Activation and Antagonism of RIG-I-Mediated Innate Immune Signaling by Herpes Simplex Virus 1

Abstract

The cytosolic innate immune receptor retinoic acid-inducible gene-I (RIG-I) recognizes double-stranded RNA (dsRNA) that emerges during viral infection and initiates an antiviral response comprised of interferon (IFN) and proinflammatory cytokine induction. Although RIG-I plays a role in the immune response to DNA viruses such as herpes simplex virus 1 (HSV-1), little is known about the nature of RNA ligands that activate RIG-I during DNA virus infection, and moreover, how these viruses antagonize RIG-I signaling. To identify physiological RNA ligands of RIG-I during HSV-1 infection, we performed RNA-Seq on RIG-I-bound RNA from HSV-1-infected cells and found that the 5S rRNA pseudogene RNA5SP141 was highly enriched with RIG-I specifically in infected cells and elicited a robust RIG-I-dependent antiviral response. In uninfected cells, RNA5SP141 is found primarily in the nucleus, but upon HSV-1 infection, its localization becomes predominantly cytoplasmic. Furthermore, HSV-1-induced shutoff of host protein expression results in the downregulation of proteins that normally interact with and shield RNA5SP141 from RIG-I detection. Depletion of endogenous RNA5SP141 strongly dampened the antiviral response to HSV-1 and the related Epstein-Barr virus, as well as influenza A virus, an RNA virus. Taken together, our data show that viral infection can lead to deshielding of endogenous RNAs that activate innate immunity. The innate immune system is tightly regulated by a variety of regulatory mechanisms that prevent aberrant signaling. However, these pathways can be exploited by viruses to suppress antiviral signaling during infection. Here we show that the serine/threonine kinase US3 of HSV-1 suppresses RIG-I-mediated signaling by phosphorylating a regulatory residue in the RIG-I signaling domain. A recombinant HSV-1 encoding catalytically-inactive US3 was unable to phosphorylate RIG-I and elicited higher levels of IFNs and proinflammatory cytokines compared to wild-type (WT) HSV-1. In summary, these studies have uncovered both a novel host mechanism for detecting DNA virus infection by sensing ‘exposed’ endogenous RNAs and a viral mechanism that co-opts a host regulatory pathway to suppress antiviral signaling. Our findings provide insight into the molecular details governing innate immunity and illustrate the complex interconnectedness of virus and host.