Understanding the antiviral roles of acellular RNA quality control pathway

Abstract Eukaryotic cells use multi-layered strategies to ensure the fidelity of gene expression. One of the best-studied RNA quality control pathways is Nonsense-mediated mRNA decay (NMD), a ribosome-associated surveillance machinery that recognizes and degrades cellular transcripts with premature termination codons (PTC). Initially identified as a mechanism to rid the cell of faulty mRNAs, it is now known that NMD also regulates the expression of 5-10% of cellular transcripts with important functions in cell differentiation, homeostasis, cellular stress responses, and more. In addition, recent studies have shown that many proteins of the NMD pathway function in the cell-autonomous defense against RNA viruses, including human-pathogenic alphaviruses, coronaviruses and flaviviruses. As obligate intracellular parasites, these viruses interface closely with cellular mRNA processing pathways, and we can gain new insight to NMD functions by understanding how the machinery is repurposed to fight viral infection. We currently have a very incomplete picture of NMD functions during viral infection. Many viruses lack PTCs or other NMD-inducing features, and it is not known whether NMD proteins recognize viral RNA in manners similar to canonical NMD, or through new and unusual interactions or mechanisms. Moreover, NMD is often globally downregulated during virus infection, suggesting that viruses have mechanisms to rewire the antiviral NMD network. Using the flavivirus Zika virus (ZIKV) as a model RNA virus, we aim to understand the molecular interactions between the NMD machinery and viral infection. We will dissect the NMD-ZIKV protein-protein and protein-RNA interaction network with a multi-disciplinary approach that combines virology with RNA biochemistry and high-throughput assays to link molecular interactions to cellular phenotypes. Specific questions addressed within this study are: 1) How do NMD proteins interact to fight viral infection? 2) Are there specific features in the viral RNA that trigger NMD, and if so, how are they recognized by the NMD machinery? 3) How do viral proteins inhibit NMD? And 4) Are antiviral NMD functions conserved in the important mosquito host of flaviviruses? Collectively, our study will provide new insight into an important cell-autonomous antiviral defense network. In addition, by studying the unusual ways in which NMD is regulated during virus infection, we hope to discover new cellular functions of the NMD machinery itself.