title: Solitary restriction endonucleases in prokaryotic genomes.
abstract: 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.
authors.affiliation: Department of Mathematical Methods in Biology, Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992, Moscow, Russia. asershova@gmail.com
authors.forename: Anna S
authors.initials: AS
authors.lastname: Ershova
authors.forename: Anna S
authors.initials: AS
authors.lastname: Karyagina
authors.forename: Mikhail O
authors.initials: MO
authors.lastname: Vasiliev
authors.forename: Alexander M
authors.initials: AM
authors.lastname: Lyashchuk
authors.forename: Vladimir G
authors.initials: VG
authors.lastname: Lunin
authors.forename: Sergey A
authors.initials: SA
authors.lastname: Spirin
authors.forename: Andrei V
authors.initials: AV
authors.lastname: Alexeevski
mesh_terms: D015254:DNA Modification Methylases / Q000235:genetics; D004262:DNA Restriction Enzymes / Q000145:classification / Q000235:genetics*; D015253:Deoxyribonucleases, Type I Site-Specific / Q000235:genetics; D015252:Deoxyribonucleases, Type II Site-Specific / Q000235:genetics; D020745:Genome, Archaeal; D016680:Genome, Bacterial; D023281:Genomics
chemical_list: D015254:DNA Modification Methylases; D004262:DNA Restriction Enzymes; D015253:Deoxyribonucleases, Type I Site-Specific; D015252:Deoxyribonucleases, Type II Site-Specific