RUI: Hfq and sRNA Function in Shewanella oneidensis Growth and Adaptation to Stress

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Changes in environmental conditions control the expression of bacterial small noncoding RNAs (sRNAs) that regulate the expression of other genes. Though sRNAs play important roles in adjusting bacterial gene expression and physiology, there are significant hurdles to understanding their function. This project combines genetic, physiological, and transcriptomic approaches to identify sRNA genes and elucidate how expression of these sRNAs impacts bacterial cell physiology. This work is being performed in Shewanella oneidensis, a bacterium with the intriguing capacity to respire using metals in the place of oxygen. Students participate fully in all aspects of the study, including experimental design, performing experiments, data analyses, and manuscript preparation and revision. Students also regularly present their work at scientific conferences. The principle investigator and his students participate in community outreach by mentoring local primary and secondary school students performing science projects.The project will investigate the role of a highly-conserved RNA chaperone molecule, Hfq, in regulation of sRNA signaling in S. oneidensis metabolism and stress responses. The research couples discovery-based systematics (next generation RNA sequencing) with molecular, genetic, and physiological approaches. RNA-Seq is used to identify putative sRNAs expressed under conditions of interest. Manipulating sRNA expression using genetic loss-of-function and gain-of-function approaches will be used to test whether sRNAs regulate predicted mRNA targets and to determine how sRNA expression impacts cell physiology. Given the large number of sRNA genes in bacteria, this study focuses on sRNA functions likely to be linked to the metal reducing metabolism of S. oneidensis. Results from the research effort will be disseminated through peer-reviewed journal publications, and through presentations at regional, national, and international meetings.