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Mitrea L, Teleky BE, Nemes SA, Plamada D, Varvara RA, Pascuta MS, Ciont C, Cocean AM, Medeleanu M, Nistor A, Rotar AM, Pop CR, Vodnar DC. Succinic acid - A run-through of the latest perspectives of production from renewable biomass. Heliyon 2024; 10:e25551. [PMID: 38327454 PMCID: PMC10848017 DOI: 10.1016/j.heliyon.2024.e25551] [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: 05/30/2023] [Revised: 01/18/2024] [Accepted: 01/29/2024] [Indexed: 02/09/2024] Open
Abstract
Succinic acid (SA) production is continuously rising, as its applications in diverse end-product generation are getting broader and more expansive. SA is an eco-friendly bulk product that acts as a valuable intermediate in different processes and might substitute other petrochemical-based products due to the inner capacity of microbes to biosynthesize it. Moreover, large amounts of SA can be obtained through biotechnological ways starting from renewable resources, imprinting at the same time the concept of a circular economy. In this context, the target of the present review paper is to bring an overview of SA market demands, production, biotechnological approaches, new strategies of production, and last but not least, the possible limitations and the latest perspectives in terms of natural biosynthesis of SA.
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Affiliation(s)
- Laura Mitrea
- Department of Food Science, Faculty of Food Science and Technology, University of Agricultural Sciences and Veterinary Medicine, Cluj-Napoca, Calea Mănăștur 3-5, 400372, Cluj-Napoca, Romania
- Life Science Institute, University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca, 400372, Cluj-Napoca, Romania
| | - Bernadette-Emőke Teleky
- Life Science Institute, University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca, 400372, Cluj-Napoca, Romania
| | - Silvia-Amalia Nemes
- Department of Food Science, Faculty of Food Science and Technology, University of Agricultural Sciences and Veterinary Medicine, Cluj-Napoca, Calea Mănăștur 3-5, 400372, Cluj-Napoca, Romania
- Life Science Institute, University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca, 400372, Cluj-Napoca, Romania
| | - Diana Plamada
- Department of Food Science, Faculty of Food Science and Technology, University of Agricultural Sciences and Veterinary Medicine, Cluj-Napoca, Calea Mănăștur 3-5, 400372, Cluj-Napoca, Romania
- Life Science Institute, University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca, 400372, Cluj-Napoca, Romania
| | - Rodica-Anita Varvara
- Department of Food Science, Faculty of Food Science and Technology, University of Agricultural Sciences and Veterinary Medicine, Cluj-Napoca, Calea Mănăștur 3-5, 400372, Cluj-Napoca, Romania
- Life Science Institute, University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca, 400372, Cluj-Napoca, Romania
| | - Mihaela-Stefana Pascuta
- Department of Food Science, Faculty of Food Science and Technology, University of Agricultural Sciences and Veterinary Medicine, Cluj-Napoca, Calea Mănăștur 3-5, 400372, Cluj-Napoca, Romania
- Life Science Institute, University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca, 400372, Cluj-Napoca, Romania
| | - Calina Ciont
- Department of Food Science, Faculty of Food Science and Technology, University of Agricultural Sciences and Veterinary Medicine, Cluj-Napoca, Calea Mănăștur 3-5, 400372, Cluj-Napoca, Romania
- Life Science Institute, University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca, 400372, Cluj-Napoca, Romania
| | - Ana-Maria Cocean
- Department of Food Science, Faculty of Food Science and Technology, University of Agricultural Sciences and Veterinary Medicine, Cluj-Napoca, Calea Mănăștur 3-5, 400372, Cluj-Napoca, Romania
- Life Science Institute, University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca, 400372, Cluj-Napoca, Romania
| | - Madalina Medeleanu
- Department of Food Science, Faculty of Food Science and Technology, University of Agricultural Sciences and Veterinary Medicine, Cluj-Napoca, Calea Mănăștur 3-5, 400372, Cluj-Napoca, Romania
| | - Alina Nistor
- Department of Food Science, Faculty of Food Science and Technology, University of Agricultural Sciences and Veterinary Medicine, Cluj-Napoca, Calea Mănăștur 3-5, 400372, Cluj-Napoca, Romania
| | - Ancuta-Mihaela Rotar
- Department of Food Science, Faculty of Food Science and Technology, University of Agricultural Sciences and Veterinary Medicine, Cluj-Napoca, Calea Mănăștur 3-5, 400372, Cluj-Napoca, Romania
| | - Carmen-Rodica Pop
- Department of Food Science, Faculty of Food Science and Technology, University of Agricultural Sciences and Veterinary Medicine, Cluj-Napoca, Calea Mănăștur 3-5, 400372, Cluj-Napoca, Romania
| | - Dan-Cristian Vodnar
- Department of Food Science, Faculty of Food Science and Technology, University of Agricultural Sciences and Veterinary Medicine, Cluj-Napoca, Calea Mănăștur 3-5, 400372, Cluj-Napoca, Romania
- Life Science Institute, University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca, 400372, Cluj-Napoca, Romania
