Post-Exponential Phase Gene Expression in Escherichia coli

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Many bacterial genes that are important for adaptation and long-term survival are poorly-expressed under the exponential phase conditions. My laboratory has helped to characterize many adaptive genes that ares expressed under nutrient limiting conditions, particularly those that are controlled by the RpoS alternative sigma factor in Escherichia coli. We have shown that the non-essential rpoS gene, while important for long-term survival, may be lost under selection as rpoS mutants have enhanced metabolic capability for growth on non-preferred carbon sources. These studies, combined with our gene expression studies, continue to be a major focus for my laboratory. We have recently found that other poorly-understood regulatory processes, in addition to and independent of RpoS, are important for long-term gene expression and these will also be examined. We will construct targeted combinatorial mutants deficient in RpoS-controlled functions to examine the role in bacterial metabolism using microarray, RNA Seq and next generation sequencing. In addition to characterizing RpoS-dependent genes, we will investigate specific questions that have arisen from our previous studies regarding expression RpoS-dependent paralogs including a key system for balance carbon utilization namely Transaldolase/Transketolase. Each of these stationary-specific genes are likely important in helping the cell adapt to stress conditions since we have found that they are expressed only in stationary phase when cells are in a starved state--they are poorly-expressed under normal conditions. To characterize non-RpoS genes that are highly expressed in long-term (> 1 day) cultures, we will construct appropriate deletion mutants of genes that we have previously identified (unpublished) and will examine bacterial survival using standard plate assays. To extend our studies further, we will also examine post exponential physiology in environmental bacterial isolates. Our long term goal is to enhance our understanding of how bacteria adapt to sub-optimal growth conditions and validate regulatory models for post-exponential gene expression, which have been developed using E. coli laboratory strains of , to natural E. coli populations in the environment. ***Our short term objectives are to: ***1. Examine how expression of the RpoS regulon is controlled by other sigma factors and by the Crl regulatory protein. ***2. Identify and characterize the Post-Stationary Phase (PSP) regulon. ***3. Examine the physiological role of key RpoS-dependent paralogs in E. coli.  *** **