Geometry of the process of transcription activation at the sigma 54-dependent nifH promoter of Klebsiella pneumoniae

Abstract

The Klebsiella pneumoniae nifH promoter is very strictly controlled by nitrogen availability and highly dependent on sigma 54 and integration host factor (IHF) for expression. This promoter region has been used to examine the role of IHF in the activation of transcription from sigma 54-dependent promoters and to analyze the positional restrictions which may exist for an activation mechanism from distant sites such as this one. By functionally replacing the binding site of IHF by sequence-directed curved DNA fragments, it has been shown that the role of IHF in stimulating transcription is structural; it brings the molecules directly involved in the process into close proximity. Unlike other promoter regions with an activation mechanism at a distance, this IHF-dependent promoter requires a precise geometry for efficient transcription. In this sense, it resembles an activation mechanism from near sites. However, alternative functional structures which are very different from the native one can be isolated.