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DNA Restriction-Modification Enzymes (2):
Recent article
DNA Restriction-Modification Enzymes
Biosystems (100)3 2010
Abstract
An individual-based model (IbM) for bacterial adaptation and evolution, COSMIC-Rules, has been employed to simulate interactions of virtual temperate bacteriophages (phages) and their bacterial hosts. Outcomes of infection mimic those of a phage such as lambda, which can enter either the lytic or ly...
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PMID: 20211223
PDF is available here.
PDF is available here.
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Abstract
We established experimental conditions which enabled the achievement of hemimethylated and unmethylated states for the specific bases of the recognition sequences of the host's DNA. To achieve this, we constructed the MboII R-M system containing only one (i.e. M2.MboII) out of two functional MboII m...
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PMID: 20134230
PDF is available here.
PDF is available here.
Abstract
Lactobacillus helveticus is a versatile dairy bacterium found to possess heterogeneous genotypes depending on the ecosystem from which it was isolated. The recently published genome sequence showed the remarkable flexibility of its structure, demonstrated by a substantial level of insertion sequence...
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PMID: 19880644
PDF is available here.
PDF is available here.
Abstract
Are plasmids selfish parasitic DNA molecules or an integrated part of the bacterial genome? This chapter reviews the current understanding of the persistence mechanisms of conjugative plasmids harbored by bacterial cells and populations. The diversity and intricacy of mechanisms affecting the succes...
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PMID: 19271180
PDF is available here.
PDF is available here.
Abstract
Digestion patterns of chromosomal DNAs of Bacillus cereus and Bacillus weihenstephanensis strains suggest that Sau3AI-type restriction modification systems are widely present among the isolates tested. In vitro methylation of plasmid DNA was used to enhance poor plasmid transfer upon electroporation...
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PMID: 18952874
PDF is available here.
PDF is available here.
Journal of Molecular Biology (383)5 2008
Abstract
I R/M enzymes both in vivo and in vitro. These R/M systems are present in over 50% of sequenced prokaryotic genomes. Our results suggest that ArdA can overcome the restriction barrier following conjugation and so helps increase the spread of antibiotic resistance genes by horizontal gene transfer....
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PMID: 18838147
PDF is available here.
PDF is available here.
Abstract
We observed a 10.9-kb band on a Southern blot assay from an autistic girl with language delay. Further investigation identified a novel G-to-A transition at an EcoRI cleavage site, upstream of the CGG repeat region of the FMRI gene. This base change abolished the EcoRI restriction site, resulting in...
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PMID: 18687789
PDF is available here.
PDF is available here.
Abstract
We describe the history of our understanding of this plasmid and the type I restriction-modification (R-M) system that it encodes, which will allow an opportunity to correct errors, or misunderstandings, that have arisen in the literature. We also describe the characterization of the R-M enzyme EcoR...
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PMID: 18535150
PDF is available here.
PDF is available here.
Abstract
We introduced the restriction and modification system cglI gene complex into Corynebacterium crenatum and studied their phage-resistance. The cglI gene complex was amplified from Corynebacterium glutamicum by PCR and constructed into pJL23 vector. The recombinant strains were obtained by transformat...
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PMID: 18724694
PDF is available here.
PDF is available here.
Journal of Bacteriology (190)6 2008
Abstract
We characterize a mutant form of the EcoRII gene complex that shows stronger capacity in such maintenance. This phenotype is conferred by an L80P amino acid substitution (T239C nucleotide substitution) mutation in the modification enzyme. This mutant enzyme showed decreased DNA methyltransferase act...
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PMID: 18192396
PDF is available here.
PDF is available here.
Abstract
I restriction modification systems (RMS) identified in Bacillus licheniformis DSM13. Single as well as double knock-outs resulted in strains being readily transformable with plasmids isolated from Bacilli. Introduction of shuttle plasmids isolated from Escherichia coli was routinely possible when th...
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PMID: 18046550
PDF is available here.
PDF is available here.
Bioinformatics (24)3 2008
Abstract
The new algorithm was applied to 52 Helicobacter pylori strains from different geographical regions and compared with conventional clustering methods. The algorithm works by first grouping strains that share a common minimum set of R-M systems and gradually adds strains according to the number of th...
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PMID: 18086685
PDF is available here.
PDF is available here.
BMC Genomics (9)1 2008
Abstract
Deciphering the 5,172,804 bp sequence of Microcystis aeruginosa PCC 7806 has revealed the high plasticity of its genome: 11.7% DNA repeats containing more than 1,000 bases, 6.8% putative transposases and 21 putative restriction enzymes. Compared to the genomes of other cyanobacterial lineages, strai...
