Coupling σ Factor Conformation to RNA Polymerase Reorganisation for DNA Melting

Patricia C. Burrows, Nicolas Joly, Wendy V. Cannon, Beatriz P. Cámara, Mathieu Rappas, Xiaodong Zhang, Kathleen Dawes, B. Tracy Nixon, Siva R. Wigneshweraraj, Martin Buck

Research output: Contribution to journalArticle

15 Citations (Scopus)

Abstract

ATP-driven remodelling of initial RNA polymerase (RNAP) promoter complexes occurs as a major post recruitment strategy used to control gene expression. Using a model-enhancer-dependent bacterial system (σ54-RNAP, Eσ54) and a slowly hydrolysed ATP analogue (ATPγS), we provide evidence for a nucleotide-dependent temporal pathway leading to DNA melting involving a small set of σ54-DNA conformational states. We demonstrate that the ATP hydrolysis-dependent remodelling of Eσ54 occurs in at least two distinct temporal steps. The first detected remodelling phase results in changes in the interactions between the promoter specificity σ54 factor and the promoter DNA. The second detected remodelling phase causes changes in the relationship between the promoter DNA and the core RNAP catalytic β/β′ subunits, correlating with the loading of template DNA into the catalytic cleft of RNAP. It would appear that, for Eσ54 promoters, loading of template DNA within the catalytic cleft of RNAP is dependent on fast ATP hydrolysis steps that trigger changes in the β′ jaw domain, thereby allowing acquisition of the open complex status.

Original languageEnglish (US)
Pages (from-to)306-319
Number of pages14
JournalJournal of Molecular Biology
Volume387
Issue number2
DOIs
StatePublished - Mar 27 2009

Fingerprint

Nucleic Acid Denaturation
DNA-Directed RNA Polymerases
Adenosine Triphosphate
DNA
Catalytic RNA
Hydrolysis
Jaw
Catalytic Domain
Nucleotides
Gene Expression

All Science Journal Classification (ASJC) codes

  • Structural Biology
  • Molecular Biology

Cite this

Burrows, P. C., Joly, N., Cannon, W. V., Cámara, B. P., Rappas, M., Zhang, X., ... Buck, M. (2009). Coupling σ Factor Conformation to RNA Polymerase Reorganisation for DNA Melting. Journal of Molecular Biology, 387(2), 306-319. https://doi.org/10.1016/j.jmb.2009.01.052
Burrows, Patricia C. ; Joly, Nicolas ; Cannon, Wendy V. ; Cámara, Beatriz P. ; Rappas, Mathieu ; Zhang, Xiaodong ; Dawes, Kathleen ; Nixon, B. Tracy ; Wigneshweraraj, Siva R. ; Buck, Martin. / Coupling σ Factor Conformation to RNA Polymerase Reorganisation for DNA Melting. In: Journal of Molecular Biology. 2009 ; Vol. 387, No. 2. pp. 306-319.
@article{bc52b8d45de84007b070ee0e320acc7f,
title = "Coupling σ Factor Conformation to RNA Polymerase Reorganisation for DNA Melting",
abstract = "ATP-driven remodelling of initial RNA polymerase (RNAP) promoter complexes occurs as a major post recruitment strategy used to control gene expression. Using a model-enhancer-dependent bacterial system (σ54-RNAP, Eσ54) and a slowly hydrolysed ATP analogue (ATPγS), we provide evidence for a nucleotide-dependent temporal pathway leading to DNA melting involving a small set of σ54-DNA conformational states. We demonstrate that the ATP hydrolysis-dependent remodelling of Eσ54 occurs in at least two distinct temporal steps. The first detected remodelling phase results in changes in the interactions between the promoter specificity σ54 factor and the promoter DNA. The second detected remodelling phase causes changes in the relationship between the promoter DNA and the core RNAP catalytic β/β′ subunits, correlating with the loading of template DNA into the catalytic cleft of RNAP. It would appear that, for Eσ54 promoters, loading of template DNA within the catalytic cleft of RNAP is dependent on fast ATP hydrolysis steps that trigger changes in the β′ jaw domain, thereby allowing acquisition of the open complex status.",
author = "Burrows, {Patricia C.} and Nicolas Joly and Cannon, {Wendy V.} and C{\'a}mara, {Beatriz P.} and Mathieu Rappas and Xiaodong Zhang and Kathleen Dawes and Nixon, {B. Tracy} and Wigneshweraraj, {Siva R.} and Martin Buck",
year = "2009",
month = "3",
day = "27",
doi = "10.1016/j.jmb.2009.01.052",
language = "English (US)",
volume = "387",
pages = "306--319",
journal = "Journal of Molecular Biology",
issn = "0022-2836",
publisher = "Academic Press Inc.",
number = "2",

