Glycolysis Metabolic Pathway in Saccharomyces cerevisiae

Metabolic networks are highly complex nonlinear reaction systems whose functions are tightly co-ordinated and regulated by feedback mechanisms to meet the physiological demands of living organisms. Dynamic mathematical models of metabolic networks allow prediction as to how metabolism will respond to manipulation.

In 1997, Manfred Rizzi, Michael Baltes, Uwe Theobald and Matthias Reuss published a kinetic model of glycolysis in the yeast Saccharomyces cerevisiae (see Figure 1 below). The model is based on rate equations for the individual reactions of the glycolysis pathway, and it aims to predict changes in the concentrations of intra- and extracellular metabolites after a glucose pulse. The model structure and experimental observations are related to the aerobic growth of yeast.

The kinetic equations for the various enzyme-catalysed reactions have been taken from the results of several previous studies carried out by other researchers. The reactions are diverse in nature and they include Hill kinetics, Michaelis-Menten kinetics, allosteric regulation, competitive inhibition, substrate inhibition, activation, reversible and irreversible reactions.

The complete original paper reference is cited below:

In Vivo Analysis of Metabolic Dynamics in Saccharomyces cerevisiae:II. Mathematical Model, Manfred Rizzi, Michael Baltes, Uwe Theobald and Matthias Reuss, 1997, Biotechnology and Bioengineering, 55, 592-608. (The PDF of the article is available on the Wiley InterScience website.)

The raw CellML description of the glycolysis pathway model can be downloaded in various formats as described in the section “Download This Model”. For an example of a more complete documentation of another real reaction pathway, see The Bhalla Iyengar EGF Pathway Model, 1999.

Figure 1. A rendering of the glycolysis pathway in Saccharomyces cerevisiae. Species are represented by rounded rectangles, and reactions by arrows. The action of a catalyst on a reaction is represented by dashed lines. Reactions involving adenine nucleotides and/or pyridine nucleotides are represented by dotted lines.

In CellML, models are thought of as connected networks of discrete components. These components may correspond to physiologically separated regions or chemically distinct objects, or may be useful modelling abstractions. This model has 58 components representing chemically distinct objects (25 metabolites, 16 enzymes and 17 reactions) and one component defined for modelling convenience which stores the universal variable time. Because this model has so many components, its CellML rendering would be complex. For an example of a CellML rendering of a reaction pathway see The Bhalla Iyengar EGF Pathway Model, 1999.