Summary of the intermediates in the process of initiation of RNA synthesis for which structural and/or kinetic evidence has been obtained; see the text for details. The complexes are shown in cartoon form at the top with a descriptive notation below. In the designation of structurally characterized complexes, R stands for RNA polymerase, P stands for promoter DNA, and c and o indicate closed and open complexes, respectively (where strand separation has not or has occurred, respectively). I₁ and I₂ are the kinetically significant intermediates, shown by DNA footprinting to be RP_c2-like complexes. AP stands for abortive RNA product, and TC stands for the transcribing complex in elongation mode. Also indicated are examples of agents or conditions that can affect (inhibit or activate) the interconversion of intermediates; some of these (CRP, cI, and arc) have different effects, depending on the promoter or RNA polymerase. Some are E. coli proteins: the lac repressor (LacR [78]), CRP (which activates different processes, depending on the promoter [18, 34, 52, 55, 62]), and elongation factors GreA and GreB (which can affect promoter escape in vitro [36]). Phage-encoded proteins cI (lambda) and arc (P22) display polymerase- or promoter-dependent effects: cI inhibits the binding of a mutant RNA polymerase (mut RNAP) (49) but affects I₁-I₂ isomerization with wild-type RNA polymerase (31); arc represses wild-type promoters by slowing I₁-I₂ isomerization but activates a consensus promoter mutant by accelerating clearance (85). Rifampin is an antibiotic which targets the β subunit of RNA polymerase; heparin binds and inactivates free RNA polymerase. The latter two agents have been useful tools in the study of RNA polymerase-promoter interactions. Growth rate control (20) and reiterative (Reit.) RNA synthesis (synth.) (50) are responsive to NTP levels (see text).

Summary of RNA polymerase-promoter interactions. A promoter with consensus sequences for the −10 and −35 regions (boxed) is shown; the sequences of actual promoters deviate from those shown here. In general, the more closely a promoter resembles the one shown, the stronger (more active) the promoter will be. Also shown is the TGN sequence just upstream of the −10 region; together, they comprise an “extended” −10 region which has promoter activity even in the absence of a −35 sequence. The model of RNA polymerase shown is based on recently available evidence (27, 60, 98); however, it is intended to show contacts between the subunits and promoter DNA and not necessarily to reflect the precise orientation of the subunits. The “jaws” of RNA polymerase are shown on the right of the molecule. This region of the RNA polymerase would grasp the DNA downstream of the catalytic site. Contacts between RNA polymerase and promoter DNA are shown by the solid lines. Not all contacts occur in every RNA polymerase-promoter interaction, but in all known cases (including promoters activated by regulator proteins), at a minimum, some contacts between ς and the −10 region appear to be required.