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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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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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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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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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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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Kuijpers, N.G. (author), Solis-Escalante, D. (author), Bosman, L. (author), Van den Broek, M. (author), Pronk, J.T. (author), Daran, J.M. (author), Daran-Lapujade, P.A.S. (author)
Background: In vivo recombination of overlapping DNA fragments for assembly of large DNA constructs in the yeast Saccharomyces cerevisiae holds great potential for pathway engineering on a small laboratory scale as well as for automated high-throughput strain construction. However, the current in vivo assembly methods are not consistent with...
journal article 2013
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Knijnenburg, T.A. (author), Daran, J.M.G. (author), Van den Broek, M.A. (author), Daran-Lapujade, P.A.S. (author), De Winde, J.H. (author), Pronk, J.T. (author), Reinders, M.J.T. (author), Wessels, L.F.A. (author)
OA Fund TU delft Background: Microorganisms adapt their transcriptome by integrating multiple chemical and physical signals from their environment. Shake-flask cultivation does not allow precise manipulation of individual culture parameters and therefore precludes a quantitative analysis of the (combinatorial) influence of these parameters on...
journal article 2009
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