SARS-CoV-2 Nsp1 Suppresses Host But Not Viral Translation Through a Bipartite Mechanism

Abstract

The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a highly contagious virus that underlies the current COVID-19 pandemic. SARS-CoV-2 infection exhibits many features of viral immune evasion of host defense, and the SARS-CoV-2 nonstructural protein 1 (Nsp1) suppresses host defense by inhibiting host protein translation and could be a target for antiviral therapy against COVID-19. However, how SARS-CoV-2 circumvents this translational blockage for the production of its own proteins is an open question. Here we report a bipartite mechanism of SARS-CoV-2 Nsp1 in hijacking the host ribosome by a direct interaction with the small ribosomal subunit 40S through its C-terminal domain (CT) and in lifting this inhibition by a direct interaction with the 5' untranslated region (5’ UTR) of viral mRNA through its N-terminal domain (NT). We show that Nsp1-CT is sufficient for binding to 40S and inhibition of host protein translation, and that 5’ UTR of SARS-CoV-2 mRNA removes this inhibition by binding to Nsp1-NT, suggesting that the Nsp1-NT-UTR interaction is incompatible with the Nsp1-CT-40S interaction. Indeed, lengthening the linker between Nsp1-NT and Nsp1-CT of Nsp1 progressively reduced the ability of SARS-CoV-2 5’ UTR to escape the translational inhibition, supporting that the incompatibility is likely steric in nature. The short SL1 region of the 5’ UTR is required for viral mRNA translation in the presence of Nsp1. Thus, our data provide a comprehensive view on how Nsp1 switches infected cells from host mRNA translation to SARS-CoV-2 mRNA translation, and that Nsp1 and 5’ UTR may be targeted for anti-COVID-19 therapeutics.Funding: L.W. was supported by funding from an NIH T32 grant (5T32AI007512-34). T.-M.F. was supported by funding from an NIH T32 grant (5T32HL066987-18 to L.E.S.) and by start-up funds from the Ohio State University Comprehensive Cancer Center.Conflict of Interest: The authors declare no competing interests.