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Wang S, Liu P, Shu W, Li C, Li H, Liu S, Xia J, Noorman H. Dynamic response of Aspergillus niger to single pulses of glucose with high and low concentrations. BIORESOUR BIOPROCESS 2019. [DOI: 10.1186/s40643-019-0251-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Suarez-Mendez C, Hanemaaijer M, ten Pierick A, Wolters J, Heijnen J, Wahl S. Interaction of storage carbohydrates and other cyclic fluxes with central metabolism: A quantitative approach by non-stationary 13C metabolic flux analysis. Metab Eng Commun 2016; 3:52-63. [PMID: 29468113 PMCID: PMC5779734 DOI: 10.1016/j.meteno.2016.01.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Revised: 11/30/2015] [Accepted: 01/19/2016] [Indexed: 12/11/2022] Open
Abstract
13C labeling experiments in aerobic glucose limited cultures of Saccharomyces cerevisiae at four different growth rates (0.054; 0.101, 0.207, 0.307 h-1) are used for calculating fluxes that include intracellular cycles (e.g., storage carbohydrate cycles, exchange fluxes with amino acids), which are rearranged depending on the growth rate. At low growth rates the impact of the storage carbohydrate recycle is relatively more significant than at high growth rates due to a higher concentration of these materials in the cell (up to 560-fold) and higher fluxes relative to the glucose uptake rate (up to 16%). Experimental observations suggest that glucose can be exported to the extracellular space, and that its source is related to storage carbohydrates, most likely via the export and subsequent extracellular breakdown of trehalose. This hypothesis is strongly supported by 13C-labeling experimental data, measured extracellular trehalose, and the corresponding flux estimations.
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Key Words
- 2PG, 2-phosphoglycerate
- 3PG, 3-phosphoglycerate
- 6PG, 6-phospho gluconate
- ACO, aconitate hydratase
- AK, adenylate kinase
- ALA, alanine
- ASP, aspartate
- Amino acids
- CoA, coenzyme-A
- DHAP, dihydroxy acetone phosphate
- DO, dissolved oxygen
- E4P, erythrose-4-phosphate
- ENO, phosphopyruvate hydratase
- F6P, fructose-6-phosphate
- FBA, fructose-bisphosphate aldolase
- FBP, fructose-1,6-bis-phosphate
- FMH, fumarate hydratase
- FUM, fumarate
- Flux estimation
- G1P, glucose-1-phosphate
- G6P, glucose-6-phosphate
- G6PDH, glucose-6-phosphate dehydrogenase
- GAP, glyceraldehyde-3-phosphate
- GAPDH&PGK, glyceraldehyde-3-phosphate dehydrogenase+phosphoglycerate kinase
- GLN, glutamine
- GLU, glutamate
- GLY, glycine
- GPM, phosphoglycerate mutase
- Glycogen
- IDMS, Isotope dilution mass spectrometry
- Iso-Cit, isocitrate
- LEU, leucine
- LYS, lysine
- MAL, malate
- METH, methionine
- Non-stationary 13C labeling
- OAA, oxaloacetate
- OUR, Oxygen uptake rate
- PEP, phospho-enol-pyruvate
- PFK, 6-phosphofructokinase
- PGI, glucose-6-phosphate isomerase
- PGM, phosphoglucomutase
- PMI, mannose-6-phosphate isomerase
- PPP, pentose phosphate pathway
- PRO, proline
- PYK, pyruvate kinase
- PYR, pyruvate
- RPE, ribulose-phosphate 3-epimerase
- RPI, ribose-5-phosphate isomerase
- Rib5P, ribose-5-phosphate
- Ribu5P, ribulose-5-phosphate
- S7P, sedoheptulose-7-phosphate
- SER, serine
- SUC, succinate
- T6P, trehalose-6-phosphate
- TCA, tricarboxylic acid cycle.