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Zhang FL, Zhang L, Zeng DW, Liao S, Fan Y, Champreda V, Runguphan W, Zhao XQ. Engineering yeast cell factories to produce biodegradable plastics and their monomers: Current status and prospects. Biotechnol Adv 2023; 68:108222. [PMID: 37516259 DOI: 10.1016/j.biotechadv.2023.108222] [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: 04/23/2023] [Revised: 07/24/2023] [Accepted: 07/24/2023] [Indexed: 07/31/2023]
Abstract
Traditional plastic products have caused serious environmental pollution due to difficulty to be degraded in the natural environment. In the recent years, biodegradable plastics are receiving increasing attention due to advantages in natural degradability and environmental friendliness. Biodegradable plastics have potential to be used in food, agriculture, industry, medicine and other fields. However, the high production cost of such plastics is the bottleneck that limits their commercialization and application. Yeasts, including budding yeast and non-conventional yeasts, are widely studied to produce biodegradable plastics and their organic acid monomers. Compared to bacteria, yeast strains are more tolerable to multiple stress conditions including low pH and high temperature, and also have other advantages such as generally regarded as safe, and no phage infection. In addition, synthetic biology and metabolic engineering of yeast have enabled its rapid and efficient engineering for bioproduction using various renewable feedstocks, especially lignocellulosic biomass. This review focuses on the recent progress in biosynthesis technology and strategies of monomeric organic acids for biodegradable polymers, including polylactic acid (PLA), polyhydroxyalkanoate (PHA), polybutylene succinate (PBS), and polybutylene adipate terephthalate (PBAT) using yeast cell factories. Improving the performance of yeast as a cell factory and strategies to improve yeast acid stress tolerance are also discussed. In addition, the critical challenges and future prospects for the production of biodegradable plastic monomer using yeast are also discussed.
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Affiliation(s)
- Feng-Li Zhang
- Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lin Zhang
- SINOPEC Dalian Research Institute of Petroleum and Petrochemicals Co., Ltd., Dalian 116045, China
| | - Du-Wen Zeng
- Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Sha Liao
- SINOPEC Dalian Research Institute of Petroleum and Petrochemicals Co., Ltd., Dalian 116045, China
| | - Yachao Fan
- SINOPEC Dalian Research Institute of Petroleum and Petrochemicals Co., Ltd., Dalian 116045, China
| | - Verawat Champreda
- National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Phaholyothin Road, Khlong Luang, Pathumthani 12120, Thailand
| | - Weerawat Runguphan
- National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Phaholyothin Road, Khlong Luang, Pathumthani 12120, Thailand
| | - Xin-Qing Zhao
- Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
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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: 12] [Impact Index Per Article: 6.0] [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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Liu Y, Esen O, Pronk JT, van Gulik WM. Uncoupling growth and succinic acid production in an industrial Saccharomyces cerevisiae strain. Biotechnol Bioeng 2021; 118:1576-1586. [PMID: 33410171 PMCID: PMC8048565 DOI: 10.1002/bit.27672] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 12/13/2020] [Accepted: 12/29/2020] [Indexed: 12/12/2022]
Abstract
This study explores the relation between biomass‐specific succinic acid (SA) production rate and specific growth rate of an engineered industrial strain of Saccharomyces cerevisiae, with the aim to investigate the extent to which growth and product formation can be uncoupled. Ammonium‐limited aerobic chemostat and retentostat cultures were grown at different specific growth rates under industrially relevant conditions, that is, at a culture pH of 3 and with sparging of a 1:1 CO2–air mixture. Biomass‐specific SA production rates decreased asymptotically with decreasing growth rate. At near‐zero growth rates, the engineered strain maintained a stable biomass‐specific SA production rate for over 500 h, with a SA yield on glucose of 0.61 mol mol−1. These results demonstrate that uncoupling of growth and SA production could indeed be achieved. A linear relation between the biomass‐specific SA production rate and glucose consumption rate indicated the coupling of SA production rate and the flux through primary metabolism. The low culture pH resulted in an increased death rate, which was lowest at near‐zero growth rates. Nevertheless, a significant amount of non‐viable biomass accumulated in the retentostat cultures, thus underlining the importance of improving low‐pH tolerance in further strain development for industrial SA production with S. cerevisiae.
