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Dissecting the stochastic transcription initiation process in live Escherichia coli

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Dissecting the stochastic transcription initiation process in live Escherichia coli. / Lloyd-Price, Jason; Startceva, Sofia; Kandavalli, Vinodh; Chandraseelan, Jerome G.; Goncalves, Nadia; Oliveira, Samuel M.D.; Häkkinen, Antti; Sanches Ribeiro, Andre.

In: DNA Research, Vol. 23, No. 3, 29.03.2016, p. 203-214.

Research output: Contribution to journalArticleScientificpeer-review

Harvard

Lloyd-Price, J, Startceva, S, Kandavalli, V, Chandraseelan, JG, Goncalves, N, Oliveira, SMD, Häkkinen, A & Sanches Ribeiro, A 2016, 'Dissecting the stochastic transcription initiation process in live Escherichia coli', DNA Research, vol. 23, no. 3, pp. 203-214. https://doi.org/10.1093/dnares/dsw009

APA

Lloyd-Price, J., Startceva, S., Kandavalli, V., Chandraseelan, J. G., Goncalves, N., Oliveira, S. M. D., ... Sanches Ribeiro, A. (2016). Dissecting the stochastic transcription initiation process in live Escherichia coli. DNA Research, 23(3), 203-214. https://doi.org/10.1093/dnares/dsw009

Vancouver

Lloyd-Price J, Startceva S, Kandavalli V, Chandraseelan JG, Goncalves N, Oliveira SMD et al. Dissecting the stochastic transcription initiation process in live Escherichia coli. DNA Research. 2016 Mar 29;23(3):203-214. https://doi.org/10.1093/dnares/dsw009

Author

Lloyd-Price, Jason ; Startceva, Sofia ; Kandavalli, Vinodh ; Chandraseelan, Jerome G. ; Goncalves, Nadia ; Oliveira, Samuel M.D. ; Häkkinen, Antti ; Sanches Ribeiro, Andre. / Dissecting the stochastic transcription initiation process in live Escherichia coli. In: DNA Research. 2016 ; Vol. 23, No. 3. pp. 203-214.

Bibtex - Download

@article{c3b316afddd944daaafdb9a809856a75,
title = "Dissecting the stochastic transcription initiation process in live Escherichia coli",
abstract = "We investigate the hypothesis that, in Escherichia coli, while the concentration of RNA polymerases differs in different growth conditions, the fraction of RNA polymerases free for transcription remains approximately constant within a certain range of these conditions. After establishing this, we apply a standard model-fitting procedure to fully characterize the in vivo kinetics of the rate-limiting steps in transcription initiation of the Plac/ara-1 promoter from distributions of intervals between transcription events in cells with different RNA polymerase concentrations. We find that, under full induction, the closed complex lasts ∼788 s while subsequent steps last ∼193 s, on average. We then establish that the closed complex formation usually occurs multiple times prior to each successful initiation event. Furthermore, the promoter intermittently switches to an inactive state that, on average, lasts ∼87 s. This is shown to arise from the intermittent repression of the promoter by LacI. The methods employed here should be of use to resolve the rate-limiting steps governing the in vivo dynamics of initiation of prokaryotic promoters, similar to established steady-state assays to resolve the in vitro dynamics.",
author = "Jason Lloyd-Price and Sofia Startceva and Vinodh Kandavalli and Chandraseelan, {Jerome G.} and Nadia Goncalves and Oliveira, {Samuel M.D.} and Antti H{\"a}kkinen and {Sanches Ribeiro}, Andre",
year = "2016",
month = "3",
day = "29",
doi = "10.1093/dnares/dsw009",
language = "English",
volume = "23",
pages = "203--214",
journal = "DNA Research",
issn = "1340-2838",
publisher = "Oxford University Press",
number = "3",

}

RIS (suitable for import to EndNote) - Download

TY - JOUR

T1 - Dissecting the stochastic transcription initiation process in live Escherichia coli

AU - Lloyd-Price, Jason

AU - Startceva, Sofia

AU - Kandavalli, Vinodh

AU - Chandraseelan, Jerome G.

AU - Goncalves, Nadia

AU - Oliveira, Samuel M.D.

AU - Häkkinen, Antti

AU - Sanches Ribeiro, Andre

PY - 2016/3/29

Y1 - 2016/3/29

N2 - We investigate the hypothesis that, in Escherichia coli, while the concentration of RNA polymerases differs in different growth conditions, the fraction of RNA polymerases free for transcription remains approximately constant within a certain range of these conditions. After establishing this, we apply a standard model-fitting procedure to fully characterize the in vivo kinetics of the rate-limiting steps in transcription initiation of the Plac/ara-1 promoter from distributions of intervals between transcription events in cells with different RNA polymerase concentrations. We find that, under full induction, the closed complex lasts ∼788 s while subsequent steps last ∼193 s, on average. We then establish that the closed complex formation usually occurs multiple times prior to each successful initiation event. Furthermore, the promoter intermittently switches to an inactive state that, on average, lasts ∼87 s. This is shown to arise from the intermittent repression of the promoter by LacI. The methods employed here should be of use to resolve the rate-limiting steps governing the in vivo dynamics of initiation of prokaryotic promoters, similar to established steady-state assays to resolve the in vitro dynamics.

AB - We investigate the hypothesis that, in Escherichia coli, while the concentration of RNA polymerases differs in different growth conditions, the fraction of RNA polymerases free for transcription remains approximately constant within a certain range of these conditions. After establishing this, we apply a standard model-fitting procedure to fully characterize the in vivo kinetics of the rate-limiting steps in transcription initiation of the Plac/ara-1 promoter from distributions of intervals between transcription events in cells with different RNA polymerase concentrations. We find that, under full induction, the closed complex lasts ∼788 s while subsequent steps last ∼193 s, on average. We then establish that the closed complex formation usually occurs multiple times prior to each successful initiation event. Furthermore, the promoter intermittently switches to an inactive state that, on average, lasts ∼87 s. This is shown to arise from the intermittent repression of the promoter by LacI. The methods employed here should be of use to resolve the rate-limiting steps governing the in vivo dynamics of initiation of prokaryotic promoters, similar to established steady-state assays to resolve the in vitro dynamics.

U2 - 10.1093/dnares/dsw009

DO - 10.1093/dnares/dsw009

M3 - Article

VL - 23

SP - 203

EP - 214

JO - DNA Research

JF - DNA Research

SN - 1340-2838

IS - 3

ER -