SPECIFIC BINDING OF THE TRANSCRIPTION FACTOR SIGMA-54 TO PROMOTER DNA

A CENTRAL event in transcription is the assembly on DNA of specific complexes near the initiation sites for RNA synthesis. Activation of transcription by one class of enhancer-binding proteins requires an RNA polymerase holoenzyme1 containing the specialized transcription factor, sigma-54 (sigma-54). We report here that sigma-54 alone specifically binds to promoter DNA and is responsible for many of the close contacts between RNA polymerase holoenzyme and promoter DNA, a property proposed for the major sigma-70 protein family. Binding of simga-54 to promoter DNA is not equivalent to that of holoenzyme suggesting that there is a constraint on sigma-54 conformation when bound with core RNA polymerase. Footprints indicate sigma-54 is at the leading edge of DNA-bound holoenzyme. Like the holoenzyme1-4, sigma-54-binding to promoter DNA does not result in DNA strand separation. Instead the specific DNA-binding activity of sigma-54 assists assembly of a closed promoter complex. This complex can be isomerized to the open (DNA melted) complex by activator protein5,6, but promoter-bound sigma-54 alone cannot be induced to melt DNA. The pathway leading to productive transcription is similar to that proposed for eukaryotic RNA polymerase II systems.