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Boender, L.G.M. (author), De Hulster, E.A.F. (author), Van Maris, A.J.A. (author), Daran-Lapujade, P.A.S. (author), Pronk, J.T. (author)
Growth at near-zero specific growth rates is a largely unexplored area of yeast physiology. To investigate the physiology of Saccharomyces cerevisiae under these conditions, the effluent removal pipe of anaerobic, glucose-limited chemostat culture (dilution rate, 0.025 h–1) was fitted with a 0.22-µm-pore-size polypropylene filter unit. This...
journal article 2009
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Tai, S.L. (author), Daran-Lapujade, P. (author), Luttik, M.A. (author), Walsh, M.C. (author), Diderich, J.A. (author), Krijger, G.C. (author), Van Gulik, W.M. (author), Pronk, J.T. (author), Daran, J.M. (author)
journal article 2007
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Nijkamp, J.F. (author), Van den Broek, M.A. (author), Datema, E. (author), De Kok, S. (author), Bosman, L. (author), Luttik, M.A.H. (author), Daran-Lapujade, P.A.S. (author), Vongsangnak, W. (author), Nielsen, J. (author), Heijne, W.H.M. (author), Klaassen, P. (author), Paddon, C.J. (author), Platt, D. (author), Kötter, P. (author), Van Ham, R.C. (author), Reinders, M.J.T. (author), Pronk, J.T. (author), De Ridder, D. (author), Daran, J.M. (author)
Saccharomyces cerevisiae CEN.PK 113-7D is widely used for metabolic engineering and systems biology research in industry and academia. We sequenced, assembled, annotated and analyzed its genome. Single-nucleotide variations (SNV), insertions/deletions (indels) and differences in genome organization compared to the reference strain S. cerevisiae...
journal article 2012
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Vos, T. (author), Hakkaart, X.D.V. (author), de Hulster, A.F. (author), van Maris, A.J.A. (author), Pronk, J.T. (author), Daran-Lapujade, P.A.S. (author)
Background: Saccharomyces cerevisiae is an established microbial platform for production of native and non-native compounds. When product pathways compete with growth for precursors and energy, uncoupling of growth and product formation could increase product yields and decrease formation of biomass as a by-product. Studying non-growing,...
journal article 2016
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Van Den Brink, J. (author), Daran-Lapujade, P. (author), Pronk, J.T. (author), De Winde, J.H. (author)
OA Fund
journal article 2008
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Knijnenburg, T.A. (author), De Winde, J.H. (author), Daran, J.M. (author), Daran-Lapujade, P. (author), Pronk, J.T. (author), Reinders, M.J.T. (author), Wessels, L.F.A. (author)
journal article 2007
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Mendes, F. (author), Sieuwerts, S. (author), De Hulster, E. (author), Almering, M.J. (author), Luttik, M.A. (author), Pronk, J.T. (author), Smid, E.J. (author), Bron, P.A. (author), Daran-Lapujade, P. (author)
Mixed populations of Saccharomyces cerevisiae yeasts and lactic acid bacteria occur in many dairy, food, and beverage fermentations, but knowledge about their interactions is incomplete. In the present study, interactions between Saccharomyces cerevisiae and Lactobacillus delbrueckii subsp. bulgaricus, two microorganisms that co-occur in kefir...
journal article 2013
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Rebnegger, C. (author), Vos, T. (author), Graf, Alexandra B. (author), Valli, Minoska (author), Pronk, J.T. (author), Daran-Lapujade, P.A.S. (author), Mattanovicha, Diethard (author)
The yeast Pichia pastoris is a widely used host for recombinant protein production. Understanding its physiology at extremely low growth rates is a first step in the direction of decoupling product formation from cellular growth and therefore of biotechnological relevance. Retentostat cultivation is an excellent tool for studying microbes at...
journal article 2016
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Knijnenburg, T.A. (author), De Winde, J.H. (author), Daran, J.M. (author), Daran-Lapujade, P. (author), Pronk, J.T. (author), Reinders, M.J.T. (author), Wessels, L.F.A. (author)
journal article 2007
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Daran, J.M. (author), Bakker, B.M. (author), Pronk, J.T. (author), Westerhoff, H.V. (author), De Winde, J.H. (author), Heck, A.J.R. (author), Slijper, M. (author), De Groot, M.J.L. (author), Luttik, M.A.H. (author), Van Gulik, W.M. (author), Rossell, S. (author), Daran-Lapujade, P. (author)
Metabolic fluxes may be regulated ‘‘hierarchically,’’ e.g., by changes of gene expression that adjust enzyme capacities (Vmax) and/or ‘‘metabolically’’ by interactions of enzymes with substrates, products, or allosteric effectors. In the present study, a method is developed to dissect the hierarchical regulation into contributions by...
