Differential retention of metabolic genes following whole-genome duplication
- PMID: 19218282
- DOI: 10.1093/molbev/msp026
Differential retention of metabolic genes following whole-genome duplication
Abstract
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 nonmetabolic 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 preduplication copy number. This is rationalized on the basis of the classical concave relationship relating metabolic fluxes with enzyme expression.
Similar articles
-
Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia.Nature. 2006 Nov 9;444(7116):171-8. doi: 10.1038/nature05230. Epub 2006 Nov 1. Nature. 2006. PMID: 17086204
-
Whole-genome duplications contributed to the expansion of cytochrome b5 genes in Paramecium tetraurelia.Genet Mol Res. 2013 Jun 13;12(2):1882-96. doi: 10.4238/2013.January.9.1. Genet Mol Res. 2013. PMID: 23359053
-
Metabolic adaptation after whole genome duplication.Mol Biol Evol. 2009 Nov;26(11):2441-53. doi: 10.1093/molbev/msp160. Epub 2009 Jul 22. Mol Biol Evol. 2009. PMID: 19625390
-
Turning a hobby into a job: how duplicated genes find new functions.Nat Rev Genet. 2008 Dec;9(12):938-50. doi: 10.1038/nrg2482. Nat Rev Genet. 2008. PMID: 19015656 Review.
-
Gene duplication, co-option and recruitment during the origin of the vertebrate brain from the invertebrate chordate brain.Brain Behav Evol. 2008;72(2):91-105. doi: 10.1159/000151470. Epub 2008 Oct 7. Brain Behav Evol. 2008. PMID: 18836256 Review.
Cited by
-
Horizontal transfer and evolution of the biosynthetic gene cluster for benzoxazinoids in plants.Plant Commun. 2022 May 9;3(3):100320. doi: 10.1016/j.xplc.2022.100320. Epub 2022 Mar 25. Plant Commun. 2022. PMID: 35576160 Free PMC article.
-
Expression properties exhibit correlated patterns with the fate of duplicated genes, their divergence, and transcriptional plasticity in Saccharomycotina.DNA Res. 2017 Dec 1;24(6):559-570. doi: 10.1093/dnares/dsx025. DNA Res. 2017. PMID: 28633360 Free PMC article.
-
Differential retention and divergent resolution of duplicate genes following whole-genome duplication.Genome Res. 2014 Oct;24(10):1665-75. doi: 10.1101/gr.173740.114. Epub 2014 Aug 1. Genome Res. 2014. PMID: 25085612 Free PMC article.
-
A Systems Approach to Elucidate Heterosis of Protein Abundances in Yeast.Mol Cell Proteomics. 2015 Aug;14(8):2056-71. doi: 10.1074/mcp.M115.048058. Epub 2015 May 13. Mol Cell Proteomics. 2015. PMID: 25971257 Free PMC article.
-
Evolutionary dynamics of a conserved sequence motif in the ribosomal genes of the ciliate Paramecium.BMC Evol Biol. 2010 May 4;10:129. doi: 10.1186/1471-2148-10-129. BMC Evol Biol. 2010. PMID: 20441586 Free PMC article.
Publication types
MeSH terms
LinkOut - more resources
Full Text Sources
