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.

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About the authors

S. A. Spirin

Lomonosov Moscow State University; Higher School of Economics; Scientific Research Institute of System Development

Author for correspondence.
Email: sas@belozersky.msu.ru
Russian Federation, Moscow; Moscow; Moscow

A. V. Grishin

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

Email: sas@belozersky.msu.ru
Russian Federation, Moscow; Moscow

I. S. Rusinov

Lomonosov Moscow State University

Email: sas@belozersky.msu.ru
Russian Federation, Moscow

A. V. Alexeevsky

Lomonosov Moscow State University; Scientific Research Institute of System Development

Email: sas@belozersky.msu.ru
Russian Federation, Moscow; Moscow

A. S. Karyagina

Lomonosov Moscow State University; Gamaleya National Research Center for Epidemiology and Microbiology; All-Russia Research Institute of Agricultural Biotechnology

Email: sas@belozersky.msu.ru
Russian Federation, Moscow; Moscow; Moscow

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Supplementary files

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2. Appendix
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3. Fig. 1. Plot of the ER sequence alignment of our class together with the sequence of the Nt.BstNBI nickase. Red stars indicate residues E418, D456, E469, E482 of the Nt.BstNBI nickase, the role of which in catalytic activity was confirmed experimentally, yellow star - residue H489, presumably involved in catalysis

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4. Fig. 2. Tree of 12 MTases with GGATC, GATGC and GATGG specificities together with the MTases M.EcoKDam, M.EcoT4Dam and M1.DpnII, for which spatial structures are known, and the well-studied M.EcoRV, M.FokI and M1.Bst19I. For the two-domain MTases, phylogeny was reconstructed separately for the N-terminal and C-terminal domains. The colours of the names correspond to specificity: red - GGATC, green - GATGG, blue - GATGC. Numbers on branches indicate bootstrap support; branches with less than 25% support have been removed (‘collapsed’)

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5. Fig. 3. Schematic of gene structure and recognisable sequences of MTase representatives from systems recognising GGATG, GATGG, GATGC and GGATC sites. The figure uses images of red and yellow flags taken from the REBASE website, which mark the positions of the conserved F-x-G-x-G and D-P-P-Y motifs; a blue asterisk at the flag indicates that the motif is imprecise (F-x-G-x-A and D-T-P-Y, respectively). Two hypothetical methylation variants are shown for each GGATC site, with the pink background highlighting the more likely variant

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6. Fig. 4. Models of the structures of complexes of group B MTases and similar complexes with DNA. Blue indicates the catalytic domain of MTase, green - TRD, red - a loop potentially involved in the recognition of the right nucleotide pairs of the recognised site in the figure, magenta - a site presumably involved in the recognition of the left nucleotide pairs. Four nucleotides corresponding to the nucleotides of the GATC recognition site of M.EcoKDam are highlighted in pale pink on the DNA, and the nucleotide pairs framing them are highlighted in light lilac and pink. The nucleotide designations of the recognition site and ends refer to the chain containing adenine methylated by MTase B

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7. Fig. 5. LOGO-diagrams for the alignments of MTase loops of group B, highlighted in red in Fig. 4. a - Diagram for MTase loops with GGATC specificity homologous to the loop indicated in red on the M.AlwI-N structure (M.AlwI residues 199-218, sequence VPISEYSDFKRYTKEQFYLE). b - Diagram for MTase loops with GGATG specificity homologous to the loop indicated in red on the M.FokI-C structure (M.FokI residues 552-571, sequence LITTGSYNDGNRGNRGFKDWNRL). The recognition site of MTases of the corresponding family is shown below each LOGO diagram, the nucleotide pair presumably recognised by the corresponding loop is shown in bold, with the arrowed G probably bound by a conserved arginine

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8. Fig. 6. LOGO-diagrams for the alignments of MTase loops of group B, highlighted in magenta in Fig. 4. a - Diagram for MTase loops with GATGC specificity (blue) homologous to the one marked in magenta on the M.SfaNI-C structure (M.SfaNI residues 490-509, sequence LSNSKMYGYNYNYYYKTSSAKGL). b - Diagram for loops of length 23 of MTase with GATGG specificity (green) homologous to that indicated in magenta on the M2.McaCI structure (residues 111-133, sequence in M2.McaCI LSCSYLSITVPDELKKKYVKYVKTYY). c - Same as b but for loops of length 24. The recognition site of MTases of the corresponding family is given under each LOGO diagram, with the nucleotide pair presumably recognised by the corresponding loop in bold

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9. Fig. 7. Phylogenetic trees of representatives of group A MTases (a), group B MTases (b), and ERs (c) with GATGC (blue) and GATGG (green) specificity, and a model of the spatial structure of group A MTase M1.Hmu12714II (d). The GC pair corresponding to the 3′-terminal cytosine in the GATGC sequence is highlighted in red on the DNA model. The protein rod model shows S-adenosyl-L-homocysteine and side chains of the N-x-R-S-N motif, the catalytic domain of the MTase is indicated in blue, and TRD is shown in green

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