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

---

Anastasiya S. Fokina¹, Anna S. Karyagina^2,3,4, Ivan S. Rusinov³, Denis M. Moshensky^1,3, Sergey A. Spirin^3,5,6,a*, and Andrey V. Alexeevski^1,3,6

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

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

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

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

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

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

^* To whom correspondence should be addressed.

Received November 28, 2022; Revised January 15, 2023; Accepted January 15, 2023

---

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.

---

KEY WORDS: restriction–modification system, DNA methyltransferase, restriction endonuclease, evolutionary domains, protein evolution, horizontal gene transfer

DOI: 10.1134/S0006297923020086

---