Sequences in σN determining holoenzyme formation and properties

Sigma subunits of bacterial RNA polymerases are closely involved in many steps of promoter-specific transcription initiation. Holoenzyme formed with the specialised minor sigma-N (sigma(N)) protein binds rare promoters in a transcriptionally inactive state and functions in enhancer-dependent transcription. Using competition and dissociation assays, we show that sigma(N)-holoenzyme has a stability comparable to the major sigma(70)-holoenzyme. Purified partial sequences of sigma(N) were prepared and assayed for retention of core RNA polymerase binding activity. Two discrete fragments of sigma(N) which both bind the core but with significantly different affinities were identified, demonstrating that the sigma(N) interface with core RNA polymerase is extensive. The low affinity segment of sigma(N) included region I sequences, an amino terminal domain which mediates activator responsiveness and formation of open promoter complexes. The higher affinity site Lies within a 95 residue fragment of region III. We propose that the fore to region I contact mediates properties of the sigma(N)-holoenzyme important for enhancer responsiveness. Heparin is shown to dissociate sigma(N) and core, indicating that disruption of the holoenzyme is involved in the heparin sensitivity of the sigma(N) closed complex. (C) 1999 Academic Press.