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- Weusthuis, R.A. (author), Visser, W. (author), Pronk, J.T. (author), Scheffers, W.A. (author), Van Dijken, J.P. (author) journal article 1994
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Abbott, D.A. (author), Knijnenburg, T.A. (author), De Poorter, L.M. (author), Reinders, M.J. (author), Pronk, J.T. (author), Van Maris, A.J. (author)Transcriptional responses to four weak organic acids (benzoate, sorbate, acetate and propionate) were investigated in anaerobic, glucose-limited chemostat cultures of Saccharomyces cerevisiae. To enable quantitative comparison of the responses to the acids, their concentrations were chosen such that they caused a 50% decrease of the biomass...journal article 2007
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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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Solis-Escalante, D. (author), Kuijpers, N.G.A. (author), Bongaerts, N. (author), Bolat, I. (author), Bosman, L. (author), Pronk, J.T. (author), Daran, J.M. (author), Daran-Lapujade, P.A.S. (author)Despite the large collection of selectable marker genes available for Saccharomyces cerevisiae, marker availability can still present a hurdle when dozens of genetic manipulations are required. Recyclable markers, counterselectable cassettes that can be removed from the targeted genome after use, are therefore valuable assets in ambitious...journal article 2012
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Guadalupe-Medina, V. (author), Wisselink, H.W. (author), Luttik, M.A.H. (author), De Hulster, E. (author), Daran, J.M. (author), Pronk, J.T. (author), Van Maris, A.J.A. (author)Background Redox-cofactor balancing constrains product yields in anaerobic fermentation processes. This challenge is exemplified by the formation of glycerol as major by-product in yeast-based bioethanol production, which is a direct consequence of the need to reoxidize excess NADH and causes a loss of conversion efficiency. Enabling the use of...journal article 2013
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Milne, N. (author), Luttik, M.A.H. (author), Cueto Rojas, H.F. (author), Wahl, A. (author), Van Maris, A.J.A. (author), Pronk, J.T. (author), Daran, J.G. (author)In microbial processes for production of proteins, biomass and nitrogen-containing commodity chemicals, ATP requirements for nitrogen assimilation affect product yields on the energy producing substrate. In Saccharomyces cerevisiae, a current host for heterologous protein production and potential platform for production of nitrogen-containing...journal article 2015
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Rossum, Harmen M. (author), Kozak, B.U. (author), Niemeijer, M.S. (author), Duine, Hendrik J. (author), Luttik, M.A.H. (author), Boer, VM (author), Kötter, P (author), Daran, J.G. (author), van Maris, A.J.A. (author), Pronk, J.T. (author)Pyruvate and acetyl-coenzyme A, located at the interface between glycolysis and TCA cycle, are important intermediates in yeast metabolism and key precursors for industrially relevant products. Rational engineering of their supply requires knowledge of compensatory reactions that replace predominant pathways when these are inactivated. This...journal article 2016
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Badia, Mariana Beatriz (author), Mans, R. (author), Lis, A.V. (author), Tronconi, Marcos Ariel (author), Arias, Cintia Lucía (author), Maurino, Verónica Graciela (author), Andreo, Carlos Santiago (author), Drincovich, María Fabiana (author), van Maris, A.J.A. (author), Gerrard Wheeler, Mariel Claudia (author)NAD(P)-malic enzyme (NAD(P)-ME) catalyzes the reversible oxidative decarboxylation of malate to pyruvate, CO<sub>2</sub>, and NAD(P)H and is present as a multigene family in Arabidopsis thaliana. The carboxylation reaction catalyzed by purified recombinant Arabidopsis NADP-ME proteins is faster than those reported for other animal or plant...journal article 2017
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Salazar, A.N. (author), Gorter de Vries, A.R. (author), van den Broek, M.A. (author), Wijsman, M. (author), de la Torre, P. (author), Brickwedde, A. (author), Brouwers, N. (author), Daran, J.G. (author), Abeel, T.E.P.M.F. (author)The haploid Saccharomyces cerevisiae strain CEN.PK113–7D is a popular model system for metabolic engineering and systems biology research. Current genome assemblies are based on short-read sequencing data scaffolded based on homology to strain S288C. However, these assemblies contain large sequence gaps, particularly in subtelomeric regions, and...journal article 2017
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Wahl, S.A. (author), Bernal Martinez, C. (author), Zhao, Zheng (author), van Gulik, W.M. (author), Jansen, Mickel L.A. (author)Background: The metabolic engineering of Saccharomyces cerevisiae for the production of succinic acid has progressed dramatically, and a series of high-producing hosts are available. At low cultivation pH and high titers, the product transport can become bidirectional, i.e. the acid is reentering the cell and is again exported or even...journal article 2017
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Bracher, J.M. (author), de Hulster, A.F. (author), Koster, C.C. (author), van den Broek, M.A. (author), Daran, J.G. (author), van Maris, A.J.A. (author), Pronk, J.T. (author)Biotin prototrophy is a rare, incompletely understood, and industrially relevant characteristic of Saccharomyces cerevisiae strains. The genome of the haploid laboratory strain CEN.PK113-7D contains a full complement of biotin biosynthesis genes, but its growth in biotin-free synthetic medium is extremely slow (specific growth rate [μ] ≈ 0.01...journal article 2017
