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Restriction-Modification systems interplay causes avoidance of GATC site in prokaryotic genomes

Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia

Gamaleya Center for Epidemiology and Microbiology, the Ministry of Health of the Russian Federation, Moscow 123098, Russia

Institute of Agricultural Biotechnology, the Russian Academy of Sciences, Moscow 127550, Russia

E-mail Address: asershova@gmail.com

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Ivan Rusinov

Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia

Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Moscow 119992, Russia

E-mail Address: isrusinov@gmail.com

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Mikhail Vasiliev

Moscow Institute of Physics and Technology, the Ministry of Education and Science of the Russian Federation, Dolgoprudny, Moscow Region, 141700, Russia

E-mail Address: mickvav@gmail.com

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Sergey Spirin

Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia

Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Moscow 119992, Russia

Scientific Research Institute for System Studies, the Russian Academy of Science (NIISI RAS), Moscow 117218, Russia

E-mail Address: sas@belozersky.msu.ru

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Anna Karyagina

Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia

Gamaleya Center for Epidemiology and Microbiology, the Ministry of Health of the Russian Federation, Moscow 123098, Russia

Institute of Agricultural Biotechnology, the Russian Academy of Sciences, Moscow 127550, Russia

E-mail Address: akaryagina@gmail.com

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https://doi.org/10.1142/S0219720016410031Cited by:3 (Source: Crossref)

Abstract

Palindromes are frequently underrepresented in prokaryotic genomes. Palindromic 5 $^{'}$ -GATC-3 $^{'}$ site is a recognition site of different Restriction-Modification (R-M) systems, as well as solitary methyltransferase Dam. Classical GATC-specific R-M systems methylate GATC and cleave unmethylated GATC. On the contrary, methyl-directed Type II restriction endonucleases cleave methylated GATC. Methylation of GATC by Dam methyltransferase is involved in the regulation of different cellular processes. The diversity of functions of GATC-recognizing proteins makes GATC sequence a good model for studying the reasons of palindrome avoidance in prokaryotic genomes.

In this work, the influence of R-M systems and solitary proteins on the GATC site avoidance is described by a mathematical model. GATC avoidance is strongly associated with the presence of alternate (methyl-directed or classical Type II R-M system) genes in different strains of the same species, as we have shown for Streptococcus pneumoniae, Neisseria meningitidis, Eubacterium rectale, and Moraxella catarrhalis. We hypothesize that GATC avoidance can result from a DNA exchange between strains with different methylation status of GATC site within the process of natural transformation. If this hypothesis is correct, the GATC avoidance is a sign of a DNA exchange between bacteria with different methylation status in a mixed population.

Keywords:

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