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Rendulić T, Perpelea A, Ortiz JPR, Casal M, Nevoigt E. Mitochondrial membrane transporters as attractive targets for the fermentative production of succinic acid from glycerol in Saccharomyces cerevisiae. FEMS Yeast Res 2024; 24:foae009. [PMID: 38587863 PMCID: PMC11014245 DOI: 10.1093/femsyr/foae009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 02/08/2024] [Accepted: 04/05/2024] [Indexed: 04/09/2024] Open
Abstract
Previously, we reported an engineered Saccharomyces cerevisiae CEN.PK113-1A derivative able to produce succinic acid (SA) from glycerol with net CO2 fixation. Apart from an engineered glycerol utilization pathway that generates NADH, the strain was equipped with the NADH-dependent reductive branch of the TCA cycle (rTCA) and a heterologous SA exporter. However, the results indicated that a significant amount of carbon still entered the CO2-releasing oxidative TCA cycle. The current study aimed to tune down the flux through the oxidative TCA cycle by targeting the mitochondrial uptake of pyruvate and cytosolic intermediates of the rTCA pathway, as well as the succinate dehydrogenase complex. Thus, we tested the effects of deletions of MPC1, MPC3, OAC1, DIC1, SFC1, and SDH1 on SA production. The highest improvement was achieved by the combined deletion of MPC3 and SDH1. The respective strain produced up to 45.5 g/L of SA, reached a maximum SA yield of 0.66 gSA/gglycerol, and accumulated the lowest amounts of byproducts when cultivated in shake-flasks. Based on the obtained data, we consider a further reduction of mitochondrial import of pyruvate and rTCA intermediates highly attractive. Moreover, the approaches presented in the current study might also be valuable for improving SA production when sugars (instead of glycerol) are the source of carbon.
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Affiliation(s)
- Toni Rendulić
- School of Science, Constructor University, Campus Ring 1, 28759 Bremen, Germany
- Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Andreea Perpelea
- School of Science, Constructor University, Campus Ring 1, 28759 Bremen, Germany
| | | | - Margarida Casal
- Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Elke Nevoigt
- School of Science, Constructor University, Campus Ring 1, 28759 Bremen, Germany
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2
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Yatabe F, Seike T, Okahashi N, Ishii J, Matsuda F. Improvement of ethanol and 2,3-butanediol production in Saccharomyces cerevisiae by ATP wasting. Microb Cell Fact 2023; 22:204. [PMID: 37807050 PMCID: PMC10560415 DOI: 10.1186/s12934-023-02221-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 09/30/2023] [Indexed: 10/10/2023] Open
Abstract
BACKGROUND "ATP wasting" has been observed in 13C metabolic flux analyses of Saccharomyces cerevisiae, a yeast strain commonly used to produce ethanol. Some strains of S. cerevisiae, such as the sake strain Kyokai 7, consume approximately two-fold as much ATP as laboratory strains. Increased ATP consumption may be linked to the production of ethanol, which helps regenerate ATP. RESULTS This study was conducted to enhance ethanol and 2,3-butanediol (2,3-BDO) production in the S. cerevisiae strains, ethanol-producing strain BY318 and 2,3-BDO-producing strain YHI030, by expressing the fructose-1,6-bisphosphatase (FBPase) and ATP synthase (ATPase) genes to induce ATP dissipation. The introduction of a futile cycle for ATP consumption in the pathway was achieved by expressing various FBPase and ATPase genes from Escherichia coli and S. cerevisiae in the yeast strains. The production of ethanol and 2,3-BDO was evaluated using high-performance liquid chromatography and gas chromatography, and fermentation tests were performed on synthetic media under aerobic conditions in batch culture. The results showed that in the BY318-opt_ecoFBPase (expressing opt_ecoFBPase) and BY318-ATPase (expressing ATPase) strains, specific glucose consumption was increased by 30% and 42%, respectively, and the ethanol production rate was increased by 24% and 45%, respectively. In contrast, the YHI030-opt_ecoFBPase (expressing opt_ecoFBPase) and YHI030-ATPase (expressing ATPase) strains showed increased 2,3-BDO yields of 26% and 18%, respectively, and the specific production rate of 2,3-BDO was increased by 36%. Metabolomic analysis confirmed the introduction of the futile cycle. CONCLUSION ATP wasting may be an effective strategy for improving the fermentative biosynthetic capacity of S. cerevisiae, and increased ATP consumption may be a useful tool in some alcohol-producing strains.
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Affiliation(s)
- Futa Yatabe
- Department of Bioinformatics Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Taisuke Seike
- Department of Bioinformatics Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan
- Industrial Biotechnology Initiative Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Nobuyuki Okahashi
- Department of Bioinformatics Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan
- Industrial Biotechnology Initiative Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
- Analytical Innovation Research Laboratory, Graduate School of Engineering, Osaka University Shimadzu, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Jun Ishii
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe, Hyogo, 657-8501, Japan
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, Hyogo, 657-8501, Japan
| | - Fumio Matsuda
- Department of Bioinformatics Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan.
- Industrial Biotechnology Initiative Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan.
- Analytical Innovation Research Laboratory, Graduate School of Engineering, Osaka University Shimadzu, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan.
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Volke DC, Gurdo N, Milanesi R, Nikel PI. Time-resolved, deuterium-based fluxomics uncovers the hierarchy and dynamics of sugar processing by Pseudomonas putida. Metab Eng 2023; 79:159-172. [PMID: 37454792 DOI: 10.1016/j.ymben.2023.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 06/30/2023] [Accepted: 07/13/2023] [Indexed: 07/18/2023]
Abstract
Pseudomonas putida, a microbial host widely adopted for metabolic engineering, processes glucose through convergent peripheral pathways that ultimately yield 6-phosphogluconate. The periplasmic gluconate shunt (PGS), composed by glucose and gluconate dehydrogenases, sequentially transforms glucose into gluconate and 2-ketogluconate. Although the secretion of these organic acids by P. putida has been extensively recognized, the mechanism and spatiotemporal regulation of the PGS remained elusive thus far. To address this challenge, we adopted a dynamic 13C- and 2H-metabolic flux analysis strategy, termed D-fluxomics. D-fluxomics demonstrated that the PGS underscores a highly dynamic metabolic architecture in glucose-dependent batch cultures of P. putida, characterized by hierarchical carbon uptake by the PGS throughout the cultivation. Additionally, we show that gluconate and 2-ketogluconate accumulation and consumption can be solely explained as a result of the interplay between growth rate-coupled and decoupled metabolic fluxes. As a consequence, the formation of these acids in the PGS is inversely correlated to the bacterial growth rate-unlike the widely studied overflow metabolism of Escherichia coli and yeast. Our findings, which underline survival strategies of soil bacteria thriving in their natural environments, open new avenues for engineering P. putida towards efficient, sugar-based bioprocesses.
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Affiliation(s)
- Daniel C Volke
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark.
| | - Nicolas Gurdo
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Riccardo Milanesi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126, Milano, Italy
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark.
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4
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Alam S, Gu Y, Reichert P, Bähler J, Oliferenko S. Optimization of energy production and central carbon metabolism in a non-respiring eukaryote. Curr Biol 2023; 33:2175-2186.e5. [PMID: 37164017 PMCID: PMC7615655 DOI: 10.1016/j.cub.2023.04.046] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 03/30/2023] [Accepted: 04/18/2023] [Indexed: 05/12/2023]
Abstract
Most eukaryotes respire oxygen, using it to generate biomass and energy. However, a few organisms have lost the capacity to respire. Understanding how they manage biomass and energy production may illuminate the critical points at which respiration feeds into central carbon metabolism and explain possible routes to its optimization. Here, we use two related fission yeasts, Schizosaccharomyces pombe and Schizosaccharomyces japonicus, as a comparative model system. We show that although S. japonicus does not respire oxygen, unlike S. pombe, it is capable of efficient NADH oxidation, amino acid synthesis, and ATP generation. We probe possible optimization strategies through the use of stable isotope tracing metabolomics, mass isotopologue distribution analysis, genetics, and physiological experiments. S. japonicus appears to have optimized cytosolic NADH oxidation via glycerol-3-phosphate synthesis. It runs a fully bifurcated TCA pathway, sustaining amino acid production. Finally, we propose that it has optimized glycolysis to maintain high ATP/ADP ratio, in part by using the pentose phosphate pathway as a glycolytic shunt, reducing allosteric inhibition of glycolysis and supporting biomass generation. By comparing two related organisms with vastly different metabolic strategies, our work highlights the versatility and plasticity of central carbon metabolism in eukaryotes, illuminating critical adaptations supporting the preferential use of glycolysis over oxidative phosphorylation.
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Affiliation(s)
- Sara Alam
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London SE1 1UL, UK
| | - Ying Gu
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London SE1 1UL, UK
| | - Polina Reichert
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London SE1 1UL, UK; School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Jürg Bähler
- Institute of Healthy Ageing, Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Snezhana Oliferenko
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London SE1 1UL, UK.
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Impact of Calcium and Nitrogen Addition on Bioethanol Production by S. cerevisiae Fermentation from Date By-Products: Physicochemical Characterization and Technical Design. FERMENTATION-BASEL 2022. [DOI: 10.3390/fermentation8110583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Given crude oil prices and their environmental impacts, the use of sustainable renewable alternative energies such as biofuels is rapidly progressing in numerous countries. Among biofuels, bioethanol is a renewable and clean fuel that can be obtained from the fermentation of several raw agricultural materials, including date fruit. However, the low product yield, mainly due to the low-grade nutrient content, limits its use as a promising alternative biofuel. This current study investigated bioethanol production from date by-products in Saudi Arabia and examined the impact of calcium and nitrogen sources added at different concentrations (0 to 1 g/L) on the productivity and ethanol concentration using Saccharomyces cerevisiae. Yeast extracts and ammonium chloride (NH4Cl) were tested as nitrogen sources for bioethanol fermentation from date juice. Calcium chloride (CaCl2) and calcium carbonate (CaCO3) were evaluated as calcium sources for the same purpose mentioned above. The results showed that both calcium and nitrogen sources improved ethanol production efficiencies. The addition of calcium sources such as CaCl2 at 0.4 g/L resulted in maximum ethanol concentration (41.5 ± 0.85 g/L) and the highest productivity of 0.511 g/L/h. Thus, an increase of 31.3% compared to the control sample was acquired. Ammonium chloride was found to be the best nitrogen supplement among them. Indeed, supplementing the fermentation medium with 1 g/L NH4Cl gave an optimal ethanol concentration and productivity, reaching more than 65 g/L and 0.83 g/L/h, respectively. This is an increase of 106.6%. The functional group of ethanol (C2H5OH) for all the elaborated samples was confirmed by Fourier-transform infrared spectroscopy (FTIR) and NMR analyses. Moreover, the results confirmed the high quality and purity of the bioethanol products. Thus, the “Khodhari” date variety of low market value is a privileged substrate for industrial bioethanol production. For this reason, a proposed flow diagram of a designed plant for bioethanol industrialization is provided and detailed.
