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De novo sequencing, assembly and analysis of the genome of the laboratory strain Saccharomyces cerevisiae CEN.PK113-7D, a model for modern industrial biotechnology

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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Engineering Acetyl Coenzyme A Supply: Functional Expression of a Bacterial Pyruvate Dehydrogenase Complex in the Cytosol of Saccharomyces cerevisiae

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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Regulation of alcohol-oxidizing capacity in chemostat cultures of Acetobacter pasteurianus

Salgueiro Machado, S. (author), Luttik, M.A.H. (author), van Dijken, J.P. (author), Jongejan, J.A. (author), Pronk, J.T. (author)

journal article 1995

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Overproduction of Threonine Aldolase Circumvents the Biosynthetic Role of Pyruvate Decarboxylase in Glucose-Limited Chemostat Cultures of Saccharomyces cerevisiae

van Maris, A.J. (author), Luttik, M.A. (author), Winkler, A.A. (author), van Dijken, J.P. (author), Pronk, J.T. (author)

journal article 2003

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Metabolic Engineering of Glycerol Production in Saccharomyces cerevisiae

Overkamp, K.M. (author), Bakker, B.M. (author), Kotter, P. (author), Luttik, M.A. (author), Van Dijken, J.P. (author), Pronk, J.T. (author)

journal article 2002

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Transcriptome-Based Characterization of Interactions between Saccharomyces cerevisiae and Lactobacillus delbrueckii subsp. bulgaricus in Lactose-Grown Chemostat Cocultures

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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The fluxes through glycolytic enzymes in Saccharomyces cerevisiae are predominantly regulated at posttranscriptional levels

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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The Mitochondrial Alcohol Dehydrogenase Adh3p Is Involved in a Redox Shuttle in Saccharomyces cerevisiae

Bakker, B.M. (author), Bro, C. (author), Kotter, P. (author), Luttik, M.A. (author), van Dijken, J.P. (author), Pronk, J.T. (author)

journal article 2000

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Substrate Specificity of Thiamine Pyrophosphate-Dependent 2-Oxo-Acid Decarboxylases in Saccharomyces cerevisiae

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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Functional expression of a heterologous nickel-dependent, ATP-independent urease in Saccharomyces cerevisiae

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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Carbon dioxide fixation by Calvin-Cycle enzymes improves ethanol yield in yeast

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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Control of the Glycolytic Flux in Saccharomyces cerevisiae Grown at Low Temperature: A multi-level analysis in anaerobic chemostat cultures

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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Novel Pathway for Alcoholic Fermentation of delta-Gluconolactone in the Yeast Saccharomyces bulderi

van Dijken, J.P. (author), van Tuijl, A. (author), Luttik, M.A. (author), Middelhoven, W.J. (author), Pronk, J.T. (author)

journal article 2002

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Chromosomal Copy Number Variation in Saccharomyces pastorianus Is Evidence for Extensive Genome Dynamics in Industrial Lager Brewing Strains

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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The Saccharomyces cerevisiae ICL2 Gene Encodes a Mitochondrial 2-Methylisocitrate Lyase Involved in Propionyl-Coenzyme A Metabolism

Luttik, M.A. (author), Kotter, P. (author), Salomons, F.A. (author), van der Klei, I.J. (author), van Dijken, J.P. (author), Pronk, J.T. (author)

journal article 2000

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Identity of the Growth-Limiting Nutrient Strongly Affects Storage Carbohydrate Accumulation in Anaerobic Chemostat Cultures of Saccharomyces cerevisiae

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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Physiological Characterization of the ARO10-Dependent, Broad-Substrate-Specificity 2-Oxo Acid Decarboxylase Activity of Saccharomyces cerevisiae

Vuralhan, Z. (author), Luttik, M.A. (author), Tai, S.L. (author), Boer, V.M. (author), Morais, M.A. (author), Schipper, D. (author), Almering, M.J. (author), Kotter, P. (author), Dickinson, J.R. (author), Daran, J.M. (author), Pronk, J.T. (author)

journal article 2005

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Metabolic engineering of ?-oxidation in Penicillium chrysogenum for improved semi-synthetic cephalosporin biosynthesis

Veiga, T. (author), Gombert, A.K. (author), Landes, N. (author), Verhoeven, M.D. (author), Kiel, J.A.K.W. (author), Krikken, A. (author), Nijland, J.G. (author), Touw, H. (author), Luttik, M.A.H. (author), Van der Toorn, J.C. (author), Driessen, A.J.M. (author), Bovenberg, R.A.L. (author), Van den Berg, M.A. (author), Van der Klei, I.J. (author), Pronk, J.T. (author), Daran, J.M. (author)

Industrial production of semi-synthetic cephalosporins by Penicillium chrysogenum requires supplementation of the growth media with the side-chain precursor adipic acid. In glucose-limited chemostat cultures of P. chrysogenum, up to 88% of the consumed adipic acid was not recovered in cephalosporin-related products, but used as an additional...

journal article 2012

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Engineering acetyl coenzyme A supply: Functional expression of a bacterial pyruvate dehydrogenase complex in the cytosol of Saccharomyces cerevisiae

Kozak, B.U. (author), Van Rossum, M.H. (author), Luttik, M.A. (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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Correction to: Class‑II dihydroorotate dehydrogenases from three phylogenetically distant fungi support anaerobic pyrimidine biosynthesis (Fungal Biology and Biotechnology, (2021), 8, 1, (10), 10.1186/s40694-021-00117-4)

Bouwknegt, J. (author), Koster, C.C. (author), Vos, A.M. (author), Ortiz Merino, R.A. (author), Wassink, Mats (author), Luttik, M.A.H. (author), van den Broek, M.A. (author), Hagedoorn, P.L. (author), Pronk, J.T. (author)

Following publication of the original article [1], the authors reported errors in the text of the Results section and in Table 2. It refers to a mutation in a yeast gene as VPS1^I410L and to the corresponding change in the Vps1 amino-acid sequence as I410L. The correct descriptions should read VPS1^I401L and I401L,...

journal article 2021