![]() ![]() coli, for example, the response regulator KdpD appears to govern transcription of a single promoter, whereas the response regulator ArcA modulates expression of >30 operons ( Georgellis et al., 1999 Salgado et al., 2004). The number of targets that a response regulator controls varies among the different systems found in a given bacterial species and between homologous systems in related bacterial species. In contrast, Escherichia coli has a genome size of 4.5 Mb encoding 30 such systems ( Blattner et al., 1997), and the environmental microbe and opportunistic pathogen Pseudomonas aeruginosa, with a genome size of 6.3 Mb, harbors 118 two-component system proteins ( Stover et al., 2000). For example, the aphid endosymbiont Buchnera aphidicola has a genome size of approximately 640 kb that does not encode two-component systems ( Shigenobu et al., 2000). In addition, organisms that live in varied environments tend to have a larger number of two-component systems than those that occupy a single environment. Genomic analysis revealed that there is a direct correlation between genome size and the number of two-component systems present in a given bacterial species. Because the phosphorylated form of the response regulator binds to target promoters with higher affinity than the unphosphorylated one, sensor-promoted changes in the phosphorylated state of a response regulator can have a profound impact in the gene expression profile of an organism. The majority of response regulators are DNA-binding proteins that modulate gene transcription. Typically, a two-component system consists of a sensor kinase that responds to a specific signal by modifying the phosphorylated state of a cognate response regulator. The two-component system constitutes a major form of bacterial signal transduction. The predictions made by GPS were validated experimentally to establish that the PhoP protein uses multiple mechanisms to control gene transcription and is a central element in a highly connected network. Application of this method to the PhoP/PhoQ two-component regulatory system of Escherichia coli and Salmonella enterica uncovered novel members of the PhoP regulon, as well as regulatory interactions that had not been discovered using previous approaches. This chapter describes a method, termed gene promoter scan (GPS), that discriminates among coregulated promoters by simultaneously considering a variety of cis-acting regulatory features. The fact that coregulated genes may be differentially expressed suggests that subtle differences in the shared cis-acting regulatory elements are likely to be significant. However, little is known about what determines the differential expression of genes within a particular network, even when it involves a single transcription factor. Genetic and genomic approaches have been used successfully to assign genes to distinct regulatory networks in both prokaryotes and eukaryotes. ![]() A critical challenge of the postgenomic era is to understand how genes are differentially regulated.
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