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Garcia I, Cornely K, Peterson CN, Berkmen MB. Roles of the oncometabolite enantiomers of 2-hydroxyglutarate and their metabolism by diverse dehydrogenases. Essays Biochem 2024:EBC20230077. [PMID: 38919140 DOI: 10.1042/ebc20230077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 06/09/2024] [Accepted: 06/11/2024] [Indexed: 06/27/2024]
Abstract
2-Hydroxyglutarate (2HG) is an oncometabolite that can contribute to tumor progression. Two enantiomer forms, L-2HG and D-2HG, arise from independent pathways starting from the precursor α-ketoglutarate (αKG). L-2HG production occurs through the promiscuous activities of malate dehydrogenase (MDH) and lactate dehydrogenase (LDH) under acidic and/or hypoxic conditions. D-2HG frequently accumulates by gain-of-function mutations in the genes encoding two isoforms of isocitrate dehydrogenase (IDH1 and IDH2). Cognate metabolite repair enzymes, L- and D-2-hydroxyglutarate dehydrogenases, oxidize the enantiomers and cause abnormally high 2HG accumulation and disease when mutated. Elevated levels of either oncometabolite affect redox homeostasis, metabolism, and immune system functioning. Moreover, the oncometabolites inhibit several α-ketoglutarate-dependent dioxygenases resulting in epigenetic changes such as DNA and histone hypermethylation as well as deficiencies in DNA repair. L-2HG, and D-2HG in some cases, inhibit degradation of hypoxia-inducible factor (HIF1α), a transcription factor that alters gene expression to adapt to hypoxic conditions, favoring tumorigenesis. Patients with the rare disease 2-hydroxyglutaric aciduria (2HGA) have exceedingly high levels of 2HG, which is neurotoxic, causing developmental delays and brain abnormalities. D-2HG also has specific effects on collagen production and NADPH pools. Recently, D-2HG has been targeted in new chemotherapies aimed at disrupting the gain-of-function IDH1 and IDH2 mutants, resulting in successful clinical trials for several cancers.
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Affiliation(s)
- Ivelitza Garcia
- Department of Chemistry, Allegheny College, Meadville, PA, U.S.A
| | - Kathleen Cornely
- Department of Chemistry and Biochemistry, Providence College, Providence, RI, U.S.A
| | | | - Melanie B Berkmen
- Department of Biochemistry, Chemistry, Environment, and Physics, Suffolk University, Boston, MA, U.S.A
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2
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Bi S, Lv QZ, Wang TT, Fuchs BB, Hu DD, Anastassopoulou CG, Desalermos A, Muhammed M, Wu CL, Jiang YY, Mylonakis E, Wang Y. SDH2 is involved in proper hypha formation and virulence in Candida albicans. Future Microbiol 2018; 13:1141-1156. [PMID: 30113213 DOI: 10.2217/fmb-2018-0033] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AIM To investigate the role of SDH2 in Candida albicans filamentation and virulence. MATERIALS & METHODS Caenorhabditis elegans and mouse candidiasis models were used to assess the virulence of a sdh2Δ/Δ mutant. Various hypha-inducing media were used to evaluate the hyphal development of C. albicans. DCFH-DA was used to measure intracellular Reactive Oxygen Species (ROS) levels. RESULTS The sdh2Δ/Δ mutant was avirulent in the C. elegans model, hypovirulent in a murine candidiasis model, and defective to form filaments both in vitro and in vivo. Intracellular ROS level increased in the sdh2Δ/Δ mutant, and the filamentation defects of sdh2Δ/Δ were rescued by decreasing intracellular ROS. CONCLUSION SDH2 plays an important role in C. albicans filamentation and virulence probably through affecting intracellular ROS. [Formula: see text].
