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Chapter 16 : How Transcription Initiation Can Be Regulated in Bacteria

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Abstract:

Most activators of transcription initiation that affect s-containing RNA polymerase (RNAP) are sequence-specific DNA-binding proteins that bind to recognition sites located upstream of the core promoter. The chapter explains the mechanism of action of one of the most thoroughly characterized activators of σ-dependent transcription in , the cyclic AMP receptor protein (CRP), also known as the catabolite activator protein. A possible explanation for the change in the kinetics of λcI-dependent activation is discussed in the chapter. The chapter talks about activators that bind to DNA and affect the process of transcription initiation by making direct contacts with RNAP. The detailed structural basis for this activator induced promoter remodeling has recently been revealed by the crystal structure of the BmrR protein, in complex with promoter DNA and a drug cofactor. In general, transcription activators that bind DNA and contact RNAP are thought to bind their specific DNA recognition sites and then, once appropriately positioned on the DNA, to interact with RNAP. The chapter discusses examples of activators that work only when bound to specific sites on the DNA, an activator that must be tethered to the DNA but remain mobile, and activators that can work directly from solution.

Citation: Dove S, Hochschild A. 2005. How Transcription Initiation Can Be Regulated in Bacteria, p 297-310. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch16

Key Concept Ranking

Core Promoter
0.4316974
Transcription Start Site
0.4287223
Upstream Promoter
0.42522633
0.4316974
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Figures

Image of Figure 1.
Figure 1.

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.

Citation: Dove S, Hochschild A. 2005. How Transcription Initiation Can Be Regulated in Bacteria, p 297-310. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch16
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Image of Figure 2.
Figure 2.

Transcription activation in bacteria. (A) RNAP (subunit composition αββ′σ) bound to α σ-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 σ-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 O2. The activating region of lcI (shaded black) is shown contacting the σ subunit.

Citation: Dove S, Hochschild A. 2005. How Transcription Initiation Can Be Regulated in Bacteria, p 297-310. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch16
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Image of Figure 3.
Figure 3.

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 σ tethered to the αNTD can activate transcription. The activating region of λcI (shaded black) is shown contacting the tethered σ moiety and stabilizing its binding to an ectopic -35 element. (C) Model for kinetic effect of λcI working at P. Activating region of λcI (shaded black) and target surface on σ (shaded black) are misaligned in the closed complex, but come into alignment during the transition to the transcriptionally active open complex.

Citation: Dove S, Hochschild A. 2005. How Transcription Initiation Can Be Regulated in Bacteria, p 297-310. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch16
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Image of Figure 4.
Figure 4.

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.

Citation: Dove S, Hochschild A. 2005. How Transcription Initiation Can Be Regulated in Bacteria, p 297-310. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch16
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Image of Figure 5.
Figure 5.

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).

Citation: Dove S, Hochschild A. 2005. How Transcription Initiation Can Be Regulated in Bacteria, p 297-310. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch16
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Image of Figure 6.
Figure 6.

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.

Citation: Dove S, Hochschild A. 2005. How Transcription Initiation Can Be Regulated in Bacteria, p 297-310. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch16
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Image of Figure 7.
Figure 7.

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 .

Citation: Dove S, Hochschild A. 2005. How Transcription Initiation Can Be Regulated in Bacteria, p 297-310. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch16
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