Restriction enzymes and methylases database
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Restriction enzymes and methylases database
metasource: Fairsharing.org
version: FAIRsharing.org: REBASE; Restriction enzymes and methylases database; DOI: https://doi.org/10.25504/FAIRsharing.9sb9qh; Last edited: April 26, 2021, 2:42 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
REBASE
metasource: Fairsharing.org
version: FAIRsharing.org: REBASE; Restriction enzymes and methylases database; DOI: https://doi.org/10.25504/FAIRsharing.9sb9qh; Last edited: April 26, 2021, 2:42 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: re3data.org
version: re3data.org: REBASE; editing status 2017-11-21; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3J930 last accessed: 2022-11-04
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:47.988817
The Restriction Enzyme Database
metasource: re3data.org
version: re3data.org: REBASE; editing status 2017-11-21; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3J930 last accessed: 2022-11-04
rebase
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:47.988817
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Restriction enzymes and methylases database
metasource: Fairsharing.orgversion: FAIRsharing.org: REBASE; Restriction enzymes and methylases database; DOI: https://doi.org/10.25504/FAIRsharing.9sb9qh; Last edited: April 26, 2021, 2:42 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
REBASE
metasource: Fairsharing.orgversion: FAIRsharing.org: REBASE; Restriction enzymes and methylases database; DOI: https://doi.org/10.25504/FAIRsharing.9sb9qh; Last edited: April 26, 2021, 2:42 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: re3data.org
version: re3data.org: REBASE; editing status 2017-11-21; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3J930 last accessed: 2022-11-04
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:47.988817
The Restriction Enzyme Database
metasource: re3data.orgversion: re3data.org: REBASE; editing status 2017-11-21; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3J930 last accessed: 2022-11-04
rebase
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:34:47.988817
Other names: REBASE, The Restriction Enzyme Database, rebase
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More detailed information about this field from each metasource.
Restriction enzymes and methylases database
metasource: Fairsharing.orgversion: FAIRsharing.org: REBASE; Restriction enzymes and methylases database; DOI: https://doi.org/10.25504/FAIRsharing.9sb9qh; Last edited: April 26, 2021, 2:42 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
REBASE
metasource: Fairsharing.orgversion: FAIRsharing.org: REBASE; Restriction enzymes and methylases database; DOI: https://doi.org/10.25504/FAIRsharing.9sb9qh; Last edited: April 26, 2021, 2:42 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: re3data.org
version: re3data.org: REBASE; editing status 2017-11-21; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3J930 last accessed: 2022-11-04
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:47.988817
The Restriction Enzyme Database
metasource: re3data.orgversion: re3data.org: REBASE; editing status 2017-11-21; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3J930 last accessed: 2022-11-04
rebase
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:34:47.988817
This source may no longer be available. No known URL could be resolved successfully.
A collection of information about restriction enzymes and related proteins. It contains published and unpublished references, recognition and cleavage sites, isoschizomers, commercial availability, methylation sensitivity, crystal, genome, and sequence data.
Description
More detailed information about this field from each metasource.
A collection of information about restriction enzymes and related proteins. It contains published and unpublished references, recognition and cleavage sites, isoschizomers, commercial availability, methylation sensitivity, crystal, genome, and sequence data.
metasource: Fairsharing.orgversion: FAIRsharing.org: REBASE; Restriction enzymes and methylases database; DOI: https://doi.org/10.25504/FAIRsharing.9sb9qh; Last edited: April 26, 2021, 2:42 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
REBASE is a comprehensive database of information about restriction enzymes, DNA methyltransferases and related proteins involved in the biological process of restriction-modification. It contains fully referenced information about recognition and cleavage sites, isoschizomers, neoschizomers, commercial availability, methylation sensitivity, crystal and sequence data. Experimentally characterized homing endonucleases are also included. All newly sequenced genomes are analyzed for the presence of putative restriction systems and this data is included within REBASE.The contents of REBASE may be browsed from the web (http://rebase.neb.com) and selected compilations can be downloaded by ftp (ftp.neb.com). Additionally, monthly updates can be requested via email.Currently, there are 19,442 enzymes (including subunits) and 10,032 references stored in REBASE. The references are collected from journals, books, patents, as well as unpublished observations.There are currently 3,945 biochemically or genetically characterized restriction enzymes in REBASE and of the 3,698 Type II restriction enzymes, 641 are commercially available, including 235 distinct specificities.Among the 5,105 restriction enzyme genes and 8,022 DNA methyltransferase genes that can be identified in GenBank, the sequenced microbial genomes now account for 9,597 of these genes!The number of sequenced bacterial and archaeal genomes has risen to more than 1,000 and the total number of complete restriction-modification (R-M) systems in REBASE is now almost 4,000 for well-characterized systems and more than 5,800 for putative R-M systems, whose existence is predicted on the basis of a bioinformatic analysis of DNA sequences in GenBank.
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
The Restriction Enzyme Database is a collection of information about restriction enzymes, methylases, the microorganisms from which they have been isolated, recognition sequences, cleavage sites, methylation specificity, the commercial availability of the enzymes, and references - both published and unpublished observations (dating back to 1952). REBASE is updated daily and is constantly expanding.
metasource: re3data.orgversion: re3data.org: REBASE; editing status 2017-11-21; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3J930 last accessed: 2022-11-04
Comprehensive database of information about restriction enzymes, DNA methyltransferases and related proteins involved in the biological process of restriction-modification (R-M). It contains fully referenced information about recognition and cleavage sites, isoschizomers, neoschizomers, commercial availability, methylation sensitivity, crystal and sequence data. Experimentally characterized homing endonucleases are also included.
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:34:47.988817
Webpage:
http://rebase.neb.comWebpage
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http://rebase.neb.com
metasource: Fairsharing.orgversion: FAIRsharing.org: REBASE; Restriction enzymes and methylases database; DOI: https://doi.org/10.25504/FAIRsharing.9sb9qh; Last edited: April 26, 2021, 2:42 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
http://rebase.neb.com/rebase/rebase.html
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
metasource: re3data.org
version: re3data.org: REBASE; editing status 2017-11-21; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3J930 last accessed: 2022-11-04
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:47.988817
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Name: Open Data Commons (ODC) Public Domain Dedication and Licence (PDDL) 1.0Licence name
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Open Data Commons (ODC) Public Domain Dedication and Licence (PDDL) 1.0
metasource: Fairsharing.orgversion: FAIRsharing.org: REBASE; Restriction enzymes and methylases database; DOI: https://doi.org/10.25504/FAIRsharing.9sb9qh; Last edited: April 26, 2021, 2:42 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
Copyrights
metasource: re3data.orgversion: re3data.org: REBASE; editing status 2017-11-21; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3J930 last accessed: 2022-11-04
Licence URL
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http://opendatacommons.org/licenses/pddl/1.0/
metasource: Fairsharing.orgversion: FAIRsharing.org: REBASE; Restriction enzymes and methylases database; DOI: https://doi.org/10.25504/FAIRsharing.9sb9qh; Last edited: April 26, 2021, 2:42 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
http://rebase.neb.com/rebase/rebhelp.html
metasource: re3data.orgversion: re3data.org: REBASE; editing status 2017-11-21; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3J930 last accessed: 2022-11-04
Publications:
Publications
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REBASE--a database for DNA restriction and modification: enzymes, genes and genomes
PMID: 25378308
metasource: Fairsharing.org
version: FAIRsharing.org: REBASE; Restriction enzymes and methylases database; DOI: https://doi.org/10.25504/FAIRsharing.9sb9qh; Last edited: April 26, 2021, 2:42 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
REBASE--a database for DNA restriction and modification: enzymes, genes and genomes
PMID: 19846593
metasource: Fairsharing.org
version: FAIRsharing.org: REBASE; Restriction enzymes and methylases database; DOI: https://doi.org/10.25504/FAIRsharing.9sb9qh; Last edited: April 26, 2021, 2:42 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:47.988817
http://dx.doi.org/10.1093/nar/gku1046
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Publications
More detailed information about this field from each metasource.
REBASE--a database for DNA restriction and modification: enzymes, genes and genomes
PMID: 25378308
metasource: Fairsharing.org
version: FAIRsharing.org: REBASE; Restriction enzymes and methylases database; DOI: https://doi.org/10.25504/FAIRsharing.9sb9qh; Last edited: April 26, 2021, 2:42 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
REBASE--a database for DNA restriction and modification: enzymes, genes and genomes
PMID: 19846593
metasource: Fairsharing.org
version: FAIRsharing.org: REBASE; Restriction enzymes and methylases database; DOI: https://doi.org/10.25504/FAIRsharing.9sb9qh; Last edited: April 26, 2021, 2:42 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:47.988817
http://dx.doi.org/10.1093/nar/gku1046
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
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REBASE--a database for DNA restriction and modification: enzymes, genes and genomes
PubMed citations: 360.