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Affiliation(s)
- Yaya Liu
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Osman Esen
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Jack T Pronk
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Walter M van Gulik
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
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Zhang J, van den Herik BM, Wahl SA. Alpha-ketoglutarate utilization in Saccharomyces cerevisiae: transport, compartmentation and catabolism. Sci Rep 2020; 10:12838. [PMID: 32733060 PMCID: PMC7393084 DOI: 10.1038/s41598-020-69178-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 06/30/2020] [Indexed: 12/20/2022] Open
Abstract
α-Ketoglutarate (αKG) is a metabolite of the tricarboxylic acid cycle, important for biomass synthesis and a precursor for biotechnological products like 1,4-butanediol. In the eukaryote Saccharomyces cerevisiae αKG is present in different compartments. Compartmentation and (intra-)cellular transport could interfere with heterologous product pathways, generate futile cycles and reduce product yields. Batch and chemostat cultivations at low pH (≤ 5) showed that αKG can be transported, catabolized and used for biomass synthesis. The uptake mechanism of αKG was further investigated under αKG limited chemostat conditions at different pH (3, 4, 5, and 6). At very low pH (3, 4) there is a fraction of undissociated αKG that could diffuse over the periplasmic membrane. At pH 5 this fraction is very low, and the observed growth and residual concentration requires a permease/facilitated uptake mechanism of the mono-dissociated form of αKG. Consumption of αKG under mixed substrate conditions was only observed for low glucose concentrations in chemostat cultivations, suggesting that the putative αKG transporter is repressed by glucose. Fully 13C-labeled αKG was introduced as a tracer during a glucose/αKG co-feeding chemostat to trace αKG transport and utilization. The measured 13C enrichments suggest the major part of the consumed 13C αKG was used for the synthesis of glutamate, and the remainder was transported into the mitochondria and fully oxidized. There was no enrichment observed in glycolytic intermediates, suggesting that there was no gluconeogenic activity under the co-feeding conditions. 13C based flux analysis suggests that the intracellular transport is bi-directional, i.e. there is a fast exchange between the cytosol and mitochondria. The model further estimates that most intracellular αKG (88%) was present in the cytosol. Using literature reported volume fractions, the mitochondria/cytosol concentration ratio was 1.33. Such ratio will not require energy investment for transport towards the mitochondria (based on thermodynamic driving forces calculated with literature pH values). Growth on αKG as sole carbon source was observed, suggesting that S. cerevisiae is not fully Krebs-negative. Using 13C tracing and modelling the intracellular use of αKG under co-feeding conditions showed a link with biomass synthesis, transport into the mitochondria and catabolism. For the engineering of strains that use cytosolic αKG as precursor, both observed sinks should be minimized to increase the putative yields.
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Affiliation(s)
- Jinrui Zhang
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Bas Mees van den Herik
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Sebastian Aljoscha Wahl
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, The Netherlands.
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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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Hakkaart X, Liu Y, Hulst M, El Masoudi A, Peuscher E, Pronk J, van Gulik W, Daran-Lapujade P. Physiological responses of Saccharomyces cerevisiae to industrially relevant conditions: Slow growth, low pH, and high CO 2 levels. Biotechnol Bioeng 2020; 117:721-735. [PMID: 31654410 PMCID: PMC7028085 DOI: 10.1002/bit.27210] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 10/12/2019] [Accepted: 10/22/2019] [Indexed: 12/21/2022]
Abstract
Engineered strains of Saccharomyces cerevisiae are used for industrial production of succinic acid. Optimal process conditions for dicarboxylic‐acid yield and recovery include slow growth, low pH, and high CO2. To quantify and understand how these process parameters affect yeast physiology, this study investigates individual and combined impacts of low pH (3.0) and high CO2 (50%) on slow‐growing chemostat and retentostat cultures of the reference strain S. cerevisiae CEN.PK113‐7D. Combined exposure to low pH and high CO2 led to increased maintenance‐energy requirements and death rates in aerobic, glucose‐limited cultures. Further experiments showed that these effects were predominantly caused by low pH. Growth under ammonium‐limited, energy‐excess conditions did not aggravate or ameliorate these adverse impacts. Despite the absence of a synergistic effect of low pH and high CO2 on physiology, high CO2 strongly affected genome‐wide transcriptional responses to low pH. Interference of high CO2 with low‐pH signaling is consistent with low‐pH and high‐CO2 signals being relayed via common (MAPK) signaling pathways, notably the cell wall integrity, high‐osmolarity glycerol, and calcineurin pathways. This study highlights the need to further increase robustness of cell factories to low pH for carboxylic‐acid production, even in organisms that are already applied at industrial scale.
