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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NAR Breakthrough Article SURVEY AND SUMMARY 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: The discovery of restriction enzymes gave rise to recombinant DNA technology that has transformed molecular biology and medicine, and their continuing impact on molecularbiology and medicine is traced.
Journal ArticleDOI
A random six-phase switch regulates pneumococcal virulence via global epigenetic changes
Ana Sousa Manso,Melissa H. Chai,John M. Atack,Leonardo Furi,Megan De Ste Croix,Richard D. Haigh,Claudia Trappetti,Abiodun D. Ogunniyi,Lucy K. Shewell,Matthew Boitano,Tyson A. Clark,Jonas Korlach,Matthew Blades,Evgeny M. Mirkes,Alexander N. Gorban,James C. Paton,Michael P. Jennings,Marco R. Oggioni +17 more
TL;DR: This work demonstrates distinct virulence in experimental infection and in vivo selection for switching between SpnD39III variants, which is ubiquitous in pneumococci, indicating an essential role in its biology.
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Major bacterial lineages are essentially devoid of CRISPR-Cas viral defence systems
David Burstein,Christine L. Sun,Christine L. Sun,Christopher T. Brown,Itai Sharon,Karthik Anantharaman,Alexander J. Probst,Brian C. Thomas,Jillian F. Banfield +8 more
TL;DR: This work investigates thousands of viral and microbial genomes recovered using a cultivation-independent approach to study the frequency, variety and taxonomic distribution of viral defence mechanisms and correlates absence of CRISPR-Cas with lack of nucleotide biosynthesis capacity and a symbiotic lifestyle.
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DISARM is a widespread bacterial defence system with broad anti-phage activities.
Gal Ofir,Sarah Melamed,Hila Sberro,Hila Sberro,Zohar Mukamel,Shahar Silverman,Gilad Yaakov,Shany Doron,Rotem Sorek +8 more
TL;DR: The results suggest that DISARM is a new type of multi-gene restriction–modification module, expanding the arsenal of defence systems known to be at the disposal of prokaryotes against their viruses.
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Genomic encyclopedia of type strains of the genus Bifidobacterium.
Christian Milani,Gabriele Andrea Lugli,Sabrina Duranti,Francesca Turroni,Francesca Bottacini,Marta Mangifesta,Borja Sánchez,Alice Viappiani,Leonardo Mancabelli,Bernard Taminiau,Véronique Delcenserie,Rodolphe Barrangou,Abelardo Margolles,Douwe van Sinderen,Marco Ventura +14 more
TL;DR: In this paper, the genomes of 42 representative (sub)species across the Bifidobacterium genus were sequenced and used to explore the overall genetic picture of this bacterial group.
References
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TL;DR: During 2004, tens of thousands of Knowledgebase records got manually annotated or updated; the UniProt keyword list got augmented by additional keywords; the documentation of the keywords and are continuously overhauling and standardizing the annotation of post-translational modifications.
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