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Initial events in bacterial transcription initiation.

Ruff EF, Record MT, Artsimovitch I - Biomolecules (2015)

Bottom Line: At some promoters, this initial open complex is greatly stabilized by rearrangements of the discriminator region between the -10 element and +1 base of the nontemplate strand and of mobile in-cleft and downstream elements of RNAP.Intrinsic DNA opening-closing appears less regulated.This noncovalent mechanism and its regulation exhibit many analogies to mechanisms of enzyme catalysis.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry, University of Wisconsin-Madison, 1101 University Ave. Madison, Madison, WI 53706, USA. eruff@wisc.edu.

ABSTRACT
Transcription initiation is a highly regulated step of gene expression. Here, we discuss the series of large conformational changes set in motion by initial specific binding of bacterial RNA polymerase (RNAP) to promoter DNA and their relevance for regulation. Bending and wrapping of the upstream duplex facilitates bending of the downstream duplex into the active site cleft, nucleating opening of 13 bp in the cleft. The rate-determining opening step, driven by binding free energy, forms an unstable open complex, probably with the template strand in the active site. At some promoters, this initial open complex is greatly stabilized by rearrangements of the discriminator region between the -10 element and +1 base of the nontemplate strand and of mobile in-cleft and downstream elements of RNAP. The rate of open complex formation is regulated by effects on the rapidly-reversible steps preceding DNA opening, while open complex lifetime is regulated by effects on the stabilization of the initial open complex. Intrinsic DNA opening-closing appears less regulated. This noncovalent mechanism and its regulation exhibit many analogies to mechanisms of enzyme catalysis.

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Related in: MedlinePlus

Sequence-specific interactions between σ70 RNAP and regions of the promoter. Schematic representations of the subunits of RNAP core, σ70, and promoter DNA. RNAP: α2: cyan; β and β': gray; ω: black. σ regions: as shown. Promoter: UP element: cyan; −35 element: blue; extended −10: red; −10 element: yellow; discriminator: orange; transcription start site: green; DNA downstream of the transcription start site: gray. Linker regions in α and σ subunits are shown as springs. Nontemplate strand sequences of a “consensus” and λPR, T7A1 and rrnB P1 promoters are shown below; missing bases are indicated by dashes.
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biomolecules-05-01035-f001: Sequence-specific interactions between σ70 RNAP and regions of the promoter. Schematic representations of the subunits of RNAP core, σ70, and promoter DNA. RNAP: α2: cyan; β and β': gray; ω: black. σ regions: as shown. Promoter: UP element: cyan; −35 element: blue; extended −10: red; −10 element: yellow; discriminator: orange; transcription start site: green; DNA downstream of the transcription start site: gray. Linker regions in α and σ subunits are shown as springs. Nontemplate strand sequences of a “consensus” and λPR, T7A1 and rrnB P1 promoters are shown below; missing bases are indicated by dashes.

Mentions: Transcription is the first step of gene expression and is therefore one of the most fundamental processes of life. All living organisms, as well as many viruses, encode at least one RNA polymerase (RNAP) enzyme that synthesizes an RNA copy of the template DNA; the core structure and many mechanistic and regulatory elements are shared by bacterial, eukaryotic and archaeal RNAPs (reviewed in [1,2]). Bacterial RNAPs are composed of a core enzyme, which carries out RNA synthesis, and a specificity (σ) subunit for recognition of promoter DNA sequence and subsequent events of initiation (Figure 1 and Figure 2). Specific binding to promoter DNA forms an initial closed complex and sets in motion a series of large conformational changes which bend the downstream duplex DNA into the active site cleft of RNAP and then open the DNA to form a transcription bubble, placing the template DNA strand into the active site. At some (but not all) promoters, subsequent conformational changes in RNAP and the nontemplate strand stabilize this initial open complex (reviewed in [3]). Many steps of this process are highly regulated by promoter DNA sequence, accessory protein factors and small ligands, nucleotide concentration, temperature, salt and solute concentrations, and other environmental variables; aspects of regulation are reviewed in [1,4,5,6,7].


