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Optimizing anaerobic growth rate and fermentation kinetics in Saccharomyces cerevisiae strains expressing Calvin-cycle enzymes for improved ethanol yield

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⁺ balance....

journal article 2018

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The Penicillium chrysogenum transporter PcAraT enables high-affinity, glucose-insensitive l-arabinose transport in Saccharomyces cerevisiae

Bracher, J.M. (author), Verhoeven, M.D. (author), Wisselink, H. Wouter (author), Crimi, B. (author), Nijland, Jeroen G. (author), Driessen, Arnold J.M. (author), Klaassen, Paul (author), van Maris, A.J.A. (author), Daran, J.G. (author), Pronk, J.T. (author)

Background: l-Arabinose occurs at economically relevant levels in lignocellulosic hydrolysates. Its low-affinity uptake via the Saccharomyces cerevisiae Gal2 galactose transporter is inhibited by d-glucose. Especially at low concentrations of l-arabinose, uptake is an important rate-controlling step in the complete conversion of these...

journal article 2018

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Combined engineering of disaccharide transport and phosphorolysis for enhanced ATP yield from sucrose fermentation in Saccharomyces cerevisiae

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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Evaluation of a novel cloud-based software platform for structured experiment design and linked data analytics

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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Reassessment of requirements for anaerobic xylose fermentation by engineered, non-evolved Saccharomyces cerevisiae strains

Bracher, J.M. (author), Martinez-Rodriguez, Oscar A. (author), Dekker, W.J.C. (author), Verhoeven, M.D. (author), van Maris, A.J.A. (author), Pronk, J.T. (author)

Expression of a heterologous xylose isomerase, deletion of the GRE3 aldose-reductase gene and overexpression of genes encoding xylulokinase (XKS1) and non-oxidative pentose-phosphate-pathway enzymes (RKI1, RPE1, TAL1, TKL1) enables aerobic growth of Saccharomyces cerevisiae on d-xylose. However, literature reports differ on whether anaerobic...

journal article 2018

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Laboratory evolution for forced glucose-xylose co-consumption enables identification of mutations that improve mixed-sugar fermentation by xylose-fermenting Saccharomyces cerevisiae

Papapetridis, I. (author), Verhoeven, M.D. (author), Wiersma, S.J. (author), Goudriaan, M. (author), van Maris, A.J.A. (author), Pronk, J.T. (author)

Simultaneous fermentation of glucose and xylose can contribute to improved productivity and robustness of yeast-based processes for bioethanol production from lignocellulosic hydrolysates. This study explores a novel laboratory evolution strategy for identifying mutations that contribute to simultaneous utilisation of these sugars in batch...

journal article 2018

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Fermentation of glucose-xylose-arabinose mixtures by a synthetic consortium of single-sugar-fermenting Saccharomyces cerevisiae strains

Verhoeven, M.D. (author), de Valk, S.C. (author), Daran, J.G. (author), van Maris, A.J.A. (author), Pronk, J.T. (author)

D-Glucose, D-xylose and L-arabinose are major sugars in lignocellulosic hydrolysates. This study explores fermentation of glucose-xylose-arabinose mixtures by a consortium of three ‘specialist’ Saccharomyces cerevisiae strains. A D-glucose- and L-arabinose-tolerant xylose specialist was constructed by eliminating hexose phosphorylation in an...

journal article 2018

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Laboratory evolution and physiological analysis of Saccharomyces cerevisiae strains dependent on sucrose uptake via the Phaseolus vulgaris Suf1 transporter

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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A CRISPR/Cas9-based exploration into the elusive mechanism for lactate export in Saccharomyces cerevisiae

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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Laboratory evolution of a biotin-requiring Saccharomyces cerevisiae strain for full biotin prototrophy and identification of causal mutations

Bracher, J.M. (author), de Hulster, A.F. (author), Koster, C.C. (author), van den Broek, M.A. (author), Daran, J.G. (author), van Maris, A.J.A. (author), Pronk, J.T. (author)

Biotin prototrophy is a rare, incompletely understood, and industrially relevant characteristic of Saccharomyces cerevisiae strains. The genome of the haploid laboratory strain CEN.PK113-7D contains a full complement of biotin biosynthesis genes, but its growth in biotin-free synthetic medium is extremely slow (specific growth rate [μ] ≈ 0.01...

journal article 2017

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Metabolic engineering strategies for optimizing acetate reduction, ethanol yield and osmotolerance in Saccharomyces cerevisiae

Papapetridis, I. (author), van Dijk, M. (author), van Maris, A.J.A. (author), Pronk, J.T. (author)

Background: Glycerol, whose formation contributes to cellular redox balancing and osmoregulation in Saccharomyces cerevisiae, is an important by-product of yeast-based bioethanol production. Replacing the glycerol pathway by an engineered pathway for NAD⁺-dependent acetate reduction has been shown to improve ethanol yields and...

journal article 2017

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Mutations in PMR1 stimulate xylose isomerase activity and anaerobic growth on xylose of engineered Saccharomyces cerevisiae by influencing manganese homeostasis

Verhoeven, M.D. (author), Lee, Misun (author), Kamoen, L. (author), van den Broek, M.A. (author), Janssen, Dick B. (author), Daran, J.G. (author), van Maris, A.J.A. (author), Pronk, J.T. (author)

