Selection for Synonymous Codon Usage

The genetic code is degenerate, and synonymous codons are not used with equal frequency. Rare codons are hypothesized to be associated with generally slower translation and lower translational accuracy. Historically, rare codons were believed to be deleterious, and were thought to persist in coding sequences mostly as the result of random genetic drift. However, rare codons have also been hypothesized to encode translation rate, thus promoting proper co-translation folding of the nascent chain and allowing time for co-translational interactions. Prior work by the Clark lab established that rare codons form clusters within the coding sequences of most species, raising the possibility that these clusters resulted from positive selection. Rare codons have been shown to have functional significance in specific protein coding sequences, but there is still no consensus on how widespread such mechanisms are or how to identify functional rare codon clusters. The studies described here seek to identify genome-wide trends in codon usage to aid in building hypotheses about the function of rare codons and identifying functionally significant codon usage. If rare codons modulate co-translational protein folding, their positions are expected to be correlated with the locations of protein structural features. Here we report that rare codon clusters are enriched at predicted domain boundaries, at a genome-wide level, in both human and E. coli. Transmembrane helices were also shown to have biased codon usage, but in this case codon usage preferences were associated with codon GC content rather than commonness or rareness. Functional sequence features are often conserved in evolution, so homologous coding sequences from multiple eukaryotes, archaea, and bacteria were analyzed to determine if rare codon clusters are conserved. This study revealed that such conservation is widespread across the tree of life, and homolog families with conserved rare codon clusters are enriched in functions associated with growth and development. Finally, the functional significance of rare codons will have to be verified experimentally. Here we describe the design of an experimental system to identify the effects of synonymous codon usage on the fitness of bacteria.