The substrate selectivity of papain-like proteases from human-infecting coronaviruses correlates with innate immune suppression

Abstract

Coronaviruses that can infect humans can cause either common colds (HCoV-NL63, HCoV-229E, HCoV-HKU1, and HCoV-OC43) or severe respiratory symptoms (SARS-CoV-2, SARS-CoV, and MERS-CoV). The papain-like proteases (PLPs) of SARS-CoV, SARS-CoV-2, MERS-CoV, and HCoV-NL63 function in viral innate immune evasion and have deubiquitinating (DUB) and deISGylating activities. We identified the PLPs of HCoV-229E, HCoV-HKU1, and HCoV-OC43 and found that their enzymatic properties correlated with their ability to suppress innate immune responses. A conserved noncatalytic aspartic acid residue was critical for both DUB and deISGylating activities, but the PLPs had differing ubiquitin (Ub) chain cleavage selectivities and binding affinities for Ub, K48-linked diUb, and interferon-stimulated gene 15 (ISG15) substrates. The crystal structure of HKU1-PLP2 in complex with Ub revealed binding interfaces that accounted for the unusually high binding affinity between this PLP and Ub. In cellular assays, the PLPs from the severe disease–causing coronaviruses strongly suppressed innate immune IFN-I and NF-κB signaling and stimulated autophagy, whereas the PLPs from the mild disease–causing coronaviruses generally showed weaker effects on immune suppression and autophagy induction. In addition, a PLP from a SARS-CoV-2 variant of concern showed increased suppression of innate immune signaling pathways. Overall, these results demonstrated that the DUB and deISGylating activities and substrate selectivities of these PLPs differentially contribute to viral innate immune evasion and may affect viral pathogenicity.

Abstract

The preference of a protease for ubiquitin or ISG15 is associated with coronavirus pathogenicity.

Papain-like proteases and coronavirus pathogenicity

The papain-like proteases (PLPs) from highly pathogenic coronaviruses, including SARS-CoV-2, have deubiquitylating and deISGylating activities that enable them to interfere with innate immune signaling pathways. By identifying and characterizing the deubiquitylation and deISGylation activities of PLPs from weakly pathogenic coronaviruses, Xiong et al. uncovered a relationship between the enzymatic properties of PLPs and pathogenicity. In contrast to those from the highly pathogenic coronaviruses, PLPs from the mildly pathogenic coronaviruses preferred ubiquitin over ISG15. The structural basis of this substrate preference was revealed by a crystal structure of PLP2 from the weak pathogen HCoV-HKU1. Although all PLPs inhibited innate immune signaling pathways to varying extents, those from the highly pathogenic viruses did so more strongly, including the PLP from a SARS-CoV-2 variant of concern. These differences likely contribute to the differences in immune evasion and pathogenicity among the coronaviruses. —AMV