360 articles citing: REBASE--a database for DNA restriction and modification: enzymes, genes and genomes
Detecting DNA Methylations in the Hyperthermoacidophilic Crenarchaeon Sulfolobus acidocaldarius Using SMRT Sequencing. PMID:35922620
Genomic and epigenetic landscapes drive CRISPR-based genome editing in Bifidobacterium. PMID:35857876
m4C DNA methylation regulates biosynthesis of daptomycin in Streptomyces roseosporus L30. PMID:35801092
Novel thermophilic polyhydroxyalkanoates producing strain Aneurinibacillus thermoaerophilus CCM 8960. PMID:35759037
SeqScreen: accurate and sensitive functional screening of pathogenic sequences via ensemble learning. PMID:35725628
Growth rate determines prokaryote-provirus network modulated by temperature and host genetic traits. PMID:35701838
Design of typical genes for heterologous gene expression. PMID:35688911
MIAOME: Human microbiome affect the host epigenome. PMID:35664224
Expression and Purification of BsaXI Restriction Endonuclease and Engineering New Specificity From BsaXI Specificity Subunit. PMID:35663886
Complete Genome Sequence of Weissella cibaria NH9449 and Comprehensive Comparative-Genomic Analysis: Genomic Diversity and Versatility Trait Revealed. PMID:35663880
Integration of the Salmonella Typhimurium Methylome and Transcriptome Reveals That DNA Methylation and Transcriptional Regulation Are Largely Decoupled under Virulence-Related Conditions. PMID:35658533
Mobility of extracellular DNA within gonococcal colonies. PMID:35647521
PADLOC: a web server for the identification of antiviral defence systems in microbial genomes. PMID:35639517
Understanding the Mechanisms That Drive Phage Resistance in Staphylococci to Prevent Phage Therapy Failure. PMID:35632803
Characterization of Three Novel Virulent Aeromonas Phages Provides Insights into the Diversity of the Autographiviridae Family. PMID:35632757
Systematic and quantitative view of the antiviral arsenal of prokaryotes. PMID:35538097
Identification and characterization of the WYL BrxR protein and its gene as separable regulatory elements of a BREX phage restriction system. PMID:35511079
Metagenomic methylation patterns resolve bacterial genomes of unusual size and structural complexity. PMID:35459792
Beyond the ABCs-Discovery of Three New Plasmid Types in Rhodobacterales (RepQ, RepY, RepW). PMID:35456790
Characterisation of Waterborne Psychrophilic Massilia Isolates with Violacein Production and Description of Massilia antarctica sp. nov. PMID:35456753
Reassembling a cannon in the DNA defense arsenal: Genetics of StySA, a BREX phage exclusion system in Salmonella lab strains. PMID:35377874
A GCDGC-specific DNA (cytosine-5) methyltransferase that methylates the GCWGC sequence on both strands and the GCSGC sequence on one strand. PMID:35312710
Precipitous Increase of Bacterial CRISPR-Cas Abundance at Around 45°C. PMID:35300480
A mobile restriction-modification system provides phage defence and resolves an epigenetic conflict with an antagonistic endonuclease. PMID:35286398
Complete Genome Sequence of Morganella morganii CTX51T, Isolated from a Human Cecal Adenocarcinoma. PMID:35254123
Complete Genome Sequence of Clostridium cadaveris IFB3C5, Isolated from a Human Colonic Adenocarcinoma. PMID:35234492
Bacterial N4-methylcytosine as an epigenetic mark in eukaryotic DNA. PMID:35228526
Comparative genomic analysis of Staphylococcus aureus isolates associated with either bovine intramammary infections or human infections demonstrates the importance of restriction-modification systems in host adaptation. PMID:35179459
A Reinforcement Learning Framework for Pooled Oligonucleotide Design. PMID:35143615
Cleavage of viral DNA by restriction endonucleases stimulates the type II CRISPR-Cas immune response. PMID:35134339
Genomic, Antimicrobial, and Aphicidal Traits of Bacillus velezensis ATR2, and Its Biocontrol Potential against Ginger Rhizome Rot Disease Caused by Bacillus pumilus. PMID:35056513
Diverse DNA modification in marine prokaryotic and viral communities. PMID:35051998
Genome Sequence of the Early 20th-Century Extreme Halophile Halobacterium sp. Strain NRC-34001. PMID:35023769
Differences in the Accessory Genomes and Methylomes of Strains of Streptococcus equi subsp. equi and of Streptococcus equi subsp. zooepidemicus Obtained from the Respiratory Tract of Horses from Texas. PMID:35019696
Methylation Motifs in Promoter Sequences May Contribute to the Maintenance of a Conserved m5C Methyltransferase in Helicobacter pylori. PMID:34946076
DNA Methylation Patterns Differ between Free-Living Rhizobium leguminosarum RCAM1026 and Bacteroids Formed in Symbiosis with Pea (Pisum sativum L.). PMID:34946059
Comparative Genomics and Physiological Investigation of a New Arthrospira/Limnospira Strain O9.13F Isolated from an Alkaline, Winter Freezing, Siberian Lake. PMID:34943919
The genetic basis of phage susceptibility, cross-resistance and host-range in Salmonella. PMID:34910616
Genome Sequence of Halobacterium sp. Strain BOL4-2, Isolated and Cultured from Salar de Uyuni, Bolivia. PMID:34854697
Characterization of the Type I Restriction Modification System Broadly Conserved among Group A Streptococci. PMID:34787444
Systematic exploration of Escherichia coli phage-host interactions with the BASEL phage collection. PMID:34784345
Dynamic changes in DNA methylation during seahorse (Hippocampus reidi) postnatal development and settlement. PMID:34627317
Identification and classification of antiviral defence systems in bacteria and archaea with PADLOC reveals new system types. PMID:34606606
Evaluation of the Properties of the DNA Methyltransferase from Aeropyrum pernix K1. PMID:34585946
Genomic Stability and Genetic Defense Systems in Dolosigranulum pigrum, a Candidate Beneficial Bacterium from the Human Microbiome. PMID:34546072
Genome archaeology of two laboratory Salmonella enterica enterica sv Typhimurium. PMID:34544129
Arms race in a cell: genomic, transcriptomic, and proteomic insights into intracellular phage-bacteria interplay in deep-sea snail holobionts. PMID:34479645
Diagnosing the drug resistance signature in Plasmodium falciparum: a review from contemporary methods to novel approaches. PMID:34475670
Complete Genome and Methylome Analysis of the Box-Shaped Halophilic Archaeon Haloarcula sinaiiensis ATCC 33800. PMID:34435862
ENDO-Pore: high-throughput linked-end mapping of single DNA cleavage events using nanopore sequencing. PMID:34417616
Rapid identification of methylase specificity (RIMS-seq) jointly identifies methylated motifs and generates shotgun sequencing of bacterial genomes. PMID:34417598
A Type I Restriction Modification System Influences Genomic Evolution Driven by Horizontal Gene Transfer in Paenibacillus polymyxa. PMID:34413842
Bacterial Epigenomics: Coming of Age. PMID:34402642
Complete Genome Sequence and Methylome of the Type Strain of Shewanella algae. PMID:34351223
Temporal shifts in antibiotic resistance elements govern phage-pathogen conflicts. PMID:34326207
Phylogenomic disentangling of the Bifidobacterium longum subsp. infantis taxon. PMID:34319225
Lowering DNA binding affinity of SssI DNA methyltransferase does not enhance the specificity of targeted DNA methylation in E. coli. PMID:34315949
Improving Mobilization of Foreign DNA into Zymomonas mobilis Strain ZM4 by Removal of Multiple Restriction Systems. PMID:34288704
Characterization of BisI Homologs. PMID:34276622
Complete Genome Sequence of an Extremely Halophilic Archaeon from Great Salt Lake, Halobacterium sp. GSL-19. PMID:34264097
Production and сharacterization of the exopolysaccharide from strain Paenibacillus polymyxa 2020. PMID:34228741
Structural and functional diversity among Type III restriction-modification systems that confer host DNA protection via methylation of the N4 atom of cytosine. PMID:34228724
DNA methylation by three Type I restriction modification systems of Escherichia coli does not influence gene regulation of the host bacterium. PMID:34181709
Epigenomic Landscape of Lyme Disease Spirochetes Reveals Novel Motifs. PMID:34156261
Phage-encoded ten-eleven translocation dioxygenase (TET) is active in C5-cytosine hypermodification in DNA. PMID:34155108
Unique phage-bacterium interplay in sponge holobionts from the southern Okinawa Trough hydrothermal vent. PMID:34128329
Differences in the genome, methylome, and transcriptome do not differentiate isolates of Streptococcus equi subsp. equi from horses with acute clinical signs from isolates of inapparent carriers. PMID:34125848
Identical sequences found in distant genomes reveal frequent horizontal transfer across the bacterial domain. PMID:34121661
Clostridioides difficile specific DNA adenine methyltransferase CamA squeezes and flips adenine out of DNA helix. PMID:34103525
The Hyperthermophilic Restriction-Modification Systems of Thermococcus kodakarensis Protect Genome Integrity. PMID:34093470
Novel Identification of Bacterial Epigenetic Regulations Would Benefit From a Better Exploitation of Methylomic Data. PMID:34054792
Preselector.uni-jena.de: optimize your cloning-a resource for identifying restriction enzymes for preselection reactions. PMID:34037777
A new family of globally distributed lytic roseophages with unusual deoxythymidine to deoxyuridine substitution. PMID:34033748
Detecting and phasing minor single-nucleotide variants from long-read sequencing data. PMID:34031367
VCF2CAPS-A high-throughput CAPS marker design from VCF files and its test-use on a genotyping-by-sequencing (GBS) dataset. PMID:34014924
Genome-wide identification of 5-methylcytosine sites in bacterial genomes by high-throughput sequencing of MspJI restriction fragments. PMID:33974631
Genome Sequence and Methylation Pattern of Haloterrigena salifodinae BOL5-1, an Extremely Halophilic Archaeon from a Bolivian Salt Mine. PMID:33958400
Zymomonas diversity and potential for biofuel production. PMID:33933155
Cocultivation of an ultrasmall environmental parasitic bacterium with lytic ability against bacteria associated with wastewater foams. PMID:33927381
Characterisation of Phage Susceptibility Variation in Salmonellaenterica Serovar Typhimurium DT104 and DT104b. PMID:33920555
Genome analysis provides insights into the biocontrol ability of Mitsuaria sp. strain TWR114. PMID:33880605
Extreme C-to-A Hypermutation at a Site of Cytosine-N4 Methylation. PMID:33849975
Discovering multiple types of DNA methylation from bacteria and microbiome using nanopore sequencing. PMID:33820988
Comparison of long read sequencing technologies in interrogating bacteria and fly genomes. PMID:33768248
In vitro exploration of the Xanthomonas hortorum pv. vitians genome using transposon insertion sequencing and comparative genomics to discriminate between core and contextual essential genes. PMID:33760724
Investigation of Burkholderia cepacia Complex Methylomes via Single-Molecule, Real-Time Sequencing and Mutant Analysis. PMID:33753468
DNA damage-signaling, homologous recombination and genetic mutation induced by 5-azacytidine and DNA-protein crosslinks in Escherichia coli. PMID:33743507
Genome-wide methylome analysis of two strains belonging to the hypervirulent Neisseria meningitidis serogroup W ST-11 clonal complex. PMID:33737546
Transcriptional rewiring of the GcrA/CcrM bacterial epigenetic regulatory system in closely related bacteria. PMID:33705385
