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PMID: 17760998 Published · epublish English Journal Article Research Support, Non-U.S. Gov't

Phylogenomic analysis of natural selection pressure in Streptococcus genomes.

BMC evolutionary biology ·Vol. 7 ·2007-08-30 ·Pages 154

Anisimova M, Bielawski J, Dunn K, Yang Z

Abstract

In comparative analyses of bacterial pathogens, it has been common practice to discriminate between two types of genes: (i) those shared by pathogens and their non-pathogenic relatives (core genes), and (ii) those found exclusively in pathogens (pathogen-specific accessory genes). Rather than attempting to a priori delineate genes into sets more or less relevant to pathogenicity, we took a broad approach to the analysis of Streptococcus species by investigating the strength of natural selection in all clusters of homologous genes. The genus Streptococcus is comprised of a wide variety of both pathogenic and commensal lineages, and we relate our findings to the pre-existing knowledge of Streptococcus virulence factors. Our analysis of 1730 gene clusters revealed 136 cases of positive Darwinian selection, which we suggest is most likely to result from an antagonistic interaction between the host and pathogen at the molecular level. A two-step validation procedure suggests that positive selection was robustly identified in our genomic survey. We found no evidence to support the notion that pathogen specific accessory genes are more likely to be subject to positive selection than core genes. Indeed, we even uncovered a few cases of essential gene evolution by positive selection. Among the gene clusters subject to positive selection, a large fraction (29%) can be connected to virulence. The most striking finding was that a considerable fraction of the positively selected genes are also known to have tissue specific patterns of expression during invasive disease. As current expression data is far from comprehensive, we suggest that this fraction was underestimated. Our findings suggest that pathogen specific genes, although a popular focus of research, do not provide a complete picture of the evolutionary dynamics of virulence. The results of this study, and others, support the notion that the products of both core and accessory genes participate in complex networks that comprise the molecular basis of virulence. Future work should seek to understand the evolutionary dynamics of both core and accessory genes as a function of the networks in which they participate.

MeSH Terms
Biological Evolution Gene Expression Regulation, Bacterial Genome, Bacterial Multigene Family Phylogeny Selection, Genetic Streptococcus/genetics,pathogenicity Virulence/genetics
Authors & Affiliations
4 authors, click to expand affiliations / ORCID
Anisimova Maria
Department of Biology, University College London, London, UK. [email protected]
Bielawski Joseph
Dunn Katherine
Yang Ziheng
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Article Info
Journal
BMC evolutionary biology
Abbr.
BMC Evol Biol
ISSN
1471-2148
DOI
10.1186/1471-2148-7-154
Email
[email protected]
Published
2007-08-30
Epub
2007-00-30
Pages
154
Language
English
Region
England
NLM ID
100966975
PMCID
PMC2031904
Subset
IM
External Links
PubMed source DOI: 10.1186/1471-2148-7-154 PMC Full Text View journal details
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