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Using Kinetic Modelling to Infer Adaptations in Saccharomyces cerevisiae Carbohydrate Storage Metabolism to Dynamic Substrate Conditions. Metabolites 2023; 13:metabo13010088. [PMID: 36677014 PMCID: PMC9862193 DOI: 10.3390/metabo13010088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 12/14/2022] [Accepted: 12/23/2022] [Indexed: 01/07/2023] Open
Abstract
Microbial metabolism is strongly dependent on the environmental conditions. While these can be well controlled under laboratory conditions, large-scale bioreactors are characterized by inhomogeneities and consequently dynamic conditions for the organisms. How Saccharomyces cerevisiae response to frequent perturbations in industrial bioreactors is still not understood mechanistically. To study the adjustments to prolonged dynamic conditions, we used published repeated substrate perturbation regime experimental data, extended it with proteomic measurements and used both for modelling approaches. Multiple types of data were combined; including quantitative metabolome, 13C enrichment and flux quantification data. Kinetic metabolic modelling was applied to study the relevant intracellular metabolic response dynamics. An existing model of yeast central carbon metabolism was extended, and different subsets of enzymatic kinetic constants were estimated. A novel parameter estimation pipeline based on combinatorial enzyme selection supplemented by regularization was developed to identify and predict the minimum enzyme and parameter adjustments from steady-state to dynamic substrate conditions. This approach predicted proteomic changes in hexose transport and phosphorylation reactions, which were additionally confirmed by proteome measurements. Nevertheless, the modelling also hints at a yet unknown kinetic or regulation phenomenon. Some intracellular fluxes could not be reproduced by mechanistic rate laws, including hexose transport and intracellular trehalase activity during substrate perturbation cycles.
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Minden S, Aniolek M, Sarkizi Shams Hajian C, Teleki A, Zerrer T, Delvigne F, van Gulik W, Deshmukh A, Noorman H, Takors R. Monitoring Intracellular Metabolite Dynamics in Saccharomyces cerevisiae during Industrially Relevant Famine Stimuli. Metabolites 2022; 12:metabo12030263. [PMID: 35323706 PMCID: PMC8953226 DOI: 10.3390/metabo12030263] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 03/08/2022] [Accepted: 03/16/2022] [Indexed: 11/16/2022] Open
Abstract
Carbon limitation is a common feeding strategy in bioprocesses to enable an efficient microbiological conversion of a substrate to a product. However, industrial settings inherently promote mixing insufficiencies, creating zones of famine conditions. Cells frequently traveling through such regions repeatedly experience substrate shortages and respond individually but often with a deteriorated production performance. A priori knowledge of the expected strain performance would enable targeted strain, process, and bioreactor engineering for minimizing performance loss. Today, computational fluid dynamics (CFD) coupled to data-driven kinetic models are a promising route for the in silico investigation of the impact of the dynamic environment in the large-scale bioreactor on microbial performance. However, profound wet-lab datasets are needed to cover relevant perturbations on realistic time scales. As a pioneering study, we quantified intracellular metabolome dynamics of Saccharomyces cerevisiae following an industrially relevant famine perturbation. Stimulus-response experiments were operated as chemostats with an intermittent feed and high-frequency sampling. Our results reveal that even mild glucose gradients in the range of 100 µmol·L−1 impose significant perturbations in adapted and non-adapted yeast cells, altering energy and redox homeostasis. Apparently, yeast sacrifices catabolic reduction charges for the sake of anabolic persistence under acute carbon starvation conditions. After repeated exposure to famine conditions, adapted cells show 2.7% increased maintenance demands.
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Affiliation(s)
- Steven Minden
- Institute of Biochemical Engineering, University of Stuttgart, 70569 Stuttgart, Germany; (S.M.); (M.A.); (C.S.S.H.); (A.T.); (T.Z.)
| | - Maria Aniolek
- Institute of Biochemical Engineering, University of Stuttgart, 70569 Stuttgart, Germany; (S.M.); (M.A.); (C.S.S.H.); (A.T.); (T.Z.)
| | - Christopher Sarkizi Shams Hajian
- Institute of Biochemical Engineering, University of Stuttgart, 70569 Stuttgart, Germany; (S.M.); (M.A.); (C.S.S.H.); (A.T.); (T.Z.)
| | - Attila Teleki
- Institute of Biochemical Engineering, University of Stuttgart, 70569 Stuttgart, Germany; (S.M.); (M.A.); (C.S.S.H.); (A.T.); (T.Z.)
| | - Tobias Zerrer
- Institute of Biochemical Engineering, University of Stuttgart, 70569 Stuttgart, Germany; (S.M.); (M.A.); (C.S.S.H.); (A.T.); (T.Z.)
| | - Frank Delvigne
- Microbial Processes and Interactions (MiPI), TERRA Research and Teaching Centre, Gembloux Agro Bio Tech, University of Liege, 5030 Gembloux, Belgium;
| | - Walter van Gulik
- Department of Biotechnology, Delft University of Technology, van der Maasweg 6, 2629 HZ Delft, The Netherlands;
| | - Amit Deshmukh
- Royal DSM, 2613 AX Delft, The Netherlands; (A.D.); (H.N.)
| | - Henk Noorman
- Royal DSM, 2613 AX Delft, The Netherlands; (A.D.); (H.N.)
- Department of Biotechnology, Delft University of Technology, 2628 CD Delft, The Netherlands
| | - Ralf Takors
- Institute of Biochemical Engineering, University of Stuttgart, 70569 Stuttgart, Germany; (S.M.); (M.A.); (C.S.S.H.); (A.T.); (T.Z.)
- Correspondence:
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Lao-Martil D, Verhagen KJA, Schmitz JPJ, Teusink B, Wahl SA, van Riel NAW. Kinetic Modeling of Saccharomyces cerevisiae Central Carbon Metabolism: Achievements, Limitations, and Opportunities. Metabolites 2022; 12:74. [PMID: 35050196 PMCID: PMC8779790 DOI: 10.3390/metabo12010074] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/11/2022] [Accepted: 01/12/2022] [Indexed: 11/23/2022] Open
Abstract
Central carbon metabolism comprises the metabolic pathways in the cell that process nutrients into energy, building blocks and byproducts. To unravel the regulation of this network upon glucose perturbation, several metabolic models have been developed for the microorganism Saccharomyces cerevisiae. These dynamic representations have focused on glycolysis and answered multiple research questions, but no commonly applicable model has been presented. This review systematically evaluates the literature to describe the current advances, limitations, and opportunities. Different kinetic models have unraveled key kinetic glycolytic mechanisms. Nevertheless, some uncertainties regarding model topology and parameter values still limit the application to specific cases. Progressive improvements in experimental measurement technologies as well as advances in computational tools create new opportunities to further extend the model scale. Notably, models need to be made more complex to consider the multiple layers of glycolytic regulation and external physiological variables regulating the bioprocess, opening new possibilities for extrapolation and validation. Finally, the onset of new data representative of individual cells will cause these models to evolve from depicting an average cell in an industrial fermenter, to characterizing the heterogeneity of the population, opening new and unseen possibilities for industrial fermentation improvement.