Significant non-existence of sequences in genomes and proteomes. PMID:33693858
Novel Genes Required for Surface-Associated Motility in Acinetobacter baumannii. PMID:33666749
Evolutionary Dynamics Based on Comparative Genomics of Pathogenic Escherichia coli Lineages Harboring Polyketide Synthase (pks) Island. PMID:33653937
Genetic and metabolic engineering challenges of C1-gas fermenting acetogenic chassis organisms. PMID:33595667
Novel Two-Component System-Like Elements Reveal Functional Domains Associated with Restriction-Modification Systems and paraMORC ATPases in Bacteria. PMID:33565597
Pangenome analysis reveals genetic isolation in Campylobacter hyointestinalis subspecies adapted to different mammalian hosts. PMID:33564053
Genome analysis of Salmonella enterica serovar Typhimurium bacteriophage L, indicator for StySA (StyLT2III) restriction-modification system action. PMID:33561243
Approaches to genetic tool development for rapid domestication of non-model microorganisms. PMID:33494801
The impact of genetic diversity on gene essentiality within the Escherichia coli species. PMID:33462433
Comparative Methylome Analysis of Campylobacter jejuni Strain YH002 Reveals a Putative Novel Motif and Diverse Epigenetic Regulations of Virulence Genes. PMID:33424813
Isolation and characterisation of Methylocystis spp. for poly-3-hydroxybutyrate production using waste methane feedstocks. PMID:33409745
Identification of New Helicobacter pylori Subpopulations in Native Americans and Mestizos From Peru. PMID:33381095
Comparative genome analyses of Mycobacteroides immunogenum reveals two potential novel subspecies. PMID:33295861
In vitro Type II Restriction of Bacteriophage DNA With Modified Pyrimidines. PMID:33193286
The Effect of Iodine-Containing Nano-Micelles, FS-1, on Antibiotic Resistance, Gene Expression and Epigenetic Modifications in the Genome of Multidrug Resistant MRSA Strain Staphylococcus aureus ATCC BAA-39. PMID:33193215
Epigenomics, genomics, resistome, mobilome, virulome and evolutionary phylogenomics of carbapenem-resistant Klebsiella pneumoniae clinical strains. PMID:33170117
Arrayed CRISPRi and quantitative imaging describe the morphotypic landscape of essential mycobacterial genes. PMID:33155979
Decoding the Genomic Variability among Members of the Bifidobacterium dentium Species. PMID:33152994
Plasmid- and strain-specific factors drive variation in ESBL-plasmid spread in vitro and in vivo. PMID:33149210
Prevalence of phase variable epigenetic invertons among host-associated bacteria. PMID:33119758
Budding yeast as a factory to engineer partial and complete microbial genomes. PMID:33015421
MamA essentiality in Mycobacterium smegmatis is explained by the presence of an apparent cognate restriction endonuclease. PMID:32993774
A High-Efficacy CRISPR Interference System for Gene Function Discovery in Zymomonas mobilis. PMID:32978126
Single-pass transcription by T7 RNA polymerase. PMID:32958559
Contribution of DNA adenine methylation to gene expression heterogeneity in Salmonella enterica. PMID:32954419
Limitations of Ribotyping as Genotyping Method for Corynebacterium ulcerans. PMID:32946740
Computational methods and next-generation sequencing approaches to analyze epigenetics data: Profiling of methods and applications. PMID:32941995
Structure of the space of taboo-free sequences. PMID:32940748
Accurate prediction of DNA N4-methylcytosine sites via boost-learning various types of sequence features. PMID:32917152
Analysis of Resistance to Florfenicol and the Related Mechanism of Dissemination in Different Animal-Derived Bacteria. PMID:32903722
The Draft Genome Sequence of Clostridium butyricum QXYZ514, a Potent Bacterium for Converting Glycerol into Fuels and Bioproducts in the Waste-Based Biorefinery. PMID:32902703
Exploring the Remarkable Diversity of Culturable Escherichia coli Phages in the Danish Wastewater Environment. PMID:32899836
Type II Restriction-Modification System from Gardnerella vaginalis ATCC 14018. PMID:32867033
Abundance, Diversity and Role of ICEs and IMEs in the Adaptation of Streptococcus salivarius to the Environment. PMID:32858915
Diverse enzymatic activities mediate antiviral immunity in prokaryotes. PMID:32855333
In Vivo Genome and Methylome Adaptation of cag-Negative Helicobacter pylori during Experimental Human Infection. PMID:32843556
Comprehensive genome data analysis establishes a triple whammy of carbapenemases, ICEs and multiple clinically relevant bacteria. PMID:32841111
Systematic Analysis of REBASE Identifies Numerous Type I Restriction-Modification Systems with Duplicated, Distinct hsdS Specificity Genes That Can Switch System Specificity by Recombination. PMID:32723795
Comparative genomic insights into Yersinia hibernica - a commonly misidentified Yersinia enterocolitica-like organism. PMID:32701425
Complete Genome Sequences and Methylome Analyses of Cutibacterium acnes subsp. acnes Strains DSM 16379 and DSM 1897T. PMID:32675190
DNA Methylation Epigenetically Regulates Gene Expression in Burkholderia cenocepacia and Controls Biofilm Formation, Cell Aggregation, and Motility. PMID:32669472
Bulk and single-molecule analysis of a bacterial DNA2-like helicase-nuclease reveals a single-stranded DNA looping motor. PMID:32621607
Genomic characterization of the most barotolerant Listeria monocytogenes RO15 strain compared to reference strains used to evaluate food high pressure processing. PMID:32615922
GapMind: Automated Annotation of Amino Acid Biosynthesis. PMID:32576650
IncC conjugative plasmids and SXT/R391 elements repair double-strand breaks caused by CRISPR-Cas during conjugation. PMID:32556263
SMRT Sequencing of Paramecium Bursaria Chlorella Virus-1 Reveals Diverse Methylation Stability in Adenines Targeted by Restriction Modification Systems. PMID:32508769
Nick-seq for single-nucleotide resolution genomic maps of DNA modifications and damage. PMID:32484547
The DNA methylation landscape of giant viruses. PMID:32461636
Restriction endonucleases that cleave RNA/DNA heteroduplexes bind dsDNA in A-like conformation. PMID:32459314
Beta class amino methyltransferases from bacteria to humans: evolution and structural consequences. PMID:32453412
Conserved DNA Methyltransferases: A Window into Fundamental Mechanisms of Epigenetic Regulation in Bacteria. PMID:32417228
High Synteny and Sequence Identity between Genomes of Nitrosococcus oceani Strains Isolated from Different Oceanic Gyres Reveals Genome Economization and Autochthonous Clonal Evolution. PMID:32397339
PCR-RFLP Detection and Genogroup Identification of Piscirickettsia salmonis in Field Samples. PMID:32397152
Evolutionary selection against short nucleotide sequences in viruses and their related hosts. PMID:32339222
Complete Genome Sequences and Methylome Analysis of Two Environmental Spirochaetes. PMID:32273363
Endogenous Type I CRISPR-Cas: From Foreign DNA Defense to Prokaryotic Engineering. PMID:32195227
Low-level expression of the Type II restriction-modification system confers potent bacteriophage resistance in Escherichia coli. PMID:32167561
Complete genome and methylome analysis of Neisseria meningitidis associated with increased serogroup Y disease. PMID:32108139
A novel DNA methylation motif identified in Bacillus pumilus BA06 and possible roles in the regulation of gene expression. PMID:32088759
Prophage-Mediated Disruption of Genetic Competence in Staphylococcus pseudintermedius. PMID:32071159
Integrated Genome-Wide Analysis of an Isogenic Pair of Pseudomonas aeruginosa Clinical Isolates with Differential Antimicrobial Resistance to Ceftolozane/Tazobactam, Ceftazidime/Avibactam, and Piperacillin/Tazobactam. PMID:32033143
Meningococcal Disease-Associated Prophage-Like Elements Are Present in Neisseria gonorrhoeae and Some Commensal Neisseria Species. PMID:32031617
Comparative Genomics of Streptococcus thermophilus Support Important Traits Concerning the Evolution, Biology and Technological Properties of the Species. PMID:31956321
DNA sequence repeats identify numerous Type I restriction-modification systems that are potential epigenetic regulators controlling phase-variable regulons; phasevarions. PMID:31914596
Structure of HhaI endonuclease with cognate DNA at an atomic resolution of 1.0 Å. PMID:31879785
Genome Analyses and Genome-Centered Metatranscriptomics of Methanothermobacter wolfeii Strain SIV6, Isolated from a Thermophilic Production-Scale Biogas Fermenter. PMID:31861790
Multiple Origins and Specific Evolution of CRISPR/Cas9 Systems in Minimal Bacteria (Mollicutes). PMID:31824468
The Pseudomonas aeruginosa accessory genome elements influence virulence towards Caenorhabditis elegans. PMID:31823826
Epigenomic characterization of Clostridioides difficile finds a conserved DNA methyltransferase that mediates sporulation and pathogenesis. PMID:31768029
Complete Genome Sequence and Methylome Analysis of Sphaerotilus natans subsp. sulfidivorans D-507. PMID:31727714
Toward a Mechanistic Understanding of DNA Methylation Readout by Transcription Factors. PMID:31689433
Non-typeable Haemophilus influenzae isolates from patients with chronic obstructive pulmonary disease contain new phase-variable modA methyltransferase alleles controlling phasevarions. PMID:31685916
Red-Brown Pigmentation of Acidipropionibacterium jensenii Is Tied to Haemolytic Activity and cyl-Like Gene Cluster. PMID:31671651
Restriction enzymes use a 24 dimensional coding space to recognize 6 base long DNA sequences. PMID:31671158
Methylome Characterization of Burkholderia pseudomallei Strain 982 at Single-Base Resolution. PMID:31649075
Detection of DNA Modifications by Sequence-Specific Transcription Factors. PMID:31626807
PADS Arsenal: a database of prokaryotic defense systems related genes. PMID:31620779
Genetic variation regulates the activation and specificity of Restriction-Modification systems in Neisseria gonorrhoeae. PMID:31605008
Synergistic Activity of Mobile Genetic Element Defences in Streptococcus pneumoniae. PMID:31540216
Random transposon insertion in the Mycoplasma hominis minimal genome. PMID:31537861
Complete Genome Sequence of Cupriavidus necator H16 (DSM 428). PMID:31515345
A protein architecture guided screen for modification dependent restriction endonucleases. PMID:31504772
N 4-Cytosine DNA Methylation Is Involved in the Maintenance of Genomic Stability in Deinococcus radiodurans. PMID:31497001
Escherichia coli belonging to ST131 rarely transfers bla ctx-m-15 to fecal Escherichia coli. PMID:31496755
Genome-wide systematic identification of methyltransferase recognition and modification patterns. PMID:31427571
Genome Sequences and Methylation Patterns of Natrinema versiforme BOL5-4 and Natrinema pallidum BOL6-1, Two Extremely Halophilic Archaea from a Bolivian Salt Mine. PMID:31416876
A Novel Bacteriophage Exclusion (BREX) System Encoded by the pglX Gene in Lactobacillus casei Zhang. PMID:31399407
Complete Genome Sequence and Methylome Analysis of Thermoactinomyces vulgaris 2H. PMID:31395639
Commensal Neisseria Kill Neisseria gonorrhoeae through a DNA-Dependent Mechanism. PMID:31378677
A Molecular Biology Tool Kit for the Phototrophic Firmicute Heliobacterium modesticaldum. PMID:31375483
