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Kuzmin A, Grigoryeva T, Gorshkov A. Assessment of stable carbon isotope 13С/ 12С ratio in phthalates from surface waters using HPLC-HRMS-TOF approach. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:87734-87742. [PMID: 37430082 DOI: 10.1007/s11356-023-28494-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 06/25/2023] [Indexed: 07/12/2023]
Abstract
A method for estimating the ratio of stable carbon isotopes 13С/12С in the composition of phthalates from surface water at a trace concentration level is proposed. It is based on the concentration of hydrophobic components of water using an analytical reversed phase HPLC column followed by their gradient separation and detection of eluted phthalates using a high-resolution time-of-flight mass spectrometer (ESI-HRMS-TOF) in the form of molecular ions. The ratio of stable carbon isotopes 13С/12C in phthalates is calculated as a ratio of integrals under the monoisotopic [M+1+H]+ and [M+H]+ peaks. The Δ13C value is calculated relatively to the 13C/12C ratio in commercial DnBP and DEHP phthalates used as standards. The minimal concentration of DnBP and DEHP in water required for a reliable determination of Δ13C value is estimated by the level of ca. 0.2 μg L-1. The technique has been verified during the monitoring of priority phthalates in the waters of Lake Baikal.
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Affiliation(s)
- Anton Kuzmin
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences, 3 Ulan-Batorskaya Str, 664033, Irkutsk, Russia.
| | - Tatyana Grigoryeva
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences, 3 Ulan-Batorskaya Str, 664033, Irkutsk, Russia
| | - Alexander Gorshkov
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences, 3 Ulan-Batorskaya Str, 664033, Irkutsk, Russia
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2
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Richter C, Grafahrend-Belau E, Ziegler J, Raorane ML, Junker BH. Improved 13C metabolic flux analysis in Escherichia coli metabolism: application of a high-resolution MS (GC-EI-QTOF) for comprehensive assessment of MS/MS fragments. J Ind Microbiol Biotechnol 2023; 50:kuad039. [PMID: 37960978 PMCID: PMC10716738 DOI: 10.1093/jimb/kuad039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 11/10/2023] [Indexed: 11/15/2023]
Abstract
Gas chromatography-tandem mass spectrometry with electron ionization (GC-EI-MS/MS) provides rich information on stable-isotope labeling for 13C-metabolic flux analysis (13C-MFA). To pave the way for the routine application of tandem MS data for metabolic flux quantification, we aimed to compile a comprehensive library of GC-EI-MS/MS fragments of tert-butyldimethylsilyl (TBDMS) derivatized proteinogenic amino acids. First, we established an analytical workflow that combines high-resolution gas chromatography-quadrupole time-of-flight mass spectrometry and fully 13C-labeled biomass to identify and structurally elucidate tandem MS amino acid fragments. Application of the high-mass accuracy MS procedure resulted into the identification of 129 validated precursor-product ion pairs of 13 amino acids with 30 fragments being accepted for 13C-MFA. The practical benefit of the novel tandem MS data was demonstrated by a proof-of-concept study, which confirmed the importance of the compiled library for high-resolution 13C-MFA. ONE SENTENCE SUMMARY An analytical workflow that combines high-resolution mass spectrometry (MS) and fully 13C-labeled biomass to identify and structurally elucidate tandem MS amino acid fragments, which provide positional information and therefore offering significant advantages over traditional MS to improve 13C-metabolic flux analysis.