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Affiliation(s)
- Xavier Hakkaart
- Department of Biotechnology, Delft University of Technology, van der Maasweg, Delft, The Netherlands
| | - Yaya Liu
- Department of Biotechnology, Delft University of Technology, van der Maasweg, Delft, The Netherlands
| | - Mandy Hulst
- Department of Biotechnology, Delft University of Technology, van der Maasweg, Delft, The Netherlands
| | - Anissa El Masoudi
- Department of Biotechnology, Delft University of Technology, van der Maasweg, Delft, The Netherlands
| | - Eveline Peuscher
- Department of Biotechnology, Delft University of Technology, van der Maasweg, Delft, The Netherlands
| | - Jack Pronk
- Department of Biotechnology, Delft University of Technology, van der Maasweg, Delft, The Netherlands
| | - Walter van Gulik
- Department of Biotechnology, Delft University of Technology, van der Maasweg, Delft, The Netherlands
| | - Pascale Daran-Lapujade
- Department of Biotechnology, Delft University of Technology, van der Maasweg, Delft, The Netherlands
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Zhang J, Martinez-Gomez K, Heinzle E, Wahl SA. Metabolic switches from quiescence to growth in synchronized Saccharomyces cerevisiae. Metabolomics 2019; 15:121. [PMID: 31468142 PMCID: PMC6715666 DOI: 10.1007/s11306-019-1584-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Accepted: 08/09/2019] [Indexed: 12/27/2022]
Abstract
INTRODUCTION The switch from quiescence (G0) into G1 and cell cycle progression critically depends on specific nutrients and metabolic capabilities. Conversely, metabolic networks are regulated by enzyme-metabolite interaction and transcriptional regulation that lead to flux modifications to support cell growth. How cells process and integrate environmental information into coordinated responses is challenging to analyse and not yet described quantitatively. OBJECTIVES To quantitatively monitor the central carbon metabolism during G0 exit and the first 2 h after reentering the cell cycle from synchronized Saccharomyces cerevisiae. METHODS Dynamic tailored 13C metabolic flux analysis was used to observe the intracellular metabolite flux changes, and the metabolome and proteome were observed to identify regulatory mechanisms. RESULTS G0 cells responded immediately to an extracellular increase of glucose. The intracellular metabolic flux changed in time and specific events were observed. High fluxes into trehalose and glycogen synthesis were observed during the G0 exit. Both fluxes then decreased, reaching a minimum at t = 65 min. Here, storage degradation contributed significantly (i.e. 21%) to the glycolytic flux. In contrast to these changes, the glucose uptake rate remained constant after the G0 exit. The flux into the oxidative pentose phosphate pathway was highest (29-fold increase, 36.4% of the glucose uptake) at t = 65 min, while it was very low at other time points. The maximum flux seems to correlate with a late G1 state preparing for the S phase transition. In the G1/S phase (t = 87 min), anaplerotic reactions such as glyoxylate shunt increased. Protein results show that during this transition, proteins belonging to clusters related with ribosome biogenesis and assembly, and initiation transcription factors clusters were continuously synthetised. CONCLUSION The intracellular flux distribution changes dynamically and these major rearrangements highlight the coordinate reorganization of metabolic flux to meet requirements for growth during different cell state.
