Structure, function, and dynamics of viral RNAs and RNA-containing complexes

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 DESCRIPTION (provided by applicant): RNA is a central molecule in biology, performing a large number of diverse and essential tasks. The diversity of RNA function is conferred, in part, by its ability to adopt many different architectures. This includes the ability to form compactly folded structures that interact with other macromolecules to achieve a biological outcome. The discovery of RNAs with novel functions is accelerating, but our understanding of the diversity of RNA structure and how these structures drive function is not keeping pace. Given the importance of RNA in biology, this is an important knowledge gap. The research program described here focuses on understanding important, diverse, biologically active RNAs produced by viruses. This program is motivated by the fact that many viruses use RNA-based mechanisms to manipulate host cell components, altering cellular conditions to favor infection. Thus, viral RNAs are powerful models to discover new RNA structures, to understand how these structures fold, to examine how they interact with and manipulate other macromolecules, and ultimately to describe how the structure drives a specific function. In addition, by studying how viral RNAs manipulate cellular machines, we learn about the machinery itself and we may find new important fundamental RNA-based cellular processes. Finally, viral disease remains a substantial threat to human health, but for most viral infections there is no effective therapy. Learning how viral RNAs work reveals the molecular basis of virus-induced disease, a necessary understanding for developing needed therapies. The number of unexplored viral RNAs is vast, therefore our strategy is to study a set of model viral RNAs with diverse functions. This includes viral RNAs that manipulate the protein synthesis machinery, RNAs that interfere with or co-opt the function of cellular enzymes, and viral RNAs that mimic cellular RNAs and may be molecular "hijackers". For each, we aim to understand the details of their structure-based mechanisms by linking atomic-resolution structural data with the function of these structures within cells. In addition, we are particularly interested in understanding how these RNAs may use programmed conformational dynamics to regulate their function. To achieve this understanding we are using quantitative biochemistry, biophysics, structural biology, and virology in an integrated approach. Our overarching goal is to discover important fundamental rules of RNA-based mechanisms of high impact and with broad applicability to many biological systems, simultaneously characterizing new therapeutic targets to inform the development of treatments for human disease.