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Affiliation(s)
- David Lao-Martil
- Department of Biomedical Engineering, Eindhoven University of Technology, Groene Loper 5, 5612 AE Eindhoven, The Netherlands;
| | - Koen J. A. Verhagen
- Lehrstuhl für Bioverfahrenstechnik, FAU Erlangen-Nürnberg, 91052 Erlangen, Germany; (K.J.A.V.); (S.A.W.)
| | - Joep P. J. Schmitz
- DSM Biotechnology Center, Alexander Fleminglaan 1, 2613 AX Delft, The Netherlands;
| | - Bas Teusink
- Systems Biology Lab, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, 1081 HZ Amsterdam, The Netherlands;
| | - S. Aljoscha Wahl
- Lehrstuhl für Bioverfahrenstechnik, FAU Erlangen-Nürnberg, 91052 Erlangen, Germany; (K.J.A.V.); (S.A.W.)
| | - Natal A. W. van Riel
- Department of Biomedical Engineering, Eindhoven University of Technology, Groene Loper 5, 5612 AE Eindhoven, The Netherlands;
- Amsterdam University Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
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5
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Fast Sampling of the Cellular Metabolome. Methods Mol Biol 2021. [PMID: 34718989 DOI: 10.1007/978-1-0716-1585-0_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Obtaining meaningful snapshots of the metabolome of microorganisms requires rapid sampling and immediate quenching of all metabolic activity, to prevent any changes in metabolite levels after sampling. Furthermore, a suitable extraction method is required ensuring complete extraction of metabolites from the cells and inactivation of enzymatic activity, with minimal degradation of labile compounds. Finally, a sensitive, high-throughput analysis platform is needed to quantify a large number of metabolites in a small amount of sample. An issue which has often been overlooked in microbial metabolomics is the fact that many intracellular metabolites are also present in significant amounts outside the cells and may interfere with the quantification of the endo metabolome. Attempts to remove the extracellular metabolites with dedicated quenching methods often induce release of intracellular metabolites into the quenching solution. For eukaryotic microorganisms, this release can be minimized by adaptation of the quenching method. For prokaryotic cells, this has not yet been accomplished, so the application of a differential method whereby metabolites are measured in the culture supernatant as well as in total broth samples, to calculate the intracellular levels by subtraction, seems to be the most suitable approach. Here we present an overview of different sampling, quenching, and extraction methods developed for microbial metabolomics, described in the literature. Detailed protocols are provided for rapid sampling, quenching, and extraction, for measurement of metabolites in total broth samples, washed cell samples, and supernatant, to be applied for quantitative metabolomics of both eukaryotic and prokaryotic microorganisms.
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Liu P, Wang S, Li C, Zhuang Y, Xia J, Noorman H. Dynamic response of Aspergillus niger to periodical glucose pulse stimuli in chemostat cultures. Biotechnol Bioeng 2021; 118:2265-2282. [PMID: 33666237 DOI: 10.1002/bit.27739] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 01/05/2021] [Accepted: 01/21/2021] [Indexed: 12/15/2022]
Abstract
In industrial large-scale bioreactors, microorganisms encounter heterogeneous substrate concentration conditions, which can impact growth or product formation. Here we carried out an extended (12 h) experiment of repeated glucose pulsing with a 10-min period to simulate fluctuating glucose concentrations with Aspergillus niger producing glucoamylase, and investigated its dynamic response by rapid sampling and quantitative metabolomics. The 10-min period represents worst-case conditions, as in industrial bioreactors the average cycling duration is usually in the order of 1 min. We found that cell growth and the glucoamylase productivity were not significantly affected, despite striking metabolomic dynamics. Periodical dynamic responses were found across all central carbon metabolism pathways, with different time scales, and the frequently reported ATP paradox was confirmed for this A. niger strain under the dynamic conditions. A thermodynamics analysis revealed that several reactions of the central carbon metabolism remained in equilibrium even under periodical dynamic conditions. The dynamic response profiles of the intracellular metabolites did not change during the pulse exposure, showing no significant adaptation of the strain to the more than 60 perturbation cycles applied. The apparent high tolerance of the glucoamylase producing A. niger strain for extreme variations in the glucose availability presents valuable information for the design of robust industrial microbial hosts.
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Affiliation(s)
- Peng Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Shuai Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Chao Li
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Yingping Zhuang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Jianye Xia
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Henk Noorman
- DSM Biotechnology Center, Delft, The Netherlands
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Xia J, Wang G, Fan M, Chen M, Wang Z, Zhuang Y. Understanding the scale-up of fermentation processes from the viewpoint of the flow field in bioreactors and the physiological response of strains. Chin J Chem Eng 2021. [DOI: 10.1016/j.cjche.2020.12.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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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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Heins AL, Johanson T, Han S, Lundin L, Carlquist M, Gernaey KV, Sørensen SJ, Eliasson Lantz A. Quantitative Flow Cytometry to Understand Population Heterogeneity in Response to Changes in Substrate Availability in Escherichia coli and Saccharomyces cerevisiae Chemostats. Front Bioeng Biotechnol 2019; 7:187. [PMID: 31448270 PMCID: PMC6691397 DOI: 10.3389/fbioe.2019.00187] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 07/18/2019] [Indexed: 12/20/2022] Open
Abstract
Microbial cells in bioprocesses are usually described with averaged parameters. But in fact, single cells within populations vary greatly in characteristics such as stress resistance, especially in response to carbon source gradients. Our aim was to introduce tools to quantify population heterogeneity in bioprocesses using a combination of reporter strains, flow cytometry, and easily comprehensible parameters. We calculated mean, mode, peak width, and coefficient of variance to describe distribution characteristics and temporal shifts in fluorescence intensity. The skewness and the slope of cumulative distribution function plots illustrated differences in distribution shape. These parameters are person-independent and precise. We demonstrated this by quantifying growth-related population heterogeneity of Saccharomyces cerevisiae and Escherichia coli reporter strains in steady-state of aerobic glucose-limited chemostat cultures at different dilution rates and in response to glucose pulses. Generally, slow-growing cells showed stronger responses to glucose excess than fast-growing cells. Cell robustness, measured as membrane integrity after exposure to freeze-thaw treatment, of fast-growing cells was strongly affected in subpopulations of low membrane robustness. Glucose pulses protected subpopulations of fast-growing but not slower-growing yeast cells against membrane damage. Our parameters could successfully describe population heterogeneity, thereby revealing physiological characteristics that might have been overlooked during traditional averaged analysis.
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Affiliation(s)
- Anna-Lena Heins
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Lyngby, Denmark
| | | | - Shanshan Han
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Luisa Lundin
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Magnus Carlquist
- Division of Applied Microbiology, Department of Chemistry, Lund University, Lund, Sweden
| | - Krist V Gernaey
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Lyngby, Denmark
| | - Søren J Sørensen
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Anna Eliasson Lantz
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Lyngby, Denmark
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Wang G, Chu J, Zhuang Y, van Gulik W, Noorman H. A dynamic model-based preparation of uniformly-13C-labeled internal standards facilitates quantitative metabolomics analysis of Penicillium chrysogenum. J Biotechnol 2019; 299:21-31. [DOI: 10.1016/j.jbiotec.2019.04.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 04/03/2019] [Accepted: 04/25/2019] [Indexed: 01/03/2023]
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11
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Wang S, Liu P, Shu W, Li C, Li H, Liu S, Xia J, Noorman H. Dynamic response of Aspergillus niger to single pulses of glucose with high and low concentrations. BIORESOUR BIOPROCESS 2019. [DOI: 10.1186/s40643-019-0251-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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12
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Li C, Shu W, Wang S, Liu P, Zhuang Y, Zhang S, Xia J. Dynamic metabolic response of Aspergillus niger to glucose perturbation: evidence of regulatory mechanism for reduced glucoamylase production. J Biotechnol 2018; 287:28-40. [PMID: 30134150 DOI: 10.1016/j.jbiotec.2018.08.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 06/20/2018] [Accepted: 08/18/2018] [Indexed: 01/14/2023]
Abstract
Environmental gradient is an important common issue during scale-up process for protein production. To address the dynamic regulatory mechanism of Aspergillus niger being exposed to inhomogeneous glucose concentrations, glucose perturbation were experimented on the steady state of A. niger chemostat culture, and dynamic profiles of the intracellular metabolites in central carbon metabolism were tracked in a time scale of seconds. The upper glycolysis and pentose phosphate pathway showed sharp variations after glucose perturbation, while the lower glycolysis, TCA cycle and amino acid pools represented a moderate and prolonged response due to the allosteric regulation of enzymes and buffering function of metabolites with large pool sizes. Improved glucose-6-phosphate enhanced the metabolic flux to PP pathway remarkably, which provided not only more redox cofactors (NADPH) for protein synthesis but also more precursors (phosphoribosyl pyrophosphate and ribose-5-phosphate) for cell growth. Moreover, reduction of the total adenine nucleotides and major precursor amino acids indicated the upregulated RNA synthesis was required to produce stress proteins, and partially explained the drop of glucoamylase production when A. niger experienced a fluctuated glucose concentration environment. These findings would be valuable for improving bioreactor operation, design, and scale-up from engineering or genetic aspects.
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Affiliation(s)
- Chao Li
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Wei Shu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Shuai Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Peng Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Yingpping Zhuang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Siliang Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Jianye Xia
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China.
