TY - JOUR
T1 - Using Kinetic Modelling to Infer Adaptations in Saccharomyces cerevisiae Carbohydrate Storage Metabolism to Dynamic Substrate Conditions
AU - Lao-Martil, David
AU - Verhagen, Koen J. A.
AU - Valdeira Caetano, Ana H.
AU - Pardijs, Ilse H.
AU - van Riel, Natal A. W.
AU - Wahl, S. Aljoscha
N1 - Funding Information: This work is part of the project “Yeast 3M: Monitor, Model and Master the dynamics of Yeast central metabolism” (with project number 737.016.00) of the research programme “Building Blocks of Life” which is (partly) financed by the Dutch Research Council (NWO). Publisher Copyright: © 2023 by the authors.
PY - 2023/1/1
Y1 - 2023/1/1
N2 - Microbial metabolism is strongly dependent on the environmental conditions. While these can be well controlled under laboratory conditions, large-scale bioreactors are characterized by inhomogeneities and consequently dynamic conditions for the organisms. How Saccharomyces cerevisiae response to frequent perturbations in industrial bioreactors is still not understood mechanistically. To study the adjustments to prolonged dynamic conditions, we used published repeated substrate perturbation regime experimental data, extended it with proteomic measurements and used both for modelling approaches. Multiple types of data were combined; including quantitative metabolome, 13C enrichment and flux quantification data. Kinetic metabolic modelling was applied to study the relevant intracellular metabolic response dynamics. An existing model of yeast central carbon metabolism was extended, and different subsets of enzymatic kinetic constants were estimated. A novel parameter estimation pipeline based on combinatorial enzyme selection supplemented by regularization was developed to identify and predict the minimum enzyme and parameter adjustments from steady-state to dynamic substrate conditions. This approach predicted proteomic changes in hexose transport and phosphorylation reactions, which were additionally confirmed by proteome measurements. Nevertheless, the modelling also hints at a yet unknown kinetic or regulation phenomenon. Some intracellular fluxes could not be reproduced by mechanistic rate laws, including hexose transport and intracellular trehalase activity during substrate perturbation cycles.
AB - Microbial metabolism is strongly dependent on the environmental conditions. While these can be well controlled under laboratory conditions, large-scale bioreactors are characterized by inhomogeneities and consequently dynamic conditions for the organisms. How Saccharomyces cerevisiae response to frequent perturbations in industrial bioreactors is still not understood mechanistically. To study the adjustments to prolonged dynamic conditions, we used published repeated substrate perturbation regime experimental data, extended it with proteomic measurements and used both for modelling approaches. Multiple types of data were combined; including quantitative metabolome, 13C enrichment and flux quantification data. Kinetic metabolic modelling was applied to study the relevant intracellular metabolic response dynamics. An existing model of yeast central carbon metabolism was extended, and different subsets of enzymatic kinetic constants were estimated. A novel parameter estimation pipeline based on combinatorial enzyme selection supplemented by regularization was developed to identify and predict the minimum enzyme and parameter adjustments from steady-state to dynamic substrate conditions. This approach predicted proteomic changes in hexose transport and phosphorylation reactions, which were additionally confirmed by proteome measurements. Nevertheless, the modelling also hints at a yet unknown kinetic or regulation phenomenon. Some intracellular fluxes could not be reproduced by mechanistic rate laws, including hexose transport and intracellular trehalase activity during substrate perturbation cycles.
KW - Saccharomyces cerevisiae
KW - adaptation
KW - carbon storage metabolism
KW - glucose transport
KW - kinetic modeling
KW - parameter estimation
KW - repeated substrate perturbation regime
UR - http://www.scopus.com/inward/record.url?scp=85146822108&partnerID=8YFLogxK
U2 - https://doi.org/10.3390/metabo13010088
DO - https://doi.org/10.3390/metabo13010088
M3 - Article
C2 - 36677014
SN - 2218-1989
VL - 13
JO - Metabolites
JF - Metabolites
IS - 1
M1 - 88
ER -