Fnr activates transcription from the P6 promoter of the pfl operon in vitro.

Expression of the Escherichia coli focA-pfl operon is induced by anaerobiosis and transcription is controlled by seven promoters. Anaerobic induction is mediated by the ArcA and Fnr transcription factors. Fnr was purified and its specific interaction with the pfl promoter-regulatory region was characterized. A single binding site could be identified by DNase I footprinting, which was centred at -40.5 bp relative to the start site of promoter 6 (P6) transcription. Activation of P6 transcription in vitro was completely dependent on the Fnr protein. Fnr-dependent transcription could be prevented by mutating the Fnr-binding site, indicating that Fnr must bind to its recognition sequence to be able to activate transcription. An Fnr-independent promoter, which overlaps the P6 promoter, was also identified and characterized in vivo and in vitro. Transcription from this promoter (termed P6A) initiated 10 bp upstream of the P6 start site and assures that low-level synthesis of the FocA protein occurs under aerobic growth conditions.