Our current understanding of gene regulation in Escherichia coli suggests three hierarchical levels of control: 1) global control of basal level gene expression by chromosome structure; 2) global regulatory proteinmediated control of stimulons and regulons; and, 3) operon specific controls. The first level of control is exemplified by the DNA-supercoiling-dependent mechanisms described for the coordination of basal level expression of operons of the ilv regulon. It has been shown that these controls can be influenced by the topological structure of the chromosome, and that DNA architectural proteins such as IHF are able to modulate the formation and location of these structures. The experiments described in this proposal are designed to further characterize this first level of global gene regulation. It is proposed that regulation of gene expression by chromosome structure is influenced by the energy charge of the cell, which in turn is influenced by nutritional and environmental conditions that require transitions from one growth state to another. To test this idea, computational and genomic methods will be employed. DNA arrays will be used to determine differential gene expression profiles, and cellular energy charge and DNA supercoiling levels will be monitored during aerobic to anaerobic growth transitions in the presence and absence of IHF. Computational predictions of IHF binding sites and predictions of the topological state of the E. coli chromosome will be used to analyze these data. It is expected that these experiments will identify additional operons that respond to energy charge and DNA supercoiling-mediated signals for further characterization. These experiments will further provide a wealth of information for future studies concerning the operon specific and global regulation of carbon and energy metabolism genes during aerobic to anaerobic growth transitions.