journal article 2007
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Vos, T. (author), De la Torre Cortes, P. (author), Van Gulik, W.M. (author), Pronk, J.T. (author), Daran-Lapujade, P.A.S. (author)
Introduction: Saccharomyces cerevisiae has become a popular host for production of non-native compounds. The metabolic pathways involved generally require a net input of energy. To maximize the ATP yield on sugar in S. cerevisiae, industrial cultivation is typically performed in aerobic, sugar-limited fed-batch reactors which, due to constraints...
journal article 2015
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Hebly, M. (author), De Ridder, D. (author), De Hulster, E.A. (author), De la Torre Cortes, P. (author), Pronk, J.T. (author), Daran-Lapujade, P.A.S. (author)
Diurnal temperature cycling is an intrinsic characteristic of many exposed microbial ecosystems. However, its influence on yeast physiology and the yeast transcriptome has not been studied in detail. In this study, 24-h sinusoidal temperature cycles, oscillating between 12°C and 30°C, were imposed on anaerobic, glucose-limited chemostat cultures...
journal article 2014
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Jansen, M.L.A. (author), Daran-Lapujade, P. (author), de Winde, J.H. (author), Piper, M.D. (author), Pronk, J.T. (author)
journal article 2004
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Heijnen, J.J. (author), Daran, J.M. (author), Pronk, J.T. (author), Daran-Lapujade, P. (author), Knijnenburg, T.A. (author), Ras, C. (author), Ten Pierick, A. (author), Akmering, M.J. (author), Van Winden, W.A. (author), Kresnowati, M.T. (author)
Within the first 5 min after a sudden relief from glucose limitation, Saccharomyces cerevisiae exhibited fast changes of intracellular metabolite levels and a major transcriptional reprogramming. Integration of transcriptome and metabolome data revealed tight relationships between the changes at these two levels. Transcriptome as well as...
journal article 2006
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Jansen, M.L.A. (author), Diderich, J.A. (author), Mashego, M. (author), Hassane, A. (author), de Winde, J.H. (author), Daran-Lapujade, P. (author), Pronk, J.T. (author)
journal article 2005
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Fazio, A. (author), Jewett, M.C. (author), Daran-Lapujade, P. (author), Mustacchi, R. (author), Usaite, R. (author), Pronk, J.T. (author), Workman, C.T. (author), Nielsen, J. (author)
journal article 2008
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Kuijpers, N.G.A. (author), Chroumpi, S. (author), Vos, T. (author), Solis-Escalante, D. (author), Bosman, D. (author), Pronk, J.T. (author), Daran, J.G. (author), Daran-Lapujade, P.A.S. (author)
In vivo assembly of overlapping fragments by homologous recombination in Saccharomyces cerevisiae is a powerful method to engineer large DNA constructs. Whereas most in vivo assembly methods reported to date result in circular vectors, stable integrated constructs are often preferred for metabolic engineering as they are required for large-scale...
journal article 2013
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Hazelwood, L.A. (author), Walsh, M.C. (author), Luttik, M.A.H. (author), Daran-Lapujade, P. (author), Pronk, J.T. (author), Daran, J.M. (author)
OA Fund TU Delft Accumulation of glycogen and trehalose in nutrient-limited cultures of Saccharomyces cerevisiae is negatively correlated with the specific growth rate. Additionally, glucose-excess conditions (i.e., growth limitation by nutrients other than glucose) are often implicated in high-level accumulation of these storage carbohydrates....
journal article 2009
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Boender, L.G.M. (author), Van Maris, A.J.A. (author), De Hulster, E.A.F. (author), Almering, M.J.H. (author), Van der Klei, I.J. (author), Veenhuis, M. (author), De Winde, J.H. (author), Pronk, J.T. (author), Daran-Lapujade, P.A.S. (author)
Extremely low specific growth rates (below 0.01 h?1) represent a largely unexplored area of microbial physiology. In this study, anaerobic, glucose-limited retentostats were used to analyse physiological and genome-wide transcriptional responses of Saccharomyces cerevisiae to cultivation at near-zero specific growth rates. While quiescence is...
journal article 2011
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Tai, S.L. (author), Daran-Lapujade, P. (author), Walsh, M.C. (author), Pronk, J.T. (author), Daran, J.M. (author)
Effects of suboptimal temperatures on transcriptional regulation in yeast have been extensively studied in batch cultures. To eliminate indirect effects of specific growth rates that are inherent to batch-cultivation studies, genome-wide transcriptional responses to low temperatures were analyzed in steady-state chemostats, grown at a fixed...
journal article 2007
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