Structural basis of ribosomal frameshifting during translation of the SARS-CoV-2 RNA genome

Bhatt, Pramod R.; Scaiola, Alain; Loughran, Gary; Leibundgut, Marc; Kratzel, Annika; Meurs, Romane; Dreos, René; O’Connor, Kate M.; McMillan, Angus; Bode, Jeffrey W.; Thiel, Volker; Gatfield, David; Atkins, John F.; Ban, Nenad

Programmed ribosomal frameshifting is a key event during translation of the SARS-CoV-2 RNA genome allowing synthesis of the viral RNA-dependent RNA polymerase and downstream proteins. Here we present the cryo-electron microscopy structure of a translating mammalian ribosome primed for frameshifting on the viral RNA. The viral RNA adopts a pseudoknot structure that lodges at the entry to the ribosomal mRNA channel to generate tension in the mRNA and promote frameshifting, whereas the nascent viral polyprotein forms distinct interactions with the ribosomal tunnel. Biochemical experiments validate the structural observations and reveal mechanistic and regulatory features that influence frameshifting efficiency. Finally, we compare compounds previously shown to reduce frameshifting with respect to their ability to inhibit SARS-CoV-2 replication, establishing coronavirus frameshifting as a target for antiviral intervention.