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.

Grant Number: 5R35GM145359-05
NIH Institute/Center: NIH
Principal Investigator: JOEL BELASCO