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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Transcriptional rewiring of the GcrA/CcrM bacterial epigenetic regulatory system in closely related bacteria
TL;DR: In this article, the regulatory targets of GcrA and CcrM were analyzed by SMRT-seq, RNA-seq and ChIP-seq technologies in the Alphaproteobacterium Brevundimonas subvibrioides, and then compared to those of its close relative C. crescentus that inhabits the same environment.
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Escherichia coli belonging to ST131 rarely transfers bla ctx-m-15 to fecal Escherichia coli
Karen Rønø Thingholm,Frederik Boëtius Hertz,Anders Løbner-Olesen,Niels Frimodt-Møller,Karen Leth Nielsen +4 more
TL;DR: The results indicate that blaCTX-M-15 is rarely transferred by conjugation to E. coli isolates of the intestinal flora, even when the gene is plasmid-borne.
Journal ArticleDOI
Structure of HhaI endonuclease with cognate DNA at an atomic resolution of 1.0 Å.
John R. Horton,Jie Yang,Xing Zhang,Theresa Petronzio,Alexey Fomenkov,Geoffrey G. Wilson,Richard J. Roberts,Xiaodong Cheng +7 more
TL;DR: The structure of HhaI, a Type II restriction endonuclease, recognizes the symmetric sequence 5′-GCG↓C-3′ in duplex DNA and cleaves (‘↓’) to produce fragments with 2-base, 3′-overhangs, and is characterized in atomic detail.
Journal ArticleDOI
Identification and prioritization of novel uncharacterized peptidases for biochemical characterization
TL;DR: The 42 most widely distributed of these putative peptidases have been identified and discussed here and are prioritized as ideal candidates for biochemical characterization.
References
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