Evidence for non-optimal codon choice in highly transcribed sex-biased genes of Drosophila melanogaster

Abstract Biases in synonymous codon use occur in many unicellular and multicellular organisms. Optimal codons, defined as those most commonly used in highly transcribed genes, are thought to arise from selection for cost-efficient translation, which would favor codons with abundant matching tRNAs. Such presumed selection is described as optimal codon choice. Non-optimal codons, defined as those least commonly used in highly transcribed genes, may in principle also play important roles, but the dynamics of their use remain understudied. Here we examine non-optimal codon use, using sex-biased genes expressed in the gonads of Drosophila melanogaster as a case study. We show that genes with sex-biased expression exhibit a preference for non-optimal codon use, especially testis-biased genes. Further we show that the use of non-optimal codons is not random. Instead, specific non-optimal codons are favored, again especially in testis-biased genes. Non-optimal codon use is positively linked to elevated disorder of the encoded proteins. Remarkably, all 18 degenerate amino acids were associated with higher disorder when encoded by the identified primary non-optimal codon, than when encoded by its sister optimal codon. We hypothesize that selection may have promoted non-optimal codon choice for a subset of favored non-optimal codons to regulate translation. We discuss the putative roles of tRNA gene copy numbers, pleiotropy, and sex-biased expression in the evolution of this level of gene regulation. Significance Statement Optimal codons, those codons most commonly used in highly expressed protein-coding genes, are thought to improve translational efficiency in a range of organisms. However, relatively minimal attention has been given to non-optimal codons, those least often used in highly transcribed genes, and their potential roles in translation. Here, using sex-biased gonadal genes of Drosophila melanogaster as a model system, we demonstrate that non-optimal codons are preferentially used in sex-biased genes, particularly within highly expressed testis-biased genes, and are associated with disordered proteins. Moreover, the preference for a specific non-optimal codon (per amino acid) is ubiquitous across all degenerate amino acids. We propose that non-optimal codon use is non-random and may have evolved under selection for roles in translational regulation and protein folding in sex-biased genes, and in a manner associated with their tRNA abundances. The findings have significant implications for the understanding of pacing of translation, protein conformation and protein functionality. Competing Interest Statement The authors have declared no competing interest. Footnotes Competing Interest Statement: None we have added new supplementary figures and tables to support the analyses and conclusions.