Rapid evolution of the sequences and gene repertoires of secreted proteins in bacteria.

Proteins secreted to the extracellular environment or to the periphery of the cell envelope, the secretome, play essential roles in foraging, antagonistic and mutualistic interactions. We hypothesize that arms races, genetic conflicts and varying selective pressures should lead to the rapid change o...

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Autores principales:	Teresa Nogueira, Marie Touchon, Eduardo P C Rocha
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/11baf6a7905d4bf2a9ad0b9c24f0f5a8
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spelling	oai:doaj.org-article:11baf6a7905d4bf2a9ad0b9c24f0f5a82021-11-18T08:07:39ZRapid evolution of the sequences and gene repertoires of secreted proteins in bacteria.1932-620310.1371/journal.pone.0049403https://doaj.org/article/11baf6a7905d4bf2a9ad0b9c24f0f5a82012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23189144/?tool=EBIhttps://doaj.org/toc/1932-6203Proteins secreted to the extracellular environment or to the periphery of the cell envelope, the secretome, play essential roles in foraging, antagonistic and mutualistic interactions. We hypothesize that arms races, genetic conflicts and varying selective pressures should lead to the rapid change of sequences and gene repertoires of the secretome. The analysis of 42 bacterial pan-genomes shows that secreted, and especially extracellular proteins, are predominantly encoded in the accessory genome, i.e. among genes not ubiquitous within the clade. Genes encoding outer membrane proteins might engage more frequently in intra-chromosomal gene conversion because they are more often in multi-genic families. The gene sequences encoding the secretome evolve faster than the rest of the genome and in particular at non-synonymous positions. Cell wall proteins in Firmicutes evolve particularly fast when compared with outer membrane proteins of Proteobacteria. Virulence factors are over-represented in the secretome, notably in outer membrane proteins, but cell localization explains more of the variance in substitution rates and gene repertoires than sequence homology to known virulence factors. Accordingly, the repertoires and sequences of the genes encoding the secretome change fast in the clades of obligatory and facultative pathogens and also in the clades of mutualists and free-living bacteria. Our study shows that cell localization shapes genome evolution. In agreement with our hypothesis, the repertoires and the sequences of genes encoding secreted proteins evolve fast. The particularly rapid change of extracellular proteins suggests that these public goods are key players in bacterial adaptation.Teresa NogueiraMarie TouchonEduardo P C RochaPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 11, p e49403 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Teresa Nogueira Marie Touchon Eduardo P C Rocha Rapid evolution of the sequences and gene repertoires of secreted proteins in bacteria.
description	Proteins secreted to the extracellular environment or to the periphery of the cell envelope, the secretome, play essential roles in foraging, antagonistic and mutualistic interactions. We hypothesize that arms races, genetic conflicts and varying selective pressures should lead to the rapid change of sequences and gene repertoires of the secretome. The analysis of 42 bacterial pan-genomes shows that secreted, and especially extracellular proteins, are predominantly encoded in the accessory genome, i.e. among genes not ubiquitous within the clade. Genes encoding outer membrane proteins might engage more frequently in intra-chromosomal gene conversion because they are more often in multi-genic families. The gene sequences encoding the secretome evolve faster than the rest of the genome and in particular at non-synonymous positions. Cell wall proteins in Firmicutes evolve particularly fast when compared with outer membrane proteins of Proteobacteria. Virulence factors are over-represented in the secretome, notably in outer membrane proteins, but cell localization explains more of the variance in substitution rates and gene repertoires than sequence homology to known virulence factors. Accordingly, the repertoires and sequences of the genes encoding the secretome change fast in the clades of obligatory and facultative pathogens and also in the clades of mutualists and free-living bacteria. Our study shows that cell localization shapes genome evolution. In agreement with our hypothesis, the repertoires and the sequences of genes encoding secreted proteins evolve fast. The particularly rapid change of extracellular proteins suggests that these public goods are key players in bacterial adaptation.
format	article
author	Teresa Nogueira Marie Touchon Eduardo P C Rocha
author_facet	Teresa Nogueira Marie Touchon Eduardo P C Rocha
author_sort	Teresa Nogueira
title	Rapid evolution of the sequences and gene repertoires of secreted proteins in bacteria.
title_short	Rapid evolution of the sequences and gene repertoires of secreted proteins in bacteria.
title_full	Rapid evolution of the sequences and gene repertoires of secreted proteins in bacteria.
title_fullStr	Rapid evolution of the sequences and gene repertoires of secreted proteins in bacteria.
title_full_unstemmed	Rapid evolution of the sequences and gene repertoires of secreted proteins in bacteria.
title_sort	rapid evolution of the sequences and gene repertoires of secreted proteins in bacteria.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/11baf6a7905d4bf2a9ad0b9c24f0f5a8
work_keys_str_mv	AT teresanogueira rapidevolutionofthesequencesandgenerepertoiresofsecretedproteinsinbacteria AT marietouchon rapidevolutionofthesequencesandgenerepertoiresofsecretedproteinsinbacteria AT eduardopcrocha rapidevolutionofthesequencesandgenerepertoiresofsecretedproteinsinbacteria
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Rapid evolution of the sequences and gene repertoires of secreted proteins in bacteria.

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