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Evolution of Restriction–Modification Systems Consisting of One Restriction Endonuclease and Two DNA Methyltransferases

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Abstract

Some restriction–modification systems contain two DNA methyltransferases. In the present work, we have classified such systems according to the families of catalytic domains present in the restriction endonucleases and both DNA methyltransferases. Evolution of the restriction–modification systems containing an endonuclease with a NOV_C family domain and two DNA methyltransferases, both with DNA_methylase family domains, was investigated in detail. Phylogenetic tree of DNA methyltransferases from the systems of this class consists of two clades of the same size. Two DNA methyltransferases of each restriction–modification system of this class belong to the different clades. This indicates independent evolution of the two methyltransferases. We detected multiple cross-species horizontal transfers of the systems as a whole, as well as the cases of gene transfer between the systems.

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Abbreviations

HGT:

horizontal gene transfer

MTase:

DNA-methyltransferase

REase:

restriction endonuclease

RM systems:

restriction–modification systems

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Funding

This work was financially supported by the Russian Science Foundation (Grant no. 21-14-00135).

Author information

Authors and Affiliations

  1. Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119234, Moscow, Russia

    Anastasiya S. Fokina, Denis M. Moshensky & Andrey V. Alexeevski

  2. N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Healthcare of the Russian Federation, 123098, Moscow, Russia

    Anna S. Karyagina

  3. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992, Moscow, Russia

    Anna S. Karyagina, Ivan S. Rusinov, Denis M. Moshensky, Sergey A. Spirin & Andrey V. Alexeevski

  4. All-Russia Research Institute of Agricultural Biotechnology, 127550, Moscow, Russia

    Anna S. Karyagina

  5. National Research University Higher School of Economics, 109028, Moscow, Russia

    Sergey A. Spirin

  6. Federal State Institution “Scientific Research Institute for System Analysis of the Russian Academy of Sciences”, 117218, Moscow, Russia

    Sergey A. Spirin & Andrey V. Alexeevski

Authors
  1. Anastasiya S. Fokina
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  2. Anna S. Karyagina
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  3. Ivan S. Rusinov
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  4. Denis M. Moshensky
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  5. Sergey A. Spirin
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  6. Andrey V. Alexeevski
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Contributions

A.V. Alekseevsky – concept and management of the work; A.S. Fokina – computer analysis of the data; I.S. Rusinov – preparation of the data on domains in REBASE proteins; D.M. Moshensky – assistance in searching for protein genes; A.S. Fokina, S.A. Spirin, A.S. Karyagina – discussion of the results, writing and editing of the article text.

Corresponding author

Correspondence to Sergey A. Spirin.

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The authors declare no conflict of interest in financial or any other sphere. This article does not contain any studies with human participants or animals performed by any of the authors.

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Fokina, A.S., Karyagina, A.S., Rusinov, I.S. et al. Evolution of Restriction–Modification Systems Consisting of One Restriction Endonuclease and Two DNA Methyltransferases. Biochemistry Moscow 88, 253–261 (2023). https://doi.org/10.1134/S0006297923020086

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  • DOI: https://doi.org/10.1134/S0006297923020086

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