Catalysis and Cooperativity in Regulatory RNAs

Klein, Daniel

Abstract

RNA, once thought of as a passive intermediate in the flow of genetic information, is now recognized as an active participant in the control of gene expression. The focus of this research program is to understand the structural, biophysical, and biochemical properties of riboswitches, a widespread class of cis-acting regulatory RNAs that sense cellular metabolites. Riboswitches are relevant to public health because they directly affect the cellular processes of transcription, translation, and mRNA splicing. Moreover, many riboswitches are promising targets for novel antibiotics because they regulate essential genes in human pathogens such as Staphylococcus aureus, Bacillus anthracis, and Vibrio cholerae. I am focusing on two riboswitches, the glmS ribozyme and the glycine riboswitch, that are distinguished from currently known natural RNAs by their respective catalytic and cooperative ligand binding mechanisms. The research I propose capitalizes on the synergism of high-resolution structural studies and detailed biochemical analyses.
The specific aims of this research are: (1) to determine the catalytic mechanism of the glmS ribozyme, (2) to elucidate the molecular basis of cooperative ligand binding by the glycine riboswitch, and (3) to determine a high-resolution crystal structure of the glycine riboswitch. This research program will allow me to complete my training and provide me with new skills in fluorescence spectroscopy, ribozyme kinetics and thermodynamic analyses of RNA. The proposed training is connected to my long-term objective of establishing an independent research program dedicated to understanding the structure-function relationships of RNAs that play important catalytic and regulatory roles in biology. The laboratory of Dr. Adrian Ferre-D'Amare provides an exceptional environment for this research and training, owing to the laboratory's past success in structural and biophysical studies of catalytic RNA.

Public Health Relevance

All living organisms must precisely control the activation, or expression, of thousands of genes. This research program aims to address how gene expression is controlled by a specific set of RNA molecules that are thought to be necessary for the survival of harmful bacteria. With an urgent need to develop new drugs to combat the rise of bacteria that are resistant to current antibiotics, this work will provide a starting point to develop novel antibiotics that inhibit these RNA molecules. ? ? ?