Understanding start-up problems in yeast glycolysis

• Published in: Mathematical biosciences Vol. 299; pp. 117 - 126
• Main Authors: Overal, Gosse B., Teusink, Bas, Bruggeman, Frank J., Hulshof, Josephus, Planqué, Robert
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01.05.2018; Elsevier Science Ltd
• Subjects: Bifurcation analysis; Bifurcations; Biochemical pathways; Bistability; Cell death; Differential equations; Enzymes; Fluctuations; Fluxes; Glucose; Glycolysis; Intermediates; Mathematical analysis; Mathematical models; Metabolism; NADH; Nicotinamide adenine dinucleotide; Nutrient concentrations; Nutrients; Parameters; Phenotypes; Qualitative analysis; Yeast; Glycolysis; Yeast; Biochemical pathways; Bifurcation analysis; Differential equations
• ISSN: 0025-5564; 1879-3134
• DOI: 10.1016/j.mbs.2018.03.007

•We present an exhaustive steady state analysis for a core model of yeast glycolysis.•The model contains both ATP and NADH householding.•We give new insight into the bistability between regular and imbalanced states.•We explain the difference in expression levels of upper and lower glycolytic enzymes•We show how fructose-1,6-biphosphate may act as flux sensor on metabolic time scales. Yeast glycolysis has been the focus of research for decades, yet a number of dynamical aspects of yeast glycolysis remain poorly understood at present. If nutrients are scarce, yeast will provide its catabolic and energetic needs with other pathways, but the enzymes catalysing upper glycolytic fluxes are still expressed. We conjecture that this overexpression facilitates the rapid transition to glycolysis in case of a sudden increase in nutrient concentration. However, if starved yeast is presented with abundant glucose, it can enter into an imbalanced state where glycolytic intermediates keep accumulating, leading to arrested growth and cell death. The bistability between regularly functioning and imbalanced phenotypes has been shown to depend on redox balance. We shed new light on these phenomena with a mathematical analysis of an ordinary differential equation model, including NADH to account for the redox balance. In order to gain qualitative insight, most of the analysis is parameter-free, i.e., without assigning a numerical value to any of the parameters. The model has a subtle bifurcation at the switch between an inviable equilibrium state and stable flux through glycolysis. This switch occurs if the ratio between the flux through upper glycolysis and ATP consumption rate of the cell exceeds a fixed threshold. If the enzymes of upper glycolysis would be barely expressed, our model predicts that there will be no glycolytic flux, even if external glucose would be at growth-permissable levels. The existence of the imbalanced state can be found for certain parameter conditions independent of the mentioned bifurcation. The parameter-free analysis proved too complex to directly gain insight into the imbalanced states, but the starting point of a branch of imbalanced states can be shown to exist in detail. Moreover, the analysis offers the key ingredients necessary for successful numerical continuation, which highlight the existence of this bistability and the influence of the redox balance.