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Vos T, Hakkaart XDV, de Hulster EAF, van Maris AJA, Pronk JT, Daran-Lapujade P. Maintenance-energy requirements and robustness of Saccharomyces cerevisiae at aerobic near-zero specific growth rates. Microb Cell Fact 2016; 15:111. [PMID: 27317316 PMCID: PMC4912818 DOI: 10.1186/s12934-016-0501-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 05/31/2016] [Indexed: 11/24/2022] Open
Abstract
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, metabolically active yeast cultures is a first step towards developing S. cerevisiae as a robust, non-growing cell factory. Microbial physiology at near-zero growth rates can be studied in retentostats, which are continuous-cultivation systems with full biomass retention. Hitherto, retentostat studies on S. cerevisiae have focused on anaerobic conditions, which bear limited relevance for aerobic industrial processes. The present study uses aerobic, glucose-limited retentostats to explore the physiology of non-dividing, respiring S. cerevisiae cultures, with a focus on industrially relevant features. Results Retentostat feeding regimes for smooth transition from exponential growth in glucose-limited chemostat cultures to near-zero growth rates were obtained by model-aided experimental design. During 20 days of retentostats cultivation, the specific growth rate gradually decreased from 0.025 h−1 to below 0.001 h−1, while culture viability remained above 80 %. The maintenance requirement for ATP (mATP) was estimated at 0.63 ± 0.04 mmol ATP (g biomass)−1 h−1, which is ca. 35 % lower than previously estimated for anaerobic retentostats. Concomitant with decreasing growth rate in aerobic retentostats, transcriptional down-regulation of genes involved in biosynthesis and up-regulation of stress-responsive genes resembled transcriptional regulation patterns observed for anaerobic retentostats. The heat-shock tolerance in aerobic retentostats far exceeded previously reported levels in stationary-phase batch cultures. While in situ metabolic fluxes in retentostats were intentionally low due to extreme caloric restriction, off-line measurements revealed that cultures retained a high metabolic capacity. Conclusions This study provides the most accurate estimation yet of the maintenance-energy coefficient in aerobic cultures of S. cerevisiae, which is a key parameter for modelling of industrial aerobic, glucose-limited fed-batch processes. The observed extreme heat-shock tolerance and high metabolic capacity at near-zero growth rates demonstrate the intrinsic potential of S. cerevisiae as a robust, non-dividing microbial cell factory for energy-intensive products. Electronic supplementary material The online version of this article (doi:10.1186/s12934-016-0501-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tim Vos
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Xavier D V Hakkaart
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Erik A F de Hulster
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Antonius J A van Maris
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Jack T Pronk
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Pascale Daran-Lapujade
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands.
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van Rossum HM, Kozak BU, Pronk JT, van Maris AJA. Engineering cytosolic acetyl-coenzyme A supply in Saccharomyces cerevisiae: Pathway stoichiometry, free-energy conservation and redox-cofactor balancing. Metab Eng 2016; 36:99-115. [PMID: 27016336 DOI: 10.1016/j.ymben.2016.03.006] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Revised: 03/20/2016] [Accepted: 03/21/2016] [Indexed: 11/18/2022]
Abstract
Saccharomyces cerevisiae is an important industrial cell factory and an attractive experimental model for evaluating novel metabolic engineering strategies. Many current and potential products of this yeast require acetyl coenzyme A (acetyl-CoA) as a precursor and pathways towards these products are generally expressed in its cytosol. The native S. cerevisiae pathway for production of cytosolic acetyl-CoA consumes 2 ATP equivalents in the acetyl-CoA synthetase reaction. Catabolism of additional sugar substrate, which may be required to generate this ATP, negatively affects product yields. Here, we review alternative pathways that can be engineered into yeast to optimize supply of cytosolic acetyl-CoA as a precursor for product formation. Particular attention is paid to reaction stoichiometry, free-energy conservation and redox-cofactor balancing of alternative pathways for acetyl-CoA synthesis from glucose. A theoretical analysis of maximally attainable yields on glucose of four compounds (n-butanol, citric acid, palmitic acid and farnesene) showed a strong product dependency of the optimal pathway configuration for acetyl-CoA synthesis. Moreover, this analysis showed that combination of different acetyl-CoA production pathways may be required to achieve optimal product yields. This review underlines that an integral analysis of energy coupling and redox-cofactor balancing in precursor-supply and product-formation pathways is crucial for the design of efficient cell factories.
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Affiliation(s)
- Harmen M van Rossum
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
| | - Barbara U Kozak
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
| | - Jack T Pronk
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
| | - Antonius J A van Maris
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands.
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Tomàs-Gamisans M, Ferrer P, Albiol J. Integration and Validation of the Genome-Scale Metabolic Models of Pichia pastoris: A Comprehensive Update of Protein Glycosylation Pathways, Lipid and Energy Metabolism. PLoS One 2016; 11:e0148031. [PMID: 26812499 PMCID: PMC4734642 DOI: 10.1371/journal.pone.0148031] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 01/12/2016] [Indexed: 01/21/2023] Open
Abstract
Motivation Genome-scale metabolic models (GEMs) are tools that allow predicting a phenotype from a genotype under certain environmental conditions. GEMs have been developed in the last ten years for a broad range of organisms, and are used for multiple purposes such as discovering new properties of metabolic networks, predicting new targets for metabolic engineering, as well as optimizing the cultivation conditions for biochemicals or recombinant protein production. Pichia pastoris is one of the most widely used organisms for heterologous protein expression. There are different GEMs for this methylotrophic yeast of which the most relevant and complete in the published literature are iPP668, PpaMBEL1254 and iLC915. However, these three models differ regarding certain pathways, terminology for metabolites and reactions and annotations. Moreover, GEMs for some species are typically built based on the reconstructed models of related model organisms. In these cases, some organism-specific pathways could be missing or misrepresented. Results In order to provide an updated and more comprehensive GEM for P. pastoris, we have reconstructed and validated a consensus model integrating and merging all three existing models. In this step a comprehensive review and integration of the metabolic pathways included in each one of these three versions was performed. In addition, the resulting iMT1026 model includes a new description of some metabolic processes. Particularly new information described in recently published literature is included, mainly related to fatty acid and sphingolipid metabolism, glycosylation and cell energetics. Finally the reconstructed model was tested and validated, by comparing the results of the simulations with available empirical physiological datasets results obtained from a wide range of experimental conditions, such as different carbon sources, distinct oxygen availability conditions, as well as producing of two different recombinant proteins. In these simulations, the iMT1026 model has shown a better performance than the previous existing models.
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Affiliation(s)
- Màrius Tomàs-Gamisans
- Departament d'Enginyeria Química, Biològica i Ambiental, Universitat Autònoma de Barcelona, 08193 Bellaterra (Cerdanyola del Vallès), Barcelona, Spain
| | - Pau Ferrer
- Departament d'Enginyeria Química, Biològica i Ambiental, Universitat Autònoma de Barcelona, 08193 Bellaterra (Cerdanyola del Vallès), Barcelona, Spain
| | - Joan Albiol
- Departament d'Enginyeria Química, Biològica i Ambiental, Universitat Autònoma de Barcelona, 08193 Bellaterra (Cerdanyola del Vallès), Barcelona, Spain
- * E-mail:
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Metabolic flux analysis model for optimizing xylose conversion into ethanol by the natural C5-fermenting yeast Candida shehatae. Appl Microbiol Biotechnol 2015; 100:1489-1499. [DOI: 10.1007/s00253-015-7085-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Revised: 09/17/2015] [Accepted: 10/13/2015] [Indexed: 10/22/2022]
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Janthanomsuk P, Verduyn C, Chauvatcharin S. Improved docosahexaenoic acid production in Aurantiochytrium by glucose limited pH-auxostat fed-batch cultivation. BIORESOURCE TECHNOLOGY 2015; 196:592-599. [PMID: 26298403 DOI: 10.1016/j.biortech.2015.08.023] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 08/07/2015] [Accepted: 08/08/2015] [Indexed: 06/04/2023]
Abstract
Fed-batch, pH auxostat cultivation of the docosahexaenoic acid (DHA)-producing microorganism Aurantiochytrium B072 was performed to obtain high cell density and record high productivity of both total fatty acid (TFA) and DHA. Using glucose feeding by carbon excess (C-excess) and by C-limitation at various feeding rates (70%, 50% or 20% of C-excess), high biomass density was obtained and DHA/TFA content (w/w) was improved from 30% to 37% with a 50% glucose feed rate when compared with C-excess. To understand the biochemistry behind these improvements, lipogenic enzyme assays and in silico metabolic flux calculations were used and revealed that enzyme activity and C-fluxes to TFA were reduced with C-limited feeding but that the carbon flux to the polyketide synthase pathway increased relative to the fatty acid synthase pathway. As a result, a new strategy to improve the DHA to TFA content while maintaining relatively high DHA productivity is proposed.
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Affiliation(s)
- Panyawut Janthanomsuk
- Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Cornelis Verduyn
- Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Somchai Chauvatcharin
- Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand.