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PMID: 18534010
PDF is available here.
PDF is available here.
BMC Microbiology (8)1 2008
Abstract
We have characterised a restriction-modification system EcoA0ORF42P of the commensal Escherichia coli strain A0 34/86 (O83: K24: H31). This system, designated as EcoAO83I, is a new functional member of the Type IB family, whose specificity differs from those of known Type IB enzymes, as was demonstr...
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PMID: 18588664
PDF is available here.
PDF is available here.
Abstract
The DNA sequences of the genes for the BsaHI methyltransferase, bsaHIM, and restriction endonuclease, bsaHIR, have been determined (GenBank accession #EU386360), cloned and expressed in E. coli. Both the restriction endonuclease and methyltransferase enzymes share significant similarity with a group...
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PMID: 18479503
PDF is available here.
PDF is available here.
BMC Genomics (9)1 2008
Abstract
To further the understanding of genetic attenuation that may be occurring in bifidobacteria cultures, we obtained the complete genome sequence of an intestinal isolate, Bifidobacterium longum DJO10A that was minimally cultured in the laboratory, and compared it to that of a culture collection strain...
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PMID: 18505588
PDF is available here.
PDF is available here.
BMC Microbiology (8)1 2008
Abstract
Using bioinformatics, we identified genes in the unfinished enteropathogenic Escherichia coli (EPEC) strain E2348/69 genome whose predicted products bear homology to the HsdM methyltransferases, HsdS specificity subunits, and HsdR restriction endonucleases of type I restriction-modification systems....
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PMID: 18681975
PDF is available here.
PDF is available here.
Abstract
We analyzed transcription of the modification gene and its regulation within the EcoRI R-M system. Northern blotting revealed that the downstream ecoRIM gene is transcribed as a monocistronic mRNA and as part of a larger bicistronic mRNA together with the upstream ecoRIR gene. Primer extension, RNas...
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PMID: 17618069
PDF is available here.
PDF is available here.
Molecular Microbiology (65)6 2007
Abstract
Phase variation, the high-frequency on/off switching of gene expression, is a common feature of host-adapted bacterial pathogens. Restriction-modification (R-M) systems, which are ubiquitous among bacteria, are classically assigned the role of cellular defence against invasion of foreign DNA. These...
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PMID: 17714447
PDF is available here.
PDF is available here.
Molecular Microbiology (65)4 2007
Abstract
We demonstrated that Slg01, a P4-like integrase, was sufficient to promote SLG integration, excision and circularization. Eleven counterpart dnd clusters, which also mapped to GIs in 10 chromosomes and a plasmid, were found in taxonomically unrelated bacterial species from various geographic niches....
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PMID: 17640271
PDF is available here.
PDF is available here.
Microbiology (153)Pt 8 2007
Abstract
I restriction-modification system (designated yrmI) of Y. pseudotuberculosis. This system is composed of three adjacent genes which could potentially encode an N6-adenine DNA methylase (YamA), an enzyme involved in site-specific recognition (YrsA) and a restriction endonuclease (YreA). Screening of...
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PMID: 17660407
PDF is available here.
PDF is available here.
Abstract
I or Type III R-M systems, thus expanding the range of phages against which the host population is immune. The most counter-intuitive observation, however, is the prevalence of phase variation in many restriction systems, but recent arguments suggest that switching off expression of R-M systems can...
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PMID: 17719266
PDF is available here.
PDF is available here.
Abstract
We present a method for cloning restriction-modification (R-M) systems that is based on the use of a lethal plasmid (pKILLER). The plasmid carries a functional gene for a restriction endonuclease having the same DNA specificity as the R-M system of interest. The first step is the standard preparatio...
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PMID: 17468281
PDF is available here.
PDF is available here.
Abstract
We studied the expression of H. pylori methyltransferases by digesting the genomic DNAs of 50 strains with 31 restriction endonucleases. We conclude that methyltransferase diversity is sufficiently high to enable the use of the genomic methylation status as a typing tool. The stability of methyltran...
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PMID: 17483255
PDF is available here.
PDF is available here.
FEMS Microbiology Letters (272)1 2007
Abstract
A novel restriction-modification (R-M) system, designated as xveIIRM, from chromosomal DNA of the Xanthomonas campestris pv. vesicatoria strain 7-1 (Xcv7-1) was cloned and characterized. The xveIIRM genes involved in this R-M system are aligned in a tail-to-tail orientation and overlapped by 12 base...
