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Postma, E.D. (author), Else-Hassing, J. (author), Mangkusaputra, Venda (author), Geelhoed, J. (author), de la Torre, P. (author), van den Broek, M.A. (author), Mooiman, C. (author), Pabst, Martin (author), Daran, J.G. (author), Daran-Lapujade, P.A.S. (author)The construction of powerful cell factories requires intensive genetic engineering for the addition of new functionalities and the remodeling of native pathways and processes. The present study demonstrates the feasibility of extensive genome reprogramming using modular, specialized de novo-assembled neochromosomes in yeast. The in vivo...journal article 2022
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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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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<sup>I410L</sup> and to the corresponding change in the Vps1 amino-acid sequence as I410L. The correct descriptions should read VPS1<sup>I401L</sup> and I401L,...journal article 2021
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Wronska, A.K. (author), van den Broek, M.A. (author), Perli, T. (author), de Hulster, A.F. (author), Pronk, J.T. (author), Daran, J.G. (author)An oxygen requirement for de novo biotin synthesis in Saccharomyces cerevisiae precludes the application of biotin-prototrophic strains in anoxic processes that use biotin-free media. To overcome this issue, this study explores introduction of the oxygen-independent Escherichia coli biotin-biosynthesis pathway in S. cerevisiae. Implementation...journal article 2021
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A supernumerary designer chromosome for modular in vivo pathway assembly in Saccharomyces cerevisiaePostma, E.D. (author), Dashko, S. (author), van Breemen, Lars (author), Taylor Parkins, S.K. (author), van den Broek, M.A. (author), Daran, J.G. (author), Daran-Lapujade, P.A.S. (author)The construction of microbial cell factories for sustainable production of chemicals and pharmaceuticals requires extensive genome engineering. Using Saccharomyces cerevisiae, this study proposes synthetic neochromosomes as orthogonal expression platforms for rewiring native cellular processes and implementing new functionalities....journal article 2021
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Perli, T. (author), van der Vorm, Daan N.A. (author), Wassink, Mats (author), van den Broek, M.A. (author), Pronk, J.T. (author), Daran, J.G. (author)Metabolic capabilities of cells are not only defined by their repertoire of enzymes and metabolites, but also by availability of enzyme cofactors. The molybdenum cofactor (Moco) is widespread among eukaryotes but absent from the industrial yeast Saccharomyces cerevisiae. No less than 50 Moco-dependent enzymes covering over 30 catalytic...journal article 2021
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Valk, L.C. (author), Luttik, M.A.H. (author), de Ram, C. (author), Pabst, M. (author), van den Broek, M.A. (author), van Loosdrecht, Mark C.M. (author), Pronk, J.T. (author)D-galacturonate, a key constituent of pectin, is a ubiquitous monomer in plant biomass. Anaerobic, fermentative conversion of D-galacturonate is therefore relevant in natural environments as well as in microbial processes for microbial conversion of pectin-containing agricultural residues. In currently known microorganisms that anaerobically...journal article 2020
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Frederick, Joni (author), Hennessy, Fritha (author), Horn, Uli (author), de la Torre Cortés, Pilar (author), van den Broek, M.A. (author), Strych, Ulrich (author), Willson, Richard (author), Daran, J.G. (author), Otten, L.G. (author)BACKGROUND: Rhodococci are industrially important soil-dwelling Gram-positive bacteria that are well known for both nitrile hydrolysis and oxidative metabolism of aromatics. Rhodococcus rhodochrous ATCC BAA-870 is capable of metabolising a wide range of aliphatic and aromatic nitriles and amides. The genome of the organism was sequenced and...journal article 2020
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Perli, T. (author), Moonen, Dewi P.I. (author), van den Broek, M.A. (author), Pronk, J.T. (author), Daran, J.G. (author)Quantitative physiological studies on Saccharomyces cerevisiae commonly use synthetic media (SM) that contain a set of water-soluble growth factors that, based on their roles in human nutrition, are referred to as B vitamins. Previous work demonstrated that in S. cerevisiae CEN. PK113-7D, requirements for biotin were eliminated by laboratory...journal article 2020
