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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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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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- 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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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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Bajaj, I. (author), Veiga, T. (author), Van Dissel, D. (author), Pronk, J.T. (author), Daran, J.M. (author)Background Microbial gene expression is strongly influenced by environmental growth conditions. Comparison of gene expression under different conditions is frequently used for functional analysis and to unravel regulatory networks, however, gene expression responses to co-cultivation with other microorganisms, a common occurrence in nature, is...journal article 2014
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Kozak, B.U. (author), Van Rossum, H.M. (author), Benjamin, K.R. (author), Wu, L. (author), Daran, J.G. (author), Pronk, J.T. (author), Van Maris, A.J.A. (author)Cytosolic acetyl-coenzyme A is a precursor for many biotechnologically relevant compounds produced by Saccharomyces cerevisiae. In this yeast, cytosolic acetyl-CoA synthesis and growth strictly depend on expression of either the Acs1 or Acs2 isoenzyme of acetyl-CoA synthetase (ACS). Since hydrolysis of ATP to AMP and pyrophosphate in the ACS...journal article 2013
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Oud, B. (author), Guadalupe-Medina, V. (author), Nijkamp, J.F. (author), De Ridder, D. (author), Pronk, J.T. (author), Van Maris, A.J.A. (author), Daran, J.G. (author)Laboratory evolution of the yeast Saccharomyces cerevisiae in bioreactor batch cultures yielded variants that grow as multicellular, fast-sedimenting clusters. Knowledge of the molecular basis of this phenomenon may contribute to the understanding of natural evolution of multicellularity and to manipulating cell sedimentation in laboratory and...journal article 2013
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Kuijpers, N.G.A. (author), Chroumpi, S. (author), Vos, T. (author), Solis-Escalante, D. (author), Bosman, D. (author), Pronk, J.T. (author), Daran, J.G. (author), Daran-Lapujade, P.A.S. (author)In vivo assembly of overlapping fragments by homologous recombination in Saccharomyces cerevisiae is a powerful method to engineer large DNA constructs. Whereas most in vivo assembly methods reported to date result in circular vectors, stable integrated constructs are often preferred for metabolic engineering as they are required for large-scale...journal article 2013
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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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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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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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Daran, J.M. (author), Pronk, J.T. (author)In this feature, leading researchers in the field of environmental microbiology speculate on the technical and conceptual developments that will drive innovative research and open new vistas over the next few years. For the better part of four decades, genetic engineering has relied on a universal toolbox containing three indispensable...journal article 2012
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Solis-Escalante, D. (author), Kuijpers, N.G.A. (author), Bongaerts, N. (author), Bolat, I. (author), Bosman, L. (author), Pronk, J.T. (author), Daran, J.M. (author), Daran-Lapujade, P.A.S. (author)Despite the large collection of selectable marker genes available for Saccharomyces cerevisiae, marker availability can still present a hurdle when dozens of genetic manipulations are required. Recyclable markers, counterselectable cassettes that can be removed from the targeted genome after use, are therefore valuable assets in ambitious...journal article 2012
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Koopman, F.W. (author), Beekwilder, J. (author), Crimi, B. (author), Van Houwelingen, A. (author), Hall, R.D. (author), Bosch, D. (author), Van Maris, A.J.A. (author), Pronk, J.T. (author), Daran, J.M. (author)Background Flavonoids comprise a large family of secondary plant metabolic intermediates that exhibit a wide variety of antioxidant and human health-related properties. Plant production of flavonoids is limited by the low productivity and the complexity of the recovered flavonoids. Thus to overcome these limitations, metabolic engineering of...journal article 2012
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Oud, B. (author), Flores, C.L. (author), Gancedo, C. (author), Zhang, X. (author), Trueheart, J. (author), Daran, J.M. (author), Pronk, J.T. (author), Van Maris, A.J.A. (author)Background Pyruvate-decarboxylase negative (Pdc-) strains of Saccharomyces cerevisiae combine the robustness and high glycolytic capacity of this yeast with the absence of alcoholic fermentation. This makes Pdc-S. cerevisiae an interesting platform for efficient conversion of glucose towards pyruvate-derived products without formation of ethanol...journal article 2012
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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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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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Veiga, T. (author), Nijland, J.G. (author), Driessen, A.J.M. (author), Bovenberg, R.A.L. (author), Touw, H. (author), Van den Berg, M.A. (author), Pronk, J.T. (author), Daran, J.M. (author)The multicomponent global regulator Velvet complex has been identified as a key regulator of secondary metabolite production in Aspergillus and Penicillium species. Previous work indicated a massive impact of PcvelA and PclaeA deletions on penicillin production in prolonged batch cultures of P. chrysogenum, as well as substantial changes in...journal article 2012
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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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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