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From qualitative data to quantitative models: analysis of the phage shock protein stress response in Escherichia coli

BACKGROUND: Bacteria have evolved a rich set of mechanisms for sensing and adapting to adverse conditions in their environment. These are crucial for their survival, which requires them to react to extracellular stresses such as heat shock, ethanol treatment or phage infection. Here we focus on stud...

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Autores principales: Toni, Tina, Jovanovic, Goran, Huvet, Maxime, Buck, Martin, Stumpf, Michael PH
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2011
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3127791/
https://www.ncbi.nlm.nih.gov/pubmed/21569396
http://dx.doi.org/10.1186/1752-0509-5-69
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author Toni, Tina
Jovanovic, Goran
Huvet, Maxime
Buck, Martin
Stumpf, Michael PH
author_facet Toni, Tina
Jovanovic, Goran
Huvet, Maxime
Buck, Martin
Stumpf, Michael PH
author_sort Toni, Tina
collection PubMed
description BACKGROUND: Bacteria have evolved a rich set of mechanisms for sensing and adapting to adverse conditions in their environment. These are crucial for their survival, which requires them to react to extracellular stresses such as heat shock, ethanol treatment or phage infection. Here we focus on studying the phage shock protein (Psp) stress response in Escherichia coli induced by a phage infection or other damage to the bacterial membrane. This system has not yet been theoretically modelled or analysed in silico. RESULTS: We develop a model of the Psp response system, and illustrate how such models can be constructed and analyzed in light of available sparse and qualitative information in order to generate novel biological hypotheses about their dynamical behaviour. We analyze this model using tools from Petri-net theory and study its dynamical range that is consistent with currently available knowledge by conditioning model parameters on the available data in an approximate Bayesian computation (ABC) framework. Within this ABC approach we analyze stochastic and deterministic dynamics. This analysis allows us to identify different types of behaviour and these mechanistic insights can in turn be used to design new, more detailed and time-resolved experiments. CONCLUSIONS: We have developed the first mechanistic model of the Psp response in E. coli. This model allows us to predict the possible qualitative stochastic and deterministic dynamic behaviours of key molecular players in the stress response. Our inferential approach can be applied to stress response and signalling systems more generally: in the ABC framework we can condition mathematical models on qualitative data in order to delimit e.g. parameter ranges or the qualitative system dynamics in light of available end-point or qualitative information.
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spelling pubmed-31277912011-07-01 From qualitative data to quantitative models: analysis of the phage shock protein stress response in Escherichia coli Toni, Tina Jovanovic, Goran Huvet, Maxime Buck, Martin Stumpf, Michael PH BMC Syst Biol Research Article BACKGROUND: Bacteria have evolved a rich set of mechanisms for sensing and adapting to adverse conditions in their environment. These are crucial for their survival, which requires them to react to extracellular stresses such as heat shock, ethanol treatment or phage infection. Here we focus on studying the phage shock protein (Psp) stress response in Escherichia coli induced by a phage infection or other damage to the bacterial membrane. This system has not yet been theoretically modelled or analysed in silico. RESULTS: We develop a model of the Psp response system, and illustrate how such models can be constructed and analyzed in light of available sparse and qualitative information in order to generate novel biological hypotheses about their dynamical behaviour. We analyze this model using tools from Petri-net theory and study its dynamical range that is consistent with currently available knowledge by conditioning model parameters on the available data in an approximate Bayesian computation (ABC) framework. Within this ABC approach we analyze stochastic and deterministic dynamics. This analysis allows us to identify different types of behaviour and these mechanistic insights can in turn be used to design new, more detailed and time-resolved experiments. CONCLUSIONS: We have developed the first mechanistic model of the Psp response in E. coli. This model allows us to predict the possible qualitative stochastic and deterministic dynamic behaviours of key molecular players in the stress response. Our inferential approach can be applied to stress response and signalling systems more generally: in the ABC framework we can condition mathematical models on qualitative data in order to delimit e.g. parameter ranges or the qualitative system dynamics in light of available end-point or qualitative information. BioMed Central 2011-05-12 /pmc/articles/PMC3127791/ /pubmed/21569396 http://dx.doi.org/10.1186/1752-0509-5-69 Text en Copyright ©2011 Toni et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Toni, Tina
Jovanovic, Goran
Huvet, Maxime
Buck, Martin
Stumpf, Michael PH
From qualitative data to quantitative models: analysis of the phage shock protein stress response in Escherichia coli
title From qualitative data to quantitative models: analysis of the phage shock protein stress response in Escherichia coli
title_full From qualitative data to quantitative models: analysis of the phage shock protein stress response in Escherichia coli
title_fullStr From qualitative data to quantitative models: analysis of the phage shock protein stress response in Escherichia coli
title_full_unstemmed From qualitative data to quantitative models: analysis of the phage shock protein stress response in Escherichia coli
title_short From qualitative data to quantitative models: analysis of the phage shock protein stress response in Escherichia coli
title_sort from qualitative data to quantitative models: analysis of the phage shock protein stress response in escherichia coli
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3127791/
https://www.ncbi.nlm.nih.gov/pubmed/21569396
http://dx.doi.org/10.1186/1752-0509-5-69
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