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Affiliation(s)
- Chris Richter
- Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Hoher Weg 8, D-06120Halle (Saale), Germany
| | - Eva Grafahrend-Belau
- Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Hoher Weg 8, D-06120Halle (Saale), Germany
| | - Jörg Ziegler
- Leibniz Institute of Plant Biochemistry, Weinberg 3, D-06120Halle (Saale), Germany
| | - Manish L Raorane
- Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Hoher Weg 8, D-06120Halle (Saale), Germany
| | - Björn H Junker
- Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Hoher Weg 8, D-06120Halle (Saale), Germany
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3
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Wang Q, Kalathil S, Pornrungroj C, Sahm CD, Reisner E. Bacteria–photocatalyst sheet for sustainable carbon dioxide utilization. Nat Catal 2022. [DOI: 10.1038/s41929-022-00817-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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4
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Correa SM, Fernie AR, Nikoloski Z, Brotman Y. Towards model-driven characterization and manipulation of plant lipid metabolism. Prog Lipid Res 2020; 80:101051. [PMID: 32640289 DOI: 10.1016/j.plipres.2020.101051] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 06/20/2020] [Accepted: 06/21/2020] [Indexed: 01/09/2023]
Abstract
Plant lipids have versatile applications and provide essential fatty acids in human diet. Therefore, there has been a growing interest to better characterize the genetic basis, regulatory networks, and metabolic pathways that shape lipid quantity and composition. Addressing these issues is challenging due to context-specificity of lipid metabolism integrating environmental, developmental, and tissue-specific cues. Here we systematically review the known metabolic pathways and regulatory interactions that modulate the levels of storage lipids in oilseeds. We argue that the current understanding of lipid metabolism provides the basis for its study in the context of genome-wide plant metabolic networks with the help of approaches from constraint-based modeling and metabolic flux analysis. The focus is on providing a comprehensive summary of the state-of-the-art of modeling plant lipid metabolic pathways, which we then contrast with the existing modeling efforts in yeast and microalgae. We then point out the gaps in knowledge of lipid metabolism, and enumerate the recent advances of using genome-wide association and quantitative trait loci mapping studies to unravel the genetic regulations of lipid metabolism. Finally, we offer a perspective on how advances in the constraint-based modeling framework can propel further characterization of plant lipid metabolism and its rational manipulation.
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Affiliation(s)
- Sandra M Correa
- Genetics of Metabolic Traits Group, Max Planck Institute for Molecular Plant Physiology, Potsdam 14476, Germany; Department of Life Sciences, Ben-Gurion University of the Negev, 8410501 Beer-Sheva, Israel; Departamento de Ciencias Exactas y Naturales, Universidad de Antioquia, Medellín 050010, Colombia.
| | - Alisdair R Fernie
- Central Metabolism Group, Max Planck Institute for Molecular Plant Physiology, Potsdam 14476, Germany; Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria
| | - Zoran Nikoloski
- Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria; Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany; Systems Biology and Mathematical Modelling Group, Max Planck Institute for Molecular Plant Physiology, Potsdam-Golm 14476, Germany.
| | - Yariv Brotman
- Genetics of Metabolic Traits Group, Max Planck Institute for Molecular Plant Physiology, Potsdam 14476, Germany; Department of Life Sciences, Ben-Gurion University of the Negev, 8410501 Beer-Sheva, Israel
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5
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Schlicker L, Boers HM, Dudek CA, Zhao G, Barua A, Trezzi JP, Meyer-Hermann M, Jacobs DM, Hiller K. Postprandial Metabolic Effects of Fiber Mixes Revealed by in vivo Stable Isotope Labeling in Humans. Metabolites 2019; 9:metabo9050091. [PMID: 31067731 PMCID: PMC6571904 DOI: 10.3390/metabo9050091] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 05/02/2019] [Accepted: 05/05/2019] [Indexed: 12/22/2022] Open
Abstract
Food supplementation with a fiber mix of guar gum and chickpea flour represents a promising approach to reduce the risk of type 2 diabetes mellitus (T2DM) by attenuating postprandial glycemia. To investigate the effects on postprandial metabolic fluxes of glucose-derived metabolites in response to this fiber mix, a randomized, cross-over study was designed. Twelve healthy, male subjects consumed three different flatbreads either supplemented with 2% guar gum or 4% guar gum and 15% chickpea flour or without supplementation (control). The flatbreads were enriched with ~2% of 13C-labeled wheat flour. Blood was collected at 16 intervals over a period of 360 min after bread intake and plasma samples were analyzed by GC-MS based metabolite profiling combined with stable isotope-assisted metabolomics. Although metabolite levels of the downstream metabolites of glucose, specifically lactate and alanine, were not altered in response to the fiber mix, supplementation of 4% guar gum was shown to significantly delay and reduce the exogenous formation of these metabolites. Metabolic modeling and computation of appearance rates revealed that the effects induced by the fiber mix were strongest for glucose and attenuated downstream of glucose. Further investigations to explore the potential of fiber mix supplementation to counteract the development of metabolic diseases are warranted.
