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

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

doi:10.1126/science.abf3546

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

Science. 2021 Jun 18;372(6548):1306-1313. doi: 10.1126/science.abf3546. Epub 2021 May 13.

Authors

Pramod R Bhatt^#^{1

2

3}, Alain Scaiola^#¹, Gary Loughran², Marc Leibundgut¹, Annika Kratzel^{4

5

6}, Romane Meurs⁷, René Dreos⁷, Kate M O'Connor², Angus McMillan⁸, Jeffrey W Bode⁸, Volker Thiel^{4

5}, David Gatfield⁷, John F Atkins^{9

3

10}, Nenad Ban¹¹

Affiliations

¹ Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland.
² School of Biochemistry and Cell Biology, University College Cork, Cork T12 XF62, Ireland.
³ School of Microbiology, University College Cork, Cork T12 K8AF, Ireland.
⁴ Institute of Virology and Immunology, University of Bern, Bern, Switzerland.
⁵ Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.
⁶ Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland.
⁷ Center for Integrative Genomics, Génopode, University of Lausanne, 1015 Lausanne, Switzerland.
⁸ Laboratorium für Organische Chemie, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland.
⁹ School of Biochemistry and Cell Biology, University College Cork, Cork T12 XF62, Ireland. j.atkins@ucc.ie ban@mol.biol.ethz.ch.
¹⁰ MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK.
¹¹ Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland. j.atkins@ucc.ie ban@mol.biol.ethz.ch.

^# Contributed equally.

Abstract

Programmed ribosomal frameshifting is a key event during translation of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA genome that allows 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 messenger RNA (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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Antiviral Agents / pharmacology
Codon, Terminator
Coronavirus RNA-Dependent RNA Polymerase / biosynthesis
Coronavirus RNA-Dependent RNA Polymerase / chemistry
Coronavirus RNA-Dependent RNA Polymerase / genetics
Cryoelectron Microscopy
Fluoroquinolones / pharmacology
Frameshifting, Ribosomal* / drug effects
Genome, Viral
Humans
Image Processing, Computer-Assisted
Models, Molecular
Nucleic Acid Conformation
Open Reading Frames
Protein Folding
RNA, Messenger / chemistry
RNA, Messenger / genetics
RNA, Messenger / metabolism
RNA, Ribosomal, 18S / chemistry
RNA, Ribosomal, 18S / genetics
RNA, Ribosomal, 18S / metabolism
RNA, Viral / chemistry
RNA, Viral / genetics*
RNA, Viral / metabolism
Ribosomal Proteins / metabolism
Ribosomes / metabolism
Ribosomes / ultrastructure*
SARS-CoV-2 / drug effects
SARS-CoV-2 / genetics*
SARS-CoV-2 / physiology
Viral Proteins / biosynthesis*
Viral Proteins / chemistry
Viral Proteins / genetics
Virus Replication / drug effects

Substances

Antiviral Agents
Codon, Terminator
Fluoroquinolones
RNA, Messenger
RNA, Ribosomal, 18S
RNA, Viral
Ribosomal Proteins
Viral Proteins
CI 934
Coronavirus RNA-Dependent RNA Polymerase
NSP12 protein, SARS-CoV-2