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Wronska, A.K. (author), Haak, Meinske P. (author), Geraats, Ellen (author), Bruins Slot, Eva (author), van den Broek, M.A. (author), Pronk, J.T. (author), Daran, J.G. (author)Biotin, an important cofactor for carboxylases, is essential for all kingdoms of life. Since native biotin synthesis does not always suffice for fast growth and product formation, microbial cultivation in research and industry often requires supplementation of biotin. De novo biotin biosynthesis in yeasts is not fully understood, which...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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Gorter de Vries, A.R. (author), Knibbe, E. (author), van Roosmalen, Roderick (author), van den Broek, M.A. (author), de la Torre, P. (author), O’Herne, Stephanie F. (author), Vijverberg, Pascal A. (author), el Masoudi, Anissa (author), Brouwers, N. (author), Pronk, J.T. (author), Daran, J.G. (author)The lager-brewing yeast Saccharomyces pastorianus is a hybrid between S. cerevisiae and S. eubayanus with an exceptional degree of aneuploidy. While chromosome copy number variation (CCNV) is present in many industrial Saccharomyces strains and has been linked to various industrially-relevant traits, its impact on the brewing performance of S...journal article 2020
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Busch, H. (author), Tonin, F. (author), Alvarenga Da Silva, N. (author), van den Broek, M.A. (author), Lu, Simona (author), Daran, J.G. (author), Hanefeld, U. (author), Hagedoorn, P.L. (author)Oleate hydratases (Ohys, EC 4.2.1.53) are a class of enzymes capable of selective water addition reactions to a broad range of unsaturated fatty acids leading to the respective chiral alcohols. Much research was dedicated to improving the applications of existing Ohys as well as to the identification of undescribed Ohys with potentially novel...journal article 2020
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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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de Jong, S.I. (author), van den Broek, M.A. (author), Merkel, Alexander Y. (author), de la Torre Cortes, Pilar (author), Kalamorz, Falk (author), Cook, Gregory M. (author), van Loosdrecht, Mark C.M. (author), McMillan, D.G.G. (author)The aerobic thermoalkaliphile Caldalkalibacillus thermarum strain TA2.A1 is a member of a separate order of alkaliphilic bacteria closely related to the Bacillales order. Efforts to relate the genomic information of this evolutionary ancient organism to environmental adaptation have been thwarted by the inability to construct a complete...journal article 2020
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Salazar, A.N. (author), Gorter de Vries, A.R. (author), van den Broek, M.A. (author), Brouwers, N. (author), de la Torre, P. (author), Kuijpers, N.G.A. (author), Daran, J.G. (author), Abeel, T.E.P.M.F. (author)Background: The lager brewing yeast, S. pastorianus, is a hybrid between S. cerevisiae and S. eubayanus with extensive chromosome aneuploidy. S. pastorianus is subdivided into Group 1 and Group 2 strains, where Group 2 strains have higher copy number and a larger degree of heterozygosity for S. cerevisiae chromosomes. As a result, Group 2...journal article 2019
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Brouwers, N. (author), Gorter de Vries, A.R. (author), van den Broek, M.A. (author), Weening, S.M. (author), Elink Schuurman, Tom D. (author), Kuijpers, Niels G.A. (author), Pronk, J.T. (author), Daran, J.G. (author)Saccharomyces eubayanus is the non-S. cerevisiae parent of the lager-brewing hybrid S. pastorianus. In contrast to most S. cerevisiae and Frohberg-type S. pastorianus strains, S. eubayanus cannot utilize the α-tri-glucoside maltotriose, a major carbohydrate in brewer's wort. In Saccharomyces yeasts, utilization of maltotriose is encoded by...journal article 2019
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Gorter de Vries, A.R. (author), Voskamp, Maaike (author), van Aalst, Aafke (author), Kristensen, L.H. (author), Jansen, Liset (author), Salazar, A.N. (author), van den Broek, M.A. (author), Brouwers, N. (author), Abeel, T.E.P.M.F. (author), Pronk, J.T. (author), Daran, J.G. (author)Saccharomyces pastorianus lager-brewing yeasts are domesticated hybrids of S. cerevisiae x S. eubayanus that display extensive inter-strain chromosome copy number variation and chromosomal recombinations. It is unclear to what extent such genome rearrangements are intrinsic to the domestication of hybrid brewing yeasts and whether they...journal article 2019
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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<sup>+</sup> balance....journal article 2018
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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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