Mechanisms of bacterial RNA degradation

PROJECT SUMMARY The overarching goal of this research project is to understand the basic principles that govern messenger RNA degradation, a cellular process that plays a key role in regulating gene expression in all organisms. The immediate goal is to elucidate the impact of the 5′ end on bacterial mRNA lifetimes. In particular, this research will focus on understanding the influence of 5′-terminal caps and 5′-end-dependent endonucleolytic cleavage on rates of mRNA degradation in bacteria. Long thought to reside exclusively on eukaryotic RNA transcripts, caps of various kinds have now been found on RNA 5′ ends in bacteria, yet many important aspects of their function remain unexplained. In addition, the regulatory endonuclease RNase E has recently been shown to locate cleavage sites in monophosphorylated RNA by a novel scanning mechanism akin to linear diffusion from the 5′ end, but how it does so is unknown. The specific objectives of this research project are to elucidate the structural and phylogenetic diversity of bacterial mRNA capping and the interplay between capping, cell physiology, and stress and to determine the molecular mechanism by which RNase E scans RNA in search of cleavage sites, the influence of the cellular environment on this process, and the breadth of its regulatory impact. A combination of molecular biological, biochemical, biophysical, and genetic methods will be employed to achieve these objectives. The knowledge gained from these studies will provide fundamental insights into novel aspects of gene regulation that have been implicated in bacterial pathogenesis and antibiotic sensitivity.