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Affiliation(s)
- Lisa Schlicker
- Department for Bioinformatics and Biochemistry, BRICS, Technische Universität Braunschweig, Rebenring 56, 38106 Braunschweig, Germany.
| | - Hanny M Boers
- Unilever R&D Vlaardingen, Olivier van Noortlaan 120, 3133 AT Vlaardingen, The Netherlands.
| | - Christian-Alexander Dudek
- Department for Bioinformatics and Biochemistry, BRICS, Technische Universität Braunschweig, Rebenring 56, 38106 Braunschweig, Germany.
| | - Gang Zhao
- Department of Systems Immunology and Braunschweig Integrated Centre of Systems Biology, Helmholtz Centre for Infection Research, Rebenring 56, 38106 Braunschweig, Germany.
- Centre for Individualised Infection Medicine (CIIM), Feodor-Lynen-Straße 15, 30625 Hannover, Germany.
| | - Arnab Barua
- Department of Systems Immunology and Braunschweig Integrated Centre of Systems Biology, Helmholtz Centre for Infection Research, Rebenring 56, 38106 Braunschweig, Germany.
- Centre for Individualised Infection Medicine (CIIM), Feodor-Lynen-Straße 15, 30625 Hannover, Germany.
| | - Jean-Pierre Trezzi
- Integrated Biobank of Luxembourg, Luxembourg Institute of Health, 1 rue Louis Rech, 3555 Dudelange, Luxembourg.
- Luxembourg Centre for Systems Biomedicine, Université du Luxembourg, 7 avenue des Hauts-Fourneaux, 4362 Esch-sur-Alzette, Luxembourg.
| | - Michael Meyer-Hermann
- Department of Systems Immunology and Braunschweig Integrated Centre of Systems Biology, Helmholtz Centre for Infection Research, Rebenring 56, 38106 Braunschweig, Germany.
- Centre for Individualised Infection Medicine (CIIM), Feodor-Lynen-Straße 15, 30625 Hannover, Germany.
- Institute of Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany.
| | - Doris M Jacobs
- Unilever R&D Vlaardingen, Olivier van Noortlaan 120, 3133 AT Vlaardingen, The Netherlands.
| | - Karsten Hiller
- Department for Bioinformatics and Biochemistry, BRICS, Technische Universität Braunschweig, Rebenring 56, 38106 Braunschweig, Germany.
- Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124 Braunschweig, Germany.
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6
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A guide to 13C metabolic flux analysis for the cancer biologist. Exp Mol Med 2018; 50:1-13. [PMID: 29657327 PMCID: PMC5938039 DOI: 10.1038/s12276-018-0060-y] [Citation(s) in RCA: 162] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 12/21/2017] [Indexed: 01/15/2023] Open
Abstract
Cancer metabolism is significantly altered from normal cellular metabolism allowing cancer cells to adapt to changing microenvironments and maintain high rates of proliferation. In the past decade, stable-isotope tracing and network analysis have become powerful tools for uncovering metabolic pathways that are differentially activated in cancer cells. In particular, 13C metabolic flux analysis (13C-MFA) has emerged as the primary technique for quantifying intracellular fluxes in cancer cells. In this review, we provide a practical guide for investigators interested in getting started with 13C-MFA. We describe best practices in 13C-MFA, highlight potential pitfalls and alternative approaches, and conclude with new developments that can further enhance our understanding of cancer metabolism. Tracing tagged molecules can help researchers understand the altered metabolism of cancer cells. The abilities of cancer cells to multiply rapidly and invade new tissues are supported by metabolic alterations, which can be investigated by feeding tagged molecules to cells and tracing how they are metabolized. These techniques, such as 13C metabolic flux analysis (13C-MFA), have been perceived as difficult to use, but recent advances are making them more accessible. Maciek Antoniewicz, University of Delaware, Newark, USA, has published a practical guide for researchers wanting to use 13C-MFA. The review includes best practices, pitfalls, alternative approaches, and new developments, especially new user-friendly software that allows researchers without extensive training in mathematics, statistics, or coding to perform 13C-MFA. Broadening access to tools for investigating altered metabolic pathways may spur development of new cancer therapies targeting these pathways.
