Advances in biological techniques have led to the availability of genome-scale metabolic reconstructions for yeast. The size and complexity of such networks impose limits on what types of analyses one can perform. Constraint-based modelling overcomes some of these restrictions by using physicochemical constraints to describe the potential behaviour of an organism. FBA (flux balance analysis) highlights flux patterns through a network that serves to achieve a particular objective and requires a minimal amount of data to make quantitative inferences about network behaviour. Even though FBA is a powerful tool for system predictions, its general formulation sometimes results in unrealistic flux patterns. A typical example is fermentation in yeast: ethanol is produced during aerobic growth in excess glucose, but this pattern is not present in a typical FBA solution. In the present paper, we examine the issue of yeast fermentation against respiration during growth. We have studied a number of hypotheses from the modelling perspective, and novel formulations of the FBA approach have been tested. By making the observation that more respiration requires the synthesis of more mitochondria, an energy cost related to mitochondrial synthesis is added to the FBA formulation. Results, although still approximate, are closer to experimental observations than earlier FBA analyses, at least on the issue of fermentation.
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Conference Article|
September 24 2010
Why does yeast ferment? A flux balance analysis study
Evangelos Simeonidis;
Evangelos Simeonidis
1
*Manchester Centre for Integrative Systems Biology, Manchester Interdisciplinary Biocentre, 131 Princess Street, Manchester M1 7DN, U.K.
†School of Chemical Engineering and Analytical Science, University of Manchester, Oxford Road, Manchester M13 9PL, U.K.
1To whom correspondence should be addressed (email [email protected]).
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Ettore Murabito;
Ettore Murabito
†School of Chemical Engineering and Analytical Science, University of Manchester, Oxford Road, Manchester M13 9PL, U.K.
‡Doctoral Training Centre Integrative Systems Biology from Molecules to Life, Manchester Interdisciplinary Biocentre, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
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Kieran Smallbone;
Kieran Smallbone
*Manchester Centre for Integrative Systems Biology, Manchester Interdisciplinary Biocentre, 131 Princess Street, Manchester M1 7DN, U.K.
§School of Mathematics, University of Manchester, Oxford Road, Manchester M13 9PL, U.K.
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Hans V. Westerhoff
Hans V. Westerhoff
*Manchester Centre for Integrative Systems Biology, Manchester Interdisciplinary Biocentre, 131 Princess Street, Manchester M1 7DN, U.K.
†School of Chemical Engineering and Analytical Science, University of Manchester, Oxford Road, Manchester M13 9PL, U.K.
∥Department of Molecular Cell Physiology, Vrije Universiteit, de Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
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Publisher: Portland Press Ltd
Received:
March 08 2010
Online ISSN: 1470-8752
Print ISSN: 0300-5127
© The Authors Journal compilation © 2010 Biochemical Society
2010
Biochem Soc Trans (2010) 38 (5): 1225–1229.
Article history
Received:
March 08 2010
Citation
Evangelos Simeonidis, Ettore Murabito, Kieran Smallbone, Hans V. Westerhoff; Why does yeast ferment? A flux balance analysis study. Biochem Soc Trans 1 October 2010; 38 (5): 1225–1229. doi: https://doi.org/10.1042/BST0381225
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