Metabolites 2012, 2(1), 221-241; doi:10.3390/metabo2010221
Article

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

1,2email, 2email and 2,* email
Received: 30 December 2011; in revised form: 8 February 2012 / Accepted: 10 February 2012 / Published: 27 February 2012
(This article belongs to the Special Issue Metabolic Network Models)
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Abstract: 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.
Keywords: biochemical systems theory; canonical modeling; dynamical model; heat stress; metabolic regulation; multi-scale control; sphingolipid metabolism; systems biology; trehalose
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MDPI and ACS Style

Fonseca, L.L.; Chen, P.-W.; Voit, E.O. Canonical Modeling of the Multi-Scale Regulation of the Heat Stress Response in Yeast. Metabolites 2012, 2, 221-241.

AMA Style

Fonseca LL, Chen P-W, Voit EO. Canonical Modeling of the Multi-Scale Regulation of the Heat Stress Response in Yeast. Metabolites. 2012; 2(1):221-241.

Chicago/Turabian Style

Fonseca, Luis L.; Chen, Po-Wei; Voit, Eberhard O. 2012. "Canonical Modeling of the Multi-Scale Regulation of the Heat Stress Response in Yeast." Metabolites 2, no. 1: 221-241.


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