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PMID: 17488332
PDF is available here.
PDF is available here.
Abstract
We employed an alternative method, which involves engineering bacterial artificial chromosomes (BACs) by inducible, plasmid encoded "Red/ET recombinase" expression system. Here, we report rapid and efficient construction of PTPRF and NWC TgVs without using restriction endonucleases....
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PMID: 17498650
PDF is available here.
PDF is available here.
Journal of Medical Microbiology (56)Pt 5 2007
Abstract
Multilocus sequence typing (MLST) and multi-strain microarray analysis have shown that most human Staphylococcus aureus strains belong to ten dominant clonal complexes (CCs) or lineages, each with unique surface architecture. Meticillin-resistant S. aureus (MRSA) strains currently belong to six of t...
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PMID: 17446283
PDF is available here.
PDF is available here.
Abstract
We modeled the interaction between a bacteriophage and a bacterium carrying a restriction enzyme as antagonistic coevolution. We assume a locus on the bacteriophage genome has either a restriction-sensitive or a restriction-resistant allele, and another locus determines whether it is recombination/r...
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PMID: 17409094
PDF is available here.
PDF is available here.
Abstract
We describe an insertion of mobE into the nrdA gene of Aeromonas hydrophila phage Aeh1. The insertion creates a unique genes-in-pieces arrangement, where nrdA is split into two independent genes, nrdA-a and nrdA-b, each encoding cysteine residues that correspond to the active-site residues of uninte...
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PMID: 17395719
PDF is available here.
PDF is available here.
Research in Microbiology (158)3 2007
Abstract
Helicobacter pylori is unique because of the unusually high number and diversity of its restriction modification (R-M) systems. HpyC1I R-M was recently characterized and contains an endonuclease which is an isoschizomer of the endonuclease BccI. This R-M is involved in adherence to gastric epithelia...
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PMID: 17346936
PDF is available here.
PDF is available here.
Abstract
The erythromycin resistance plasmid pRSB105 was previously isolated from an activated sludge bacterial community of a municipal wastewater treatment plant. Compilation of the complete pRSB105 nucleotide sequence revealed that the plasmid is 57,137 bp in size and has a mean G+C conten...
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PMID: 17261525
PDF is available here.
PDF is available here.
Journal of Bacteriology (189)6 2007
Abstract
Mycoplasma pulmonis possesses a cassette of genes that are predicted to code for type III restriction and modification (R-M) enzymes. Transposon disruption of a gene predicted to code for the endonuclease subunit of the enzyme resulted in loss of R-M activity. Genomic data indicate that the cassette...
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PMID: 17209015
PDF is available here.
PDF is available here.
Abstract
We compared FokI with four other distinct enzymes HgaI, BsmFI, BbsI, and BseMII, and found their differential independence on T4 DNA ligase when performing automaton reactions. Since DNA automaton is a potential powerful tool to tackle gene relationship in genomic network scale, the feasible ligase-...
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PMID: 17196173
PDF is available here.
PDF is available here.
Journal of Molecular Biology (365)2 2007
Abstract
I restriction-modification (R-M) systems in Escherichia coli cells. In addition, a lot of the putative ardA genes encoded by plasmids and bacterial chromosomes are found as a result of sequencing of complete genomic sequences, suggesting that ArdA proteins and type I R-M systems that seem to be wide...
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PMID: 17069852
PDF is available here.
PDF is available here.
Abstract
A nucleotide sequence was established for the full-length Sporosarcina species 9D operon coding for enzymes of type II restriction-modification system Sse9I. These enzymes recognize the tetranucleotide DNA sequence 5'-AATT-3'. The operon was shown to consist of three genes that are situated with the...
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PMID: 17685226
PDF is available here.
PDF is available here.
Abstract
Genes coding for the restriction-modification system Fsp4HI, recognizing the sequence 5'-GCNGC-3' have been cloned in Escherichia coli ER2267 cells and its primary structure has been determined. This RM system consists of two genes: the DNA-methyltransferase gene which is followed by the restriction...
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PMID: 17380890
PDF is available here.
PDF is available here.
Nucleic Acids Research (35)8 2007
Abstract
Controller proteins such as C.AhdI regulate the expression of bacterial restriction-modification genes, and ensure that methylation of the host DNA precedes restriction by delaying transcription of the endonuclease. The operator DNA sequence to which C.AhdI binds consists of two adjacent binding sit...
