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Published online before print May 8, 2001, 10.1101/gr.GR-1531RR
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Vol. 11, Issue 6, 946-958, June 2001

Evolutionary Role of Restriction/Modification Systems as Revealed by Comparative Genome Analysis

Eduardo P.C. Rocha,1,2,5 Antoine Danchin,2,3 and Alain Viari1,4

1 Atelier de BioInformatique, Université Paris VI, 75005 Paris, France; 2 Unité de Régulation de l'Expression Génétique, Institut Pasteur, 75724 Paris, France; 3 Hong Kong University Pasteur Research Centre, Dexter HC Man Building, Pokfulam, Hong Kong; 4 Action Helix, INRIA-Rhône-Alpes, 38330 Montbonnot-Saint Martin, France

Type II restriction modification systems (RMSs) have been regarded either as defense tools or as molecular parasites of bacteria. We extensively analyzed 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 with the infective behavior of the phage. We observe that the degree of palindrome and restriction site avoidance is significantly and consistently less important in phages than in their bacterial hosts. This result brings to the fore a larger selective load for palindrome and restriction site avoidance on the bacterial hosts than on their infecting phages. It is then consistent with a view where type II RMSs are considered as parasites possibly at the verge of mutualism. As a consequence, RMSs constitute a nontrivial third player in the host-parasite relationship between bacteria and phages.

5 Corresponding author.

11:946-958 ©2001 by Cold Spring Harbor Laboratory Press  ISSN 1088-9051/01 $5.00
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