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Canonical Modeling of the Multi-Scale Regulation of the Heat Stress Response in Yeast

Heat is one of the most fundamental and ancient environmental stresses, and response mechanisms are found in prokaryotes and shared among most eukaryotes. In the budding yeast Saccharomyces cerevisiae, the heat stress response involves coordinated changes at all biological levels, from gene expressi...

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Autores principales: Fonseca, Luis L., Chen, Po-Wei, Voit, Eberhard O.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3901190/
https://www.ncbi.nlm.nih.gov/pubmed/24957376
http://dx.doi.org/10.3390/metabo2010221
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author Fonseca, Luis L.
Chen, Po-Wei
Voit, Eberhard O.
author_facet Fonseca, Luis L.
Chen, Po-Wei
Voit, Eberhard O.
author_sort Fonseca, Luis L.
collection PubMed
description Heat is one of the most fundamental and ancient environmental stresses, and response mechanisms are found in prokaryotes and shared among most eukaryotes. In the budding yeast Saccharomyces cerevisiae, the heat stress response involves coordinated changes at all biological levels, from gene expression to protein and metabolite abundances, and to temporary adjustments in physiology. Due to its integrative multi-level-multi-scale nature, heat adaptation constitutes a complex dynamic process, which has forced most experimental and modeling analyses in the past to focus on just one or a few of its aspects. Here we review the basic components of the heat stress response in yeast and outline what has been done, and what needs to be done, to merge the available information into computational structures that permit comprehensive diagnostics, interrogation, and interpretation. We illustrate the process in particular with the coordination of two metabolic responses, namely the dramatic accumulation of the protective disaccharide trehalose and the substantial change in the profile of sphingolipids, which in turn affect gene expression. The proposed methods primarily use differential equations in the canonical modeling framework of Biochemical Systems Theory (BST), which permits the relatively easy construction of coarse, initial models even in systems that are incompletely characterized.
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spelling pubmed-39011902014-05-27 Canonical Modeling of the Multi-Scale Regulation of the Heat Stress Response in Yeast Fonseca, Luis L. Chen, Po-Wei Voit, Eberhard O. Metabolites Article Heat is one of the most fundamental and ancient environmental stresses, and response mechanisms are found in prokaryotes and shared among most eukaryotes. In the budding yeast Saccharomyces cerevisiae, the heat stress response involves coordinated changes at all biological levels, from gene expression to protein and metabolite abundances, and to temporary adjustments in physiology. Due to its integrative multi-level-multi-scale nature, heat adaptation constitutes a complex dynamic process, which has forced most experimental and modeling analyses in the past to focus on just one or a few of its aspects. Here we review the basic components of the heat stress response in yeast and outline what has been done, and what needs to be done, to merge the available information into computational structures that permit comprehensive diagnostics, interrogation, and interpretation. We illustrate the process in particular with the coordination of two metabolic responses, namely the dramatic accumulation of the protective disaccharide trehalose and the substantial change in the profile of sphingolipids, which in turn affect gene expression. The proposed methods primarily use differential equations in the canonical modeling framework of Biochemical Systems Theory (BST), which permits the relatively easy construction of coarse, initial models even in systems that are incompletely characterized. MDPI 2012-02-27 /pmc/articles/PMC3901190/ /pubmed/24957376 http://dx.doi.org/10.3390/metabo2010221 Text en © 2012 by the authors; licensee MDPI, Basel, Switzerland. http://creativecommons.org/licenses/by/3.0/ This article is an open-access article distributed under the terms and conditions of the Creative Commons Attribution license (http://creativecommons.org/licenses/by/3.0/).
spellingShingle Article
Fonseca, Luis L.
Chen, Po-Wei
Voit, Eberhard O.
Canonical Modeling of the Multi-Scale Regulation of the Heat Stress Response in Yeast
title Canonical Modeling of the Multi-Scale Regulation of the Heat Stress Response in Yeast
title_full Canonical Modeling of the Multi-Scale Regulation of the Heat Stress Response in Yeast
title_fullStr Canonical Modeling of the Multi-Scale Regulation of the Heat Stress Response in Yeast
title_full_unstemmed Canonical Modeling of the Multi-Scale Regulation of the Heat Stress Response in Yeast
title_short Canonical Modeling of the Multi-Scale Regulation of the Heat Stress Response in Yeast
title_sort canonical modeling of the multi-scale regulation of the heat stress response in yeast
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3901190/
https://www.ncbi.nlm.nih.gov/pubmed/24957376
http://dx.doi.org/10.3390/metabo2010221
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