Novel DNA Binding and Regulatory Activities for σ54 (RpoN) in Salmonella enterica Serovar Typhimurium 14028s

The variable sigma (sigma) subunit of the bacterial RNA polymerase (RNAP) holoenzyme, which is responsible for promoter specificity and open complex formation, plays a strategic role in the response to environmental changes. Salmonella enterica serovar Typhimurium utilizes the housekeeping sigma(70) and five alternative sigma factors, including sigma(54). The sigma(54)-RNAP differs from other sigma-RNAP holoenzymes in that it forms a stable closed complex with the promoter and requires ATP hydrolysis by an activated cognate bacterial enhancer binding protein (bEBP) to transition to an open complex and initiate transcription. In S. Typhimurium, sigma(54)-dependent promoters normally respond to one of 13 different bEBPs, each of which is activated under a specific growth condition. Here, we utilized a constitutively active, promiscuous bEBP to perform a genome-wide identification of sigma(54)-RNAP DNA binding sites and the transcriptome of the sigma(54) regulon of S. Typhimurium. The position and context of many of the identified sigma(54) RNAP DNA binding sites suggest regulatory roles for sigma(54)RNAP that connect the sigma(54) regulon to regulons of other sigma factors to provide a dynamic response to rapidly changing environmental conditions. IMPORTANCE The alternative sigma factor sigma(54) (RpoN) is required for expression of genes involved in processes with significance in agriculture, bioenergy production, bioremediation, and host-microbe interactions. The characterization of the sigma(54) regulon of the versatile pathogen S. Typhimurium has expanded our understanding of the scope of the sigma(54) regulon and how it links to other sigma regulons within the complex regulatory network for gene expression in bacteria.