Restriction–Modification Systems Specific toward GGATC, GATGC, and GATGG. Part 2. Functionality and Structure

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Sergey Spirin^1,2,3,a*, Alexander Grishin^4,5, Ivan Rusinov¹, Andrei Alexeevski^1,3, Anna Karyagina^1,4,5

¹Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia

²Higher School of Economics National Research University, 109028 Moscow, Russia

³NRC “Kurchatov Institute” - SRISA, 117218 Moscow, Russia

⁴Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Healthcare of the Russian Federation, 123098 Moscow, Russia

⁵All-Russia Research Institute of Agricultural Biotechnology, 127550 Moscow, Russia

^* To whom correspondence should be addressed.

Received: January 21, 2025; Revised: March 23, 2025; Accepted: March 25, 2025

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The structural and functional basics of protein functionality of restriction–modification systems recognizing GGATC/GATCC, GATGC/GCATC, and GATGG/CCATC sites have been studied using bioinformatics methods. Such systems include a single restriction endonuclease and either two separate DNA methyltransferases or a single fusion DNA methyltransferase with two catalytic domains. It is known that some of these systems methylate both adenines in the recognition sites to 6-methyladenine, but the role of each of the two DNA methyltransferases remained unknown. In this work, we proved the functionality of most known systems. Based on the analysis of structures of related DNA methyltransferases, we hypothesized which of the adenines within the recognition site is modified by each of the DNA methyltransferases and suggested a possible molecular mechanism of changes in the DNA methyltransferase specificity from GATGG to GATGC during horizontal transfer of its gene.

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KEY WORDS: restriction–modification system, 3D structure, DNA methyltransferase, restriction endonuclease, horizontal gene transfer

DOI: 10.1134/S0006297925600152

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