NDLI: Positive selection for unpreferred codon usage in eukaryotic genomes

Content Provider	Springer Nature : BioMed Central
Author	Neafsey, Daniel E Galagan, James E
Abstract	Background Natural selection has traditionally been understood as a force responsible for pushing genes to states of higher translational efficiency, whereas lower translational efficiency has been explained by neutral mutation and genetic drift. We looked for evidence of directional selection resulting in increased unpreferred codon usage (and presumably reduced translational efficiency) in three divergent clusters of eukaryotic genomes using a simple optimal-codon-based metric (Kp/Ku). Results Here we show that for some genes natural selection is indeed responsible for causing accelerated unpreferred codon substitution, and document the scope of this selection. In Cryptococcus and to a lesser extent Drosophila, we find many genes showing a statistically significant signal of selection for unpreferred codon usage in one or more lineages. We did not find evidence for this type of selection in Saccharomyces. The signal of positive selection observed from unpreferred synonymous codon substitutions is coincident in Cryptococcus and Drosophila with the distribution of upstream open reading frames (uORFs), another genic feature known to reduce translational efficiency. Functional enrichment analysis of genes exhibiting low Kp/Ku ratios reveals that genes in regulatory roles are particularly subject to this type of selection. Conclusion Through genome-wide scans, we find recent selection for unpreferred codon usage at approximately 1% of genetic loci in a Cryptococcus and several genes in Drosophila. Unpreferred codons can impede translation efficiency, and we find that genes with translation-impeding uORFs are enriched for this selection signal. We find that regulatory genes are particularly likely to be subject to selection for unpreferred codon usage. Given that expression noise can propagate through regulatory cascades, and that low translational efficiency can reduce expression noise, this finding supports the hypothesis that translational efficiency may be suppressed in some cases to reduce stochastic noise in gene expression.
Related Links	https://bmcecolevol.biomedcentral.com/counter/pdf/10.1186/1471-2148-7-119.pdf
Ending Page	10
Page Count	10
Starting Page	1
File Format	HTM / HTML
ISSN	27307182
DOI	10.1186/1471-2148-7-119
Journal	BMC Ecology and Evolution
Issue Number	1
Volume Number	7
Language	English
Publisher	BioMed Central
Publisher Date	2007-07-18
Access Restriction	Open
Subject Keyword	Evolutionary Biology Animal Systematics Taxonomy Biogeography Entomology Genetics and Population Dynamics Life Sciences Codon Usage Synonymous Substitution Translational Efficiency Synonymous Codon Codon Bias Animal Systematics/Taxonomy/Biogeography
Content Type	Text
Resource Type	Article
Subject	Ecology, Evolution, Behavior and Systematics
Journal Impact Factor	2.3/2023
5-Year Journal Impact Factor	2.3/2023

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