Prokaryote Genome Fluidity: Toward a System Approach of the Mobilome

Part of the Methods in Molecular Biology book series (MIMB, volume 804)

Abstract

The importance of horizontal/lateral gene transfer (LGT) in shaping the genomes of prokaryotic organisms has been recognized in recent years as a result of analysis of the increasing number of available genome sequences. LGT is largely due to the transfer and recombination activities of mobile genetic elements (MGEs). Bacterial and archaeal genomes are mosaics of vertically and horizontally transmitted DNA segments. This generates reticulate relationships between members of the prokaryotic world that are better represented by networks than by “classical” phylogenetic trees. In this review we summarize the nature and activities of MGEs, and the problems that presently limit their analysis on a large scale. We propose routes to improve their annotation in the flow of genomic and metagenomic sequences that currently exist and those that become available. We describe network analysis of evolutionary relationships among some MGE categories and sketch out possible developments of this type of approach to get more insight into the role of the mobilome in bacterial adaptation and evolution.

Key words

Mobile genetic elements Intercellular gene transfer Recombination Reticulate classification Prokaryotes adaptation and ev0olution 

Notes

Acknowledgments

We wish to thank Hans Geiselmann for his encouragement and useful comments, Raphael Leplae and Gipsi Lima-Mendez for discussion and comments, and Laurence van Melderen and Shannon Williamson for their critical reading of the manuscript. Work on the ACLAME project in the BiGRe laboratory is financed by the European Space Agency (ESA-PRODEX) and the Belgian Science Policy (Belspo) through the EXANAM project (PRODEX agreements No. C90358), the Fonds de la Recherche Scientifique Médicale (FRSM), the Belgian Program on Interuniversity Attraction Poles, initiated by the Belgian Federal Science Policy Office, project P6/25 (BioMaGNet), the BioSapiens Network of excellence funded under the sixth Framework program of the European Communities (LSHG-CT-2003-503265) and the intramural programme of the CNRS (LMGM Toulouse).

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© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  1. 1.Laboratoire de Bioinformatique des Génomes et des Réseaux (BiGRe)Université Libre de BruxellesBruxellesBelgium
  2. 2.Laboratoire de Microbiologie et Génétique Moléculaire (UMR 5100)ToulouseFrance

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