Assembly Mechanisms of RNA-Protein Complexes for Genetic Control

Johns Hopkins University, Baltimore MD

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Abstract

Non-coding RNA acts at every step of gene expression, assembling with protein partners to form the cellular machines responsible for protein synthesis and RNA processing, and regulate the output of individual mRNAs over their life cycles. Even subtle defects in the assembly and localization of non-coding RNA-protein complexes can result in development disorders, metabolic misfunction, high cancer risks, and neurodegeneration. The promise of non-coding RNAs as targets for therapy and as therapeutics and vaccines is now being realized. Previous work showed that RNA and proteins change shape as they come together, and that the fidelity of gene control by non-coding RNAs arises from a dynamic competition between alternative RNA-RNA and RNA- protein interactions. Therefore, the performance of RNA molecules in cells depends on which other RNA and protein molecules are also present and the network of interactions among these components. The goal of this research program is to define the physical principles of RNA-protein assembly and dynamics that can predict how large RNA-protein complexes are formed and how small non-coding RNAs rapidly search out their regulatory targets. These concepts will be addressed using ribosome biosynthesis in bacteria and yeast as model systems. New approaches for single molecule fluorescence microscopy of live cells and of biochemically reconstituted systems will be used to visualize how RNA folding and protein binding is coupled to transcription, and how small RNAs in the nucleolus capture their target sites. The results of this research will lead to new concepts related to how RNA-protein complexes assemble faithfully to produce functional ribosomes during normal growth and how ribosome biosynthesis is affected by stress.