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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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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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Kozak, B.U. (author), Van Rossum, H.M. (author), Luttik, M.A.H. (author), Akeroyd, M. (author), Benjamin, K.R. (author), Wu, L. (author), De Vries, S. (author), Daran, J.M. (author), Pronk, J.T. (author), Van Maris, A.J.A. (author)
The energetic (ATP) cost of biochemical pathways critically determines the maximum yield of metabolites of vital or commercial relevance. Cytosolic acetyl coenzyme A (acetyl-CoA) is a key precursor for biosynthesis in eukaryotes and for many industrially relevant product pathways that have been introduced into Saccharomyces cerevisiae, such as...
journal article 2014
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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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Hazelwood, L.A. (author), Walsh, M.C. (author), Pronk, J.T. (author), Daran, J.M. (author)
The hop plant, Humulus lupulus L., has an exceptionally high content of secondary metabolites, the hop -acids, which possess a range of beneficial properties, including antiseptic action. Studies performed on the mode of action of hop iso--acids have hitherto been restricted to lactic acid bacteria. The present study investigated molecular...
journal article 2009
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Harris, D.M. (author), Van der Krogt, Z.A. (author), Klaassen, P. (author), Raamsdonk, L.M. (author), Hage, S. (author), Van den Berg, M.A. (author), Bovenberg, R.A.L. (author), Pronk, J.T. (author), Daran, J.M. (author)
OA Fund TU Delft Background Since the discovery of the antibacterial activity of penicillin by Fleming 80 years ago, improvements of penicillin titer were essentially achieved by classical strain improvement through mutagenesis and screening. The recent sequencing of Penicillium chrysogenum strain Wisconsin1255-54 and the availability of...
journal article 2009
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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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Kozak, B.U. (author), Van Rossum, H.M. (author), Benjamin, K.R. (author), Wu, L. (author), Daran, J.G. (author), Pronk, J.T. (author), Van Maris, A.J.A. (author)
Cytosolic acetyl-coenzyme A is a precursor for many biotechnologically relevant compounds produced by Saccharomyces cerevisiae. In this yeast, cytosolic acetyl-CoA synthesis and growth strictly depend on expression of either the Acs1 or Acs2 isoenzyme of acetyl-CoA synthetase (ACS). Since hydrolysis of ATP to AMP and pyrophosphate in the ACS...
journal article 2013
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De Kok, S. (author), Marques, W.L. (author), Mans, R. (author), Yilmaz, D. (author), Suir, E. (author), Pronk, J.T. (author), Gombert, A.K. (author), Daran, J.M. (author), Van Maris, A.J.A. (author)
journal article 2014
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Romagnoli, G. (author), Luttik, M.A.H. (author), Kötter, P. (author), Pronk, J.T. (author), Daran, J.M. (author)
Fusel alcohols are precursors and contributors to flavor and aroma compounds in fermented beverages, and some are under investigation as biofuels. The decarboxylation of 2-oxo acids is a key step in the Ehrlich pathway for fusel alcohol production. In Saccharomyces cerevisiae, five genes share sequence similarity with genes encoding thiamine...
journal article 2012
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Hazelwood, L.A. (author), Daran, J.M. (author), Van Maris, A.J.A. (author), Pronk, J.T. (author), Dickinson, J.R. (author)
journal article 2008
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Bajaj, I. (author), Veiga, T. (author), Van Dissel, D. (author), Pronk, J.T. (author), Daran, J.M. (author)
Background Microbial gene expression is strongly influenced by environmental growth conditions. Comparison of gene expression under different conditions is frequently used for functional analysis and to unravel regulatory networks, however, gene expression responses to co-cultivation with other microorganisms, a common occurrence in nature, is...
journal article 2014
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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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Gonzalez-Ramos, D. (author), Van den Broek, M. (author), Van Maris, A.J.A. (author), Pronk, J.T. (author), Daran, J.M.G. (author)
Background n-Butanol and isobutanol produced from biomass-derived sugars are promising renewable transport fuels and solvents. Saccharomyces cerevisiae has been engineered for butanol production, but its high butanol sensitivity poses an upper limit to product titers that can be reached by further pathway engineering. A better understanding of...
journal article 2013
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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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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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Solis-Escalante, D. (author), Kuijpers, N.G.A. (author), Barrajon-Simancas, N. (author), Van den Broek, M. (author), Pronk, J.T. (author), Daran, J.M. (author), Daran-Lapujade, P. (author)
As a result of ancestral whole-genome and small-scale duplication events, the genomes of Saccharomyces cerevisiae and many eukaryotes still contain a substantial fraction of duplicated genes. In all investigated organisms, metabolic pathways, and more particularly glycolysis, are specifically enriched for functionally redundant paralogs. In...
journal article 2015
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Veiga, T. (author), Solis-Escalante, D. (author), Romagnoli, G. (author), Ten Pierick, A. (author), Hanemaaijer, M. (author), Deshmuhk, A. (author), Wahl, A. (author), Pronk, J.T. (author), Daran, J.M. (author)
The industrial production of penicillin G by Penicillium chrysogenum requires the supplementation of the growth medium with the side chain precursor phenylacetate. The growth of P. chrysogenum with phenylalanine as the sole nitrogen source resulted in the extracellular production of phenylacetate and penicillin G. To analyze this natural pathway...
journal article 2011
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Oud, B. (author), Flores, C.L. (author), Gancedo, C. (author), Zhang, X. (author), Trueheart, J. (author), Daran, J.M. (author), Pronk, J.T. (author), Van Maris, A.J.A. (author)
Background Pyruvate-decarboxylase negative (Pdc-) strains of Saccharomyces cerevisiae combine the robustness and high glycolytic capacity of this yeast with the absence of alcoholic fermentation. This makes Pdc-S. cerevisiae an interesting platform for efficient conversion of glucose towards pyruvate-derived products without formation of ethanol...
journal article 2012
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Van den Broek, M. (author), Bolat, I. (author), Nijkamp, J.F. (author), Ramos, E. (author), Luttik, M.A.H. (author), Koopman, F. (author), Geertman, J.M. (author), De Ridder, D. (author), Pronk, J.T. (author), Daran, J.M. (author)
Lager brewing strains of Saccharomyces pastorianus are natural interspecific hybrids originating from the spontaneous hybridization of Saccharomyces cerevisiae and Saccharomyces eubayanus. Over the past 500 years, S. pastorianus has been domesticated to become one of the most important industrial microorganisms. Production of lager-type beers...
journal article 2015
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