We are interested in determining the role of RNA-binding and RNA chaperone activities of the multifunctional StpA protein in its regulation of other genes. Regulatory features will be compared with the structurally similar DNA-binding nucleoid protein H-BS, with which StpA interacts. Not only does it appear that StpA and H-NS can form heterodimers, but they regulate each others synthesis and that of specific cellular proteins. The property that sets StpA apart is its distinctive RNA chaperone activity. The degree to which the RNA-chaperone activity dictates (StpA's ability to act in cellular riboregulation (regulation via RNA) forms the crux of this application. Genes controlled by StpA and H-NS will be identified, to distinguish functions differentially regulated by StpA. The experimental approaches will be differential display PCR and reporter fusion technology, in different genetic backgrounds and under a variety of environmental conditions. These experiments are designed to define StpA's global role as a riboregulator. For a specific case of such regulation, we are investigating the silencing of h-NS by a small RNA produced by the DsrA gene. StpA's ability to form heterodimers with H-NS, together with its RNA chaperone activities, make it a strong candidate for the mediator of DsrA riboregulation of h-NS. We are currently studying the cross-regulation of DsrA, StpA and HNS. We will also analyze the effect of DsrA on StpA-H-NS heterodimerization, as the basis for an altered affinity of H-NS for its target genes. Together these approaches will probe both the global and specific riboregulatory potential of StpA.
