Fundamental to all cells is the ability to alter the pattern of gene expression in response to environmental and metabolic signals. In prokaryotes most signal transduction and stress response systems ultimately act at the transcriptional level to express sets of genes needed to adapt to changing conditions. Our experimental focus is the role of RNA polymerase in controlling stationary phase gene expression in the Gram positive bacterium Bacillus subtilis. This analysis will contribute to understanding the functions, interactions, and regulation of the transcriptional machinery of a model developmental system, including the RNA polymerase catalytic core, the sigma factors that determine promoter recognition, and interacting accessory factors. Bacillus subtilis cells manifest diverse responses in stationary phase, including expression of genes important for transition to the non-growing state, initiation of the sporulation process, development of genetic competence, and production of extracellular enzymes and antibiotics. Alternative sigma factors have a central role in coordinating these stationary phase events. Thus it is important to understand the molecular mechanisms that regulate sigma factor activity and interaction with the RNA polymerase core enzyme. The primary goal of this proposal is to investigate the physiological role and regulation of sigma-B, an alternative sigma factor implicated in stationary phase stress response. A combined biochemical and genetic approach will address the following questions: (l) What stationary phase genes are controlled by sigma-B, and how is their expression regulated; (2) What are the molecular mechanisms controlling sigma-B activity in response to stationary phase signals; (3) How do sigma-B and other dispensable sigma factors interact with RNA polymerase core; and, in an extension of this process, (4) What developmental functions are mediated by genes directly controlled by the stationary phase transcription factor sigma-F? Specific aspects of this research will be directly relevant to understanding stationary phase regulation in a broad range of bacteria, including antibiotic biosynthesis by Streptomyces species and the production of virulence factors by bacterial pathogens. The problem of ordered regulation of gene expression in response to environmental, metabolic, and morphological signals is common in biology, and the biochemical principles that govern sigma factor regulation and interaction with RNA polymerase are likely relevant to proteins that associate with RNA polymerases in all organisms.
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