Restriction–Modification Systems with Specificity GGATC, GATGC and GATGG. Part 2. Functionality and Structural Issues

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Abstract

The structural and functional issues of protein functionality of restriction-modification systems recognizing one of the 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. For a subset of these systems, it was known that both adenines within the site are methylated to form 6-methyladenine, but the role of each of the two DNA methyltransferases comprising the system was unknown. In this work, the functionality of most known systems of this kind is proven. Based on analysis of the structures of related DNA methyltransferases, it is hypothesized which of the adenines within the site is modified by each of the DNA methyltransferases of the system. A possible molecular mechanism of DNA methyltransferase specificity change from GATGG to GATGC during horizontal transfer of its gene is described.

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

A. V. Grishin

N. F. Gamaleya National Research Center for Epidemiology and Microbiology; All-Russia Research Institute of Agricultural Biotechnology

123098 Moscow, Russia; 127550 Moscow, Russia

I. S. Rusinov

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

119234 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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2. Fig. P1. Alignment of MTase A and B sequences together with MTase M.DpnII, M.EcoRV, M1.Bst19I, and M.EcoKDam sequences, M.EcoT4Dam and the N- and C-terminal parts of the MTase of M.FokI. Group A MTase sequences together with their close N-terminal part M.FokI sequences are above the black line. The specificity of the investigated MTases is indicated by the color of the bar after the name, red GGATC, green GATGG and blue GATGC. The degree of conservation of amino acid residues is indicated by blue background of different intensities. Yellow, green, and red stars indicate residues from conserved clusters on the surface of the proteins (see details in the text of the article). Colored bars under the alignment mark structural elements (see Fig. 4 of the article)
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