Transcriptome analyses of cells carrying the Type II Csp231I restriction-modification system reveal cross-talk between two unrelated transcription factors: C protein and the Rac prophage repressor. PMID:31372643
Rational development of transformation in Clostridium thermocellum ATCC 27405 via complete methylome analysis and evasion of native restriction-modification systems. PMID:31342224
Genome sequencing and analysis of Salmonella enterica subsp. enterica serovar Stanley UPM 517: Insights on its virulence-associated elements and their potentials as vaccine candidates. PMID:31293824
Methylomes of Two Extremely Halophilic Archaea Species, Haloarcula marismortui and Haloferax mediterranei. PMID:31270201
A novel conjugal donor strain for improved DNA transfer into Clostridium spp. PMID:31269456
Long-read based de novo assembly of low-complexity metagenome samples results in finished genomes and reveals insights into strain diversity and an active phage system. PMID:31238873
Recent mixing of Vibrio parahaemolyticus populations. PMID:31235840
Characterization of the virome of Paracoccus spp. (Alphaproteobacteria) by combined in silico and in vivo approaches. PMID:31133656
Comparative genome analysis of the Lactobacillus brevis species. PMID:31122208
Systematic evasion of the restriction-modification barrier in bacteria. PMID:31097593
Development of a metabolic pathway transfer and genomic integration system for the syngas-fermenting bacterium Clostridium ljungdahlii. PMID:31086564
DNAmod: the DNA modification database. PMID:31016417
Natural tuning of restriction endonuclease synthesis by cluster of rare arginine codons. PMID:30967604
Curated BLAST for Genomes. PMID:30944879
Complete Genome Sequence and Methylome Analysis of Deinococcus wulumuqiensis 479. PMID:30938698
Bci528I, a new isoschizomer of EcoRI isolated from Bacillus circulans 528. PMID:30937821
Determinants of Phage Host Range in Staphylococcus Species. PMID:30902858
The Patchy Distribution of Restriction⁻Modification System Genes and the Conservation of Orphan Methyltransferases in Halobacteria. PMID:30893937
Deoxyuridine in DNA has an inhibitory and promutagenic effect on RNA transcription by diverse RNA polymerases. PMID:30892639
Genomic Characteristics of Desulfonema ishimotonii Tokyo 01T Implying Horizontal Gene Transfer Among Phylogenetically Dispersed Filamentous Gliding Bacteria. PMID:30837965
The complete genome and methylome of Helicobacter pylori hpNEAfrica strain HP14039. PMID:30820249
Genomic Analysis of Shewanella sp. O23S-The Natural Host of the pSheB Plasmid Carrying Genes for Arsenic Resistance and Dissimilatory Reduction. PMID:30813619
Unveiling Genomic Diversity among Members of the Species Bifidobacterium pseudolongum, a Widely Distributed Gut Commensal of the Animal Kingdom. PMID:30737347
Single-molecule sequencing detection of N6-methyladenine in microbial reference materials. PMID:30718479
The Genome Sequence of M228, a Chinese Isolate of Pseudomonas syringae pv. actinidiae, Illustrates Insertion Sequence Element Mobility. PMID:30637393
The core genome m5C methyltransferase JHP1050 (M.Hpy99III) plays an important role in orchestrating gene expression in Helicobacter pylori. PMID:30624738
Insight Into the Diversity and Possible Role of Plasmids in the Adaptation of Psychrotolerant and Metalotolerant Arthrobacter spp. to Extreme Antarctic Environments. PMID:30619210
Genome-wide association study reveals novel loci associated with body size and carcass yields in Pekin ducks. PMID:30606130
Deciphering bacterial epigenomes using modern sequencing technologies. PMID:30546107
Complete Genome Sequences of Two Rhodobacter Strains. PMID:30533667
Avoidance of recognition sites of restriction-modification systems is a widespread but not universal anti-restriction strategy of prokaryotic viruses. PMID:30526500
Impacts of horizontal gene transfer on the compact genome of the clavulanic acid-producing Streptomyces strain F613-1. PMID:30456006
Unique mechanism of target recognition by PfoI restriction endonuclease of the CCGG-family. PMID:30445642
Isolation of A Novel Bacillus thuringiensis Phage Representing A New Phage Lineage and Characterization of Its Endolysin. PMID:30404215
Structure, subunit organization and behavior of the asymmetric Type IIT restriction endonuclease BbvCI. PMID:30395313
A Type I Restriction-Modification System Associated with Enterococcus faecium Subspecies Separation. PMID:30389763
Excision-reintegration at a pneumococcal phase-variable restriction-modification locus drives within- and between-strain epigenetic differentiation and inhibits gene acquisition. PMID:30321375
Streptococcus suis contains multiple phase-variable methyltransferases that show a discrete lineage distribution. PMID:30304532
Controller protein of restriction-modification system Kpn2I affects transcription of its gene by acting as a transcription elongation roadblock. PMID:30295835
Methylation-Induced Hypermutation in Natural Populations of Bacteria. PMID:30275280
A genomic view of experimental intraspecies and interspecies transformation of a rifampicin-resistance allele into Neisseria meningitidis. PMID:30251949
DNA Methylation by Restriction Modification Systems Affects the Global Transcriptome Profile in Borrelia burgdorferi. PMID:30249703
Spread of Carbapenem Resistance by Transposition and Conjugation Among Pseudomonas aeruginosa. PMID:30233535
Prokaryotic horizontal gene transfer within the human holobiont: ecological-evolutionary inferences, implications and possibilities. PMID:30223892
Activity of Vsr endonucleases encoded by Neisseria gonorrhoeae FA1090 is influenced by MutL and MutS proteins. PMID:30165819
A model for the evolution of prokaryotic DNA restriction-modification systems based upon the structural malleability of Type I restriction-modification enzymes. PMID:30165537
Identification of the minimal bacterial 2'-deoxy-7-amido-7-deazaguanine synthesis machinery. PMID:30159947
Comparative genomic analysis of Staphylococcus lugdunensis shows a closed pan-genome and multiple barriers to horizontal gene transfer. PMID:30126366
Large plasmidome of dairy Lactococcus lactis subsp. lactis biovar diacetylactis FM03P encodes technological functions and appears highly unstable. PMID:30119641
The complete methylome of an entomopathogenic bacterium reveals the existence of loci with unmethylated Adenines. PMID:30108278
Crystal structure of a novel domain of the motor subunit of the Type I restriction enzyme EcoR124 involved in complex assembly and DNA binding. PMID:30054276
Comparative genomics of Salmonella enterica serovar Montevideo reveals lineage-specific gene differences that may influence ecological niche association. PMID:30052174
Comparison between complete genomes of an isolate of Pseudomonas syringae pv. actinidiae from Japan and a New Zealand isolate of the pandemic lineage. PMID:30026612
MetClo: methylase-assisted hierarchical DNA assembly using a single type IIS restriction enzyme. PMID:29986052
Comparative Genomics of Lactobacillus acidipiscis ACA-DC 1533 Isolated From Traditional Greek Kopanisti Cheese Against Species Within the Lactobacillus salivarius Clade. PMID:29942291
Isospecific adenine DNA methyltransferases show distinct preferences towards DNA substrates. PMID:29844340
Randomized DNA libraries construction tool: a new 3-bp 'frequent cutter' TthHB27I/sinefungin endonuclease with chemically-induced specificity. PMID:29751745
Circularly permuted variants of two CG-specific prokaryotic DNA methyltransferases. PMID:29746549
Engineering altered protein-DNA recognition specificity. PMID:29718463
An Attenuated CRISPR-Cas System in Enterococcus faecalis Permits DNA Acquisition. PMID:29717009
Complete Genome Sequence of the Freshwater Bacterium Beggiatoa leptomitoformis Strain D-401. PMID:29700149
Sequence, genome organization, annotation and proteomics of the thermophilic, 47.7-kb Geobacillus stearothermophilus bacteriophage TP-84 and its classification in the new Tp84virus genus. PMID:29624616
Analyzing AbrB-Knockout Effects through Genome and Transcriptome Sequencing of Bacillus licheniformis DW2. PMID:29599755
Revisiting Francisella tularensis subsp. holarctica, Causative Agent of Tularemia in Germany With Bioinformatics: New Insights in Genome Structure, DNA Methylation and Comparative Phylogenetic Analysis. PMID:29593661
A survey of Type III restriction-modification systems reveals numerous, novel epigenetic regulators controlling phase-variable regulons; phasevarions. PMID:29554328
Synthetic Biology Approaches to Engineer Probiotics and Members of the Human Microbiota for Biomedical Applications. PMID:29528686
The DNA Methylome of the Hyperthermoacidophilic Crenarchaeon Sulfolobus acidocaldarius. PMID:29472906
The H-subunit of the restriction endonuclease CglI contains a prototype DEAD-Z1 helicase-like motor. PMID:29471489
Function analysis of 5'-UTR of the cellulosomal xyl-doc cluster in Clostridium papyrosolvens. PMID:29467821
Phasevarions of Bacterial Pathogens: Methylomics Sheds New Light on Old Enemies. PMID:29452952
Complete Genome Sequence and Methylome Analysis of Bacillus caldolyticus NEB414. PMID:29439055
Comparative genome and methylome analysis reveals restriction/modification system diversity in the gut commensal Bifidobacterium breve. PMID:29294107
Toward Understanding Phage:Host Interactions in the Rumen; Complete Genome Sequences of Lytic Phages Infecting Rumen Bacteria. PMID:29259581
Genome-scale model guided design of Propionibacterium for enhanced propionic acid production. PMID:29255672
The non-specific adenine DNA methyltransferase M.EcoGII. PMID:29228259
Metagenomic binning and association of plasmids with bacterial host genomes using DNA methylation. PMID:29227468
Comparative genomics of Spiraeoideae-infecting Erwinia amylovora strains provides novel insight to genetic diversity and identifies the genetic basis of a low-virulence strain. PMID:29178620
DISARM is a widespread bacterial defence system with broad anti-phage activities. PMID:29085076
Analysis of somaclonal variation in transgenic and regenerated plants of Arabidopsis thaliana using methylation related metAFLP and TMD markers. PMID:29038910
De novo assembly of genomes from long sequence reads reveals uncharted territories of Propionibacterium freudenreichii. PMID:29037147
cuRRBS: simple and robust evaluation of enzyme combinations for reduced representation approaches. PMID:29036576
Insights into Epigenome Evolution from Animal and Plant Methylomes. PMID:29036466
Comparative genomics of Lactobacillus kefiranofaciens ZW3 and related members of Lactobacillus. spp reveal adaptations to dairy and gut environments. PMID:28993659
Global Survey and Genome Exploration of Bacteriophages Infecting the Lactic Acid Bacterium Streptococcus thermophilus. PMID:28955321
UbaLAI is a monomeric Type IIE restriction enzyme. PMID:28934493
Restriction-modification mediated barriers to exogenous DNA uptake and incorporation employed by Prevotella intermedia. PMID:28934361
Pseudomonas stutzeri as an alternative host for membrane proteins. PMID:28931397
DNA Adenine Methyltransferase (Dam) Overexpression Impairs Photorhabdus luminescens Motility and Virulence. PMID:28919886
Adaptation of Surface-Associated Bacteria to the Open Ocean: A Genomically Distinct Subpopulation of Phaeobacter gallaeciensis Colonizes Pacific Mesozooplankton. PMID:28912769
