Repressor activity of the RpoS/σS- dependent RNA polymerase requires DNA binding

The RpoS/sigma(s) sigma subunit of RNA polymerase (RNAP) activates transcription of stationary phase genes in many Gram-negative bacteria and controls adaptive functions, including stress resistance, biofilm formation and virulence. In this study, we address an important but poorly understood aspect of sigma(s)-dependent control, that of a repressor. Negative regulation by sigma(s) has been proposed to result largely from competition between sigma(s) and other sigma factors for binding to a limited amount of core RNAP (E). To assess whether sigma(s) binding to E alone results in significant downregulation of gene expression by other sigma factors, we characterized an rpoS mutant of Salmonella enterica serovar Typhimurium producing a sigma(s) protein proficient for E sigma(s) complex formation but deficient in promoter DNA binding. Genome expression profiling and physiological assays revealed that this mutant was defective for negative regulation, indicating that gene repression by sigma(s) requires its binding to DNA. Although the mechanisms of repression by sigma(s) are likely specific to individual genes and environmental conditions, the study of transcription downregulation of the succinate dehydrogenase operon suggests that sigma competition at the promoter DNA level plays an important role in gene repression by E sigma(s).