Transcriptional activation of the Klebsiella pneumoniae nifLA promoter by NTRC is face‐of‐the‐helix dependent and the activator stabilizes the interaction of sigma 54‐RNA polymerase with the promoter.

Activation of transcription at the Klebsiella pneumoniae nifLA promoter requires the phosphorylated form of the positive control protein NTRC, together with RNA polymerase modified by the alternative sigma factor sigma 54. Dimethylsulphate and potassium permanganate were used as probes to analyse the interaction of NTRC and sigma 54‐RNA polymerase with supercoiled nifLA promoter DNA in vitro. In contrast to the glnAp2 promoter, sigma 54 holoenzyme did not protect guanine residues in the nifLA promoter from methylation in the absence of the activator. We propose that NTRC stabilizes the interaction of sigma 54‐RNA polymerase with the ‐24, ‐12 region, in addition to its role in catalysing open complex formation. Phosphorylated NTRC binds to two sites located greater than 100 nucleotides upstream of the ‐24, ‐12 region; it also induces hyper‐methylation of a G residue at ‐23. Enhanced methylation at ‐23 is not co‐operative with the binding of activator to the upstream sites and may account for the ability of NTRC, when present at high concentration, to activate transcription in the absence of the upstream binding sites. The insertion of spacer mutations at ‐86 indicates that transcriptional activation of the nifLA promoter at low NTRC concentrations is face‐of‐the‐helix dependent, both in vivo and in vitro. We propose that correct positioning of activator molecules at the upstream binding sites stabilizes the interaction of sigma 54‐RNA polymerase with the downstream region via the formation of a DNA loop.