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Tröndle J, Albermann C, Weiner M, Sprenger GA, Weuster-Botz D. Phosphoenolpyruvate Transporter Enables Targeted Perturbation During Metabolic Analysis of L-Phenylalanine Production With Escherichia coli. Biotechnol J 2017; 13:e1700611. [DOI: 10.1002/biot.201700611] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 11/14/2017] [Indexed: 12/25/2022]
Affiliation(s)
- Julia Tröndle
- Institute of Biochemical Engineering; Technical University of Munich; Boltzmannstr. 15 85748 Garching Germany
| | | | - Michael Weiner
- Institute of Biochemical Engineering; Technical University of Munich; Boltzmannstr. 15 85748 Garching Germany
| | - Georg A. Sprenger
- Institute of Microbiology; University of Stuttgart; Stuttgart Germany
| | - Dirk Weuster-Botz
- Institute of Biochemical Engineering; Technical University of Munich; Boltzmannstr. 15 85748 Garching Germany
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Pinu FR, Villas-Boas SG, Aggio R. Analysis of Intracellular Metabolites from Microorganisms: Quenching and Extraction Protocols. Metabolites 2017; 7:E53. [PMID: 29065530 PMCID: PMC5746733 DOI: 10.3390/metabo7040053] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 10/11/2017] [Accepted: 10/21/2017] [Indexed: 11/17/2022] Open
Abstract
Sample preparation is one of the most important steps in metabolome analysis. The challenges of determining microbial metabolome have been well discussed within the research community and many improvements have already been achieved in last decade. The analysis of intracellular metabolites is particularly challenging. Environmental perturbations may considerably affect microbial metabolism, which results in intracellular metabolites being rapidly degraded or metabolized by enzymatic reactions. Therefore, quenching or the complete stop of cell metabolism is a pre-requisite for accurate intracellular metabolite analysis. After quenching, metabolites need to be extracted from the intracellular compartment. The choice of the most suitable metabolite extraction method/s is another crucial step. The literature indicates that specific classes of metabolites are better extracted by different extraction protocols. In this review, we discuss the technical aspects and advancements of quenching and extraction of intracellular metabolite analysis from microbial cells.
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Affiliation(s)
- Farhana R Pinu
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 92169, Auckland 1142, New Zealand.
| | - Silas G Villas-Boas
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland 1010, New Zealand.
| | - Raphael Aggio
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Crown Street, Liverpool L693BX, UK.
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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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Wahl SA, Bernal Martinez C, Zhao Z, van Gulik WM, Jansen MLA. Intracellular product recycling in high succinic acid producing yeast at low pH. Microb Cell Fact 2017; 16:90. [PMID: 28535757 PMCID: PMC5442661 DOI: 10.1186/s12934-017-0702-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 05/12/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The metabolic engineering of Saccharomyces cerevisiae for the production of succinic acid has progressed dramatically, and a series of high-producing hosts are available. At low cultivation pH and high titers, the product transport can become bidirectional, i.e. the acid is reentering the cell and is again exported or even catabolized. Here, a quantitative approach for the identification of product recycling fluxes is developed. RESULTS The metabolic flux distributions at two time-points of the fermentation process were analyzed. 13C labeled succinic acid was added to the extracellular space and intracellular enrichments were measured and subsequently used for the estimation of metabolic fluxes. The labeling was introduced by a labeling switch experiment, leading to an immediate labeling of about 85% of the acid while keeping the total acid concentration constant. Within 100 s significant labeling enrichment of the TCA cycle intermediates fumarate, iso-citrate and α-ketoglutarate was observed, while no labeling was detected for malate and citrate. These findings suggest that succinic acid is rapidly exchanged over the cellular membrane and enters the oxidative TCA cycle. Remarkably, in the oxidative direction malate 13C enrichment was not detected, indicating that there is no flux going through this metabolite pool. Using flux modeling and thermodynamic assumptions on compartmentation it was concluded that malate must be predominantly cytosolic while fumarate and iso-citrate were more dominant in the mitochondria. CONCLUSIONS Adding labeled product without changing the extracellular environment allowed to quantify intracellular metabolic fluxes under high producing conditions and identify product degradation cycles. In the specific case of succinic acid production, compartmentation was found to play a major role, i.e. the presence of metabolic activity in two different cellular compartments lead to intracellular product degradation reducing the yield. We also observed that the flux from glucose to succinic acid branches at two points in metabolism: (1) At the level of pyruvate, and (2) at cytosolic malate which was not expected.
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Affiliation(s)
- S Aljoscha Wahl
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands.
| | - Cristina Bernal Martinez
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands.,Applikon Biotechnology B.V., Heertjeslaan 2, 2629 JG, Delft, The Netherlands
| | - Zheng Zhao
- DSM Biotechnology Center, Alexander Fleminglaan 1, 2613 AX, 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 Center, Alexander Fleminglaan 1, 2613 AX, Delft, The Netherlands
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17
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Velasco Alvarez MI, Ten Pierick A, van Dam PTN, Maleki Seifar R, van Loosdrecht MCM, Wahl SA. Microscale Quantitative Analysis of Polyhydroxybutyrate in Prokaryotes Using IDMS. Metabolites 2017; 7:metabo7020019. [PMID: 28513556 PMCID: PMC5487990 DOI: 10.3390/metabo7020019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 05/13/2017] [Accepted: 05/15/2017] [Indexed: 12/02/2022] Open
Abstract
Poly(3-hydroxybutyrate) (PHB) is an interesting biopolymer for replacing petroleum-based plastics, its biological production is performed in natural and engineered microorganisms. Current metabolic engineering approaches rely on high-throughput strain construction and screening. Analytical procedures have to be compatible with the small scale and speed of these approaches. Here, we present a method based on isotope dilution mass spectrometry (IDMS) and propanolysis extraction of poly(3-hydroxybutyrate) from an Escherichia coli strain engineered for PHB production. As internal standard (IS), we applied an uniformly labeled 13C-cell suspension, of an E. coli PHB producing strain, grown on U-13C-glucose as C-source. This internal 13C-PHB standard enables to quantify low concentrations of PHB (LOD of 0.01 µg/gCDW) from several micrograms of biomass. With this method, a technical reproducibility of about 1.8% relative standard deviation is achieved. Furthermore, the internal standard is robust towards different sample backgrounds and dilutions. The early addition of the internal standard also enables higher reproducibility and increases sensitivity and throughput by simplified sample preparation steps.
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Affiliation(s)
- Mariana Itzel Velasco Alvarez
- Cell Systems Engineering Group, Department of Biotechnology, Delft University of Technology, 2629 HZ Delft, The Netherlands.
| | - Angela Ten Pierick
- BioAnalytical Chemistry, Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands.
| | - Patricia T N van Dam
- Cell Systems Engineering Group, Department of Biotechnology, Delft University of Technology, 2629 HZ Delft, The Netherlands.
| | - Reza Maleki Seifar
- Cell Systems Engineering Group, Department of Biotechnology, Delft University of Technology, 2629 HZ Delft, The Netherlands.
| | - Mark C M van Loosdrecht
- Cell Systems Engineering Group, Department of Biotechnology, Delft University of Technology, 2629 HZ Delft, The Netherlands.
| | - S Aljoscha Wahl
- Cell Systems Engineering Group, Department of Biotechnology, Delft University of Technology, 2629 HZ Delft, The Netherlands.
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18
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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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19
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Suarez-Mendez C, Hanemaaijer M, ten Pierick A, Wolters J, Heijnen J, Wahl S. Interaction of storage carbohydrates and other cyclic fluxes with central metabolism: A quantitative approach by non-stationary 13C metabolic flux analysis. Metab Eng Commun 2016; 3:52-63. [PMID: 29468113 PMCID: PMC5779734 DOI: 10.1016/j.meteno.2016.01.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Revised: 11/30/2015] [Accepted: 01/19/2016] [Indexed: 12/11/2022] Open
Abstract
13C labeling experiments in aerobic glucose limited cultures of Saccharomyces cerevisiae at four different growth rates (0.054; 0.101, 0.207, 0.307 h-1) are used for calculating fluxes that include intracellular cycles (e.g., storage carbohydrate cycles, exchange fluxes with amino acids), which are rearranged depending on the growth rate. At low growth rates the impact of the storage carbohydrate recycle is relatively more significant than at high growth rates due to a higher concentration of these materials in the cell (up to 560-fold) and higher fluxes relative to the glucose uptake rate (up to 16%). Experimental observations suggest that glucose can be exported to the extracellular space, and that its source is related to storage carbohydrates, most likely via the export and subsequent extracellular breakdown of trehalose. This hypothesis is strongly supported by 13C-labeling experimental data, measured extracellular trehalose, and the corresponding flux estimations.
