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Microbial metabolomics: Past, present and future methodologies

Mashego, M.R. (author), Rumbold, K. (author), De Mey, M. (author), Vandamme, E. (author), Soetaert, W. (author), Heijnen, J.J. (author)

journal article 2007

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In vivo analysis of Saccharomyces cerevisiae plasma membrane ATPase Pma1p isoforms with increased in vitro H+/ATP stoichiometry

De Kok, S. (author), Yilmaz, D. (author), Daran, J.M. (author), Pronk, J.T. (author), Van Maris, A.J.A. (author)

Plasma membrane H+-ATPase isoforms with increased H+/ATP ratios represent a desirable asset in yeast metabolic engineering. In vivo proton coupling of two previously reported Pma1p isoforms (Ser800Ala, Glu803Gln) with increased in vitro H+/ATP stoichiometries was analysed by measuring biomass yields of anaerobic maltose-limited chemostat...

journal article 2012

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Pyruvate Metabolism in Saccharomyces cerevisiae

Pronk, J.T. (author), Steensma, H.Y. (author), van Dijken, J.P. (author)

journal article 1996

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Regulatory control circuits for stabilizing long-term anabolic product formation in yeast

D'Ambrosio, Vasil (author), Dore, Eleonora (author), Di Blasi, Roberto (author), van den Broek, M.A. (author), Sudarsan, Suresh (author), Horst, Jolanda ter (author), Ambri, Francesca (author), Keasling, Jay D. (author), Mans, R. (author)

Engineering living cells for production of chemicals, enzymes and therapeutics can burden cells due to use of limited native co-factor availability and/or expression burdens, totalling a fitness deficit compared to parental cells encoded through long evolutionary trajectories to maximise fitness. Ultimately, this discrepancy puts a selective...

journal article 2020

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A squalene-hopene cyclase in Schizosaccharomyces japonicus represents a eukaryotic adaptation to sterol-limited anaerobic environments

Bouwknegt, J. (author), Wiersma, S.J. (author), Ortiz Merino, R.A. (author), Doornenbal, E.S.R. (author), Buitenhuis, Petrik (author), Giera, Martin (author), Müller, Christoph (author), Pronk, J.T. (author)

Biosynthesis of sterols, which are key constituents of canonical eukaryotic membranes, requiresmolecular oxygen. Anaerobic protists and deep-branching anaerobic fungi are the only eukaryotes in which a mechanism for sterol-independent growth has been elucidated. In these organisms, tetrahymanol, formed through oxygen-independent cyclization...

journal article 2021

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Class-II dihydroorotate dehydrogenases from three phylogenetically distant fungi support anaerobic pyrimidine biosynthesis

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)

Background: In most fungi, quinone-dependent Class-II dihydroorotate dehydrogenases (DHODs) are essential for pyrimidine biosynthesis. Coupling of these Class-II DHODHs to mitochondrial respiration makes their in vivo activity dependent on oxygen availability. Saccharomyces cerevisiae and closely related yeast species harbor a cytosolic Class...

journal article 2021

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Carbon dioxide fixation via production of succinic acid from glycerol in engineered Saccharomyces cerevisiae

Malubhoy, Zahabiya (author), Bahia, Frederico Mendonça (author), de Valk, Sophie Claire (author), de Hulster, A.F. (author), Rendulić, Toni (author), Ortiz, Juan Paulo Ragas (author), Xiberras, Joeline (author), Klein, Mathias (author), Mans, R. (author), Nevoigt, Elke (author)

Background: The microbial production of succinic acid (SA) from renewable carbon sources via the reverse TCA (rTCA) pathway is a process potentially accompanied by net-fixation of carbon dioxide (CO₂). Among reduced carbon sources, glycerol is particularly attractive since it allows a nearly twofold higher CO₂-fixation...

journal article 2022

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Proteome Dynamics During Transition From Exponential to Stationary Phase Under Aerobic and Anaerobic Conditions in Yeast

den Ridder, M.J. (author), van den Brandeler, Wiebeke (author), Altiner, Meryem (author), Daran-Lapujade, P.A.S. (author), Pabst, Martin (author)