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Affiliation(s)
- Shuang Bi
- School of Pharmacy, Second Military Medical University, Shanghai 200433, PR China
| | - Quan-Zhen Lv
- School of Pharmacy, Second Military Medical University, Shanghai 200433, PR China
| | - Tian-Tian Wang
- School of Pharmacy, Second Military Medical University, Shanghai 200433, PR China
| | - Beth Burgwyn Fuchs
- Division of Infectious Diseases, Rhode Island Hospital, Alpert Medical School of Brown University, RI 02903, USA
| | - Dan-Dan Hu
- School of Pharmacy, Second Military Medical University, Shanghai 200433, PR China
| | - Cleo G Anastassopoulou
- Division of Genetics, Cell & Developmental Biology, Department of Biology, University of Patras, Patras, Greece.,Division of Infectious Diseases, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Athanasios Desalermos
- Division of Infectious Diseases, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Maged Muhammed
- Division of Infectious Diseases, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.,Division of Infectious Diseases, and Division of Gastroenterology, Boston Children's Hospital. Department of Medicine, Department of Adult Inpatient Medicine, Newton Wellesley Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Chin-Lee Wu
- Department of Urology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Yuan-Ying Jiang
- School of Pharmacy, Second Military Medical University, Shanghai 200433, PR China
| | - Eleftherios Mylonakis
- Division of Infectious Diseases, Rhode Island Hospital, Alpert Medical School of Brown University, RI 02903, USA.,Division of Genetics, Cell & Developmental Biology, Department of Biology, University of Patras, Patras, Greece
| | - Yan Wang
- School of Pharmacy, Second Military Medical University, Shanghai 200433, PR China.,Division of Infectious Diseases, Rhode Island Hospital, Alpert Medical School of Brown University, RI 02903, USA.,Division of Infectious Diseases, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
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3
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Ezeogu LI, Ogbonna JC. Tryptic Digests of Sorghum Malt Sprouts: An Assessment of Their Usefulness as Organic Nitrogen Sources for the YeastSaccharomyces Cerevisiae. JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS 2018. [DOI: 10.1094/asbcj-63-0050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Lewis I. Ezeogu
- Brewing Science Laboratory, Department of Microbiology, University of Nigeria, Nsukka, Nigeria
| | - James C. Ogbonna
- Institute of Applied Biochemistry, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8572 Japan
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4
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Management of Multiple Nitrogen Sources during Wine Fermentation by Saccharomyces cerevisiae. Appl Environ Microbiol 2017; 83:AEM.02617-16. [PMID: 28115380 DOI: 10.1128/aem.02617-16] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 12/14/2016] [Indexed: 11/20/2022] Open
Abstract
During fermentative growth in natural and industrial environments, Saccharomyces cerevisiae must redistribute the available nitrogen from multiple exogenous sources to amino acids in order to suitably fulfill anabolic requirements. To exhaustively explore the management of this complex resource, we developed an advanced strategy based on the reconciliation of data from a set of stable isotope tracer experiments with labeled nitrogen sources. Thus, quantifying the partitioning of the N compounds through the metabolism network during fermentation, we demonstrated that, contrary to the generally accepted view, only a limited fraction of most of the consumed amino acids is directly incorporated into proteins. Moreover, substantial catabolism of these molecules allows for efficient redistribution of nitrogen, supporting the operative de novo synthesis of proteinogenic amino acids. In contrast, catabolism of consumed amino acids plays a minor role in the formation of volatile compounds. Another important feature is that the α-keto acid precursors required for the de novo syntheses originate mainly from the catabolism of sugars, with a limited contribution from the anabolism of consumed amino acids. This work provides a comprehensive view of the intracellular fate of consumed nitrogen sources and the metabolic origin of proteinogenic amino acids, highlighting a strategy of distribution of metabolic fluxes implemented by yeast as a means of adapting to environments with changing and scarce nitrogen resources.IMPORTANCE A current challenge for the wine industry, in view of the extensive competition in the worldwide market, is to meet consumer expectations regarding the sensory profile of the product while ensuring an efficient fermentation process. Understanding the intracellular fate of the nitrogen sources available in grape juice is essential to the achievement of these objectives, since nitrogen utilization affects both the fermentative activity of yeasts and the formation of flavor compounds. However, little is known about how the metabolism operates when nitrogen is provided as a composite mixture, as in grape must. Here we quantitatively describe the distribution through the yeast metabolic network of the N moieties and C backbones of these nitrogen sources. Knowledge about the management of a complex resource, which is devoted to improvement of the use of the scarce N nutrient for growth, will be useful for better control of the fermentation process and the sensory quality of wines.
