Loss of IKK subunits limits NF-κB signaling in reovirus infected cells.

Viruses commonly antagonize innate immune pathways that are primarily driven by Nuclear Factor-kappaB (NF-kappaB), Interferon Regulatory Factor (IRF) and Signal Transducer and Activator of Transcription proteins (STAT) family of transcription factors. Such a strategy allows viruses to evade immune surveillance and maximize their replication. Using an unbiased RNA-seq based approach to measure gene expression induced by transfected viral genomic RNA (vgRNA) and reovirus infection, we discovered that mammalian reovirus inhibits host cell innate immune signaling. We found that, while vgRNA and reovirus infection both induce a similar IRF dependent gene expression program, gene expression driven by the NF-kappaB family of transcription factors is lower in infected cells. Potent agonists of NF-kappaB such as Tumor Necrosis Factor alpha (TNFalpha) and vgRNA failed to induce NF-kappaB dependent gene expression in infected cells. We demonstrate that NF-kappaB signaling is blocked due to loss of critical members of the Inhibitor of KappaB Kinase (IKK) complex, NF-kappaB Essential MOdifier (NEMO) and IKKbeta. The loss of the IKK complex components prevents nuclear translocation and phosphorylation of NF-kappaB, thereby preventing gene expression. Our studies demonstrate that reovirus infection selectively blocks NF-kappaB, likely to counteract its antiviral effects and promote efficient viral replication.IMPORTANCEHost cells mount a response to curb virus replication in infected cells and prevent spread of virus to neighboring, as yet uninfected cells. The NF-kappaB family of proteins is important for the cell to mediate this response. In this study, we show that in cells infected with mammalian reovirus, NF-kappaB is inactive. Further, we demonstrate that NF-kappaB is rendered inactive because virus infection results in reduced levels of upstream intermediaries (called IKKs) that are needed for NF-kappaB function. Based on previous evidence that active NF-kappaB limits reovirus infection, we conclude that inactivating NF-kappaB is a viral strategy to produce a cellular environment that is favorable for virus replication.