title: Restriction-Modification systems interplay causes avoidance of GATC site in prokaryotic genomes.
abstract: Palindromes are frequently underrepresented in prokaryotic genomes. Palindromic 5[Formula: see text]-GATC-3[Formula: see text] 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.
authors.affiliation: * 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.
authors.forename: Anna
authors.initials: A
authors.lastname: Ershova
authors.affiliation: * 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.
authors.forename: Ivan
authors.initials: I
authors.lastname: Rusinov
authors.affiliation: ¶ Moscow Institute of Physics and Technology, the Ministry of Education and Science of the Russian Federation, Dolgoprudny, Moscow Region, 141700, Russia.
authors.forename: Mikhail
authors.initials: M
authors.lastname: Vasiliev
authors.affiliation: * 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.
authors.forename: Sergey
authors.initials: S
authors.lastname: Spirin
authors.affiliation: * 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.
authors.forename: Anna
authors.initials: A
authors.lastname: Karyagina
mesh_terms: D019175:DNA Methylation; D015280:DNA Restriction-Modification Enzymes / Q000145:classification / Q000235:genetics / Q000378:metabolism*; D016678:Genome; D055029:Inverted Repeat Sequences / Q000235:genetics*; D008954:Models, Biological; D005810:Multigene Family; D011387:Prokaryotic Cells; D015265:Site-Specific DNA-Methyltransferase (Adenine-Specific) / Q000235:genetics / Q000378:metabolism
chemical_list: D015280:DNA Restriction-Modification Enzymes; C058693:Dam methyltransferase; D015265:Site-Specific DNA-Methyltransferase (Adenine-Specific)
keywords: GATC; Restriction-modification systems; bacteria; horizontal gene transfer; recognition site; site avoidance