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5
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Marsit S, Sanchez I, Galeote V, Dequin S. Horizontally acquired oligopeptide transporters favour adaptation ofSaccharomyces cerevisiaewine yeast to oenological environment. Environ Microbiol 2016; 18:1148-61. [DOI: 10.1111/1462-2920.13117] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Revised: 10/30/2015] [Accepted: 10/30/2015] [Indexed: 12/01/2022]
Affiliation(s)
- Souhir Marsit
- INRA; UMR1083 Sciences pour l'Oenology; Montpellier France
| | | | | | - Sylvie Dequin
- INRA; UMR1083 Sciences pour l'Oenology; Montpellier France
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6
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Becker-Kettern J, Paczia N, Conrotte JF, Kay DP, Guignard C, Jung PP, Linster CL. Saccharomyces cerevisiae Forms D-2-Hydroxyglutarate and Couples Its Degradation to D-Lactate Formation via a Cytosolic Transhydrogenase. J Biol Chem 2016; 291:6036-58. [PMID: 26774271 DOI: 10.1074/jbc.m115.704494] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Indexed: 12/23/2022] Open
Abstract
The D or L form of 2-hydroxyglutarate (2HG) accumulates in certain rare neurometabolic disorders, and high D-2-hydroxyglutarate (D-2HG) levels are also found in several types of cancer. Although 2HG has been detected in Saccharomyces cerevisiae, its metabolism in yeast has remained largely unexplored. Here, we show that S. cerevisiae actively forms the D enantiomer of 2HG. Accordingly, the S. cerevisiae genome encodes two homologs of the human D-2HG dehydrogenase: Dld2, which, as its human homolog, is a mitochondrial protein, and the cytosolic protein Dld3. Intriguingly, we found that a dld3Δ knock-out strain accumulates millimolar levels of D-2HG, whereas a dld2Δ knock-out strain displayed only very moderate increases in D-2HG. Recombinant Dld2 and Dld3, both currently annotated as D-lactate dehydrogenases, efficiently oxidized D-2HG to α-ketoglutarate. Depletion of D-lactate levels in the dld3Δ, but not in the dld2Δ mutant, led to the discovery of a new type of enzymatic activity, carried by Dld3, to convert D-2HG to α-ketoglutarate, namely an FAD-dependent transhydrogenase activity using pyruvate as a hydrogen acceptor. We also provide evidence that Ser3 and Ser33, which are primarily known for oxidizing 3-phosphoglycerate in the main serine biosynthesis pathway, in addition reduce α-ketoglutarate to D-2HG using NADH and represent major intracellular sources of D-2HG in yeast. Based on our observations, we propose that D-2HG is mainly formed and degraded in the cytosol of S. cerevisiae cells in a process that couples D-2HG metabolism to the shuttling of reducing equivalents from cytosolic NADH to the mitochondrial respiratory chain via the D-lactate dehydrogenase Dld1.
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Affiliation(s)
- Julia Becker-Kettern
- From the Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4367 Belvaux and
| | - Nicole Paczia
- From the Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4367 Belvaux and
| | - Jean-François Conrotte
- From the Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4367 Belvaux and
| | - Daniel P Kay
- From the Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4367 Belvaux and
| | - Cédric Guignard
- the Luxembourg Institute of Science and Technology, 41 Rue du Brill, L-4422 Belvaux, Luxembourg
| | - Paul P Jung
- From the Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4367 Belvaux and
| | - Carole L Linster
- From the Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4367 Belvaux and
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7
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Gomes D, Aguiar TQ, Dias O, Ferreira EC, Domingues L, Rocha I. Genome-wide metabolic re-annotation of Ashbya gossypii: new insights into its metabolism through a comparative analysis with Saccharomyces cerevisiae and Kluyveromyces lactis. BMC Genomics 2014; 15:810. [PMID: 25253284 PMCID: PMC4190384 DOI: 10.1186/1471-2164-15-810] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 08/15/2014] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Ashbya gossypii is an industrially relevant microorganism traditionally used for riboflavin production. Despite the high gene homology and gene order conservation comparatively with Saccharomyces cerevisiae, it presents a lower level of genomic complexity. Its type of growth, placing it among filamentous fungi, questions how close it really is from the budding yeast, namely in terms of metabolism, therefore raising the need for an extensive and thorough study of its entire metabolism. This work reports the first manual enzymatic genome-wide re-annotation of A. gossypii as well as the first annotation of membrane transport proteins. RESULTS After applying a developed enzymatic re-annotation pipeline, 847 genes were assigned with metabolic functions. Comparatively to KEGG's annotation, these data corrected the function for 14% of the common genes and increased the information for 52 genes, either completing existing partial EC numbers or adding new ones. Furthermore, 22 unreported enzymatic functions were found, corresponding to a significant increase in the knowledge of the metabolism of this organism. The information retrieved from the metabolic re-annotation and transport annotation was used for a comprehensive analysis of A. gossypii's metabolism in comparison to the one of S. cerevisiae (post-WGD - whole genome duplication) and Kluyveromyces lactis (pre-WGD), suggesting some relevant differences in several parts of their metabolism, with the majority being found for the metabolism of purines, pyrimidines, nitrogen and lipids. A considerable number of enzymes were found exclusively in A. gossypii comparatively with K. lactis (90) and S. cerevisiae (13). In a similar way, 176 and 123 enzymatic functions were absent on A. gossypii comparatively to K. lactis and S. cerevisiae, respectively, confirming some of the well-known phenotypes of this organism. CONCLUSIONS This high quality metabolic re-annotation, together with the first membrane transporters annotation and the metabolic comparative analysis, represents a new important tool for the study and better understanding of A. gossypii's metabolism.
