Bat RNA viruses employ viral RHIMs orchestrating species-specific cell death programs linked to Z-RNA sensing and ZBP1-RIPK3 signaling

Abstract

Interferons and regulated cell death pathways counteract virus spread and mount immune responses, but their deregulation often results in inflammatory pathologies. The RIP-homotypic interaction motif (RHIM) is a conserved protein domain critical for assembling higher-order amyloid-like signaling complexes inducing cell death. A few DNA viruses employ viral RHIMs mimicking host RHIMs to alleviate cell death-mediated antiviral defenses. Whether RNA viruses operate such viral RHIMs remains unknown. Host RHIM-protein signaling promotes lung damage and cytokine storm in respiratory RNA virus infections, arguing the presence of viral RHIMs in RNA viruses. Here, we report the identification of novel viral RHIMs in Nsp13 and Nsp14 of SARS-CoV-2 and other bat RNA viruses and provide a basis for bats as the hosts for the evolution of RHIMs in RNA viruses. Nsp13 expression promoted CoV-RHIM-1-dependent cell death after SARS-CoV-2 infection, and its RNA-binding channel conformation was critical for cell death function. Nsp13 interacted and promoted the formation of large insoluble complexes of ZBP1 and RIPK3. Unlike DNA virus RHIMs, SARS-CoV-2 Nsp13 did not restrict host RHIM-dependent cell death. Instead, it promoted ZBP1-RIPK3 signaling-mediated cell death dependent on intracellular RNA ligands. Intriguingly, SARS-CoV-2 genome fragments showed high Z-RNA forming propensity which bound to Z-RNA sensing Zα domains and promoted Nsp13-dependent cell death. Our findings reveal the functional viral RHIMs in RNA viruses and the role of SARS-CoV-2 Nsp13 in cell death associated with Z-RNAs and ZBP1-RIPK3 signaling, allowing the understanding of mechanisms of cellular damage and cytokine storm in respiratory virus infections and COVID-19.