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

Abstract

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 the 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 (2...

Translational efficiency across healthy and tumor tissues is proliferation‐related

“…Although a more accurate SDA would have determined the supply and demand based on the aminoacylated portion of tRNAs (Evans et al , ) and the ribosome‐bound mRNAs (Ingolia et al , ), respectively, we approximate such measures by our tRNA quantifications and the publicly available mRNA‐seq data of TCGA. In agreement with current studies showing that a dynamic codon usage needs to compete for a limited tRNA pool (Frumkin et al , ; Eraslan et al , ), we demonstrate that SDA is better measure of codon optimality than previously published metrics such as the tAI (dos Reis et al , , ). However, far from explaining the translation process, the still low but significant correlations of protein‐SDA in human, in contrast to unicellular organisms, suggest that protein expression is also dependent on other layers of regulation, such as transcriptional and post‐transcriptional machineries, translation initiation, epigenetic modifications of DNA and RNAs, or protein degradation mechanisms (Rudolph et al , ).…”

“…The so‐called translational efficiency is defined as the rate of protein production from mRNA, and multiple indices and models can be described to estimate it (Gingold & Pilpel, ). In this article, and based on previous studies underscoring the global control role of codon usage as a competition for a limited tRNA pool (Gingold et al , ; Pechmann & Frydman, ; Frumkin et al , ), we define the Supply‐to‐Demand Adaptation (SDA) as the balance between the supply (i.e., the anticodon tRNA abundances) and demand (i.e., the weighted codon usage based on the mRNA levels) for each of the 60 codons (excluding methionine and stop codons). Furthermore, we normalize both the codon and anticodon abundances within each amino acid family (i.e., relative to the most abundant synonymous codon/anticodon), in order to remove the effect of amino acid biases and get a cleaner measure of codon optimality (Eraslan et al , ).…”

“…In doing so, it constitutes a global measure of translation control, since the efficiency of a certain codon depends both on its complementary anticodon abundance and the demand for such anticodon by other transcripts. This global control has been indeed established to play an important role in defining optimal translation programs (Frumkin et al, 2018). The definition of the SDA is based on similar previously published metrics (Gingold et al, 2012;Pechmann & Frydman, 2013), which consists of a ratio between the anticodon supply and demand.…”

Transcript degradation and codon usage regulate gene expression in a lytic phage

“…Some codons are always translated more quickly than others. However, in living E. coli cells, abundances of charged tRNAs may change during infection, due to the stress the cells experience during infection, and such changes would affect codon-specific translation rates [35,36]. Thus, further work may be needed to extend Pinetree to include a realistic translation model.…”

Evolutionary Analyses of RNA Editing and Amino Acid Recoding in Cephalopods

“…Besides nucleotide composition, another potential consequence of widespread RNA editing is changes in codon usage bias, in which certain codons are used at higher frequencies than other synonymous codons ( 12 ). Codon usage bias has various influences on processes related to gene expression--for example, codon usage of highly expressed genes is selected to increase translation efficiency ( 13 ). Within the context of RNA editing in cephalopods, given synonymous codons that code for the identical amino acid, we might expect the codon containing a "A" to be preferred since it enables further editing that may diversify the protein.…”