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Key Words
- 2PG, 2-phosphoglycerate
- 3PG, 3-phosphoglycerate
- 6PG, 6-phospho gluconate
- ACO, aconitate hydratase
- AK, adenylate kinase
- ALA, alanine
- ASP, aspartate
- Amino acids
- CoA, coenzyme-A
- DHAP, dihydroxy acetone phosphate
- DO, dissolved oxygen
- E4P, erythrose-4-phosphate
- ENO, phosphopyruvate hydratase
- F6P, fructose-6-phosphate
- FBA, fructose-bisphosphate aldolase
- FBP, fructose-1,6-bis-phosphate
- FMH, fumarate hydratase
- FUM, fumarate
- Flux estimation
- G1P, glucose-1-phosphate
- G6P, glucose-6-phosphate
- G6PDH, glucose-6-phosphate dehydrogenase
- GAP, glyceraldehyde-3-phosphate
- GAPDH&PGK, glyceraldehyde-3-phosphate dehydrogenase+phosphoglycerate kinase
- GLN, glutamine
- GLU, glutamate
- GLY, glycine
- GPM, phosphoglycerate mutase
- Glycogen
- IDMS, Isotope dilution mass spectrometry
- Iso-Cit, isocitrate
- LEU, leucine
- LYS, lysine
- MAL, malate
- METH, methionine
- Non-stationary 13C labeling
- OAA, oxaloacetate
- OUR, Oxygen uptake rate
- PEP, phospho-enol-pyruvate
- PFK, 6-phosphofructokinase
- PGI, glucose-6-phosphate isomerase
- PGM, phosphoglucomutase
- PMI, mannose-6-phosphate isomerase
- PPP, pentose phosphate pathway
- PRO, proline
- PYK, pyruvate kinase
- PYR, pyruvate
- RPE, ribulose-phosphate 3-epimerase
- RPI, ribose-5-phosphate isomerase
- Rib5P, ribose-5-phosphate
- Ribu5P, ribulose-5-phosphate
- S7P, sedoheptulose-7-phosphate
- SER, serine
- SUC, succinate
- T6P, trehalose-6-phosphate
- TCA, tricarboxylic acid cycle.
- TPP, trehalose- phosphatase
- TPS, alpha,alpha-trehalose-phosphate synthase
- Trehalose
- UDP, uridine-5-diphosphate
- UDPG, UDP-glucose
- UTP, uridine-5-triphosphate
- X5P, xylulose-5-phosphate
- α-KG, oxoglutarate
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Affiliation(s)
- C.A. Suarez-Mendez
- Department of Biotechnology, Delft University of Technology, Julianalaan 67 – 2628 BC Delft, The Netherlands
- Kluyver Centre for Genomics of Industrial Fermentation, P.O. Box 5057, 2600 GA Delft, The Netherlands
| | - M. Hanemaaijer
- Department of Biotechnology, Delft University of Technology, Julianalaan 67 – 2628 BC Delft, The Netherlands
| | - Angela ten Pierick
- Department of Biotechnology, Delft University of Technology, Julianalaan 67 – 2628 BC Delft, The Netherlands
| | - J.C. Wolters
- Department of Analytical Biochemistry, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - J.J. Heijnen
- Department of Biotechnology, Delft University of Technology, Julianalaan 67 – 2628 BC Delft, The Netherlands
- Kluyver Centre for Genomics of Industrial Fermentation, P.O. Box 5057, 2600 GA Delft, The Netherlands
| | - S.A. Wahl
- Department of Biotechnology, Delft University of Technology, Julianalaan 67 – 2628 BC Delft, The Netherlands
- Kluyver Centre for Genomics of Industrial Fermentation, P.O. Box 5057, 2600 GA Delft, The Netherlands
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20
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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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21
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Current state and challenges for dynamic metabolic modeling. Curr Opin Microbiol 2016; 33:97-104. [PMID: 27472025 DOI: 10.1016/j.mib.2016.07.008] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Revised: 06/28/2016] [Accepted: 07/06/2016] [Indexed: 01/06/2023]
Abstract
While the stoichiometry of metabolism is probably the best studied cellular level, the dynamics in metabolism can still not be well described, predicted and, thus, engineered. Unknowns in the metabolic flux behavior arise from kinetic interactions, especially allosteric control mechanisms. While the stoichiometry of enzymes is preserved in vitro, their activity and kinetic behavior differs from the in vivo situation. Next to this challenge, it is infeasible to test the interaction of each enzyme with each intracellular metabolite in vitro exhaustively. As a consequence, the whole interacting metabolome has to be studied in vivo to identify the relevant enzymes properties. In this review we discuss current approaches for in vivo perturbation experiments, that is, stimulus response experiments using different setups and quantitative analytical approaches, including dynamic carbon tracing. Next to reliable and informative data, advanced modeling approaches and computational tools are required to identify kinetic mechanisms and their parameters.
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22
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Accurate Measurement of the in vivo Ammonium Concentration in Saccharomyces cerevisiae. Metabolites 2016; 6:metabo6020012. [PMID: 27120628 PMCID: PMC4931543 DOI: 10.3390/metabo6020012] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 04/13/2016] [Accepted: 04/20/2016] [Indexed: 11/16/2022] Open
Abstract
Ammonium (NH4+) is the most common N-source for yeast fermentations, and N-limitation is frequently applied to reduce growth and increase product yields. While there is significant molecular knowledge on NH4+ transport and assimilation, there have been few attempts to measure the in vivo concentration of this metabolite. In this article, we present a sensitive and accurate analytical method to quantify the in vivo intracellular ammonium concentration in Saccharomycescerevisiae based on standard rapid sampling and metabolomics techniques. The method validation experiments required the development of a proper sample processing protocol to minimize ammonium production/consumption during biomass extraction by assessing the impact of amino acid degradation—an element that is often overlooked. The resulting cold chloroform metabolite extraction method, together with quantification using ultra high performance liquid chromatography-isotope dilution mass spectrometry (UHPLC-IDMS), was not only more sensitive than most of the existing methods but also more accurate than methods that use electrodes, enzymatic reactions, or boiling water or boiling ethanol biomass extraction because it minimized ammonium consumption/production during sampling processing and interference from other metabolites in the quantification of intracellular ammonium. Finally, our validation experiments showed that other metabolites such as pyruvate or 2-oxoglutarate (αKG) need to be extracted with cold chloroform to avoid measurements being biased by the degradation of other metabolites (e.g., amino acids).
