REBASE—a database for DNA restriction and modification: enzymes, genes and genomes
TLDR
REBASE is a comprehensive and fully curated database of information about the components of restriction-modification (RM) systems that contains fully referenced information about recognition and cleavage sites for both restriction enzymes and methyltransferases as well as commercial availability, methylation sensitivity, crystal and sequence data.Abstract:
REBASE is a comprehensive and fully curated database of information about the components of restriction-modification (RM) systems. It contains fully referenced information about recognition and cleavage sites for both restriction enzymes and methyltransferases as well as commercial availability, methylation sensitivity, crystal and sequence data. All genomes that are completely sequenced are analyzed for RM system components, and with the advent of PacBio sequencing, the recognition sequences of DNA methyltransferases (MTases) are appearing rapidly. Thus, Type I and Type III systems can now be characterized in terms of recognition specificity merely by DNA sequencing. 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). Monthly updates are also available via email.read more
Citations
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Journal ArticleDOI
Mining bacterial NGS data vastly expands the complete genomes of temperate phages
TL;DR: TemPhD as mentioned in this paper mines both the integrated active prophages and their spontaneously induced forms (temperate phages) from next-generation sequencing raw data to detect temperate phages.
Book ChapterDOI
Epigenetics Mediated by Restriction Modification Systems
Iwona Mruk,Ichizo Kobayashi +1 more
Journal ArticleDOI
DNA methylation by three Type I restriction modification systems of Escherichia coli does not influence gene regulation of the host bacterium.
TL;DR: This article showed that three distinct non-phase-variable restriction modification systems (RMSs) in Escherichia coli have no measurable impact on gene expression, in vivo virulence, or any of 1190 in vitro growth phenotypes.
Posted ContentDOI
Ecology Shapes Microbial Immune Strategy: Temperature and Oxygen as Determinants of the Incidence of CRISPR Adaptive Immunity
TL;DR: A strong but hitherto-unknown negative interaction between CRISPR and aerobicity is discovered, which it is hypothesize may result from interference betweenCRISPR associated proteins and non-homologous end-joining DNA repair due to oxidative stress.
Journal ArticleDOI
Development of an efficient host-vector system of Ruminiclostridium josui.
TL;DR: This is the first report on the establishment of fundamental technology for molecular breeding of R. josui by electroporation and characterization showed that RjoI is an isoschizomer of DpnI, recognizing the sequence 5′‐GmetATC‐3′, where the A nucleotide is Dam‐methylated.
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