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27. Vitamin requirements and biosynthesis in Saccharomyces cerevisiae

Author

Perli, Thomas, Wronska, Anna K., Ortiz‐Merino, Raúl A., Pronk, Jack T., and Daran, Jean‐Marc

Subjects
0106 biological sciences, Vitamin, Saccharomyces cerevisiae Proteins, Auxotrophy, Saccharomyces cerevisiae, Yeast Extracts, Biotin, Bioengineering, Biology, 01 natural sciences, Applied Microbiology and Biotechnology, Biochemistry, Saccharomyces, Niacin, Pantothenic Acid, 03 medical and health sciences, chemistry.chemical_compound, growth requirements, synthetic media, 010608 biotechnology, Genetics, Biomass, Thiamine, fermentation, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, Structural gene, Pyridoxine, Reproducibility of Results, Vitamins, Vitamin biosynthesis, biology.organism_classification, Yeast, vitamin biosynthesis, chemistry, Fermentation, Inositol, Biotechnology
Abstract

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 their synthesis. Despite the widespread use of CDMY in fundamental and applied yeast research, the relation of their design and composition to the actual vitamin requirements of yeasts has not been subjected to critical review since their first development in the 1940s. Vitamins are formally defined as essential organic molecules that cannot be synthesized by an organism. In yeast physiology, use of the term “vitamin” is primarily based on essentiality for humans, but the genome of the Saccharomyces cerevisiae reference strain S288C harbours most of the structural genes required for synthesis of the vitamins included in popular CDMY. Here, we review the biochemistry and genetics of the biosynthesis of these compounds by S. cerevisiae and, based on a comparative genomics analysis, assess the diversity within the Saccharomyces genus with respect to vitamin prototrophy.

Published
2020

28. Additional file 5 of An engineered non-oxidative glycolytic bypass based on Calvin-cycle enzymes enables anaerobic co-fermentation of glucose and sorbitol by Saccharomyces cerevisiae

Author

van Aalst, Aafke C. A., Mans, Robert, and Pronk, Jack T.

Abstract

Additional file 5: Table S1. Predicted ethanol yields on substrate, biomass-specific substrate-uptake rates (qsubstrate) and biomass yields on substrate for wild-type S. cerevisiae (WT) and strains with an engineered PRK-RuBisCO bypass of the oxidative reaction in glycolysis on both glucose and on sorbitol. Rates and yields were predicted for cultures growing at different specific growth rates, using an extended stoichiometric model of the core metabolic network of S. cerevisiae (1, 2). A Cmol biomass (CH1.8O0.5N0.2, (3)) corresponds to 26.4 g dry biomass. Table S2 Maximum specific growth rates in aerobic batch cultures of S. cerevisiae strains IMX2506 (gpd2∆ {PRK-RuBisCO} HXT15↑ SOR2↑) and IME611 (GPD2 HXT15↑ SOR2↑) on synthetic medium, supplemented with either 20 g L-1 of glucose or 20 g L-1 of sorbitol. Specific growth rates were calculated from quadruplicate cultures in a Growth Profiler, using at least 9 measurement points obtained during the exponential growth phase. Strain IME324 (GPD2) was inoculated in duplicate aerobic shake-flask cultures containing synthetic medium supplemented with 20 g L-1 of sorbitol as sole carbon source. No growth was observed after 4 weeks of incubation. N.D.: not determined. Table S3 Segmental aneuploidies observed in two prolonged anaerobic chemostat cultivation experiments with S. cerevisiae IMX2506 (gpd2∆ {PRK-RuBisCO} HXT15↑ SOR2↑) on glucose- sorbitol mixtures (see Fig. 5). Table S4 Oligonucleotide primers used in this study. Figure S1A Copy number variation across yeast chromosomes in prolonged anaerobic chemostat cultivation experiment 1 with S. cerevisiae IMX2506 (gpd2∆ {PRK-RuBisCO} HXT15↑ SOR2↑) on glucose- sorbitol mixtures (see Fig. 5). Copy number variations were visualized with the Magnolya algorithm (4). Figure S1B Copy number variation across yeast chromosomes in prolonged anaerobic chemostat cultivation experiment 2 with S. cerevisiae IMX2506 (gpd2∆ {PRK-RuBisCO} HXT15↑ SOR2↑) on glucose–sorbitol mixtures (see Fig. 5). Copy number variations were visualized with the Magnolya algorithm (4). Figure S1C Reference data for copy-number assessment with the Magnolya algorithm (4) for the reference strain S. cerevisiae IMX2506 (gpd2∆ {PRK-RuBisCO} HXT15↑ SOR2↑). Figure S2 Optical density at 660 nm (OD660), sorbitol concentration, ethanol concentration and glycerol concentration in duplicate aerobic shake-flask cultures of S. cerevisiae IMX2506 (gpd2∆ {PRK-RuBisCO} HXT15↑ SOR2↑) on 20 g L-1 sorbitol.