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23
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Taymaz-Nikerel H, De Mey M, Baart GJE, Maertens J, Foulquié-Moreno MR, Charlier D, Heijnen JJ, van Gulik WM. Comparative fluxome and metabolome analysis for overproduction of succinate in Escherichia coli. Biotechnol Bioeng 2015; 113:817-29. [PMID: 26444867 DOI: 10.1002/bit.25850] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Revised: 09/08/2015] [Accepted: 09/28/2015] [Indexed: 11/10/2022]
Abstract
An aerobic succinate-producing Escherichia coli mutant was compared to its wild-type by quantitatively analyzing both the metabolome and fluxome, during glucose-limited steady-state and succinate excess dynamic conditions, in order to identify targets for further strain engineering towards more efficient succinate production. The mutant had four functional mutations under the conditions investigated: increased expression of a succinate exporter (DcuC), deletion of a succinate importer (Dct), deletion of succinate dehydrogenase (SUCDH) and expression of a PEP carboxylase (PPC) with increased capacity due to a point mutation. The steady-state and dynamic patterns of the intracellular metabolite levels and fluxes in response to changes were used to locate the quantitative differences in the physiology/metabolism of the mutant strain. Unexpectedly the mutant had a higher energy efficiency, indicated by a much lower rate of oxygen consumption, under glucose-limited conditions, caused by the deletion of the transcription factors IclR and ArcA. Furthermore the mutant had a much lower uptake capacity for succinate (26-fold) and oxygen (17-fold under succinate excess) compared to the wild-type strain. The mutant strain produced 7.9 mmol.CmolX(-1).h(-1) succinate during chemostat cultivation, showing that the choice of the applied genetic modifications was a successful strategy. Furthermore, the applied genetic modifications resulted in multiple large changes in metabolite levels (FBP, pyruvate, 6PG, NAD(+) /NADH ratio, α-ketogluarate) corresponding to large changes in fluxes. Compared to the wild-type a considerable flux shift occurred from the tricarboxylic acid (TCA) cycle to the oxidative part of the pentose phosphate pathway, including an inversion of the pyruvate kinase flux. The mutant responded very differently to excess of succinate, with a remarkable possible reversal of the TCA cycle. The mutant and the wild-type both showed homeostatic behaviour with respect to the energy charge. In contrast, large changes in redox ratios (NAD(+) /NADH) occurred in the wild-type, while the mutant showed even larger changes. This large redox change can be associated to the reversal of flux directions. The observed large flexibility in the central metabolism following genetic (deletions) and environmental (substrate excess) perturbations of the mutant, indicates that introducing a more efficient succinate exporter could result in an even higher succinate production rate.
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Affiliation(s)
- Hilal Taymaz-Nikerel
- Department of Biotechnology, Delft University of Technology, Kluyver Centre for Genomics of Industrial Fermentation, Julianalaan 67, 2628 BC Delft, The Netherlands. .,Present address: Department of Chemical Engineering, Bogazici University, 34342 Bebek, Istanbul, Turkey.
| | - Marjan De Mey
- Department of Biochemical and Microbial Technology, Centre of Expertise-Industrial Biotechnology and Biocatalysis, Ghent University, Ghent, Belgium
| | - Gino J E Baart
- Department of Applied Mathematics, Biometrics and Process Control, Ghent University, Ghent, Belgium.,Present address: Leuven Institute for Beer Research, CMPG Lab for Genetics and Genomics, University of Leuven, Leuven, Belgium
| | - Jo Maertens
- Department of Biochemical and Microbial Technology, Centre of Expertise-Industrial Biotechnology and Biocatalysis, Ghent University, Ghent, Belgium.,Department of Applied Mathematics, Biometrics and Process Control, Ghent University, Ghent, Belgium
| | - Maria Remedios Foulquié-Moreno
- Department of Applied Biological Sciences, Research Group of Microbiology, Vrije Universiteit Brussel, Brussels, Belgium.,Present address: Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Flanders, Belgium.,Present address: Department of Molecular Microbiology, VIB, Kasteelpark Arenberg 31, Flanders, Belgium
| | - Daniel Charlier
- Department of Applied Biological Sciences, Research Group of Microbiology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Joseph J Heijnen
- Department of Biotechnology, Delft University of Technology, Kluyver Centre for Genomics of Industrial Fermentation, Julianalaan 67, 2628 BC Delft, The Netherlands
| | - Walter M van Gulik
- Department of Biotechnology, Delft University of Technology, Kluyver Centre for Genomics of Industrial Fermentation, Julianalaan 67, 2628 BC Delft, The Netherlands
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24
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Zhang J, Pierick AT, van Rossum HM, Maleki Seifar R, Ras C, Daran JM, Heijnen JJ, Aljoscha Wahl S. Determination of the Cytosolic NADPH/NADP Ratio in Saccharomyces cerevisiae using Shikimate Dehydrogenase as Sensor Reaction. Sci Rep 2015; 5:12846. [PMID: 26243542 PMCID: PMC4525286 DOI: 10.1038/srep12846] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 07/14/2015] [Indexed: 12/04/2022] Open
Abstract
Eukaryotic metabolism is organised in complex networks of enzyme catalysed reactions which are distributed over different organelles. To quantify the compartmentalised reactions, quantitative measurements of relevant physiological variables in different compartments are needed, especially of cofactors. NADP(H) are critical components in cellular redox metabolism. Currently, available metabolite measurement methods allow whole cell measurements. Here a metabolite sensor based on a fast equilibrium reaction is introduced to monitor the cytosolic NADPH/NADP ratio in Saccharomyces cerevisiae: NADP + shikimate ⇄ NADPH + H(+) + dehydroshikimate. The cytosolic NADPH/NADP ratio was determined by measuring the shikimate and dehydroshikimate concentrations (by GC-MS/MS). The cytosolic NADPH/NADP ratio was determined under batch and chemostat (aerobic, glucose-limited, D = 0.1 h(-1)) conditions, to be 22.0 ± 2.6 and 15.6 ± 0.6, respectively. These ratios were much higher than the whole cell NADPH/NADP ratio (1.05 ± 0.08). In response to a glucose pulse, the cytosolic NADPH/NADP ratio first increased very rapidly and restored the steady state ratio after 3 minutes. In contrast to this dynamic observation, the whole cell NADPH/NADP ratio remained nearly constant. The novel cytosol NADPH/NADP measurements provide new insights into the thermodynamic driving forces for NADP(H)-dependent reactions, like amino acid synthesis, product pathways like fatty acid production or the mevalonate pathway.
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Affiliation(s)
- Jinrui Zhang
- Department of Biotechnology, Delft University of Technology, Delft, 2628BC, The Netherlands
| | - Angela ten Pierick
- Department of Biotechnology, Delft University of Technology, Delft, 2628BC, The Netherlands
| | - Harmen M. van Rossum
- Department of Biotechnology, Delft University of Technology, Delft, 2628BC, The Netherlands
| | - Reza Maleki Seifar
- Department of Biotechnology, Delft University of Technology, Delft, 2628BC, The Netherlands
| | - Cor Ras
- Department of Biotechnology, Delft University of Technology, Delft, 2628BC, The Netherlands
| | - Jean-Marc Daran
- Department of Biotechnology, Delft University of Technology, Delft, 2628BC, The Netherlands
| | - Joseph J. Heijnen
- Department of Biotechnology, Delft University of Technology, Delft, 2628BC, The Netherlands
| | - S. Aljoscha Wahl
- Department of Biotechnology, Delft University of Technology, Delft, 2628BC, The Netherlands
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25
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Zhang J, Sassen T, ten Pierick A, Ras C, Heijnen JJ, Wahl SA. A fast sensor for in vivo quantification of cytosolic phosphate in Saccharomyces cerevisiae. Biotechnol Bioeng 2015; 112:1033-46. [PMID: 25502731 DOI: 10.1002/bit.25516] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Revised: 11/13/2014] [Accepted: 12/01/2014] [Indexed: 11/07/2022]
Abstract
Eukaryotic metabolism consists of a complex network of enzymatic reactions and transport processes which are distributed over different subcellular compartments. Currently, available metabolite measurement protocols allow to measure metabolite whole cell amounts which hinder progress to describe the in vivo dynamics in different compartments, which are driven by compartment specific concentrations. Phosphate (Pi) is an essential component for: (1) the metabolic balance of upper and lower glycolytic flux; (2) Together with ATP and ADP determines the phosphorylation energy. Especially, the cytosolic Pi has a critical role in disregulation of glycolysis in tps1 knockout. Here we developed a method that enables us to monitor the cytosolic Pi concentration in S. cerevisiae using an equilibrium sensor reaction: maltose + Pi < = > glucose + glucose-1-phosphate. The required enzyme, maltose phosphorylase from L. sanfranciscensis was overexpressed in S. cerevisiae. With this reaction in place, the cytosolic Pi concentration was obtained from intracellular glucose, G1P and maltose concentrations. The cytosolic Pi concentration was determined in batch and chemostat (D = 0.1 h(-1) ) conditions, which was 17.88 µmol/gDW and 25.02 µmol/gDW, respectively under Pi-excess conditions. Under Pi-limited steady state (D = 0.1 h(-1) ) conditions, the cytosolic Pi concentration dropped to only 17.7% of the cytosolic Pi in Pi-excess condition (4.42 µmol/gDW vs. 25.02 µmol/gDW). In response to a Pi pulse, the cytosolic Pi increased very rapidly, together with the concentration of sugar phosphates. Main sources of the rapid Pi increase are vacuolar Pi (and not the polyPi), as well as Pi uptake from the extracellular space. The temporal increase of cytosolic Pi increases the driving force of GAPDH reaction of the lower glycolytic reactions. The novel cytosol specific Pi concentration measurements provide new insight into the thermodynamic driving force for ATP hydrolysis, GAPDH reaction, and Pi transport over the plasma and vacuolar membranes.