The yeast Saccharomyces cerevisiae is a widely-used eukaryotic model organism and a promising cell factory for industry. However, despite decades of research, the regulation of its metabolism is not yet fully understood, and its complexity represents a major challenge for engineering and optimizing biosynthetic routes. Recent studies have...

journal article 2023

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Maintenance-energy requirements and robustness of Saccharomyces cerevisiae at aerobic near-zero specific growth rates

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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Replacement of the initial steps of ethanol metabolism in Saccharomyces cerevisiae by ATP-independent acetylating acetaldehyde dehydrogenase

Kozak, B.U. (author), Rossum, Harmen M. (author), Niemeijer, M.S. (author), van Dijk, M. (author), Benjamin, Kirsten (author), Wu, Liang (author), Daran, J.G. (author), Pronk, J.T. (author), van Maris, A.J.A. (author)

In Saccharomyces cerevisiae ethanol dissimilation is initiated by its oxidation and activation to cytosolic acetyl-CoA. The associated consumption of ATP strongly limits yields of biomass and acetyl-CoA-derived products. Here, we explore the implementation of an ATP-independent pathway for acetyl-CoA synthesis from ethanol that, in theory,...

journal article 2016

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Improving ethanol yield in acetate-reducing Saccharomyces cerevisiae by cofactor engineering of 6-phosphogluconate dehydrogenase and deletion of ALD6

Papapetridis, I. (author), van Dijk, M. (author), Dobbe, Arthur P A (author), Metz, B. (author), Pronk, J.T. (author), van Maris, A.J.A. (author)

Background: Acetic acid, an inhibitor of sugar fermentation by yeast, is invariably present in lignocellulosic hydrolysates which are used or considered as feedstocks for yeast-based bioethanol production. Saccharomyces cerevisiae strains have been constructed, in which anaerobic reduction of acetic acid to ethanol replaces glycerol formation...

journal article 2016

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A new laboratory evolution approach to select for constitutive acetic acid tolerance in Saccharomyces cerevisiae and identification of causal mutations

Gonzalez Ramos, D. (author), Gorter de Vries, A.R. (author), Grijseels, Sietske S. (author), van Berkum, M.C. (author), Swinnen, Steve (author), van den Broek, M.A. (author), Nevoigt, Elke (author), Daran, J.G. (author), Pronk, J.T. (author), van Maris, A.J.A. (author)

Background: Acetic acid, released during hydrolysis of lignocellulosic feedstocks for second generation bioethanol production, inhibits yeast growth and alcoholic fermentation. Yeast biomass generated in a propagation step that precedes ethanol production should therefore express a high and constitutive level of acetic acid tolerance before...

journal article 2016

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Genetic bases for the metabolism of the DMS precursor S-methylmethionine by Saccharomyces cerevisiae

Eder, Matthias (author), Sanchez, Isabelle (author), Camarasa, Carole (author), Daran, J.G. (author), Legras, Jean Luc (author), Dequin, Sylvie (author)

Dimethyl sulfide (DMS) is a sulfur containing volatile that enhances general fruity aroma and imparts aromatic notes in wine. The most important precursor of DMS is S-methylmethionine (SMM), which is synthesized by grapes and can be metabolized by the yeast S. cerevisiae during wine fermentation. Precursor molecules left after fermentation...

journal article 2022

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The Penicillium chrysogenum transporter PcAraT enables high-affinity, glucose-insensitive l-arabinose transport in Saccharomyces cerevisiae

Bracher, J.M. (author), Verhoeven, M.D. (author), Wisselink, H. Wouter (author), Crimi, B. (author), Nijland, Jeroen G. (author), Driessen, Arnold J.M. (author), Klaassen, Paul (author), van Maris, A.J.A. (author), Daran, J.G. (author), Pronk, J.T. (author)