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Affiliation(s)
- Daniel Gomes
- CEB - Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Tatiana Q Aguiar
- CEB - Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Oscar Dias
- CEB - Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Eugénio C Ferreira
- CEB - Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Lucília Domingues
- CEB - Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Isabel Rocha
- CEB - Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar, 4710-057 Braga, Portugal
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8
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Johansson N, Persson KO, Quehl P, Norbeck J, Larsson C. Ethylene production in relation to nitrogen metabolism in Saccharomyces cerevisiae. FEMS Yeast Res 2014; 14:1110-8. [PMID: 25195797 DOI: 10.1111/1567-1364.12208] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Revised: 08/05/2014] [Accepted: 08/31/2014] [Indexed: 11/30/2022] Open
Abstract
We have previously shown that ethylene production in Saccharomyces cerevisiae expressing the ethylene-forming enzyme (EFE) from Pseudomonas syringae is strongly influenced by variations in the mode of cultivation as well as the choice of nitrogen source. Here, we have studied the influence of nitrogen metabolism on the production of ethylene further. Using ammonium, glutamate, glutamate/arginine, and arginine as nitrogen sources, it was found that glutamate (with or without arginine) correlates with a high ethylene production, most likely linked to an observed increase in 2-oxoglutarate levels. Arginine as a sole nitrogen source caused a reduced ethylene production. A reduction of arginine levels, accomplished using an arginine auxotrophic ARG4-deletion strain in the presence of limiting amounts of arginine or through CAR1 overexpression, did however not correlate with an increased ethylene production. As expected, arginine was necessary for ethylene production as ethylene production in the ARG4-deletion strain ceased at the time when arginine was depleted. In conclusion, our data suggest that high levels of 2-oxoglutarate and a limited amount of arginine are required for successful ethylene production in yeast.
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Affiliation(s)
- Nina Johansson
- Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
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9
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de Castro A, Sánchez AH, Beato VM, Casado FJ, Montaño A. Stability of monosodium glutamate in green table olives and pickled cucumbers as a function of packing conditions and storage time. Food Addit Contam Part A Chem Anal Control Expo Risk Assess 2014; 31:1158-64. [PMID: 24720705 DOI: 10.1080/19440049.2014.913320] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The effects of different packing conditions and storage times on the stability of monosodium glutamate (MSG) added to two different fermented vegetables (Spanish-type green table olives and pickled cucumbers) were studied. Factors such as packaging material (glass bottle versus plastic pouch), heat treatment (pasteurisation versus non-pasteurisation), and the presence or not of a preservative compound (potassium sorbate) were considered. The MSG content of pickled cucumbers was stable for up to 1 year of storage in all packing conditions studied. The MSG content also remained stable in pasteurised green table olives. On the contrary, MSG was extensively degraded (>75% degradation) after 54 weeks of storage in unpasteurised green olives with a higher degradation rate in glass bottles compared with plastic pouches. In the presence of potassium sorbate, MSG was also considerably degraded in olives packed in plastic pouches (>50% degradation), but hardly degraded in glass bottles. The results indicate that MSG degradation in olives is due to the action of both lactic acid bacteria and yeasts, with the formation of γ-aminobutyric acid as the major end-product.
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Affiliation(s)
- Antonio de Castro
- a Food Biotechnology Department , Instituto de la Grasa (C.S.I.C.) , Seville , Spain
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10
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Engqvist MKM, Eßer C, Maier A, Lercher MJ, Maurino VG. Mitochondrial 2-hydroxyglutarate metabolism. Mitochondrion 2014; 19 Pt B:275-81. [PMID: 24561575 DOI: 10.1016/j.mito.2014.02.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2013] [Revised: 02/13/2014] [Accepted: 02/14/2014] [Indexed: 01/03/2023]
Abstract
2-Hydroxyglutarate (2-HG) is a five-carbon dicarboxylic acid with a hydroxyl group at the alpha position, which forms a stereocenter in this molecule. Although the existence of mitochondrial D- and L-2HG metabolisms has long been known in different eukaryotes, the biosynthetic pathways, especially in plants, have not been completely elucidated. While D-2HG is involved in intermediary metabolism, L-2HG may not have a cellular function but it needs to be recycled through a metabolic repair reaction. Independent of their metabolic origin, D- and L-2HG are oxidized in plant mitochondria to 2-ketoglutarate through the action of two stereospecific enzymes, D- and L-2-hydroxyacid dehydrogenases. While plants are to a large extent unaffected by high cellular concentrations of D-2HG, deficiencies in the metabolism of D- and L-2HG result in fatal disorders in humans. We present current data gathered on plant D- and L-2HG metabolisms and relate it to existing knowledge on 2HG metabolism in other organisms. We focus on the metabolic origin of these compounds, the mitochondrial catabolic steps catalyzed by the stereospecific dehydrogenases, and phylogenetic relationships between different studied 2-hydroxyacid dehydrogenases.