The third restriction-modification system from Thermus aquaticus YT-1: solving the riddle of two TaqII specificities. PMID:28911108
Complete Genome Sequence of Geobacillus thermodenitrificans T12, A Potential Host for Biotechnological Applications. PMID:28900693
Tuning DNA binding affinity and cleavage specificity of an engineered gene-targeting nuclease via surface display, flow cytometry and cellular analyses. PMID:28873986
Live attenuated enterovirus vaccine (OPV) is not associated with islet autoimmunity in children with genetic susceptibility to type 1 diabetes: prospective cohort study. PMID:28866779
Designing Randomized DNA Sequences Free of Restriction Enzyme Recognition Sites. PMID:28865135
Whole-Genome Sequence and Methylome Analysis of the Freshwater Colorless Sulfur Bacterium Thioflexothrix psekupsii D3. PMID:28860255
Methylation-dependent DNA discrimination in natural transformation of Campylobacter jejuni. PMID:28855338
Restriction endonuclease triggered bacterial apoptosis as a mechanism for long time survival. PMID:28854737
Restriction and modification of deoxyarchaeosine (dG+)-containing phage 9 g DNA. PMID:28827753
A Case Study into Microbial Genome Assembly Gap Sequences and Finishing Strategies. PMID:28769883
Toward a genetic tool development pipeline for host-associated bacteria. PMID:28624690
Analysis of the Genome and Mobilome of a Dissimilatory Arsenate Reducing Aeromonas sp. O23A Reveals Multiple Mechanisms for Heavy Metal Resistance and Metabolism. PMID:28611742
A genome-scale metabolic reconstruction of Lysinibacillus sphaericus unveils unexploited biotechnological potentials. PMID:28604819
Design of synthetic epigenetic circuits featuring memory effects and reversible switching based on DNA methylation. PMID:28537256
Anti-Restriction Protein, KlcAHS, Promotes Dissemination of Carbapenem Resistance. PMID:28512626
DNA sequence homology induces cytosine-to-thymine mutation by a heterochromatin-related pathway in Neurospora. PMID:28459455
The dynamics of the monomeric restriction endonuclease BcnI during its interaction with DNA. PMID:28453854
Complete Genome Sequence of the Original Escherichia coli Isolate, Strain NCTC86. PMID:28428314
Genomic Analysis of Factors Associated with Low Prevalence of Antibiotic Resistance in Extraintestinal Pathogenic Escherichia coli Sequence Type 95 Strains. PMID:28405633
Convergence of DNA methylation and phosphorothioation epigenetics in bacterial genomes. PMID:28400512
A machine learning approach for viral genome classification. PMID:28399797
Reconstruction of the evolution of microbial defense systems. PMID:28376755
TfoI produced by Tepidimonas fonticaldi PL17, a moderate thermophilic bacterium, is an isoschizomer of MseI. PMID:28315976
Complete Genome and Methylome Analysis of Psychrotrophic Bacterial Isolates from Lake Untersee in Antarctica. PMID:28302790
Complete Genome and Methylome Sequences of Salmonella enterica subsp. enterica Serovars Typhimurium, Saintpaul, and Stanleyville from the SARA/SARB Collection. PMID:28302778
Genome Sequence of the Thermotolerant Foodborne Pathogen Salmonella enterica Serovar Senftenberg ATCC 43845 and Phylogenetic Analysis of Loci Encoding Increased Protein Quality Control Mechanisms. PMID:28293682
DNA recognition by the SwaI restriction endonuclease involves unusual distortion of an 8 base pair A:T-rich target. PMID:28180307
DNA target recognition domains in the Type I restriction and modification systems of Staphylococcus aureus. PMID:28180279
Protein Bioinformatics Databases and Resources. PMID:28150231
The 24th annual Nucleic Acids Research database issue: a look back and upcoming changes. PMID:28053160
Use of single molecule sequencing for comparative genomics of an environmental and a clinical isolate of Clostridium difficile ribotype 078. PMID:27964731
An Enrichment of CRISPR and Other Defense-Related Features in Marine Sponge-Associated Microbial Metagenomes. PMID:27877161
Distribution of Type I Restriction-Modification Systems in Streptococcus suis: An Outlook. PMID:27869755
SNP discovery and genotyping using Genotyping-by-Sequencing in Pekin ducks. PMID:27845353
Complete Genome Sequence of Brevibacterium linens SMQ-1335. PMID:27834701
DNA Base Flipping: A General Mechanism for Writing, Reading, and Erasing DNA Modifications. PMID:27826845
Genomic analyses of multidrug resistant Pseudomonas aeruginosa PA1 resequenced by single-molecule real-time sequencing. PMID:27765811
Implementation and Data Analysis of Tn-seq, Whole-Genome Resequencing, and Single-Molecule Real-Time Sequencing for Bacterial Genetics. PMID:27672193
Diverse fates of uracilated HIV-1 DNA during infection of myeloid lineage cells. PMID:27644592
Genome-directed analysis of prophage excision, host defence systems, and central fermentative metabolism in Clostridium pasteurianum. PMID:27641836
Novel Methyltransferase Recognition Motif Identified in Chania multitudinisentens RB-25(T) gen. nov., sp. nov. PMID:27630623
The First Siphoviridae Family Bacteriophages Infecting Bordetella bronchiseptica Isolated from Environment. PMID:27628741
Steady at the wheel: conservative sex and the benefits of bacterial transformation. PMID:27619692
Novel m4C modification in type I restriction-modification systems. PMID:27580720
Identification of DNA Methyltransferase Genes in Human Pathogenic Bacteria by Comparative Genomics. PMID:27570304
Comparative Methylome Analysis of the Occasional Ruminant Respiratory Pathogen Bibersteinia trehalosi. PMID:27556252
AdoMet analog synthesis and utilization: current state of the art. PMID:27506965
A Novel Approach to Helicobacter pylori Pan-Genome Analysis for Identification of Genomic Islands. PMID:27504980
Two Inducible Prophages of an Antarctic Pseudomonas sp. ANT_H14 Use the Same Capsid for Packaging Their Genomes - Characterization of a Novel Phage Helper-Satellite System. PMID:27387973
An emerging zoonotic clone in the Netherlands provides clues to virulence and zoonotic potential of Streptococcus suis. PMID:27381348
Expression and purification of the modification-dependent restriction enzyme BisI and its homologous enzymes. PMID:27353146
Complete Genome Sequence and Methylome Analysis of Bacillus globigii ATCC 49760. PMID:27231364
The evolutionary pathway from a biologically inactive polypeptide sequence to a folded, active structural mimic of DNA. PMID:27095198
Structure of Type IIL Restriction-Modification Enzyme MmeI in Complex with DNA Has Implications for Engineering New Specificities. PMID:27082731
Evaluation of genetic diversity among strains of the human gut commensal Bifidobacterium adolescentis. PMID:27035119
Complete Genome and Methylome Sequences of Salmonella enterica subsp. enterica Serovar Panama (ATCC 7378) and Salmonella enterica subsp. enterica Serovar Sloterdijk (ATCC 15791). PMID:26988049
RiboFR-Seq: a novel approach to linking 16S rRNA amplicon profiles to metagenomes. PMID:26984526
Structural insights into DNA sequence recognition by Type ISP restriction-modification enzymes. PMID:26975655
A putative Type IIS restriction endonuclease GeoICI from Geobacillus sp.--A robust, thermostable alternative to mezophilic prototype BbvI. PMID:26949085
Complete Genome Sequence and Methylome Analysis of Aeromonas hydrophila Strain YL17, Isolated from a Compost Pile. PMID:26941143
Complete Genome Sequence and Comparative Genomics of a Novel Myxobacterium Myxococcus hansupus. PMID:26900859
The Epigenomic Landscape of Prokaryotes. PMID:26870957
Major bacterial lineages are essentially devoid of CRISPR-Cas viral defence systems. PMID:26837824
The Role of DNA Restriction-Modification Systems in the Biology of Bacillus anthracis. PMID:26834729
Electroporation-Based Genetic Manipulation in Type I Methanotrophs. PMID:26801578
Complete Genome and Methylome Sequences of Two Salmonella enterica spp. PMID:26798102
Phase variation of a Type IIG restriction-modification enzyme alters site-specific methylation patterns and gene expression in Campylobacter jejuni strain NCTC11168. PMID:26786317
Complete genome sequence of the potato pathogen Ralstonia solanacearum UY031. PMID:26779304
The Complete Genome Sequence of the Murine Pathobiont Helicobacter typhlonius. PMID:26779178
An innovative platform for quick and flexible joining of assorted DNA fragments. PMID:26758940
Type III Methyltransferase M.NgoAX from Neisseria gonorrhoeae FA1090 Regulates Biofilm Formation and Interactions with Human Cells. PMID:26733970
Complete Genome Sequence of Streptomyces sp. Strain CCM_MD2014, Isolated from Topsoil in Woods Hole, Massachusetts. PMID:26722012
Complete Genome Sequence of Curtobacterium sp. Strain MR_MD2014, Isolated from Topsoil in Woods Hole, Massachusetts. PMID:26722011
Precision methylome characterization of Mycobacterium tuberculosis complex (MTBC) using PacBio single-molecule real-time (SMRT) technology. PMID:26704977
SMRT sequencing of the Campylobacter coli BfR-CA-9557 genome sequence reveals unique methylation motifs. PMID:26689587
Lifespan of restriction-modification systems critically affects avoidance of their recognition sites in host genomes. PMID:26689194
Natural C-independent expression of restriction endonuclease in a C protein-associated restriction-modification system. PMID:26656489
On the role of steric clashes in methylation control of restriction endonuclease activity. PMID:26635397
Complete genome sequence of Salinicoccus halodurans H3B36, isolated from the Qaidam Basin in China. PMID:26634017
Re-evaluating the kinetics of ATP hydrolysis during initiation of DNA sliding by Type III restriction enzymes. PMID:26538601
Mapping DNA cleavage by the Type ISP restriction-modification enzymes following long-range communication between DNA sites in different orientations. PMID:26507855
Complete DNA Sequence of Pseudomonas syringae pv. actinidiae, the Causal Agent of Kiwifruit Canker Disease. PMID:26383666
Complete Genome Sequence of Enteroinvasive Escherichia coli O96:H19 Associated with a Severe Foodborne Outbreak. PMID:26251502
A Modified Shuttle Plasmid Facilitates Expression of a Flavin Mononucleotide-Based Fluorescent Protein in Treponema denticola ATCC 35405. PMID:26162875
Genetic Stabilization of the Drug-Resistant PMEN1 Pneumococcus Lineage by Its Distinctive DpnIII Restriction-Modification System. PMID:26081630
Single molecule-level detection and long read-based phasing of epigenetic variations in bacterial methylomes. PMID:26074426
Structural basis of asymmetric DNA methylation and ATP-triggered long-range diffusion by EcoP15I. PMID:26067164
Engineering a Nickase on the Homing Endonuclease I-DmoI Scaffold. PMID:26045557
Genome-wide DNA methylation analysis of Haloferax volcanii H26 and identification of DNA methyltransferase related PD-(D/E)XK nuclease family protein HVO_A0006. PMID:25904898
Highly Iterated Palindromic Sequences (HIPs) and Their Relationship to DNA Methyltransferases. PMID:25789551
Restriction-modification system with methyl-inhibited base excision and abasic-site cleavage activities. PMID:25697504
The 2015 Nucleic Acids Research Database Issue and molecular biology database collection. PMID:25593347 -
REBASE--a database for DNA restriction and modification: enzymes, genes and genomes
PubMed citations: 261.
