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Solitary restriction endonucleases in prokaryotic genomes

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...

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Autores principales: Ershova, Anna S., Karyagina, Anna S., Vasiliev, Mikhail O., Lyashchuk, Alexander M., Lunin, Vladimir G., Spirin, Sergey A., Alexeevski, Andrei V.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3488263/
https://www.ncbi.nlm.nih.gov/pubmed/22965118
http://dx.doi.org/10.1093/nar/gks853
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author Ershova, Anna S.
Karyagina, Anna S.
Vasiliev, Mikhail O.
Lyashchuk, Alexander M.
Lunin, Vladimir G.
Spirin, Sergey A.
Alexeevski, Andrei V.
author_facet Ershova, Anna S.
Karyagina, Anna S.
Vasiliev, Mikhail O.
Lyashchuk, Alexander M.
Lunin, Vladimir G.
Spirin, Sergey A.
Alexeevski, Andrei V.
author_sort Ershova, Anna S.
collection PubMed
description 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.
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spelling pubmed-34882632012-11-06 Solitary restriction endonucleases in prokaryotic genomes Ershova, Anna S. Karyagina, Anna S. Vasiliev, Mikhail O. Lyashchuk, Alexander M. Lunin, Vladimir G. Spirin, Sergey A. Alexeevski, Andrei V. Nucleic Acids Res Computational Biology 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. Oxford University Press 2012-11 2012-09-08 /pmc/articles/PMC3488263/ /pubmed/22965118 http://dx.doi.org/10.1093/nar/gks853 Text en © The Author(s) 2012. Published by Oxford University Press. http://creativecommons.org/licenses/by/3.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Computational Biology
Ershova, Anna S.
Karyagina, Anna S.
Vasiliev, Mikhail O.
Lyashchuk, Alexander M.
Lunin, Vladimir G.
Spirin, Sergey A.
Alexeevski, Andrei V.
Solitary restriction endonucleases in prokaryotic genomes
title Solitary restriction endonucleases in prokaryotic genomes
title_full Solitary restriction endonucleases in prokaryotic genomes
title_fullStr Solitary restriction endonucleases in prokaryotic genomes
title_full_unstemmed Solitary restriction endonucleases in prokaryotic genomes
title_short Solitary restriction endonucleases in prokaryotic genomes
title_sort solitary restriction endonucleases in prokaryotic genomes
topic Computational Biology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3488263/
https://www.ncbi.nlm.nih.gov/pubmed/22965118
http://dx.doi.org/10.1093/nar/gks853
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