The gene of encodes a non-proton-translocating NADH dehydrogenase (NdhII) that is anaerobically repressed by the global transcription regulator, FNR. FNR binds at two sites (centred at -50.5 and -94.5) in the promoter but the mechanism of FNR-mediated repression appears not to be due to promoter occlusion. This mechanism has been investigated using an aerobically active derivative of FNR, FNR(FNR-D154A), with promoters containing altered FNR-binding sites. FNRrepressed ndh gene expression both aerobically and anaerobically Gel retardation analysis and DNase I footprinting with purified FNRprotein confirmed that FNR interacts at two sites in the promoter, and that FNR and RNA polymerase (RNAP) can bind simultaneously. Studies with three altered ndh promoters, each containing an impaired or improved FNR-site, indicated that both FNR-sites are needed for efficient repression The α-subunit of RNAP interacted with two regions (centred at -105 and -46), each overlapping one of the FNR-sites in the promoter. Footprints of the FNR-RNAP- ternary complex indicated that FNR-binding at -50.5 prevents the α-subunit of RNAP from docking with the DNA just upstream of the -35 element. Binding of a second FNRmolecule at the -105 site likewise prevents binding of the α-subunit at its alternative site, thus providing a plausible mechanism for FNR-mediated repression based on displacement of the α-subunit of RNAP.


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