Core RNA polymerase assists binding of the transcription factor sigma 54 to promoter DNA

The sigma subunit of bacterial RNA polymerase is necessary for the specific binding of RNA polymerase holoenzyme to promoter DNA. Promoter complexes which form with holoenzyme containing sigma 54 remain as closed complexes unless they are activated by one class of enhancer binding protein. The sigma 54 transcription factor can bind specifically to certain promoter sites in the absence of the core RNA polymerase subunits. This property has allowed demonstration of a new role for core polymerase in transcription, namely that it assists the binding of sigma 54 to promoter DNA. An altered form of sigma 54 with a deletion within the amino-terminal region showed increased affinity for specific DNA-binding sites. Although able to complex with core RNA polymerase the mutant sigma 54 failed to respond to core polymerase in the manner characteristic of the wild-type sigma 54 by altering its footprint. This result indicates that sigma 54 has a latent DNA-binding activity which is revealed by core RNA polymerase, and possibly involves a change in sigma 54 conformation. Promoter complexes which formed with sigma 54-holoenzyme appeared to be qualitatively different, depending upon the target promoter sequence, suggesting that different activatable complexes form at different promoter sequences.