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Zhou X, Zhao L, Wang X, Wang X, Wei J, Fang Z, Li S, Rong X, Luo Z, Liang Z, Dai Z, Wu Z, Liu Z. Organic and inorganic nitrogen removals by an ureolytic heterotrophic nitrification and aerobic denitrification strain Acinetobacter sp. Z1: Elucidating its physiological characteristics and metabolic mechanisms. BIORESOURCE TECHNOLOGY 2022; 362:127792. [PMID: 35985460 DOI: 10.1016/j.biortech.2022.127792] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 08/09/2022] [Accepted: 08/13/2022] [Indexed: 06/15/2023]
Abstract
Although heterotrophic nitrification-aerobic denitrification (HN-AD) is promising in nitrogen removal, it remains unclear for most HN-AD strains in physiological characteristics and metabolic mechanisms. In this study, a newly isolated strain Acinetobacter sp. Z1 converted not only inorganic nitrogen, but also organic nitrogen to N2. Among them, urea was the preferential nitrogen substrate. Single-factor experiments showed that efficient HN-AD process occurred with acetate as carbon source, C/N ratios of 12 for NH4+-N and 15 for NO3--N, pH 8, 30 °C, DO of ∼5.8 mg/L and salinity less than 1.5 %. Subsequently, response surface analysis was applied to predict the optimal growth conditions. Its complete genome annotation in combination with enzymatic activity assay and nitrogen balance calculation showed that at least four pathways involved in nitrogen metabolism. This work indicates that ureolytic strain Z1 could be prepared as bacterial agents with other HN-AD strains to treat urea-containing wastewater like urine from urban community.
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Affiliation(s)
- Xiangtong Zhou
- Institute of Environmental Health and Ecological Safety, Jiangsu University, Zhenjiang, Jiang Su 212013, China
| | - Liang Zhao
- Institute of Environmental Health and Ecological Safety, Jiangsu University, Zhenjiang, Jiang Su 212013, China
| | - Xiao Wang
- School of Chemical Engineering, Qinghai University, No. 251, Ningda Road, Chengbei District, Xining, Qinghai 810016, China
| | - Xiaochun Wang
- Institute of Environmental Health and Ecological Safety, Jiangsu University, Zhenjiang, Jiang Su 212013, China
| | - Jing Wei
- Institute of Environmental Health and Ecological Safety, Jiangsu University, Zhenjiang, Jiang Su 212013, China; Jiangsu Collaborative Innovation Center of Technology and Material of WaterTreatment, Suzhou University of Science and Technology, Suzhou, Jiangsu 215009, China
| | - Zhen Fang
- Biofuels Institute, Jiangsu University, Zhenjiang, Jiang Su 212013, China
| | - Shanwei Li
- Institute of Environmental Health and Ecological Safety, Jiangsu University, Zhenjiang, Jiang Su 212013, China
| | - Xinshan Rong
- Institute of Environmental Health and Ecological Safety, Jiangsu University, Zhenjiang, Jiang Su 212013, China
| | - Zhijun Luo
- Institute of Environmental Health and Ecological Safety, Jiangsu University, Zhenjiang, Jiang Su 212013, China
| | - Zhishui Liang
- School of Civil Engineering, Southeast University, No. 2 Sipailou, Nanjing, Jiangsu 210096, China
| | - Zhidong Dai
- Biotechnology Center of Danyang Environmental Ecological Restoration, Zhenjiang, Jiang Su 212013, China
| | - Zhiren Wu
- Institute of Environmental Health and Ecological Safety, Jiangsu University, Zhenjiang, Jiang Su 212013, China
| | - Zhigang Liu
- Institute of Environmental Health and Ecological Safety, Jiangsu University, Zhenjiang, Jiang Su 212013, China.
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7
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The Dicarboxylate Transporters from the AceTr Family and Dct-02 Oppositely Affect Succinic Acid Production in S. cerevisiae. J Fungi (Basel) 2022; 8:jof8080822. [PMID: 36012810 PMCID: PMC9409672 DOI: 10.3390/jof8080822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 07/28/2022] [Accepted: 08/04/2022] [Indexed: 11/17/2022] Open
Abstract
Membrane transporters are important targets in metabolic engineering to establish and improve the production of chemicals such as succinic acid from renewable resources by microbial cell factories. We recently provided a Saccharomyces cerevisiae strain able to strongly overproduce succinic acid from glycerol and CO2 in which the Dct-02 transporter from Aspergillus niger, assumed to be an anion channel, was used to export succinic acid from the cells. In a different study, we reported a new group of succinic acid transporters from the AceTr family, which were also described as anion channels. Here, we expressed these transporters in a succinic acid overproducing strain and compared their impact on extracellular succinic acid accumulation with that of the Dct-02 transporter. The results show that the tested transporters of the AceTr family hinder succinic acid accumulation in the extracellular medium at low pH, which is in strong contrast to Dct-02. Data suggests that the AceTr transporters prefer monovalent succinate, whereas Dct-02 prefers divalent succinate anions. In addition, the results provided deeper insights into the characteristics of Dct-02, showing its ability to act as a succinic acid importer (thus being bidirectional) and verifying its capability of exporting malate.
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8
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Malubhoy Z, Bahia FM, de Valk SC, de Hulster E, Rendulić T, Ortiz JPR, Xiberras J, Klein M, Mans R, Nevoigt E. Carbon dioxide fixation via production of succinic acid from glycerol in engineered Saccharomyces cerevisiae. Microb Cell Fact 2022; 21:102. [PMID: 35643577 PMCID: PMC9148483 DOI: 10.1186/s12934-022-01817-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 05/06/2022] [Indexed: 12/21/2022] Open
Abstract
Background The microbial production of succinic acid (SA) from renewable carbon sources via the reverse TCA (rTCA) pathway is a process potentially accompanied by net-fixation of carbon dioxide (CO2). Among reduced carbon sources, glycerol is particularly attractive since it allows a nearly twofold higher CO2-fixation yield compared to sugars. Recently, we described an engineered Saccharomyces cerevisiae strain which allowed SA production in synthetic glycerol medium with a maximum yield of 0.23 Cmol Cmol−1. The results of that previous study suggested that the glyoxylate cycle considerably contributed to SA accumulation in the respective strain. The current study aimed at improving the flux into the rTCA pathway accompanied by a higher CO2-fixation and SA yield. Results By changing the design of the expression cassettes for the rTCA pathway, overexpressing PYC2, and adding CaCO3 to the batch fermentations, an SA yield on glycerol of 0.63 Cmol Cmol−1 was achieved (i.e. 47.1% of the theoretical maximum). The modifications in this 2nd-generation SA producer improved the maximum biomass-specific glycerol consumption rate by a factor of nearly four compared to the isogenic baseline strain solely equipped with the dihydroxyacetone (DHA) pathway for glycerol catabolism. The data also suggest that the glyoxylate cycle did not contribute to the SA production in the new strain. Cultivation conditions which directly or indirectly increased the concentration of bicarbonate, led to an accumulation of malate in addition to the predominant product SA (ca. 0.1 Cmol Cmol−1 at the time point when SA yield was highest). Off-gas analysis in controlled bioreactors with CO2-enriched gas-phase indicated that CO2 was fixed during the SA production phase. Conclusions The data strongly suggest that a major part of dicarboxylic acids in our 2nd-generation SA-producer was formed via the rTCA pathway enabling a net fixation of CO2. The greatly increased capacity of the rTCA pathway obviously allowed successful competition with other pathways for the common precursor pyruvate. The overexpression of PYC2 and the increased availability of bicarbonate, the co-substrate for the PYC reaction, further strengthened this capacity. The achievements are encouraging to invest in future efforts establishing a process for SA production from (crude) glycerol and CO2. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01817-1.
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van Aalst AC, de Valk SC, van Gulik WM, Jansen ML, Pronk JT, Mans R. Pathway engineering strategies for improved product yield in yeast-based industrial ethanol production. Synth Syst Biotechnol 2022; 7:554-566. [PMID: 35128088 PMCID: PMC8792080 DOI: 10.1016/j.synbio.2021.12.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/22/2021] [Accepted: 12/23/2021] [Indexed: 12/16/2022] Open
Abstract
Product yield on carbohydrate feedstocks is a key performance indicator for industrial ethanol production with the yeast Saccharomyces cerevisiae. This paper reviews pathway engineering strategies for improving ethanol yield on glucose and/or sucrose in anaerobic cultures of this yeast by altering the ratio of ethanol production, yeast growth and glycerol formation. Particular attention is paid to strategies aimed at altering energy coupling of alcoholic fermentation and to strategies for altering redox-cofactor coupling in carbon and nitrogen metabolism that aim to reduce or eliminate the role of glycerol formation in anaerobic redox metabolism. In addition to providing an overview of scientific advances we discuss context dependency, theoretical impact and potential for industrial application of different proposed and developed strategies.
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Affiliation(s)
- Aafke C.A. van Aalst
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629, HZ Delft, the Netherlands
| | - Sophie C. de Valk
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629, HZ Delft, the Netherlands
| | - Walter M. van Gulik
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629, HZ Delft, the Netherlands
| | - Mickel L.A. Jansen
- DSM Biotechnology Centre, Alexander Fleminglaan 1, 2613, AX Delft, the Netherlands
| | - Jack T. Pronk
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629, HZ Delft, the Netherlands
| | - Robert Mans
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629, HZ Delft, the Netherlands
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Havukainen S, Pujol-Giménez J, Valkonen M, Hediger MA, Landowski CP. Functional characterization of a highly specific L-arabinose transporter from Trichoderma reesei. Microb Cell Fact 2021; 20:177. [PMID: 34496831 PMCID: PMC8425032 DOI: 10.1186/s12934-021-01666-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 08/25/2021] [Indexed: 11/10/2022] Open
Abstract
Background Lignocellulose biomass has been investigated as a feedstock for second generation biofuels and other value-added products. Some of the processes for biofuel production utilize cellulases and hemicellulases to convert the lignocellulosic biomass into a range of soluble sugars before fermentation with microorganisms such as yeast Saccharomyces cerevisiae. One of these sugars is l-arabinose, which cannot be utilized naturally by yeast. The first step in l-arabinose catabolism is its transport into the cells, and yeast lacks a specific transporter, which could perform this task. Results We identified Trire2_104072 of Trichoderma reesei as a potential l-arabinose transporter based on its expression profile. This transporter was described already in 2007 as d-xylose transporter XLT1. Electrophysiology experiments with Xenopus laevis oocytes and heterologous expression in yeast revealed that Trire2_104072 is a high-affinity l-arabinose symporter with a Km value in the range of \documentclass[12pt]{minimal}
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\begin{document}$$\sim$$\end{document}∼ 0.1–0.2 mM. It can also transport d-xylose but with low affinity (Km\documentclass[12pt]{minimal}
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\begin{document}$$\sim$$\end{document}∼ 9 mM). In yeast, l-arabinose transport was inhibited slightly by d-xylose but not by d-glucose in an assay with fivefold excess of the inhibiting sugar. Comparison with known l-arabinose transporters revealed that the expression of Trire2_104072 enabled yeast to uptake l-arabinose at the highest rate in conditions with low extracellular l-arabinose concentration. Despite the high specificity of Trire2_104072 for l-arabinose, the growth of its T. reesei deletion mutant was only affected at low l-arabinose concentrations. Conclusions Due to its high affinity for l-arabinose and low inhibition by d-glucose or d-xylose, Trire2_104072 could serve as a good candidate for improving the existing pentose-utilizing yeast strains. The discovery of a highly specific l-arabinose transporter also adds to our knowledge of the primary metabolism of T. reesei. The phenotype of the deletion strain suggests the involvement of other transporters in l-arabinose transport in this species. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01666-4.
