Figure 1

RNAP holoenzyme and the interaction of RNAP with σ⁷⁰-dependent promoters. Structure-based cartoons (left to right) depict RNAP holoenzyme, RPc (closed complex), RPo (open complex), and EC (elongating complex) with σ⁷⁰ in yellow, core (β,β',α₂, and ω) in turquoise, DNA in magenta, and RNA in purple. In holoenzyme, the positions of σ⁷⁰ Regions 1.1, 2, 3, and 4, the α-CTDs, the β-flap, and the β,β' jaws are identified. In RPc, contact can be made between RNAP and promoter dsDNA elements: two UP elements with each of the α-CTDs, the -35 element with σ⁷⁰ Region 4, TGn (positions -15 to -13) with σ⁷⁰ Region 3, and positions -12/-11 of the -10 element with σ⁷⁰ Region 2. σ⁷⁰ Region 1.1 lies in the downstream DNA channel formed by portions of β and β' and the β',β' jaws are open. In RPo, unwinding of the DNA and conformational changes within RNAP result in a sharp bend of the DNA into the active site with the formation of the transcription bubble surrounding the start of transcription, the interaction of σ⁷⁰ Region 2 with nontemplate ssDNA in the -10 element, movement of Region 1.1 from the downstream DNA channel, and contact between the downstream DNA and the β' clamp. In EC, σ⁷⁰ and the promoter DNA have been released. The newly synthesized RNA remains annealed to the DNA template in the RNA/DNA hybrid as the previously synthesized RNA is extruded through the RNA exit channel past the β-flap.