Interplay between coronaviruses and nonsense-mediated mRNA decay pathway

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Coronaviruses (CoVs), which carry a large, single-stranded, positive-sense RNA genome, cause a variety of diseases in humans and domestic animals. Human CoVs (HCoVs) usually infect the respiratory tract and cause a range of symptoms varying from mild, such as the common cold, to more serious respiratory illnesses like severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS), caused by two highly pathogenic HCoVs, SARS-CoV and MERS-CoV. SARS-CoV caused a worldwide epidemic in 2002- 2003, resulting in more than 8,000 cases with an approximate mortality of 10%, while MERS-CoV emerged in Saudi Arabia in 2012 and has been disseminated into other countries in the Middle East, North Africa, Europe, and East Asia. HCoVs represent a major threat to public health and have the potential to cause a significant negative economic impact. Currently, there are no approved vaccines and therapeutic agents against HCoVs. The development of effective control measures against CoVs requires a comprehensive understanding of viral gene expression strategies and host-CoV interactions. A plethora of studies have focused on investigating CoV biology and have significantly contributed to our understanding of CoV replication mechanisms, including the structure-function analyses of viral RNA elements as well as the viral proteins that are involved in viral replication and assembly. However, there are still gaps in our knowledge of the post-transcriptional regulation of viral gene expression, as only a limited number of studies have addressed this area of CoV research. Particularly, very little is known about the cis-acting viral RNA elements and trans-acting host and viral factors that regulate CoV mRNA transcript stability. One newly emerging research area in virology is understanding interactions between viruses and host mRNA surveillance pathways that prevent generation/accumulation of unwanted gene products. We have demonstrated that CoV mRNAs are the targets of the nonsense-mediated mRNA decay (NMD) pathway, one of the host mRNA surveillance pathways, and that viral N protein protects CoV mRNAs from NMD. Our data suggest the importance of N-mediated NMD suppression for efficient virus replication. The present application will study the interplay between the NMD pathway and CoVs by testing the following hypotheses: UPF1, the principal orchestrator of NMD, binds to the 3’ UTR of CoV mRNAs having specific motifs, undergoes phosphorylation, and recruits SMG6, an endonuclease, leading to endonucleolytic RNA cleavage; N binds to the 3’ UTRs of NMD targets and prevents an NMD factor(s) from accessing these targets and/or N interacts with an NMD factor(s) and sequesters it away from the NMD pathway; and CoV mutants having an increased susceptibility to NMD, cannot replicate as efficiently as the parental viruses. The data obtained from these studies will provide mechanistic insights into NMD of CoV mRNAs and N-mediated NMD pathway suppression, and will reveal the feasibility of novel strategies for attenuating CoVs through increased susceptibility to the NMD pathway.