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Affiliation(s)
- Jinrui Zhang
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC, Delft, The Netherlands; Kluyver Centre for Genomics of Industrial Fermentation, 2600 GA, Delft, The Netherlands.
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26
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Perturbation Experiments: Approaches for Metabolic Pathway Analysis in Bioreactors. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2015; 152:91-136. [PMID: 25981857 DOI: 10.1007/10_2015_326] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
In the last decades, targeted metabolic engineering of microbial cells has become one of the major tools in bioprocess design and optimization. For successful application, a detailed knowledge is necessary about the relevant metabolic pathways and their regulation inside the cells. Since in vitro experiments cannot display process conditions and behavior properly, process data about the cells' metabolic state have to be collected in vivo. For this purpose, special techniques and methods are necessary. Therefore, most techniques enabling in vivo characterization of metabolic pathways rely on perturbation experiments, which can be divided into dynamic and steady-state approaches. To avoid any process disturbance, approaches which enable perturbation of cell metabolism in parallel to the continuing production process are reasonable. Furthermore, the fast dynamics of microbial production processes amplifies the need of parallelized data generation. These points motivate the development of a parallelized approach for multiple metabolic perturbation experiments outside the operating production reactor. An appropriate approach for in vivo characterization of metabolic pathways is presented and applied exemplarily to a microbial L-phenylalanine production process on a 15 L-scale.
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Wang G, Tang W, Xia J, Chu J, Noorman H, van Gulik WM. Integration of microbial kinetics and fluid dynamics toward model-driven scale-up of industrial bioprocesses. Eng Life Sci 2014. [DOI: 10.1002/elsc.201400172] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
- Guan Wang
- State Key Laboratory of Bioreactor Engineering; East China University of Science and Technology; Shanghai P. R. China
| | - Wenjun Tang
- State Key Laboratory of Bioreactor Engineering; East China University of Science and Technology; Shanghai P. R. China
| | - Jianye Xia
- State Key Laboratory of Bioreactor Engineering; East China University of Science and Technology; Shanghai P. R. China
| | - Ju Chu
- State Key Laboratory of Bioreactor Engineering; East China University of Science and Technology; Shanghai P. R. China
| | | | - Walter M. van Gulik
- Department of Biotechnology, Kluyver Centre for Genomics of Industrial Fermentation; Delft University of Technology; Delft The Netherlands
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Suarez-Mendez CA, Sousa A, Heijnen JJ, Wahl A. Fast "Feast/Famine" Cycles for Studying Microbial Physiology Under Dynamic Conditions: A Case Study with Saccharomyces cerevisiae. Metabolites 2014; 4:347-72. [PMID: 24957030 PMCID: PMC4101510 DOI: 10.3390/metabo4020347] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Revised: 05/01/2014] [Accepted: 05/06/2014] [Indexed: 01/24/2023] Open
Abstract
Microorganisms are constantly exposed to rapidly changing conditions, under natural as well as industrial production scale environments, especially due to large-scale substrate mixing limitations. In this work, we present an experimental approach based on a dynamic feast/famine regime (400 s) that leads to repetitive cycles with moderate changes in substrate availability in an aerobic glucose cultivation of Saccharomyces cerevisiae. After a few cycles, the feast/famine produced a stable and repetitive pattern with a reproducible metabolic response in time, thus providing a robust platform for studying the microorganism's physiology under dynamic conditions. We found that the biomass yield was slightly reduced (-5%) under the feast/famine regime, while the averaged substrate and oxygen consumption as well as the carbon dioxide production rates were comparable. The dynamic response of the intracellular metabolites showed specific differences in comparison to other dynamic experiments (especially stimulus-response experiments, SRE). Remarkably, the frequently reported ATP paradox observed in single pulse experiments was not present during the repetitive perturbations applied here. We found that intracellular dynamic accumulations led to an uncoupling of the substrate uptake rate (up to 9-fold change at 20 s.) Moreover, the dynamic profiles of the intracellular metabolites obtained with the feast/famine suggest the presence of regulatory mechanisms that resulted in a delayed response. With the feast famine setup many cellular states can be measured at high frequency given the feature of reproducible cycles. The feast/famine regime is thus a versatile platform for systems biology approaches, which can help us to identify and investigate metabolite regulations under realistic conditions (e.g., large-scale bioreactors or natural environments).
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Affiliation(s)
- Camilo A Suarez-Mendez
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands.
| | - Andre Sousa
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands.
| | - Joseph J Heijnen
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands.
| | - Aljoscha Wahl
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands.
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de Jonge L, Heijnen J, van Gulik W. Reconstruction of the oxygen uptake and carbon dioxide evolution rates of microbial cultures at near-neutral pH during highly dynamic conditions. Biochem Eng J 2014. [DOI: 10.1016/j.bej.2013.12.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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van Heerden JH, Wortel MT, Bruggeman FJ, Heijnen JJ, Bollen YJM, Planqué R, Hulshof J, O'Toole TG, Wahl SA, Teusink B. Lost in transition: start-up of glycolysis yields subpopulations of nongrowing cells. Science 2014; 343:1245114. [PMID: 24436182 DOI: 10.1126/science.1245114] [Citation(s) in RCA: 221] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Cells need to adapt to dynamic environments. Yeast that fail to cope with dynamic changes in the abundance of glucose can undergo growth arrest. We show that this failure is caused by imbalanced reactions in glycolysis, the essential pathway in energy metabolism in most organisms. The imbalance arises largely from the fundamental design of glycolysis, making this state of glycolysis a generic risk. Cells with unbalanced glycolysis coexisted with vital cells. Spontaneous, nongenetic metabolic variability among individual cells determines which state is reached and, consequently, which cells survive. Transient ATP (adenosine 5'-triphosphate) hydrolysis through futile cycling reduces the probability of reaching the imbalanced state. Our results reveal dynamic behavior of glycolysis and indicate that cell fate can be determined by heterogeneity purely at the metabolic level.
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Affiliation(s)
- Johan H van Heerden
- Systems Bioinformatics/Amsterdam Institute for Molecules, Medicines and Systems (AIMMS)/Netherlands Institute for Systems Biology, VU University, De Boelelaan 1085, 1081 HV Amsterdam, Netherlands
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Wang G, Chu J, Noorman H, Xia J, Tang W, Zhuang Y, Zhang S. Prelude to rational scale-up of penicillin production: a scale-down study. Appl Microbiol Biotechnol 2014; 98:2359-69. [DOI: 10.1007/s00253-013-5497-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Revised: 12/19/2013] [Accepted: 12/22/2013] [Indexed: 12/16/2022]
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Antoniewicz MR. Dynamic metabolic flux analysis—tools for probing transient states of metabolic networks. Curr Opin Biotechnol 2013; 24:973-8. [DOI: 10.1016/j.copbio.2013.03.018] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2012] [Revised: 03/21/2013] [Accepted: 03/22/2013] [Indexed: 12/16/2022]
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33
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Villafaña-Rojas J, González-Reynoso O, Alcaraz-González V, González-García Y, González-Álvarez V, Solís-Pacheco JR, Aguilar-Uscanga B, Gómez-Hermosillo C. Asymptotic Observers a tool to estimate metabolite concentrations under transient state conditions in biological systems: Determination of intermediate metabolites in the pentose phosphate pathway of Saccharomyces cerevisiae. Chem Eng Sci 2013. [DOI: 10.1016/j.ces.2013.09.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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34
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Spadiut O, Rittmann S, Dietzsch C, Herwig C. Dynamic process conditions in bioprocess development. Eng Life Sci 2013. [DOI: 10.1002/elsc.201200026] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Oliver Spadiut
- Vienna University of Technology; Institute of Chemical Engineering; Research Area Biochemical Engineering; Vienna; Austria
| | - Simon Rittmann
- Vienna University of Technology; Institute of Chemical Engineering; Research Area Biochemical Engineering; Vienna; Austria
| | - Christian Dietzsch
- Vienna University of Technology; Institute of Chemical Engineering; Research Area Biochemical Engineering; Vienna; Austria
| | - Christoph Herwig
- Vienna University of Technology; Institute of Chemical Engineering; Research Area Biochemical Engineering; Vienna; Austria
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35
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An advanced monitoring platform for rational design of recombinant processes. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2012. [PMID: 23207722 DOI: 10.1007/10_2012_169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register]
Abstract
Bioprocess engineering is an application-oriented science in an interdisciplinary environment, and a meaningful combination of different scientific disciplines is the only way to meet the challenges of bioprocess complexity. Setting up a reasoned process monitoring platform is the first step in an iterative procedure aiming at process and systems understanding, being the key to rational and innovative bioprocess design. This chapter describes a comprehensive process monitoring platform and how the resulting knowledge is translated into new strategies in process and/or host cell design.