- TPP, trehalose- phosphatase
- TPS, alpha,alpha-trehalose-phosphate synthase
- Trehalose
- UDP, uridine-5-diphosphate
- UDPG, UDP-glucose
- UTP, uridine-5-triphosphate
- X5P, xylulose-5-phosphate
- α-KG, oxoglutarate
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Affiliation(s)
- C.A. Suarez-Mendez
- Department of Biotechnology, Delft University of Technology, Julianalaan 67 – 2628 BC Delft, The Netherlands
- Kluyver Centre for Genomics of Industrial Fermentation, P.O. Box 5057, 2600 GA Delft, The Netherlands
| | - M. Hanemaaijer
- Department of Biotechnology, Delft University of Technology, Julianalaan 67 – 2628 BC Delft, The Netherlands
| | - Angela ten Pierick
- Department of Biotechnology, Delft University of Technology, Julianalaan 67 – 2628 BC Delft, The Netherlands
| | - J.C. Wolters
- Department of Analytical Biochemistry, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - J.J. Heijnen
- Department of Biotechnology, Delft University of Technology, Julianalaan 67 – 2628 BC Delft, The Netherlands
- Kluyver Centre for Genomics of Industrial Fermentation, P.O. Box 5057, 2600 GA Delft, The Netherlands
| | - S.A. Wahl
- Department of Biotechnology, Delft University of Technology, Julianalaan 67 – 2628 BC Delft, The Netherlands
- Kluyver Centre for Genomics of Industrial Fermentation, P.O. Box 5057, 2600 GA Delft, The Netherlands
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Pires RH, Cataldi TR, Franceschini LM, Labate MV, Fusco-Almeida AM, Labate CA, Palma MS, Soares Mendes-Giannini MJ. Metabolic profiles of planktonic and biofilm cells of Candida orthopsilosis. Future Microbiol 2016; 11:1299-1313. [PMID: 27662506 DOI: 10.2217/fmb-2016-0025] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
AIM This study aims to understand which Candida orthopsilosis protein aids fungus adaptation upon its switching from planktonic growth to biofilm. MATERIALS & METHODS Ion mobility separation within mass spectrometry analysis combination were used. RESULTS Proteins mapped for different biosynthetic pathways showed that selective ribosome autophagy might occur in biofilms. Glucose, used as a carbon source in the glycolytic flux, changed to glycogen and trehalose. CONCLUSION Candida orthopsilosis expresses proteins that combine a variety of mechanisms to provide yeasts with the means to adjust the catalytic properties of enzymes. Adjustment of the enzymes helps modulate the biosynthesis/degradation rates of the available nutrients, in order to control and coordinate the metabolic pathways that enable cells to express an adequate response to nutrient availability.
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Affiliation(s)
- Regina Helena Pires
- Department of Clinical Analysis, Clinical Mycology Laboratory, Faculdade de Ciências Farmacêuticas, UNESP - Univ Estadual Paulista Júlio de Mesquita Filho, FCFAr, Rodovia Araraquara-Jaú, km1, Araraquara 14801-902, SP, Brazil
| | - Thaís Regiani Cataldi
- Department of Genetics, ESALQ/USP - Univ de São Paulo, Laboratory Max Feffer Plant Genetics, Av. Pádua Dias 11, Caixa Postal 83, Piracicaba 13400-970, SP, Brazil
| | - Livia Maria Franceschini
- Department of Genetics, ESALQ/USP - Univ de São Paulo, Laboratory Max Feffer Plant Genetics, Av. Pádua Dias 11, Caixa Postal 83, Piracicaba 13400-970, SP, Brazil
| | - Mônica Veneziano Labate
- Department of Genetics, ESALQ/USP - Univ de São Paulo, Laboratory Max Feffer Plant Genetics, Av. Pádua Dias 11, Caixa Postal 83, Piracicaba 13400-970, SP, Brazil
| | - Ana Marisa Fusco-Almeida
- Department of Clinical Analysis, Clinical Mycology Laboratory, Faculdade de Ciências Farmacêuticas, UNESP - Univ Estadual Paulista Júlio de Mesquita Filho, FCFAr, Rodovia Araraquara-Jaú, km1, Araraquara 14801-902, SP, Brazil
| | - Carlos Alberto Labate
- Department of Genetics, ESALQ/USP - Univ de São Paulo, Laboratory Max Feffer Plant Genetics, Av. Pádua Dias 11, Caixa Postal 83, Piracicaba 13400-970, SP, Brazil
| | - Mario Sérgio Palma
- Department of Biology, Lab. Structural Biology & Zoochemistry, CEIS, Univ Estadual Paulista Júlio de Mesquita Filho, UNESP, Institute of Biosciences, Av. 24-A, 1515. Bela Vista, Rio Claro 13506-900, SP, Brazil
| | - Maria José Soares Mendes-Giannini
- Department of Clinical Analysis, Clinical Mycology Laboratory, Faculdade de Ciências Farmacêuticas, UNESP - Univ Estadual Paulista Júlio de Mesquita Filho, FCFAr, Rodovia Araraquara-Jaú, km1, Araraquara 14801-902, SP, Brazil
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Richard L, Guillouet SE, Uribelarrea JL. Quantification of the transient and long-term response of Saccharomyces cerevisiae to carbon dioxide stresses of various intensities. Process Biochem 2014. [DOI: 10.1016/j.procbio.2014.07.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Wang G, Chu J, Noorman H, Xia J, Tang W, Zhuang Y, Zhang S. Prelude to rational scale-up of penicillin production: a scale-down study. Appl Microbiol Biotechnol 2014; 98:2359-69. [DOI: 10.1007/s00253-013-5497-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Revised: 12/19/2013] [Accepted: 12/22/2013] [Indexed: 12/16/2022]
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Ask M, Bettiga M, Duraiswamy VR, Olsson L. Pulsed addition of HMF and furfural to batch-grown xylose-utilizing Saccharomyces cerevisiae results in different physiological responses in glucose and xylose consumption phase. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:181. [PMID: 24341320 PMCID: PMC3878631 DOI: 10.1186/1754-6834-6-181] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 11/29/2013] [Indexed: 05/07/2023]
