The differential effect of SARS-COV-2 NSP1 on mRNA translation and stability reveals new insights linking ribosome recruitment, codon usage and virus evolution

Summary The non-structural protein 1 (NSP1) of SARS-CoV-2 blocks the mRNA entry channel of the 40S ribosomal subunit, causing inhibition of translation initiation and subsequent degradation of host mRNAs. However, target mRNA specificity and the way in which viral mRNAs escape NSP1-mediated degradation have not been clarified to date. Here we found that NSP1 acts as a translational switch capable of blocking or enhancing translation depending on how preinitiation complex 43S-PIC is recruited to the mRNA, whereas NSP1-mediated mRNA degradation mostly depends on codon usage bias. Thus, fast-translating mRNAs with optimal codon usage for human cells that preferentially recruit 43S-PIC by threading, showed a dramatic sensitivity to NSP1. On the contrary, slow-translating mRNAs with suboptimal codon usage and 5’ UTR that enabled slotting on 43S-PIC were resistant to or even enhanced by NSP1. Translation of SARS-CoV-2 mRNAs escapes NSP1-mediated inhibition by a proper combination of suboptimal codon usage and slotting-prone 5’ UTR that also confers efficient translation. Thus, the prevalence of non-optimal codons found in SARS-CoV-2 and other coronavirus genomes is favored by the distinctive effect that NSP1 plays on translation and mRNA stability.