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Optimization of lipid production with a genome-scale model of Yarrowia lipolytica. BMC SYSTEMS BIOLOGY 2015; 9:72. [PMID: 26503450 PMCID: PMC4623914 DOI: 10.1186/s12918-015-0217-4] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 10/07/2015] [Indexed: 12/19/2022]
Abstract
Background Yarrowia lipolytica is a non-conventional yeast that is extensively investigated for its ability to excrete citrate or to accumulate large amounts of storage lipids, which is of great significance for single cell oil production. Both traits are thus of interest for basic research as well as for biotechnological applications but they typically occur simultaneously thus lowering the respective yields. Therefore, engineering of strains with high lipid content relies on novel concepts such as computational simulation to better understand the two competing processes and to eliminate citrate excretion. Results Using a genome-scale model (GSM) of baker's yeast as a scaffold, we reconstructed the metabolic network of Y. lipolytica and optimized it for use in flux balance analysis (FBA), with the aim to simulate growth and lipid production phases of this yeast. We validated our model and found the predictions of the growth behavior of Y. lipolytica in excellent agreement with experimental data. Based on these data, we successfully designed a fed-batch strategy to avoid citrate excretion during the lipid production phase. Further analysis of the network suggested that the oxygen demand of Y. lipolytica is reduced upon induction of lipid synthesis. According to this finding we hypothesized that a reduced aeration rate might induce lipid accumulation. This prediction was indeed confirmed experimentally. In a fermentation combining these two strategies lipid content of the biomass was increased by 80 %, and lipid yield was improved more than four-fold, compared to standard conditions. Conclusions Genome scale network reconstructions provide a powerful tool to predict the effects of genetic modifications and the metabolic response to environmental conditions. The high accuracy and the predictive value of a newly reconstructed GSM of Y. lipolytica to optimize growth conditions for lipid accumulation are demonstrated. Based on these findings, further strategies for engineering Y. lipolytica towards higher efficiency in single cell oil production are discussed. Electronic supplementary material The online version of this article (doi:10.1186/s12918-015-0217-4) contains supplementary material, which is available to authorized users.
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Bisschops MM, Vos T, Martínez-Moreno R, Cortés PT, Pronk JT, Daran-Lapujade P. Oxygen availability strongly affects chronological lifespan and thermotolerance in batch cultures of Saccharomyces cerevisiae. MICROBIAL CELL (GRAZ, AUSTRIA) 2015; 2:429-444. [PMID: 28357268 PMCID: PMC5349206 DOI: 10.15698/mic2015.11.238] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 09/13/2015] [Indexed: 01/08/2023]
Abstract
Stationary-phase (SP) batch cultures of Saccharomyces cerevisiae, in which growth has been arrested by carbon-source depletion, are widely applied to study chronological lifespan, quiescence and SP-associated robustness. Based on this type of experiments, typically performed under aerobic conditions, several roles of oxygen in aging have been proposed. However, SP in anaerobic yeast cultures has not been investigated in detail. Here, we use the unique capability of S. cerevisiae to grow in the complete absence of oxygen to directly compare SP in aerobic and anaerobic bioreactor cultures. This comparison revealed strong positive effects of oxygen availability on adenylate energy charge, longevity and thermotolerance during SP. A low thermotolerance of anaerobic batch cultures was already evident during the exponential growth phase and, in contrast to the situation in aerobic cultures, was not substantially increased during transition into SP. A combination of physiological and transcriptome analysis showed that the slow post-diauxic growth phase on ethanol, which precedes SP in aerobic, but not in anaerobic cultures, endowed cells with the time and resources needed for inducing longevity and thermotolerance. When combined with literature data on acquisition of longevity and thermotolerance in retentostat cultures, the present study indicates that the fast transition from glucose excess to SP in anaerobic cultures precludes acquisition of longevity and thermotolerance. Moreover, this study demonstrates the importance of a preceding, calorie-restricted conditioning phase in the acquisition of longevity and stress tolerance in SP yeast cultures, irrespective of oxygen availability.
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Affiliation(s)
- Markus M. Bisschops
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
- Current address: Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering & The Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg, Sweden
| | - Tim Vos
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Rubén Martínez-Moreno
- Instituto de Ciencias de la Vid y del Vino, CSIC, Universidad de La Rioja, Gobierno de La Rioja, Logroño, Spain
- Current address: Quercus Europe S.L., L’Hospitalet de Llobregat, Catalonia, Spain
| | - Pilar T. Cortés
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Jack T. Pronk
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
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Goyal N, Padhiary M, Karimi IA, Zhou Z. Flux measurements and maintenance energy for carbon dioxide utilization by Methanococcus maripaludis. Microb Cell Fact 2015; 14:146. [PMID: 26376868 PMCID: PMC4573941 DOI: 10.1186/s12934-015-0336-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 09/03/2015] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND The rapidly growing mesophilic methanogen Methanococcus maripaludis S2 has a unique ability to consume both CO2 and N2, the main components of a flue gas, and produce methane with H2 as the electron donor. The existing literature lacks experimental measurements of CO2 and H2 uptake rates and CH4 production rates on M. maripaludis. Furthermore, it lacks estimates of maintenance energies for use with genome-scale models. In this paper, we performed batch culture experiments on M. maripaludis S2 using CO2 as the sole carbon substrate to quantify three key extracellular fluxes (CO2, H2, and CH4) along with specific growth rates. For precise computation of these fluxes from experimental measurements, we developed a systematic process simulation approach. Then, using an existing genome-scale model, we proposed an optimization procedure to estimate maintenance energy parameters: growth associated maintenance (GAM) and non-growth associated maintenance (NGAM). RESULTS The measured extracellular fluxes for M. maripaludis showed excellent agreement with in silico predictions from a validated genome-scale model (iMM518) for NGAM = 7.836 mmol/gDCW/h and GAM = 27.14 mmol/gDCW. M. maripaludis achieved a CO2 to CH4 conversion yield of 70-95 % and a growth yield of 3.549 ± 0.149 g DCW/mol CH4 during the exponential phase. The ATP gain of 0.35 molATP/molCH4 for M. maripaludis, computed using NGAM, is in the acceptable range of 0.3-0.7 mol ATP/molCH4 reported for methanogens. Interestingly, the uptake distribution of amino acids, quantified using iMM518, confirmed alanine to be the most preferred amino acids for growth and methanogenesis. CONCLUSIONS This is the first study to report experimental gas consumption and production rates for the growth of M. maripaludis on CO2 and H2 in minimal media. A systematic process simulation and optimization procedure was successfully developed to precisely quantify extracellular fluxes along with cell growth and maintenance energy parameters. Our growth yields, ATP gain, and energy parameters fall within acceptable ranges known in the literature for hydrogenotrophic methanogens.
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Affiliation(s)
- Nishu Goyal
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore.
| | - Mrutyunjay Padhiary
- Department of Civil and Environmental Engineering, National University of Singapore, 1 Engineering Drive 2, Singapore, 117576, Singapore.
| | - Iftekhar A Karimi
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore.
| | - Zhi Zhou
- Department of Civil and Environmental Engineering, National University of Singapore, 1 Engineering Drive 2, Singapore, 117576, Singapore.
- Division of Environmental and Ecological Engineering and School of Civil Engineering, Purdue University, 550 Stadium Mall Drive, West Lafayette, IN, 47907, USA.
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Vos T, de la Torre Cortés P, van Gulik WM, Pronk JT, Daran-Lapujade P. Growth-rate dependency of de novo resveratrol production in chemostat cultures of an engineered Saccharomyces cerevisiae strain. Microb Cell Fact 2015; 14:133. [PMID: 26369953 PMCID: PMC4570684 DOI: 10.1186/s12934-015-0321-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 08/21/2015] [Indexed: 01/28/2023] Open
Abstract
Introduction Saccharomyces cerevisiae has become a popular host for production of non-native compounds. The metabolic pathways involved generally require a net input of energy. To maximize the ATP yield on sugar in S. cerevisiae, industrial cultivation is typically performed in aerobic, sugar-limited fed-batch reactors which, due to constraints in oxygen transfer and cooling capacities, have to be operated at low specific growth rates. Because intracellular levels of key metabolites are growth-rate dependent, slow growth can significantly affect biomass-specific productivity. Using an engineered Saccharomyces cerevisiae strain expressing a heterologous pathway for resveratrol production as a model energy-requiring product, the impact of specific growth rate on yeast physiology and productivity was investigated in aerobic, glucose-limited chemostat cultures. Results Stoichiometric analysis revealed that de novo resveratrol production from glucose requires 13 moles of ATP per mole of produced resveratrol. The biomass-specific production rate of resveratrol showed a strong positive correlation with the specific growth rate. At low growth rates a substantial fraction of the carbon source was invested in cellular maintenance-energy requirements (e.g. 27 % at 0.03 h−1). This distribution of resources was unaffected by resveratrol production. Formation of the by-products coumaric, phloretic and cinnamic acid had no detectable effect on maintenance energy requirement and yeast physiology in chemostat. Expression of the heterologous pathway led to marked differences in transcript levels in the resveratrol-producing strain, including increased expression levels of genes involved in pathways for precursor supply (e.g. ARO7 and ARO9 involved in phenylalanine biosynthesis). The observed strong differential expression of many glucose-responsive genes in the resveratrol producer as compared to a congenic reference strain could be explained from higher residual glucose concentrations and higher relative growth rates in cultures of the resveratrol producer. Conclusions De novo resveratrol production by engineered S. cerevisiae is an energy demanding process. Resveratrol production by an engineered strain exhibited a strong correlation with specific growth rate. Since industrial production in fed-batch reactors typically involves low specific growth rates, this study emphasizes the need for uncoupling growth and product formation via energy-requiring pathways. Electronic supplementary material The online version of this article (doi:10.1186/s12934-015-0321-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tim Vos
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC, Delft, The Netherlands.
| | - Pilar de la Torre Cortés
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC, Delft, The Netherlands.
| | - Walter M van Gulik
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC, Delft, The Netherlands.
| | - Jack T Pronk
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC, Delft, The Netherlands.
| | - Pascale Daran-Lapujade
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC, Delft, The Netherlands.
