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Chromosomal Copy Number Variation in Saccharomyces pastorianus Is Evidence for Extensive Genome Dynamics in Industrial Lager Brewing Strains

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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Effect of sludge age on methanogenic and glycogen accumulating organisms in an aerobic granular sludge process fed with methanol and acetate

Pronk, M. (author), Abbas, B. (author), Kleerebezem, R. (author), Van Loosdrecht, M.C.M. (author)

The influence of sludge age on granular sludge formation and microbial population dynamics in a methanol- and acetate-fed aerobic granular sludge system operated at 35°C was investigated. During anaerobic feeding of the reactor, methanol was initially converted to methane by methylotrophic methanogens. These methanogens were able to withstand...

journal article 2015

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Physiological and Transcriptional Responses of Different Industrial Microbes at Near-Zero Specific Growth Rates

Ercan, O. (author), Bisschops, M.M. (author), Overkamp, W. (author), Jørgensen, T.R. (author), Rama, A.F. (author), Smid, E.J. (author), Pronk, J.T. (author), Kuipers, O.P. (author), Daran-Lapujade, P. (author), Kleerebezem, M. (author)

The current knowledge of the physiology and gene expression of industrially relevant microorganisms is largely based on laboratory studies under conditions of rapid growth and high metabolic activity. However, in natural ecosystems and industrial processes, microbes frequently encounter severe calorie restriction. As a consequence, microbial...

journal article 2015

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Title microbial linear polysacchrides being soluble at a low pH and precipitating at a high pH

Van Loosdrecht, M.C.M. (author), Lin, Y. (author), Pronk, M. (author)

The present invention concerns a method of producing linear polysaccharides, bacteria capable of producing such linear polysaccharides, and uses of such linear polysaccharides, as a medicament, in agriculture, in food processing, as a coating, as a thickening agent, as a flocculating agent, and for water processing.

patent 2015

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Functional expression of a heterologous nickel-dependent, ATP-independent urease in Saccharomyces cerevisiae

Milne, N. (author), Luttik, M.A.H. (author), Cueto Rojas, H.F. (author), Wahl, A. (author), Van Maris, A.J.A. (author), Pronk, J.T. (author), Daran, J.G. (author)

In microbial processes for production of proteins, biomass and nitrogen-containing commodity chemicals, ATP requirements for nitrogen assimilation affect product yields on the energy producing substrate. In Saccharomyces cerevisiae, a current host for heterologous protein production and potential platform for production of nitrogen-containing...

journal article 2015

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A Minimal Set of Glycolytic Genes Reveals Strong Redundancies in Saccharomyces cerevisiae Central Metabolism

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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CRISPR/Cas9: A molecular Swiss army knife for simultaneous introduction of multiple genetic modifications in Saccharomyces cerevisiae

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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Effect and behaviour of different substrates in relation to the formation of aerobic granular sludge

Pronk, M. (author), Abbas, B. (author), Al-zuhairy, S.H.K. (author), Kraan, R. (author), Kleerebezem, R. (author), Van Loosdrecht, M.C.M. (author)

When aerobic granular sludge is applied for industrial wastewater treatment, different soluble substrates can be present. For stable granular sludge formation on volatile fatty acids (e.g. acetate), production of storage polymers under anaerobic feeding conditions has been shown to be important. This prevents direct aerobic growth on readily...

journal article 2015

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Engineering Acetyl Coenzyme A Supply: Functional Expression of a Bacterial Pyruvate Dehydrogenase Complex in the Cytosol of Saccharomyces cerevisiae

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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Engineering acetyl coenzyme A supply: Functional expression of a bacterial pyruvate dehydrogenase complex in the cytosol of Saccharomyces cerevisiae

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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Increasing ATP conservation in maltose consuming yeast, a challenge for industrial organic acid production in non-aerated reactors

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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Recombinant micro-organism for use in method with increased product yield

Van Maris, A.J.A. (author), Pronk, J.T. (author), Guadalupe Medina, V.G. (author), Wisselink, H.W. (author)

The invention relates to a recombinant yeast cell, in particular a transgenic yeast cell, functionally expressing one or more recombinant, in particular heterologous, nucleic acid sequences encoding ribulose-1,5-biphosphate carboxylase oxygenase (Rubisco) and phosphoribulokinase (PRK). The invention further relates to the use of carbon dioxide...

patent 2014

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An alternative, arginase-independent pathway for arginine metabolism in Kluyveromyces lactis involves guanidinobutyrase as a key enzyme

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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Physiological and transcriptional responses of anaerobic chemostat cultures of Saccharomyces cerevisiae subjected to diurnal temperature cycles

Hebly, M. (author), De Ridder, D. (author), De Hulster, E.A. (author), De la Torre Cortes, P. (author), Pronk, J.T. (author), Daran-Lapujade, P.A.S. (author)

Diurnal temperature cycling is an intrinsic characteristic of many exposed microbial ecosystems. However, its influence on yeast physiology and the yeast transcriptome has not been studied in detail. In this study, 24-h sinusoidal temperature cycles, oscillating between 12°C and 30°C, were imposed on anaerobic, glucose-limited chemostat cultures...

journal article 2014

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Functional characterization of a Penicillium chrysogenum mutanase gene induced upon co-cultivation with Bacillus subtilis

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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Replacement of the Saccharomyces cerevisiae acetyl-CoA synthetases by alternative pathways for cytosolic acetyl-CoA synthesis

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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Stochastic Evolution Equations with Adapted Drift

Pronk, M. (author)

In this thesis we study stochastic evolution equations in Banach spaces. We restrict ourselves to the two following cases. First, we consider equations in which the drift is a closed linear operator that depends on time and is random. Such equations occur as mathematical models in for instance mathematical finance and filtration theory. Second,...

doctoral thesis 2013

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Genome duplication and mutations in ACE2 cause multicellular, fast-sedimenting phenotypes in evolved Saccharomyces cerevisiae

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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One-step assembly and targeted integration of multigene constructs assisted by the I-SceI meganuclease in Saccharomyces cerevisiae

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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Evolutionary engineering of a glycerol-3-phosphate dehydrogenase-negative, acetate-reducing Saccharomyces cerevisiae strain enables anaerobic growth at high glucose concentrations

Guadalupe-Medina, V. (author), Metz, B. (author), Oud, B. (author), Van der Graaf, C.M. (author), Pronk, J.T. (author), Van Maris, A.J.A. (author)

Glycerol production by Saccharomyces cerevisiae, which is required for redox-cofactor balancing in anaerobic cultures, causes yield reduction in industrial bioethanol production. Recently, glycerol formation in anaerobic S.?cerevisiae cultures was eliminated by expressing Escherichia coli (acetylating) acetaldehyde dehydrogenase (encoded by mhpF...

journal article 2013