Gene repression by sigmaS: sigma competition for binding to RNA polymerase or more?
The alternative subunit of RNA polymerase RpoS/sS controls a global adaptive response allowing many Gram-negative bacteria to survive nutrient deprivation and various stresses and contributes to biofilm formation and virulence of Salmonella enterica serovar Typhimurium. We have addressed an important but poorly understood aspect of sS-dependent control; that of a repressor. The general assumption is that negative regulation of gene expression by sS is mainly a passive phenomenon, due to competition between sS and other sigma factors for binding to a limited amount of core RNA polymerase (RNAP). Genome expression profiling and physiological characterization of mutants of Salmonella ser. Typhimurium deleted for rpoS or producing a sS protein efficient for binding to RNAP, but not to the -10 promoter element, revealed that gene repression by sS requires its binding to DNA. Therefore, gene repression by sS is an active phenomenon rather than the sole cause of sS competing with other sigma factors for RNAP binding. Overall design: RNA profiles of the wild type strain and two rpoS mutants of Salmonella enterica serotype Typhimurium were generated by RNA sequencing, using three biological replicates. One rpoS mutant is deleted for rpoS (delta-rpoS), while the other (rpoSdb) contains two point mutations in rpoS (C421A and G469A) and produces an sS protein inefficient for binding to the -10 promoter element.