Evolutionary role of restriction modification systems as revealed by comparative genome analysis

Type II restriction modification systems (RMSs) have been regarded either a s defense tools or as molecular parasites of bacteria. We extensively analy zed their evolutionary role from the study of their impact in the complete genomes of 26 bacteria and 35 phages in terms of palindrome avoidance. This analysis reveals that palindrome avoidance is not universally spread among bacterial species and that it does not correlate with taxonomic proximity. Palindrome avoidance is also not universal among bacteriophage, even when their hosts code for RMSs, and depends strongly on the genetic material of the phage. Interestingly, palindrome avoidance is intimately correlated wit h the infective behavior of the phage. We observe that the degree of palind rome and restriction site avoidance is significantly and consistently less important in phages than in their bacterial hosts. This result brings to th e fore a larger selective load for palindrome and restriction site avoidanc e on the bacterial hosts than on their infecting phages. It is then consist ent with a view where type II RMSs are considered as parasites possibly at the verge of mutualism. As a consequence, RMSs constitute a nontrivial thir d player in the host-parasite relationship between bacteria and phages.