We will investigate regulatory pathways in E. coli by monitoring global gene expression on microarrays. In particular, we will study nitrogen regulatory pathways and their connection to osmoregulatory pathways through the common intermediate glutamate. We will create microarrays of E. coli genes and develop methods for fluorescent labeling of E. coli cDNAs. As a first exercise, we will use microarrays to determine which genes are under regulatory control of the nitrogen regulatory C (NtrC ) protein in E. coli. Then we will investigate expression levels of all genes under nitrogen limiting conditions to determine how nitrogen limitation propagates downstream of a primary glutamine limitation to slow the growth rate of E. coli. Finally, we will investigate the roles of glutamate and K+ in cellular osmoregulation and the dual role of glutamate in osmoregulation and biosynthesis. Our development of a system for gene expression monitoring in bacteria will facilitate global expression analyses in bacteria.
