Mechanism of Bacterial Transcription Initiation: RNA Polymerase - Promoter Binding, Isomerization to Initiation-competent Open Complexes, and Initiation of RNA Synthesis

Overview

Journal J Mol Biol

Publisher Elsevier

Specialties Microbiology
Molecular Biology

Date 2011 Mar 5

PMID 21371479

Citations 188

Authors

Ruth M Saecker

M Thomas Record Jr

Pieter L deHaseth

Affiliations

Soon will be listed here.

Abstract

Initiation of RNA synthesis from DNA templates by RNA polymerase (RNAP) is a multi-step process, in which initial recognition of promoter DNA by RNAP triggers a series of conformational changes in both RNAP and promoter DNA. The bacterial RNAP functions as a molecular isomerization machine, using binding free energy to remodel the initial recognition complex, placing downstream duplex DNA in the active site cleft and then separating the nontemplate and template strands in the region surrounding the start site of RNA synthesis. In this initial unstable "open" complex the template strand appears correctly positioned in the active site. Subsequently, the nontemplate strand is repositioned and a clamp is assembled on duplex DNA downstream of the open region to form the highly stable open complex, RP(o). The transcription initiation factor, σ(70), plays critical roles in promoter recognition and RP(o) formation as well as in early steps of RNA synthesis.

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References

Kontur W, Saecker R, Capp M, Record Jr M . Late steps in the formation of E. coli RNA polymerase-lambda P R promoter open complexes: characterization of conformational changes by rapid [perturbant] upshift experiments. J Mol Biol. 2008; 376(4):1034-47. PMC: 2396949. DOI: 10.1016/j.jmb.2007.11.064. View

Ghosh T, Bose D, Zhang X . Mechanisms for activating bacterial RNA polymerase. FEMS Microbiol Rev. 2010; 34(5):611-27. DOI: 10.1111/j.1574-6976.2010.00239.x. View

Lonetto M, Gribskov M, Gross C . The sigma 70 family: sequence conservation and evolutionary relationships. J Bacteriol. 1992; 174(12):3843-9. PMC: 206090. DOI: 10.1128/jb.174.12.3843-3849.1992. View

Saecker R, Tsodikov O, McQuade K, Schlax Jr P, Capp M, Record Jr M . Kinetic studies and structural models of the association of E. coli sigma(70) RNA polymerase with the lambdaP(R) promoter: large scale conformational changes in forming the kinetically significant intermediates. J Mol Biol. 2002; 319(3):649-71. DOI: 10.1016/S0022-2836(02)00293-0. View

Devi P, Campbell E, Darst S, Nickels B . Utilization of variably spaced promoter-like elements by the bacterial RNA polymerase holoenzyme during early elongation. Mol Microbiol. 2010; 75(3):607-22. PMC: 3274365. DOI: 10.1111/j.1365-2958.2009.07021.x. View

Sevim E, Gaballa A, Belduz A, Helmann J . DNA-binding properties of the Bacillus subtilis and Aeribacillus pallidus AC6 σ(D) proteins. J Bacteriol. 2010; 193(2):575-9. PMC: 3019834. DOI: 10.1128/JB.01193-10. View

Naryshkin N, Revyakin A, Kim Y, Mekler V, Ebright R . Structural organization of the RNA polymerase-promoter open complex. Cell. 2000; 101(6):601-11. DOI: 10.1016/s0092-8674(00)80872-7. View

Ross W, Schneider D, Paul B, Mertens A, Gourse R . An intersubunit contact stimulating transcription initiation by E coli RNA polymerase: interaction of the alpha C-terminal domain and sigma region 4. Genes Dev. 2003; 17(10):1293-307. PMC: 196054. DOI: 10.1101/gad.1079403. View

Hsu L, Cobb I, Ozmore J, Khoo M, Nahm G, Xia L . Initial transcribed sequence mutations specifically affect promoter escape properties. Biochemistry. 2006; 45(29):8841-54. PMC: 2528282. DOI: 10.1021/bi060247u. View

10.

Paget M, Helmann J . The sigma70 family of sigma factors. Genome Biol. 2003; 4(1):203. PMC: 151288. DOI: 10.1186/gb-2003-4-1-203. View

11.

Hudson B, Quispe J, Lara-Gonzalez S, Kim Y, Berman H, Arnold E . Three-dimensional EM structure of an intact activator-dependent transcription initiation complex. Proc Natl Acad Sci U S A. 2009; 106(47):19830-5. PMC: 2775702. DOI: 10.1073/pnas.0908782106. View

12.

Kolb A, Igarashi K, Ishihama A, Lavigne M, Buckle M, Buc H . E. coli RNA polymerase, deleted in the C-terminal part of its alpha-subunit, interacts differently with the cAMP-CRP complex at the lacP1 and at the galP1 promoter. Nucleic Acids Res. 1993; 21(2):319-26. PMC: 309109. DOI: 10.1093/nar/21.2.319. View

13.

Cowing D, Mecsas J, Record Jr M, Gross C . Intermediates in the formation of the open complex by RNA polymerase holoenzyme containing the sigma factor sigma 32 at the groE promoter. J Mol Biol. 1989; 210(3):521-30. DOI: 10.1016/0022-2836(89)90128-9. View

14.

Gourse R, Ross W, Gaal T . UPs and downs in bacterial transcription initiation: the role of the alpha subunit of RNA polymerase in promoter recognition. Mol Microbiol. 2000; 37(4):687-95. DOI: 10.1046/j.1365-2958.2000.01972.x. View

15.

Cook V, deHaseth P . Strand opening-deficient Escherichia coli RNA polymerase facilitates investigation of closed complexes with promoter DNA: effects of DNA sequence and temperature. J Biol Chem. 2007; 282(29):21319-26. DOI: 10.1074/jbc.M702232200. View

16.

Gruber T, Gross C . Multiple sigma subunits and the partitioning of bacterial transcription space. Annu Rev Microbiol. 2003; 57:441-66. DOI: 10.1146/annurev.micro.57.030502.090913. View

17.

Malhotra A, Severinova E, Darst S . Crystal structure of a sigma 70 subunit fragment from E. coli RNA polymerase. Cell. 1996; 87(1):127-36. DOI: 10.1016/s0092-8674(00)81329-x. View

18.

Kovacic R . The 0 degree C closed complexes between Escherichia coli RNA polymerase and two promoters, T7-A3 and lacUV5. J Biol Chem. 1987; 262(28):13654-61. View

19.

Busby S, Ebright R . Transcription activation by catabolite activator protein (CAP). J Mol Biol. 1999; 293(2):199-213. DOI: 10.1006/jmbi.1999.3161. View

20.

deHaseth P, Zupancic M, Record Jr M . RNA polymerase-promoter interactions: the comings and goings of RNA polymerase. J Bacteriol. 1998; 180(12):3019-25. PMC: 107799. DOI: 10.1128/JB.180.12.3019-3025.1998. View