Codon usage of highly expressed genes affects proteome-wide translation efficiency

Idan Frumkin, Marc J. Lajoie, Christopher J. Gregg, Gil Hornung, George M. Church, Yitzhak Pilpel
2018 Proceedings of the National Academy of Sciences of the United States of America  
Although the genetic code is redundant, synonymous codons for the same amino acid are not used with equal frequencies in genomes, a phenomenon termed "codon usage bias." Previous studies have demonstrated that synonymous changes in a coding sequence can exert significant cis effects on the gene's expression level. However, whether the codon composition of a gene can also affect the translation efficiency of other genes has not been thoroughly explored. To study how codon usage bias influences
more » ... e cellular economy of translation, we massively converted abundant codons to their rare synonymous counterpart in several highly expressed genes in Escherichia coli. This perturbation reduces both the cellular fitness and the translation efficiency of genes that have high initiation rates and are naturally enriched with the manipulated codon, in agreement with theoretical predictions. Interestingly, we could alleviate the observed phenotypes by increasing the supply of the tRNA for the highly demanded codon, thus demonstrating that the codon usage of highly expressed genes was selected in evolution to maintain the efficiency of global protein translation. codon usage evolution | tRNA | codon-to-tRNA balance | translation efficiency | genome engineering S ince there are 61 sense codons but only 20 amino acids, most amino acids are encoded by more than a single codon. However, synonymous codons for the same amino acid are not utilized to the same extent across different genes or genomes. This phenomenon, termed "codon usage bias," has been the subject of intense research and was shown to affect gene expression and cellular function through varied processes in bacteria, yeast, and mammals (1-4). Although differential codon usage can result from neutral processes of mutational biases and drift (5-7), certain codon choices could be specifically favored as they increase the efficiency (8-12) or accuracy (13-17) of protein synthesis. These forces would typically lead to codon biases in a gene because they locally exert their effect on the gene in which the codons reside. Indeed, there is a positive correlation between a gene's expression level and the degree of its codon bias (1). Various systems have demonstrated how altering the codon usage synonymously can alter the expression levels of the manipulated genes (18-21), an effect that could reach more than 1,000-fold (22). In addition to such cis effects, it is possible that codon usage also acts in trans, namely, that the codon choice of some genes would affect the translation of others due to a "shared economy" of the entire translation apparatus (23-25). Previous theoretical works have suggested that an increase in the elongation rate may reduce the number of ribosomes on mRNAs and therefore may indirectly increase the rate of initiation of other transcripts due to an increase in the pool of free ribosomes (6, 26). In addition, a recent computational study in yeast has also examined the indirect effects of synonymous codon changes on the translation of the entire transcriptome (27). However, experimental evidence of such changes is absent. Here we ask how manipulating the frequency of a single codon on a small subset of genes influences the synthesis of other proteins. To tackle this question, we replaced common codons with a synonymous, rare counterpart in several highly expressed genes. We then asked how this massive change in the codon representation in the transcriptome would affect the manipulated genes, other genes, and the physiology and well-being of the cell (Fig. 1) . Interestingly, our genetic manipulation did not consistently affect the translation efficiency of the mutated genes, but it did show a profound proteome-wide effect on the translation process. Importantly, the translation efficiency of genes changed in a way that was dependent on the extent to which they contained the affected codons. These observations demonstrate that trans effects of codon usage could have strong implications in the cell. We could alleviate these physiological and molecular defects by increasing the tRNA supply for the manipulated codon in a manner that restored codon-to-tRNA balance. Our work demonstrates that codon choice not only tunes the expression level of individual genes but also maintains the efficiency of global protein translation in the cell.
doi:10.1073/pnas.1719375115 pmid:29735666 fatcat:7uyxypjapjfanj2v7hmc3c7iii