Universal features of Nsp1-mediated translational shutdown by coronaviruses

Schubert, K.; Karousis, E. D.; Ban, I.; Lapointe, C.; Leibundgut, M.; Baeumlin, E.; Kummerant, E.; Scaiola, A.; Schoenhut, T.; Ziegelmueller, J.; Puglisi, J.; Muehlemann, O.; Ban, N.

doi:10.1101/2023.05.31.543022

bioRxiv · 10.1101/2023.05.31.543022

Universal features of Nsp1-mediated translational shutdown by coronaviruses

Schubert, K.·Karousis, E. D.·Ban, I.·Lapointe, C.·Leibundgut, M.·Baeumlin, E.·Kummerant, E.·Scaiola, A.·Schoenhut, T.·Ziegelmueller, J.·Puglisi, J.·Muehlemann, O.·Ban, N.

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Abstract

Nonstructural protein 1 (Nsp1) produced by coronaviruses shuts down host protein synthesis in infected cells. The C-terminal domain of SARS-CoV-2 Nsp1 was shown to bind to the small ribosomal subunit to inhibit translation, but it is not clear whether this mechanism is broadly used by coronaviruses, whether the N-terminal domain of Nsp1 binds the ribosome, or how Nsp1 specifically permits translation of viral mRNAs. Here, we investigated Nsp1 from three representative Betacoronaviruses - SARS-CoV-2, MERS-CoV, and Bat-Hp-CoV - using structural, biophysical, and biochemical assays. We revealed a conserved mechanism of host translational shutdown across the three coronaviruses. We further demonstrated that the N-terminal domain of Bat-Hp-CoV Nsp1 binds to the decoding center of the 40S subunit, where it would prevent mRNA and eIF1A binding. Structure-based biochemical experiments identified a conserved role of these inhibitory interactions in all three coronaviruses and showed that the same regions of Nsp1 are responsible for the preferential translation of viral mRNAs. Our results provide a mechanistic framework to understand how Betacoronaviruses overcome translational inhibition to produce viral proteins.

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Schubert, K., Karousis, E. D., Ban, I., Lapointe, C., Leibundgut, M., Baeumlin, E., Kummerant, E., Scaiola, A., Schoenhut, T., Ziegelmueller, J., Puglisi, J., Muehlemann, O., Ban, N.. 2023-06-01. Universal features of Nsp1-mediated translational shutdown by coronaviruses. https://doi.org/10.1101/2023.05.31.543022

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