}

Burrows, PC, Joly, N, Cannon, WV, Cámara, BP, Rappas, M, Zhang, X, Dawes, K, Nixon, BT, Wigneshweraraj, SR & Buck, M 2009, 'Coupling σ Factor Conformation to RNA Polymerase Reorganisation for DNA Melting', Journal of Molecular Biology, vol. 387, no. 2, pp. 306-319. https://doi.org/10.1016/j.jmb.2009.01.052

Coupling σ Factor Conformation to RNA Polymerase Reorganisation for DNA Melting. / Burrows, Patricia C.; Joly, Nicolas; Cannon, Wendy V.; Cámara, Beatriz P.; Rappas, Mathieu; Zhang, Xiaodong; Dawes, Kathleen; Nixon, B. Tracy; Wigneshweraraj, Siva R.; Buck, Martin.

In: Journal of Molecular Biology, Vol. 387, No. 2, 27.03.2009, p. 306-319.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Coupling σ Factor Conformation to RNA Polymerase Reorganisation for DNA Melting

AU - Burrows, Patricia C.

AU - Joly, Nicolas

AU - Cannon, Wendy V.

AU - Cámara, Beatriz P.

AU - Rappas, Mathieu

AU - Zhang, Xiaodong

AU - Dawes, Kathleen

AU - Nixon, B. Tracy

AU - Wigneshweraraj, Siva R.

AU - Buck, Martin

PY - 2009/3/27

Y1 - 2009/3/27

N2 - ATP-driven remodelling of initial RNA polymerase (RNAP) promoter complexes occurs as a major post recruitment strategy used to control gene expression. Using a model-enhancer-dependent bacterial system (σ54-RNAP, Eσ54) and a slowly hydrolysed ATP analogue (ATPγS), we provide evidence for a nucleotide-dependent temporal pathway leading to DNA melting involving a small set of σ54-DNA conformational states. We demonstrate that the ATP hydrolysis-dependent remodelling of Eσ54 occurs in at least two distinct temporal steps. The first detected remodelling phase results in changes in the interactions between the promoter specificity σ54 factor and the promoter DNA. The second detected remodelling phase causes changes in the relationship between the promoter DNA and the core RNAP catalytic β/β′ subunits, correlating with the loading of template DNA into the catalytic cleft of RNAP. It would appear that, for Eσ54 promoters, loading of template DNA within the catalytic cleft of RNAP is dependent on fast ATP hydrolysis steps that trigger changes in the β′ jaw domain, thereby allowing acquisition of the open complex status.

AB - ATP-driven remodelling of initial RNA polymerase (RNAP) promoter complexes occurs as a major post recruitment strategy used to control gene expression. Using a model-enhancer-dependent bacterial system (σ54-RNAP, Eσ54) and a slowly hydrolysed ATP analogue (ATPγS), we provide evidence for a nucleotide-dependent temporal pathway leading to DNA melting involving a small set of σ54-DNA conformational states. We demonstrate that the ATP hydrolysis-dependent remodelling of Eσ54 occurs in at least two distinct temporal steps. The first detected remodelling phase results in changes in the interactions between the promoter specificity σ54 factor and the promoter DNA. The second detected remodelling phase causes changes in the relationship between the promoter DNA and the core RNAP catalytic β/β′ subunits, correlating with the loading of template DNA into the catalytic cleft of RNAP. It would appear that, for Eσ54 promoters, loading of template DNA within the catalytic cleft of RNAP is dependent on fast ATP hydrolysis steps that trigger changes in the β′ jaw domain, thereby allowing acquisition of the open complex status.

UR - http://www.scopus.com/inward/record.url?scp=61849128326&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=61849128326&partnerID=8YFLogxK

U2 - 10.1016/j.jmb.2009.01.052

DO - 10.1016/j.jmb.2009.01.052

M3 - Article

C2 - 19356588

AN - SCOPUS:61849128326

VL - 387

SP - 306

EP - 319

JO - Journal of Molecular Biology

JF - Journal of Molecular Biology

SN - 0022-2836

IS - 2

ER -

Burrows PC, Joly N, Cannon WV, Cámara BP, Rappas M, Zhang X et al. Coupling σ Factor Conformation to RNA Polymerase Reorganisation for DNA Melting. Journal of Molecular Biology. 2009 Mar 27;387(2):306-319. https://doi.org/10.1016/j.jmb.2009.01.052