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Abstract
The author looks back on his development in microbiology and yeast research, and on the establishment in Delft of the FEMS Central Office, FEMS Publications Office and the birth of FEMS Yeast Research.
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Affiliation(s)
- W Alexander Scheffers
- Department of Microbiology, Delft University of Technology, Julianalaan 67A, NL-2628 BC, the Netherlands
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Transcriptional remodeling in response to transfer upon carbon-limited or metformin-supplemented media in S. cerevisiae and its effect on chronological life span. Appl Microbiol Biotechnol 2015; 99:6775-89. [PMID: 26099330 DOI: 10.1007/s00253-015-6728-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 05/17/2015] [Accepted: 05/25/2015] [Indexed: 12/16/2022]
Abstract
One of the factors affecting chronological life span (CLS) in budding yeast is nutrient, especially carbon limitation. Aside from metabolites in the growth medium such as glucose, amino acids, and acetic acid, many pharmaceuticals have also been proven to alter CLS. Besides their impact on life span, these drugs are also prospective chemicals to treat the age-associated diseases, so the identification of their action mechanism and their potential side effects is of crucial importance. In this study, the effects of caloric restriction and metformin, a dietary mimetic pharmaceutical, on yeast CLS are compared. Saccharomyces cerevisiae cells grown in synthetic dextrose complete (SDC) up to mid-exponential phase were either treated with metformin or were subjected to glucose limitation. The impacts of these perturbations were analyzed via transcriptomics, and the common (stimulation of glucose uptake, induction of mitochondrial maintenance, and reduction of protein translation) and divergent (stimulation of aerobic respiration and reprogramming of respiratory electron transport chain (ETC)) cellular responses specific to each treatment were determined. These results revealed that both glucose limitation and metformin treatment stimulate CLS extension and involve the mitochondrial function, probably by creating an efficient mitochondria-to-nucleus signaling of either aerobic respiration or ETC signaling stimulation, respectively.
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Dikicioglu D, Kırdar B, Oliver SG. Biomass composition: the "elephant in the room" of metabolic modelling. Metabolomics 2015; 11:1690-1701. [PMID: 26491422 PMCID: PMC4605984 DOI: 10.1007/s11306-015-0819-2] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2015] [Accepted: 05/25/2015] [Indexed: 12/17/2022]
Abstract
Genome-scale stoichiometric models, constrained to optimise biomass production are often used to predict mutant phenotypes. However, for Saccharomyces cerevisiae, the representation of biomass in its metabolic model has hardly changed in over a decade, despite major advances in analytical technologies. Here, we use the stoichiometric model of the yeast metabolic network to show that its ability to predict mutant phenotypes is particularly poor for genes encoding enzymes involved in energy generation. We then identify apparently inefficient energy-generating pathways in the model and demonstrate that the network suffers from the high energy burden associated with the generation of biomass. This is tightly connected to the availability of phosphate since this macronutrient links energy generation and structural biomass components. Variations in yeast's biomass composition, within experimentally-determined bounds, demonstrated that flux distributions are very sensitive to such changes and to the identity of the growth-limiting nutrient. The predictive accuracy of the yeast metabolic model is, therefore, compromised by its failure to represent biomass composition in an accurate and context-dependent manner.
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Affiliation(s)
- Duygu Dikicioglu
- Cambridge Systems Biology Centre & Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA UK
- Department of Chemical Engineering, Bogazici University, Istanbul, Turkey
| | - Betul Kırdar
- Department of Chemical Engineering, Bogazici University, Istanbul, Turkey
| | - Stephen G. Oliver
- Cambridge Systems Biology Centre & Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA UK
- Department of Chemical Engineering, Bogazici University, Istanbul, Turkey
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Contreras A, Hidalgo C, Schmidt S, Henschke PA, Curtin C, Varela C. The application of non-Saccharomyces yeast in fermentations with limited aeration as a strategy for the production of wine with reduced alcohol content. Int J Food Microbiol 2015; 205:7-15. [PMID: 25866906 DOI: 10.1016/j.ijfoodmicro.2015.03.027] [Citation(s) in RCA: 116] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Revised: 03/10/2015] [Accepted: 03/24/2015] [Indexed: 10/23/2022]
Abstract
High alcohol concentrations reduce the complexity of wine sensory properties. In addition, health and economic drivers have the wine industry actively seeking technologies that facilitate the production of wines with lower alcohol content. One of the simplest approaches to achieve this aim would be the use of wine yeast strains which are less efficient at transforming grape sugars into ethanol, however commercially available wine yeasts produce very similar ethanol yields. Non-conventional yeast, in particular non-Saccharomyces species, have shown potential for producing wines with lower alcohol content. These yeasts are naturally present in the early stages of fermentation but in general are not capable of completing alcoholic fermentation. We have evaluated 48 non-Saccharomyces isolates to identify strains that, with limited aeration and in sequential inoculation regimes with S. cerevisiae, could be used for the production of wine with lower ethanol concentration. Two of these, Torulaspora delbrueckii AWRI1152 and Zygosaccharomyces bailii AWRI1578, enabled the production of wine with reduced ethanol concentration under limited aerobic conditions. Depending on the aeration regime T. delbrueckii AWRI1152 and Z. bailii AWRI1578 showed a reduction in ethanol concentration of 1.5% (v/v) and 2.0% (v/v) respectively, compared to the S. cerevisiae anaerobic control.
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Affiliation(s)
- A Contreras
- The Australian Wine Research Institute, PO Box 197, Glen Osmond, Adelaide, South Australia, 5064, Australia; Department of Chemical and Bioprocess Engineering, College of Engineering, Pontificia Universidad Católica de Chile, Casilla 306 Correo 22, Santiago, Chile
| | - C Hidalgo
- The Australian Wine Research Institute, PO Box 197, Glen Osmond, Adelaide, South Australia, 5064, Australia; Instituto de Investigaciones Agropecuarias, La Platina Research Station, Avenida Santa Rosa 11610, La Pintana, 8831314, Santiago, Chile
| | - S Schmidt
- The Australian Wine Research Institute, PO Box 197, Glen Osmond, Adelaide, South Australia, 5064, Australia
| | - P A Henschke
- The Australian Wine Research Institute, PO Box 197, Glen Osmond, Adelaide, South Australia, 5064, Australia; School of Agriculture, Food and Wine, The University of Adelaide, PMB 1, Glen Osmond, SA 5064, Australia
| | - C Curtin
- The Australian Wine Research Institute, PO Box 197, Glen Osmond, Adelaide, South Australia, 5064, Australia
| | - C Varela
- The Australian Wine Research Institute, PO Box 197, Glen Osmond, Adelaide, South Australia, 5064, Australia.
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Hebly M, Brickwedde A, Bolat I, Driessen MRM, de Hulster EAF, van den Broek M, Pronk JT, Geertman JM, Daran JM, Daran-Lapujade P. S. cerevisiae × S. eubayanus interspecific hybrid, the best of both worlds and beyond. FEMS Yeast Res 2015; 15:fov005. [PMID: 25743788 DOI: 10.1093/femsyr/fov005] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/27/2015] [Indexed: 12/16/2022] Open
Abstract
Saccharomyces pastorianus lager-brewing yeasts have descended from natural hybrids of S. cerevisiae and S. eubayanus. Their alloploidy has undoubtedly contributed to successful domestication and industrial exploitation. To understand the early events that have led to the predominance of S. pastorianus as lager-brewing yeast, an interspecific hybrid between S. cerevisiae and S. eubayanus was experimentally constructed. Alloploidy substantially improved the performance of the S. cerevisiae × S. eubayanus hybrid as compared to either parent regarding two cardinal features of brewing yeasts: tolerance to low temperature and oligosaccharide utilization. The hybrid's S. eubayanus subgenome conferred better growth rates and biomass yields at low temperature, both on glucose and on maltose. Conversely, the ability of the hybrid to consume maltotriose, which was absent in the S. eubayanus CBS12357 type strain, was inherited from its S. cerevisiae parent. The S. cerevisiae × S. eubayanus hybrid even outperformed its parents, a phenomenon known as transgression, suggesting that fast growth at low temperature and oligosaccharide utilization may have been key selective advantages of the natural hybrids in brewing environments. To enable sequence comparisons of the parental and hybrid strains, the genome of S. eubayanus CBS12357 type strain (Patagonian isolate) was resequenced, resulting in an improved publicly available sequence assembly.
