RT Journal Article
SR Electronic
T1 Natural selection on gene-specific codon usage bias is common across eukaryotes
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 292938
DO 10.1101/292938
A1 Zhen Peng
A1 Hani Zaher
A1 Yehuda Ben-Shahar
YR 2018
UL http://biorxiv.org/content/early/2018/03/31/292938.abstract
AB Genomic data from diverse taxa indicate that synonymous codon usage frequencies are often not random. Although the molecular evolutionary forces that shape codon usage remain poorly understood, synonymous mutations are generally assumed to be neutral because they do not affect protein sequences. However, empirical evidence indicates that some synonymous mutations can have phenotypic consequences. Here we show that in contrast to the current dogma, natural selection on gene-specific codon usage bias is common across Eukaryota. Furthermore, by using bioinformatic and experimental approaches, we demonstrate that specific combinations of rare codons contribute to spatial and sex-related regulation of protein expression in Drosophila melanogaster. These data indicate that natural selection shapes gene-specific codon usage biases, and therefore, it represents an overlooked genomic feature that plays an important role in the spatial and temporal regulation of gene functions. Hence, the broadly accepted dogma that synonymous mutations are generally functionally neutral should be reevaluated.