Figure 7. Models for σ_3.2 Displacement During Initial transcription.

Core RNAP (gray), σ regions 2 and 4 (tan), σ_3.2 (brown), non-template DNA strand (light blue), template DNA strand (dark blue), RNA (green). The RNA exit channel is depicted as a tube composed of the β flap (cyan) and the β′ clamp (pink). (A) RP_O. σ_3.2 approaches the active site and is then threaded through the RNA exit channel. (B) The template strand impingement model for RP_ITC5. The 5′ end of the 5-mer RNA comes close to σ_3.2. The template strand bulge approaches the entrance to the RNA exit channel and disrupts β flap-β′ clamp-σ_3.2 interactions. (C) The template strand impingement model for longer initial transcripts (RP_ITC>5). The template strand (TS) bulge continues into the RNA exit channel as the bulge is pushed upstream by the growing RNA-DNA hybrid resulting in further disruption of β flap-β′ clamp-σ_3.2 interactions. This impingement, along with growth of the RNA chain (green), could help displace σ_3.2 from the RNA exit channel. (D) Template strand extrusion model for RP_ITC>5. As the RNA-DNA hybrid lengthens, the TS bulge is extruded out of the TS tunnel into bulk solvent, and the growing RNA chain (green arrow) continues σ_3.2 displacement from the RNA exit channel (see Discussion). In C and D we do not mean to imply that σ is lost from the complex upon formation of a 5-mer, only that σ_3.2 is displaced during promoter escape.