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
A Modified Shuttle Plasmid Facilitates Expression of a Flavin Mononucleotide-Based Fluorescent Protein in Treponema denticola ATCC 35405
Valentina Godovikova,M. Paula Goetting-Minesky,Jae M. Shin,Yvonne L. Kapila,Alexander H. Rickard,J. Christopher Fenno +5 more
TL;DR: Routine transformation of T. denticola ATCC 35405 with shuttle plasmids is reported, independently of both plasmid methylation status and activity of the type II restriction endonuclease encoded by TDE0911 to enable more-rigorous and -detailed studies of the behavior of this organism.
Journal ArticleDOI
Development of a shuttle plasmid without host restriction sites for efficient transformation and heterologous gene expression in Clostridium cellulovorans
TL;DR: A new shuttle plasmid (pYL001) was developed to remove all restriction sites of two major RM systems of C. cellulovorans and can facilitate further metabolic engineering of this organism for cellulosic butanol production.
Journal ArticleDOI
Flexibility of the linker between the domains of DNA methyltransferase SsoII revealed by small-angle X-ray scattering: implications for transcription regulation in SsoII restriction-modification system.
Petr V. Konarev,Galina S. Kachalova,Alexandra Yu Ryazanova,Elena A. Kubareva,Anna S. Karyagina,Hans D. Bartunik,Dmitri I. Svergun +6 more
TL;DR: Homology modeling of the M.SsoII structure is performed by using the model of M.HhaI for the methyltransferase domain and representing the N-terminal region either as a flexible chain of dummy residues or as a rigid structure of a homologous protein connected to the methyl transferase domain by a short flexible linker.
Journal ArticleDOI
Genome Analyses and Genome-Centered Metatranscriptomics of Methanothermobacter wolfeii Strain SIV6, Isolated from a Thermophilic Production-Scale Biogas Fermenter.
TL;DR: Detailed analysis of the archaeal isolate M. wolfeii SIV6 indicates its role and function within the microbial community of the thermophilic biogas fermenter, towards a better understanding of theBiogas production process and a microbial-based management of this complex process.
Posted ContentDOI
The Genetic Basis of phage susceptibility, cross-resistance and host-range in Salmonella
Benjamin A. Adler,Alexey E. Kazakov,Crystal Zhong,Hualan Liu,Elizabeth Kutter,Lauren M. Lui,Torben Nielsen,Heloise Carion,Adam M. Deutschbauer,Adam M. Deutschbauer,Vivek K. Mutalik,Vivek K. Mutalik,Adam P. Arkin,Adam P. Arkin +13 more
TL;DR: Adler et al. as mentioned in this paper employed genome-wide screens in Salmonella enterica serovar Typhimurium to discover host determinants involved in resistance to eleven diverse lytic phages including 4 new phages isolated from a therapeutic phage cocktail.
References
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