The SARS-CoV-2 protein ORF3c is a mitochondrial modulator of innate immunity
Hazel Stewart,
Yongxu Lu,
Sarah O’Keefe,
Anusha Valpadashi,
Luis Daniel Cruz-Zaragoza,
Hendrik A. Michel,
Samantha K. Nguyen,
George W. Carnell,
Nina Lukhovitskaya,
Rachel Milligan,
Yasmin Adewusi,
Irwin Jungreis,
Valeria Lulla,
David A. Matthews,
Stephen High,
Peter Rehling,
Edward Emmott,
Jonathan L. Heeney,
Andrew D. Davidson,
James R. Edgar,
Geoffrey L. Smith,
Andrew E. Firth
Affiliations
Hazel Stewart
Department of Pathology, University of Cambridge, Cambridge, UK; Corresponding author
Yongxu Lu
Department of Pathology, University of Cambridge, Cambridge, UK
Sarah O’Keefe
Faculty of Biology, Medicine and Health, School of Biological Sciences, University of Manchester, Manchester, UK
Anusha Valpadashi
Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
Luis Daniel Cruz-Zaragoza
Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
Hendrik A. Michel
Department of Pathology, University of Cambridge, Cambridge, UK
Samantha K. Nguyen
Department of Pathology, University of Cambridge, Cambridge, UK
George W. Carnell
Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
Nina Lukhovitskaya
Department of Pathology, University of Cambridge, Cambridge, UK
Rachel Milligan
School of Cellular and Molecular Medicine, Faculty of Life Sciences, University of Bristol, Bristol, UK
Yasmin Adewusi
Department of Pathology, University of Cambridge, Cambridge, UK
Irwin Jungreis
Broad Institute of MIT and Harvard, Cambridge, MA, USA; MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA
Valeria Lulla
Department of Pathology, University of Cambridge, Cambridge, UK
David A. Matthews
School of Cellular and Molecular Medicine, Faculty of Life Sciences, University of Bristol, Bristol, UK
Stephen High
Faculty of Biology, Medicine and Health, School of Biological Sciences, University of Manchester, Manchester, UK
Peter Rehling
Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
Edward Emmott
Centre for Proteome Research, Department of Biochemistry & Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
Jonathan L. Heeney
Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
Andrew D. Davidson
School of Cellular and Molecular Medicine, Faculty of Life Sciences, University of Bristol, Bristol, UK
James R. Edgar
Department of Pathology, University of Cambridge, Cambridge, UK; Corresponding author
Geoffrey L. Smith
Department of Pathology, University of Cambridge, Cambridge, UK; Corresponding author
Andrew E. Firth
Department of Pathology, University of Cambridge, Cambridge, UK; Corresponding author
Summary: The SARS-CoV-2 genome encodes a multitude of accessory proteins. Using comparative genomic approaches, an additional accessory protein, ORF3c, has been predicted to be encoded within the ORF3a sgmRNA. Expression of ORF3c during infection has been confirmed independently by ribosome profiling. Despite ORF3c also being present in the 2002–2003 SARS-CoV, its function has remained unexplored. Here we show that ORF3c localizes to mitochondria, where it inhibits innate immunity by restricting IFN-β production, but not NF-κB activation or JAK-STAT signaling downstream of type I IFN stimulation. We find that ORF3c is inhibitory after stimulation with cytoplasmic RNA helicases RIG-I or MDA5 or adaptor protein MAVS, but not after TRIF, TBK1 or phospho-IRF3 stimulation. ORF3c co-immunoprecipitates with the antiviral proteins MAVS and PGAM5 and induces MAVS cleavage by caspase-3. Together, these data provide insight into an uncharacterized mechanism of innate immune evasion by this important human pathogen.
