MCA: Using Multiple Approaches for Understanding RNA Binding by Enzymes in Intermediary Metabolism

University Of Illinois At Chicago, Chicago IL

Investigators

Abstract

All cells need methods to adjust their activities in a coordinated fashion to respond to changes in their environment. In recent years, dozens of proteins that have central roles in obtaining energy from food have, surprisingly, been found to have direct interactions with specific RNA molecules that are key players in turning up or down other cellular activities. A greater understanding of how these proteins interact with and control RNA functions may lead to the design and development of novel methods to regulate many kinds of cellular activities, as well as commercial biotechnology applications. This Mid-Career Advancement (MCA) project will enable the principal investigator to receive hands-on training in determining the structures of protein/RNA complexes at a national cryo-electron microscopy research facility. The PI will also work with an expert collaborator to gain experience in using computational methods for analysis and prediction of protein/RNA interactions. The project will generate opportunities for undergraduate students to gain research experience and with it the mentoring and training needed to prepare them for future careers in science. Training of individuals with these skills is important to the high-tech industries in the United States. Dynamic interactions between RNA and RBPs play key roles in all aspects of post-transcriptional gene regulation, including splicing, transport, translation, and maintaining RNA stability or promoting RNA degradation. Combining catalytic and RNA binding functions in one multifunctional protein can be a mechanism to coordinate cellular activities, for example, by sensing the cell’s metabolic state through availability of the enzyme’s ligands and responding by regulating translation of specific transcripts. Conversely, RNA binding could regulate the enzyme’s catalytic activity. Cryo-electron microscopy for determining the structures of enzyme/RNA complexes will complement computational methods for analysis and prediction of RNA binding sites on proteins. Structure-guided mutagenesis will be used for validation of RNA/protein interaction sites. Successful completion of the proposed project will add to the limited number of structures of complexes containing RNA bound to noncanonical RNA binding proteins and provide valuable information about the mechanisms of RNA binding. The computer-based analysis will aid in understanding the nature of the interacting surfaces and will provide a basis for identifying other unconventional RNA binding proteins. This information can be applied in the future to the design and development of novel proteins that regulate RNA translation, stability, and lifetime and RNAs that regulate enzyme function. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.