Initial events in bacterial transcription initiation.

Ruff EF, Record MT, Artsimovitch I - Biomolecules (2015)

Sequence-specific interactions between σ70 RNAP and regions of the promoter. Schematic representations of the subunits of RNAP core, σ70, and promoter DNA. RNAP: α2: cyan; β and β': gray; ω: black. σ regions: as shown. Promoter: UP element: cyan; −35 element: blue; extended −10: red; −10 element: yellow; discriminator: orange; transcription start site: green; DNA downstream of the transcription start site: gray. Linker regions in α and σ subunits are shown as springs. Nontemplate strand sequences of a “consensus” and λPR, T7A1 and rrnB P1 promoters are shown below; missing bases are indicated by dashes.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4496709&req=5

biomolecules-05-01035-f001: Sequence-specific interactions between σ70 RNAP and regions of the promoter. Schematic representations of the subunits of RNAP core, σ70, and promoter DNA. RNAP: α2: cyan; β and β': gray; ω: black. σ regions: as shown. Promoter: UP element: cyan; −35 element: blue; extended −10: red; −10 element: yellow; discriminator: orange; transcription start site: green; DNA downstream of the transcription start site: gray. Linker regions in α and σ subunits are shown as springs. Nontemplate strand sequences of a “consensus” and λPR, T7A1 and rrnB P1 promoters are shown below; missing bases are indicated by dashes.
Mentions: Transcription is the first step of gene expression and is therefore one of the most fundamental processes of life. All living organisms, as well as many viruses, encode at least one RNA polymerase (RNAP) enzyme that synthesizes an RNA copy of the template DNA; the core structure and many mechanistic and regulatory elements are shared by bacterial, eukaryotic and archaeal RNAPs (reviewed in [1,2]). Bacterial RNAPs are composed of a core enzyme, which carries out RNA synthesis, and a specificity (σ) subunit for recognition of promoter DNA sequence and subsequent events of initiation (Figure 1 and Figure 2). Specific binding to promoter DNA forms an initial closed complex and sets in motion a series of large conformational changes which bend the downstream duplex DNA into the active site cleft of RNAP and then open the DNA to form a transcription bubble, placing the template DNA strand into the active site. At some (but not all) promoters, subsequent conformational changes in RNAP and the nontemplate strand stabilize this initial open complex (reviewed in [3]). Many steps of this process are highly regulated by promoter DNA sequence, accessory protein factors and small ligands, nucleotide concentration, temperature, salt and solute concentrations, and other environmental variables; aspects of regulation are reviewed in [1,4,5,6,7].

Bottom Line: At some promoters, this initial open complex is greatly stabilized by rearrangements of the discriminator region between the -10 element and +1 base of the nontemplate strand and of mobile in-cleft and downstream elements of RNAP.Intrinsic DNA opening-closing appears less regulated.This noncovalent mechanism and its regulation exhibit many analogies to mechanisms of enzyme catalysis.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry, University of Wisconsin-Madison, 1101 University Ave. Madison, Madison, WI 53706, USA. eruff@wisc.edu.

ABSTRACT
Transcription initiation is a highly regulated step of gene expression. Here, we discuss the series of large conformational changes set in motion by initial specific binding of bacterial RNA polymerase (RNAP) to promoter DNA and their relevance for regulation. Bending and wrapping of the upstream duplex facilitates bending of the downstream duplex into the active site cleft, nucleating opening of 13 bp in the cleft. The rate-determining opening step, driven by binding free energy, forms an unstable open complex, probably with the template strand in the active site. At some promoters, this initial open complex is greatly stabilized by rearrangements of the discriminator region between the -10 element and +1 base of the nontemplate strand and of mobile in-cleft and downstream elements of RNAP. The rate of open complex formation is regulated by effects on the rapidly-reversible steps preceding DNA opening, while open complex lifetime is regulated by effects on the stabilization of the initial open complex. Intrinsic DNA opening-closing appears less regulated. This noncovalent mechanism and its regulation exhibit many analogies to mechanisms of enzyme catalysis.

Show MeSH
Related in: MedlinePlus