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Affiliation(s)
- Martin K M Engqvist
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Mail Code 210-41, Pasadena, CA 91125, United States
| | - Christian Eßer
- Institute for Computer Science, Heinrich-Heine-University, Universitätsstr. 1, D-40225 Düsseldorf, Germany
| | - Alexander Maier
- Institut of Developmental and Molecular Biology of Plants, Plant Molecular Physiology and Biotechnology Group, Heinrich-Heine-University, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Martin J Lercher
- Institute for Computer Science, Heinrich-Heine-University, Universitätsstr. 1, D-40225 Düsseldorf, Germany; Cluster of Excellence on Plant Sciences (CEPLAS), 40225 Düsseldorf, Germany
| | - Veronica G Maurino
- Institut of Developmental and Molecular Biology of Plants, Plant Molecular Physiology and Biotechnology Group, Heinrich-Heine-University, Universitätsstraße 1, 40225 Düsseldorf, Germany; Cluster of Excellence on Plant Sciences (CEPLAS), 40225 Düsseldorf, Germany.
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11
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Quirós M, Martínez-Moreno R, Albiol J, Morales P, Vázquez-Lima F, Barreiro-Vázquez A, Ferrer P, Gonzalez R. Metabolic flux analysis during the exponential growth phase of Saccharomyces cerevisiae in wine fermentations. PLoS One 2013; 8:e71909. [PMID: 23967264 PMCID: PMC3742454 DOI: 10.1371/journal.pone.0071909] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Accepted: 07/04/2013] [Indexed: 12/27/2022] Open
Abstract
As a consequence of the increase in global average temperature, grapes with the adequate phenolic and aromatic maturity tend to be overripe by the time of harvest, resulting in increased sugar concentrations and imbalanced C/N ratios in fermenting musts. This fact sets obvious additional hurdles in the challenge of obtaining wines with reduced alcohols levels, a new trend in consumer demands. It would therefore be interesting to understand Saccharomyces cerevisiae physiology during the fermentation of must with these altered characteristics. The present study aims to determine the distribution of metabolic fluxes during the yeast exponential growth phase, when both carbon and nitrogen sources are in excess, using continuous cultures. Two different sugar concentrations were studied under two different winemaking temperature conditions. Although consumption and production rates for key metabolites were severely affected by the different experimental conditions studied, the general distribution of fluxes in central carbon metabolism was basically conserved in all cases. It was also observed that temperature and sugar concentration exerted a higher effect on the pentose phosphate pathway and glycerol formation than on glycolysis and ethanol production. Additionally, nitrogen uptake, both quantitatively and qualitatively, was strongly influenced by environmental conditions. This work provides the most complete stoichiometric model used for Metabolic Flux Analysis of S. cerevisiae in wine fermentations employed so far, including the synthesis and release of relevant aroma compounds and could be used in the design of optimal nitrogen supplementation of wine fermentations.
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Affiliation(s)
- Manuel Quirós
- Instituto de Ciencias de la Vid y del Vino (Consejo Superior de Investigaciones Científicas, Universidad de la Rioja, Gobierno de La Rioja), Logroño, Spain.
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12
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Papini M, Nookaew I, Uhlén M, Nielsen J. Scheffersomyces stipitis: a comparative systems biology study with the Crabtree positive yeast Saccharomyces cerevisiae. Microb Cell Fact 2012; 11:136. [PMID: 23043429 PMCID: PMC3528450 DOI: 10.1186/1475-2859-11-136] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Accepted: 09/13/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Scheffersomyces stipitis is a Crabtree negative yeast, commonly known for its capacity to ferment pentose sugars. Differently from Crabtree positive yeasts such as Saccharomyces cerevisiae, the onset of fermentation in S. stipitis is not dependent on the sugar concentration, but is regulated by a decrease in oxygen levels. Even though S. stipitis has been extensively studied due to its potential application in pentoses fermentation, a limited amount of information is available about its metabolism during aerobic growth on glucose. Here, we provide a systems biology based comparison between the two yeasts, uncovering the metabolism of S. stipitis during aerobic growth on glucose under batch and chemostat cultivations. RESULTS Starting from the analysis of physiological data, we confirmed through 13C-based flux analysis the fully respiratory metabolism of S. stipitis when growing both under glucose limited or glucose excess conditions. The patterns observed showed similarity to the fully respiratory metabolism observed for S. cerevisiae under chemostat cultivations however, intracellular metabolome analysis uncovered the presence of several differences in metabolite patterns. To describe gene expression levels under the two conditions, we performed RNA sequencing and the results were used to quantify transcript abundances of genes from the central carbon metabolism and compared with those obtained with S. cerevisiae. Interestingly, genes involved in central pathways showed different patterns of expression, suggesting different regulatory networks between the two yeasts. Efforts were focused on identifying shared and unique families of transcription factors between the two yeasts through in silico transcription factors analysis, suggesting a different regulation of glycolytic and glucoenogenic pathways. CONCLUSIONS The work presented addresses the impact of high-throughput methods in describing and comparing the physiology of Crabtree positive and Crabtree negative yeasts. Based on physiological data and flux analysis we identified the presence of one metabolic condition for S. stipitis under aerobic batch and chemostat cultivations, which shows similarities to the oxidative metabolism observed for S. cerevisiae under chemostat cultivations. Through metabolome analysis and genome-wide transcriptomic analysis several differences were identified. Interestingly, in silico analysis of transciption factors was useful to address a different regulation of mRNAs of genes involved in the central carbon metabolism. To our knowledge, this is the first time that the metabolism of S. stiptis is investigated in details and is compared to S. cerevisiae. Our study provides useful results and allows for the possibility to incorporate these data into recently developed genome-scaled metabolic, thus contributing to improve future industrial applications of S. stipitis as cell factory.
