Codon Optimality Is a Major Determinant of mRNA Stability

Abstract

Messenger RNA degradation represents a critical regulated step in gene expression. While the major pathways in turnover have been identified, accounting for disparate half-lives has been elusive. We show that codon optimality is one feature that contributes greatly to mRNA stability. Genome-wide RNA decay analysis revealed that stable mRNAs are enriched in codons designated optimal, whereas unstable mRNAs contain predominately non-optimal codons. Substitution of optimal codons with synonymous, non-optimal codons results in dramatic mRNA destabilization, while the converse substitution significantly increases stability. Further, we demonstrate that codon optimality impacts ribosome translocation, connecting the processes of translation elongation and decay through codon optimality. Finally, we show that optimal codon content accounts for the similar stabilities observed in mRNAs encoding proteins with coordinated physiological function. This work demonstrates that codon optimization exists as an mechanism to finely tune levels of mRNAs, and ultimately, proteins.

Codon optimality and mRNA decay

“…First, optimal and non-optimal versions of the HIS3 mRNA show the same distribution on polysome gradients, which can be explained if slower elongation is coupled to reduced initiation rates [5]. Second, the amount of protein production per mRNA can be decreased up to 20-fold by converting optimal to non-optimal codons, which is more than the average difference in elongation rates between optimal and non-optimal codons (~2.5×) [8].…”

“…Moreover, specific sequence motifs that are recognized by trans-acting factors, such as microRNAs and RNA-binding proteins, often modulate mRNA stability by controlling translation initiation. This inverse relationship between translation initiation and degradation can be rationalized as the cap and poly(A) tail either being in a translationally competent mRNP or in an alternative nuclease accessible complex.Studies in organisms from E. coli to zebrafish now demonstrate that the "optimality" of an mRNA's codons modulates its stability [2][3][4][5]. The general theme is that "optimal" codons, which are recognized by abundant tRNAs and efficiently translated, are correlated with mRNA stability, whereas "non-optimal" codons, which are recognized by less abundant tRNAs, are correlated with mRNA instability.…”

“…Studies in organisms from E. coli to zebrafish now demonstrate that the "optimality" of an mRNA's codons modulates its stability [2][3][4][5]. The general theme is that "optimal" codons, which are recognized by abundant tRNAs and efficiently translated, are correlated with mRNA stability, whereas "non-optimal" codons, which are recognized by less abundant tRNAs, are correlated with mRNA instability.…”

“…optimal codons in endogenous stable mRNAs with synonymous, non-optimal codons result in faster mRNA decay, whereas replacing non-optimal codons with optimal codons stabilizes unstable mRNAs [3,5]. Since codon identity affects translation elongation speed, at least in part, via the process of cognate tRNA recognition [6], this argues that the speed of translation elongation somehow affects mRNA stability.…”

“…Thus, this model predicts that, as mRNA length increases, mRNA half-life decreases even with all optimal codons. Although there are limited examples, mRNA half-life increases with length for engineered mRNAs made of optimal codons ( Figure 1A, bottom) [5]. Thus, for this kinetic model to be viable, either the "decay" recognition events need to be somehow synergistic, or recognize a unique property of nonoptimal codons, perhaps a non-cognate tRNA in the A-site.…”