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MBE Advance Access published online on April 3, 2007
Molecular Biology and Evolution, doi:10.1093/molbev/msm065
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© The Author 2007. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org

Research Article

Testing the Neutral Fixation of Hetero-oligomerism in the Archaeal Chaperonin CCT

Valentin Ruano-Rubio1 and Mario A. Fares1,*

1 Evolutionary Genetics and Bioinformatics Laboratory, Department of Genetics, Smurfit Institute of Genetics, University of Dublin, Trinity College, Dublin, Ireland

* Corresponding author: Dr. Mario A. Fares, Telephone number: 353 1 8963521, Email address: faresm{at}tcd.ie

Received for publication December 11, 2006. Revision received February 15, 2007. Accepted for publication March 15, 2007.

The evolutionary transition from homo-oligomerism to hetero-oligomerism in multi-meric proteins and its contribution to function innovation and organism complexity remains to be investigated. Here we undertake the challenge of contributing to this theoretical ground by investigating the hetero-oligomerism in the molecular chaperonin CCT from archaea. CCT is amenable to this study because, in contrast to eukaryotic CCTs where sub-functionalisation after gene duplication has been taken to completion, archaeal CCTs present no evidence for subunit functional specialisation. Our analyses yield additional information to previous reports on archaeal CCT paralogy by identifying new duplication events. Analyses of selective constraints show that amino acid sites from one subunit have fixed slightly deleterious mutations at inter-subunit interfaces after gene duplication. These mutations have been followed by compensatory mutations in nearby regions of the same subunit and in the interface contact regions of its paralogous subunit. The strong selective constraints in these regions after speciation support the evolutionary entrapment of CCTs as hetero-oligomers. In addition, our results unveil different evolutionary dynamics depending on the degree of CCT hetero-oligomerism. Archaeal CCT protein complexes comprising three distinct classes of subunits present two evolutionary processes. First, slightly deleterious and compensatory mutations were fixed neutrally at inter-subunit regions. Second, sub-functionalisation may have occurred at substrate binding and ATP binding regions after the second gene duplication event took place. CCTs with two distinct types of subunits did not present evidence of sub-functionalisation. Our results provide the first in silico evidence for the neutral fixation of hetero-oligomerism in archaeal CCTs and provide information on the evolution of hetero-oligomerism toward sub-functionalisation in archaeal CCTs.

Key Words: Neutral Evolution • Positive Selection • Accelerated fixation rates • Coevolution • CCT • Archaea


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