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7
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Golubeva LI, Shupletsov MS, Mashko SV. Metabolic Flux Analysis Using 13C Isotopes (13C-MFA). 1. Experimental Basis of the Method and the Present State of Investigations. APPL BIOCHEM MICRO+ 2018. [DOI: 10.1134/s0003683817070031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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8
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Matsuda F, Toya Y, Shimizu H. Learning from quantitative data to understand central carbon metabolism. Biotechnol Adv 2017; 35:971-980. [DOI: 10.1016/j.biotechadv.2017.09.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 09/01/2017] [Accepted: 09/14/2017] [Indexed: 12/23/2022]
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9
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Funk AM, Anderson BL, Wen X, Hever T, Khemtong C, Kovacs Z, Sherry AD, Malloy CR. The rate of lactate production from glucose in hearts is not altered by per-deuteration of glucose. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2017; 284:86-93. [PMID: 28972888 PMCID: PMC5817885 DOI: 10.1016/j.jmr.2017.09.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 09/13/2017] [Accepted: 09/14/2017] [Indexed: 05/05/2023]
Abstract
This study was designed to determine whether perdeuterated glucose experiences a kinetic isotope effect (KIE) as glucose passes through glycolysis and is further oxidized in the tricarboxylic acid (TCA) cycle. Metabolism of deuterated glucose was investigated in two groups of perfused rat hearts. The control group was supplied with a 1:1 mixture of [U-13C6]glucose and [1,6-13C2]glucose, while the experimental group received [U-13C6,U-2H7]glucose and [1,6-13C2]glucose. Tissue extracts were analyzed by 1H, 2H and proton-decoupled 13C NMR spectroscopy. Extensive 2H-13C scalar coupling plus chemical shift isotope effects were observed in the proton-decoupled 13C NMR spectra of lactate, alanine and glutamate. A small but measureable (∼8%) difference in the rate of conversion of [U-13C6]glucose vs. [1,6-13C2]glucose to lactate, likely reflecting rates of CC bond breakage in the aldolase reaction, but conversion of [U-13C6]glucose versus [U-13C6,U-2H7]glucose to lactate did not differ. This shows that the presence of deuterium in glucose does not alter glycolytic flux. However, there were two distinct effects of deuteration on metabolism of glucose to alanine and oxidation of glucose in the TCA. First, alanine undergoes extensive exchange of methyl deuterons with solvent protons in the alanine amino transferase reaction. Second, there is a substantial kinetic isotope effect in metabolism of [U-13C6,U-2H7]glucose to alanine and glutamate. In the presence of [U-13C6,U-2H7]glucose, alanine and lactate are not in rapid exchange with the same pool of pyruvate. These studies indicate that the appearance of hyperpolarized 13C-lactate from hyperpolarized [U-13C6,U-2H7]glucose is not substantially influenced by a deuterium kinetic isotope effect.
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Affiliation(s)
- Alexander M Funk
- Advanced Imaging Research Center, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Brian L Anderson
- Advanced Imaging Research Center, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Xiaodong Wen
- Advanced Imaging Research Center, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Thomas Hever
- Advanced Imaging Research Center, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Chalermchai Khemtong
- Advanced Imaging Research Center, University of Texas Southwestern Medical Center, Dallas, TX, United States; Department of Radiology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Zoltan Kovacs
- Advanced Imaging Research Center, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - A Dean Sherry
- Advanced Imaging Research Center, University of Texas Southwestern Medical Center, Dallas, TX, United States; Department of Radiology, University of Texas Southwestern Medical Center, Dallas, TX, United States; Department of Chemistry, University of Texas at Dallas, Richardson, TX, United States
| | - Craig R Malloy
- Advanced Imaging Research Center, University of Texas Southwestern Medical Center, Dallas, TX, United States; Department of Radiology, University of Texas Southwestern Medical Center, Dallas, TX, United States; Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, United States; Veterans Affairs North Texas Healthcare System, Dallas, TX, United States.
