Bacteria must sense and respond to rapidly changing and often stressful environments. Their ability to enact rapid changes in gene expression that alter cell structure and function is key to their survival. In the last twenty years, it has become abundantly clear that post-transcriptional regulation of gene expression in bacteria is pervasive and represents an important stress response strategy. Small RNAs (sRNAs) that base pair with mRNAs and regulate transcription elongation, translation, and mRNA stability are now known to be common mediators of bacterial post-transcriptional regulation. Small RNAs (sRNAs) number from tens to hundreds in bacterial genomes and carry out diverse regulatory mechanisms, yet the molecular details of their activities and their specific roles in bacterial physiology and virulence remain poorly understood. My research group has been engaged in research to address these questions for the last 15 years. Our overall approach is to combine genomic approaches with classical genetics and biochemistry to study sRNAs from the molecular to the physiological level in Escherichia coli and Salmonella model systems. Our work has defined the target regulons of several sRNAs, revealing a number of new molecular mechanisms of sRNA-mediated regulation. We have uncovered factors that promote hierarchical regulation of multi-target sRNA regulons. We have also found stress response and metabolic phenotypes for sRNA mutants, linking the molecular mechanisms of regulation to physiological outcomes. In the next funding period, we will build on a strong and productive foundation of previous work to continue investigating novel mechanisms of sRNA-dependent regulation in E. coli and Salmonella. We will extend our work to investigate the prevalence of these regulatory mechanisms and identify new examples. A strong team of collaborators using a diverse set of techniques will allow us to interrogate sRNA interactions with target mRNAs on a global scale and at the level of single RNA molecules. This will allow us to generate quantitative models for in vivo regulation by sRNAs and elucidate an extensive sRNA regulatory network to produce an sRNA interaction map of greater precision than ever before. We envision continuing to use studies of sRNAs to connect molecular biology to cell physiology to reveal fundamental new insight into the biology of microbes.
Mapping the interactions between stress-inducible bacterial small RNAs and their mRNA partners will provide novel insights into regulatory networks. We propose to elucidate how small RNA regulators control target mRNAs to achieve precise control of complex physiological traits, including virulence. Systematic and quantitative analyses of a variety of small RNAs will expand our understanding of regulatory networks in bacteria, which may stimulate development of new therapeutic strategies for combating pathogens.