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Affiliation(s)
- Marit Hebly
- Department of Biotechnology, Delft University of Technology, 2628 BC Delft, the Netherlands Netherlands Consortium for Systems Biology, 1098 XH Amsterdam, the Netherlands
| | - Anja Brickwedde
- Department of Biotechnology, Delft University of Technology, 2628 BC Delft, the Netherlands
| | - Irina Bolat
- Department of Biotechnology, Delft University of Technology, 2628 BC Delft, the Netherlands
| | - Maureen R M Driessen
- Department of Biotechnology, Delft University of Technology, 2628 BC Delft, the Netherlands
| | - Erik A F de Hulster
- Department of Biotechnology, Delft University of Technology, 2628 BC Delft, the Netherlands
| | - Marcel van den Broek
- Department of Biotechnology, Delft University of Technology, 2628 BC Delft, the Netherlands
| | - Jack T Pronk
- Department of Biotechnology, Delft University of Technology, 2628 BC Delft, the Netherlands Netherlands Consortium for Systems Biology, 1098 XH Amsterdam, the Netherlands Platform Green Synthetic Biology, 2628 BC Delft, the Netherlands
| | - Jan-Maarten Geertman
- Heineken Global Supply Chain, Technology & Policies, 2382 PH Zoeterwoude, the Netherlands
| | - Jean-Marc Daran
- Department of Biotechnology, Delft University of Technology, 2628 BC Delft, the Netherlands Platform Green Synthetic Biology, 2628 BC Delft, the Netherlands
| | - Pascale Daran-Lapujade
- Department of Biotechnology, Delft University of Technology, 2628 BC Delft, the Netherlands Netherlands Consortium for Systems Biology, 1098 XH Amsterdam, the Netherlands
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65
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Klein T, Niklas J, Heinzle E. Engineering the supply chain for protein production/secretion in yeasts and mammalian cells. J Ind Microbiol Biotechnol 2015; 42:453-64. [PMID: 25561318 DOI: 10.1007/s10295-014-1569-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 12/16/2014] [Indexed: 12/14/2022]
Abstract
Metabolic bottlenecks play an increasing role in yeasts and mammalian cells applied for high-performance production of proteins, particularly of pharmaceutical ones that require complex posttranslational modifications. We review the present status and developments focusing on the rational metabolic engineering of such cells to optimize the supply chain for building blocks and energy. Methods comprise selection of beneficial genetic modifications, rational design of media and feeding strategies. Design of better producer cells based on whole genome-wide metabolic network analysis becomes increasingly possible. High-resolution methods of metabolic flux analysis for the complex networks in these compartmented cells are increasingly available. We discuss phenomena that are common to both types of organisms but also those that are different with respect to the supply chain for the production and secretion of pharmaceutical proteins.
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Affiliation(s)
- Tobias Klein
- Research Area Biochemical Engineering, Institute of Chemical Engineering, Vienna University of Technology, Gumpendorfer Strasse 1a, 1060, Vienna, Austria
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66
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Goyal N, Widiastuti H, Karimi IA, Zhou Z. A genome-scale metabolic model of Methanococcus maripaludis S2 for CO2 capture and conversion to methane. MOLECULAR BIOSYSTEMS 2014; 10:1043-54. [PMID: 24553424 DOI: 10.1039/c3mb70421a] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Methane is a major energy source for heating and electricity. Its production by methanogenic bacteria is widely known in nature. M. maripaludis S2 is a fully sequenced hydrogenotrophic methanogen and an excellent laboratory strain with robust genetic tools. However, a quantitative systems biology model to complement these tools is absent in the literature. To understand and enhance its methanogenesis from CO2, this work presents the first constraint-based genome-scale metabolic model (iMM518). It comprises 570 reactions, 556 distinct metabolites, and 518 genes along with gene-protein-reaction (GPR) associations, and covers 30% of open reading frames (ORFs). The model was validated using biomass growth data and experimental phenotypic studies from the literature. Its comparison with the in silico models of Methanosarcina barkeri, Methanosarcina acetivorans, and Sulfolobus solfataricus P2 shows M. maripaludis S2 to be a better organism for producing methane. Using the model, genes essential for growth were identified, and the efficacies of alternative carbon, hydrogen and nitrogen sources were studied. The model can predict the effects of reengineering M. maripaludis S2 to guide or expedite experimental efforts.
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Affiliation(s)
- Nishu Goyal
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117576.
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67
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Guo Z, Olsson L. Physiological response of Saccharomyces cerevisiae to weak acids present in lignocellulosic hydrolysate. FEMS Yeast Res 2014; 14:1234-48. [PMID: 25331461 DOI: 10.1111/1567-1364.12221] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2014] [Revised: 10/05/2014] [Accepted: 10/08/2014] [Indexed: 01/15/2023] Open
Abstract
Weak acids are present in lignocellulosic hydrolysate as potential inhibitors that can hamper the use of this renewable resource for fuel and chemical production. To study the effects of weak acids on yeast growth, physiological investigations were carried out in batch cultures using glucose as carbon source in the presence of acetic, formic, levulinic, and vanillic acid at three different concentrations at pH 5.0. The results showed that acids at moderate concentrations can stimulate the glycolytic flux, while higher levels of acid slow down the glycolytic flux for both aerobically and anaerobically grown yeast cells. In particular, the flux distribution between respiratory and fermentative growth was adjusted to achieve an optimal ATP generation to allow a maintained energy level as high as it is in nonstressed cells grown exponentially on glucose under aerobic conditions. In addition, yeast cells exposed to acids suffered from severe reactive oxygen species stress and depletion of reduced glutathione commensurate with exhaustion of the total glutathione pool. Furthermore, a higher cellular trehalose content was observed as compared to control cultivations, and this trehalose probably acts to enhance a number of stress tolerances of the yeast.
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Affiliation(s)
- Zhongpeng Guo
- Department of Chemical and Biological Engineering, Industrial Biotechnology, Chalmers University of Technology, Gothenburg, Sweden
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68
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Pfeiffer T, Morley A. An evolutionary perspective on the Crabtree effect. Front Mol Biosci 2014; 1:17. [PMID: 25988158 PMCID: PMC4429655 DOI: 10.3389/fmolb.2014.00017] [Citation(s) in RCA: 163] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 09/26/2014] [Indexed: 11/24/2022] Open
Abstract
The capability to ferment sugars into ethanol is a key metabolic trait of yeasts. Crabtree-positive yeasts use fermentation even in the presence of oxygen, where they could, in principle, rely on the respiration pathway. This is surprising because fermentation has a much lower ATP yield than respiration (2 ATP vs. approximately 18 ATP per glucose). While genetic events in the evolution of the Crabtree effect have been identified, the selective advantages provided by this trait remain controversial. In this review we analyse explanations for the emergence of the Crabtree effect from an evolutionary and game-theoretical perspective. We argue that an increased rate of ATP production is likely the most important factor behind the emergence of the Crabtree effect.
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Affiliation(s)
- Thomas Pfeiffer
- New Zealand Institute for Advanced Study, Massey University Auckland, New Zealand
| | - Annabel Morley
- New Zealand Institute for Advanced Study, Massey University Auckland, New Zealand
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69
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Sandoval CM, Ayson M, Moss N, Lieu B, Jackson P, Gaucher SP, Horning T, Dahl RH, Denery JR, Abbott DA, Meadows AL. Use of pantothenate as a metabolic switch increases the genetic stability of farnesene producing Saccharomyces cerevisiae. Metab Eng 2014; 25:215-26. [DOI: 10.1016/j.ymben.2014.07.006] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Revised: 06/27/2014] [Accepted: 07/17/2014] [Indexed: 01/19/2023]
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70
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Slavov N, Budnik BA, Schwab D, Airoldi EM, van Oudenaarden A. Constant growth rate can be supported by decreasing energy flux and increasing aerobic glycolysis. Cell Rep 2014; 7:705-14. [PMID: 24767987 DOI: 10.1016/j.celrep.2014.03.057] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Revised: 02/11/2014] [Accepted: 03/21/2014] [Indexed: 01/16/2023] Open
Abstract
Fermenting glucose in the presence of enough oxygen to support respiration, known as aerobic glycolysis, is believed to maximize growth rate. We observed increasing aerobic glycolysis during exponential growth, suggesting additional physiological roles for aerobic glycolysis. We investigated such roles in yeast batch cultures by quantifying O2 consumption, CO2 production, amino acids, mRNAs, proteins, posttranslational modifications, and stress sensitivity in the course of nine doublings at constant rate. During this course, the cells support a constant biomass-production rate with decreasing rates of respiration and ATP production but also decrease their stress resistance. As the respiration rate decreases, so do the levels of enzymes catalyzing rate-determining reactions of the tricarboxylic-acid cycle (providing NADH for respiration) and of mitochondrial folate-mediated NADPH production (required for oxidative defense). The findings demonstrate that exponential growth can represent not a single metabolic/physiological state but a continuum of changing states and that aerobic glycolysis can reduce the energy demands associated with respiratory metabolism and stress survival.
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Affiliation(s)
- Nikolai Slavov
- Departments of Physics and Biology and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Statistics and FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands.
| | - Bogdan A Budnik
- Department of Statistics and FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA
| | - David Schwab
- Department of Physics and Lewis-Sigler Institute, Princeton University, Princeton, NJ 08544, USA
| | - Edoardo M Airoldi
- Department of Statistics and FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alexander van Oudenaarden
- Departments of Physics and Biology and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands.
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71
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Mensonides FIC, Brul S, Hellingwerf KJ, Bakker BM, Teixeira de Mattos MJ. A kinetic model of catabolic adaptation and protein reprofiling in Saccharomyces cerevisiae during temperature shifts. FEBS J 2014; 281:825-41. [PMID: 24616920 DOI: 10.1111/febs.12649] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In this article, we aim to find an explanation for the surprisingly thin line, with regard to temperature, between cell growth, growth arrest and ultimately loss of cell viability. To this end, we used an integrative approach including both experimental and modelling work. We measured the short- and long-term effects of increases in growth temperature from 28 °C to 37, 39, 41, 42 or 43 °C on the central metabolism of Saccharomyces cerevisiae. Based on the experimental data, we developed a kinetic mathematical model that describes the metabolic and energetic changes in growing bakers' yeast when exposed to a specific temperature upshift. The model includes the temperature dependence of core energy-conserving pathways, trehalose synthesis, protein synthesis and proteolysis. Because our model focuses on protein synthesis and degradation, the net result of which is important in determining the cell's capacity to grow, the model includes growth, i.e. glucose is consumed and biomass and adenosine nucleotide cofactors are produced. The model reproduces both the observed initial metabolic response and the subsequent relaxation into a new steady-state, compatible with the new ambient temperature. In addition, it shows that the energy consumption for proteome reprofiling may be a major determinant of heat-induced growth arrest and subsequent recovery or cell death.