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Affiliation(s)
- Sami Havukainen
- VTT Technical Research Center of Finland Ltd, Tietotie 2, 02150, Espoo, Finland
| | - Jonai Pujol-Giménez
- Membrane Transport Discovery Lab, Department of Nephrology and Hypertension, University of Bern, Freiburgstrasse 15, 3010, Bern, Switzerland.,Department of Biomedical Research, Inselspital, University of Bern, Freiburgstrasse 15, 3010, Bern, Switzerland
| | - Mari Valkonen
- VTT Technical Research Center of Finland Ltd, Tietotie 2, 02150, Espoo, Finland
| | - Matthias A Hediger
- Membrane Transport Discovery Lab, Department of Nephrology and Hypertension, University of Bern, Freiburgstrasse 15, 3010, Bern, Switzerland.,Department of Biomedical Research, Inselspital, University of Bern, Freiburgstrasse 15, 3010, Bern, Switzerland
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11
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Montaño López J, Duran L, Avalos JL. Physiological limitations and opportunities in microbial metabolic engineering. Nat Rev Microbiol 2021; 20:35-48. [PMID: 34341566 DOI: 10.1038/s41579-021-00600-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/22/2021] [Indexed: 11/10/2022]
Abstract
Metabolic engineering can have a pivotal role in increasing the environmental sustainability of the transportation and chemical manufacturing sectors. The field has already developed engineered microorganisms that are currently being used in industrial-scale processes. However, it is often challenging to achieve the titres, yields and productivities required for commercial viability. The efficiency of microbial chemical production is usually dependent on the physiological traits of the host organism, which may either impose limitations on engineered biosynthetic pathways or, conversely, boost their performance. In this Review, we discuss different aspects of microbial physiology that often create obstacles for metabolic engineering, and present solutions to overcome them. We also describe various instances in which natural or engineered physiological traits in host organisms have been harnessed to benefit engineered metabolic pathways for chemical production.
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Affiliation(s)
- José Montaño López
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | - Lisset Duran
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - José L Avalos
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA. .,Department of Molecular Biology, Princeton University, Princeton, NJ, USA. .,Andlinger Center for Energy and the Environment, Princeton University, Princeton, NJ, USA. .,Princeton Environmental Institute, Princeton University, Princeton, NJ, USA.
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12
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Adebami GE, Kuila A, Ajunwa OM, Fasiku SA, Asemoloye MD. Genetics and metabolic engineering of yeast strains for efficient ethanol production. J FOOD PROCESS ENG 2021. [DOI: 10.1111/jfpe.13798] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
| | - Arindam Kuila
- Department of Bioscience and Biotechnology Banasthali University Vanasthali India
| | - Obinna M. Ajunwa
- Department of Microbiology Modibbo Adama University of Technology Yola Nigeria
| | - Samuel A. Fasiku
- Department of Biological Sciences Ajayi Crowther University Oyo Nigeria
| | - Michael D. Asemoloye
- Department of Pharmaceutical Science and Technology Tianjin University Tianjin China
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13
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Yang X, Yang Y, Huang J, Man D, Guo M. Comparisons of urea or ammonium on growth and fermentative metabolism of Saccharomyces cerevisiae in ethanol fermentation. World J Microbiol Biotechnol 2021; 37:98. [PMID: 33969436 DOI: 10.1007/s11274-021-03056-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 04/13/2021] [Indexed: 10/21/2022]
Abstract
This work was mainly about the understanding of how urea and ammonium affect growth, glucose consumption and ethanol production of S. cerevisiae, in particular regarding the basic physiology of cell. The basic physiology of cell included intracellular pH, ATP, NADH and enzyme activity. Results showed that fermentation time was reduced by 19% when using urea compared with ammonium. The maximal ethanol production rate using urea was 1.14 g/L/h, increasing 30% comparing with the medium prepared with ammonium. Moreover, urea could decrease the synthesis of glycerol from glucose by 26% comparing with ammonium. The by-product of acetic acid yields decreased from 40 mmol/mol of glucose (with urea) to 24 mmol/mol of glucose (with ammonium). At the end of ethanol fermentation, cell number and pH were greater with urea than ammonium. Comparing with urea, ammonium decreased the intracellular pH by 14% (from 7.1 to 6.1). Urease converting urea into ammonia resulted in a more than 50% lower of ATP when comparing with ammonium. The values of NADH/DCW were 0.21 mg/g and 0.14 mg/g respectively with urea and ammonium, suggesting a 33% lower NADH. The enzyme activity of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) was 0.0225 and 0.0275 U/mg protein respectively with urea and ammonium, which was consistent with the yields of glycerol.
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Affiliation(s)
- Xinchao Yang
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, China.
| | - Yuling Yang
- Linghua Group Limited, Jining, 272073, China
| | - Jiadong Huang
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, China
| | - Deen Man
- Linghua Group Limited, Jining, 272073, China
| | - Maihai Guo
- Linghua Group Limited, Jining, 272073, China
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14
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Rodrigues CIS, Wahl A, Gombert AK. Aerobic growth physiology of Saccharomyces cerevisiae on sucrose is strain-dependent. FEMS Yeast Res 2021; 21:6214418. [PMID: 33826723 DOI: 10.1093/femsyr/foab021] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 04/01/2021] [Indexed: 12/22/2022] Open
Abstract
Present knowledge on the quantitative aerobic physiology of the yeast Saccharomyces cerevisiae during growth on sucrose as sole carbon and energy source is limited to either adapted cells or to the model laboratory strain CEN.PK113-7D. To broaden our understanding of this matter and open novel opportunities for sucrose-based biotechnological processes, we characterized three strains, with distinct backgrounds, during aerobic batch bioreactor cultivations. Our results reveal that sucrose metabolism in S. cerevisiae is a strain-specific trait. Each strain displayed distinct extracellular hexose concentrations and invertase activity profiles. Especially, the inferior maximum specific growth rate (0.21 h-1) of the CEN.PK113-7D strain, with respect to that of strains UFMG-CM-Y259 (0.37 h-1) and JP1 (0.32 h-1), could be associated to its low invertase activity (0.04-0.09 U/mgDM). Moreover, comparative experiments with glucose or fructose alone, or in combination, suggest mixed mechanisms of sucrose utilization by the industrial strain JP1, and points out the remarkable ability of the wild isolate UFMG-CM-259 to grow faster on sucrose than on glucose in a well-controlled cultivation system. This work hints to a series of metabolic traits that can be exploited to increase sucrose catabolic rates and bioprocess efficiency.
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Affiliation(s)
- Carla Inês Soares Rodrigues
- School of Food Engineering, University of Campinas, Rua Monteiro Lobato 80, 13083-862, Campinas, SP, Brazil.,Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629HZ Delft, The Netherlands
| | - Aljoscha Wahl
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629HZ Delft, The Netherlands
| | - Andreas K Gombert
- School of Food Engineering, University of Campinas, Rua Monteiro Lobato 80, 13083-862, Campinas, SP, Brazil
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15
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Endocytosis of nutrient transporters in fungi: The ART of connecting signaling and trafficking. Comput Struct Biotechnol J 2021; 19:1713-1737. [PMID: 33897977 PMCID: PMC8050425 DOI: 10.1016/j.csbj.2021.03.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 03/14/2021] [Accepted: 03/14/2021] [Indexed: 12/11/2022] Open
Abstract
Plasma membrane transporters play pivotal roles in the import of nutrients, including sugars, amino acids, nucleobases, carboxylic acids, and metal ions, that surround fungal cells. The selective removal of these transporters by endocytosis is one of the most important regulatory mechanisms that ensures a rapid adaptation of cells to the changing environment (e.g., nutrient fluctuations or different stresses). At the heart of this mechanism lies a network of proteins that includes the arrestin‐related trafficking adaptors (ARTs) which link the ubiquitin ligase Rsp5 to nutrient transporters and endocytic factors. Transporter conformational changes, as well as dynamic interactions between its cytosolic termini/loops and with lipids of the plasma membrane, are also critical during the endocytic process. Here, we review the current knowledge and recent findings on the molecular mechanisms involved in nutrient transporter endocytosis, both in the budding yeast Saccharomyces cerevisiae and in some species of the filamentous fungus Aspergillus. We elaborate on the physiological importance of tightly regulated endocytosis for cellular fitness under dynamic conditions found in nature and highlight how further understanding and engineering of this process is essential to maximize titer, rate and yield (TRY)-values of engineered cell factories in industrial biotechnological processes.
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Key Words
- AAs, amino acids
- ACT, amino Acid/Choline Transporter
- AP, adaptor protein
- APC, amino acid-polyamine-organocation
- Arg, arginine
- Arrestins
- Arts, arrestin‐related trafficking adaptors
- Asp, aspartic acid
- Aspergilli
- Biotechnology
- C, carbon
- C-terminus, carboxyl-terminus
- Cell factories
- Conformational changes
- Cu, copper
- DUBs, deubiquitinating enzymes
- EMCs, eisosome membrane compartments
- ER, endoplasmic reticulum
- ESCRT, endosomal sorting complex required for transport
- Endocytic signals
- Endocytosis
- Fe, iron
- Fungi
- GAAC, general amino acid control
- Glu, glutamic acid
- H+, proton
- IF, inward-facing
- LAT, L-type Amino acid Transporter
- LID, loop Interaction Domain
- Lys, lysine
- MCCs, membrane compartments containing the arginine permease Can1
- MCCs/eisosomes
- MCPs, membrane compartments of Pma1
- MFS, major facilitator superfamily
- MVB, multi vesicular bodies
- Met, methionine
- Metabolism
- Mn, manganese
- N, nitrogen
- N-terminus, amino-terminus
- NAT, nucleobase Ascorbate Transporter
- NCS1, nucleobase/Cation Symporter 1
- NCS2, nucleobase cation symporter family 2
- NH4+, ammonium
- Nutrient transporters
- OF, outward-facing
- PEST, proline (P), glutamic acid (E), serine (S), and threonine (T)
- PM, plasma membrane
- PVE, prevacuolar endosome
- Saccharomyces cerevisiae
- Signaling pathways
- Structure-function
- TGN, trans-Golgi network
- TMSs, transmembrane segments
- TORC1, target of rapamycin complex 1
- TRY, titer, rate and yield
- Trp, tryptophan
- Tyr, tyrosine
- Ub, ubiquitin
- Ubiquitylation
- VPS, vacuolar protein sorting
- W/V, weight per volume
- YAT, yeast Amino acid Transporter
- Zn, Zinc
- fAATs, fungal AA transporters
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16
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Du Q, Liu Y, Song Y, Qin Y. Creation of a Low-Alcohol-Production Yeast by a Mutated SPT15 Transcription Regulator Triggers Transcriptional and Metabolic Changes During Wine Fermentation. Front Microbiol 2021; 11:597828. [PMID: 33381093 PMCID: PMC7768003 DOI: 10.3389/fmicb.2020.597828] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Accepted: 11/23/2020] [Indexed: 11/23/2022] Open
Abstract
There is significant interest in the wine industry to develop methods to reduce the ethanol content of wine. Here the global transcription machinery engineering (gTME) technology was used to engineer a yeast strain with decreased ethanol yield, based on the mutation of the SPT15 gene. We created a strain of Saccharomyces cerevisiae (YS59-409), which possessed ethanol yield reduced by 34.9%; this was accompanied by the increase in CO2, biomass, and glycerol formation. Five mutation sites were identified in the mutated SPT15 gene of YS59-409. RNA-Seq and metabolome analysis of YS59-409 were conducted compared with control strain, suggesting that ribosome biogenesis, nucleotide metabolism, glycolysis flux, Crabtree effect, NAD+/NADH homeostasis and energy metabolism might be regulated by the mutagenesis of SPT15 gene. Furthermore, two genes related to energy metabolism, RGI1 and RGI2, were found to be associated with the weakened ethanol production capacity, although the precise mechanisms involved need to be further elucidated. This study highlighted the importance of applying gTME technology when attempting to reduce ethanol production by yeast, possibly reprogramming yeast’s metabolism at the global level.
