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Massive comparative genomic analysis reveals convergent evolution of
specialized bacteria
Biology Direct 2009, 4:13

doi:10.1186/1745-6150-4-13

Vicky Merhej (vicky_merhej@hotmail.com)
Manuela Royer-Carenzi(royermanuela@yahoo.fr)
Pierre Pontarotti (Pierre.Pontarotti@univ-provence.fr)
Didier Raoult (didier.raoult@gmail.com)

ISSN
Article type

1745-6150
Research

Submission date

30 March 2009

Acceptance date

10 April 2009

Publication date

10 April 2009

Article URL

http://www.biology-direct.com/content/4/1/13

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Massive comparative genomicanalysis reveals convergent
evolution of specialized bacteria

Vicky Merhej1, Manuela Royer-Carenzi2, Pierre Pontarotti2, Didier Raoult1*

1

Unit for Research on Emergent and Tropical Infectious Diseases (URMITE), CNRS-IRD

UMR 6236 IFR48, Faculty of Medicine, University of the Mediterranean, Marseilles, France
2

Evolutionary biology and modelization, LATP UMR CNRS 6632 FR 3098 IFR 48,University of Provence, Marseilles, France

*Corresponding author: Didier Raoult

Email addresses:
VM: vicky_merhej@hotmail.com
MRC: royermanuela@yahoo.fr
PP: Pierre.Pontarotti@univ-provence.fr
DR: didier.raoult@gmail.com

1

Abstract
Background

Genome size and gene content in bacteria are associated with their lifestyles. Obligate
intracellular bacteria (i.e., mutualists andparasites) 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 metaanalysis of 317 genomes from bacteria with different lifestyles.
ResultsCompared 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 convergingaccording 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: mutualistshave significantly more
genes that enable nutrient provisioning whereas parasites have genes that encode Types II, IV,
and VI secretion pathways.
Conclusions

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 genomic meta-analysis
helps to explore the strategies by which...