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72
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Weber N, Gorwa-Grauslund M, Carlquist M. Exploiting cell metabolism for biocatalytic whole-cell transamination by recombinant Saccharomyces cerevisiae. Appl Microbiol Biotechnol 2014; 98:4615-24. [PMID: 24557569 PMCID: PMC4253539 DOI: 10.1007/s00253-014-5576-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Revised: 12/20/2013] [Accepted: 01/26/2014] [Indexed: 01/29/2023]
Abstract
The potential of Saccharomyces cerevisiae for biocatalytic whole-cell transamination was investigated using the kinetic resolution of racemic 1-phenylethylamine (1-PEA) to (R)-1-PEA as a model reaction. As native yeast do not possess any ω-transaminase activity for the reaction, a recombinant yeast biocatalyst was constructed by overexpressing the gene coding for vanillin aminotransferase from Capsicum chinense. The yeast-based biocatalyst could use glucose as the sole co-substrate for the supply of amine acceptor via cell metabolism. In addition, the biocatalyst was functional without addition of the co-factor pyridoxal-5′-phosphate (PLP), which can be explained by a high inherent cellular capacity to sustain PLP-dependent reactions in living cells. In contrast, external PLP supplementation was required when cell viability was low, as it was the case when using pyruvate as a co-substrate. Overall, the results indicate a potential for engineered S. cerevisiae as a biocatalyst for whole-cell transamination and with glucose as the only co-substrate for the supply of amine acceptor and PLP.
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Affiliation(s)
- Nora Weber
- Division of Applied Microbiology, Department of Chemistry, Lund University, Getingevägen 60, 22100 Lund, Sweden
| | - Marie Gorwa-Grauslund
- Division of Applied Microbiology, Department of Chemistry, Lund University, Getingevägen 60, 22100 Lund, Sweden
| | - Magnus Carlquist
- Division of Applied Microbiology, Department of Chemistry, Lund University, Getingevägen 60, 22100 Lund, Sweden
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73
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Overcoming the metabolic burden of protein secretion in Schizosaccharomyces pombe – A quantitative approach using 13C-based metabolic flux analysis. Metab Eng 2014; 21:34-45. [DOI: 10.1016/j.ymben.2013.11.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Revised: 10/27/2013] [Accepted: 11/11/2013] [Indexed: 01/20/2023]
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74
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Guest JS, van Loosdrecht MCM, Skerlos SJ, Love NG. Lumped pathway metabolic model of organic carbon accumulation and mobilization by the alga Chlamydomonas reinhardtii. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2013; 47:3258-3267. [PMID: 23452258 DOI: 10.1021/es304980y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Phototrophic microorganisms have significant potential as bioenergy feedstocks, but the sustainability of large-scale cultivation will require the use of wastewater as a renewable resource. A key barrier to this advancement is a lack of bioprocess understanding that would enable the design and implementation of efficient and resilient mixed community, naturally lit cultivation systems. In this study, a lumped pathway metabolic model (denoted the phototrophic process model or PPM) was developed for mixed phototrophic communities subjected to day/night cycling. State variables included functional biomass (XCPO), stored carbohydrates (XCH), stored lipids (XLI), nitrate (SNO), phosphate (SP), and others. PPM metabolic reactions and stoichiometry were based on Chlamydomonas reinhardtii , but experiments for model calibration and validation were performed in flat panel photobioreactors (PBRs) originally inoculated with biomass from a phototrophic system at a wastewater treatment plant. PBRs were operated continuously as cyclostats to poise cells for intrinsic kinetic parameter estimation in batch studies, which included nutrient-available conditions in light and dark as well as nitrogen-starved and phosphorus-starved conditions in light. The model was calibrated and validated and was shown to be a reasonable predictor of growth, lipid and carbohydrate storage, and lipid and carbohydrate mobilization by a mixed microbial community.
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Affiliation(s)
- Jeremy S Guest
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
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75
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Sansonetti S, Hobley TJ, Curcio S, Villadsen J, Sin G. Use of continuous lactose fermentation for ethanol production by Kluveromyces marxianus for verification and extension of a biochemically structured model. BIORESOURCE TECHNOLOGY 2013; 130:703-709. [PMID: 23334030 DOI: 10.1016/j.biortech.2012.12.080] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Revised: 12/10/2012] [Accepted: 12/11/2012] [Indexed: 06/01/2023]
Abstract
A biochemically structured model has been developed to describe the continuous fermentation of lactose to ethanol by Kluveromyces marxianus and allowed metabolic coefficients to be determined. Anaerobic lactose-limited chemostat fermentations at different dilution rates (0.02-0.35h(-1)) were performed. Species specific rates of consumption/formation, as well as yield coefficients were determined. Ethanol yield (0.655 C-mol ethanol(∗)C-mol lactose(-1)) was as high as 98% of theoretical. The modeling procedure allowed calculation of maintenance coefficients for lactose consumption and ethanol production of m(s)=0.6029 and m(e)=0.4218 (C-mol) and (C-molh)(-1), respectively. True yield coefficients for biomass, ethanol and glycerol production were calculated to be Y(true)(sx)=0.114, Y(true)(ex)=0.192 and Y(sg)=2.250 (C-mol) and (C-mol)(-1), respectively. Model calculated maintenance and true yield coefficients agreed very closely with those determined by regressions of the experimental data. The model developed provides a solid basis for the rational design of optimised fermentation of cheese whey.
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Affiliation(s)
- S Sansonetti
- Novozymes A/S, Solid Products Development, DK-2880 Bagsvaerd, Denmark.
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76
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Leite FCB, Basso TO, Pita WDB, Gombert AK, Simões DA, de Morais MA. Quantitative aerobic physiology of the yeast Dekkera bruxellensis, a major contaminant in bioethanol production plants. FEMS Yeast Res 2012; 13:34-43. [PMID: 23078341 DOI: 10.1111/1567-1364.12007] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2011] [Revised: 08/07/2012] [Accepted: 09/07/2012] [Indexed: 12/01/2022] Open
Abstract
Dekkera bruxellensis has been described as the major contaminant yeast of industrial ethanol production, although little is known about its physiology. The aim of this study was to investigate the growth of this yeast in diverse carbon sources and involved conducting shake-flask and glucose- or sucrose-limited chemostats experiments, and from the chemostat data, the stoichiometry of biomass formation during aerobic growth was established. As a result of the shake-flask experiments with hexoses or disaccharides, the specific growth rates were calculated, and a different behavior in rich and mineral medium was observed concerning to profile of acetate and ethanol production. In C-limited chemostats conditions, the metabolism of this yeast was completely respiratory, and the biomass yields reached values of 0.62 gDW gS(-1) . In addition, glucose pulses were applied to the glucose- or sucrose-limited chemostats. These results showed that D. bruxellensis has a short-term Crabtree effect. While the glucose pulse was at the sucrose-limited chemostat, sucrose accumulated at the reactor, indicating the presence of a glucose repression mechanism in D. bruxellensis.
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77
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Production host selection for asymmetric styrene epoxidation: Escherichia coli vs. solvent-tolerant Pseudomonas. ACTA ACUST UNITED AC 2012; 39:1125-33. [DOI: 10.1007/s10295-012-1126-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Accepted: 03/28/2012] [Indexed: 10/28/2022]
Abstract
Abstract
Selection of the ideal microbe is crucial for whole-cell biotransformations, especially if the target reaction intensively interacts with host cell functions. Asymmetric styrene epoxidation is an example of a reaction which is strongly dependent on the host cell owing to its requirement for efficient cofactor regeneration and stable expression of the styrene monooxygenase genes styAB. On the other hand, styrene epoxidation affects the whole-cell biocatalyst, because it involves toxic substrate and products besides the burden of additional (recombinant) enzyme synthesis. With the aim to compare two fundamentally different strain engineering strategies, asymmetric styrene epoxidation by StyAB was investigated using the engineered wild-type strain Pseudomonas sp. strain VLB120ΔC, a styrene oxide isomerase (StyC) knockout strain able to accumulate (S)-styrene oxide, and recombinant E. coli JM101 carrying styAB on the plasmid pSPZ10. Their performance was analyzed during fed-batch cultivation in two-liquid phase biotransformations with respect to specific activity, volumetric productivity, product titer, tolerance of toxic substrate and products, by-product formation, and product yield on glucose. Thereby, Pseudomonas sp. strain VLB120ΔC proved its great potential by tolerating high styrene oxide concentrations and by the absence of by-product formation. The E. coli-based catalyst, however, showed higher specific activities and better yields on glucose. The results not only show the importance but also the complexity of host cell selection and engineering. Finding the optimal strain engineering strategy requires profound understanding of bioprocess and biocatalyst operation. In this respect, a possible negative influence of solvent tolerance on yield and activity is discussed.
