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Two-step model for open complex formation. See text for details. Activators can influence open complex formation by exerting an effect at either step in the process.
Transcription activation in bacteria. (A) RNAP (subunit composition α2ββ′σ70) bound to α σ70-dependent promoter containing a -10 and a -35 element. The a subunits have been drawn to illustrate domain structure. aNTD designates the a N-terminal domain, and αCTD designates the a C-terminal domain. (B) RNAP bound to a σ70-dependent promoter containing an UP element. (C) CRP-mediated transcription activation of a class I promoter. The activating region ARI of CRP (shaded black) is shown contacting the αCTD. (D) CRP-mediated transcription activation of a class II promoter. The activating regions ARI and ARII of CRP (shaded black) are shown contacting the αCTD and the αNTD, respectively. (E) λcI-mediated transcription activation from PRM. λcI dimers are shown cooperatively bound to the operators OR1 and OR2. The activating region of lcI (shaded black) is shown contacting the σ70 subunit.
Use of artificial activators to probe activation mechanisms. (A) Interaction between protein domains X and Y can activate transcription. (B) Interaction between λcI and region 4 of σ70 tethered to the αNTD can activate transcription. The activating region of λcI (shaded black) is shown contacting the tethered σ70 moiety and stabilizing its binding to an ectopic -35 element. (C) Model for kinetic effect of λcI working at PRM. Activating region of λcI (shaded black) and target surface on σ70 (shaded black) are misaligned in the closed complex, but come into alignment during the transition to the transcriptionally active open complex.
Transcription activation and repression by p4 of bacteriophage f29. p4 activates transcription from the A3 promoter (A) and represses transcription from the A2c promoter (B). The same region of p4 (shaded black) contacts the aCTD to mediate both activation and repression.
Transcription activation by MerR. MerR (shaded gray) is shown bound to its recognition site positioned between the -10 and -35 elements of its target promoter, which are separated by a noncanonical spacer of 19 bp. Under noninducing conditions, DNA-bound MerR stabilizes the formation of a transcriptionally inactive promoter complex (top). Upon induction, MerR distorts its recognition site, bringing the −10 and −35 elements of the target promoter closer together (effectively creating a canonical 17-bp spacer) so that they can be contacted simultaneously by RNAP (bottom).
Transcription activation by an activator that is prebound to RNAP. (A) A classical activator of transcription that ordinarily binds to its specific recognition site on the DNA and then interacts with RNAP. (B) An activator such as MarA or SoxS that may ordinarily interact with RNAP prior to binding its specific recognition site on the DNA.
Transcription activator synergy. (A) Two DNA-bound CRP dimers activate transcription synergistically by contacting the aCTDs. The activating region of each CRP dimer (shaded black) is shown contacting an aCTD. (B) Regulatory region of malEp and malKp. Shown is the 271-bp regulatory region that mediates control of the divergent promoters malEp and malKp by MalT and CRP. Indicated are the -10 and -35 elements of the promoters (hatched boxes), the MalT recognition sites (pointed boxes), and the CRP recognition sites (open boxes). MalT sites 3/4/5 (shaded gray) are bound under repressing conditions, while MalT sites 1/2 and 30/40/50 (shaded black) are bound under activating conditions. Adapted from reference 80 .
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