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

Abstract

Viruses commonly antagonize innate immune pathways that are primarily driven by Nuclear Factor-{kappa}B (NF-{kappa}B), Interferon Regulatory Factor (IRF) and Signal Transducer and Activator of Transcription (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-{kappa}B family of transcription factors is lower in infected cells. Potent agonists of NF-{kappa}B, such as Tumor Necrosis Factor alpha (TNF) and vgRNA, failed to induce NF-{kappa}B dependent gene expression in infected cells. We demonstrate that NF-{kappa}B signaling is blocked due to loss of critical members of the Inhibitor of KappaB Kinase (IKK) complex, NF-{kappa}B Essential MOdifier (NEMO) and IKK{beta}. The loss of the IKK complex components prevents nuclear translocation and phosphorylation of NF-{kappa}B, thereby preventing gene expression. Our studies demonstrate that reovirus infection selectively blocks NF-{kappa}B, 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 infection of neighboring, as yet uninfected cells. The NF-{kappa}B 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-{kappa}B is inactive. Further, we demonstrate that NF-{kappa}B is rendered inactive because virus infection results in reduced levels of upstream intermediaries (called IKKs) that are needed for NF-{kappa}B function. Based on previous evidence that active NF-{kappa}B limits reovirus infection, we conclude that inactivating NF-{kappa}B is a viral strategy to produce a cellular environment that is favorable for virus replication.