Fig. 1.

Transcription initiation at λP_R promoter. (A) Nontemplate strand sequence of the λP_R promoter studied here, in which the ITR is modified to eliminate the incorporation of CMP before position +17, so transcription halts at a 16-mer RNA when CTP is withheld. The −35 (green), −10 (blue), and discriminator (tan) elements and the start site (+1; green) and ITR (gray) are highlighted. (B) Summary of stages in productive initiation by RNAP holoenzyme (α₂ββ’ωσ⁷⁰). Key aspects of the mechanisms of two of these stages (OC and ITC) are determined in this study. (C) Schematic representation of OC species at the λP_R promoter at 37 °C: intermediates I₂ and I₃ and stable 37 °C complex RP_O. As illustrated, interactions of in-cleft and downstream elements of RNAP with the discriminator and ITR, weak or absent in I₂, are stronger in I₃ and much stronger in RP_O at 37 °C (10). RNAP core (gray) is shown with relevant σ⁷⁰ subunits 1.1 (purple), 1.2 (green), 2 (light orange), and 4 (yellow). Linking domains between subunits are not shown for clarity. The template DNA strand is shown in black and the nontemplate strand in orange, with the −35 (light green), −10 (blue), and start site (dark green) indicated.