Temperature adaptation at homologous sites in proteins from nine thermophile-mesophile species pairs.

Genome Biology and Evolution
John H McDonald

Abstract

Whether particular amino acids are favored by selection at high temperatures over others has long been an open question in protein evolution. One way to approach this question is to compare homologous sites in proteins from one thermophile and a closely related mesophile; asymmetrical substitution patterns have been taken as evidence for selection favoring certain amino acids over others. However, most pairs of prokaryotic species that differ in optimum temperature also differ in genome-wide GC content, and amino acid content is known to be associated with GC content. Here, I compare homologous sites in nine thermophilic prokaryotes and their mesophilic relatives, all with complete published genome sequences. After adjusting for the effects of differing GC content with logistic regression, 139 of the 190 pairs of amino acids show significant substitutional asymmetry, evidence of widespread adaptive amino acid substitution. The patterns are fairly consistent across the nine pairs of species (after taking the effects of differing GC content into account), suggesting that much of the asymmetry results from adaptation to temperature. Some amino acids in some species pairs deviate from the overall pattern in ways indicating that ada...Continue Reading

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Citations

May 30, 2013·Origins of Life and Evolution of the Biosphere : the Journal of the International Society for the Study of the Origin of Life·J Dennis PollackDennis K Pearl
Jan 12, 2013·BMC Evolutionary Biology·Vera van NoortPeer Bork
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Jan 10, 2013·Journal of Biomolecular Structure & Dynamics·Andrés IriarteHéctor Musto
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Jan 16, 2021·Molecular Biology and Evolution·Michel LecocqCéline Brochier-Armanet
Feb 1, 2019·Molecular & Cellular Proteomics : MCP·Jeremy D VolkeningMichael R Sussman

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Software Mentioned

Blast
AmbiguityRemover
SAS
ClustalW
AsymmetryCounter
Pascal
Geneplot

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