- document
-
van Aalst, A.C.A. (author), de Valk, S.C. (author), van Gulik, W.M. (author), Jansen, Mickel L.A. (author), Pronk, J.T. (author), Mans, R. (author)Product yield on carbohydrate feedstocks is a key performance indicator for industrial ethanol production with the yeast Saccharomyces cerevisiae. This paper reviews pathway engineering strategies for improving ethanol yield on glucose and/or sucrose in anaerobic cultures of this yeast by altering the ratio of ethanol production, yeast growth...journal article 2022
- document
-
Dekker, W.J.C. (author), Jürgens, H. (author), Ortiz Merino, R.A. (author), Mooiman, C. (author), van den Berg, Remon (author), Kaljouw, Astrid (author), Mans, R. (author), Pronk, J.T. (author)While thermotolerance is an attractive trait for yeasts used in industrial ethanol production, oxygen requirements of known thermotolerant species are incompatible with process requirements. Analysis of oxygen-sufficient and oxygen-limited chemostat cultures of the facultatively fermentative, thermotolerant species Ogataea parapolymorpha...journal article 2022
- document
-
Bouwknegt, J. (author), Vos, A.M. (author), Ortiz Merino, R.A. (author), van Cuylenburg, Daphne C. (author), Luttik, M.A.H. (author), Pronk, J.T. (author)Analysis of predicted fungal proteomes revealed a large family of sequences that showed similarity to the Saccharomyces cerevisiae Class-I dihydroorotate dehydrogenase Ura1, which supports synthesis of pyrimidines under aerobic and anaerobic conditions. However, expression of codon-optimised representatives of this gene family, from the...journal article 2022
- document
-
van Aalst, A.C.A. (author), Mans, R. (author), Pronk, J.T. (author)Background: Saccharomyces cerevisiae is intensively used for industrial ethanol production. Its native fermentation pathway enables a maximum product yield of 2 mol of ethanol per mole of glucose. Based on conservation laws, supply of additional electrons could support even higher ethanol yields. However, this option is disallowed by the...journal article 2022
- document
-
Bouwknegt, J. (author), Wiersma, S.J. (author), Ortiz Merino, R.A. (author), Doornenbal, E.S.R. (author), Buitenhuis, Petrik (author), Giera, Martin (author), Müller, Christoph (author), Pronk, J.T. (author)Biosynthesis of sterols, which are key constituents of canonical eukaryotic membranes, requiresmolecular oxygen. Anaerobic protists and deep-branching anaerobic fungi are the only eukaryotes in which a mechanism for sterol-independent growth has been elucidated. In these organisms, tetrahymanol, formed through oxygen-independent cyclization...journal article 2021
- document
-
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
- document
-
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
- document
-
Perli, T. (author), Vos, A.M. (author), Bouwknegt, J. (author), Dekker, W.J.C. (author), Wiersma, S.J. (author), Mooiman, C. (author), Ortiz Merino, R.A. (author), Daran, J.G. (author), Pronk, J.T. (author)Neocallimastigomycetes are unique examples of strictly anaerobic eukaryotes. This study investigates how these anaerobic fungi bypass reactions involved in synthesis of pyridine nucleotide cofactors and coenzyme A that, in canonical fungal pathways, require molecular oxygen. Analysis of Neocallimastigomycetes proteomes identified a candidate...journal article 2021
- document
-
Else-Hassing, J. (author), Buijs, Joran (author), Blankerts, Nikki (author), Luttik, M.A.H. (author), de Hulster, A.F. (author), Pronk, J.T. (author), Daran, J.G. (author)Engineered strains of the yeast Saccharomyces cerevisiae are intensively studied as production platforms for aromatic compounds such as hydroxycinnamic acids, stilbenoids and flavonoids. Heterologous pathways for production of these compounds use L-phenylalanine and/or L-tyrosine, generated by the yeast shikimate pathway, as aromatic...journal article 2021
- document
-
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
- document
-
Mooiman, C. (author), Bouwknegt, J. (author), Dekker, W.J.C. (author), Wiersma, S.J. (author), Ortiz Merino, R.A. (author), de Hulster, A.F. (author), Pronk, J.T. (author)All known facultatively fermentative yeasts require molecular oxygen for growth. Only in a small number of yeast species, these requirements can be circumvented by supplementation of known anaerobic growth factors such as nicotinate, sterols and unsaturated fatty acids. Biosynthetic oxygen requirements of yeasts are typically small and,...journal article 2021
- document
-
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
- document
-
Liu, Y. (author), Esen, Osman (author), Pronk, J.T. (author), van Gulik, W.M. (author)This study explores the relation between biomass-specific succinic acid (SA) production rate and specific growth rate of an engineered industrial strain of Saccharomyces cerevisiae, with the aim to investigate the extent to which growth and product formation can be uncoupled. Ammonium-limited aerobic chemostat and retentostat cultures were...journal article 2021
- document
-
Dekker, W.J.C. (author), Ortiz Merino, R.A. (author), Kaljouw, Astrid (author), Battjes, Julius (author), Wiering, Frank W. (author), Mooiman, C. (author), de la Torre, P. (author), Pronk, J.T. (author)Current large-scale, anaerobic industrial processes for ethanol production from renewable carbohydrates predominantly rely on the mesophilic yeast Saccharomyces cerevisiae. Use of thermotolerant, facultatively fermentative yeasts such as Kluyveromyces marxianus could confer significant economic benefits. However, in contrast to S. cerevisiae,...journal article 2021
- document
-
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
- document
-
Valk, L.C. (author), Diender, Martijn (author), Stouten, G.R. (author), Petersen, Jette F. (author), Nielsen, Per H. (author), Dueholm, Morten S. (author), Pronk, J.T. (author), van Loosdrecht, Mark C.M. (author)Acetogens have the ability to fixate carbon during fermentation by employing the Wood-Ljungdahl pathway (WLP), which is highly conserved across Bacteria and Archaea. In a previous study, product stoichometries in galacturonate-limited, anaerobic enrichment cultures of “Candidatus Galacturonibacter soehngenii,” from a novel genus within the...journal article 2020
- document
-
Perli, T. (author), Wronska, A.K. (author), Ortiz Merino, R.A. (author), Pronk, J.T. (author), Daran, J.G. (author)Chemically defined media for yeast cultivation (CDMY) were developed to support fast growth, experimental reproducibility, and quantitative analysis of growth rates and biomass yields. In addition to mineral salts and a carbon substrate, popular CDMYs contain seven to nine B-group vitamins, which are either enzyme cofactors or precursors for...journal article 2020
- document
-
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
- document
-
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
- document
-
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