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Nucleic Acids Res. 2012 Nov 1;40(20):10107-15. PubMed; doi 10.1093/nar/gks853

Solitary restriction endonucleases in prokaryotic genomes.

Ershova, A. S.; Karyagina, A. S.; Vasiliev, M. O.; Lyashchuk, A. M.; Lunin, V. G.; Spirin, S. A.; Alexeevski, A. V.

Prokaryotic restriction-modification (R-M) systems defend the host cell from the invasion of a foreign DNA. They comprise two enzymatic activities: specific DNA cleavage activity and DNA methylation activity preventing cleavage. Typically, these activities are provided by two separate enzymes: a DNA methyltransferase (MTase) and a restriction endonuclease (RE). In the absence of a corresponding MTase, an RE of Type II R-M system is highly toxic for the cell. Genes of the R-M system are linked in the genome in the vast majority of annotated cases. There are only a few reported cases in which the genes of MTase and RE from one R-M system are not linked. Nevertheless, a few hundreds solitary RE genes are present in the Restriction Enzyme Database (http://rebase.neb.com) annotations. Using the comparative genomic approach, we analysed 272 solitary RE genes. For 57 solitary RE genes we predicted corresponding MTase genes located distantly in a genome. Of the 272 solitary RE genes, 99 are likely to be fragments of RE genes. Various explanations for the existence of the remaining 116 solitary RE genes are also discussed.



 


  Московский Государственный Университет имени М.В.Ломоносова



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