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Affiliation(s)
- Qing Du
- College of Enology, Northwest A&F University, Yangling, China.,Shaanxi Engineering Research Center for Viti-Viniculture, Yangling, China.,National Forestry and Grassland Administration Engineering Research Center for Viti-Viniculture, Yangling, China
| | - Yanlin Liu
- College of Enology, Northwest A&F University, Yangling, China.,Shaanxi Engineering Research Center for Viti-Viniculture, Yangling, China.,National Forestry and Grassland Administration Engineering Research Center for Viti-Viniculture, Yangling, China
| | - Yuyang Song
- College of Enology, Northwest A&F University, Yangling, China.,Shaanxi Engineering Research Center for Viti-Viniculture, Yangling, China.,National Forestry and Grassland Administration Engineering Research Center for Viti-Viniculture, Yangling, China
| | - Yi Qin
- College of Enology, Northwest A&F University, Yangling, China.,Shaanxi Engineering Research Center for Viti-Viniculture, Yangling, China.,National Forestry and Grassland Administration Engineering Research Center for Viti-Viniculture, Yangling, China
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17
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Energy coupling of membrane transport and efficiency of sucrose dissimilation in yeast. Metab Eng 2020; 65:243-254. [PMID: 33279674 DOI: 10.1016/j.ymben.2020.11.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 11/04/2020] [Accepted: 11/30/2020] [Indexed: 11/22/2022]
Abstract
Proton coupled transport of α-glucosides via Mal11 into Saccharomyces cerevisiae costs one ATP per imported molecule. Targeted mutation of all three acidic residues in the active site resulted in sugar uniport, but expression of these mutant transporters in yeast did not enable growth on sucrose. We then isolated six unique transporter variants of these mutants by directed evolution of yeast for growth on sucrose. In three variants, new acidic residues emerged near the active site that restored proton-coupled sucrose transport, whereas the other evolved transporters still catalysed sucrose uniport. The localization of mutations and transport properties of the mutants enabled us to propose a mechanistic model of proton-coupled sugar transport by Mal11. Cultivation of yeast strains expressing one of the sucrose uniporters in anaerobic, sucrose-limited chemostat cultures indicated an increase in the efficiency of sucrose dissimilation by 21% when additional changes in strain physiology were taken into account. We thus show that a combination of directed and evolutionary engineering results in more energy efficient sucrose transport, as a starting point to engineer yeast strains with increased yields for industrially relevant products.
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18
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Zahoor A, Messerschmidt K, Boecker S, Klamt S. ATPase-based implementation of enforced ATP wasting in Saccharomyces cerevisiae for improved ethanol production. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:185. [PMID: 33292464 PMCID: PMC7654063 DOI: 10.1186/s13068-020-01822-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 10/23/2020] [Indexed: 05/06/2023]
Abstract
BACKGROUND Enforced ATP wasting has been recognized as a promising metabolic engineering strategy to enhance the microbial production of metabolites that are coupled to ATP generation. It also appears to be a suitable approach to improve production of ethanol by Saccharomyces cerevisiae. In the present study, we constructed different S. cerevisiae strains with heterologous expression of genes of the ATP-hydrolyzing F1-part of the ATPase enzyme to induce enforced ATP wasting and quantify the resulting effect on biomass and ethanol formation. RESULTS In contrast to genomic integration, we found that episomal expression of the αβγ subunits of the F1-ATPase genes of Escherichia coli in S. cerevisiae resulted in significantly increased ATPase activity, while neither genomic integration nor episomal expression of the β subunit from Trichoderma reesei could enhance ATPase activity. When grown in minimal medium under anaerobic growth-coupled conditions, the strains expressing E. coli's F1-ATPase genes showed significantly improved ethanol yield (increase of 10% compared to the control strain). However, elevated product formation reduces biomass formation and, therefore, volumetric productivity. We demonstrate that this negative effect can be overcome under growth-decoupled (nitrogen-starved) operation with high and constant biomass concentration. Under these conditions, which mimic the second (production) phase of a two-stage fermentation process, the ATPase-expressing strains showed significant improvement in volumetric productivity (up to 111%) compared to the control strain. CONCLUSIONS Our study shows that expression of genes of the F1-portion of E. coli's ATPase induces ATPase activity in S. cerevisiae and can be a promising way to improve ethanol production. This ATP-wasting strategy can be easily applied to other metabolites of interest, whose formation is coupled to ATP generation.
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Affiliation(s)
- Ahmed Zahoor
- Analysis and Redesign of Biological Networks, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Katrin Messerschmidt
- Analysis and Redesign of Biological Networks, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Simon Boecker
- Analysis and Redesign of Biological Networks, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Steffen Klamt
- Analysis and Redesign of Biological Networks, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany.
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19
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Enhanced 2′-Fucosyllactose production by engineered Saccharomyces cerevisiae using xylose as a co-substrate. Metab Eng 2020; 62:322-329. [DOI: 10.1016/j.ymben.2020.10.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 10/13/2020] [Accepted: 10/17/2020] [Indexed: 12/24/2022]
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20
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de Arroyo Garcia L, Jones PR. In silico co-factor balance estimation using constraint-based modelling informs metabolic engineering in Escherichia coli. PLoS Comput Biol 2020; 16:e1008125. [PMID: 32776925 PMCID: PMC7440669 DOI: 10.1371/journal.pcbi.1008125] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 08/20/2020] [Accepted: 07/06/2020] [Indexed: 02/06/2023] Open
Abstract
In the growing field of metabolic engineering, where cells are treated as ‘factories’ that synthesize industrial compounds, it is essential to consider the ability of the cells’ native metabolism to accommodate the demands of synthetic pathways, as these pathways will alter the homeostasis of cellular energy and electron metabolism. From the breakdown of substrate, microorganisms activate and reduce key co-factors such as ATP and NAD(P)H, which subsequently need to be hydrolysed and oxidized, respectively, in order to restore cellular balance. A balanced supply and consumption of such co-factors, here termed co-factor balance, will influence biotechnological performance. To aid the strain selection and design process, we used stoichiometric modelling (FBA, pFBA, FVA and MOMA) and the Escherichia coli (E.coli) core stoichiometric model to investigate the network-wide effect of butanol and butanol precursor production pathways differing in energy and electron demand on product yield. An FBA-based co-factor balance assessment (CBA) algorithm was developed to track and categorise how ATP and NAD(P)H pools are affected in the presence of a new pathway. CBA was compared to the balance calculations proposed by Dugar et al. (Nature Biotechnol. 29 (12), 1074–1078). Predicted solutions were compromised by excessively underdetermined systems, displaying greater flexibility in the range of reaction fluxes than experimentally measured by 13C-metabolic flux analysis (MFA) and the appearance of unrealistic futile co-factor cycles. With the assumption that futile cycles are tightly regulated in reality, the FBA models were manually constrained in a step-wise manner. Solutions with minimal futile cycling diverted surplus energy and electrons towards biomass formation. As an alternative, the use of loopless FBA or constraining the models with measured flux ranges were tried but did not prevent futile co-factor cycles. The results highlight the need to account for co-factor imbalance and confirm that better-balanced pathways with minimal diversion of surplus towards biomass formation present the highest theoretical yield. The analysis also suggests that ATP and NAD(P)H balancing cannot be assessed in isolation from each other, or even from the balance of additional co-factors such as AMP and ADP. We conclude that, through revealing the source of co-factor imbalance CBA can facilitate pathway and host selection when designing new biocatalysts for implementation by metabolic engineering. The chemicals industry is a major contributor to greenhouse gas emissions and desperately requires more sustainable alternatives. Genetically engineered microorganisms can be used as ‘bio-factories’ to manufacture chemicals, replacing those currently sourced from fossil fuels or unsustainable tropical plant agriculture. However, due to the complexity of biology, the features that render one bio-factory design more efficient than others are difficult to identify. Computational modelling of such designs can enable the selection of optimally performing designs, but it remains challenging as biology is complex and not fully understood. Microorganisms require energy for their own growth and maintenance, but also to convert molecules into desired target products. The supply and consumption of such energy is through co-factors, and the balance of such co-factors influences the performance of the engineered bio-factories. This study developed a computer-aided approach for quantification of the co-factor balance of bio-factories. Using the chemical n-butanol as a case study, our study explores the impact of variant bio-factory designs with differing co-factor balance on the potential efficiency of biomanufacturing. We provide insights into the relative balance of different designs and provide a computational framework to select the best-performing designs.
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Affiliation(s)
| | - Patrik R. Jones
- Department of Life Sciences, Imperial College London, London, United Kingdom
- * E-mail:
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21
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Tiukova IA, Møller-Hansen I, Belew ZM, Darbani B, Boles E, Nour-Eldin HH, Linder T, Nielsen J, Borodina I. Identification and characterisation of two high-affinity glucose transporters from the spoilage yeast Brettanomyces bruxellensis. FEMS Microbiol Lett 2020; 366:5610216. [PMID: 31665273 PMCID: PMC6847091 DOI: 10.1093/femsle/fnz222] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 10/25/2019] [Indexed: 12/17/2022] Open
Abstract
The yeast Brettanomyces bruxellensis (syn. Dekkera bruxellensis) is an emerging and undesirable contaminant in industrial low-sugar ethanol fermentations that employ the yeast Saccharomyces cerevisiae. High-affinity glucose import in B. bruxellensis has been proposed to be the mechanism by which this yeast can outcompete S. cerevisiae. The present study describes the characterization of two B. bruxellensis genes (BHT1 and BHT3) believed to encode putative high-affinity glucose transporters. In vitro-generated transcripts of both genes as well as the S. cerevisiae HXT7 high-affinity glucose transporter were injected into Xenopus laevis oocytes and subsequent glucose uptake rates were assayed using 14C-labelled glucose. At 0.1 mM glucose, Bht1p was shown to transport glucose five times faster than Hxt7p. pH affected the rate of glucose transport by Bht1p and Bht3p, indicating an active glucose transport mechanism that involves proton symport. These results suggest a possible role for BHT1 and BHT3 in the competitive ability of B. bruxellensis.