Combined overexpression of xylulokinase, pentose-phosphate-pathway enzymes and a heterologous xylose isomerase (XI) is required but insufficient for anaerobic growth of Saccharomyces cerevisiae on d-xylose. Single-step Cas9-assisted implementation of these modifications yielded a yeast strain expressing Piromyces XI that showed fast aerobic...

journal article 2017

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A simulator-assisted workshop for teaching chemostat cultivation in academic classes on microbial physiology

Hakkaart, X.D.V. (author), Pronk, J.T. (author), van Maris, A.J.A. (author)

Understanding microbial growth and metabolism is a key learning objective of microbiology and biotechnology courses, essential for understanding microbial ecology, microbial biotechnology and medical microbiology. Chemostat cultivation, a key research tool in microbial physiology that enables quantitative analysis of growth and metabolism under...

journal article 2017

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Elimination of sucrose transport and hydrolysis in Saccharomyces cerevisiae: a platform strain for engineering sucrose metabolism

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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Saccharomyces cerevisiae strains tor second-generation ethanol production: from academie exploration to industrial implementation

Jansen, Mickel L.A. (author), Bracher, J.M. (author), Papapetridis, I. (author), Verhoeven, M.D. (author), de Bruijn, J.A. (author), de Waal, P. (author), van Maris, A.J.A. (author), Klaassen, P (author), Pronk, J.T. (author)

The recent start-up of several full-scale ‘second generation’ ethanol plants marks a major milestone in the development of Saccharomyces cerevisiae strains for fermentation of lignocellulosic hydrolysates of agricultural residues and energy crops. After a discussion of the challenges that these novel industrial contexts impose on yeast strains,...

journal article 2017

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A new laboratory evolution approach to select for constitutive acetic acid tolerance in Saccharomyces cerevisiae and identification of causal mutations

Gonzalez Ramos, D. (author), Gorter de Vries, A.R. (author), Grijseels, Sietske S. (author), van Berkum, M.C. (author), Swinnen, Steve (author), van den Broek, M.A. (author), Nevoigt, Elke (author), Daran, J.G. (author), Pronk, J.T. (author), van Maris, A.J.A. (author)

Background: Acetic acid, released during hydrolysis of lignocellulosic feedstocks for second generation bioethanol production, inhibits yeast growth and alcoholic fermentation. Yeast biomass generated in a propagation step that precedes ethanol production should therefore express a high and constitutive level of acetic acid tolerance before...

journal article 2016

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Maintenance-energy requirements and robustness of Saccharomyces cerevisiae at aerobic near-zero specific growth rates

Vos, T. (author), Hakkaart, X.D.V. (author), de Hulster, A.F. (author), van Maris, A.J.A. (author), Pronk, J.T. (author), Daran-Lapujade, P.A.S. (author)

Background: Saccharomyces cerevisiae is an established microbial platform for production of native and non-native compounds. When product pathways compete with growth for precursors and energy, uncoupling of growth and product formation could increase product yields and decrease formation of biomass as a by-product. Studying non-growing,...

journal article 2016

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Improving ethanol yield in acetate-reducing Saccharomyces cerevisiae by cofactor engineering of 6-phosphogluconate dehydrogenase and deletion of ALD6

Papapetridis, I. (author), van Dijk, M. (author), Dobbe, Arthur P A (author), Metz, B. (author), Pronk, J.T. (author), van Maris, A.J.A. (author)

Background: Acetic acid, an inhibitor of sugar fermentation by yeast, is invariably present in lignocellulosic hydrolysates which are used or considered as feedstocks for yeast-based bioethanol production. Saccharomyces cerevisiae strains have been constructed, in which anaerobic reduction of acetic acid to ethanol replaces glycerol formation...

journal article 2016

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Replacement of the initial steps of ethanol metabolism in Saccharomyces cerevisiae by ATP-independent acetylating acetaldehyde dehydrogenase

Kozak, B.U. (author), Rossum, Harmen M. (author), Niemeijer, M.S. (author), van Dijk, M. (author), Benjamin, Kirsten (author), Wu, Liang (author), Daran, J.G. (author), Pronk, J.T. (author), van Maris, A.J.A. (author)

In Saccharomyces cerevisiae ethanol dissimilation is initiated by its oxidation and activation to cytosolic acetyl-CoA. The associated consumption of ATP strongly limits yields of biomass and acetyl-CoA-derived products. Here, we explore the implementation of an ATP-independent pathway for acetyl-CoA synthesis from ethanol that, in theory,...

journal article 2016

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Requirements for carnitine shuttle-mediated translocation of mitochondrial acetyl moieties to the yeast cytosol

Rossum, Harmen M. (author), Kozak, B.U. (author), Niemeijer, M.S. (author), Dykstra, James C. (author), Luttik, M.A.H. (author), Daran, J.G. (author), van Maris, A.J.A. (author), Pronk, J.T. (author)

In many eukaryotes, the carnitine shuttle plays a key role in intracellular transport of acyl moieties. Fatty acidgrown Saccharomyces cerevisiae cells employ this shuttle to translocate acetyl units into their mitochondria. Mechanistically, the carnitine shuttle should be reversible, but previous studies indicate that carnitine shuttle...

journal article 2016