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10
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Liu N, Qiao K, Stephanopoulos G. 13C Metabolic Flux Analysis of acetate conversion to lipids by Yarrowia lipolytica. Metab Eng 2016; 38:86-97. [DOI: 10.1016/j.ymben.2016.06.006] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 06/17/2016] [Accepted: 06/20/2016] [Indexed: 12/18/2022]
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11
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Okahashi N, Kawana S, Iida J, Shimizu H, Matsuda F. GC-MS/MS survey of collision-induced dissociation of tert-butyldimethylsilyl-derivatized amino acids and its application to (13)C-metabolic flux analysis of Escherichia coli central metabolism. Anal Bioanal Chem 2016; 408:6133-40. [PMID: 27342798 DOI: 10.1007/s00216-016-9724-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 06/13/2016] [Accepted: 06/14/2016] [Indexed: 12/31/2022]
Abstract
Stable isotope labeling experiments using mass spectrometry have been employed to investigate carbon flow levels (metabolic flux) in mammalian, plant, and microbial cells. To achieve a more precise (13)C-metabolic flux analysis ((13)C-MFA), novel fragmentations of tert-butyldimethylsilyl (TBDMS)-amino acids were investigated by gas chromatography-tandem mass spectrometry (GC-MS/MS). The product ion scan analyses of 15 TBDMS-amino acids revealed 24 novel fragment ions. The amino acid-derived carbons included in the five fragment ions were identified by the analyses of (13)C-labeled authentic standards. The identification of the fragment ion at m/z 170 indicated that the isotopic abundance of S-methyl carbon in methionine could be determined from the cleavage of C5 in the precursor of [M-159](+) (m/z 218). It was also confirmed that the precision of (13)C-MFA in Escherichia coli central carbon metabolism could be improved by introducing (13)C-labeling data derived from novel fragmentations. Graphical Abstract Novel collision-induced dissociation fragmentations of tert-butyldimethylsilyl amino acids were investigated and identified by GC-MS/MS.
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Affiliation(s)
- Nobuyuki Okahashi
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Shuichi Kawana
- Analytical and Measuring Instruments Division, Shimadzu Corporation, 1 Nishinokyo Kuwabara-cho, Nakagyo-ku, Kyoto, 604-8511, Japan
| | - Junko Iida
- Analytical and Measuring Instruments Division, Shimadzu Corporation, 1 Nishinokyo Kuwabara-cho, Nakagyo-ku, Kyoto, 604-8511, Japan.,Osaka University Shimadzu Analytical Innovation Research Laboratory, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Hiroshi Shimizu
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Fumio Matsuda
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan.
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12
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Sandberg TE, Long CP, Gonzalez JE, Feist AM, Antoniewicz MR, Palsson BO. Evolution of E. coli on [U-13C]Glucose Reveals a Negligible Isotopic Influence on Metabolism and Physiology. PLoS One 2016; 11:e0151130. [PMID: 26964043 PMCID: PMC4786092 DOI: 10.1371/journal.pone.0151130] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 02/24/2016] [Indexed: 12/16/2022] Open
Abstract
13C-Metabolic flux analysis (13C-MFA) traditionally assumes that kinetic isotope effects from isotopically labeled compounds do not appreciably alter cellular growth or metabolism, despite indications that some biochemical reactions can be non-negligibly impacted. Here, populations of Escherichia coli were adaptively evolved for ~1000 generations on uniformly labeled 13C-glucose, a commonly used isotope for 13C-MFA. Phenotypic characterization of these evolved strains revealed ~40% increases in growth rate, with no significant difference in fitness when grown on either labeled (13C) or unlabeled (12C) glucose. The evolved strains displayed decreased biomass yields, increased glucose and oxygen uptake, and increased acetate production, mimicking what is observed after adaptive evolution on unlabeled glucose. Furthermore, full genome re-sequencing revealed that the key genetic changes underlying these phenotypic alterations were essentially the same as those acquired during adaptive evolution on unlabeled glucose. Additionally, glucose competition experiments demonstrated that the wild-type exhibits no isotopic preference for unlabeled glucose, and the evolved strains have no preference for labeled glucose. Overall, the results of this study indicate that there are no significant differences between 12C and 13C-glucose as a carbon source for E. coli growth.
