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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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Mans, R. (author), Van Rossum, H.M. (author), Wijsman, M. (author), Backx, A. (author), Kuijpers, N.G.A. (author), van den Broek, M. (author), Daran-Lapujade, P.A.S. (author), Pronk, J.T. (author), Van Maris, A.J.A. (author), Daran, J.G. (author)
A variety of techniques for strain engineering in Saccharomyces cerevisiae have recently been developed. However, especially when multiple genetic manipulations are required, strain construction is still a time-consuming process. This study describes new CRISPR/Cas9-based approaches for easy, fast strain construction in yeast and explores their...
journal article 2015
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Romagnoli, G. (author), Verhoeven, M.D. (author), Mans, R. (author), Fleury Rey, Y. (author), Bel-Rhlid, R. (author), Van den Broek, M. (author), Maleki Seifar, R. (author), Ten Pierick, A. (author), Thompson, M. (author), Müller, V. (author), Wahl, S.A. (author), Pronk, J.T. (author), Daran, J.M. (author)
Most available knowledge on fungal arginine metabolism is derived from studies on Saccharomyces cerevisiae, in which arginine catabolism is initiated by releasing urea via the arginase reaction. Orthologues of the S. cerevisiae genes encoding the first three enzymes in the arginase pathway were cloned from Kluyveromyces lactis and shown to...
journal article 2014
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Jürgens, H. (author), Varela, Javier A. (author), Gorter de Vries, A.R. (author), Perli, T. (author), Gast, V.J.M. (author), Gyurchev, N.Y. (author), Rajkumar, Arun S. (author), Mans, R. (author), Pronk, J.T. (author), Morrissey, John P. (author), Daran, J.G. (author)
While CRISPR-Cas9-mediated genome editing has transformed yeast research, current plasmids and cassettes for Cas9 and guide-RNA expression are species specific. CRISPR tools that function in multiple yeast species could contribute to the intensifying research on non-conventional yeasts. A plasmid carrying a pangenomic origin of replication...
journal article 2018
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Marques, W.L. (author), Mans, R. (author), Marella, Eko Roy (author), Cordeiro, Rosa Lorizolla (author), van den Broek, M.A. (author), Daran, J.G. (author), Pronk, J.T. (author), Gombert, Andreas K. (author), van Maris, A.J.A. (author)
Many relevant options to improve efficacy and kinetics of sucrose metabolism in Saccharomyces cerevisiae and, thereby, the economics of sucrose-based processes remain to be investigated. An essential first step is to identify all native sucrose-hydrolysing enzymes and sucrose transporters in this yeast, including those that can be activated...
journal article 2017
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Mans, R. (author), Else-Hassing, J. (author), Wijsman, M. (author), Giezekamp, Annabel (author), Pronk, J.T. (author), Daran, J.G. (author), van Maris, A.J.A. (author)
CRISPR/Cas9-based genome editing allows rapid, simultaneous modification of multiple genetic loci in Saccharomyces cerevisiae. Here, this technique was used in a functional analysis study aimed at identifying the hitherto unknown mechanism of lactate export in this yeast. First, an S. cerevisiae strain was constructed with deletions in 25...
journal article 2017
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Marques, W.L. (author), van der Woude, L.N. (author), Luttik, M.A.H. (author), van den Broek, M.A. (author), Nijenhuis, J.M. (author), Pronk, J.T. (author), van Maris, A.J.A. (author), Mans, R. (author), Gombert, Andreas K. (author)
Knowledge on the genetic factors important for the efficient expression of plant transporters in yeast is still very limited. Phaseolus vulgaris sucrose facilitator 1 (PvSuf1), a presumable uniporter, was an essential component in a previously published strategy aimed at increasing ATP yield in Saccharomyces cerevisiae. However, attempts to...
journal article 2018
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Jürgens, H. (author), Niemeijer, M.S. (author), Jennings-Antipov, Laura D. (author), Mans, R. (author), Morel, Jack (author), van Maris, A.J.A. (author), Pronk, J.T. (author), Gardner, Timothy S. (author)
Open data in science requires precise definition of experimental procedures used in data generation, but traditional practices for sharing protocols and data cannot provide the required data contextualization. Here, we explore implementation, in an academic research setting, of a novel cloud-based software system designed to address this...
