Figure 7. The three promoter-recognition structural motifs of N4 and T7 RNAPs.
(A) The −11 recognition site (gray), specificity loop (cyan) and β-intercalating hairpin (orange) of N4 vRNAP in the binary complex. The promoter hairpin is depicted by a pink ribbon.
(B) The AT-rich recognition loop (gray), specific loop (cyan) and β-intercalating hairpin of T7 RNAP in the binary complex (PDB: 2PI5). Template and non-template DNA strands are depicted by pink and yellow ribbons, respectively. The orientation of the T7 RNAP binary complex has been aligned with the N4 mini-vRNAP binary complex in panel A by superimposing their Palm cores. Amino acid residues involved in promoter recognition are shown as stick and labeled.
(C) Sequential remodeling of the N4 phage genome DNA and vRNAP to achieve phage early gene transcription. Both N4 vRNAP promoters and vRNAP are injected into the host cell in inactive conformations. Host factors, DNA gyrase and EcoSSB, play a role in remodeling the N4 genome DNA to produce three hairpin-form promoters (P1, P2 and P3) that, upon binding to vRNAP, remodel the vRNAP conformation to form the transcription-ready binary complexes. EcoSSB also participates in transcription elongation as a DNA-template recycling factor. Structures of N4 mini-vRNAP in the apo-form (left, inactive) and binary complex (right, active) are shown. Color scheme is the same as in Fig. 1C.