TI - Oxygen and nitrate -dependent regulation of dmsABC operon expression in Escherichia coli : sites for Fnr and NarL protein interactions . AB - Background Escherichia coli can respire anaerobically using dimethyl sulfoxide ( DMSO ) or trimethylamine-N-oxide ( TMAO ) as the terminal electron acceptor for anaerobic energy generation . Expression of the dmsABC 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 . Results The regions of dmsA 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 dmsA-lacZ expression . The region for PHOSphorylated NarL ( NarL-phosphate ) binding at the dmsA 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 dmsA 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 . Conclusion These findings suggest that multiple molecules of PHOSphorylated NarL bind one face of the DNA and may interfere with Fnr and/or RNA polymerase interactions at the dmsA regulatory region . The interplay of these transcription factors insures a hierarchical expression of the dmsABC genes when respiration of the preferred electron acceptors , oxygen and nitrate , is not possible .