The short isoform of the host antiviral protein ZAP acts as an inhibitor of SARS-CoV-2 programmed ribosomal frameshifting

Matthias M. Zimmer, Anuja Kibe, Ulfert Rand, Lukas Pekarek, Liqing Ye, Stefan Buck, Redmond P. Smyth, Luka Cicin-Sain and Neva Caliskan ()
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Matthias M. Zimmer: Helmholtz Zentrum für Infektionsforschung (Helmholtz Centre for Infection Research)
Anuja Kibe: Helmholtz Zentrum für Infektionsforschung (Helmholtz Centre for Infection Research)
Ulfert Rand: Helmholtz Zentrum für Infektionsforschung, Inhoffenstrasse 7
Lukas Pekarek: Helmholtz Zentrum für Infektionsforschung (Helmholtz Centre for Infection Research)
Liqing Ye: Helmholtz Zentrum für Infektionsforschung (Helmholtz Centre for Infection Research)
Stefan Buck: Helmholtz Zentrum für Infektionsforschung (Helmholtz Centre for Infection Research)
Redmond P. Smyth: Helmholtz Zentrum für Infektionsforschung (Helmholtz Centre for Infection Research)
Luka Cicin-Sain: Helmholtz Zentrum für Infektionsforschung, Inhoffenstrasse 7
Neva Caliskan: Helmholtz Zentrum für Infektionsforschung (Helmholtz Centre for Infection Research)

Nature Communications, 2021, vol. 12, issue 1, 1-15

Abstract: Abstract Programmed ribosomal frameshifting (PRF) is a fundamental gene expression event in many viruses, including SARS-CoV-2. It allows production of essential viral, structural and replicative enzymes that are encoded in an alternative reading frame. Despite the importance of PRF for the viral life cycle, it is still largely unknown how and to what extent cellular factors alter mechanical properties of frameshift elements and thereby impact virulence. This prompted us to comprehensively dissect the interplay between the SARS-CoV-2 frameshift element and the host proteome. We reveal that the short isoform of the zinc-finger antiviral protein (ZAP-S) is a direct regulator of PRF in SARS-CoV-2 infected cells. ZAP-S overexpression strongly impairs frameshifting and inhibits viral replication. Using in vitro ensemble and single-molecule techniques, we further demonstrate that ZAP-S directly interacts with the SARS-CoV-2 RNA and interferes with the folding of the frameshift RNA element. Together, these data identify ZAP-S as a host-encoded inhibitor of SARS-CoV-2 frameshifting and expand our understanding of RNA-based gene regulation.

Date: 2021
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DOI: 10.1038/s41467-021-27431-0

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