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Temperature-Dependent Model of Multi-step Transcription Initiation in Escherichia coli Based on Live Single-Cell Measurements

Transcription kinetics is limited by its initiation steps, which differ between promoters and with intra- and extracellular conditions. Regulation of these steps allows tuning both the rate and stochasticity of RNA production. We used time-lapse, single-RNA microscopy measurements in live Escherichi...

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Autores principales: Oliveira, Samuel M. D., Häkkinen, Antti, Lloyd-Price, Jason, Tran, Huy, Kandavalli, Vinodh, Ribeiro, Andre S.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5085040/
https://www.ncbi.nlm.nih.gov/pubmed/27792724
http://dx.doi.org/10.1371/journal.pcbi.1005174
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author Oliveira, Samuel M. D.
Häkkinen, Antti
Lloyd-Price, Jason
Tran, Huy
Kandavalli, Vinodh
Ribeiro, Andre S.
author_facet Oliveira, Samuel M. D.
Häkkinen, Antti
Lloyd-Price, Jason
Tran, Huy
Kandavalli, Vinodh
Ribeiro, Andre S.
author_sort Oliveira, Samuel M. D.
collection PubMed
description Transcription kinetics is limited by its initiation steps, which differ between promoters and with intra- and extracellular conditions. Regulation of these steps allows tuning both the rate and stochasticity of RNA production. We used time-lapse, single-RNA microscopy measurements in live Escherichia coli to study how the rate-limiting steps in initiation of the P(lac/ara-1) promoter change with temperature and induction scheme. For this, we compared detailed stochastic models fit to the empirical data in maximum likelihood sense using statistical methods. Using this analysis, we found that temperature affects the rate limiting steps unequally, as nonlinear changes in the closed complex formation suffice to explain the differences in transcription dynamics between conditions. Meanwhile, a similar analysis of the P(tetA) promoter revealed that it has a different rate limiting step configuration, with temperature regulating different steps. Finally, we used the derived models to explore a possible cause for why the identified steps are preferred as the main cause for behavior modifications with temperature: we find that transcription dynamics is either insensitive or responds reciprocally to changes in the other steps. Our results suggests that different promoters employ different rate limiting step patterns that control not only their rate and variability, but also their sensitivity to environmental changes.
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spelling pubmed-50850402016-11-04 Temperature-Dependent Model of Multi-step Transcription Initiation in Escherichia coli Based on Live Single-Cell Measurements Oliveira, Samuel M. D. Häkkinen, Antti Lloyd-Price, Jason Tran, Huy Kandavalli, Vinodh Ribeiro, Andre S. PLoS Comput Biol Research Article Transcription kinetics is limited by its initiation steps, which differ between promoters and with intra- and extracellular conditions. Regulation of these steps allows tuning both the rate and stochasticity of RNA production. We used time-lapse, single-RNA microscopy measurements in live Escherichia coli to study how the rate-limiting steps in initiation of the P(lac/ara-1) promoter change with temperature and induction scheme. For this, we compared detailed stochastic models fit to the empirical data in maximum likelihood sense using statistical methods. Using this analysis, we found that temperature affects the rate limiting steps unequally, as nonlinear changes in the closed complex formation suffice to explain the differences in transcription dynamics between conditions. Meanwhile, a similar analysis of the P(tetA) promoter revealed that it has a different rate limiting step configuration, with temperature regulating different steps. Finally, we used the derived models to explore a possible cause for why the identified steps are preferred as the main cause for behavior modifications with temperature: we find that transcription dynamics is either insensitive or responds reciprocally to changes in the other steps. Our results suggests that different promoters employ different rate limiting step patterns that control not only their rate and variability, but also their sensitivity to environmental changes. Public Library of Science 2016-10-28 /pmc/articles/PMC5085040/ /pubmed/27792724 http://dx.doi.org/10.1371/journal.pcbi.1005174 Text en © 2016 Oliveira et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Oliveira, Samuel M. D.
Häkkinen, Antti
Lloyd-Price, Jason
Tran, Huy
Kandavalli, Vinodh
Ribeiro, Andre S.
Temperature-Dependent Model of Multi-step Transcription Initiation in Escherichia coli Based on Live Single-Cell Measurements
title Temperature-Dependent Model of Multi-step Transcription Initiation in Escherichia coli Based on Live Single-Cell Measurements
title_full Temperature-Dependent Model of Multi-step Transcription Initiation in Escherichia coli Based on Live Single-Cell Measurements
title_fullStr Temperature-Dependent Model of Multi-step Transcription Initiation in Escherichia coli Based on Live Single-Cell Measurements
title_full_unstemmed Temperature-Dependent Model of Multi-step Transcription Initiation in Escherichia coli Based on Live Single-Cell Measurements
title_short Temperature-Dependent Model of Multi-step Transcription Initiation in Escherichia coli Based on Live Single-Cell Measurements
title_sort temperature-dependent model of multi-step transcription initiation in escherichia coli based on live single-cell measurements
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5085040/
https://www.ncbi.nlm.nih.gov/pubmed/27792724
http://dx.doi.org/10.1371/journal.pcbi.1005174
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