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
Highlights of the DNA cutters: a short history of the restriction enzymes
Wil A. M. Loenen,David T. F. Dryden,Elisabeth A. Raleigh,Geoffrey G. Wilson,Noreen E. Murray +4 more
TL;DR: In the early 1950's, it was reported that host-controlled variation in bacterial viruses was a non-hereditary phenomenon: one cycle of viral growth on certain bacterial hosts affected the ability of progeny virus to grow on other hosts by either restricting or enlarging their host range.
Journal ArticleDOI
Diverse enzymatic activities mediate antiviral immunity in prokaryotes
Linyi Gao,Linyi Gao,Linyi Gao,Han Altae-Tran,Han Altae-Tran,Han Altae-Tran,Francisca Böhning,Francisca Böhning,Kira S. Makarova,Michael Segel,Jonathan L. Schmid-Burgk,Jeremy Koob,Jeremy Koob,Yuri I. Wolf,Eugene V. Koonin,Feng Zhang +15 more
TL;DR: 29 widespread antiviral gene cassettes are discovered that mediate protection against specific bacteriophages that incorporate enzymatic activities not previously implicated in antiviral defense, including RNA editing and retron satellite DNA synthesis.
Journal ArticleDOI
DNA methylation in bacteria: from the methyl group to the methylome.
TL;DR: Bacterial methylomes provide a wealth of information on the methylation marks present in bacterial genomes, and may open a new era in bacterial epigenomics.
Journal ArticleDOI
To be or not to be: regulation of restriction–modification systems and other toxin–antitoxin systems
Iwona Mruk,Ichizo Kobayashi +1 more
TL;DR: Drawing parallels between some TA systems and restriction–modification systems (RM systems) is demonstrated, intended to generalize the concept of TA systems in studies of stress responses, programmed death, genetic conflict and epigenetics.
Journal ArticleDOI
Type II restriction endonucleases—a historical perspective and more
TL;DR: The mechanisms of sequence recognition and catalysis, and the varied oligomeric modes in which Type II REases act are discussed; the surprising heterogeneity revealed by comparisons of their sequences and structures is described.
References
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