Bioinformatics Advance Access originally published online on April 6, 2006
Bioinformatics 2006 22(12):1418-1423; doi:10.1093/bioinformatics/btl135
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Gene fusion/fission is a major contributor to evolution of multi-domain bacterial proteins
1 Laboratoire Statistique et Génome 523 Place des Terrasses, 91034 Evry cedex, France
2 Soluscience, Biopôle Clermont-Limagne 63360 Saint-Beauzire, France
*To whom correspondence should be addressed.
Most proteins comprise one or several domains. New domain architectures can be created by combining previously existing domains. The elementary events that create new domain architectures may be categorized into three classes, namely domain(s) insertion or deletion (indel), exchange and repetition. Using ‘DomainTeam’, a tool dedicated to the search for microsyntenies of domains, we quantified the relative contribution of these events. This tool allowed us to collect homologous bacterial genes encoding proteins that have obviously evolved by modular assembly of domains. We show that indels are the most frequent elementary events and that they occur in most cases at either the N- or C-terminus of the proteins. As revealed by the genomic neighbourhood/context of the corresponding genes, we show that a substantial number of these terminal indels are the consequence of gene fusions/fissions. We provide evidence showing that the contribution of gene fusion/fission to the evolution of multi-domain bacterial proteins is lower-bounded by 27% and upper-bounded by 64%. We conclude that gene fusion/fission is a major contributor to the evolution of multi-domain bacterial proteins.
Contact: pasek{at}genopole.cnrs.fr
Supplementary information: Supplementary data are available at http://stat.genopole.cnrs.fr/domainteams/Bioinformatics/results.html
Received on February 13, 2006; revised on March 22, 2006; accepted on April 3, 2006
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