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PMID: 19361336 Published · epublish English Comparative Study Journal Article

Massive comparative genomic analysis reveals convergent evolution of specialized bacteria.

Biology direct ·Vol. 4 ·2009-04-10 ·Pages 13

Merhej V, Royer-Carenzi M, Pontarotti P, Raoult D

Abstract

Genome size and gene content in bacteria are associated with their lifestyles. Obligate intracellular bacteria (i.e., mutualists and parasites) have small genomes that derived from larger free-living bacterial ancestors; however, the different steps of bacterial specialization from free-living to intracellular lifestyle have not been studied comprehensively. The growing number of available sequenced genomes makes it possible to perform a statistical comparative analysis of 317 genomes from bacteria with different lifestyles. Compared to free-living bacteria, host-dependent bacteria exhibit fewer rRNA genes, more split rRNA operons and fewer transcriptional regulators, linked to slower growth rates. We found a function-dependent and non-random loss of the same 100 orthologous genes in all obligate intracellular bacteria. Thus, we showed that obligate intracellular bacteria from different phyla are converging according to their lifestyle. Their specialization is an irreversible phenomenon characterized by translation modification and massive gene loss, including the loss of transcriptional regulators. Although both mutualists and parasites converge by genome reduction, these obligate intracellular bacteria have lost distinct sets of genes in the context of their specific host associations: mutualists have significantly more genes that enable nutrient provisioning whereas parasites have genes that encode Types II, IV, and VI secretion pathways. Our findings suggest that gene loss, rather than acquisition of virulence factors, has been a driving force in the adaptation of parasites to eukaryotic cells. This comparative genomic analysis helps to explore the strategies by which obligate intracellular genomes specialize to particular host-associations and contributes to advance our knowledge about the mechanisms of bacterial evolution.

MeSH Terms
Bacteria/genetics,growth & development Evolution, Molecular Genes, Bacterial Genome, Bacterial/genetics Genomics Intracellular Space/microbiology Open Reading Frames/genetics Phylogeny Principal Component Analysis Protein Biosynthesis Time Factors Transcription, Genetic
Authors & Affiliations
4 authors, click to expand affiliations / ORCID
Merhej Vicky
Faculty of Medicine, Unit for Research on Emergent and Tropical Infectious Diseases, CNRS-IRD UMR 6236 IFR48, University of the Mediterranean, Marseilles, France. [email protected]
Royer-Carenzi Manuela
Pontarotti Pierre
Raoult Didier
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Article Info
Journal
Biology direct
Abbr.
Biol Direct
ISSN
1745-6150
DOI
10.1186/1745-6150-4-13
Email
[email protected]
Published
2009-04-10
Epub
2009-00-10
Pages
13
Language
English
Region
England
NLM ID
101258412
PMCID
PMC2688493
Subset
IM
External Links
PubMed source DOI: 10.1186/1745-6150-4-13 PMC Full Text View journal details
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