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Affiliation(s)
- Marta Papini
- Novo Nordisk Foundation Center for Biosustainability, Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, SE, 412 96, Sweden
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13
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Larsson C, Snoep JL, Norbeck J, Albers E. Flux balance analysis for ethylene formation in genetically engineered Saccharomyces cerevisiae. IET Syst Biol 2011; 5:245-51. [PMID: 21823755 DOI: 10.1049/iet-syb.2010.0027] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Biosynthesis of ethylene (ethene) is mainly performed by plants and some bacteria and fungi, via two distinct metabolic routes. Plants use two steps, starting with S-adenosylmethionine, while the ethylene-forming microbes perform an oxygen dependent reaction using 2-oxoglutarate and arginine. Introduction of these systems into Saccharomyces cerevisiae was studied in silico. The reactions were added to a metabolic network of yeast and flux over the two networks was optimised for maximal ethylene formation. The maximal ethylene yields obtained for the two systems were similar in the range of 7-8 mol ethylene/10 mol glucose. The microbial metabolic network was used for testing different strategies to increase the ethylene formation. It was suggested that supplementation of exogenous proline, using a solely NAD-coupled glutamate dehydrogenase, and using glutamate as the nitrogen source, could increase the ethylene formation. Comparison of these in silico results with published experimental data for yeast expressing the microbial system confirmed an increased ethylene formation when changing nitrogen source from ammonium to glutamate. The theoretical analysis methods indicated a much higher maximal yield per glucose for ethylene than was experimentally observed. However, such high ethylene yields could only be obtained with a concomitant very high respiration (per glucose). Accordingly, when ethylene production was optimised under the additional constraint of restricted respiratory capacity (i.e. limited to experimentally measured values) the theoretical maximal ethylene yield was much lower at 0.2/10 mol glucose, and closer to the experimentally observed values.
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Affiliation(s)
- C Larsson
- Chalmers University of Technology, Department of Chemical and Biological Engineering - Life Sciences, Gothenburg, Sweden
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Engqvist MKM, Kuhn A, Wienstroer J, Weber K, Jansen EEW, Jakobs C, Weber APM, Maurino VG. Plant D-2-hydroxyglutarate dehydrogenase participates in the catabolism of lysine especially during senescence. J Biol Chem 2011; 286:11382-90. [PMID: 21296880 DOI: 10.1074/jbc.m110.194175] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
D-2-Hydroxyglutarate dehydrogenase (D-2HGDH) catalyzes the specific and efficient oxidation of D-2-hydroxyglutarate (D-2HG) to 2-oxoglutarate using FAD as a cofactor. In this work, we demonstrate that D-2HGDH localizes to plant mitochondria and that its expression increases gradually during developmental and dark-induced senescence in Arabidopsis thaliana, indicating an enhanced demand of respiration of alternative substrates through this enzymatic system under these conditions. Using loss-of-function mutants in D-2HGDH (d2hgdh1) and stable isotope dilution LC-MS/MS, we found that the D-isomer of 2HG accumulated in leaves of d2hgdh1 during both forms of carbon starvation. In addition to this, d2hgdh1 presented enhanced levels of most TCA cycle intermediates and free amino acids. In contrast to the deleterious effects caused by a deficiency in D-2HGDH in humans, d2hgdh1 and overexpressing lines of D-2HGDH showed normal developmental and senescence phenotypes, indicating a mild role of D-2HGDH in the tested conditions. Moreover, metabolic fingerprinting of leaves of plants grown in media supplemented with putative precursors indicated that D-2HG most probably originates during the catabolism of lysine. Finally, the L-isomer of 2HG was also detected in leaf extracts, indicating that both chiral forms of 2HG participate in plant metabolism.