Background: l-Arabinose occurs at economically relevant levels in lignocellulosic hydrolysates. Its low-affinity uptake via the Saccharomyces cerevisiae Gal2 galactose transporter is inhibited by d-glucose. Especially at low concentrations of l-arabinose, uptake is an important rate-controlling step in the complete conversion of these...

journal article 2018

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Metabolic adjustment upon repetitive substrate perturbations using dynamic ¹³C-tracing in yeast

Suarez Mendez, C.A. (author), Ras, C. (author), Wahl, S.A. (author)

Background: Natural and industrial environments are dynamic with respect to substrate availability and other conditions like temperature and pH. Especially, metabolism is strongly affected by changes in the extracellular space. Here we study the dynamic flux of central carbon metabolism and storage carbohydrate metabolism under dynamic feast...

journal article 2017

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A systematic evaluation of yeast sample preparation protocols for spectral identifications, proteome coverage and post-isolation modifications

den Ridder, M.J. (author), Knibbe, E. (author), van den Brandeler, Wiebeke (author), Daran-Lapujade, P.A.S. (author), Pabst, Martin (author)

The importance of obtaining comprehensive and accurate information from cellular proteomics experiments asks for a systematic investigation of sample preparation protocols. In particular when working with unicellular organisms with strong cell walls, such as found in the model organism and cell factory Saccharomyces cerevisiae. Here, we...

journal article 2022

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Optimizing anaerobic growth rate and fermentation kinetics in Saccharomyces cerevisiae strains expressing Calvin-cycle enzymes for improved ethanol yield

Papapetridis, I. (author), Goudriaan, M. (author), Vazquez Vitali, M. (author), De Keijzer, Nikita A. (author), van den Broek, M.A. (author), van Maris, A.J.A. (author), Pronk, J.T. (author)

Background: Reduction or elimination of by-product formation is of immediate economic relevance in fermentation processes for industrial bioethanol production with the yeast Saccharomyces cerevisiae. Anaerobic cultures of wild-type S. cerevisiae require formation of glycerol to maintain the intracellular NADH/NAD⁺ balance....

journal article 2018

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Structural, physiological and regulatory analysis of maltose transporter genes in Saccharomyces eubayanus CBS 12357^T

Brickwedde, A. (author), Brouwers, N. (author), van den Broek, M.A. (author), Gallego Murillo, Joan Sebastián (author), Fraiture, J.L. (author), Pronk, J.T. (author), Daran, J.G. (author)

Saccharomyces pastorianus lager brewing yeasts are domesticated hybrids of Saccharomyces cerevisiae and cold-tolerant Saccharomyces eubayanus. To understand the contribution of both parental genomes to maltose metabolism in brewing wort, this study focuses on maltose transport in the S. eubayanus type strain CBS 12357^T/FM1318. To...

journal article 2018

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An engineered non-oxidative glycolytic bypass based on Calvin-cycle enzymes enables anaerobic co-fermentation of glucose and sorbitol by Saccharomyces cerevisiae

van Aalst, A.C.A. (author), Mans, R. (author), Pronk, J.T. (author)

Background: Saccharomyces cerevisiae is intensively used for industrial ethanol production. Its native fermentation pathway enables a maximum product yield of 2 mol of ethanol per mole of glucose. Based on conservation laws, supply of additional electrons could support even higher ethanol yields. However, this option is disallowed by the...

journal article 2022

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Metabolic engineering strategies for optimizing acetate reduction, ethanol yield and osmotolerance in Saccharomyces cerevisiae

Papapetridis, I. (author), van Dijk, M. (author), van Maris, A.J.A. (author), Pronk, J.T. (author)

Background: Glycerol, whose formation contributes to cellular redox balancing and osmoregulation in Saccharomyces cerevisiae, is an important by-product of yeast-based bioethanol production. Replacing the glycerol pathway by an engineered pathway for NAD⁺-dependent acetate reduction has been shown to improve ethanol yields and...

journal article 2017