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
Improving Mobilization of Foreign DNA into Zymomonas mobilis Strain ZM4 by Removal of Multiple Restriction Systems.
Piyush Behari Lal,Piyush Behari Lal,Fritz M. Wells,Fritz M. Wells,Kevin S. Myers,Kevin S. Myers,Rajdeep Banerjee,Adam M. Guss,Patricia J. Kiley,Patricia J. Kiley +9 more
TL;DR: In this paper, the authors characterized the contribution of several defense systems of Zymomonas mobilis strain ZM4 to impeding heterologous gene transfer from an Escherichia coli donor.
Patent
Tnt cloning system
TL;DR: In this paper, the authors present vectors and components for a nucleic acid cloning system, and methods of use of the vectors and component in cloning nucleic acids fragments of interest.
Posted ContentDOI
A high quality reference genome for the fish pathogen Streptococcus iniae
Areej S. Alsheikh-Hussain,Nouri L. Ben Zakour,Nouri L. Ben Zakour,Brian M. Forde,Oleksandra Silayeva,Andrew J. Barnes,Scott A. Beatson +6 more
TL;DR: This study presents the complete genome sequence of Streptococcus iniae strain QMA0248, isolated from farmed barramundi in South Australia, and provides a high quality reference genome that will assist future S. iniae comparative genomic and evolutionary studies.
Journal ArticleDOI
Genomic Features and Pervasive Negative Selection in Rhodanobacter Strains Isolated from Nitrate and Heavy Metal Contaminated Aquifer
Mu Peng,Dongyu Wang,Lauren M. Lui,Torben Nielsen,Renmao Tian,Megan L. Kempher,Xuanyu Tao,Chongle Pan,Romy Chakraborty,Adam M. Deutschbauer,Michael P. Thorgersen,M. R. Adams,Matthew W. Fields,Terry C. Hazen,Adam P. Arkin,Aifen Zhou,Jizhong Zhou +16 more
TL;DR: The sequence comparison results demonstrate the important roles of horizontal gene transfer and negative selection in adaptation in Rhodanobacter strains isolated from the ORR site and suggest these strains may be recalcitrant to genetic manipulation due to the complex restriction-modification systems and methylations.
Journal ArticleDOI
Novel Two-Component System-Like Elements Reveal Functional Domains Associated with Restriction-Modification Systems and paraMORC ATPases in Bacteria.
TL;DR: In this article, the authors reported two newly predicted protein domains, Response_reg_2 and HEF_HK, in bacteria which exhibit high structural similarity, respectively, with typical domains of RRs and HKs, and the genes encoding for these predicted domains exhibit a 91.6% linkage observed across 644 genomic regions recovered from 628 different bacterial strains.
References
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