The principal investigator proposes to study the AbrB protein Bacillus subtilis. AbrB is a key global regulator which adjusts gene expression to fit metabolic needs in suboptimal environments, stress and the initial stages of the developmental process of sporulation. In addition to preventing inappropriate expression of stationary phase associated functions during rapid growth, recent evidence suggests that AbrB also plays a role in modulating catabolite repression and could affect growth-rate dependent regulation of components of the translational apparatus. AbrB is a transcriptional regulator whose N-terminal domain represents a novel DNA-binding motif that primarily recognizes subtle three-dimensional DNA structures that are assumed by a subset of varying sequences. The PI argues that elucidation of the factors responsible for flexible AbrB binding specificity will provide insights in protein-DNA recognition mechanisms and how a cell can economically use a single protein to coordinate a variety of stress responses and developmental options. Currently, over 35 genes encoding a wide array of metabolic functions, including some essential for normal sporulation, are known to have AbrB binding sites, usually in the promoter regions. To better define the exact structural parameters of the DNA targets recognized by AbrB, binding to select sites will be probed by high resolution footprinting techniques and kinetics examined using a sensitive real-time assay. The relationship of protein structure to DNA- binding properties will be probed by a combination o mutant analysis, NMR of isolated DNA-binding domain, C domain multimerization studies and crystallography of AbrB-DNA complexes. In vitro transcription and binding assays will test hypotheses regarding AbrB-mediated regulatory mechanisms at representative promoters where different classes of AbrB-dependent effects are suspected. Where necessary, confirmatory in vivo genetic evidence will be obtained.
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