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.

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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

I. S. Rusinov

Lomonosov Moscow State University

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

O. L. Makarikova

Moscow Institute of Physics and Technology

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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4. Appendix 3
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6. Fig. 1. Phylogenetic trees of ERs and MTases from three R-M systems with two MTases and three with one (fused) MTase. The name is followed by the recognisable sequence according to REBASE. a - Tree constructed from ER sequences. Asterisk indicates enzymes from systems with a fused MTase. b - Tree constructed by MTase domain sequences. For domains from separate MTases the names of these MTases from REBASE are used, for domains of fusion MTases the suffixes N for N-terminal domains or C for C-terminal domains are assigned to the names of proteins on the tree. The letters A and B denote two groups of MTases

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7. Fig. 2. ER tree from P-M systems with GATGC specificity with the gene order marked. Cluster representatives were selected based on 70% sequence identity. The letter F at the beginning of the name means that the MTases of the system are fused, gene order is labelled with three letters, similar to the table. Numbers on the branches denote bootstrap support

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8. Fig. 3. Phylogenetic trees of MTases of MethyltransfD12 family from P-M systems with specificities GGATC, GATGC and GATGG and close to them. a - Group A MTase tree, b - Group B MTase tree. Branches with bootstrap support less than 40% have been removed. Monophyletic groups of MTases with the same specificity are combined and indicated by rhombuses; for each such group the recognition site is indicated, then, in parentheses, the composition of systems occurring in the group, where M stands for MTase, 2M - two MTases, R - restriction endonuclease, MR - fusion bifunctional protein including methyltransferase and endonuclease domains. If systems have ERs in the composition, the identifiers of the catalytic domain families found in these ERs are given in other brackets; Unk means that Pfam profiles do not find domains in the ER sequence. The number of systems in which the indicated site was experimentally confirmed by PacBio technology is given after the composition. The MTase B tree includes the M.EcoT4Dam MTase whose GATC specificity was not confirmed by PacBio data

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9. Fig. 4. Phylogenetic tree of ERs close to ERs with specificities GGATC, GATGC, and GATGG. Clades consisting of ERs of the same specificity are indicated by rhombuses. The recognised sequence is followed by the number of ERs of this clade that are part of systems with MTases with this specificity confirmed by PacBio

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