Hfq RNA Chaperone and the Mechanism of RNA-Dependent Regulation

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Small non-coding RNAs (sRNAs) in bacteria regulate cell growth and stress response in conjunction with an RNA chaperone protein Hfq. sRNAs control the expression of virulence factors and toxins in pathogenic bacteria, and allow bacteria to survive harsh environmental conditions such as dessication, oxidation or acidity that allow them to defeat host defenses or persist in hospital environments. Conversely, the virulence of many strains is reduced or attenuated when sRNAs are disabled. Although thousands of sRNAs have been identified in diverse bacterial species, how sRNAs and Hfq physically recognize mRNA targets to change gene expression is much less understood. The basic RNA-Hfq interaction motifs have been identified. The goal of this research is to investigate how these modular interaction motifs combine to upregulate or downregulate different gene targets. Single-molecule spectroscopy will used to study how Hfq facilitates sRNA-mRNA base pairing, while biochemical, physical and genetic methods will be used to probe the three-dimensional structure of different classes of Hfq-RNA complexes. Finally, a new model for auto-regulation of Hfq by an intrinsically disordered peptide will be investigated. Understanding how sRNAs turn genes on and off in bacteria is critical for understanding and treating microbial disease. The results of this research will uncover new antibacterial drug targets and aid the engineering of sRNAs for the control of bacterial growth. As Hfq is homologous to Sm proteins, the results will be relevant to how human Sm and Lsm proteins act in mRNA turnover and pre-mRNA splicing.