261 articles citing: REBASE--a database for DNA restriction and modification: enzymes, genes and genomes
Detecting DNA Methylations in the Hyperthermoacidophilic Crenarchaeon Sulfolobus acidocaldarius Using SMRT Sequencing. PMID:35922620
Plant DNA Methylation Responds to Nutrient Stress. PMID:35741754
Intracellular Salmonella Paratyphi A is motile and differs in the expression of flagella-chemotaxis, SPI-1 and carbon utilization pathways in comparison to intracellular S. Typhimurium. PMID:35381053
A high-quality reference genome for the fish pathogen Streptococcus iniae. PMID:35229712
Genomic Features and Pervasive Negative Selection in Rhodanobacter Strains Isolated from Nitrate and Heavy Metal Contaminated Aquifer. PMID:35107332
Characterization of the Type I Restriction Modification System Broadly Conserved among Group A Streptococci. PMID:34787444
The Influence of 5'R and 5'S cdA and cdG on the Activity of BsmAI and SspI Restriction Enzymes. PMID:34205449
Epigenomic Landscape of Lyme Disease Spirochetes Reveals Novel Motifs. PMID:34156261
Nutrient Loading and Viral Memory Drive Accumulation of Restriction Modification Systems in Bloom-Forming Cyanobacteria. PMID:34060332
Persistent Bacterial Coinfection of a COVID-19 Patient Caused by a Genetically Adapted Pseudomonas aeruginosa Chronic Colonizer. PMID:33816347
Novel Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV2) and Other Coronaviruses: A Genome-wide Comparative Annotation and Analysis. PMID:33564990
Evolutionary Ecology and Interplay of Prokaryotic Innate and Adaptive Immune Systems. PMID:33022264
Methylase-assisted subcloning for high throughput BioBrick assembly. PMID:32974095
Experimental approaches to tracking mobile genetic elements in microbial communities. PMID:32672812
Linking high GC content to the repair of double strand breaks in prokaryotic genomes. PMID:31703064
Functional screening of a soil metagenome for DNA endonucleases by acquired resistance to bacteriophage infection. PMID:31643043
A Stable Genetic Transformation System and Implications of the Type IV Restriction System in the Nitrogen-Fixing Plant Endosymbiont Frankia alni ACN14a. PMID:31608043
Genome-wide systematic identification of methyltransferase recognition and modification patterns. PMID:31427571
SMRT sequencing reveals differential patterns of methylation in two O111:H- STEC isolates from a hemolytic uremic syndrome outbreak in Australia. PMID:31263188
Visualization and prediction of CRISPR incidence in microbial trait-space to identify drivers of antiviral immune strategy. PMID:31239539
Adaptive dif Modules in Permafrost Strains of Acinetobacter lwoffii and Their Distribution and Abundance Among Present Day Acinetobacter Strains. PMID:30984151
A new type of DNA phosphorothioation-based antiviral system in archaea. PMID:30975999
Bci528I, a new isoschizomer of EcoRI isolated from Bacillus circulans 528. PMID:30937821
Metaepigenomic analysis reveals the unexplored diversity of DNA methylation in an environmental prokaryotic community. PMID:30635580
The Need for Speed: Run-On Oligomer Filament Formation Provides Maximum Speed with Maximum Sequestration of Activity. PMID:30518649
Moraxella catarrhalis Restriction-Modification Systems Are Associated with Phylogenetic Lineage and Disease. PMID:30335144
DNA phosphorothioate modification-a new multi-functional epigenetic system in bacteria. PMID:30289455
Thermosipho spp. Immune System Differences Affect Variation in Genome Size and Geographical Distributions. PMID:30239713
Evaluating the Safety of Potential Probiotic Enterococcus durans KLDS6.0930 Using Whole Genome Sequencing and Oral Toxicity Study. PMID:30186262
REHUNT: a reliable and open source package for restriction enzyme hunting. PMID:30092755
Genome editing of Ralstonia eutropha using an electroporation-based CRISPR-Cas9 technique. PMID:29951116
LraI from Lactococcus raffinolactis BGTRK10-1, an Isoschizomer of EcoRI, Exhibits Ion Concentration-Dependent Specific Star Activity. PMID:29789800
Characterizing the DNA Methyltransferases of Haloferax volcanii via Bioinformatics, Gene Deletion, and SMRT Sequencing. PMID:29495512
The DNA Methylome of the Hyperthermoacidophilic Crenarchaeon Sulfolobus acidocaldarius. PMID:29472906
Function analysis of 5'-UTR of the cellulosomal xyl-doc cluster in Clostridium papyrosolvens. PMID:29467821
Identification of the DNA methyltransferases establishing the methylome of the cyanobacterium Synechocystis sp. PCC 6803. PMID:29444255
Characterization of Sinorhizobium sp. LM21 Prophages and Virus-Encoded DNA Methyltransferases in the Light of Comparative Genomic Analyses of the Sinorhizobial Virome. PMID:28672885
Convergence of DNA methylation and phosphorothioation epigenetics in bacterial genomes. PMID:28400512
Complete Genome Sequence and Methylome Analysis of Acinetobacter calcoaceticus 65. PMID:28336599
Mobile Introns Shape the Genetic Diversity of Their Host Genes. PMID:28193728
The complete genome sequence of the yogurt isolate Streptococcus thermophilus ACA-DC 2. PMID:28163827
Networking in microbes: conjugative elements and plasmids in the genus Alteromonas. PMID:28056800
Methylome Analysis of Two Xanthomonas spp. Using Single-Molecule Real-Time Sequencing. PMID:27904456
Comparative Genomics Reveals the Diversity of Restriction-Modification Systems and DNA Methylation Sites in Listeria monocytogenes. PMID:27836852
Is the Evolution of Salmonella enterica subsp. enterica Linked to Restriction-Modification Systems? PMID:27822532
Resistance of Permafrost and Modern Acinetobacter lwoffii Strains to Heavy Metals and Arsenic Revealed by Genome Analysis. PMID:27795957
Listeria monocytogenes in Stone Fruits Linked to a Multistate Outbreak: Enumeration of Cells and Whole-Genome Sequencing. PMID:27694232
Vibrio natriegens as a fast-growing host for molecular biology. PMID:27571549
OGS2: genome re-annotation of the jewel wasp Nasonia vitripennis. PMID:27561358
Contrasting Patterns of rDNA Homogenization within the Zygosaccharomyces rouxii Species Complex. PMID:27501051
Epigenetic Switch Driven by DNA Inversions Dictates Phase Variation in Streptococcus pneumoniae. PMID:27427949
Whole genomic DNA sequencing and comparative genomic analysis of Arthrospira platensis: high genome plasticity and genetic diversity. PMID:27330141
Regulation of genetic flux between bacteria by restriction-modification systems. PMID:27140615
FN-Identify: Novel Restriction Enzymes-Based Method for Bacterial Identification in Absence of Genome Sequencing. PMID:26880910
Complete genome sequence and genomic characterization of Microcystis panniformis FACHB 1757 by third-generation sequencing. PMID:26823957
Complete Genome Sequence of a Strain of Azospirillum thiophilum Isolated from a Sulfide Spring. PMID:26744373
Lifespan of restriction-modification systems critically affects avoidance of their recognition sites in host genomes. PMID:26689194
How quantum entanglement in DNA synchronizes double-strand breakage by type II restriction endonucleases. PMID:26682627
Complete Genome Sequence of the Freshwater Colorless Sulfur Bacterium Beggiatoa leptomitoformis [corrected] Neotype Strain D-402T. PMID:26659680
DNA Methylation Assessed by SMRT Sequencing Is Linked to Mutations in Neisseria meningitidis Isolates. PMID:26656597
Whole genome sequencing provides possible explanations for the difference in phage susceptibility among two Salmonella Typhimurium phage types (DT8 and DT30) associated with a single foodborne outbreak. PMID:26613761
A Cytosine Methyltransferase Modulates the Cell Envelope Stress Response in the Cholera Pathogen [corrected]. PMID:26588462
Lineage-Specific Methyltransferases Define the Methylome of the Globally Disseminated Escherichia coli ST131 Clone. PMID:26578678
Complete genome sequence of Propionibacterium freudenreichii DSM 20271(T). PMID:26500719
Dormant phages of Helicobacter pylori reveal distinct populations in Europe. PMID:26387443
MmoSTI restriction endonuclease, isolated from Morganella morganii infecting a tropical moth, Actias selene, cleaving 5'-|CCNGG-3' sequences. PMID:26280518
Intraspecies Genomic Diversity and Long-Term Persistence of Bifidobacterium longum. PMID:26275230
Systematic Mapping of Protein Mutational Space by Prolonged Drift Reveals the Deleterious Effects of Seemingly Neutral Mutations. PMID:26274323
A biphasic epigenetic switch controls immunoevasion, virulence and niche adaptation in non-typeable Haemophilus influenzae. PMID:26215614
Restriction site free cloning (RSFC) plasmid family for seamless, sequence independent cloning in Pichia pastoris. PMID:26169367
Restriction modification systems as engines of diversity. PMID:26082758
Misassembly detection using paired-end sequence reads and optical mapping data. PMID:26072512
Functional coupling of duplex translocation to DNA cleavage in a type I restriction enzyme. PMID:26039067
The complete methylome of Helicobacter pylori UM032. PMID:26031894
Structure-guided sequence specificity engineering of the modification-dependent restriction endonuclease LpnPI. PMID:26001968
Genomic analysis of a ginger pathogen Bacillus pumilus providing the understanding to the pathogenesis and the novel control strategy. PMID:25989507
Expression and purification of a single-chain Type IV restriction enzyme Eco94GmrSD and determination of its substrate preference. PMID:25988532
Characterization of LlaKI, a New Metal Ion-Independent Restriction Endonuclease from Lactococcus lactis KLDS4. PMID:25969755
Complete Genome Sequence Analysis of Bacillus subtilis T30. PMID:25953183
Genome-wide methylation patterns in Salmonella enterica Subsp. enterica Serovars. PMID:25860355
Specificity of the ModA11, ModA12 and ModD1 epigenetic regulator N(6)-adenine DNA methyltransferases of Neisseria meningitidis. PMID:25845594
Genome Modification in Enterococcus faecalis OG1RF Assessed by Bisulfite Sequencing and Single-Molecule Real-Time Sequencing. PMID:25825433
Multiplexed locus-specific analysis of DNA methylation in single cells. PMID:25811896
Insights into the Origin of Clostridium botulinum Strains: Evolution of Distinct Restriction Endonuclease Sites in rrs (16S rRNA gene). PMID:25805900
Archaeal extrachromosomal genetic elements. PMID:25694123
Analysis of the HindIII-catalyzed reaction by time-resolved crystallography. PMID:25664735
A comparative analysis of methylome profiles of Campylobacter jejuni sheep abortion isolate and gastroenteric strains using PacBio data. PMID:25642218
Endonuclease specificity and sequence dependence of type IIS restriction enzymes. PMID:25629514
Multilocus sequence typing of Leuconostoc gelidum subsp. gasicomitatum, a Psychrotrophic lactic acid bacterium causing spoilage of packaged perishable foods. PMID:25616799
Complete Genome Sequence of Bifidobacterium longum 105-A, a Strain with High Transformation Efficiency. PMID:25523770
Enzymatic synthesis of modified oligonucleotides by PEAR using Phusion and KOD DNA polymerases. PMID:25517220
Sequence-specific labeling of nucleic acids and proteins with methyltransferases and cofactor analogues. PMID:25490674
Expansion of the genetic toolkit for metabolic engineering of Clostridium pasteurianum: chromosomal gene disruption of the endogenous CpaAI restriction enzyme. PMID:25431621
DNA cleavage by CgII and NgoAVII requires interaction between N- and R-proteins and extensive nucleotide hydrolysis. PMID:25429977
Plasmids of psychrophilic and psychrotolerant bacteria and their role in adaptation to cold environments. PMID:25426110
Diversification of bacterial genome content through distinct mechanisms over different timescales. PMID:25407023
qDNAmod: a statistical model-based tool to reveal intercellular heterogeneity of DNA modification from SMRT sequencing data. PMID:25404133
REBASE--a database for DNA restriction and modification: enzymes, genes and genomes. PMID:25378308
Computational tools and algorithms for designing customized synthetic genes. PMID:25340050
The genomic landscape of the verrucomicrobial methanotroph Methylacidiphilum fumariolicum SolV. PMID:25331649
Selective microbial genomic DNA isolation using restriction endonucleases. PMID:25279840
Methyltransferases acquired by lactococcal 936-type phage provide protection against restriction endonuclease activity. PMID:25269955
A random six-phase switch regulates pneumococcal virulence via global epigenetic changes. PMID:25268848
ClpXP protease targets long-lived DNA translocation states of a helicase-like motor to cause restriction alleviation. PMID:25260590
The interplay of restriction-modification systems with mobile genetic elements and their prokaryotic hosts. PMID:25120263
Selective whole genome amplification for resequencing target microbial species from complex natural samples. PMID:25096321
Genomic encyclopedia of type strains of the genus Bifidobacterium. PMID:25085493
