The surprising negative correlation of gene length and optimal codon use--disentangling translational selection from GC-biased gene conversion in yeast

BMC Evolutionary Biology
Nina Stoletzki

Abstract

Surprisingly, in several multi-cellular eukaryotes optimal codon use correlates negatively with gene length. This contrasts with the expectation under selection for translational accuracy. While suggested explanations focus on variation in strength and efficiency of translational selection, it has rarely been noticed that the negative correlation is reported only in organisms whose optimal codons are biased towards codons that end with G or C (-GC). This raises the question whether forces that affect base composition--such as GC-biased gene conversion--contribute to the negative correlation between optimal codon use and gene length. Yeast is a good organism to study this as equal numbers of optimal codons end in -GC and -AT and one may hence compare frequencies of optimal GC- with optimal AT-ending codons to disentangle the forces. Results of this study demonstrate in yeast frequencies of GC-ending (optimal AND non-optimal) codons decrease with gene length and increase with recombination. A decrease of GC-ending codons along genes contributes to the negative correlation with gene length. Correlations with recombination and gene expression differentiate between GC-ending and optimal codons, and also substitution patterns support...Continue Reading

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Related Concepts

Sense Codon
Yeast Proteins
Saccharomyces cerevisiae
Protein Biosynthesis
Gene Expression Regulation, Fungal
Gene Expression
Genes
Guanosine
Kidney Failure, Chronic
Recombination, Genetic

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