Koen Verhagen

Monitor, Model , Master Yeast (Yeast 3M)


Saccharomyces cerevisiae is a very common microorganism used for the production of bio-based fuels, chemicals and also foods and pharmaceuticals. Next to its industrial relevance, S. cerevisiae is also an important model organism for studying physiology, genetics and metabolic interactions of eukaryotic cells. The organism is even used as model for human metabolism (Castrillo et al., 2007). 


In our project we focus on dynamics of S. cerevisiae metabolism and its regulation that will generate significant novel insights for both industrial applications and fundamental knowledge. We aim to provide a better operational understanding of the dynamics of the central carbon metabolism of S. cerevisiae. To replicate the dynamic gradients of substrate and oxygen concentrations S. cerevisiae is subjected to in large-scale reactors, scale-down approaches will be used (Suarez Mendez et al., 2012). The response of the metabolism will be measured using quantitative metabolomics in combination with rapid sampling to capture ‘snapshots’ of the metabolism. In addition, dynamic 13C metabolomics will be used to elucidate the intracellular fluxes in the central carbon metabolism (Abate et al., 2012). To elucidate compartment-specific metabolite concentrations, equilibrium-reaction based metabolite sensors will be employed (Canelas et al., 2008).

Dynamic conditions are generated using feast/famine cultivation. Intracellular metabolites are monitored using rapid sampling, the intracellular flux will be monitored by tracer experiments (dynamic 13C flux analysis).


VU Amsterdam is the project leader, working especially on single cell analysis and development of novel intracellular sensors.

TU Eindhoven will engage with novel modelling approaches like ADAPT.

Our industrial partner DSM will perform advanced Proteomics measurements.


Abate, A., Hillen, R. C. and Wahl, S. A. (2012), Piecewise affine approximations of fluxes and enzyme kinetics from in vivo 13C labeling experiments. Int. J. Robust. Nonlinear Control, 22: 1120–1139. doi:10.1002/rnc.2798

Canelas, A. B., van Gulik, W. M. and Heijnen, J. J. (2008), Determination of the cytosolic free NAD/NADH ratio in Saccharomyces cerevisiae under steady-state and highly dynamic conditions. Biotechnol. Bioeng., 100: 734–743. doi:10.1002/bit.21813

Castrillo, J., Zeef, L., Hoyle, D., Zhang, N., Hayes, A., Gardner, D., Cornell, M., Petty, J., Hakes, L., Wardleworth, L. (2007), Growth control of the eukaryote cell: a systems biology study in yeast, Journal of Biology. 6(2): 4, doi:10.1186/jbiol54

Suarez-Mendez, C. A., Sousa, A., Heijnen, J. J. and Wahl, S. A. (2012), Fast “Feast/Famine” Cycles for Studying Microbial Physiology Under Dynamic Conditions: A Case Study with Saccharomyces cerevisiae, Metabolites, 4(2): 347-372 doi:10.3390/metabo4020347

Suarez-Mendez, C. A. (2015), Dynamics of Storage Carbohydrates Metabolism in Saccharomyces cerevisiae (Doctoral dissertation). Retrieved from TU Delft Repository, doi:10.4233/uuid:2504bd76-9811-4d3c-a66b-3aae7fbb40b5

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