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Affiliation(s)
- Ievgeniia A Tiukova
- Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Kemigården 4, 412 96 Gothenburg, Sweden
| | - Iben Møller-Hansen
- The Novo Nordisk Foundation for Biosustainability, Technical University of Denmark, Building 220, 2800 Kongens Lyngby, Denmark
| | - Zeinu M Belew
- Department of Plant and Environmental Sciences, DynaMo Center, Copenhagen Plant Science Center, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
| | - Behrooz Darbani
- The Novo Nordisk Foundation for Biosustainability, Technical University of Denmark, Building 220, 2800 Kongens Lyngby, Denmark
| | - Eckhard Boles
- Institute of Molecular Biosciences, Faculty of Biological Sciences, Goethe University Frankfurt, Max-von-Laue Straße 9, 60438, Frankfurt am Main, Germany
| | - Hussam H Nour-Eldin
- Department of Plant and Environmental Sciences, DynaMo Center, Copenhagen Plant Science Center, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
| | - Tomas Linder
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Almas allé 5, 750 07 Uppsala, Sweden
| | - Jens Nielsen
- Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Kemigården 4, 412 96 Gothenburg, Sweden
| | - Irina Borodina
- The Novo Nordisk Foundation for Biosustainability, Technical University of Denmark, Building 220, 2800 Kongens Lyngby, Denmark
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22
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Abstract
Metabolic engineering is crucial in the development of production strains for platform chemicals, pharmaceuticals and biomaterials from renewable resources. The central carbon metabolism (CCM) of heterotrophs plays an essential role in the conversion of biomass to the cellular building blocks required for growth. Yet, engineering the CCM ultimately aims toward a maximization of flux toward products of interest. The most abundant dissimilative carbohydrate pathways amongst prokaryotes (and eukaryotes) are the Embden-Meyerhof-Parnas (EMP) and the Entner-Doudoroff (ED) pathways, which build the basics for heterotrophic metabolic chassis strains. Although the EMP is regarded as the textbook example of a carbohydrate pathway owing to its central role in production strains like Escherichia coli, Saccharomyces cerevisiae and Bacillus subtilis, it is either modified, complemented or even replaced by alternative carbohydrate pathways in different organisms. The ED pathway also plays key roles in biotechnological relevant bacteria, like Zymomonas mobilis and Pseudomonas putida, and its importance was recently discovered in photoautotrophs and marine microorganisms. In contrast to the EMP, the ED pathway and its variations are not evolutionary optimized for high ATP production and it differs in key principles such as protein cost, energetics and thermodynamics, which can be exploited in the construction of unique metabolic designs. Single ED pathway enzymes and complete ED pathway modules have been used to rewire carbon metabolisms in production strains and for the construction of cell-free enzymatic pathways. This review focuses on the differences of the ED and EMP pathways including their variations and discusses the use of alternative pathway strategies for in vivo and cell-free metabolic engineering.
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Affiliation(s)
- Dominik Kopp
- Department of Molecular Sciences, Macquarie University, Sydney, Australia
| | - Anwar Sunna
- Department of Molecular Sciences, Macquarie University, Sydney, Australia.,Biomolecular Discovery Research Centre, Macquarie University, Sydney, Australia
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23
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Xiberras J, Klein M, de Hulster E, Mans R, Nevoigt E. Engineering Saccharomyces cerevisiae for Succinic Acid Production From Glycerol and Carbon Dioxide. Front Bioeng Biotechnol 2020; 8:566. [PMID: 32671027 PMCID: PMC7332542 DOI: 10.3389/fbioe.2020.00566] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 05/11/2020] [Indexed: 12/11/2022] Open
Abstract
Previously, our lab replaced the endogenous FAD-dependent pathway for glycerol catabolism in S. cerevisiae by the synthetic NAD-dependent dihydroxyacetone (DHA) pathway. The respective modifications allow the full exploitation of glycerol’s higher reducing power (compared to sugars) for the production of the platform chemical succinic acid (SA) via a reductive, carbon dioxide fixing and redox-neutral pathway in a production host robust for organic acid production. Expression cassettes for three enzymes converting oxaloacetate to SA in the cytosol (“SA module”) were integrated into the genome of UBR2CBS-DHA, an optimized CEN.PK derivative. Together with the additional expression of the heterologous dicarboxylic acid transporter DCT-02 from Aspergillus niger, a maximum SA titer of 10.7 g/L and a yield of 0.22 ± 0.01 g/g glycerol was achieved in shake flask (batch) cultures. Characterization of the constructed strain under controlled conditions in a bioreactor supplying additional carbon dioxide revealed that the carbon balance was closed to 96%. Interestingly, the results of the current study indicate that the artificial “SA module” and endogenous pathways contribute to the SA production in a highly synergistic manner.
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Affiliation(s)
- Joeline Xiberras
- Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, Bremen, Germany
| | - Mathias Klein
- Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, Bremen, Germany
| | - Erik de Hulster
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Robert Mans
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Elke Nevoigt
- Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, Bremen, Germany
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24
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Bellut K, Krogerus K, Arendt EK. Lachancea fermentati Strains Isolated From Kombucha: Fundamental Insights, and Practical Application in Low Alcohol Beer Brewing. Front Microbiol 2020; 11:764. [PMID: 32390994 PMCID: PMC7191199 DOI: 10.3389/fmicb.2020.00764] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 03/30/2020] [Indexed: 01/05/2023] Open
Abstract
With a growing interest in non-alcoholic and low alcohol beer (NABLAB), researchers are looking into non-conventional yeasts to harness their special metabolic traits for their production. One of the investigated species is Lachancea fermentati, which possesses the uncommon ability to produce significant amounts of lactic acid during alcoholic fermentation, resulting in the accumulation of lactic acid while exhibiting reduced ethanol production. In this study, four Lachancea fermentati strains isolated from individual kombucha cultures were investigated. Whole genome sequencing was performed, and the strains were characterized for important brewing characteristics (e.g., sugar utilization) and sensitivities toward stress factors. A screening in wort extract was performed to elucidate strain-dependent differences, followed by fermentation optimization to enhance lactic acid production. Finally, a low alcohol beer was produced at 60 L pilot-scale. The genomes of the kombucha isolates were diverse and could be separated into two phylogenetic groups, which were related to their geographical origin. Compared to a Saccharomyces cerevisiae brewers' yeast, the strains' sensitivities to alcohol and acidic conditions were low, while their sensitivities toward osmotic stress were higher. In the screening, lactic acid production showed significant, strain-dependent differences. Fermentation optimization by means of response surface methodology (RSM) revealed an increased lactic acid production at a low pitching rate, high fermentation temperature, and high extract content. It was shown that a high initial glucose concentration led to the highest lactic acid production (max. 18.0 mM). The data indicated that simultaneous lactic acid production and ethanol production occurred as long as glucose was present. When glucose was depleted and/or lactic acid concentrations were high, the production shifted toward the ethanol pathway as the sole pathway. A low alcohol beer (<1.3% ABV) was produced at 60 L pilot-scale by means of stopped fermentation. The beer exhibited a balanced ratio of sweetness from residual sugars and acidity from the lactic acid produced (13.6 mM). However, due to the stopped fermentation, high levels of diacetyl were present, which could necessitate further process intervention to reduce concentrations to acceptable levels.
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Affiliation(s)
- Konstantin Bellut
- School of Food and Nutritional Sciences, University College Cork, Cork, Ireland
| | | | - Elke K. Arendt
- School of Food and Nutritional Sciences, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
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25
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Functional expression of a bacterial α-ketoglutarate dehydrogenase in the cytosol of Saccharomyces cerevisiae. Metab Eng 2019; 56:190-197. [DOI: 10.1016/j.ymben.2019.10.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 09/20/2019] [Accepted: 10/01/2019] [Indexed: 11/23/2022]
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26
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Kalnenieks U, Balodite E, Rutkis R. Metabolic Engineering of Bacterial Respiration: High vs. Low P/O and the Case of Zymomonas mobilis. Front Bioeng Biotechnol 2019; 7:327. [PMID: 31781557 PMCID: PMC6861446 DOI: 10.3389/fbioe.2019.00327] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 10/28/2019] [Indexed: 11/13/2022] Open
Abstract
Respiratory chain plays a pivotal role in the energy and redox balance of aerobic bacteria. By engineering respiration, it is possible to alter the efficiency of energy generation and intracellular redox state, and thus affect the key bioprocess parameters: cell yield, productivity and stress resistance. Here we summarize the current metabolic engineering and synthetic biology approaches to bacterial respiratory metabolism, with a special focus on the respiratory chain of the ethanologenic bacterium Zymomonas mobilis. Electron transport in Z. mobilis can serve as a model system of bacterial respiration with low oxidative phosphorylation efficiency. Its application for redox balancing and relevance for improvement of stress tolerance are analyzed.
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Affiliation(s)
- Uldis Kalnenieks
- Institute of Microbiology and Biotechnology, University of Latvia, Riga, Latvia
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27
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Ruchala J, Kurylenko OO, Dmytruk KV, Sibirny AA. Construction of advanced producers of first- and second-generation ethanol in Saccharomyces cerevisiae and selected species of non-conventional yeasts (Scheffersomyces stipitis, Ogataea polymorpha). J Ind Microbiol Biotechnol 2019; 47:109-132. [PMID: 31637550 PMCID: PMC6970964 DOI: 10.1007/s10295-019-02242-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 10/01/2019] [Indexed: 12/20/2022]
Abstract
This review summarizes progress in the construction of efficient yeast ethanol producers from glucose/sucrose and lignocellulose. Saccharomyces cerevisiae is the major industrial producer of first-generation ethanol. The different approaches to increase ethanol yield and productivity from glucose in S. cerevisiae are described. Construction of the producers of second-generation ethanol is described for S. cerevisiae, one of the best natural xylose fermenters, Scheffersomyces stipitis and the most thermotolerant yeast known Ogataea polymorpha. Each of these organisms has some advantages and drawbacks. S. cerevisiae is the primary industrial ethanol producer and is the most ethanol tolerant natural yeast known and, however, cannot metabolize xylose. S. stipitis can effectively ferment both glucose and xylose and, however, has low ethanol tolerance and requires oxygen for growth. O. polymorpha grows and ferments at high temperatures and, however, produces very low amounts of ethanol from xylose. Review describes how the mentioned drawbacks could be overcome.
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Affiliation(s)
- Justyna Ruchala
- Department of Microbiology and Biotechnology, University of Rzeszow, Zelwerowicza 4, 35-601, Rzeszow, Poland
| | - Olena O Kurylenko
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology, NAS of Ukraine, Drahomanov Street, 14/16, Lviv, 79005, Ukraine
| | - Kostyantyn V Dmytruk
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology, NAS of Ukraine, Drahomanov Street, 14/16, Lviv, 79005, Ukraine
| | - Andriy A Sibirny
- Department of Microbiology and Biotechnology, University of Rzeszow, Zelwerowicza 4, 35-601, Rzeszow, Poland.
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28
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Alcohol dehydrogenase 1 participates in the Crabtree effect and connects fermentative and oxidative metabolism in the Zygomycete Mucor circinelloides. J Microbiol 2019; 57:606-617. [DOI: 10.1007/s12275-019-8680-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 03/11/2019] [Accepted: 03/25/2019] [Indexed: 12/19/2022]
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29
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Boecker S, Zahoor A, Schramm T, Link H, Klamt S. Broadening the Scope of Enforced ATP Wasting as a Tool for Metabolic Engineering in Escherichia coli. Biotechnol J 2019; 14:e1800438. [PMID: 30927494 DOI: 10.1002/biot.201800438] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 02/25/2019] [Indexed: 01/21/2023]
Abstract
The targeted increase of cellular adenosine triphosphate (ATP) turnover (enforced ATP wasting) has recently been recognized as a promising tool for metabolic engineering when product synthesis is coupled with net ATP formation. The goal of the present study is to further examine and to further develop the concept of enforced ATP wasting and to broaden its scope for potential applications. In particular, considering the fermentation products synthesized by Escherichia coli under anaerobic conditions as a proxy for target chemical(s), i) a new genetic module for dynamic and gradual induction of the F1 -part of the ATPase is developed and it is found that ii) induction of the ATPase leads to higher metabolic activity and increased product formation in E. coli under anaerobic conditions, and that iii) ATP wasting significantly increases substrate uptake and productivity of growth-arrested cells, which is vital for its use in two-stage processes. To the best of the authors' knowledge, the glucose uptake rate of 6.49 mmol gCDW-1 h-1 achieved with enforced ATP wasting is the highest value reported for nongrowing E. coli cells. In summary, this study shows that enforced ATP wasting can be used to improve yield and titer (in growth-coupled processes) as well as volumetric productivity (in two-stage processes) depending on which of the performance measures is more crucial for the process and product of interest.
