Coronaviruses encode multiple interferon antagonists that modulate the host response to virus replication. Here, we evaluated pathogenesis and host transcription in response to infection with murine coronaviruses encoding independent mutations in two different viral antagonists: the deubiquitinase (DUB) within nonstructural protein 3 and the endoribonuclease (EndoU) within nonstructural protein 15. The virus with reduced ability to deubiquitinate proteins, herein termed the DUBmut virus, was engineered via X-ray structure-guided mutagenesis and activates an earlier interferon response than the wild type virus. However, the replication kinetics of DUBmut in cultured cells are similar to wild type virus and pat... More
Coronaviruses encode multiple interferon antagonists that modulate the host response to virus replication. Here, we evaluated pathogenesis and host transcription in response to infection with murine coronaviruses encoding independent mutations in two different viral antagonists: the deubiquitinase (DUB) within nonstructural protein 3 and the endoribonuclease (EndoU) within nonstructural protein 15. The virus with reduced ability to deubiquitinate proteins, herein termed the DUBmut virus, was engineered via X-ray structure-guided mutagenesis and activates an earlier interferon response than the wild type virus. However, the replication kinetics of DUBmut in cultured cells are similar to wild type virus and pathogenesis in mice is also similar to what was observed during infection with wild type virus. On the other hand, we previously reported that an EndoUmut virus containing an inactivated endoribonuclease activity elicited rapid and robust activation of type I interferon, which limited virus replication and pathogenesis. Here, using a transcriptomics approach, we compared the scope and kinetics of the host response to the wild type, DUBmut, and EndoUmut viruses in infected macrophages. We found that the EndoUmut virus activates a focused response, predominantly involving type I interferons and a subset of interferon-responsive genes, within 12 hours after infection. In contrast, the wild type and DUBmut viruses stimulate upregulation of over 2,800 genes, including activation of unfolded protein response (UPR) pathways and a proinflammatory profile associated with viral pathogenesis. This study highlights the role of viral interferon antagonists in shaping the kinetics and magnitude of the host response during virus infection and demonstrates that inactivation of a dominant viral antagonist, the coronavirus endoribonuclease, dramatically alters the host response in macrophages and the disease process.
