Codon bias and mRNA folding stability: Two natural controls of protein expression dynamics

Introduction: Connections between genetic variation and trait variation are complex and dynamic; the critical link between the two is gene expression variation. Though proteins are the functional products of most genes, the relative ease and throughput level of various measurement approaches has meant that gene expression is typically studied via transcript-level rather than protein-level techniques. Recent studies however, suggest that certain genetic factors act post-transcriptionally to modify rates of protein synthesis, making transcript levels imperfect indicators of protein levels. A gene’s bias for ‘optimal’ codons (i.e., its codon bias) and a gene’s mRNA folding stability appear to be two such factors, though until the present work, their individual effects on protein synthesis rates have not been systematically confirmed and quantified in a large number of genes or in a natural (non-genetically engineered) system. Methods: Our study is based on sequence, mRNA and protein expression data for 1620 genes across a diverse set of 22 Saccharomyces cerevisiae isolates. For each gene, we model how across-isolate changes in codon bias and in mRNA folding stability relate to the across-isolate variations in the steady-state ratio of protein level to mRNA level, our approximation of protein synthesis rate. Results: In general for each gene, the alleles with higher codon biases are also those with higher ratios of protein per mRNA (PPR). This relationship is especially pronounced when the gene’s alleles have high mRNA folding stabilities. On a finer scale, changes in the biases of four local gene regions (protein-domainencoding, inter-domain-encoding, 5’coding, and 3’coding) differentially contribute to the PPR of the gene. In parallel, for each gene, alleles with more stable mRNA folding are also those with higher PPR. This is particularly true if their codon biases are already high, though it does not occur through the proposed mechanisms acting on mRNA structures near the start and stop codons. Lastly, we conclude that a gene’s codon bias and mRNA folding stability act synergistically to tune its PPR