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Affiliation(s)
- Simon Boecker
- Analysis and Redesign of Biological Networks, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstr. 1, 39106, Magdeburg, Germany
| | - Ahmed Zahoor
- Analysis and Redesign of Biological Networks, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstr. 1, 39106, Magdeburg, Germany
| | - Thorben Schramm
- Dynamic Control of Metabolic Networks, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 16, 35043, Marburg, Germany
| | - Hannes Link
- Dynamic Control of Metabolic Networks, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 16, 35043, Marburg, Germany
| | - Steffen Klamt
- Analysis and Redesign of Biological Networks, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstr. 1, 39106, Magdeburg, Germany
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30
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Marques WL, van der Woude LN, Luttik MAH, van den Broek M, Nijenhuis JM, Pronk JT, van Maris AJA, Mans R, Gombert AK. Laboratory evolution and physiological analysis of Saccharomyces cerevisiae strains dependent on sucrose uptake via the Phaseolus vulgaris Suf1 transporter. Yeast 2018; 35:639-652. [PMID: 30221387 DOI: 10.1002/yea.3357] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 08/17/2018] [Accepted: 09/10/2018] [Indexed: 01/03/2023] Open
Abstract
Knowledge on the genetic factors important for the efficient expression of plant transporters in yeast is still very limited. Phaseolus vulgaris sucrose facilitator 1 (PvSuf1), a presumable uniporter, was an essential component in a previously published strategy aimed at increasing ATP yield in Saccharomyces cerevisiae. However, attempts to construct yeast strains in which sucrose metabolism was dependent on PvSUF1 led to slow sucrose uptake. Here, PvSUF1-dependent S. cerevisiae strains were evolved for faster growth. Of five independently evolved strains, two showed an approximately twofold higher anaerobic growth rate on sucrose than the parental strain (μ = 0.19 h-1 and μ = 0.08 h-1 , respectively). All five mutants displayed sucrose-induced proton uptake (13-50 μmol H+ (g biomass)-1 min-1 ). Their ATP yield from sucrose dissimilation, as estimated from biomass yields in anaerobic chemostat cultures, was the same as that of a congenic strain expressing the native sucrose symporter Mal11p. Four out of six observed amino acid substitutions encoded by evolved PvSUF1 alleles removed or introduced a cysteine residue and may be involved in transporter folding and/or oligomerization. Expression of one of the evolved PvSUF1 alleles (PvSUF1I209F C265F G326C ) in an unevolved strain enabled it to grow on sucrose at the same rate (0.19 h-1 ) as the corresponding evolved strain. This study shows how laboratory evolution may improve sucrose uptake in yeast via heterologous plant transporters, highlights the importance of cysteine residues for their efficient expression, and warrants reinvestigation of PvSuf1's transport mechanism.
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Affiliation(s)
- Wesley Leoricy Marques
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands.,School of Food Engineering, University of Campinas, Campinas, Brazil
| | | | - Marijke A H Luttik
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Marcel van den Broek
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | | | - Jack T Pronk
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | | | - Robert Mans
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Andreas K Gombert
- School of Food Engineering, University of Campinas, Campinas, Brazil
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31
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Hayakawa K, Matsuda F, Shimizu H. 13C-metabolic flux analysis of ethanol-assimilating Saccharomyces cerevisiae for S-adenosyl-L-methionine production. Microb Cell Fact 2018; 17:82. [PMID: 29855316 PMCID: PMC5977476 DOI: 10.1186/s12934-018-0935-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 05/22/2018] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Saccharomyces cerevisiae is a host for the industrial production of S-adenosyl-L-methionine (SAM), which has been widely used in pharmaceutical and nutritional supplement industries. It has been reported that the intracellular SAM content in S. cerevisiae can be improved by the addition of ethanol during cultivation. However, the metabolic state in ethanol-assimilating S. cerevisiae remains unclear. In this study, 13C-metabolic flux analysis (13C-MFA) was conducted to investigate the metabolic regulation responsible for the high SAM production from ethanol. RESULTS The comparison between the metabolic flux distributions of central carbon metabolism showed that the metabolic flux levels of the tricarboxylic acid cycle and glyoxylate shunt in the ethanol culture were significantly higher than that of glucose. Estimates of the ATP balance from the 13C-MFA data suggested that larger amounts of excess ATP was produced from ethanol via increased oxidative phosphorylation. The finding was confirmed by the intracellular ATP level under ethanol-assimilating condition being similarly higher than glucose. CONCLUSIONS These results suggest that the enhanced ATP regeneration due to ethanol assimilation was critical for the high SAM accumulation.
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Affiliation(s)
- Kenshi Hayakawa
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan.,KANEKA Fundamental Technology Research Alliance Laboratories, Graduate School of Engineering, Osaka University, 2-8 Yamadaoka, Suita, Osaka, 565-0871, Japan.,Biotechnology Development Laboratories, Health Care Solutions Research Institute, Kaneka Corporation, 1-8 Miyamae-cho, Takasago-cho, Takasago, Hyogo, 676-8688, Japan
| | - Fumio Matsuda
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Hiroshi Shimizu
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan.
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32
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Zhou N, Bottagisi S, Katz M, Schacherer J, Friedrich A, Gojkovic Z, Swamy KBS, Knecht W, Compagno C, Piškur J. Yeast-bacteria competition induced new metabolic traits through large-scale genomic rearrangements in Lachancea kluyveri. FEMS Yeast Res 2018; 17:4064365. [PMID: 28910985 DOI: 10.1093/femsyr/fox060] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 08/03/2017] [Indexed: 12/28/2022] Open
Abstract
Large-scale chromosomal rearrangements are an important source of evolutionary novelty that may have reshaped the genomes of existing yeast species. They dramatically alter genome organization and gene expression fueling a phenotypic leap in response to environmental constraints. Although the emergence of such signatures of genetic diversity is thought to be associated with human exploitation of yeasts, less is known about the driving forces operating in natural habitats. Here we hypothesize that an ecological battlefield characteristic of every autumn when fruits ripen accounts for the genomic innovations in natural populations. We described a long-term cross-kingdom competition experiment between Lachancea kluyveri and five species of bacteria. Now, we report how we further subjected the same yeast to a sixth species of bacteria, Pseudomonas fluorescens, resulting in the appearance of a fixed and stably inherited large-scale genomic rearrangement in two out of three parallel evolution lines. The 'extra-banded' karyotype, characterized by a higher fitness and an elevated fermentative capacity, conferred the emergence of new metabolic traits in most carbon sources and osmolytes. We tracked down the event to a duplication and translocation event involving a 261-kb segment. Such an experimental setup described here is an attractive method for developing industrial strains without genetic engineering strategies.
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Affiliation(s)
- Nerve Zhou
- Department of Biology, Lund University, Sölvegatan 35, 22362 Lund, Sweden.,Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology, P Bag 16, 00267 Palapye, Botswana
| | - Samuele Bottagisi
- Department of Biology, Lund University, Sölvegatan 35, 22362 Lund, Sweden.,Department of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy
| | - Michael Katz
- Carlsberg Laboratories, Gamle Carlsberg Vej 10, 1799 Copenhagen V, Denmark
| | - Joseph Schacherer
- Department of Genetics, Genomics and Microbiology, University of Strasbourg, CNRS UMR7156, 67083 Strasbourg, France
| | - Anne Friedrich
- Department of Genetics, Genomics and Microbiology, University of Strasbourg, CNRS UMR7156, 67083 Strasbourg, France
| | - Zoran Gojkovic
- Carlsberg Laboratories, Gamle Carlsberg Vej 10, 1799 Copenhagen V, Denmark
| | - Krishna B S Swamy
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Wolfgang Knecht
- Department of Biology, Lund University, Sölvegatan 35, 22362 Lund, Sweden.,Lund Protein Production Platform, Lund University, Sölvegatan 35, 22362 Lund, Sweden
| | - Concetta Compagno
- Department of Food, Environmental and Nutritional Sciences, University of Milan, Via Giovanni Celoria 2, 20133 Milan, Italy
| | - Jure Piškur
- Department of Biology, Lund University, Sölvegatan 35, 22362 Lund, Sweden
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33
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Nagai H, Masuda A, Toya Y, Matsuda F, Shimizu H. Metabolic engineering of mevalonate-producing Escherichia coli strains based on thermodynamic analysis. Metab Eng 2018; 47:1-9. [DOI: 10.1016/j.ymben.2018.02.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 12/07/2017] [Accepted: 02/25/2018] [Indexed: 01/07/2023]
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34
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Combined engineering of disaccharide transport and phosphorolysis for enhanced ATP yield from sucrose fermentation in Saccharomyces cerevisiae. Metab Eng 2017; 45:121-133. [PMID: 29196124 DOI: 10.1016/j.ymben.2017.11.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 09/27/2017] [Accepted: 11/24/2017] [Indexed: 11/24/2022]
Abstract
Anaerobic industrial fermentation processes do not require aeration and intensive mixing and the accompanying cost savings are beneficial for production of chemicals and fuels. However, the free-energy conservation of fermentative pathways is often insufficient for the production and export of the desired compounds and/or for cellular growth and maintenance. To increase free-energy conservation during fermentation of the industrially relevant disaccharide sucrose by Saccharomyces cerevisiae, we first replaced the native yeast α-glucosidases by an intracellular sucrose phosphorylase from Leuconostoc mesenteroides (LmSPase). Subsequently, we replaced the native proton-coupled sucrose uptake system by a putative sucrose facilitator from Phaseolus vulgaris (PvSUF1). The resulting strains grew anaerobically on sucrose at specific growth rates of 0.09 ± 0.02h-1 (LmSPase) and 0.06 ± 0.01h-1 (PvSUF1, LmSPase). Overexpression of the yeast PGM2 gene, which encodes phosphoglucomutase, increased anaerobic growth rates on sucrose of these strains to 0.23 ± 0.01h-1 and 0.08 ± 0.00h-1, respectively. Determination of the biomass yield in anaerobic sucrose-limited chemostat cultures was used to assess the free-energy conservation of the engineered strains. Replacement of intracellular hydrolase with a phosphorylase increased the biomass yield on sucrose by 31%. Additional replacement of the native proton-coupled sucrose uptake system by PvSUF1 increased the anaerobic biomass yield by a further 8%, resulting in an overall increase of 41%. By experimentally demonstrating an energetic benefit of the combined engineering of disaccharide uptake and cleavage, this study represents a first step towards anaerobic production of compounds whose metabolic pathways currently do not conserve sufficient free-energy.