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Boonekamp, F.J. (author), Dashko, S. (author), van den Broek, M.A. (author), Gehrmann, T. (author), Daran, J.G. (author), Daran-Lapujade, P.A.S. (author)The ability of the yeast Saccharomyces cerevisiae to convert glucose, even in the presence of oxygen, via glycolysis and the fermentative pathway to ethanol has played an important role in its domestication. Despite the extensive knowledge on these pathways in S. cerevisiae, relatively little is known about their genetic makeup in other...journal article 2018
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Perez-Samper, Gemma (author), Cerulus, Bram (author), Jariani, Abbas (author), Vermeersch, Lieselotte (author), Barrajon Simancas, N. (author), Bisschops, M.M.M. (author), van den Brink, Joost (author), Solis Escalante, D. (author), Gallone, Brigida (author), De Maeyer, Dries (author), Daran-Lapujade, P.A.S. (author)When faced with environmental changes, microbes often enter a temporary growth arrest during which they reprogram the expression of specific genes to adapt to the new conditions. A prime example of such a lag phase occurs when microbes need to switch from glucose to other, less-preferred carbon sources. Despite its industrial relevance, the...journal article 2018
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Levisson, Mark (author), Patinios, Constantinos (author), Hein, Sascha (author), de Groot, P.A. (author), Daran, J.G. (author), Martens, Stefan (author), Hall, Robert D. (author), Beekwilder, Jules (author)Background: Anthocyanins are polyphenolic pigments which provide pink to blue colours in fruits and flowers. There is an increasing demand for anthocyanins, as food colorants and as health-promoting substances. Plant production of anthocyanins is often seasonal and cannot always meet demand due to low productivity and the complexity of the...journal article 2018
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Levisson, Mark (author), Araya-Cloutier, Carla (author), De Bruijn, Wouter J.C. (author), Van Der Heide, Menno (author), Salvador López, José Manuel (author), Daran, J.G. (author), Vincken, Jean Paul (author), Beekwilder, Jules (author)Prenylated flavonoids possess a wide variety of biological activities, including estrogenic, antioxidant, antimicrobial, and anticancer activities. Hence, they have potential applications in food products, medicines, or supplements with health-promoting activities. However, the low abundance of prenylated flavonoids in nature is limiting...journal article 2019
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Else-Hassing, J. (author), de Groot, P.A. (author), Marquenie, Vita R. (author), Pronk, J.T. (author), Daran, J.G. (author)The organic compound 2-phenylethanol (2PE) has a pleasant floral scent and is intensively used in the cosmetic and food industries. Microbial production of 2PE by phenylalanine bioconversion or de novo biosynthesis from sugar offer sustainable, reliable and natural production processes compared to chemical synthesis. Despite the ability of...journal article 2019
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Hajian, Christopher Sarkizi Shams (author), Haringa, C. (author), Noorman, H.J. (author), Takors, Ralf (author)Scaling up bioprocesses is one of the most crucial steps in the commercialization of bioproducts. While it is known that concentration and shear rate gradients occur at larger scales, it is often too risky, if feasible at all, to conduct validation experiments at such scales. Using computational fluid dynamics equipped with mechanistic...journal article 2020
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Perli, T. (author), Wronska, A.K. (author), Ortiz Merino, R.A. (author), Pronk, J.T. (author), Daran, J.G. (author)Chemically defined media for yeast cultivation (CDMY) were developed to support fast growth, experimental reproducibility, and quantitative analysis of growth rates and biomass yields. In addition to mineral salts and a carbon substrate, popular CDMYs contain seven to nine B-group vitamins, which are either enzyme cofactors or precursors for...journal article 2020
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Boonekamp, F.J. (author), Dashko, S. (author), Duiker, Donna (author), Gehrmann, T. (author), van den Broek, M.A. (author), den Ridder, M.J. (author), Pabst, Martin (author), Robert, Vincent (author), Abeel, T.E.P.M.F. (author), Postma, E.D. (author), Daran, J.G. (author), Daran-Lapujade, P.A.S. (author)The construction of powerful cell factories requires intensive and extensive remodelling of microbial genomes. Considering the rapidly increasing number of these synthetic biology endeavors, there is an increasing need for DNA watermarking strategies that enable the discrimination between synthetic and native gene copies. While it is well...journal article 2020
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Wiersma, S.J. (author), Mooiman, C. (author), Giera, Martin (author), Pronk, J.T. (author)Biosynthesis of sterols, which are considered essential components of virtually all eukaryotic membranes, requires molecular oxygen. Anaerobic growth of the yeast Saccharomyces cerevisiae therefore strictly depends on sterol supplementation of synthetic growth media. Neocallimastigomycota are a group of strictly anaerobic fungi which, instead...journal article 2020
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