title: Why does yeast ferment? A flux balance analysis study.
abstract: 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.
authors.affiliation: Manchester Centre for Integrative Systems Biology, Manchester Interdisciplinary Biocentre, 131 Princess Street, Manchester M1 7DN, UK. v.simeonidis@manchester.ac.uk
authors.forename: Evangelos
authors.initials: E
authors.lastname: Simeonidis
authors.forename: Ettore
authors.initials: E
authors.lastname: Murabito
authors.forename: Kieran
authors.initials: K
authors.lastname: Smallbone
authors.forename: Hans V
authors.initials: HV
authors.lastname: Westerhoff
mesh_terms: D000465:Algorithms; D019069:Cell Respiration / Q000502:physiology; D005285:Fermentation / Q000502:physiology*; D012441:Saccharomyces cerevisiae / Q000254:growth & development / Q000378:metabolism*; D049490:Systems Biology / Q000379:methods