Genomic characterization and transcriptional studies of the starch-utilizing strain Bifidobacterium adolescentis 22L. PMID:25063659
Whole-genome sequencing reveals clonal expansion of multiresistant Staphylococcus haemolyticus in European hospitals. PMID:25038069
Molecular bases and role of viruses in the human microbiome. PMID:25020228
Progressive genomic convergence of two Helicobacter pylori strains during mixed infection of a patient with chronic gastritis. PMID:25007814
Protein and DNA modifications: evolutionary imprints of bacterial biochemical diversification and geochemistry on the provenance of eukaryotic epigenetics. PMID:24984775
Identification of essential alphaproteobacterial genes reveals operational variability in conserved developmental and cell cycle systems. PMID:24975755
Type II restriction endonucleases--a historical perspective and more. PMID:24878924
Identification of restriction-modification systems of Bifidobacterium animalis subsp. lactis CNCM I-2494 by SMRT sequencing and associated methylome analysis. PMID:24743599
Helicobacter pylori DNA methyltransferases and the epigenetic field effect in cancerization. PMID:24723914
Methylome diversification through changes in DNA methyltransferase sequence specificity. PMID:24722038
Comparative genomics of the dairy isolate Streptococcus macedonicus ACA-DC 198 against related members of the Streptococcus bovis/Streptococcus equinus complex. PMID:24713045
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. PMID:24710319
TstI, a Type II restriction-modification protein with DNA recognition, cleavage and methylation functions in a single polypeptide. PMID:24634443
Engineering nicking enzymes that preferentially nick 5-methylcytosine-modified DNA. PMID:24609382
Reliable differentiation of Meyerozyma guilliermondii from Meyerozyma caribbica by internal transcribed spacer restriction fingerprinting. PMID:24575831
A base composition analysis of natural patterns for the preprocessing of metagenome sequences. PMID:24564274
Genomic analysis of thermophilic Bacillus coagulans strains: efficient producers for platform bio-chemicals. PMID:24473268
Super-resolution optical DNA Mapping via DNA methyltransferase-directed click chemistry. PMID:24452797
Characterization of cleavage intermediate and star sites of RM.Tth111II. PMID:24452415
Bacterial community dynamics and activity in relation to dissolved organic matter availability during sea-ice formation in a mesocosm experiment. PMID:24443388
Cofactor analogue-induced chemical reactivation of endonuclease activity in a DNA cleavage/methylation deficient TspGWI N₄₇₃A variant in the NPPY motif. PMID:24442320
The functions of DNA methylation by CcrM in Caulobacter crescentus: a global approach. PMID:24398711
How to interpret methylation sensitive amplified polymorphism (MSAP) profiles? PMID:24393618
ArdA proteins from different mobile genetic elements can bind to the EcoKI Type I DNA methyltransferase of E. coli K12. PMID:24368349
Online exercise for the design and simulation of PCR and PCR-RFLP experiments. PMID:24314313
The complex methylome of the human gastric pathogen Helicobacter pylori. PMID:24302578
Global methylation state at base-pair resolution of the Caulobacter genome throughout the cell cycle. PMID:24218615
Cytosine-to-uracil deamination by SssI DNA methyltransferase. PMID:24205358
High-throughput, cost-effective verification of structural DNA assembly. PMID:24203706
Highlights of the DNA cutters: a short history of the restriction enzymes. PMID:24141096
Bacteriophage orphan DNA methyltransferases: insights from their bacterial origin, function, and occurrence. PMID:24123737
Directional cloning of DNA fragments using deoxyinosine-containing oligonucleotides and endonuclease V. PMID:24090222
Naturally-occurring, dually-functional fusions between restriction endonucleases and regulatory proteins. PMID:24083337
Type I restriction enzymes and their relatives. PMID:24068554
Allosteric regulation of DNA cleavage and sequence-specificity through run-on oligomerization. PMID:24055317
Structure determination and biochemical characterization of a putative HNH endonuclease from Geobacter metallireducens GS-15. PMID:24039739
Exploring the roles of DNA methylation in the metal-reducing bacterium Shewanella oneidensis MR-1. PMID:23995632
The other face of restriction: modification-dependent enzymes. PMID:23990325
To be or not to be: regulation of restriction-modification systems and other toxin-antitoxin systems. PMID:23945938
Mutations of the domain forming the dimeric interface of the ArdA protein affect dimerization and antimodification activity but not antirestriction activity. PMID:23910724
Homologous recombination drives both sequence diversity and gene content variation in Neisseria meningitidis. PMID:23902748
DNA methylation impacts gene expression and ensures hypoxic survival of Mycobacterium tuberculosis. PMID:23853579
Ubiquitin reference technique and its use in ubiquitin-lacking prokaryotes. PMID:23825692
Combined methylation mapping of 5mC and 5hmC during early embryonic stages in bovine. PMID:23773395
Impact of target site distribution for Type I restriction enzymes on the evolution of methicillin-resistant Staphylococcus aureus (MRSA) populations. PMID:23771140
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. PMID:23724933
Overcoming restriction as a barrier to DNA transformation in Caldicellulosiruptor species results in efficient marker replacement. PMID:23714229
Comparison of restriction enzymes for pulsed-field gel electrophoresis typing of Moraxella catarrhalis. PMID:23678064
Construction of a stable replicating shuttle vector for Caldicellulosiruptor species: use for extending genetic methodologies to other members of this genus. PMID:23658781
Comparative genomics of Bifidobacterium animalis subsp. lactis reveals a strict monophyletic bifidobacterial taxon. PMID:23645200
A bistable hysteretic switch in an activator-repressor regulated restriction-modification system. PMID:23630319
Evidence for the widespread distribution of CRISPR-Cas system in the Phylum Cyanobacteria. PMID:23628889
Massively parallel characterization of restriction endonucleases. PMID:23605040
Mobile elements in a single-filament orange Guaymas Basin Beggiatoa ("Candidatus Maribeggiatoa") sp. draft genome: evidence for genetic exchange with cyanobacteria. PMID:23603674
Identification and prioritization of novel uncharacterized peptidases for biochemical characterization. PMID:23584835
Development of an electrotransformation protocol for genetic manipulation of Clostridium pasteurianum. PMID:23570573
Homologues of bacterial TnpB_IS605 are widespread in diverse eukaryotic transposable elements. PMID:23548000
Restriction endonuclease TseI cleaves A:A and T:T mismatches in CAG and CTG repeats. PMID:23525471
Fully assembled genome sequence for Salmonella enterica subsp. enterica Serovar Javiana CFSAN001992. PMID:23516208
Diverse functions of restriction-modification systems in addition to cellular defense. PMID:23471617
Entering the era of bacterial epigenomics with single molecule real time DNA sequencing. PMID:23434113
Enhanced 5-methylcytosine detection in single-molecule, real-time sequencing via Tet1 oxidation. PMID:23339471
Tough nuts to crack: site-directed mutagenesis of bifidobacteria remains a challenge. PMID:23314785
Comprehensive methylome characterization of Mycoplasma genitalium and Mycoplasma pneumoniae at single-base resolution. PMID:23300489
CpG underrepresentation and the bacterial CpG-specific DNA methyltransferase M.MpeI. PMID:23248272
Genomic analysis of cold-active Colwelliaphage 9A and psychrophilic phage-host interactions. PMID:23224375
The Type ISP Restriction-Modification enzymes LlaBIII and LlaGI use a translocation-collision mechanism to cleave non-specific DNA distant from their recognition sites. PMID:23222132
EcoGene 3.0. PMID:23197660
Genome-derived insights into the biology of the hepatotoxic bloom-forming cyanobacterium Anabaena sp. strain 90. PMID:23148582
Organization of the BcgI restriction-modification protein for the cleavage of eight phosphodiester bonds in DNA. PMID:23147005
Organization of the BcgI restriction-modification protein for the transfer of one methyl group to DNA. PMID:23147004
Genome-wide mapping of methylated adenine residues in pathogenic Escherichia coli using single-molecule real-time sequencing. PMID:23138224
Natural zinc ribbon HNH endonucleases and engineered zinc finger nicking endonuclease. PMID:23125367
Evolutionary transitions to new DNA methyltransferases through target site expansion and shrinkage. PMID:23074188
The methylomes of six bacteria. PMID:23034806
A mimicking-of-DNA-methylation-patterns pipeline for overcoming the restriction barrier of bacteria. PMID:23028379
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. PMID:23002145
Solitary restriction endonucleases in prokaryotic genomes. PMID:22965118
Methylation by a unique α-class N4-cytosine methyltransferase is required for DNA transformation of Caldicellulosiruptor bescii DSM6725. PMID:22928042
Identification of Cj1051c as a major determinant for the restriction barrier of Campylobacter jejuni strain NCTC11168. PMID:22923403
Comparative genomics evidence that only protein toxins are tagging bad bugs. PMID:22919573
Movement of DNA sequence recognition domains between non-orthologous proteins. PMID:22821560
Restriction and sequence alterations affect DNA uptake sequence-dependent transformation in Neisseria meningitidis. PMID:22768309
Screening for catalytically active Type II restriction endonucleases using segregation-induced methylation deficiency. PMID:22753027
Rational engineering of sequence specificity in R.MwoI restriction endonuclease. PMID:22735699
Exploring the DNA mimicry of the Ocr protein of phage T7. PMID:22684506
Superfamily 2 helicases. PMID:22652765
Replacing and additive horizontal gene transfer in Streptococcus. PMID:22617954
Context-dependent conservation of DNA methyltransferases in bacteria. PMID:22573173
LAHEDES: the LAGLIDADG homing endonuclease database and engineering server. PMID:22570419
The recognition domain of the methyl-specific endonuclease McrBC flips out 5-methylcytosine. PMID:22570415
Dcm methylation is detrimental to plasmid transformation in Clostridium thermocellum. PMID:22559230
Aberrant DNA methylation and prostate cancer. PMID:22547956
Dissociation from DNA of Type III Restriction-Modification enzymes during helicase-dependent motion and following endonuclease activity. PMID:22523084
Structural mechanisms of the degenerate sequence recognition by Bse634I restriction endonuclease. PMID:22495930
Origin of the diversity in DNA recognition domains in phasevarion associated modA genes of pathogenic Neisseria and Haemophilus influenzae. PMID:22457715
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. PMID:22392282
DNA looping by FokI: the impact of synapse geometry on loop topology at varied site orientations. PMID:22362745
Two novel type II restriction-modification systems occupying genomically equivalent locations on the chromosomes of Listeria monocytogenes strains. PMID:22327591
A vast collection of microbial genes that are toxic to bacteria. PMID:22300632
A novel restriction-modification system is responsible for temperature-dependent phage resistance in Listeria monocytogenes ECII. PMID:22247158
Structure and operation of the DNA-translocating type I DNA restriction enzymes. PMID:22215814
Type III restriction endonuclease EcoP15I is a heterotrimeric complex containing one Res subunit with several DNA-binding regions and ATPase activity. PMID:22199260
Methylation-dependent DNA restriction in Bacillus anthracis. PMID:22178763
Characterization of DNA methyltransferase specificities using single-molecule, real-time DNA sequencing. PMID:22156058
Bifunctional TaqII restriction endonuclease: redefining the prototype DNA recognition site and establishing the Fidelity Index for partial cleaving. PMID:22141927
On the evolutionary origin of eukaryotic DNA methyltransferases and Dnmt2. PMID:22140515
Speed, sensitivity, and bistability in auto-activating signaling circuits. PMID:22125482
A versatile element for gene addition in bacterial chromosomes. PMID:22123741
DNAtraffic--a new database for systems biology of DNA dynamics during the cell life. PMID:22110027
Novel non-specific DNA adenine methyltransferases. PMID:22102579
Databases and bioinformatics tools for the study of DNA repair. PMID:22091405
Characterization of type II and III restriction-modification systems from Bacillus cereus strains ATCC 10987 and ATCC 14579. PMID:22037402
Illuminating the reaction pathway of the FokI restriction endonuclease by fluorescence resonance energy transfer. PMID:21993298
Rapid genotyping of soybean cultivars using high throughput sequencing. PMID:21949759
Cloning and characterization of the TneDI restriction: modification system of Thermotoga neapolitana. PMID:21918796