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78
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Jouhten P, Wiebe M, Penttilä M. Dynamic flux balance analysis of the metabolism ofSaccharomyces cerevisiaeduring the shift from fully respirative or respirofermentative metabolic states to anaerobiosis. FEBS J 2012; 279:3338-54. [DOI: 10.1111/j.1742-4658.2012.08649.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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79
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Olson DG, McBride JE, Joe Shaw A, Lynd LR. Recent progress in consolidated bioprocessing. Curr Opin Biotechnol 2012; 23:396-405. [DOI: 10.1016/j.copbio.2011.11.026] [Citation(s) in RCA: 370] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2011] [Revised: 11/08/2011] [Accepted: 11/23/2011] [Indexed: 12/30/2022]
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80
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Golmakani MT, Rezaei K, Mazidi S, Razavi SH. Effect of alternative C2 carbon sources on the growth, lipid, and γ-linolenic acid production of spirulina (Arthrospira platensis). Food Sci Biotechnol 2012. [DOI: 10.1007/s10068-012-0047-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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81
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Caspeta L, Shoaie S, Agren R, Nookaew I, Nielsen J. Genome-scale metabolic reconstructions of Pichia stipitis and Pichia pastoris and in silico evaluation of their potentials. BMC SYSTEMS BIOLOGY 2012; 6:24. [PMID: 22472172 PMCID: PMC3364918 DOI: 10.1186/1752-0509-6-24] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Accepted: 04/04/2012] [Indexed: 11/18/2022]
Abstract
Background Pichia stipitis and Pichia pastoris have long been investigated due to their native abilities to metabolize every sugar from lignocellulose and to modulate methanol consumption, respectively. The latter has been driving the production of several recombinant proteins. As a result, significant advances in their biochemical knowledge, as well as in genetic engineering and fermentation methods have been generated. The release of their genome sequences has allowed systems level research. Results In this work, genome-scale metabolic models (GEMs) of P. stipitis (iSS884) and P. pastoris (iLC915) were reconstructed. iSS884 includes 1332 reactions, 922 metabolites, and 4 compartments. iLC915 contains 1423 reactions, 899 metabolites, and 7 compartments. Compared with the previous GEMs of P. pastoris, PpaMBEL1254 and iPP668, iLC915 contains more genes and metabolic functions, as well as improved predictive capabilities. Simulations of physiological responses for the growth of both yeasts on selected carbon sources using iSS884 and iLC915 closely reproduced the experimental data. Additionally, the iSS884 model was used to predict ethanol production from xylose at different oxygen uptake rates. Simulations with iLC915 closely reproduced the effect of oxygen uptake rate on physiological states of P. pastoris expressing a recombinant protein. The potential of P. stipitis for the conversion of xylose and glucose into ethanol using reactors in series, and of P. pastoris to produce recombinant proteins using mixtures of methanol and glycerol or sorbitol are also discussed. Conclusions In conclusion the first GEM of P. stipitis (iSS884) was reconstructed and validated. The expanded version of the P. pastoris GEM, iLC915, is more complete and has improved capabilities over the existing models. Both GEMs are useful frameworks to explore the versatility of these yeasts and to capitalize on their biotechnological potentials.
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Affiliation(s)
- Luis Caspeta
- Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
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82
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Celton M, Goelzer A, Camarasa C, Fromion V, Dequin S. A constraint-based model analysis of the metabolic consequences of increased NADPH oxidation in Saccharomyces cerevisiae. Metab Eng 2012; 14:366-79. [PMID: 22709677 DOI: 10.1016/j.ymben.2012.03.008] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2011] [Revised: 01/22/2012] [Accepted: 03/16/2012] [Indexed: 11/28/2022]
Abstract
Controlling the amounts of redox cofactors to manipulate metabolic fluxes is emerging as a useful approach to optimizing byproduct yields in yeast biotechnological processes. Redox cofactors are extensively interconnected metabolites, so predicting metabolite patterns is challenging and requires in-depth knowledge of how the metabolic network responds to a redox perturbation. Our aim was to analyze comprehensively the metabolic consequences of increased cytosolic NADPH oxidation during yeast fermentation. Using a genetic device based on the overexpression of a modified 2,3-butanediol dehydrogenase catalyzing the NADPH-dependent reduction of acetoin into 2,3-butanediol, we increased the NADPH demand to between 8 and 40-fold the anabolic demand. We developed (i) a dedicated constraint-based model of yeast fermentation and (ii) a constraint-based modeling method based on the dynamical analysis of mass distribution to quantify the in vivo contribution of pathways producing NADPH to the maintenance of redox homeostasis. We report that yeast responds to NADPH oxidation through a gradual increase in the flux through the PP and acetate pathways, providing 80% and 20% of the NADPH demand, respectively. However, for the highest NADPH demand, the model reveals a saturation of the PP pathway and predicts an exchange between NADH and NADPH in the cytosol that may be mediated by the glycerol-DHA futile cycle. We also reveal the contribution of mitochondrial shuttles, resulting in a net production of NADH in the cytosol, to fine-tune the NADH/NAD(+) balance. This systems level study helps elucidate the physiological adaptation of yeast to NADPH perturbation. Our findings emphasize the robustness of yeast to alterations in NADPH metabolism and highlight the role of the glycerol-DHA cycle as a redox valve, providing additional NADPH from NADH under conditions of very high demand.
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Affiliation(s)
- Magalie Celton
- INRA, UMR1083, Sciences Pour l'Oenologie, 2 Place Viala, F-34060 Montpellier, France.
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83
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Huberts DHEW, Niebel B, Heinemann M. A flux-sensing mechanism could regulate the switch between respiration and fermentation. FEMS Yeast Res 2011; 12:118-28. [DOI: 10.1111/j.1567-1364.2011.00767.x] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Revised: 10/28/2011] [Accepted: 11/16/2011] [Indexed: 12/20/2022] Open
Affiliation(s)
- Daphne H. E. W. Huberts
- Molecular Systems Biology; Groningen Biomolecular Sciences and Biotechnology Institute; University of Groningen; Groningen; The Netherlands
| | - Bastian Niebel
- Molecular Systems Biology; Groningen Biomolecular Sciences and Biotechnology Institute; University of Groningen; Groningen; The Netherlands
| | - Matthias Heinemann
- Molecular Systems Biology; Groningen Biomolecular Sciences and Biotechnology Institute; University of Groningen; Groningen; The Netherlands
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84
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Postmus J, Tuzun I, Bekker M, Müller WH, Teixeira de Mattos MJ, Brul S, Smits GJ. Dynamic regulation of mitochondrial respiratory chain efficiency in Saccharomyces cerevisiae. MICROBIOLOGY-SGM 2011; 157:3500-3511. [PMID: 21964735 DOI: 10.1099/mic.0.050039-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
To adapt to changes in the environment, cells have to dynamically alter their phenotype in response to, for instance, temperature and oxygen availability. Interestingly, mitochondrial function in Saccharomyces cerevisiae is inherently temperature sensitive; above 37 °C, yeast cells cannot grow on respiratory carbon sources. To investigate this phenomenon, we studied the effect of cultivation temperature on the efficiency (production of ATP per atom of oxygen consumed, or P/O) of the yeast respiratory chain in glucose-limited chemostats. We determined that even though the specific oxygen consumption rate did not change with temperature, oxygen consumption no longer contributed to mitochondrial ATP generation at temperatures higher than 37 °C. Remarkably, between 30 and 37 °C, we observed a linear increase in respiratory efficiency with growth temperature, up to a P/O of 1.4, close to the theoretical maximum that can be reached in vivo. The temperature-dependent increase in efficiency required the presence of the mitochondrial glycerol-3-phosphate dehydrogenase GUT2. Respiratory chain efficiency was also altered in response to changes in oxygen availibility. Our data show that, even in the absence of alternative oxidases or uncoupling proteins, yeast has retained the ability to dynamically regulate the efficiency of coupling of oxygen consumption to proton translocation in the respiratory chain in response to changes in the environment.
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Affiliation(s)
- Jarne Postmus
- Department of Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Işil Tuzun
- Department of Molecular Microbial Physiology, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Martijn Bekker
- Department of Molecular Microbial Physiology, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Wally H Müller
- Department of Biology, Biomolecular Imaging, Institute of Biomembranes, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - M Joost Teixeira de Mattos
- Department of Molecular Microbial Physiology, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Stanley Brul
- Department of Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Gertien J Smits
- Department of Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
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85
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Sansonetti S, Hobley TJ, Calabrò V, Villadsen J, Sin G. A biochemically structured model for ethanol fermentation by Kluyveromyces marxianus: A batch fermentation and kinetic study. BIORESOURCE TECHNOLOGY 2011; 102:7513-7520. [PMID: 21632239 DOI: 10.1016/j.biortech.2011.05.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Revised: 05/05/2011] [Accepted: 05/06/2011] [Indexed: 05/30/2023]
Abstract
Anaerobic batch fermentations of ricotta cheese whey (i.e. containing lactose) were performed under different operating conditions. Ethanol concentrations of ca. 22g L(-1) were found from whey containing ca. 44g L(-1) lactose, which corresponded to up to 95% of the theoretical ethanol yield within 15h. The experimental data could be explained by means of a simple knowledge-driven biochemically structured model that was built on bioenergetics principles applied to the metabolic pathways through which lactose is converted into major products. Use of the model showed that the observed concentrations of ethanol, lactose, biomass and glycerol during batch fermentation could be described within a ca. 6% deviation, as could the yield coefficients for biomass and ethanol produced on lactose. The model structure confirmed that the thermodynamics considerations on the stoichiometry of the system constrain the metabolic coefficients within a physically meaningful range thereby providing valuable and reliable insight into fermentation processes.
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Affiliation(s)
- S Sansonetti
- Computer Aided Process Engineering Center, Department of Chemical and Biochemical Engineering, Technical University of Denmark, DK-2800 Lyngby, Denmark.
