Proteome-Wide Analysis of Functional Divergence in Bacteria: Exploring a Host of Ecological Adaptations

Functional divergence is the process by which new genes and functions originate through the modification of existing ones. Both genetic and environmental factors influence the evolution of new functions, including gene duplication or changes in the ecological requirements of an organism. Novel funct...

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Main Authors:	Caffrey, Brian E., Williams, Tom A., Jiang, Xiaowei, Toft, Christina, Hokamp, Karsten, Fares, Mario A.
Format:	Online
Language:	English
Published:	Public Library of Science 2012
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3338524/

id	pubmed-3338524
recordtype	oai_dc
spelling	pubmed-33385242012-05-04 Proteome-Wide Analysis of Functional Divergence in Bacteria: Exploring a Host of Ecological Adaptations Caffrey, Brian E. Williams, Tom A. Jiang, Xiaowei Toft, Christina Hokamp, Karsten Fares, Mario A. Research Article Functional divergence is the process by which new genes and functions originate through the modification of existing ones. Both genetic and environmental factors influence the evolution of new functions, including gene duplication or changes in the ecological requirements of an organism. Novel functions emerge at the expense of ancestral ones and are generally accompanied by changes in the selective forces at constrained protein regions. We present software capable of analyzing whole proteomes, identifying putative amino acid replacements leading to functional change in each protein and performing statistical tests on all tabulated data. We apply this method to 750 complete bacterial proteomes to identify high-level patterns of functional divergence and link these patterns to ecological adaptations. Proteome-wide analyses of functional divergence in bacteria with different ecologies reveal a separation between proteins involved in information processing (Ribosome biogenesis etc.) and those which are dependent on the environment (energy metabolism, defense etc.). We show that the evolution of pathogenic and symbiotic bacteria is constrained by their association with the host, and also identify unusual events of functional divergence even in well-studied bacteria such as Escherichia coli. We present a description of the roles of phylogeny and ecology in functional divergence at the level of entire proteomes in bacteria. Public Library of Science 2012-04-26 /pmc/articles/PMC3338524/ /pubmed/22563391 http://dx.doi.org/10.1371/journal.pone.0035659 Text en Caffrey et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Caffrey, Brian E. Williams, Tom A. Jiang, Xiaowei Toft, Christina Hokamp, Karsten Fares, Mario A.
spellingShingle	Caffrey, Brian E. Williams, Tom A. Jiang, Xiaowei Toft, Christina Hokamp, Karsten Fares, Mario A. Proteome-Wide Analysis of Functional Divergence in Bacteria: Exploring a Host of Ecological Adaptations
author_facet	Caffrey, Brian E. Williams, Tom A. Jiang, Xiaowei Toft, Christina Hokamp, Karsten Fares, Mario A.
author_sort	Caffrey, Brian E.
title	Proteome-Wide Analysis of Functional Divergence in Bacteria: Exploring a Host of Ecological Adaptations
title_short	Proteome-Wide Analysis of Functional Divergence in Bacteria: Exploring a Host of Ecological Adaptations
title_full	Proteome-Wide Analysis of Functional Divergence in Bacteria: Exploring a Host of Ecological Adaptations
title_fullStr	Proteome-Wide Analysis of Functional Divergence in Bacteria: Exploring a Host of Ecological Adaptations
title_full_unstemmed	Proteome-Wide Analysis of Functional Divergence in Bacteria: Exploring a Host of Ecological Adaptations
title_sort	proteome-wide analysis of functional divergence in bacteria: exploring a host of ecological adaptations
description	Functional divergence is the process by which new genes and functions originate through the modification of existing ones. Both genetic and environmental factors influence the evolution of new functions, including gene duplication or changes in the ecological requirements of an organism. Novel functions emerge at the expense of ancestral ones and are generally accompanied by changes in the selective forces at constrained protein regions. We present software capable of analyzing whole proteomes, identifying putative amino acid replacements leading to functional change in each protein and performing statistical tests on all tabulated data. We apply this method to 750 complete bacterial proteomes to identify high-level patterns of functional divergence and link these patterns to ecological adaptations. Proteome-wide analyses of functional divergence in bacteria with different ecologies reveal a separation between proteins involved in information processing (Ribosome biogenesis etc.) and those which are dependent on the environment (energy metabolism, defense etc.). We show that the evolution of pathogenic and symbiotic bacteria is constrained by their association with the host, and also identify unusual events of functional divergence even in well-studied bacteria such as Escherichia coli. We present a description of the roles of phylogeny and ecology in functional divergence at the level of entire proteomes in bacteria.
publisher	Public Library of Science
publishDate	2012
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3338524/
_version_	1611525358872428544

Proteome-Wide Analysis of Functional Divergence in Bacteria: Exploring a Host of Ecological Adaptations

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