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Affiliation(s)
- Martin K M Engqvist
- Botanisches Institut, Biozentrum Köln, Universität zu Köln, Cologne, Germany
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15
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Pizarro F, Varela C, Martabit C, Bruno C, Pérez-Correa JR, Agosin E. Coupling kinetic expressions and metabolic networks for predicting wine fermentations. Biotechnol Bioeng 2008; 98:986-98. [PMID: 17497743 DOI: 10.1002/bit.21494] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Problematic fermentations are commonplace and cause wine industry producers substantial economic losses through wasted tank capacity and low value final products. Being able to predict such fermentations would enable enologists to take preventive actions. In this study we modeled sugar uptake kinetics and coupled them to a previously developed stoichiometric model, which describes the anaerobic metabolism of Saccharomyces cerevisiae. The resulting model was used to predict normal and slow fermentations under winemaking conditions. The effects of fermentation temperature and initial nitrogen concentration were modeled through an efficiency factor incorporated into the sugar uptake expressions. The model required few initial parameters to successfully reproduce glucose, fructose, and ethanol profiles of laboratory and industrial fermentations. Glycerol and biomass profiles were successfully predicted in nitrogen rich cultures. The time normal or slow wine fermentations needed to complete the process was predicted accurately, at different temperatures. Simulations with a model representing a genetically modified yeast fermentation, reproduced qualitatively well literature results regarding the formation of minor compounds involved in wine complexity and aroma. Therefore, the model also proves useful to explore the effects of genetic modifications on fermentation profiles.
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Affiliation(s)
- Francisco Pizarro
- Departamento de Ingeniería Química y Bioprocesos, Escuela de Ingeniería, Pontificia Universidad Católica de Chile, Santiago, Chile
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16
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Heux S, Cachon R, Dequin S. Cofactor engineering in Saccharomyces cerevisiae: Expression of a H2O-forming NADH oxidase and impact on redox metabolism. Metab Eng 2006; 8:303-14. [PMID: 16473032 DOI: 10.1016/j.ymben.2005.12.003] [Citation(s) in RCA: 114] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2005] [Revised: 12/06/2005] [Accepted: 12/13/2005] [Indexed: 10/25/2022]
Abstract
The pyridine nucleotides NAD(H) and NADP(H) play major roles in the formation of by-products. To analyse how Saccharomyces cerevisiae (S. cerevisiae) metabolism during growth on glucose might be altered when intracellular NADH pool is decreased, we expressed noxE encoding a water-forming NADH oxidase from Lactococcus lactis (L. lactis) in the S. cerevisiae strain V5. During batch fermentation under controlled microaeration conditions, expression of the NADH oxidase under the control of a yeast promoter lead to large decreases in the intracellular NADH concentration (five-fold) and NADH/NAD+ ratio (six-fold). This increased NADH consumption caused a large redistribution of metabolic fluxes. The ethanol, glycerol, succinate and hydroxyglutarate yields were significantly reduced as a result of the lower NADH availability, whereas the formation of more oxidized metabolites, acetaldehyde, acetate and acetoin was favoured. The biomass yield was low and consumption of glucose, at concentration above 10%, was impaired. The metabolic redistribution in cells expressing the NADH oxidase was a consequence of the maintenance of a redox balance and of the management of acetaldehyde formation, which accumulated at toxic levels early in the process.
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Affiliation(s)
- Stéphanie Heux
- UMR Sciences pour l'Oenologie, Microbiologie, INRA, 2 place Viala, F-34060 Montpellier Cedex 1, France
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Struys EA. D-2-Hydroxyglutaric aciduria: unravelling the biochemical pathway and the genetic defect. J Inherit Metab Dis 2006; 29:21-9. [PMID: 16601864 DOI: 10.1007/s10545-006-0317-9] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2005] [Accepted: 01/23/2006] [Indexed: 11/27/2022]
Abstract
D-2-Hydroxyglutaric aciduria (D-2-HGA) is a neurometabolic inherited disorder first described in 1980. In the following years, it became clear that the clinical phenotype of the disease varies widely from severe neonatal to asymptomatic. However, the sparse biochemical knowledge made D-2-HGA a poorly understood disease. Much progress has been made in the last five years in various studies, revealing two human enzymes that play a role in the metabolism of D-2-hydroxyglutarate (D-2-HG): hydroxyacid-oxoacid transhydrogenase (HOT) and D-2-HG dehydrogenase. HOT is expected to be responsible for the formation of D-2-HG, while D-2-HG dehydrogenase converts D-2-HG into 2-ketoglutarate. We demonstrated pathogenic mutations in the D2HGD gene in patients with D-2-HGA, helping to unravel the primary defect causing D-2-HGA. However, in approximately 50% of the patients with D-2-HGA examined, no pathogenic mutations have yet been found.
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Affiliation(s)
- Eduard A Struys
- VU University Medical Centre, De Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands.
