Tampere University of Technology

TUTCRIS Research Portal

Effects of σ factor competition are promoter initiation kinetics dependent

Research output: Contribution to journalArticleScientificpeer-review

Standard

Effects of σ factor competition are promoter initiation kinetics dependent. / Kandavalli, Vinodh K.; Tran, Huy; Ribeiro, Andre S.

In: Biochimica et Biophysica Acta: Gene Regulatory Mechanisms, Vol. 1859, No. 10, 01.10.2016, p. 1281-1288.

Research output: Contribution to journalArticleScientificpeer-review

Harvard

Kandavalli, VK, Tran, H & Ribeiro, AS 2016, 'Effects of σ factor competition are promoter initiation kinetics dependent', Biochimica et Biophysica Acta: Gene Regulatory Mechanisms, vol. 1859, no. 10, pp. 1281-1288. https://doi.org/10.1016/j.bbagrm.2016.07.011

APA

Kandavalli, V. K., Tran, H., & Ribeiro, A. S. (2016). Effects of σ factor competition are promoter initiation kinetics dependent. Biochimica et Biophysica Acta: Gene Regulatory Mechanisms, 1859(10), 1281-1288. https://doi.org/10.1016/j.bbagrm.2016.07.011

Vancouver

Kandavalli VK, Tran H, Ribeiro AS. Effects of σ factor competition are promoter initiation kinetics dependent. Biochimica et Biophysica Acta: Gene Regulatory Mechanisms. 2016 Oct 1;1859(10):1281-1288. https://doi.org/10.1016/j.bbagrm.2016.07.011

Author

Kandavalli, Vinodh K. ; Tran, Huy ; Ribeiro, Andre S. / Effects of σ factor competition are promoter initiation kinetics dependent. In: Biochimica et Biophysica Acta: Gene Regulatory Mechanisms. 2016 ; Vol. 1859, No. 10. pp. 1281-1288.

Bibtex - Download

@article{3d680d4eae5645c796c943324e797a2c,
title = "Effects of σ factor competition are promoter initiation kinetics dependent",
abstract = "In Escherichia coli, the expression of a σ factor is expected to indirectly down-regulate the expression of genes recognized by another σ factor, due to σ factor competition for a limited pool of RNA polymerase core enzymes. Evidence suggests that the sensitivity of genes to indirect down-regulation differs widely. We studied the variability in this sensitivity in promoters primarily recognized by RNAP holoenzymes carrying σ70. From qPCR and live single-cell, single-RNA measurements of the transcription kinetics of several σ70-dependent promoters in various conditions and from the analysis of σ factors population-dependent models of transcription initiation, we find that, the smaller is the time-scale of the closed complex formation relative to the open complex formation, the weaker is a promoter's responsiveness to changes in σ38 numbers. We conclude that, in E. coli, a promoter's responsiveness to indirect regulation by σ factor competition is determined by the sequence-dependent kinetics of the rate limiting steps of transcription initiation.",
keywords = "Closed Complex Formation, In vivo Transcription dynamics, Open Complex Formation, Single RNA detection, σ Factors competition",
author = "Kandavalli, {Vinodh K.} and Huy Tran and Ribeiro, {Andre S.}",
year = "2016",
month = "10",
day = "1",
doi = "10.1016/j.bbagrm.2016.07.011",
language = "English",
volume = "1859",
pages = "1281--1288",
journal = "Biochimica et Biophysica Acta: Gene Regulatory Mechanisms",
issn = "1874-9399",
publisher = "Elsevier",
number = "10",

}

RIS (suitable for import to EndNote) - Download

TY - JOUR

T1 - Effects of σ factor competition are promoter initiation kinetics dependent

AU - Kandavalli, Vinodh K.

AU - Tran, Huy

AU - Ribeiro, Andre S.

PY - 2016/10/1

Y1 - 2016/10/1

N2 - In Escherichia coli, the expression of a σ factor is expected to indirectly down-regulate the expression of genes recognized by another σ factor, due to σ factor competition for a limited pool of RNA polymerase core enzymes. Evidence suggests that the sensitivity of genes to indirect down-regulation differs widely. We studied the variability in this sensitivity in promoters primarily recognized by RNAP holoenzymes carrying σ70. From qPCR and live single-cell, single-RNA measurements of the transcription kinetics of several σ70-dependent promoters in various conditions and from the analysis of σ factors population-dependent models of transcription initiation, we find that, the smaller is the time-scale of the closed complex formation relative to the open complex formation, the weaker is a promoter's responsiveness to changes in σ38 numbers. We conclude that, in E. coli, a promoter's responsiveness to indirect regulation by σ factor competition is determined by the sequence-dependent kinetics of the rate limiting steps of transcription initiation.

AB - In Escherichia coli, the expression of a σ factor is expected to indirectly down-regulate the expression of genes recognized by another σ factor, due to σ factor competition for a limited pool of RNA polymerase core enzymes. Evidence suggests that the sensitivity of genes to indirect down-regulation differs widely. We studied the variability in this sensitivity in promoters primarily recognized by RNAP holoenzymes carrying σ70. From qPCR and live single-cell, single-RNA measurements of the transcription kinetics of several σ70-dependent promoters in various conditions and from the analysis of σ factors population-dependent models of transcription initiation, we find that, the smaller is the time-scale of the closed complex formation relative to the open complex formation, the weaker is a promoter's responsiveness to changes in σ38 numbers. We conclude that, in E. coli, a promoter's responsiveness to indirect regulation by σ factor competition is determined by the sequence-dependent kinetics of the rate limiting steps of transcription initiation.

KW - Closed Complex Formation

KW - In vivo Transcription dynamics

KW - Open Complex Formation

KW - Single RNA detection

KW - σ Factors competition

U2 - 10.1016/j.bbagrm.2016.07.011

DO - 10.1016/j.bbagrm.2016.07.011

M3 - Article

VL - 1859

SP - 1281

EP - 1288

JO - Biochimica et Biophysica Acta: Gene Regulatory Mechanisms

JF - Biochimica et Biophysica Acta: Gene Regulatory Mechanisms

SN - 1874-9399

IS - 10

ER -