StpA prevents RpoS-dependent transcription during mid-exponential growth in S. Typhimurium

StpA is a paralogue of the nucleoid associated protein H-NS that is conserved in a range of enteric bacteria and had no known function in Salmonella enterica serovar Typhimurium. Here, we show that 5% of the Salmonella genome is regulated by StpA, which contrasts with the situation in Escherichia coli where deletion of stpA only had minor effects on gene expression. The StpA-dependent genes of S. Typhimurium are a specific subset of the H-NS regulon that are predominantly under the positive control of sigma38 (RpoS), CRP-cAMP and PhoP. The regulatory role of StpA varied at different growth phases; StpA only controlled sigma38 levels at mid-exponential phase when it prevented inappropriate activation of sigma38 during rapid bacterial growth. In contrast, StpA only activated the CRP-cAMP regulon during late exponential phase. To test the hypothesis that stpA prevents Sigma38-dependent transcription during mid-exponential growth in S. Typhimurium, we analysed the effect of the stpA deletion on transcription in the presence and absence of rpoS. Three biological replicates were performed for each strain. For this study, we used Salmonella genomic DNA as the comparator which also acted as the control for spot quality.