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86
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Guo ZP, Zhang L, Ding ZY, Gu ZH, Shi GY. Development of an industrial ethanol-producing yeast strain for efficient utilization of cellobiose. Enzyme Microb Technol 2011; 49:105-12. [DOI: 10.1016/j.enzmictec.2011.02.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2011] [Revised: 02/13/2011] [Accepted: 02/16/2011] [Indexed: 10/18/2022]
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87
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Vargas FA, Pizarro F, Pérez-Correa JR, Agosin E. Expanding a dynamic flux balance model of yeast fermentation to genome-scale. BMC SYSTEMS BIOLOGY 2011; 5:75. [PMID: 21595919 PMCID: PMC3118138 DOI: 10.1186/1752-0509-5-75] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2010] [Accepted: 05/19/2011] [Indexed: 12/03/2022]
Abstract
Background Yeast is considered to be a workhorse of the biotechnology industry for the production of many value-added chemicals, alcoholic beverages and biofuels. Optimization of the fermentation is a challenging task that greatly benefits from dynamic models able to accurately describe and predict the fermentation profile and resulting products under different genetic and environmental conditions. In this article, we developed and validated a genome-scale dynamic flux balance model, using experimentally determined kinetic constraints. Results Appropriate equations for maintenance, biomass composition, anaerobic metabolism and nutrient uptake are key to improve model performance, especially for predicting glycerol and ethanol synthesis. Prediction profiles of synthesis and consumption of the main metabolites involved in alcoholic fermentation closely agreed with experimental data obtained from numerous lab and industrial fermentations under different environmental conditions. Finally, fermentation simulations of genetically engineered yeasts closely reproduced previously reported experimental results regarding final concentrations of the main fermentation products such as ethanol and glycerol. Conclusion A useful tool to describe, understand and predict metabolite production in batch yeast cultures was developed. The resulting model, if used wisely, could help to search for new metabolic engineering strategies to manage ethanol content in batch fermentations.
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Affiliation(s)
- Felipe A Vargas
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Casilla, Correo, Santiago CHILE
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88
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Expression of aspartic protease from Neurospora crassa in industrial ethanol-producing yeast and its application in ethanol production. Enzyme Microb Technol 2011; 48:148-54. [DOI: 10.1016/j.enzmictec.2010.10.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2010] [Revised: 09/26/2010] [Accepted: 10/21/2010] [Indexed: 11/19/2022]
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89
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Guo ZP, Zhang L, Ding ZY, Shi GY. Minimization of glycerol synthesis in industrial ethanol yeast without influencing its fermentation performance. Metab Eng 2011; 13:49-59. [DOI: 10.1016/j.ymben.2010.11.003] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2010] [Revised: 11/08/2010] [Accepted: 11/16/2010] [Indexed: 10/18/2022]
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90
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Guo ZP, Zhang L, Ding ZY, Wang ZX, Shi GY. Improving ethanol productivity by modification of glycolytic redox factor generation in glycerol-3-phosphate dehydrogenase mutants of an industrial ethanol yeast. J Ind Microbiol Biotechnol 2010; 38:935-43. [PMID: 20824484 DOI: 10.1007/s10295-010-0864-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2010] [Accepted: 08/25/2010] [Indexed: 11/27/2022]
Abstract
The GPD2 gene, encoding NAD(+)-dependent glycerol-3-phosphate dehydrogenase in an industrial ethanol-producing strain of Saccharomyces cerevisiae, was deleted. And then, either the non-phosphorylating NADP(+)-dependent glyceraldehyde-3-phosphate dehydrogenase (GAPN) from Bacillus cereus, or the NADP(+)-dependent glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from Kluyveromyces lactis, was expressed in the obtained mutant AG2 deletion of GPD2, respectively. The resultant recombinant strain AG2A (gpd2Δ P (PGK)-gapN) exhibited a 48.70 ± 0.34% (relative to the amount of substrate consumed) decrease in glycerol production and a 7.60 ± 0.12% (relative to the amount of substrate consumed) increase in ethanol yield, while recombinant AG2B (gpd2Δ P (PGK)-GAPDH) exhibited a 52.90 ± 0.45% (relative to the amount of substrate consumed) decrease in glycerol production and a 7.34 ± 0.15% (relative to the amount of substrate consumed) increase in ethanol yield compared with the wild-type strain. More importantly, the maximum specific growth rates (μ (max)) of the recombinant AG2A and AG2B were higher than that of the mutant gpd2Δ and were indistinguishable compared with the wild-type strain in anaerobic batch fermentations. The results indicated that the redox imbalance of the mutant could be partially solved by expressing the heterologous genes.
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Affiliation(s)
- Zhong-peng Guo
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, Center for Bioresources and Bioenergy, School of Biotechnology, Jiangnan University, 214122, Wuxi, People's Republic of China
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91
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Guo ZP, Zhang L, Ding ZY, Wang ZX, Shi GY. Improving the performance of industrial ethanol-producing yeast by expressing the aspartyl protease on the cell surface. Yeast 2010; 27:1017-27. [DOI: 10.1002/yea.1811] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2010] [Accepted: 07/05/2010] [Indexed: 11/12/2022] Open
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92
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Chung BK, Selvarasu S, Andrea C, Ryu J, Lee H, Ahn J, Lee H, Lee DY. Genome-scale metabolic reconstruction and in silico analysis of methylotrophic yeast Pichia pastoris for strain improvement. Microb Cell Fact 2010; 9:50. [PMID: 20594333 PMCID: PMC2908565 DOI: 10.1186/1475-2859-9-50] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2010] [Accepted: 07/01/2010] [Indexed: 01/21/2023] Open
Abstract
Background Pichia pastoris has been recognized as an effective host for recombinant protein production. A number of studies have been reported for improving this expression system. However, its physiology and cellular metabolism still remained largely uncharacterized. Thus, it is highly desirable to establish a systems biotechnological framework, in which a comprehensive in silico model of P. pastoris can be employed together with high throughput experimental data analysis, for better understanding of the methylotrophic yeast's metabolism. Results A fully compartmentalized metabolic model of P. pastoris (iPP668), composed of 1,361 reactions and 1,177 metabolites, was reconstructed based on its genome annotation and biochemical information. The constraints-based flux analysis was then used to predict achievable growth rate which is consistent with the cellular phenotype of P. pastoris observed during chemostat experiments. Subsequent in silico analysis further explored the effect of various carbon sources on cell growth, revealing sorbitol as a promising candidate for culturing recombinant P. pastoris strains producing heterologous proteins. Interestingly, methanol consumption yields a high regeneration rate of reducing equivalents which is substantial for the synthesis of valuable pharmaceutical precursors. Hence, as a case study, we examined the applicability of P. pastoris system to whole-cell biotransformation and also identified relevant metabolic engineering targets that have been experimentally verified. Conclusion The genome-scale metabolic model characterizes the cellular physiology of P. pastoris, thus allowing us to gain valuable insights into the metabolism of methylotrophic yeast and devise possible strategies for strain improvement through in silico simulations. This computational approach, combined with synthetic biology techniques, potentially forms a basis for rational analysis and design of P. pastoris metabolic network to enhance humanized glycoprotein production.
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Affiliation(s)
- Bevan Ks Chung
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, 28 Medical Drive, #05-01, 117456, Singapore.
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93
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van Leeuwen M, Krommenhoek EE, Heijnen JJ, Gardeniers H, van der Wielen LAM, van Gulik WM. Aerobic batch cultivation in micro bioreactor with integrated electrochemical sensor array. Biotechnol Prog 2010; 26:293-300. [PMID: 19924767 DOI: 10.1002/btpr.315] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Aerobic batch cultivations of Candida utilis were carried out in two micro bioreactors with a working volume of 100 muL operated in parallel. The dimensions of the micro bioreactors were similar as the wells in a 96-well microtiter plate, to preserve compatibility with the current high-throughput cultivation systems. Each micro bioreactor was equipped with an electrochemical sensor array for the online measurement of temperature, pH, dissolved oxygen, and viable biomass concentration. Furthermore, the CO(2) production rate was obtained from the online measurement of cumulative CO(2) production during the cultivation. The online data obtained by the sensor array and the CO(2) production measurements appeared to be very reproducible for all batch cultivations performed and were highly comparable to measurement results obtained during a similar aerobic batch cultivation carried out in a conventional 4L bench-scale bioreactor. Although the sensor chip certainly needs further improvement on some points, this work clearly shows the applicability of electrochemical sensor arrays for the monitoring of parallel micro-scale fermentations, e.g. using the 96-well microtiterplate format.
