Two roles for integration host factor at an enhancer-dependent nifA promoter

Control of transcription in prokaryotes often involves direct contact of re gulatory proteins with RNA polymerase. For the sigma(54) RNA polymerase, re gulatory proteins bound to distally located enhancers engage the polymerase via DNA looping. The sigma(54)-dependent nifA promoter of Herbaspirillum s eropedicae (Hs) is activated under nitrogen-limiting growth conditions. Pot ential enhancers for the nitrogen control activators NTRC and NIFA and bind ing sites for integration host factor (IHF) and sigma(54)-holoenzyme were i dentified. DNA footprinting experiments showed that these sites functioned for protein binding. Their involvement in the promoter regulation was explo red. In vitro, activation of the Hs nifA promoter by NTRC is stimulated by the DNA bending protein IHF. In marked contrast, activation by NIFA is grea tly reduced by IHF, thus diminishing potentially destabilizing autoactivati on of the nifA promoter by NIFA. Additionally, high levels of NIFA appear t o limit NTRC-dependent activation. This inhibition is IHF dependent. Theref ore, IHF acts positively and negatively at the nifA promoter to restrict tr anscription activation to NTRC and one signal transduction pathway.