The seven human coronavirus main proteases exhibit differential modulation of NF-κB suppression via TAB1 cleavage

The divergence in pathogenicity among human coronaviruses (HCoVs), from causing common cold to lethal pneumonia, may indicate distinct viral immune evasion strategies. However, the molecular basis of their differential immune evasion strategies remains unclear. In this study, we find that the innate immune adapter protein TGF-β activated kinase 1 (TAB1) is a universal target of the main proteases (Mpros) of all seven HCoVs. We show that Mpros from coronaviruses that cause severe disease (SARS-CoV-2, SARS-CoV, and MERS-CoV) efficiently cleave TAB1 at two distinct sites (Q10 and Q444), disrupting the TAB1-TAK1 complex and blocking Nuclear Factor kappa-B (NF-κB) signaling. In contrast, Mpro from common cold coronaviruses (HCoV-OC43, HCoV-HKU1, HCoV-NL63, and HCoV-229E) primarily cleave at Q10, resulting in only partial NF-κB suppression. Furthermore, structural analysis of SARS-CoV-2 Mpro in complex with a TAB1 peptide reveals key features of the substrate-enzyme interaction interface. Kinetic analysis shows that Mpros from the severe disease associated coronaviruses cleave Q444 more efficiently than Mpros from the common cold associated viruses. Conversely, Mpros from common cold associated coronaviruses prefer Q10 over Q444. Although Q10 cleavage is observed in all viruses, Mpros from common cold associated coronaviruses cleave Q10 more efficiently than it cleaves Q444. Overall, our findings establish the Mpro-mediated cleavage of TAB1 as a conserved strategy for immune evasion across HCoVs.