Identifying structural features of viral RNA recognized by host helicases

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Viruses hijack the host cell machinery and recruit host proteins to aid viral replication. Considerable effort has been made to identify host proteins that interact with viral RNA/proteins. However, the biochemical and structural basis of viral RNA recognition by the members of the DEAD-box family, which support viral replication, is poorly understood. My long-term research goal is to study these key host helicases that are exploited by many viruses in order to gain detailed insights into the molecular mechanisms behind a broad spectrum of host helicases and viral RNA interactions. Despite the ATP-dependent unwinding of nucleic acids being the established role of DEAD-box helicases, recent studies demonstrate that helicases influence all major aspects of RNA metabolism and often play significant roles in viral replication. Particularly, the helicases DDX3X and DDX5 interact with the viral 3' untranslated region (3' UTR) of Japanese encephalitis virus, hepatitis C virus, and SARS coronavirus, and support their replication. My laboratory will investigate the structural basis of the interactions of DDX3X/DDX5 with 3' UTRs of members of the Flavivirus genus (e.g., Japanese encephalitis, West Nile, Yellow Fever, Zika, and Dengue viruses) to identify specific patterns of viral RNA being recognized by the helicases under investigation. An interdisciplinary approach involving molecular biology, biochemistry, biophysical and structural biology techniques will be employed to achieve these goals. In the longer term, my research program will consider other members of the helicase family (e.g., DDX1, DDX6, and DDX17), as well as viruses that infect plants (e.g., tomato bushy stunt virus) to establish if the recognition of viral 3' UTR is a conserved function of DEAD-box helicases across the species. In addition, studying helicase-viral RNA and helicase-host RNA interactions will allow insights into how helicases discriminate viral and host RNAs. My research program will provide a platform for training highly qualified personnel in a multidisciplinary research area using a hands-on approach and cutting-edge techniques (e.g., light scattering, analytical ultracentrifuge, small angle X-ray scattering and X-ray crystallography).