journal article 2018
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Wijsman, M. (author), Swiat, M.A. (author), Marques, W.L. (author), Hettinga, Johanna K. (author), van den Broek, M.A. (author), Torre Cortés, Pilar de la (author), Mans, R. (author), Pronk, J.T. (author), Daran, J.G. (author), Daran-Lapujade, P.A.S. (author)
Hexose transporter-deficient yeast strains are valuable testbeds for the study of sugar transport by native and heterologous transporters. In the popular Saccharomyces cerevisiae strain EBY.VW4000, deletion of 21 transporters completely abolished hexose transport. However, repeated use of the LoxP/Cre system in successive deletion rounds also...
journal article 2018
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Dekker, W.J.C. (author), Jürgens, H. (author), Ortiz Merino, R.A. (author), Mooiman, C. (author), van den Berg, Remon (author), Kaljouw, Astrid (author), Mans, R. (author), Pronk, J.T. (author)
While thermotolerance is an attractive trait for yeasts used in industrial ethanol production, oxygen requirements of known thermotolerant species are incompatible with process requirements. Analysis of oxygen-sufficient and oxygen-limited chemostat cultures of the facultatively fermentative, thermotolerant species Ogataea parapolymorpha...
journal article 2022
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van Aalst, A.C.A. (author), Jansen, Mickel L.A. (author), Mans, R. (author), Pronk, J.T. (author)
Background: Anaerobic Saccharomyces cerevisiae cultures require glycerol formation to re-oxidize NADH formed in biosynthetic processes. Introduction of the Calvin-cycle enzymes phosphoribulokinase (PRK) and ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) has been shown to couple re-oxidation of biosynthetic NADH to ethanol...
journal article 2023
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van Aalst, Aafke C.A. (author), Geraats, Ellen H. (author), Martini, M.L.A. (author), Mans, R. (author), Pronk, J.T. (author)
In anaerobic Saccharomyces cerevisiae cultures, NADH (reduced form of nicotinamide adenine dinucleotide)-cofactor balancing by glycerol formation constrains ethanol yields. Introduction of an acetate-to-ethanol reduction pathway based on heterologous acetylating acetaldehyde dehydrogenase (A-ALD) can replace glycerol formation as 'redox-sink'...
journal article 2023
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Marques, W.L. (author), Mans, R. (author), Henderson, Ryan K. (author), Marella, Eko Roy (author), ter Horst, J. (author), de Hulster, A.F. (author), Poolman, Bert (author), Daran, J.G. (author), Pronk, J.T. (author), Gombert, Andreas K. (author), van Maris, A.J.A. (author)
Anaerobic industrial fermentation processes do not require aeration and intensive mixing and the accompanying cost savings are beneficial for production of chemicals and fuels. However, the free-energy conservation of fermentative pathways is often insufficient for the production and export of the desired compounds and/or for cellular growth...
journal article 2018
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Baldi, N. (author), Dykstra, James C. (author), Luttik, M.A.H. (author), Pabst, Martin (author), Wu, Liang (author), Benjamin, Kirsten R. (author), Vente, André (author), Pronk, J.T. (author), Mans, R. (author)
Efficient production of fuels and chemicals by metabolically engineered micro-organisms requires availability of precursor molecules for product pathways. In eukaryotic cell factories, heterologous product pathways are usually expressed in the cytosol, which may limit availability of precursors that are generated in other cellular...
journal article 2019
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van Aalst, A.C.A. (author), de Valk, S.C. (author), van Gulik, W.M. (author), Jansen, Mickel L.A. (author), Pronk, J.T. (author), Mans, R. (author)
Product yield on carbohydrate feedstocks is a key performance indicator for industrial ethanol production with the yeast Saccharomyces cerevisiae. This paper reviews pathway engineering strategies for improving ethanol yield on glucose and/or sucrose in anaerobic cultures of this yeast by altering the ratio of ethanol production, yeast growth...
journal article 2022
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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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van Aalst, A.C.A. (author), van der Meulen, Igor S. (author), Jansen, Mickel L.A. (author), Mans, R. (author), Pronk, J.T. (author)
Glycerol is the major organic byproduct of industrial ethanol production with the yeast Saccharomyces cerevisiae. Improved ethanol yields have been achieved with engineered S. cerevisiae strains in which heterologous pathways replace glycerol formation as the predominant mechanism for anaerobic re-oxidation of surplus NADH generated in...
journal article 2023
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