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Jung JY, Kim TY, Ng CY, Oh MK. Characterization of GCY1 in Saccharomyces cerevisiae by metabolic profiling. J Appl Microbiol 2012; 113:1468-78. [PMID: 22979944 DOI: 10.1111/jam.12013] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Revised: 08/29/2012] [Accepted: 09/07/2012] [Indexed: 12/20/2022]
Abstract
AIMS The analytical study of intracellular (IC) metabolites has developed with advances in chromatography-linked mass spectrometry and fast sampling procedures. We applied the IC metabolite analysis to characterize the role of GCY1 in the glycerol (GLY) catabolic pathway in Saccharomyces cerevisiae. METHODS AND RESULTS Strains with disrupted or overexpressing GLY catabolic genes such as GCY1, DAK1 and DAK2 were constructed. The strains were cultivated under different aeration conditions and quickly quenched using a novel rapid sampling port. IC concentrations of GLY, dihydroxyacetone (DHA), glycerol 3-phosphate and dihydroxyacetone phosphate were analysed in the strains by gas chromatography/mass spectrometry. DHA was not detected in the gcy1 gene-disrupted strain but accumulated 225.91 μmol g DCW(-1) in a DHA kinase gene-deficient strain under micro-aerobic conditions. Additionally, a 16.1% increase in DHA occurred by overexpressing GCY1 in the DHA kinase-deficient strain. CONCLUSIONS Metabolic profiling showed that the GCY1 gene product functions as a GLY dehydrogenase in S. cerevisiae, particularly under micro-aerobic conditions. SIGNIFICANCE AND IMPACT OF THE STUDY Metabolic profiling of the GLY dissimilation pathway was successfully demonstrated in S. cerevisiae, and the function of GCY1 was explained by the results.
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Affiliation(s)
- J-Y Jung
- Department of Chemical and Biological Engineering, Korea University, Seoul, Korea
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37
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Takors R. Scale-up of microbial processes: Impacts, tools and open questions. J Biotechnol 2012; 160:3-9. [DOI: 10.1016/j.jbiotec.2011.12.010] [Citation(s) in RCA: 134] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2011] [Revised: 12/06/2011] [Accepted: 12/13/2011] [Indexed: 11/26/2022]
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Carinhas N, Oliveira R, Alves PM, Carrondo MJ, Teixeira AP. Systems biotechnology of animal cells: the road to prediction. Trends Biotechnol 2012; 30:377-85. [DOI: 10.1016/j.tibtech.2012.03.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Revised: 03/11/2012] [Accepted: 03/14/2012] [Indexed: 12/26/2022]
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Hendrickx DM, Hoefsloot HC, Hendriks MM, Canelas AB, Smilde AK. Global test for metabolic pathway differences between conditions. Anal Chim Acta 2012; 719:8-15. [DOI: 10.1016/j.aca.2011.12.051] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2011] [Revised: 11/30/2011] [Accepted: 12/20/2011] [Indexed: 10/14/2022]
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40
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Kim IK, Roldão A, Siewers V, Nielsen J. A systems-level approach for metabolic engineering of yeast cell factories. FEMS Yeast Res 2012; 12:228-48. [DOI: 10.1111/j.1567-1364.2011.00779.x] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2011] [Revised: 12/05/2011] [Accepted: 12/09/2011] [Indexed: 12/01/2022] Open
Affiliation(s)
- Il-Kwon Kim
- Department of Chemical and Biological Engineering; Chalmers University of Technology; Gothenburg; Sweden
| | - António Roldão
- Department of Chemical and Biological Engineering; Chalmers University of Technology; Gothenburg; Sweden
| | - Verena Siewers
- Department of Chemical and Biological Engineering; Chalmers University of Technology; Gothenburg; Sweden
| | - Jens Nielsen
- Department of Chemical and Biological Engineering; Chalmers University of Technology; Gothenburg; Sweden
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Van Gulik WM, Canelas AB, Taymaz-Nikerel H, Douma RD, de Jonge LP, Heijnen JJ. Fast sampling of the cellular metabolome. Methods Mol Biol 2012; 881:279-306. [PMID: 22639217 DOI: 10.1007/978-1-61779-827-6_10] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Obtaining meaningful snapshots of the metabolome of microorganisms requires rapid sampling and immediate quenching of all metabolic activity, to prevent any changes in metabolite levels after sampling. Furthermore, a suitable extraction method is required ensuring complete extraction of metabolites from the cells and inactivation of enzymatic activity, with minimal degradation of labile compounds. Finally a sensitive, high-throughput analysis platform is needed to quantify a large number of metabolites in a small amount of sample. An issue which has often been overlooked in microbial metabolomics is the fact that many intracellular metabolites are also present in significant amounts outside the cells, and may interfere with the endometabolome measurements. Attempts to remove the extracellular metabolites with dedicated quenching methods often induce release of intracellular metabolites into the quenching solution. For eukaryotic microorganisms, leakage can be minimized by adaptation of the quenching method. For prokaryotic cells this had not yet been accomplished, so the application of a differential method whereby metabolites are measured in the culture supernatant as well as in total broth samples, to calculate the intracellular levels by subtraction, seems to be the most suitable approach. Here we present an overview of different sampling, quenching, and extraction methods developed for microbial metabolomics, described in the literature. Detailed protocols are provided for rapid sampling, quenching, and extraction for measurement of metabolites in total broth samples, washed cell samples and supernatant, to be applied for quantitative metabolomics of both eukaryotic and prokaryotic microorganisms.
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Affiliation(s)
- Walter M Van Gulik
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands.
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42
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de Jonge LP, Buijs NAA, ten Pierick A, Deshmukh A, Zhao Z, Kiel JAKW, Heijnen JJ, van Gulik WM. Scale-down of penicillin production in Penicillium chrysogenum. Biotechnol J 2011; 6:944-58. [PMID: 21751388 DOI: 10.1002/biot.201000409] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
In large-scale production reactors the combination of high broth viscosity and large broth volume leads to insufficient liquid-phase mixing, resulting in gradients in, for example, the concentrations of substrate and oxygen. This often leads to differences in productivity of the full-scale process compared with laboratory scale. In this scale-down study of penicillin production, the influence of substrate gradients on process performance and cell physiology was investigated by imposing an intermittent feeding regime on a laboratory-scale culture of a high yielding strain of Penicillium chrysogenum. It was found that penicillin production was reduced by a factor of two in the intermittently fed cultures relative to constant feed cultivations fed with the same amount of glucose per hour, while the biomass yield was the same. Measurement of the levels of the intermediates of the penicillin biosynthesis pathway, along with the enzyme levels, suggested that the reduction of the flux through the penicillin pathway is mainly the result of a lower influx into the pathway, possibly due to inhibitory levels of adenosine monophosphate and pyrophosphate and lower activating levels of adenosine triphosphate during the zero-substrate phase of each cycle of intermittent feeding.
