Transcripts with codons that trigger the P-site tRNA–mediated mRNA decay are enriched with optimal codons

Synonymous codon usage is a major determinant of mRNA half-life in yeast, functioning as a second layer of genetic information during translation. In this system, the CCR4-NOT complex plays a key role by interacting with the ribosome when both its A and E sites are vacant—a state that typically occurs when a non-optimal codon, i.e., one with low tRNA availability, occupies the A site. The complex then recruits the mRNA decay machinery, leading to shorter half-lives for transcripts enriched in non-optimal codons. In humans, the extent to which codon usage affects mRNA stability remains unclear. Recent studies have shown that CCR4-NOT recruitment in humans shares some similarities with yeast but also exhibits significant mechanistic differences. In particular, CCR4-NOT binding depends on the presence of specific arginine codons —CGG, CGA, or AGG—at the P site of the ribosome, a process termed P-site tRNA-mediated decay (PTMD). PTMD also requires slow decoding at the A site, enabling E-site vacancy and subsequent CCR4-NOT recruitment by CNOT3. Using high-throughput analyses of public datasets, we investigated how human transcripts enriched in PTMD codons differ from the rest of the transcriptome in terms of codon optimality, mRNA half-life, and protein abundance. We find that PTMD-target codons are predominantly present in transcripts with overall optimal codon usage and longer half-lives. This suggests that, in contrast to yeast, PTMD in humans preferentially shortens the half-lives of otherwise stable transcripts, rather than contributing to the degradation of inherently unstable ones.