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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DNA methylation epigenetically regulates gene expression in Burkholderia cenocepacia and controls biofilm formation, cell aggregation, and motility
TL;DR: DNA methylation plays an important role in regulating the expression of B. cenocepacia genes involved in biofilm formation, cell aggregation, and motility, and qPCR experiments showed an upregulation of several genes.
Journal ArticleDOI
Single-pass transcription by T7 RNA polymerase.
TL;DR: The results show that a controlled single-pass transcription using T7 RNAP allows precise measurement of co-transcriptional ribozyme activity, and this approach will facilitate the study of other kinetic events.
Journal ArticleDOI
Recombinant production of A1S_0222 from Acinetobacter baumannii ATCC 17978 and confirmation of its DNA-(adenine N6)-methyltransferase activity.
Ulrike Blaschke,Beneditta Suwono,Sachli Zafari,Ingo Ebersberger,Evelyn Skiebe,Cy M. Jeffries,Dmitri I. Svergun,Gottfried Wilharm +7 more
TL;DR: A mutant inactivated in a putative DNA-(adenine N6)-methyltransferase, designated A1S_0222 in strain ATCC 17978 is revealed and small angle X-ray scattering revealed that the protein is monomeric and has an extended and likely two-domain shape in solution.
Journal ArticleDOI
Complete Genome Sequence of the Freshwater Colorless Sulfur Bacterium Beggiatoa leptomitiformis Neotype Strain D-402T
Alexey Fomenkov,Tamas Vincze,Margarita Grabovich,Galina Dubinina,Maria Orlova,E. V. Belousova,Richard J. Roberts +6 more
TL;DR: A complete closed genome sequence and methylome analysis of Beggiatoa leptomitiformis neotype strain D-402T (DSM 14946, UNIQEM U 779) is announced.
Journal ArticleDOI
Genomic and epigenetic landscapes drive CRISPR-based genome editing in Bifidobacterium
Meichen Pan,Wesley Morovic,Claudio Hidalgo-Cantabrana,Avery Roberts,Kimberly K. O. Walden,Yong Jun Goh,Rodolphe Barrangou +6 more
TL;DR: The need to develop individualized CRISPR-based genome engineering approaches for distinct bacterial strains and opens avenues for engineering of next generation probiotics is highlighted and epigenetic patterns that are distributed unevenly among B. lactis strains are uncovered that may contribute to editing efficiency variability.
References
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