Proteome-wide analysis of functional divergence in bacteria: exploring a host of ecological adaptations.

PloS One
Brian E CaffreyMario A Fares

Abstract

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 diverg...Continue Reading

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Citations

May 24, 2013·Molecular Biology and Evolution·Laurent GuéguenJulien Y Dutheil
Jan 17, 2016·Journal of Experimental Botany·Edelín RoqueLuis A Cañas
Nov 1, 2013·Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution·Jianghong WuWenguang Zhang
Nov 18, 2014·Biochemical Society Transactions·Mario A Fares
Nov 30, 2014·Genome Biology and Evolution·Mauro Degli Esposti

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Software Mentioned

DIVERGE
OMA
RaxML
R
HAMAP
PAML
BIONJ
Linux
gplots
COG

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