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Affiliation(s)
- Troy E. Sandberg
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, United States of America
| | - Christopher P. Long
- Department of Chemical and Biomolecular Engineering, Metabolic Engineering and Systems Biology Laboratory, University of Delaware, Newark, DE, 19716, United States of America
| | - Jacqueline E. Gonzalez
- Department of Chemical and Biomolecular Engineering, Metabolic Engineering and Systems Biology Laboratory, University of Delaware, Newark, DE, 19716, United States of America
| | - Adam M. Feist
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, United States of America
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Lyngby, Denmark
| | - Maciek R. Antoniewicz
- Department of Chemical and Biomolecular Engineering, Metabolic Engineering and Systems Biology Laboratory, University of Delaware, Newark, DE, 19716, United States of America
| | - Bernhard O. Palsson
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, United States of America
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Lyngby, Denmark
- * E-mail:
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13
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Millard P, Portais JC, Mendes P. Impact of kinetic isotope effects in isotopic studies of metabolic systems. BMC SYSTEMS BIOLOGY 2015; 9:64. [PMID: 26410690 PMCID: PMC4583766 DOI: 10.1186/s12918-015-0213-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 09/19/2015] [Indexed: 12/30/2022]
Abstract
Background Isotope labeling experiments (ILEs) are increasingly used to investigate the functioning of metabolic systems. Some enzymes are subject to kinetic isotope effects (KIEs) which modulate reaction rates depending on the isotopic composition of their substrate(s). KIEs may therefore affect both the propagation of isotopes through metabolic networks and their operation, and ultimately jeopardize the biological value of ILEs. However, the actual impact of KIEs on metabolism has never been investigated at the system level. Results First, we developed a framework which integrates KIEs into kinetic and isotopic models of metabolism, thereby accounting for their system-wide effects on metabolite concentrations, metabolic fluxes, and isotopic patterns. Then, we applied this framework to assess the impact of KIEs on the central carbon metabolism of Escherichia coli in the context of 13C-ILEs, under different situations commonly encountered in laboratories. Results showed that the impact of KIEs strongly depends on the label input and on the variable considered but is significantly lower than expected intuitively from measurements on isolated enzymes. The global robustness of both the metabolic operation and isotopic patterns largely emerge from intrinsic properties of metabolic networks, such as the distribution of control across the network and bidirectional isotope exchange. Conclusions These results demonstrate the necessity of investigating the impact of KIEs at the level of the entire system, contradict previous hypotheses that KIEs would have a strong effect on isotopic distributions and on flux determination, and strengthen the biological value of 13C-ILEs. The proposed modeling framework is generic and can be used to investigate the impact of all the isotopic tracers (2H, 13C, 15N, 18O, etc.) on different isotopic datasets and metabolic systems. By allowing the integration of isotopic and metabolomics data collected under stationary and/or non-stationary conditions, it may also assist interpretations of ILEs and facilitate the development of more accurate kinetic models with improved explicative and predictive capabilities. Electronic supplementary material The online version of this article (doi:10.1186/s12918-015-0213-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Pierre Millard
- MCISB, Manchester Institute of Biotechnology, University of Manchester, Manchester, UK. .,School of Computer Science, University of Manchester, Manchester, UK. .,Université de Toulouse; INSA, UPS, INP; LISBP, Toulouse, France. .,INRA, UMR792, Ingénierie des Systèmes Biologiques et des Procédés, Toulouse, France. .,CNRS, UMR5504, Toulouse, France.
| | - Jean-Charles Portais
- Université de Toulouse; INSA, UPS, INP; LISBP, Toulouse, France. .,INRA, UMR792, Ingénierie des Systèmes Biologiques et des Procédés, Toulouse, France. .,CNRS, UMR5504, Toulouse, France.
| | - Pedro Mendes
- MCISB, Manchester Institute of Biotechnology, University of Manchester, Manchester, UK. .,School of Computer Science, University of Manchester, Manchester, UK. .,Center for Quantitative Medicine and Department of Cell Biology, UConn Health, Farmington, Connecticut, USA.