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PMID: 17426137
PDF is available here.
PDF is available here.
Nucleic Acids Research (35)19 2007
Abstract
The restriction endonuclease Type II R.NmeDI from Neisseria meningitidis 2120 (serogroup C, ST-11 complex) was characterized. The cloned nmeDIR gene was expressed in Escherichia coli cells, and the endonucleolytic and restriction activities of R.NmeDI were then observed in vitro and in vivo. The nme...
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PMID: 17897964
PDF is available here.
PDF is available here.
Nucleic Acids Research (35)20 2007
Abstract
Type II restriction-modification (R-M) systems comprise a restriction endonuclease (REase) and a protective methyltransferase (MTase). After R-M genes enter a new cell, MTase must appear before REase or the chromosome will be cleaved. PvuII and some other R-M systems achieve this delay by cotranscri...
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PMID: 17933763
PDF is available here.
PDF is available here.
Biochemistry (New York) (71)12 2006
Abstract
DNA duplexes bearing an aldehyde group at the 2'-position of the sugar moiety were used for affinity modification of (cytosine-5)-DNA methyltransferase SsoII. It is shown that lysine residues of M.SsoII N-terminal region are located in proximity to DNA sugar-phosphate backbone of a regulatory sequen...
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PMID: 17223787
PDF is available here.
PDF is available here.
FEMS Microbiology Letters (262)1 2006
Abstract
The human respiratory tract pathogen Moraxella catarrhalis is a naturally competent microorganism. However, electrotransformation has long been used to introduce foreign DNA into this organism. This study demonstrated that electrotransformants obtained with linear or circular nonreplicating plasmid...
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PMID: 16907741
PDF is available here.
PDF is available here.
Journal of Bacteriology (188)15 2006
Abstract
We show that it carries a mutation in the sau1hsdR gene and that complementation restored a nontransformable phenotype. Sau1 was also responsible for reduced conjugative transfer from enterococci, a model of vancomycin resistance transfer. This may explain why only four vancomycin-resistant S. aureu...
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PMID: 16855248
PDF is available here.
PDF is available here.
Journal of Molecular Biology (358)2 2006
Abstract
We provide evidence that the binding site can accommodate either one or two dimers of C.AhdI in a concentration-dependent manner. The dimer binding site is adjacent to the -35 hexamer site required for the interaction with RNA polymerase (RNAP); however, co-operative binding of a second dimer blocks...
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PMID: 16516922
PDF is available here.
PDF is available here.
Genetika (Moskva) (42)3 2006
Abstract
I restriction-modification enzymes. The ArdA of R64 is highly homologous to ColIb-P9 ArdA, differing only by four amino acid residues of the overall 166. However, unlike ColIb-P9 ArdA, which inhibits both the endonuclease and the methylase activities of EcoKI, the R64 ArdA protein inhibits only the...
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PMID: 16649659
PDF is available here.
PDF is available here.
Journal of Bacteriology (188)5 2006
Abstract
The native lactococcal plasmid, pKR223, from Lactococcus lactis subsp. lactis biovar diacetylactis KR2 encodes two distinct bacteriophage-resistant mechanisms, the LlaKR2I restriction and modification (R/M) system and the abortive infection (Abi) mechanism, AbiR, that impedes bacteriophage DNA repli...
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PMID: 16484203
PDF is available here.
PDF is available here.
Physiological Genomics (24)3 2006
Abstract
We first retrieved all the putative restriction-modification (RM) genes in the draft genome of Spirulina and then performed a range of comparative and bioinformatic analyses on RM genes from unicellular and filamentous cyanobacterial genomes. We have identified 6 gene clusters containing putative Ty...
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PMID: 16368872
PDF is available here.
PDF is available here.
Abstract
Endonuclease Pca17AI, having a relatively low temperature optimum, was identified. PCR amplification revealed that the nucleotide sequence of genes for EcoRII and Pca17AI R-M are different. Dcm methylation was observed in all strains of Pectobacterium and other Erwinia species tested. The sequence o...
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PMID: 16430511
PDF is available here.
PDF is available here.
Abstract
It has been shown that the temperate bacteriophage ZF40 Erwinia carotovora combines in it two kinds of intragenome heterogeneity--cyclic permutation and cohesive end structures. The latter reassociate more quickly than analogous cos-sites of the phage lambda Escherichia coli. A series of clear-mutan...
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PMID: 17243365
PDF is available here.
PDF is available here.