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Affiliation(s)
- Lodewijk P de Jonge
- Bioprocess Technology, Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
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43
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An in vivo data-driven framework for classification and quantification of enzyme kinetics and determination of apparent thermodynamic data. Metab Eng 2011; 13:294-306. [DOI: 10.1016/j.ymben.2011.02.005] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2010] [Revised: 01/10/2011] [Accepted: 02/15/2011] [Indexed: 01/21/2023]
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Taymaz-Nikerel H, van Gulik WM, Heijnen JJ. Escherichia coli responds with a rapid and large change in growth rate upon a shift from glucose-limited to glucose-excess conditions. Metab Eng 2011; 13:307-18. [PMID: 21439400 DOI: 10.1016/j.ymben.2011.03.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2010] [Revised: 02/24/2011] [Accepted: 03/18/2011] [Indexed: 10/18/2022]
Abstract
Glucose pulse experiments at seconds time scale resolution were performed in aerobic glucose-limited Escherichia coli chemostat cultures. The dynamic responses of oxygen-uptake and growth rate at seconds time scale were determined using a new method based on the dynamic liquid-phase mass balance for oxygen and the pseudo-steady-state ATP balance. Significant fold changes in metabolites (10-1/10) and fluxes (4-1/4) were observed during the short (200 s) period of glucose excess. During glucose excess there was no secretion of by-products and the increased glucose uptake rate led within 40s to a 3.7 fold increase in growth rate. Also within 40-60s a new pseudo-steady-state was reached for both metabolite levels and fluxes. Flux changes of reactions were strongly correlated to the concentrations of involved compounds. Surprisingly the 3.7 fold increase in growth rate and hence protein synthesis rate was not matched by a significant increase in amino acid concentrations. This poses interesting questions for the kinetic factors, which drive protein synthesis by ribosomes.
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Affiliation(s)
- Hilal Taymaz-Nikerel
- Department of Biotechnology, Delft University of Technology, Kluyver Centre for Genomics of Industrial Fermentation, Delft, The Netherlands.
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Dunn WB, Winder CL. Sample preparation related to the intracellular metabolome of yeast methods for quenching, extraction, and metabolite quantitation. Methods Enzymol 2011; 500:277-97. [PMID: 21943903 DOI: 10.1016/b978-0-12-385118-5.00015-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The determination of intracellular metabolite concentrations in Saccharomyces cerevisiae cell systems requires appropriate experimental methods to (a) collect cells and rapidly inhibit metabolism (quenching), (b) fracture cell walls and extract metabolites from within the cellular envelope(s), and (c) detect and quantify metabolites. A range of methods are applied for each of these processes, and no single method is appropriate for all metabolites. For example, the physicochemical diversity of metabolites, including solubility in water or organic solvents, is large. No single extraction solvent is appropriate for all metabolites reported in S. cerevisiae, and multiple solvent systems for extraction employing water, methanol, and chloroform at different pH are recommended for targeted extraction of metabolites. In this chapter, methods for the targeted study of organic acids present in the tricarboxylic acid cycle will be described. These include (a) the quenching of metabolism in batch cell cultures, (b) a single extraction method which provides the extraction of a wide diversity of metabolites, and (c) an analytical method applying gas chromatography-mass spectrometry for targeted analysis of six organic acids present in the tricarboxylic acid cycle metabolic pathway.
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Affiliation(s)
- Warwick B Dunn
- Manchester Centre for Integrative Systems Biology, University of Manchester, Manchester, United Kingdom
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Hendrickx DM, Hendriks MMWB, Eilers PHC, Smilde AK, Hoefsloot HCJ. Reverse engineering of metabolic networks, a critical assessment. MOLECULAR BIOSYSTEMS 2010; 7:511-20. [PMID: 21069230 DOI: 10.1039/c0mb00083c] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Inferring metabolic networks from metabolite concentration data is a central topic in systems biology. Mathematical techniques to extract information about the network from data have been proposed in the literature. This paper presents a critical assessment of the feasibility of reverse engineering of metabolic networks, illustrated with a selection of methods. Appropriate data are simulated to study the performance of four representative methods. An overview of sampling and measurement methods currently in use for generating time-resolved metabolomics data is given and contrasted with the needs of the discussed reverse engineering methods. The results of this assessment show that if full inference of a real-world metabolic network is the goal there is a large discrepancy between the requirements of reverse engineering of metabolic networks and contemporary measurement practice. Recommendations for improved time-resolved experimental designs are given.
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Affiliation(s)
- Diana M Hendrickx
- Biosystems Data Analysis, Swammerdam Institute for Life Sciences, University of Amsterdam, The Netherlands.
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De Mey M, Taymaz-Nikerel H, Baart G, Waegeman H, Maertens J, Heijnen JJ, van Gulik WM. Catching prompt metabolite dynamics in Escherichia coli with the BioScope at oxygen rich conditions. Metab Eng 2010; 12:477-87. [PMID: 20447466 DOI: 10.1016/j.ymben.2010.04.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2010] [Revised: 04/12/2010] [Accepted: 04/26/2010] [Indexed: 11/28/2022]
Abstract
The design and application of a BioScope, a mini plug-flow reactor for carrying out pulse response experiments, specifically designed for Escherichia coli is presented. Main differences with the previous design are an increased volume-specific membrane surface for oxygen transfer and significantly decreased sampling intervals. The characteristics of the new device (pressure drop, residence time distribution, plug-flow behavior and O2 mass transfer) were determined and evaluated. Subsequently, 2.8 mM glucose perturbation experiments on glucose-limited aerobic E. coli chemostat cultures were carried out directly in the chemostat as well as in the BioScope (for two time frames: 8 and 40 s). It was ensured that fully aerobic conditions were maintained during the perturbation experiments. To avoid metabolite leakage during quenching, metabolite quantification (glycolytic and TCA-cycle intermediates and nucleotides) was carried out with a differential method, whereby the amounts measured in the filtrate were subtracted from the amounts measured in total broth. The dynamic metabolite profiles obtained from the BioScope perturbations were very comparable with the profiles obtained from the chemostat perturbation. This agreement demonstrates that the BioScope is a promising device for studying in vivo kinetics in E. coli that shows much faster response (< 10 s) in comparison with eukaryotes.
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Affiliation(s)
- Marjan De Mey
- Department of Biochemical and Microbial Technology, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
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Walther T, Novo M, Rössger K, Létisse F, Loret MO, Portais JC, François JM. Control of ATP homeostasis during the respiro-fermentative transition in yeast. Mol Syst Biol 2010; 6:344. [PMID: 20087341 PMCID: PMC2824524 DOI: 10.1038/msb.2009.100] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2009] [Accepted: 11/07/2009] [Indexed: 11/09/2022] Open
Abstract
Respiring Saccharomyces cerevisiae cells respond to a sudden increase in glucose concentration by a pronounced drop of their adenine nucleotide content ([ATP]+[ADP]+[AMP]=[AXP]). The unknown fate of 'lost' AXP nucleotides represented a long-standing problem for the understanding of the yeast's physiological response to changing growth conditions. Transient accumulation of the purine salvage pathway intermediate, inosine, accounted for the apparent loss of adenine nucleotides. Conversion of AXPs into inosine was facilitated by AMP deaminase, Amd1, and IMP-specific 5'-nucleotidase, Isn1. Inosine recycling into the AXP pool was facilitated by purine nucleoside phosphorylase, Pnp1, and joint action of the phosphoribosyltransferases, Hpt1 and Xpt1. Analysis of changes in 24 intracellular metabolite pools during the respiro-fermentative growth transition in wild-type, amd1, isn1, and pnp1 strains revealed that only the amd1 mutant exhibited significant deviations from the wild-type behavior. Moreover, mutants that were blocked in inosine production exhibited delayed growth acceleration after glucose addition. It is proposed that interconversion of adenine nucleotides and inosine facilitates rapid and energy-cost efficient adaptation of the AXP pool size to changing environmental conditions.
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Affiliation(s)
- Thomas Walther
- Université de Toulouse, INSA, UPS, INP, Toulouse, France.
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Lara AR, Taymaz-Nikerel H, Mashego MR, van Gulik WM, Heijnen JJ, Ramírez OT, van Winden WA. Fast dynamic response of the fermentative metabolism ofEscherichia colito aerobic and anaerobic glucose pulses. Biotechnol Bioeng 2009; 104:1153-61. [DOI: 10.1002/bit.22503] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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