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Background  Sigma54, or RpoN, is an alternative σ factor found widely in eubacteria. A significant complication in analysis of the global σ 54  regulon in a bacterium is that the σ 54  RNA polymerase holoenzyme requires interaction with an active bacterial enhancer-binding protein (bEBP) to initiate transcription at a σ 54 -dependent promoter. Many bacteria possess multiple bEBPs, which are activated by diverse environmental stimuli. In this work, we assess the ability of a promiscuous, constitutively-active bEBP—the AAA+ ATPase domain of DctD from  Sinorhizobium meliloti —to activate transcription from all σ 54 -dependent promoters for the characterization of the σ 54  regulon of  Salmonella  Typhimurium LT2.    Results  The AAA+ ATPase domain of DctD was able to drive transcription from nearly all previously characterized or predicted σ 54 -dependent promoters in  Salmonella  under a single condition. These promoters are controlled by a variety of native activators and, under the condition tested, are not transcribed in the absence of the DctD AAA+ ATPase domain. We also identified a novel σ 54 -dependent promoter upstream of STM2939, a homolog of the  cas1  component of a CRISPR system. ChIP-chip analysis revealed at least 70 σ 54  binding sites in the chromosome, of which 58% are located within coding sequences. Promoter- lacZ  fusions with selected intragenic σ 54  binding sites suggest that many of these sites are capable of functioning as σ 54 -dependent promoters.    Conclusion  Since the DctD AAA+ ATPase domain proved effective in activating transcription from the diverse σ 54 -dependent promoters of the  S . Typhimurium LT2 σ 54  regulon under a single growth condition, this approach is likely to be valuable for examining σ 54  regulons in other bacterial species. The  S . Typhimurium σ 54  regulon included a high number of intragenic σ 54  binding sites/promoters, suggesting that σ 54  may have multiple regulatory roles beyond the initiation of transcription at the start of an operon.

Use of a promiscuous, constitutively-active bacterial enhancer-binding protein to define the σ54 (RpoN) regulon of Salmonella Typhimurium LT2