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35
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Schabort DTWP, Kilian SG, du Preez JC. Elucidation of new condition-dependent roles for fructose-1,6-bisphosphatase linked to cofactor balances. PLoS One 2017; 12:e0177319. [PMID: 28542187 PMCID: PMC5444679 DOI: 10.1371/journal.pone.0177319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 04/25/2017] [Indexed: 11/19/2022] Open
Abstract
The cofactor balances in metabolism is of paramount importance in the design of a metabolic engineering strategy and understanding the regulation of metabolism in general. ATP, NAD+ and NADP+ balances are central players linking the various fluxes in central metabolism as well as biomass formation. NADP+ is especially important in the metabolic engineering of yeasts for xylose fermentation, since NADPH is required by most yeasts in the initial step of xylose utilisation, including the fast-growing Kluyveromyces marxianus. In this simulation study of yeast metabolism, the complex interplay between these cofactors was investigated; in particular, how they may affect the possible roles of fructose-1,6-bisphosphatase, the pentose phosphate pathway, glycerol production and the pyruvate dehydrogenase bypass. Using flux balance analysis, it was found that the potential role of fructose-1,6-bisphosphatase was highly dependent on the cofactor specificity of the oxidative pentose phosphate pathway and on the carbon source. Additionally, the excessive production of ATP under certain conditions might be involved in some of the phenomena observed, which may have been overlooked to date. Based on these findings, a strategy is proposed for the metabolic engineering of a future xylose-fermenting yeast for biofuel production.
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Affiliation(s)
- Du Toit W. P. Schabort
- Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, Bloemfontein, South Africa
- * E-mail:
| | - Stephanus G. Kilian
- Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, Bloemfontein, South Africa
| | - James C. du Preez
- Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, Bloemfontein, South Africa
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36
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Zhang R, Shao M, Han X, Wang C, Li Y, Hu B, Pang D, Xie Z. ATP synthesis in the energy metabolism pathway: a new perspective for manipulating CdSe quantum dots biosynthesized in Saccharomyces cerevisiae. Int J Nanomedicine 2017; 12:3865-3879. [PMID: 28579774 PMCID: PMC5446969 DOI: 10.2147/ijn.s132719] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Due to a growing trend in their biomedical application, biosynthesized nanomaterials are of great interest to researchers nowadays with their biocompatible, low-energy consumption, economic, and tunable characteristics. It is important to understand the mechanism of biosynthesis in order to achieve more efficient applications. Since there are only rare studies on the influences of cellular energy levels on biosynthesis, the influence of energy is often overlooked. Through determination of the intracellular ATP concentrations during the biosynthesis process, significant changes were observed. In addition, ATP synthesis deficiency caused great decreases in quantum dots (QDs) biosynthesis in the Δatp1, Δatp2, Δatp14, and Δatp17 strains. With inductively coupled plasma-atomic emission spectrometry and atomic absorption spectroscopy analyses, it was found that ATP affected the accumulation of the seleno-precursor and helped with the uptake of Cd and the formation of QDs. We successfully enhanced the fluorescence intensity 1.5 or 2 times through genetic modification to increase ATP or SeAM (the seleno analog of S-adenosylmethionine, the product that would accumulate when ATP is accrued). This work explains the mechanism for the correlation of the cellular energy level and QDs biosynthesis in living cells, demonstrates control of the biosynthesis using this mechanism, and thus provides a new manipulation strategy for the biosynthesis of other nanomaterials to widen their applications.
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Affiliation(s)
- Rong Zhang
- Hubei Key Laboratory of Cell Homeostasis
- College of Life Sciences, Wuhan University
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education)
| | - Ming Shao
- Hubei Key Laboratory of Cell Homeostasis
- College of Life Sciences, Wuhan University
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education)
| | - Xu Han
- Hubei Key Laboratory of Cell Homeostasis
- College of Life Sciences, Wuhan University
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education)
| | - Chuan Wang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education)
- College of Chemistry and Molecular Science, Wuhan University, Wuhan, People’s Republic of China
| | - Yong Li
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education)
- College of Chemistry and Molecular Science, Wuhan University, Wuhan, People’s Republic of China
| | - Bin Hu
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education)
- College of Chemistry and Molecular Science, Wuhan University, Wuhan, People’s Republic of China
| | - Daiwen Pang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education)
- College of Chemistry and Molecular Science, Wuhan University, Wuhan, People’s Republic of China
| | - Zhixiong Xie
- Hubei Key Laboratory of Cell Homeostasis
- College of Life Sciences, Wuhan University
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education)
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37
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Cueto-Rojas HF, Milne N, van Helmond W, Pieterse MM, van Maris AJA, Daran JM, Wahl SA. Membrane potential independent transport of NH 3 in the absence of ammonium permeases in Saccharomyces cerevisiae. BMC SYSTEMS BIOLOGY 2017; 11:49. [PMID: 28412970 PMCID: PMC5392931 DOI: 10.1186/s12918-016-0381-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 12/20/2016] [Indexed: 01/08/2023]
Abstract
Background Microbial production of nitrogen containing compounds requires a high uptake flux and assimilation of the N-source (commonly ammonium), which is generally coupled with ATP consumption and negatively influences the product yield. In the industrial workhorse Saccharomyces cerevisiae, ammonium (NH4+) uptake is facilitated by ammonium permeases (Mep1, Mep2 and Mep3), which transport the NH4+ ion, resulting in ATP expenditure to maintain the intracellular charge balance and pH by proton export using the plasma membrane-bound H+-ATPase. Results To decrease the ATP costs for nitrogen assimilation, the Mep genes were removed, resulting in a strain unable to uptake the NH4+ ion. Subsequent analysis revealed that growth of this ∆mep strain was dependent on the extracellular NH3 concentrations. Metabolomic analysis revealed a significantly higher intracellular NHX concentration (3.3-fold) in the ∆mep strain than in the reference strain. Further proteomic analysis revealed significant up-regulation of vacuolar proteases and genes involved in various stress responses. Conclusions Our results suggest that the uncharged species, NH3, is able to diffuse into the cell. The measured intracellular/extracellular NHX ratios under aerobic nitrogen-limiting conditions were consistent with this hypothesis when NHx compartmentalization was considered. On the other hand, proteomic analysis indicated a more pronounced N-starvation stress response in the ∆mep strain than in the reference strain, which suggests that the lower biomass yield of the ∆mep strain was related to higher turnover rates of biomass components. Electronic supplementary material The online version of this article (doi:10.1186/s12918-016-0381-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hugo F Cueto-Rojas
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629HZ, Delft, The Netherlands
| | - Nicholas Milne
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629HZ, Delft, The Netherlands.,Present Address: Evolva Biotech A/S, Lersø Parkallé 42, 2100, København Ø, Denmark
| | - Ward van Helmond
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629HZ, Delft, The Netherlands.,Present Address: Nederlands Forensisch Instituut (NFI), Laan van Ypenburg 6, 2497 GB, Den Haag, The Netherlands
| | - Mervin M Pieterse
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629HZ, Delft, The Netherlands
| | - Antonius J A van Maris
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629HZ, Delft, The Netherlands.,Division of Industrial Biotechnology, School of Biotechnology, KTH Royal Institute of Technology, AlbaNova University Center, SE 106 91, Stockholm, Sweden
| | - Jean-Marc Daran
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629HZ, Delft, The Netherlands.
| | - S Aljoscha Wahl
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629HZ, Delft, The Netherlands.
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Tippmann S, Ferreira R, Siewers V, Nielsen J, Chen Y. Effects of acetoacetyl-CoA synthase expression on production of farnesene in Saccharomyces cerevisiae. J Ind Microbiol Biotechnol 2017; 44:911-922. [PMID: 28185100 PMCID: PMC5432608 DOI: 10.1007/s10295-017-1911-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 01/29/2017] [Indexed: 01/24/2023]
Abstract
Efficient production of sesquiterpenes in Saccharomyces cerevisiae requires a high flux through the mevalonate pathway. To achieve this, the supply of acetyl-CoA plays a crucial role, partially because nine moles of acetyl-CoA are necessary to produce one mole of farnesyl diphosphate, but also to overcome the thermodynamic constraint imposed on the first reaction, in which acetoacetyl-CoA is produced from two moles of acetyl-CoA by acetoacetyl-CoA thiolase. Recently, a novel acetoacetyl-CoA synthase (nphT7) has been identified from Streptomyces sp. strain CL190, which catalyzes the irreversible condensation of malonyl-CoA and acetyl-CoA to acetoacetyl-CoA and, therefore, represents a potential target to increase the flux through the mevalonate pathway. This study investigates the effect of acetoacetyl-CoA synthase on growth as well as the production of farnesene and compares different homologs regarding their efficiency. While plasmid-based expression of nphT7 did not improve final farnesene titers, the construction of an alternative pathway, which exclusively relies on the malonyl-CoA bypass, was detrimental for growth and farnesene production. The presented results indicate that the overall functionality of the bypass was limited by the efficiency of acetoacetyl-CoA synthase (nphT7). Besides modulation of the expression level, which could be used as a means to partially restore the phenotype, nphT7 from Streptomyces glaucescens showed clearly higher efficiency compared to Streptomyces sp. strain CL190.
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Affiliation(s)
- Stefan Tippmann
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE412 96, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE412 96, Gothenburg, Sweden
| | - Raphael Ferreira
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE412 96, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE412 96, Gothenburg, Sweden
| | - Verena Siewers
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE412 96, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE412 96, Gothenburg, Sweden
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE412 96, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE412 96, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK2800 Kongens Lyngby, Denmark
| | - Yun Chen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE412 96, Gothenburg, Sweden. .,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE412 96, Gothenburg, Sweden.
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39
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In Vivo Analysis of NH 4+ Transport and Central Nitrogen Metabolism in Saccharomyces cerevisiae during Aerobic Nitrogen-Limited Growth. Appl Environ Microbiol 2016; 82:6831-6845. [PMID: 27637876 DOI: 10.1128/aem.01547-16] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2016] [Accepted: 09/08/2016] [Indexed: 11/20/2022] Open
Abstract
Ammonium is the most common N source for yeast fermentations. Although its transport and assimilation mechanisms are well documented, there have been only a few attempts to measure the in vivo intracellular concentration of ammonium and assess its impact on gene expression. Using an isotope dilution mass spectrometry (IDMS)-based method, we were able to measure the intracellular ammonium concentration in N-limited aerobic chemostat cultivations using three different N sources (ammonium, urea, and glutamate) at the same growth rate (0.05 h-1). The experimental results suggest that, at this growth rate, a similar concentration of intracellular (IC) ammonium, about 3.6 mmol NH4+/literIC, is required to supply the reactions in the central N metabolism, independent of the N source. Based on the experimental results and different assumptions, the vacuolar and cytosolic ammonium concentrations were estimated. Furthermore, we identified a futile cycle caused by NH3 leakage into the extracellular space, which can cost up to 30% of the ATP production of the cell under N-limited conditions, and a futile redox cycle between Gdh1 and Gdh2 reactions. Finally, using shotgun proteomics with protein expression determined relative to a labeled reference, differences between the various environmental conditions were identified and correlated with previously identified N compound-sensing mechanisms.IMPORTANCE In our work, we studied central N metabolism using quantitative approaches. First, intracellular ammonium was measured under different N sources. The results suggest that Saccharomyces cerevisiae cells maintain a constant NH4+ concentration (around 3 mmol NH4+/literIC), independent of the applied nitrogen source. We hypothesize that this amount of intracellular ammonium is required to obtain sufficient thermodynamic driving force. Furthermore, our calculations based on thermodynamic analysis of the transport mechanisms of ammonium suggest that ammonium is not equally distributed, indicating a high degree of compartmentalization in the vacuole. Additionally, metabolomic analysis results were used to calculate the thermodynamic driving forces in the central N metabolism reactions, revealing that the main reactions in the central N metabolism are far from equilibrium. Using proteomics approaches, we were able to identify major changes, not only in N metabolism, but also in C metabolism and regulation.