Published
2022
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44. Additional file 5 of Class-II dihydroorotate dehydrogenases from three phylogenetically distant fungi support anaerobic pyrimidine biosynthesis

Author

Bouwknegt, Jonna, Koster, Charlotte C., Vos, Aurin M., Ortiz-Merino, Raúl A., Wassink, Mats, Luttik, Marijke A. H., van den Broek, Marcel, Hagedoorn, Peter L., and Pronk, Jack T.

Subjects
ComputingMethodologies_DOCUMENTANDTEXTPROCESSING, ComputingMilieux_COMPUTERSANDEDUCATION, Data_FILES, ComputerApplications_COMPUTERSINOTHERSYSTEMS
Abstract

Additional file 5. Supplementary tables and figures.

Published
2021
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46. Saccharomyces cerevisiae CEN.PK113-7D: Anaerobically evolved fungi that harbor Class II dihydroorotate dehydrogenase enzymes that function independently of the respiratory chain

Author

Bouwknegt, Jonna, Koster, Charlotte C., Vos, Aurin, Ortiz-Merino, Raúl A., Wassink, Mats, Luttik, Marijke A.H., van den Broek, Marcel, Hagedoorn, Peter L., Pronk, Jack T., Bouwknegt, Jonna, Koster, Charlotte C., Vos, Aurin, Ortiz-Merino, Raúl A., Wassink, Mats, Luttik, Marijke A.H., van den Broek, Marcel, Hagedoorn, Peter L., and Pronk, Jack T.

Abstract

The goal of this study was elucidate the respiratory chain dependency of the abovementioned Class II DHODs. The URA9 genes of Anaeromyces robustus, Sch. japonicus, D. bruxellensis, O. parapolymorpha and K. marxianus were expressed in a ura1 null mutant of S. cerevisiae and growth was studied under anaerobic conditions. The subcellular localization of the enzymes was determined by fluorescence microscopy of GFP-fused Ura9 proteins. Finally, alternative electron acceptors were determined for these proteins by enzyme assays using cell free extracts and mitochondrial extracts of S. cerevisiae ura1 null mutants expressing the URA9 genes from a multicopy plasmid.

Published
2021

47. Correction to : Class‑II dihydroorotate dehydrogenases from three phylogenetically distant fungi support anaerobic pyrimidine biosynthesis

Author

Bouwknegt, Jonna, Koster, Charlotte C., Vos, Aurin M., Ortiz-Merino, Raúl A., Wassink, Mats, Luttik, Marijke A.H., van den Broek, Marcel, Hagedoorn, Peter L., Pronk, Jack T., Bouwknegt, Jonna, Koster, Charlotte C., Vos, Aurin M., Ortiz-Merino, Raúl A., Wassink, Mats, Luttik, Marijke A.H., van den Broek, Marcel, Hagedoorn, Peter L., and Pronk, Jack T.

Abstract

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 VPS1I410L and to the corresponding change in the Vps1 amino-acid sequence as I410L. The correct descriptions should read VPS1I401L and I401L, respectively. This has been corrected with this erratum.

Published
2021

48. The Saccharomyces cerevisiae NDE1 and NDE2 genes encode separate mitochondrial NADH dehydrogenases catalyzing the oxidation of cytosolic NADH

Author

Luttik, Marijke A. H., Overkamp, Karin Martine, Kötter, Peter, Vries, Simon de, Dijken, Johannes P. van, Pronk, Jack T., Luttik, Marijke A. H., Overkamp, Karin Martine, Kötter, Peter, Vries, Simon de, Dijken, Johannes P. van, and Pronk, Jack T.

Abstract

In Saccharomyces cerevisiae, the NDI1 gene encodes a mitochondrial NADH dehydrogenase, the catalytic side of which projects to the matrix side of the inner mitochondrial membrane. In addition to this NADH dehydrogenase, S. cerevisiae exhibits another mitochondrial NADH-dehydrogenase activity, which oxidizes NADH at the cytosolic side of the inner membrane. To investigate whether open reading frames YMR145c/NDE1 and YDL 085w/NDE2, which exhibit sequence similarity with NDI1, encode the latter enzyme, NADH-dependent mitochondrial respiration was assayed in wild-type S. cerevisiae and nde deletion mutants. Mitochondria were isolated from aerobic, glucose-limited chemostat cultures grown at a dilution rate (D) of 0. 10 h-1, in which reoxidation of cytosolic NADH by wild-type cells occurred exclusively by respiration. Compared with the wild type, rates of mitochondrial NADH oxidation were about 3-fold reduced in an nde1Delta mutant and unaffected in an nde2Delta mutant. NADH-dependent mitochondrial respiration was completely abolished in an nde1Delta nde2Delta double mutant. Mitochondrial respiration of substrates other than NADH was not affected in nde mutants. In shake flasks, an nde1Delta nde2Delta mutant exhibited reduced specific growth rates on ethanol and galactose but not on glucose. Glucose metabolism in aerobic, glucose-limited chemostat cultures (D = 0.10 h-1) of an nde1Delta nde2Delta mutant was essentially respiratory. Apparently, under these conditions alternative systems for reoxidation of cytosolic NADH could replace the role of Nde1p and Nde2p in S. cerevisiae.

Published
2021

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