Papain-like protease of SARS-CoV-2 inhibits dsRNA-induced type I interferon response partly by cleaving TBK1

Abstract

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection has claimed millions of lives and has been a global threat since its emergence. Multiple SARS-CoV-2-encoded proteins have been shown to exert interferon-I (IFN–I)-antagonizing effects, which contribute to severe pathogenesis. We previously reported that the papain-like protease (PLpro) of SARS-CoV-2 and SARS-CoV, a closely related highly pathogenic coronavirus, counteracts IFN production via its deubiquitinating (DUB) activity. In this study, we reveal a new mechanism by which SARS-CoV-2 negatively regulates host innate antiviral responses. Both PLpro proteins from SARS-CoV and SARS-CoV-2 mediated the proteolytic cleavage of TBK1, the hub kinase in the IFN-I signaling pathway. Using point mutants, we demonstrated that the catalytic triad, which is composed of C111, H272, and D286, and the enzyme activity regulatory site, W93, are essential for the ability of SARS-CoV-2 PLpro to cleave the TBK1 protein and for the inhibitory effect on TBK1-triggered IFN expression. However, the mutants failed to abrogate the suppressive effect of SARS-CoV PLpro on Sendai virus (SeV)-induced IFN-I promoter activation, indicating that PLpro inhibits the dsRNA-induced IFN response partly by cleaving TBK1. Collectively, our findings suggest a conserved mechanism through which highly pathogenic SARS-CoV and SARS-CoV-2 harness their PLpro proteins to suppress IFN expression at the level of TBK1, resulting in the evasion of the host innate antiviral response.