| Summary: | <p>Abstract</p> <p>Background</p> <p><it>Escherichia coli</it> can respire anaerobically using dimethyl sulfoxide (DMSO) or trimethylamine-<it>N</it>-oxide (TMAO) as the terminal electron acceptor for anaerobic energy generation. Expression of the <it>dmsABC</it> genes that encode the membrane-associated DMSO/TMAO reductase is positively regulated during anaerobic conditions by the Fnr protein and negatively regulated by the NarL protein when nitrate is present.</p> <p>Results</p> <p>The regions of <it>dmsA</it> regulatory DNA required for Fnr and NarL interactions in response to anaerobiosis and nitrate, respectively, were examined. Mutations within the Fnr site that deviated from the wild type sequence, TTGATaccgAACAA, or that removed an entire half-site, either impaired or abolished the anaerobic activation of <it>dmsA</it>-<it>lacZ</it> expression. The region for phosphorylated NarL (NarL-phosphate) binding at the <it>dmsA</it> promoter was identified by DNase I and hydroxyl radical footprinting methods. A large 97 bp region that overlaps the Fnr and RNA polymerase recognition sites was protected by NarL-phosphate but not by the non-phosphorylated form of NarL. Hydroxyl radical footprinting analysis confirmed the NarL-phosphate DNase I protections of both <it>dmsA</it> strands and revealed 8–9 protected sites of 3–5 bp occurring at ten bp intervals that are offset by 3 bp in the 3' direction.</p> <p>Conclusion</p> <p>These findings suggest that multiple molecules of phosphorylated NarL bind along one face of the DNA and may interfere with Fnr and/or RNA polymerase interactions at the <it>dmsA</it> regulatory region. The interplay of these transcription factors insures a hierarchical expression of the <it>dmsABC</it> genes when respiration of the preferred electron acceptors, oxygen and nitrate, is not possible.</p>
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