Uncoupling the functional roles of Coronavirus Nsp1

The emergence of pathogenic coronaviruses has highlighted the interplay between viral components and host gene expression during infection. Non-structural protein 1 (Nsp1), the first viral protein produced during coronaviral infections, inhibits host protein synthesis and induces mRNA degradation to enhance viral proliferation. However, the interconnection between the two processes and whether host mRNA degradation depends on the active translation of targeted mRNAs remains enigmatic. Here, intrigued by the observation that Nsp1 does not stimulate ribosome collisions, we use a human cell-free translation system to decouple the main Nsp1 activities, showing that Nsp1 can induce mRNA degradation independently of translation inhibition. Notably, SARS-CoV-2 Nsp1 binding to the ribosome is sufficient to trigger host mRNA degradation without requiring ribosome scanning or translation elongation, stimulating degradation at the 5΄end of the transcript. Interestingly, for MERS-CoV, Nsp1 causes translation inhibition without triggering mRNA degradation. Using Nsp1 from SARS-CoV-2, MERS and Bat-Hp coronaviruses, we observe 5’UTR-specific protection of viral mRNAs, indicating a co-evolutionary adaptation mechanism of the two viral features. Our findings mirror key observations from living cells about Nsp1-mediated mRNA degradation, highlighting the utility of cell-free systems in monitoring and decoupling translation-related processes and providing new insights into this interplay.