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MBE Advance Access published online on February 13, 2009
Molecular Biology and Evolution, doi:10.1093/molbev/msp026
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© The Author 2009. 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

Differential retention of metabolic genes following whole-genome duplication

Jean-François Gout, Laurent Duret and Daniel Kahn

Université de Lyon; Université Lyon 1; CNRS; INRIA; UMR5558; Laboratoire de Biométrie et Biologie Evolutive, F-69622 Villeurbanne, France

Corresponding author: Daniel Kahn, Laboratoire Biométrie et Biologie Evolutive, UMR CNRS 5558, Université Lyon 1, 43 Bld du 11 Novembre 1918, 69622 Villeurbanne Cedex, France, Phone : +33 (0) 4 72 43 13 44, FAX : +33 (0) 4 72 43 13 88, Email : kahn{at}biomserv.univ-lyon1.fr

Received for publication December 8, 2008. Revision received January 26, 2009. Accepted for publication January 26, 2009.

Classical studies in Metabolic Control Theory have shown that metabolic fluxes usually exhibit little sensitivity to changes in individual enzyme activity, yet remain sensitive to global changes of all enzymes in a pathway. Therefore little selective pressure is expected on the dosage or expression of individual metabolic genes, yet entire pathways should still be constrained. However a direct estimate of this selective pressure had not been evaluated. Whole genome duplications (WGDs) offer a good opportunity to address this question by analyzing the fates of metabolic genes during the massive gene losses that follow. Here we take advantage of the successive rounds of WGD that occurred in the Paramecium lineage. We show that metabolic genes exhibit different gene retention patterns than non-metabolic genes. Contrary to what was expected for individual genes, metabolic genes appeared more retained than other genes after the recent WGD, which was best explained by selection for gene expression operating on entire pathways. Metabolic genes also tend to be less retained when present at high copy number before WGD, contrary to other genes that show a positive correlation between gene retention and pre-duplication copy number. This is rationalized on the basis of the classical concave relationship relating metabolic fluxes with enzyme expression.

Key Words: metabolism • gene dosage • whole genome duplication • Paramecium • expression


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M. J. A. van Hoek and P. Hogeweg
Metabolic Adaptation after Whole Genome Duplication
Mol. Biol. Evol., November 1, 2009; 26(11): 2441 - 2453.
[Abstract] [Full Text] [PDF]


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