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bioRxiv · 10.1101/2022.02.07.479471

The mechanism of RNA capping by SARS-CoV-2

Park, G. J.·Osinski, A.·Hernandez, G.·Eitson, J.·Majumdar, A.·Tonelli, M.·Henzler-Wildman, K.·Pawlowski, K.·Chen, Z.·Li, Y.·Schoggins, J.·Tagliabracci, V. S.
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Abstract

The SARS-CoV-2 RNA genome contains a 5-cap that facilitates translation of viral proteins, protection from exonucleases and evasion of the host immune response1-4. How this cap is made is not completely understood. Here, we reconstitute the SARS-CoV-2 7MeGpppA2-O-Me-RNA cap using virally encoded non-structural proteins (nsps). We show that the kinase-like NiRAN domain5 of nsp12 transfers RNA to the amino terminus of nsp9, forming a covalent RNA-protein intermediate (a process termed RNAylation). Subsequently, the NiRAN domain transfers RNA to GDP, forming the cap core structure GpppA-RNA. The nsp146 and nsp167 methyltransferases then add methyl groups to form functional cap structures. Structural analyses of the replication-transcription complex bound to nsp9 identified key interactions that mediate the capping reaction. Furthermore, we demonstrate in a reverse genetics system8 that the N-terminus of nsp9 and the kinase-like active site residues in the NiRAN domain are required for successful SARS-CoV-2 replication. Collectively, our results reveal an unconventional mechanism by which SARS-CoV-2 caps its RNA genome, thus exposing a new target in the development of antivirals to treat COVID-19.

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Park, G. J., Osinski, A., Hernandez, G., Eitson, J., Majumdar, A., Tonelli, M., Henzler-Wildman, K., Pawlowski, K., Chen, Z., Li, Y., Schoggins, J., Tagliabracci, V. S.. 2022-02-09. The mechanism of RNA capping by SARS-CoV-2. https://doi.org/10.1101/2022.02.07.479471

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