Structural bases of the functions of RNA-protein machines - Project 5

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RNAs that recognize small molecule ligands provide a widespread regulatory mechanism in biological systems. This study focuses on three RNAs that respond to small molecules, but in very different ways. Studies will be performed on the group I self-splicing RNA, the cooperative glycine riboswitch and a newly discovered riboswitch responsive to the second messenger cyclic diguanosine monophosphate (c-diGMP). 1. RNA splicing in response to the small molecule substrate guanosine. RNA splicing is the removal of an intron and the simultaneous ligation of its flanking exons in the generation of mature cellular RNA molecules. While most introns are removed by the spliceosome, some introns are able to catalyze their own removal from the primary transcript. The discovery of the group I class of introns provided the first indication that not all enzymes are proteins. Our goal is to structurally characterize each step in an RNA splicing pathway in order to understand how RNA functions as a catalyst. 2. Control of gene expression by cooperative binding of the amino acid glycine. Riboswitches are dynamic RNA folding domains that bind specific metabolites and control gene expression by modulation of transcription termination, translation initiation or RNA degradation. The glycine riboswitch comprises two similar aptamer domains that each bind glycine, but do so cooperatively. The result is a digital RNA sensor that is particularly sensitive to glycine concentration. Our goal is to understand the structural basis of glycine binding and cooperativity. 3. Analysis of a riboswitch responsive to a second messenger in the cell. c-dGMP was recently identified as a ligand for a broad collection of riboswitches, termed GEMM riboswitches. Our goal is to understand the structural and biochemical basis of c-diGMP binding by this new class of RNA molecule.