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Abstract
Cofactor engineering has been long identified as a valuable tool for metabolic engineering. Besides interventions targeting the pools of redox cofactors, many studies addressed the adenosine pools of microorganisms. In this mini-review, we discuss interventions that manipulate the availability of ATP with a special focus on ATP wasting strategies. We discuss the importance to fine-tune the ATP yield along a production pathway to balance process performance parameters like product yield and volumetric productivity.
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41
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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: 92] [Impact Index Per Article: 11.5] [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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42
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Kozak BU, van Rossum HM, Niemeijer MS, van Dijk M, Benjamin K, Wu L, Daran JMG, Pronk JT, van Maris AJA. Replacement of the initial steps of ethanol metabolism in Saccharomyces cerevisiae by ATP-independent acetylating acetaldehyde dehydrogenase. FEMS Yeast Res 2016; 16:fow006. [PMID: 26818854 PMCID: PMC5815134 DOI: 10.1093/femsyr/fow006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 01/25/2016] [Indexed: 11/17/2022] Open
Abstract
In Saccharomyces cerevisiae ethanol dissimilation is initiated by its oxidation and activation to cytosolic acetyl-CoA. The associated consumption of ATP strongly limits yields of biomass and acetyl-CoA-derived products. Here, we explore the implementation of an ATP-independent pathway for acetyl-CoA synthesis from ethanol that, in theory, enables biomass yield on ethanol that is up to 40% higher. To this end, all native yeast acetaldehyde dehydrogenases (ALDs) were replaced by heterologous acetylating acetaldehyde dehydrogenase (A-ALD). Engineered Ald− strains expressing different A-ALDs did not immediately grow on ethanol, but serial transfer in ethanol-grown batch cultures yielded growth rates of up to 70% of the wild-type value. Mutations in ACS1 were identified in all independently evolved strains and deletion of ACS1 enabled slow growth of non-evolved Ald− A-ALD strains on ethanol. Acquired mutations in A-ALD genes improved affinity—Vmax/Km for acetaldehyde. One of five evolved strains showed a significant 5% increase of its biomass yield in ethanol-limited chemostat cultures. Increased production of acetaldehyde and other by-products was identified as possible cause for lower than theoretically predicted biomass yields. This study proves that the native yeast pathway for conversion of ethanol to acetyl-CoA can be replaced by an engineered pathway with the potential to improve biomass and product yields. This manuscript investigates a metabolic engineering strategy to improve the use of ethanol as a feedstock for production of bio-based fuels and chemicals with yeast.
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Affiliation(s)
- Barbara U Kozak
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, the Netherlands
| | - Harmen M van Rossum
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, the Netherlands
| | - Matthijs S Niemeijer
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, the Netherlands
| | - Marlous van Dijk
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, the Netherlands
| | - Kirsten Benjamin
- Amyris Inc, 5885 Hollis Street, Ste. 100, Emeryville, CA94608, USA
| | - Liang Wu
- DSM Biotechnology Center, Alexander Fleminglaan 1, 2613 AX Delft, the Netherlands
| | - Jean-Marc G Daran
- 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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Dmytruk KV, Kshanovska BV, Abbas CA, Sibirny A. New methods for positive selection of yeast ethanol overproducing mutants. ACTA ACUST UNITED AC 2016. [DOI: 10.1515/bioeth-2015-0003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
AbstractFuel ethanol is an environmentally friendly alternative liquid fuel to the widely used petroleum derived transportation liquid fuels. Since 2007, worldwide fuel ethanol production has increased. Currently ethanol is primarily produced from carbohydrates such as sucrose and starch by fermentation using the yeast Saccharomyces cerevisiae. In this work, new approaches for the selection of S. cerevisiae strains with increased ethanol production from hydrolyzed corn meal are described. An industrial production strain of Saccharomyces cerevisiae AS400 was subjected to positive selection of mutants resistant to toxic concentrations of oxythiamine, trehalose, 3-bromopyruvate, glyoxylic acid, and glucosamine. The selected mutants are characterized by 5-8% increase in ethanol yield (g g-1 of consumed glucose) as compared to the parental industrial ethanol-producing strain. A three-step selection approach that consisted of the use of glyoxylic acid, glucosamine and bromopyruvate resulted in a 12% increase in ethanol yield during fermentation on industrial media. These results indicate that the selected strains are promising candidates for industrial ethanol production.
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44
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Hara KY, Kondo A. ATP regulation in bioproduction. Microb Cell Fact 2015; 14:198. [PMID: 26655598 PMCID: PMC4676173 DOI: 10.1186/s12934-015-0390-6] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 11/25/2015] [Indexed: 01/06/2023] Open
Abstract
Adenosine-5'-triphosphate (ATP) is consumed as a biological energy source by many intracellular reactions. Thus, the intracellular ATP supply is required to maintain cellular homeostasis. The dependence on the intracellular ATP supply is a critical factor in bioproduction by cell factories. Recent studies have shown that changing the ATP supply is critical for improving product yields. In this review, we summarize the recent challenges faced by researchers engaged in the development of engineered cell factories, including the maintenance of a large ATP supply and the production of cell factories. The strategies used to enhance ATP supply are categorized as follows: addition of energy substrates, controlling pH, metabolic engineering of ATP-generating or ATP-consuming pathways, and controlling reactions of the respiratory chain. An enhanced ATP supply generated using these strategies improves target production through increases in resource uptake, cell growth, biosynthesis, export of products, and tolerance to toxic compounds.
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Affiliation(s)
- Kiyotaka Y Hara
- Department of Environmental Sciences, Graduate School of Nutritional and Environmental Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, 422-8526, Japan.
| | - Akihiko Kondo
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodaicho, Nada-ku, Kobe, 657-8501, Japan.
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45
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Cueto-Rojas HF, van Maris A, Wahl SA, Heijnen J. Thermodynamics-based design of microbial cell factories for anaerobic product formation. Trends Biotechnol 2015; 33:534-46. [DOI: 10.1016/j.tibtech.2015.06.010] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2015] [Revised: 05/20/2015] [Accepted: 06/23/2015] [Indexed: 11/29/2022]
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Hädicke O, Bettenbrock K, Klamt S. Enforced ATP futile cycling increases specific productivity and yield of anaerobic lactate production in Escherichia coli. Biotechnol Bioeng 2015; 112:2195-9. [PMID: 25899755 DOI: 10.1002/bit.25623] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 03/11/2015] [Accepted: 04/13/2015] [Indexed: 11/05/2022]
Abstract
The manipulation of cofactor pools such as ATP or NAD(P)H has for long been recognized as key targets for metabolic engineering of microorganisms to improve yields and productivities of biotechnological processes. Several works in the past have shown that enforcing ATP futile cycling may enhance the synthesis of certain products under aerobic conditions. However, case studies demonstrating that ATP wasting may also have beneficial effects for anaerobic production processes are scarce. Taking lactic acid as an economically relevant product, we demonstrate that induction of ATP futile cycling in Escherichia coli leads to increased yields and specific production rates under anaerobic conditions, even in the case where lactate is already produced with high yields. Specifically, we constructed a high lactate producer strain KBM10111 (= MG1655 ΔadhE::Cam ΔackA-pta) and implemented an IPTG-inducible overexpression of ppsA encoding for PEP synthase which, together with pyruvate kinase, gives rise to an ATP consuming cycle. Under induction of ppsA, KBM10111 exhibits a 25% higher specific lactate productivity as well as an 8% higher lactate yield. Furthermore, the specific substrate uptake rate was increased by 14%. However, trade-offs between specific and volumetric productivities must be considered when ATP wasting strategies are used to shift substrate conversion from biomass to product synthesis and we discuss potential solutions to design optimal processes. In summary, enforced ATP futile cycling has great potential to optimize a variety of production processes and our study demonstrates that this holds true also for anaerobic processes.
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Affiliation(s)
- Oliver Hädicke
- Max Planck Institute for Dynamics of Complex Technical Systems1Sandtorstrasse 1, Magdeburg 39106, Germany
| | - Katja Bettenbrock
- Max Planck Institute for Dynamics of Complex Technical Systems1Sandtorstrasse 1, Magdeburg 39106, Germany
| | - Steffen Klamt
- Max Planck Institute for Dynamics of Complex Technical Systems1Sandtorstrasse 1, Magdeburg 39106, Germany.
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47
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Improving conversion yield of fermentable sugars into fuel ethanol in 1st generation yeast-based production processes. Curr Opin Biotechnol 2015; 33:81-6. [DOI: 10.1016/j.copbio.2014.12.012] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Revised: 12/08/2014] [Accepted: 12/14/2014] [Indexed: 11/22/2022]
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48
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Milne N, Luttik MAH, Cueto Rojas HF, Wahl A, van Maris AJA, Pronk JT, Daran JM. Functional expression of a heterologous nickel-dependent, ATP-independent urease in Saccharomyces cerevisiae. Metab Eng 2015; 30:130-140. [PMID: 26037463 DOI: 10.1016/j.ymben.2015.05.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Revised: 05/18/2015] [Accepted: 05/21/2015] [Indexed: 12/31/2022]
Abstract
In microbial processes for production of proteins, biomass and nitrogen-containing commodity chemicals, ATP requirements for nitrogen assimilation affect product yields on the energy producing substrate. In Saccharomyces cerevisiae, a current host for heterologous protein production and potential platform for production of nitrogen-containing chemicals, uptake and assimilation of ammonium requires 1 ATP per incorporated NH3. Urea assimilation by this yeast is more energy efficient but still requires 0.5 ATP per NH3 produced. To decrease ATP costs for nitrogen assimilation, the S. cerevisiae gene encoding ATP-dependent urease (DUR1,2) was replaced by a Schizosaccharomyces pombe gene encoding ATP-independent urease (ure2), along with its accessory genes ureD, ureF and ureG. Since S. pombe ure2 is a Ni(2+)-dependent enzyme and Saccharomyces cerevisiae does not express native Ni(2+)-dependent enzymes, the S. pombe high-affinity nickel-transporter gene (nic1) was also expressed. Expression of the S. pombe genes into dur1,2Δ S. cerevisiae yielded an in vitro ATP-independent urease activity of 0.44±0.01 µmol min(-1) mg protein(-1) and restored growth on urea as sole nitrogen source. Functional expression of the Nic1 transporter was essential for growth on urea at low Ni(2+) concentrations. The maximum specific growth rates of the engineered strain on urea and ammonium were lower than those of a DUR1,2 reference strain. In glucose-limited chemostat cultures with urea as nitrogen source, the engineered strain exhibited an increased release of ammonia and reduced nitrogen content of the biomass. Our results indicate a new strategy for improving yeast-based production of nitrogen-containing chemicals and demonstrate that Ni(2+)-dependent enzymes can be functionally expressed in S. cerevisiae.
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Affiliation(s)
- N Milne
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
| | - M A H Luttik
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
| | - H F Cueto Rojas
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
| | - A Wahl
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
| | - A J A van Maris
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
| | - J T Pronk
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
| | - J M Daran
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands.
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49
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Carrau F, Gaggero C, Aguilar PS. Yeast diversity and native vigor for flavor phenotypes. Trends Biotechnol 2015; 33:148-54. [DOI: 10.1016/j.tibtech.2014.12.009] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2014] [Revised: 10/29/2014] [Accepted: 12/31/2014] [Indexed: 01/03/2023]
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50
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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: 157] [Impact Index Per Article: 15.7] [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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