Stationary-Phase Gene Regulation in Escherichia coli §

Abstract

In their stressful natural environments, bacteria often are in stationary phase and use their limited resources for maintenance and stress survival. Underlying this activity is the general stress response, which in Escherichia coli depends on the σ S (RpoS) subunit of RNA polymerase. σ S is closely related to the vegetative sigma factor σ 70 (RpoD), and these two sigmas recognize similar but not identical promoter sequences. During the postexponential phase and entry into stationary phase, σ S is induced by a fine-tuned combination of transcriptional, translational, and proteolytic control. In addition, regulatory "short-cuts" to high cellular σ S levels, which mainly rely on the rapid inhibition of σ S proteolysis, are triggered by sudden starvation for various nutrients and other stressful shift conditons. σ S directly or indirectly activates more than 500 genes. Additional signal input is integrated by σ S cooperating with various transcription factors in complex cascades and feedforward loops. Target gene products have stress-protective functions, redirect metabolism, affect cell envelope and cell shape, are involved in biofilm formation or pathogenesis, or can increased stationary phase and stress-induced mutagenesis. This review summarizes these diverse functions and the amazingly complex regulation of σ S . At the molecular level, these processes are integrated with the partitioning of global transcription space by sigma factor competition for RNA polymerase core enzyme and signaling by nucleotide second messengers that include cAMP, (p)ppGpp, and c-di-GMP. Physiologically, σ S is the key player in choosing between a lifestyle associated with postexponential growth based on nutrient scavenging and motility and a lifestyle focused on maintenance, strong stress resistance, and increased adhesiveness. Finally, research with other proteobacteria is beginning to reveal how evolution has further adapted function and regulation of σ S to specific environmental niches.