Structural and molecular basis for Cardiovirus 2A protein as a viral gene expression switch

Chris H. Hill (), Lukas Pekarek, Sawsan Napthine, Anuja Kibe, Andrew E. Firth, Stephen C. Graham (), Neva Caliskan () and Ian Brierley ()
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Chris H. Hill: Division of Virology, Department of Pathology, University of Cambridge, Tennis Court Road
Lukas Pekarek: Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI)
Sawsan Napthine: Division of Virology, Department of Pathology, University of Cambridge, Tennis Court Road
Anuja Kibe: Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI)
Andrew E. Firth: Division of Virology, Department of Pathology, University of Cambridge, Tennis Court Road
Stephen C. Graham: Division of Virology, Department of Pathology, University of Cambridge, Tennis Court Road
Neva Caliskan: Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI)
Ian Brierley: Division of Virology, Department of Pathology, University of Cambridge, Tennis Court Road

Nature Communications, 2021, vol. 12, issue 1, 1-16

Abstract: Abstract Programmed –1 ribosomal frameshifting (PRF) in cardioviruses is activated by the 2A protein, a multi-functional virulence factor that also inhibits cap-dependent translational initiation. Here we present the X-ray crystal structure of 2A and show that it selectively binds to a pseudoknot-like conformation of the PRF stimulatory RNA element in the viral genome. Using optical tweezers, we demonstrate that 2A stabilises this RNA element, likely explaining the increase in PRF efficiency in the presence of 2A. Next, we demonstrate a strong interaction between 2A and the small ribosomal subunit and present a cryo-EM structure of 2A bound to initiated 70S ribosomes. Multiple copies of 2A bind to the 16S rRNA where they may compete for binding with initiation and elongation factors. Together, these results define the structural basis for RNA recognition by 2A, show how 2A-mediated stabilisation of an RNA pseudoknot promotes PRF, and reveal how 2A accumulation may shut down translation during virus infection.

Date: 2021
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DOI: 10.1038/s41467-021-27400-7

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