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Affiliation(s)
- Michiel van Leeuwen
- Dept. of Biotechnology, Delft University of Technology and Kluyver Centre for Genomics of Industrial Fermentation, Julianalaan 67, 2628 BC, Delft, The Netherlands
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94
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Vilaprinyo E, Alves R, Sorribas A. Minimization of biosynthetic costs in adaptive gene expression responses of yeast to environmental changes. PLoS Comput Biol 2010; 6:e1000674. [PMID: 20168993 PMCID: PMC2820516 DOI: 10.1371/journal.pcbi.1000674] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2009] [Accepted: 01/11/2010] [Indexed: 11/18/2022] Open
Abstract
Yeast successfully adapts to an environmental stress by altering physiology and fine-tuning metabolism. This fine-tuning is achieved through regulation of both gene expression and protein activity, and it is shaped by various physiological requirements. Such requirements impose a sustained evolutionary pressure that ultimately selects a specific gene expression profile, generating a suitable adaptive response to each environmental change. Although some of the requirements are stress specific, it is likely that others are common to various situations. We hypothesize that an evolutionary pressure for minimizing biosynthetic costs might have left signatures in the physicochemical properties of proteins whose gene expression is fine-tuned during adaptive responses. To test this hypothesis we analyze existing yeast transcriptomic data for such responses and investigate how several properties of proteins correlate to changes in gene expression. Our results reveal signatures that are consistent with a selective pressure for economy in protein synthesis during adaptive response of yeast to various types of stress. These signatures differentiate two groups of adaptive responses with respect to how cells manage expenditure in protein biosynthesis. In one group, significant trends towards downregulation of large proteins and upregulation of small ones are observed. In the other group we find no such trends. These results are consistent with resource limitation being important in the evolution of the first group of stress responses. Although different environmental stresses trigger specific sets of protective changes in the gene expression of yeast, the adaptive responses to these stresses also share some common features. We hypothesize that minimization of metabolic costs may contribute to shaping such adaptive responses. If this is so, then such pressure should be more noticeable in the costliest biosynthetic processes. One of these is protein synthesis. Thus, we analyze the set of genes and proteins whose expression changes during the responses and look for evidence to support or falsify our hypothesis. We find that protein properties that are indicative of protein cost correlate to changes in gene expression in a way that is consistent with that hypothesis for a large number of adaptive responses. However, if changes in gene expression are small during the adaptive response, we find no evidence of protein cost as a factor in shaping the adaptive response.
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Affiliation(s)
- Ester Vilaprinyo
- Fundació Dr Ferràn-Hospital de Tortosa Verge de la Cinta, Tortosa, Spain.
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95
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van den Brink J, Akeroyd M, van der Hoeven R, Pronk JT, de Winde JH, Daran-Lapujade P. Energetic limits to metabolic flexibility: responses of Saccharomyces cerevisiae to glucose-galactose transitions. MICROBIOLOGY-SGM 2009; 155:1340-1350. [PMID: 19332835 DOI: 10.1099/mic.0.025775-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Glucose is the favoured carbon source for Saccharomyces cerevisiae, and the Leloir pathway for galactose utilization is only induced in the presence of galactose during glucose-derepressed conditions. The goal of this study was to investigate the dynamics of glucose-galactose transitions. To this end, well-controlled, glucose-limited chemostat cultures were switched to galactose-excess conditions. Surprisingly, galactose was not consumed upon a switch to galactose excess under anaerobic conditions. However, the transcripts of the Leloir pathway were highly increased upon galactose excess under both aerobic and anaerobic conditions. Protein and enzyme-activity assays showed that impaired galactose consumption under anaerobiosis coincided with the absence of the Leloir-pathway proteins. Further results showed that absence of protein synthesis was not caused by glucose-mediated translation inhibition. Analysis of adenosine nucleotide pools revealed a fast decrease of the energy charge after the switch from glucose to galactose under anaerobic conditions. Similar results were obtained when glucose-galactose transitions were analysed under aerobic conditions with a respiratory-deficient strain. It is concluded that under fermentative conditions, the energy charge was too low to allow synthesis of the Leloir proteins. Hence, this study conclusively shows that the intracellular energy status is an important factor in the metabolic flexibility of S. cerevisiae upon changes in its environment.
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Affiliation(s)
- J van den Brink
- Kluyver Centre for Genomics of Industrial Fermentation and Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
| | - M Akeroyd
- DSM Food Specialties, PO Box 1, 2600 MA Delft, The Netherlands
| | | | - J T Pronk
- Kluyver Centre for Genomics of Industrial Fermentation and Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
| | - J H de Winde
- Kluyver Centre for Genomics of Industrial Fermentation and Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
| | - P Daran-Lapujade
- Kluyver Centre for Genomics of Industrial Fermentation and Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
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96
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van Leeuwen M, Heijnen JJ, Gardeniers H, van der Wielen LAM, van Gulik WM. Development of a system for the on-line measurement of carbon dioxide production in microbioreactors: Application to aerobic batch cultivations ofCandida utilis. Biotechnol Prog 2009; 25:892-7. [DOI: 10.1002/btpr.145] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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97
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van Leeuwen M, Buijs NA, Canelas AB, Oudshoorn A, Heijnen JJ, van Gulik WM. The Hagen–Poiseuille pump for parallel fed-batch cultivations in microbioreactors. Chem Eng Sci 2009. [DOI: 10.1016/j.ces.2009.01.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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98
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Interruption of glycerol pathway in industrial alcoholic yeasts to improve the ethanol production. Appl Microbiol Biotechnol 2008; 82:287-92. [PMID: 19018525 DOI: 10.1007/s00253-008-1777-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2008] [Revised: 10/27/2008] [Accepted: 10/29/2008] [Indexed: 10/21/2022]
Abstract
The two homologous genes GPD1 and GPD2, encoding two isoenzymes of NAD(+)-dependent glycerol-3-phosphate dehydrogenase in industrial yeast Saccharomyces cerevisiae CICIMY0086, had been deleted. The obtained two kinds of mutants gpd1Delta and gpd2Delta were studied under alcoholic fermentation conditions. gpd1Delta mutants exhibited a 4.29% (relative to the amount of substrate consumed) decrease in glycerol production and 6.83% (relative to the amount of substrate consumed) increased ethanol yield while gpd2Delta mutants exhibited a 7.95% (relative to the amount of substrate consumed) decrease in glycerol production and 7.41% (relative to the amount of substrate consumed) increased ethanol yield compared with the parental strain. The growth rate of the two mutants were slightly lower than that of the wild type under the exponential phase whereas ANG1 (gpd1Delta) and the decrease in glycerol production was not accompanied by any decline in the protein content of the strain ANG1 (gpd1Delta) but a slight decrease in the strain ANG2 (gpd2Delta). Meanwhile, dramatic decrease of acetate acid formation was observed in strain ANG1 (gpd1Delta) and ANG2 (gpd2Delta) compared to the parental strain. Therefore, it is possible to improve the ethanol yield by interruption of glycerol pathway in industrial alcoholic yeast.
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99
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Dynamics of glycolytic regulation during adaptation of Saccharomyces cerevisiae to fermentative metabolism. Appl Environ Microbiol 2008; 74:5710-23. [PMID: 18641162 DOI: 10.1128/aem.01121-08] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The ability of baker's yeast (Saccharomyces cerevisiae) to rapidly increase its glycolytic flux upon a switch from respiratory to fermentative sugar metabolism is an important characteristic for many of its multiple industrial applications. An increased glycolytic flux can be achieved by an increase in the glycolytic enzyme capacities (V(max)) and/or by changes in the concentrations of low-molecular-weight substrates, products, and effectors. The goal of the present study was to understand the time-dependent, multilevel regulation of glycolytic enzymes during a switch from fully respiratory conditions to fully fermentative conditions. The switch from glucose-limited aerobic chemostat growth to full anaerobiosis and glucose excess resulted in rapid acceleration of fermentative metabolism. Although the capacities (V(max)) of the glycolytic enzymes did not change until 45 min after the switch, the intracellular levels of several substrates, products, and effectors involved in the regulation of glycolysis did change substantially during the initial 45 min (e.g., there was a buildup of the phosphofructokinase activator fructose-2,6-bisphosphate). This study revealed two distinct phases in the upregulation of glycolysis upon a switch to fermentative conditions: (i) an initial phase, in which regulation occurs completely through changes in metabolite levels; and (ii) a second phase, in which regulation is achieved through a combination of changes in V(max) and metabolite concentrations. This multilevel regulation study qualitatively explains the increase in flux through the glycolytic enzymes upon a switch of S. cerevisiae to fermentative conditions and provides a better understanding of the roles of different regulatory mechanisms that influence the dynamics of yeast glycolysis.
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100
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Ståhlberg A, Elbing K, Andrade-Garda JM, Sjögreen B, Forootan A, Kubista M. Multiway real-time PCR gene expression profiling in yeast Saccharomyces cerevisiae reveals altered transcriptional response of ADH-genes to glucose stimuli. BMC Genomics 2008; 9:170. [PMID: 18412983 PMCID: PMC2335116 DOI: 10.1186/1471-2164-9-170] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2007] [Accepted: 04/16/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The large sensitivity, high reproducibility and essentially unlimited dynamic range of real-time PCR to measure gene expression in complex samples provides the opportunity for powerful multivariate and multiway studies of biological phenomena. In multiway studies samples are characterized by their expression profiles to monitor changes over time, effect of treatment, drug dosage etc. Here we perform a multiway study of the temporal response of four yeast Saccharomyces cerevisiae strains with different glucose uptake rates upon altered metabolic conditions. RESULTS We measured the expression of 18 genes as function of time after addition of glucose to four strains of yeast grown in ethanol. The data are analyzed by matrix-augmented PCA, which is a generalization of PCA for 3-way data, and the results are confirmed by hierarchical clustering and clustering by Kohonen self-organizing map. Our approach identifies gene groups that respond similarly to the change of nutrient, and genes that behave differently in mutant strains. Of particular interest is our finding that ADH4 and ADH6 show a behavior typical of glucose-induced genes, while ADH3 and ADH5 are repressed after glucose addition. CONCLUSION Multiway real-time PCR gene expression profiling is a powerful technique which can be utilized to characterize functions of new genes by, for example, comparing their temporal response after perturbation in different genetic variants of the studied subject. The technique also identifies genes that show perturbed expression in specific strains.
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