Enzymatic synthesis of long double-stranded DNA labeled with haloderivatives of nucleobases in a precisely pre-determined sequence. PMID:21864341
Comparative characterization of the PvuRts1I family of restriction enzymes and their application in mapping genomic 5-hydroxymethylcytosine. PMID:21813453
Labeling DNA for single-molecule experiments: methods of labeling internal specific sequences on double-stranded DNA. PMID:21734993
Characterization and crystal structure of the type IIG restriction endonuclease RM.BpuSI. PMID:21724614
The MspJI family of modification-dependent restriction endonucleases for epigenetic studies. PMID:21690366
An investigation of the structural requirements for ATP hydrolysis and DNA cleavage by the EcoKI Type I DNA restriction and modification enzyme. PMID:21685455
Concerted action at eight phosphodiester bonds by the BcgI restriction endonuclease. PMID:21653548
Construction of Japanese BAC library Yamato-2 (JY2): a set of 330K clone resources of damage-minimized DNA taken from a genetically established Japanese individual. PMID:21611881
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. PMID:21604181
Disruption of a type II endonuclease (TDE0911) enables Treponema denticola ATCC 35405 to accept an unmethylated shuttle vector. PMID:21602384
Domain movement within a gene: a novel evolutionary mechanism for protein diversification. PMID:21533192
Identification of genes and genomic islands correlated with high pathogenicity in Streptococcus suis using whole genome tiling microarrays. PMID:21479213
Antisense RNA associated with biological regulation of a restriction-modification system. PMID:21459843
A type IV modification-dependent restriction enzyme SauUSI from Staphylococcus aureus subsp. aureus USA300. PMID:21421560
Natural transformation of Myxococcus xanthus. PMID:21378184
Identification of restriction endonucleases sensitive to 5-cytosine methylation at non-CpG sites, including expanded (CAG)n/(CTG)n repeats. PMID:21364324
A novel immunity system for bacterial nucleic acid degrading toxins and its recruitment in various eukaryotic and DNA viral systems. PMID:21306995
Fused eco29kIR- and M genes coding for a fully functional hybrid polypeptide as a model of molecular evolution of restriction-modification systems. PMID:21291520
Recognition of an expanded genetic alphabet by type-II restriction endonucleases and their application to analyze polymerase fidelity. PMID:21245035
Degenerate sequence recognition by the monomeric restriction enzyme: single mutation converts BcnI into a strand-specific nicking endonuclease. PMID:21227928
Characterization of Helicobacter pylori factors that control transformation frequency and integration length during inter-strain DNA recombination. PMID:21219459
Cleavage of phosphorothioated DNA and methylated DNA by the type IV restriction endonuclease ScoMcrA. PMID:21203499
Translational independence between overlapping genes for a restriction endonuclease and its transcriptional regulator. PMID:21092102
The phage-host arms race: shaping the evolution of microbes. PMID:20979102
Nucleases: diversity of structure, function and mechanism. PMID:20854710
Differences in methylation at GATC sites in genomic DNA of Campylobacter coli from turkeys and swine. PMID:20833787
Asymmetric DNA recognition by the OkrAI endonuclease, an isoschizomer of BamHI. PMID:20833632
Natural and engineered nicking endonucleases--from cleavage mechanism to engineering of strand-specificity. PMID:20805246
Sequence-specific cleavage of RNA by Type II restriction enzymes. PMID:20702422
The type II restriction endonuclease MvaI has dual specificity. PMID:20693529
Alteration of sequence specificity of the type IIS restriction endonuclease BtsI. PMID:20668693
BspRI restriction endonuclease: cloning, expression in Escherichia coli and sequential cleavage mechanism. PMID:20587501
Unusual target site disruption by the rare-cutting HNH restriction endonuclease PacI. PMID:20541511
Cloning of NruI and Sbo13I restriction and modification sstems in E. coli and amino acid sequence comparison of M.NruI and M.Sbo13I with other amino-methyltransferases. PMID:20497557
A unique family of Mrr-like modification-dependent restriction endonucleases. PMID:20444879
GeneDesign 3.0 is an updated synthetic biology toolkit. PMID:20211837
A putative mobile genetic element carrying a novel type IIF restriction-modification system (PluTI). PMID:20071747
Genome comparison and context analysis reveals putative mobile forms of restriction-modification systems and related rearrangements. PMID:20071371 - http://dx.doi.org/10.1093/nar/gku1046
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deoxyribonucleic acid
metasource: Fairsharing.org
version: FAIRsharing.org: REBASE; Restriction enzymes and methylases database; DOI: https://doi.org/10.25504/FAIRsharing.9sb9qh; Last edited: April 26, 2021, 2:42 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
enzyme
metasource: Fairsharing.org
version: FAIRsharing.org: REBASE; Restriction enzymes and methylases database; DOI: https://doi.org/10.25504/FAIRsharing.9sb9qh; Last edited: April 26, 2021, 2:42 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
genome
metasource: Fairsharing.org
version: FAIRsharing.org: REBASE; Restriction enzymes and methylases database; DOI: https://doi.org/10.25504/FAIRsharing.9sb9qh; Last edited: April 26, 2021, 2:42 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
molecular structure
metasource: Fairsharing.org
version: FAIRsharing.org: REBASE; Restriction enzymes and methylases database; DOI: https://doi.org/10.25504/FAIRsharing.9sb9qh; Last edited: April 26, 2021, 2:42 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
protein
metasource: Fairsharing.org
version: FAIRsharing.org: REBASE; Restriction enzymes and methylases database; DOI: https://doi.org/10.25504/FAIRsharing.9sb9qh; Last edited: April 26, 2021, 2:42 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
ribonucleic acid
metasource: Fairsharing.org
version: FAIRsharing.org: REBASE; Restriction enzymes and methylases database; DOI: https://doi.org/10.25504/FAIRsharing.9sb9qh; Last edited: April 26, 2021, 2:42 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
small molecule
metasource: Fairsharing.org
version: FAIRsharing.org: REBASE; Restriction enzymes and methylases database; DOI: https://doi.org/10.25504/FAIRsharing.9sb9qh; Last edited: April 26, 2021, 2:42 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
structure
metasource: Fairsharing.org
version: FAIRsharing.org: REBASE; Restriction enzymes and methylases database; DOI: https://doi.org/10.25504/FAIRsharing.9sb9qh; Last edited: April 26, 2021, 2:42 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
protein sequence databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
databases of individual protein families
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
dna methyltransferases
metasource: re3data.org
version: re3data.org: REBASE; editing status 2017-11-21; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3J930 last accessed: 2022-11-04
crystals
metasource: re3data.org
version: re3data.org: REBASE; editing status 2017-11-21; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3J930 last accessed: 2022-11-04
endonuclease
metasource: re3data.org
version: re3data.org: REBASE; editing status 2017-11-21; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3J930 last accessed: 2022-11-04
enzymes
metasource: re3data.org
version: re3data.org: REBASE; editing status 2017-11-21; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3J930 last accessed: 2022-11-04
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:47.988817
genetics
metasource: re3data.org
version: re3data.org: REBASE; editing status 2017-11-21; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3J930 last accessed: 2022-11-04
genomics
metasource: re3data.org
version: re3data.org: REBASE; editing status 2017-11-21; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3J930 last accessed: 2022-11-04
proteins
metasource: re3data.org
version: re3data.org: REBASE; editing status 2017-11-21; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3J930 last accessed: 2022-11-04
sequences
metasource: re3data.org
version: re3data.org: REBASE; editing status 2017-11-21; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3J930 last accessed: 2022-11-04
dna
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:47.988817
protein binding sites
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:47.988817
dna binding sites
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:47.988817
Tags
More detailed information about this field from each metasource.
deoxyribonucleic acid
metasource: Fairsharing.orgversion: FAIRsharing.org: REBASE; Restriction enzymes and methylases database; DOI: https://doi.org/10.25504/FAIRsharing.9sb9qh; Last edited: April 26, 2021, 2:42 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
enzyme
metasource: Fairsharing.orgversion: FAIRsharing.org: REBASE; Restriction enzymes and methylases database; DOI: https://doi.org/10.25504/FAIRsharing.9sb9qh; Last edited: April 26, 2021, 2:42 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
genome
metasource: Fairsharing.orgversion: FAIRsharing.org: REBASE; Restriction enzymes and methylases database; DOI: https://doi.org/10.25504/FAIRsharing.9sb9qh; Last edited: April 26, 2021, 2:42 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
molecular structure
metasource: Fairsharing.orgversion: FAIRsharing.org: REBASE; Restriction enzymes and methylases database; DOI: https://doi.org/10.25504/FAIRsharing.9sb9qh; Last edited: April 26, 2021, 2:42 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
protein
metasource: Fairsharing.orgversion: FAIRsharing.org: REBASE; Restriction enzymes and methylases database; DOI: https://doi.org/10.25504/FAIRsharing.9sb9qh; Last edited: April 26, 2021, 2:42 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
ribonucleic acid
metasource: Fairsharing.orgversion: FAIRsharing.org: REBASE; Restriction enzymes and methylases database; DOI: https://doi.org/10.25504/FAIRsharing.9sb9qh; Last edited: April 26, 2021, 2:42 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
small molecule
metasource: Fairsharing.orgversion: FAIRsharing.org: REBASE; Restriction enzymes and methylases database; DOI: https://doi.org/10.25504/FAIRsharing.9sb9qh; Last edited: April 26, 2021, 2:42 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
structure
metasource: Fairsharing.orgversion: FAIRsharing.org: REBASE; Restriction enzymes and methylases database; DOI: https://doi.org/10.25504/FAIRsharing.9sb9qh; Last edited: April 26, 2021, 2:42 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
protein sequence databases
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
databases of individual protein families
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
dna methyltransferases
metasource: re3data.orgversion: re3data.org: REBASE; editing status 2017-11-21; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3J930 last accessed: 2022-11-04
crystals
metasource: re3data.orgversion: re3data.org: REBASE; editing status 2017-11-21; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3J930 last accessed: 2022-11-04
endonuclease
metasource: re3data.orgversion: re3data.org: REBASE; editing status 2017-11-21; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3J930 last accessed: 2022-11-04
enzymes
metasource: re3data.orgversion: re3data.org: REBASE; editing status 2017-11-21; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3J930 last accessed: 2022-11-04
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:47.988817
genetics
metasource: re3data.orgversion: re3data.org: REBASE; editing status 2017-11-21; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3J930 last accessed: 2022-11-04
genomics
metasource: re3data.orgversion: re3data.org: REBASE; editing status 2017-11-21; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3J930 last accessed: 2022-11-04
proteins
metasource: re3data.orgversion: re3data.org: REBASE; editing status 2017-11-21; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3J930 last accessed: 2022-11-04
sequences
metasource: re3data.orgversion: re3data.org: REBASE; editing status 2017-11-21; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3J930 last accessed: 2022-11-04
dna
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:34:47.988817
protein binding sites
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:34:47.988817
dna binding sites
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:34:47.988817
dna enzyme genome molecular structure protein rna small molecule structure protein sequence protein family dna methyltransferases crystals endonuclease enzyme genetics genomics proteins sequences dna protein binding sites dna binding sites
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