Autophagy mechanism of coronaviral infection: Lessons from enteroviruses

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The long-term objective of my research program is to understand the molecular basis of how positive RNA viruses hijack the host cellular machinery to achieve successful infection. Positive-strand RNA viruses, including enteroviruses (EVs) and coronaviruses (CoVs), cover more than one-third of all virus genera and infect a wide range of hosts, including plants, animals, and humans. The previous NSERC Discovery Grant allowed us to make substantial progress towards understanding the underlying mechanisms by which Coxsackievirus (an EV) has evolved to exploit the host recycling system to support its lifecycle. In this renewal application, I propose to extend our research to study the interaction between CoVs and autophagy, a "self-eating" process in cells by which cells recycle damaged proteins and/or organelles. CoVs are a group of single-stranded RNA viruses covered by crown-like protein spikes, which can infect humans and a variety of animals, and cause a range of disorders from asymptomatic to lethal infection. My hypothesis is that similar to EVs, CoVs subvert the host autophagy machinery to ensure successful infection by enhancing viral replication and through preventing the clearance of viral components and/or particles. This hypothesis is based on our novel observations that (1) CoVs induce autophagy through a pathway independent of enzymes known to be required for traditional autophagy; and (2) CoV-encoded proteases target a number of host proteins involved in autophagy regulation for degradation. Despite these findings, the detailed mechanisms of how CoVs hijack the host autophagy pathway and the functional consequence of the cleavage of autophagic proteins remain unclear. To test this hypothesis, we will combine the use of cutting-edge proteomics and imaging approaches with conventional molecular and cellular technologies to study how CoVs manipulate the autophagy pathway and to identify the critical enzymes and target proteins within the autophagy pathway that regulates CoV infection. Our experience in investigating enteroviral subversion of the autophagy pathway places us in a unique position to understand the interplay between host autophagy and CoVs. This research, exploring a novel autophagy-based viral mechanism, will fill a key knowledge gap in our understanding of the mechanisms underlying effective CoV infection of host cells. Knowledge acquired from this research will also have broader implications for the study of host-pathogen interactions of other viruses in the same family. The proposed research program will also benefit Canada and the Canadian economy by training 3 PhD graduate and 5 undergraduate students in natural science for future careers in academic research and teaching institutions, medical laboratories, and biotechnology companies.