Restriction-modification systems with specificity GGATC, GATGC and GATGG. Part 1. Evolution and ecology

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Abstract

The evolution of proteins from restriction–modification systems containing an endonuclease domain of the RE_AlwI family and either two DNA methyltransferases, each with a domain of the MethyltransfD12 family, or one DNA methyltransferase with two domains of this family was studied. It was found that all such systems recognize one of three DNA sequences, namely GGATC, GATGC or GATGG, and the restriction endonucleases of these systems are divided by sequence similarity into three clades that unambiguously correspond to specificities. The DNA methyltransferase domains of these systems are divided into two groups based on sequence similarity, with two domains of each system belonging to different groups. Within each group, the domains are divided into three clades according to their specificity. Evidence of multiple interspecific horizontal transfers of systems as a whole is found, as well as evidence of gene transfer between systems, including transfer of one of the DNA methyltransferases with a change in specificity. Evolutionary relationships of DNA methyltransferases from such systems with other DNA methyltransferases, including orphan DNA methyltransferases, were revealed.

About the authors

S. A. Spirin

Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University; National Research University Higher School of Economics; NRC “Kurchatov Institute” – SRISA

Email: sas@belozersky.msu.ru
119234 Moscow, Russia; 109028 Moscow, Russia; 117218 Moscow, Russia

I. S. Rusinov

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

119234 Moscow, Russia

O. L. Makarikova

National Research University Moscow Institute of Physics and Technology

117303 Moscow, Russia

A. V. Alexeevski

Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University; NRC “Kurchatov Institute” – SRISA

119234 Moscow, Russia; 117218 Moscow, Russia

A. S. Karyagina

Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University; N. F. Gamaleya National Research Center for Epidemiology and Microbiology; All-Russia Research Institute of Agricultural Biotechnology

119234 Moscow, Russia; 123098 Moscow, Russia; 127550 Moscow, Russia

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