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Jeun YS, Kim MD, Park YC, Lee TH, Yoo MS, Ryu YW, Seo JH. Expression of Azotobacter vinelandii soluble transhydrogenase perturbs xylose reductase-mediated conversion of xylose to xylitol by recombinant Saccharomyces cerevisiae. ACTA ACUST UNITED AC 2003. [DOI: 10.1016/j.molcatb.2003.07.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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19
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Camarasa C, Grivet JP, Dequin S. Investigation by 13C-NMR and tricarboxylic acid (TCA) deletion mutant analysis of pathways for succinate formation in Saccharomyces cerevisiae during anaerobic fermentation. MICROBIOLOGY (READING, ENGLAND) 2003; 149:2669-2678. [PMID: 12949191 DOI: 10.1099/mic.0.26007-0] [Citation(s) in RCA: 113] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
NMR isotopic filiation of 13C-labelled aspartate and glutamate was used to explore the tricarboxylic acid (TCA) pathway in Saccharomyces cerevisiae during anaerobic glucose fermentation. The assimilation of [3-13C]aspartate led to the formation of [2,3-13C]malate and [2,3-13C]succinate, with equal levels of 13C incorporation, whereas site-specific enrichment on C-2 and C-3 of succinate was detected only with [3-13C]glutamate. The non-random distribution of 13C labelling in malate and succinate demonstrates that the TCA pathway operates during yeast fermentation as both an oxidative and a reductive branch. The observed 13C distribution suggests that the succinate dehydrogenase (SDH) complex is not active during glucose fermentation. This hypothesis was tested by deleting the SDH1 gene encoding the flavoprotein subunit of the SDH complex. The growth, fermentation rate and metabolite profile of the sdh1 mutant were similar to those of the parental strain, demonstrating that SDH was indeed not active. Filiation experiments indicated the reductive branch of the TCA pathway was the main pathway for succinate production if aspartate was used as the nitrogen source, and that a surplus of succinate was produced by oxidative decarboxylation of 2-oxoglutarate if glutamate was the sole nitrogen source. Consistent with this finding, a kgd1 mutant displayed lower levels of succinate production on glutamate than on other nitrogen sources, and higher levels of oxoglutarate dehydrogenase activity were observed on glutamate. Thus, the reductive branch generating succinate via fumarate reductase operates independently of the nitrogen source. This pathway is the main source of succinate during fermentation, unless glutamate is the sole nitrogen source, in which case the oxidative decarboxylation of 2-oxoglutarate generates additional succinate.
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Affiliation(s)
- Carole Camarasa
- UMR-Sciences pour l'Œnologie, Microbiologie et Technologie des Fermentations, Institut National de la Recherche Agronomique, 2 Place Viala, 34060 Montpellier, France
| | - Jean-Philippe Grivet
- Centre de Biophysique Moléculaire, Centre National de la Recherche Scientifique et Université d'Orléans, Rue Charles Sadron, 45071 Orléans Cedex 2, France
| | - Sylvie Dequin
- UMR-Sciences pour l'Œnologie, Microbiologie et Technologie des Fermentations, Institut National de la Recherche Agronomique, 2 Place Viala, 34060 Montpellier, France
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Albers E, Laizé V, Blomberg A, Hohmann S, Gustafsson L. Ser3p (Yer081wp) and Ser33p (Yil074cp) are phosphoglycerate dehydrogenases in Saccharomyces cerevisiae. J Biol Chem 2003; 278:10264-72. [PMID: 12525494 DOI: 10.1074/jbc.m211692200] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Two genes YER081W and YIL074C, renamed SER3 and SER33, respectively, which encode phosphoglycerate dehydrogenases in Saccharomyces cerevisiae were identified. These dehydrogenases catalyze the first reaction of serine and glycine biosynthesis from the glycolytic metabolite 3-phosphoglycerate. Unlike either single mutant, the ser3Delta ser33Delta double mutant lacks detectable phosphoglycerate dehydrogenase activity and is auxotrophic for serine or glycine for growth on glucose media. However, the requirement for the SER-dependent "phosphoglycerate pathway" is conditional since the "glyoxylate" route of serine/glycine biosynthesis is glucose-repressed. Thus, in cells grown on ethanol both expression and activity of all SER-encoded proteins are low, including the remaining enzymes of the phosphoglycerate pathway, Ser1p and Ser2p. Moreover the available nitrogen source regulates the expression of SER genes. However, for only SER33, and not SER3, expression was regulated in relation to the available nitrogen source in a coordinated fashion with SER1 and SER2. Based on these mRNA data together with data on enzyme activities, Ser33p is likely to be the main isoenzyme of the phosphoglycerate pathway during growth on glucose. Moreover, since phosphoglycerate dehydrogenase activity requires NAD(+) as cofactor, deletion of SER3 and SER33 markedly affected redox metabolism as shown by substrate and product analysis.
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Affiliation(s)
- Eva Albers
- Department of Molecular Biotechnology, Chalmers University of Technology, Box 462, SE-405 30 Göteborg, Sweden.
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Kumar S, Punekar NS, SatyaNarayan V, Venkatesh KV. Metabolic fate of glutamate and evaluation of flux through the 4-aminobutyrate (GABA) shunt inAspergillus niger. Biotechnol Bioeng 2000. [DOI: 10.1002/(sici)1097-0290(20000305)67:5<575::aid-bit8>3.0.co;2-l] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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