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Affiliation(s)
- Jinrui Zhang
- 0000 0001 2097 4740grid.5292.cDepartment of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Karla Martinez-Gomez
- 0000 0001 2167 7588grid.11749.3aBiochemical Engineering, Saarland University, Campus A 1.5, 66123 Saarbrücken, Germany
| | - Elmar Heinzle
- 0000 0001 2167 7588grid.11749.3aBiochemical Engineering, Saarland University, Campus A 1.5, 66123 Saarbrücken, Germany
| | - Sebastian Aljoscha Wahl
- 0000 0001 2097 4740grid.5292.cDepartment of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
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Metabolomics analysis of gut barrier dysfunction in a trauma-hemorrhagic shock rat model. Biosci Rep 2019; 39:BSR20181215. [PMID: 30393232 PMCID: PMC6328858 DOI: 10.1042/bsr20181215] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Revised: 09/30/2018] [Accepted: 10/10/2018] [Indexed: 12/12/2022] Open
Abstract
Intestinal barrier dysfunction has been implicated in the development of multiorgan dysfunction syndrome caused by the trauma-hemorrhagic shock (THS). However, the mechanisms underlying THS-induced gut barrier injury are still poorly understood. In the present study, we used the metabolomics analysis to test the hypothesis that altered metabolites might be related to the development of THS-induced barrier dysfunction in the large intestine. Under the induction of THS, gut barrier failure was characterized by injury of permeability and mucus layer, which were companied by the decreased expression of zonula occludens-1 in the colon and increased levels of inflammatory factors including tumor necrosis factor-α, interferon-γ, interleukin (IL)-6, and IL-1β in the serum. A total of 16 differential metabolites were identified in colonic tissues from THS-treated rats compared with control rats. These altered metabolites included dihydroxy acetone phosphate, ribose-5-phosphate, fructose, glyceric acid, succinic acid, and adenosine, which are critical intermediates or end products that are involved in pentose phosphate pathway, glycolysis, and tricarboxylic acid cycle as well as mitochondrial adenosine triphosphate biosynthesis. These findings may offer important insight into the metabolic alterations in THS-treated gut injury, which will be helpful for developing effective metabolites-based strategies to prevent THS-induced gut barrier dysfunction.
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Suarez-Mendez CA, Ras C, Wahl SA. Metabolic adjustment upon repetitive substrate perturbations using dynamic 13C-tracing in yeast. Microb Cell Fact 2017; 16:161. [PMID: 28946905 PMCID: PMC5613340 DOI: 10.1186/s12934-017-0778-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 09/18/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Natural and industrial environments are dynamic with respect to substrate availability and other conditions like temperature and pH. Especially, metabolism is strongly affected by changes in the extracellular space. Here we study the dynamic flux of central carbon metabolism and storage carbohydrate metabolism under dynamic feast/famine conditions in Saccharomyces cerevisiae. RESULTS The metabolic flux reacts fast and sensitive to cyclic perturbations in substrate availability. Compared to well-documented stimulus-response experiments using substrate pulses, different metabolic responses are observed. Especially, cells experiencing cyclic perturbations do not show a drop in ATP with the addition of glucose, but an immediate increase in energy charge. Although a high glycolytic flux of up to 5.4 mmol g DW-1 h-1 is observed, no overflow metabolites are detected. From famine to feast the glucose uptake rate increased from 170 to 4788 μmol g DW-1 h-1 in 24 s. Intracellularly, even more drastic changes were observed. Especially, the T6P synthesis rate increased more than 100-fold upon glucose addition. This response indicates that the storage metabolism is very sensitive to changes in glycolytic flux and counterbalances these rapid changes by diverting flux into large pools to prevent substrate accelerated death and potentially refill the central metabolism when substrates become scarce. Using 13C-tracer we found a dilution in the labeling of extracellular glucose, G6P, T6P and other metabolites, indicating an influx of unlabeled carbon. It is shown that glycogen and trehalose degradation via different routes could explain these observations. Based on the 13C labeling in average 15% of the carbon inflow is recycled via trehalose and glycogen. This average fraction is comparable to the steady-state turnover, but changes significantly during the cycle, indicating the relevance for dynamic regulation of the metabolic flux. CONCLUSIONS Comparable to electric energy grids, metabolism seems to use storage units to buffer peaks and keep reserves to maintain a robust function. During the applied fast feast/famine conditions about 15% of the metabolized carbon were recycled in storage metabolism. Additionally, the resources were distributed different to steady-state conditions. Most remarkably is a fivefold increased flux towards PPP that generated a reversed flux of transaldolase and the F6P-producing transketolase reactions. Combined with slight changes in the biomass composition, the yield decrease of 5% can be explained.
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Affiliation(s)
- C. A. Suarez-Mendez
- Department of Biotechnology, Delft University of Technology, Van der Maasweg, 92629 HZ Delft, The Netherlands
- Kluyver Centre for Genomics of Industrial Fermentation, P.O. Box 5057, 2600 GA Delft, The Netherlands
- Present Address: Department of Processes and Energy, Universidad Nacional de Colombia, Carrera 80 No. 65-223, Medellin, Colombia
| | - C. Ras
- Department of Biotechnology, Delft University of Technology, Van der Maasweg, 92629 HZ Delft, The Netherlands
| | - S. A. Wahl
- Department of Biotechnology, Delft University of Technology, Van der Maasweg, 92629 HZ Delft, The Netherlands
- Kluyver Centre for Genomics of Industrial Fermentation, P.O. Box 5057, 2600 GA Delft, The Netherlands
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