The Bacillus subtilis AbrB protein is a key global regulator that adjusts gene expression to fit metabolic needs in suboptimal environments, in the face of stress and during the initial stages of the developmental process of sporulation. In addition to preventing inappropriate expression of stationary phase associated functions during rapid growth, evidence suggests that AbrB also plays roles in modulating catabolite repression and could affect growth-rate regulation of translational components. AbrB is a transcriptional regulator whose N-terminal domain is paradigmatic for a new class of DNA-binding motif that primarily recognizes subtle three-dimensional DNA structures that are assumed by a subset of varying base sequences. Over 40 operons encoding a wide array of metabolic functions, including essential sporulation genes and genes responsible for production of antimicrobial compounds, are known to have AbrB binding sites, usually in the promoter regions. At least 25 other regulatory proteins present in Bacillus, Clostridium, Listeria and Carboxydothermus species (including pathogenic species) show extensive amino acid identity and homology to the DNA-binding domain of AbrB. 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. Examining the roles played by specific residues and regions in the protein, and comparing and contrasting properties specified by sequence variations in AbrB homologs, will provide significant insights into macromolecular interactions that are exploited by proteins having this flexible binding motif in order to achieve broad, but specific, DNA recognition properties. The relationship of AbrB structure to DNA-binding properties, and the precise role played by specific amino acid residues present in and near the binding surface, will be probed by a combination of mutant selection, mutant analysis, and examination of the binding domains from selected AbrB homologs. The hypothesis that the carboxy-terminal domains of these proteins are primarily higher order multimerization domains will be tested using a variety of approaches including genetic, biochemical and biophysical analysis of mutant proteins and construction of hybrid proteins having either intact or truncated C-domains fused to the DNA-binding domains of other AbrB homologs, or to the ? Repressor. Information gained by these investigations will be a crucial step towards an ultimate goal of utilizing the unique properties of the AbrB motif in order to design, or directly select, specific variants that specifically bind any desired DNA target.
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