Abstract
A model for revealing and type identifying the systems of restriction-modification of phytopathogenic bacterium Ewinia carotovora with the help of two virulent polyvalent phages-FE 44 and T7 is proposed in the work. The joint use of the phages permits to identify both the limitations of phages devel...
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PMID: 17243364
PDF is available here.
PDF is available here.
BMC Microbiology (6)1 2006
Abstract
Detailed bioinformatics analysis confirmed the presence of a conserved GTP binding and hydrolysis domain within the C-terminal half of the R1.LlaJI amino acid sequence whilst the N-terminal half appeared to be entirely unique. This domain architecture was homologous with that of the "B" subunit of t...
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PMID: 16646963
PDF is available here.
PDF is available here.
Nucleic Acids Research (34)7 2006
Abstract
We present a structural model of the Type IC M.EcoR124I DNA methyltransferase (MTase), comprising the HsdS subunit, two HsdM subunits, the cofactor AdoMet and the substrate DNA molecule. The structure was obtained by docking models of individual subunits generated by fold-recognition and comparative...
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PMID: 16614449
PDF is available here.
PDF is available here.
Abstract
Protection from DNA invasion is afforded by restriction-modification systems in many bacteria. The efficiency of protection depends crucially on the relative expression levels of restriction versus methytransferase genes. This regulation is provided by a controller protein, named C protein. Studies...
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PMID: 16338412
PDF is available here.
PDF is available here.
Journal of Molecular Biology (351)4 2005
Abstract
I restriction and modification system. The structure consists of two globular domains, with about 150 residues each, separated by a pair of 40 residue long antiparallel alpha-helices. The globular domains correspond to the variable target recognition domains (TRDs), as previously defined for S subun...
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PMID: 16038930
PDF is available here.
PDF is available here.
Molecular Microbiology (57)6 2005
Abstract
We report the molecular mechanism by which this R/M system is transcriptionally regulated. The recognition sequence for the LlaJI MTases was deduced to be 5'GACGC'3 for M1.LlaJI and 5'GCGTC'3 for M2.LlaJI, thus together constituting an asymmetric complementary recognition site. Two recognition seque...
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PMID: 16135222
PDF is available here.
PDF is available here.
Biochimica et Biophysica Acta (1751)2 2005
Abstract
We interpret the presented experimental evidence as a suggestion that the motif 306Rx3ExHHx14Nx8H represents the active site of MnlI. Consequentially, MnlI seems to be the member of Type IIS with the active site of the H-N-H type....
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PMID: 16024301
PDF is available here.
PDF is available here.
Abstract
The phenomena of prokaryotic restriction and modification, as well as anti-restriction, were first discovered five decades ago but have yielded only gradually to rigorous analysis. Work presented at the 5th New England Biolabs Meeting on Restriction-Modification (available on REBASE, http://www.reba...
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PMID: 15979932
PDF is available here.
PDF is available here.
Analytical Biochemistry (340)2 2005
Abstract
We have developed a nonradioactive assay method for DNA methyltransferases based on the ability to protect substrate DNA from restriction. DNA immobilized to a microplate well was treated sequentially with methyltransferase and an appropriate endonuclease. The amount of methylated DNA product is ref...
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PMID: 15840507
PDF is available here.
PDF is available here.
Biochemistry (New York) (70)5 2005
Abstract
Background studies have shown that 6-methylaminopurine (m6A) and 5-methylcytosine (m5C), detected in DNA, are products of its post-synthetic modification. At variance with bacterial genomes exhibiting both, eukaryotic genomes essentially carry only m5C in m5CpG doublets. This served to establish tha...
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PMID: 15948712
PDF is available here.
PDF is available here.
Microbiology (151)Pt 4 2005
Abstract
The serotype F phage Phi42 of Staphylococcus aureus is a triple-converting bacteriophage that encodes the staphylokinase gene (sak) and the enterotoxin A gene (entA). Lysogeny results in loss of expression of the chromosomal beta-haemolysin gene (hlb) (negative conversion), the expression of staphyl...
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PMID: 15817797
PDF is available here.
PDF is available here.
Journal of Molecular Biology (346)3 2005
Abstract
We have solved the first X-ray structure of an R-M controller protein, C.AhdI, to 1.69 A resolution using selenomethionine MAD. C.AhdI is part of a Type IIH R-M system from the pathogen Aeromonas hydrophila. The structure reveals an all-alpha protein that contains a classical helix-turn-helix (HTH)...
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PMID: 15713456
PDF is available here.
PDF is available here.