Synonymous codon usage regulates translation initiation

Abstract

Synonymous codon usage regulates gene expression such that transcripts rich in optimal codons produce significantly more protein than their nonoptimal counterparts. A major unresolved issue has been understanding the mechanisms by which synonymous codons regulate gene expression. We and others have previously shown that nonoptimal codons slow translation elongation speeds and thereby trigger mRNA degradation. However, differences in transcript abundance are not always sufficient to explain differences in protein levels, suggesting there are additional mechanisms by which codon usage regulates gene expression. Using reporter assays in human and Drosophila cells, we found that transcript levels account for less than half of the variation in protein abundance. We demonstrate that the differences at the protein level are not attributable to either protein folding or stability. Instead, we find that mRNAs with nonoptimal codons are bound by fewer ribosomes and that nonoptimal codon usage represses translation initiation. Nonoptimal transcripts are also less bound by the key translation initiation factors eIF4E and eIF4G, providing a mechanistic explanation for their reduced initiation rates. Our results reveal a new mechanism of regulation by codon usage, where nonoptimal codons repress further rounds of translation.

Codon optimality modulates protein output by tuning translation initiation

“…Collectively, these observations lead us to propose that slow elongation limits translation initiation through an unknown, active mechanism. This model is corroborated by a recent report identifying depletion of cap binding proteins from non-optimal reporter transcripts; our results align with the observations of lower initiation in that study (Barrington et al 2022). The discovery of specific feedback on initiation in response to ribosome stalls (Hickey et al 2020; Juszkiewicz et al 2020; Sinha et al 2020) makes it plausible that an analogous mechanism could function on slow but non-stalled ribosomes.…”

“…A distinct pathway in which collided ribosomes inhibit translation initiation has recently been identified in mammalian cells, although this specific pathway is not thought to operate in yeast, which lack a homolog of a key component, 4EHP (Hickey et al 2020; Juszkiewicz et al 2020; Sinha et al 2020). Recent work has demonstrated that slow elongation, even without collisions, can limit initiation to decrease protein output in human and fly cells (Barrington et al 2022).…”

Translation and mRNA Stability Control

“…Differences between reporters enriched in optimal or nonoptimal codons tend to be greater at the protein level than at the RNA level, supporting translation efficiency differences (12,13,29). It was also recently proposed that enrichment of nonoptimal codons might repress translation initiation (30).…”

Model-guided design of microRNA-based gene circuits supports precise dosage of transgenic cargoes into diverse primary cells

“…However, significant variance introduced in translation may obscure noise suppression at the transcriptional level. Other forms of regulation such as translational control and protein-based circuits may be coupled with ComMAND to control expression across the Central Dogma [54][55][56][57].…”