Figure 1.

Sequence of events at λP_R'.

1. Presence of λQ (shown in blue) allows RNAP that has initiated transcription from λP_R' to read through terminator t_R'. Blow-up shows the functionally important elements at λP_R' including: the promoter −10 and −35 elements, the λQ-binding element (QBE), the pause-inducing −10-like element, and the −35-like element (TTGACT motif) positioned between the QBE and the pause-inducing element. Note that the TTGACT motif is separated by one base pair from the pause-inducing −10-like element.
2. Cartoons depict sequence of events during initiation and early elongation at λP_R'. Shown first is the initiation complex; σ⁷⁰ region 3.2 (σ_3.2) is shown dashed to indicate that it is located within the RNA exit channel, and σ⁷⁰ region 4 (σ₄) is shown bound to the β flap (blue triangle). The σ⁷⁰ region 4/β flap interaction positions σ⁷⁰ region 4 for interaction with the promoter −35 element when σ⁷⁰ region 2 is bound to the promoter −10 element (where the −10 and −35 elements are separated by ∼17 base pairs) (Kuznedelov et al., 2002). Shown just below the initiation complex is the paused early elongation complex at λP_R' with σ⁷⁰ region 2 (σ₂) bound to the pause-inducing −10-like element (shown in red). The nascent RNA (depicted as red beads) has displaced σ⁷⁰ region 3.2 from the RNA exit channel and, as illustrated in the blow-ups, displaced σ⁷⁰ region 4 from the β flap upon addition of the 17th nt.
3. λQ (shown as a dimer) binds to the QBE and engages the paused elongation complex. λQ contacts σ⁷⁰ region 4 and stabilizes its binding to the TTGACT motif (grey rectangle), causing RNAP holoenzyme to adopt a conformation in which σ⁷⁰ region 4 and σ⁷⁰ region 2 are simultaneously bound to DNA elements that are separated by 1 base pair (Nickels et al., 2002). Formation of this RNAP holoenzyme-DNA complex requires that σ⁷⁰ region 4 be displaced from the β flap. λQ is depicted as contacting a surface of RNAP core that is occluded when σ⁷⁰ region 4 is bound to the β flap.