Abstract
BACKGROUND Pretreatment of lignocellulosic biomass generates a number of undesired degradation products that can inhibit microbial metabolism. Two of these compounds, the furan aldehydes 5-hydroxymethylfurfural (HMF) and 2-furaldehyde (furfural), have been shown to be an impediment for viable ethanol production. In the present study, HMF and furfural were pulse-added during either the glucose or the xylose consumption phase in order to dissect the effects of these inhibitors on energy state, redox metabolism, and gene expression of xylose-consuming Saccharomyces cerevisiae. RESULTS Pulsed addition of 3.9 g L-1 HMF and 1.2 g L-1 furfural during either the glucose or the xylose consumption phase resulted in distinct physiological responses. Addition of furan aldehydes in the glucose consumption phase was followed by a decrease in the specific growth rate and the glycerol yield, whereas the acetate yield increased 7.3-fold, suggesting that NAD(P)H for furan aldehyde conversion was generated by acetate synthesis. No change in the intracellular levels of NAD(P)H was observed 1 hour after pulsing, whereas the intracellular concentration of ATP increased by 58%. An investigation of the response at transcriptional level revealed changes known to be correlated with perturbations in the specific growth rate, such as protein and nucleotide biosynthesis. Addition of furan aldehydes during the xylose consumption phase brought about an increase in the glycerol and acetate yields, whereas the xylitol yield was severely reduced. The intracellular concentrations of NADH and NADPH decreased by 58 and 85%, respectively, hence suggesting that HMF and furfural drained the cells of reducing power. The intracellular concentration of ATP was reduced by 42% 1 hour after pulsing of inhibitors, suggesting that energy-requiring repair or maintenance processes were activated. Transcriptome profiling showed that NADPH-requiring processes such as amino acid biosynthesis and sulfate and nitrogen assimilation were induced 1 hour after pulsing. CONCLUSIONS The redox and energy metabolism were found to be more severely affected after pulsing of furan aldehydes during the xylose consumption phase than during glucose consumption. Conceivably, this discrepancy resulted from the low xylose utilization rate, hence suggesting that xylose metabolism is a feasible target for metabolic engineering of more robust xylose-utilizing yeast strains.
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Affiliation(s)
- Magnus Ask
- Department of Chemical and Biological Engineering, Industrial Biotechnology, Chalmers University of Technology, SE-41296, Gothenburg, Sweden
| | - Maurizio Bettiga
- Department of Chemical and Biological Engineering, Industrial Biotechnology, Chalmers University of Technology, SE-41296, Gothenburg, Sweden
| | - Varuni Raju Duraiswamy
- Department of Chemical and Biological Engineering, Industrial Biotechnology, Chalmers University of Technology, SE-41296, Gothenburg, Sweden
| | - Lisbeth Olsson
- Department of Chemical and Biological Engineering, Industrial Biotechnology, Chalmers University of Technology, SE-41296, Gothenburg, Sweden
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de Jonge L, Buijs NAA, Heijnen JJ, van Gulik WM, Abate A, Wahl SA. Flux response of glycolysis and storage metabolism during rapid feast/famine conditions inPenicillium chrysogenumusing dynamic13C labeling. Biotechnol J 2013; 9:372-85. [DOI: 10.1002/biot.201200260] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Revised: 09/04/2013] [Accepted: 10/17/2013] [Indexed: 12/29/2022]
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Systematic applications of metabolomics in metabolic engineering. Metabolites 2012; 2:1090-122. [PMID: 24957776 PMCID: PMC3901235 DOI: 10.3390/metabo2041090] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Revised: 11/29/2012] [Accepted: 12/10/2012] [Indexed: 02/05/2023] Open
Abstract
The goals of metabolic engineering are well-served by the biological information provided by metabolomics: information on how the cell is currently using its biochemical resources is perhaps one of the best ways to inform strategies to engineer a cell to produce a target compound. Using the analysis of extracellular or intracellular levels of the target compound (or a few closely related molecules) to drive metabolic engineering is quite common. However, there is surprisingly little systematic use of metabolomics datasets, which simultaneously measure hundreds of metabolites rather than just a few, for that same purpose. Here, we review the most common systematic approaches to integrating metabolite data with metabolic engineering, with emphasis on existing efforts to use whole-metabolome datasets. We then review some of the most common approaches for computational modeling of cell-wide metabolism, including constraint-based models, and discuss current computational approaches that explicitly use metabolomics data. We conclude with discussion of the broader potential of computational approaches that systematically use metabolomics data to drive metabolic engineering.
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