RESEARCH ARTICLE Open Access Lifespan of restriction-modification systems

critically affects avoidance of their recognition sites in host genomes Ivan Rusinov1, Anna Ershova2,3,4, Anna Karyagina2,3,4, Sergey Spirin1,2,5 and Andrei Alexeevski1,2,5* Background: Avoidance of palindromic recognition sites of Type II restriction-modification (R-M) systems was shown for many R-M systems in dozens of prokaryotic genomes. However the phenomenon has not been investigated systematically for all presently available genomes and annotated R-M systems. We have studied all known recognition sites in thousands of prokaryotic genomes and found factors that influence their avoidance. Results: Only Type II R-M systems consisting of independently acting endonuclease and methyltransferase (called ‘orthodox ’ here) cause avoidance of their sites, both palindromic and asymmetric, in corresponding prokaryotic genomes; the avoidance takes place for ~ 50 % of 1774 studied cases. It is known that prokaryotes can acquire and lose R-M systems. Thus it is possible to talk about the lifespan of an R-M system in a genome. We have shown that the recognition site avoidance correlates with the lifespan of R-M systems. The sites of orthodox R-M systems that are encoded in host genomes for a long time are avoided more often (up to 100 % in certain cohorts) than the sites of recently acquired ones. We also found cases of site avoidance in absence of the corresponding R-M system