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PMID: 11557807 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't Review

Behavior of restriction-modification systems as selfish mobile elements and their impact on genome evolution.

Nucleic acids research ·Vol. 29 ·No. 18 ·2001-09-15 ·Pages 3742-56

Kobayashi I

Abstract

Restriction-modification (RM) systems are composed of genes that encode a restriction enzyme and a modification methylase. RM systems sometimes behave as discrete units of life, like viruses and transposons. RM complexes attack invading DNA that has not been properly modified and thus may serve as a tool of defense for bacterial cells. However, any threat to their maintenance, such as a challenge by a competing genetic element (an incompatible plasmid or an allelic homologous stretch of DNA, for example) can lead to cell death through restriction breakage in the genome. This post-segregational or post-disturbance cell killing may provide the RM complexes (and any DNA linked with them) with a competitive advantage. There is evidence that they have undergone extensive horizontal transfer between genomes, as inferred from their sequence homology, codon usage bias and GC content difference. They are often linked with mobile genetic elements such as plasmids, viruses, transposons and integrons. The comparison of closely related bacterial genomes also suggests that, at times, RM genes themselves behave as mobile elements and cause genome rearrangements. Indeed some bacterial genomes that survived post-disturbance attack by an RM gene complex in the laboratory have experienced genome rearrangements. The avoidance of some restriction sites by bacterial genomes may result from selection by past restriction attacks. Both bacteriophages and bacteria also appear to use homologous recombination to cope with the selfish behavior of RM systems. RM systems compete with each other in several ways. One is competition for recognition sequences in post-segregational killing. Another is super-infection exclusion, that is, the killing of the cell carrying an RM system when it is infected with another RM system of the same regulatory specificity but of a different sequence specificity. The capacity of RM systems to act as selfish, mobile genetic elements may underlie the structure and function of RM enzymes.

MeSH Terms
Base Sequence DNA Restriction-Modification Enzymes/genetics,metabolism DNA Transposable Elements/genetics DNA, Bacterial/genetics,metabolism Evolution, Molecular Genome, Bacterial
Chemicals
DNA Restriction-Modification Enzymes DNA Transposable Elements DNA, Bacterial
Authors & Affiliations
1 authors, click to expand affiliations / ORCID
Kobayashi I
Department of Molecular Biology, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan. ikobaya@ims.u-tokyo.ac.jp
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Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
DOI
10.1093/nar/29.18.3742
Email
ikobaya@ims.u-tokyo.ac.jp
Published
2001-09-15
Pages
3742-56
Language
English
Region
England
NLM ID
0411011
PMCID
PMC55917
Subset
IM
External Links
PubMed source DOI: 10.1093/nar/29.18.3742 PMC Full Text View journal details
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