The SARS-CoV-2 papain-like protease suppresses type I interferon responses by deubiquitinating STING

Abstract

The SARS-CoV-2 papain-like protease (PLpro), which has deubiquitinating activity, suppresses the type I interferon (IFN-I) antiviral response. We investigated the mechanism by which PLpro antagonizes cellular antiviral responses. In HEK392T cells, PLpro removed K63-linked polyubiquitin chains from Lys ²⁸⁹ of the stimulator of interferon genes (STING). PLpro-mediated deubiquitination of STING disrupted the STING-IKKε-IRF3 complex that induces the production of IFN-β and IFN-stimulated cytokines and chemokines. In human airway cells infected with SARS-CoV-2, the combined treatment with the STING agonist diABZi and the PLpro inhibitor GRL0617 resulted in the synergistic inhibition of SARS-CoV-2 replication and increased IFN-I responses. The PLpros of seven human coronaviruses (SARS-CoV-2, SARS-CoV, MERS-CoV, HCoV-229E, HCoV-HKU1, HCoV-OC43, and HCoV-NL63) and four SARS-CoV-2 variants of concern (α, β, γ, and δ) all bound to STING and suppressed STING-stimulated IFN-I responses in HEK293T cells. These findings reveal how SARS-CoV-2 PLpro inhibits IFN-I signaling through STING deubiquitination and a general mechanism used by seven human coronaviral PLpros to dysregulate STING and to facilitate viral innate immune evasion. We also identified simultaneous pharmacological STING activation and PLpro inhibition as a potentially effective strategy for antiviral therapy against SARS-CoV-2.

Abstract

A SARS-CoV-2 protease deubiquitinates STING to block antiviral signaling.

SARS-CoV-2 takes the STING out of host defenses

The papain-like proteases of human-infecting coronaviruses are important for processing viral polyproteins and have deubiquitinase activities that enable the virus to evade innate defenses. Cao et al. demonstrated that the papain-like protease of SARS-CoV-2, PLpro, suppressed antiviral signaling in cells by deubiquitinating the stimulator of interferon genes (STING). PLpro specifically removed K63-linked polyubiquitin chains at Lys ²⁸⁹ of STING, thereby blocking the interaction of STING with binding partners that are required for STING to activate interferon response factor 3 (IRF3) and downstream type I interferon responses. A STING agonist and a PLpro inhibitor synergistically inhibited SARS-CoV-2 replication in human lung cells, demonstrating the importance of PLpro-mediated STING deubiquitination for SARS-CoV-2 replication in host cells. —AMV