Specific binding of the transcription factor sigma-54 to promoter DNA

Abstract

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 holoenzyme' containing the specialized transcription factor, sigma-54 (σ⁵⁴). We report here that σ⁵⁴ 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 σ⁷⁰ protein family. Binding of σ⁵⁴ to promoter DNA is not equivalent to that of holoenzyme suggesting that there is a constraint on σ⁵⁴ conformation when bound with core RNA polymerase. Footprints indicate σ⁵⁴ is at the leading edge of DNA-bound holoenzyme. Like the holoenzyme^1–4, σ⁵⁴-binding to promoter DNA does not result in DNA strand separation. Instead the specific DNA-binding activity of σ⁵⁴ assists assembly of a closed promoter complex. This complex can be isomerized to the open (DNA melted) complex by activator protein^5,6, but promoter-bound σ⁵⁴ alone cannot be induced to melt DNA. The pathway leading to productive transcription is similar to that proposed for eukaryotic RNA polymerase II systems.