The long-range goal of this project is to learn how genes are controlled by remotely-bound activator proteins. This is a problem of great significance because most human genes are controlled in this manner. These genes include oncogenes and others controlling the production of other proteins whose functions are critical for the health of the cells and the organism. The discovery of an analogous process in bacteria provides an entry to study aspects of the complex problem in a simple and accessible system. In the simple bacterium E. coli this process requires the participation of the protein sigma 54. The current proposal centers on learning how sigma 54 modifies the bacterial transcription apparatus so that it can be sensitive to remotely bound activator proteins. First the transcription cycle of genes dependent on sigma 54 will be characterized by in vitro studies. Then the mutually interacting domains on sigma 54, activator and RNA polymerase will be identified. Particular attention will be paid to the eukaryotic - like motifs present on sigma 54 including acidic and glutamine-rich regions. Finally the role of each protein and its sub-domains will be analyzed with regard to where it participates in the enhancer-dependent mechanism. This work should serve as a guide to studies of more complex systems and facilitate the emergence of concepts important to transcription in both human cells and micro-organisms.
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