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14
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Allen DK, Bates PD, Tjellström H. Tracking the metabolic pulse of plant lipid production with isotopic labeling and flux analyses: Past, present and future. Prog Lipid Res 2015; 58:97-120. [PMID: 25773881 DOI: 10.1016/j.plipres.2015.02.002] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 01/30/2015] [Accepted: 02/11/2015] [Indexed: 11/25/2022]
Abstract
Metabolism is comprised of networks of chemical transformations, organized into integrated biochemical pathways that are the basis of cellular operation, and function to sustain life. Metabolism, and thus life, is not static. The rate of metabolites transitioning through biochemical pathways (i.e., flux) determines cellular phenotypes, and is constantly changing in response to genetic or environmental perturbations. Each change evokes a response in metabolic pathway flow, and the quantification of fluxes under varied conditions helps to elucidate major and minor routes, and regulatory aspects of metabolism. To measure fluxes requires experimental methods that assess the movements and transformations of metabolites without creating artifacts. Isotopic labeling fills this role and is a long-standing experimental approach to identify pathways and quantify their metabolic relevance in different tissues or under different conditions. The application of labeling techniques to plant science is however far from reaching it potential. In light of advances in genetics and molecular biology that provide a means to alter metabolism, and given recent improvements in instrumentation, computational tools and available isotopes, the use of isotopic labeling to probe metabolism is becoming more and more powerful. We review the principal analytical methods for isotopic labeling with a focus on seminal studies of pathways and fluxes in lipid metabolism and carbon partitioning through central metabolism. Central carbon metabolic steps are directly linked to lipid production by serving to generate the precursors for fatty acid biosynthesis and lipid assembly. Additionally some of the ideas for labeling techniques that may be most applicable for lipid metabolism in the future were originally developed to investigate other aspects of central metabolism. We conclude by describing recent advances that will play an important future role in quantifying flux and metabolic operation in plant tissues.
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Affiliation(s)
- Doug K Allen
- United States Department of Agriculture, Agricultural Research Service, 975 North Warson Road, St. Louis, MO 63132, United States; Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO 63132, United States.
| | - Philip D Bates
- Department of Chemistry and Biochemistry, University of Southern Mississippi, Hattiesburg, MS 39406, United States
| | - Henrik Tjellström
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, United States; Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI 48824, United States
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15
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Wasylenko TM, Ahn WS, Stephanopoulos G. The oxidative pentose phosphate pathway is the primary source of NADPH for lipid overproduction from glucose in Yarrowia lipolytica. Metab Eng 2015; 30:27-39. [PMID: 25747307 DOI: 10.1016/j.ymben.2015.02.007] [Citation(s) in RCA: 203] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 02/21/2015] [Indexed: 12/26/2022]
Abstract
Oleaginous microbes represent an attractive means of converting a diverse range of feedstocks into oils that can be transesterified to biodiesel. However, the mechanism of lipid overproduction in these organisms is incompletely understood, hindering the development of strategies for engineering superior biocatalysts for "single-cell oil" production. In particular, it is unclear which pathways are used to generate the large quantities of NADPH required for overproduction of the highly reduced fatty acid species. While early studies implicated malic enzyme as having a key role in production of lipogenic NADPH in oleaginous fungi, several recent reports have cast doubts as to whether malic enzyme may contribute to production of lipogenic NADPH in the model oleaginous yeast Yarrowia lipolytica. To address this problem we have used (13)C-Metabolic Flux Analysis to estimate the metabolic flux distributions during lipid accumulation in two Y. lipolytica strains; a control strain and a previously published engineered strain capable of producing lipids at roughly twice the yield. We observe a dramatic rearrangement of the metabolic flux distribution in the engineered strain which supports lipid overproduction. The NADPH-producing flux through the oxidative Pentose Phosphate Pathway is approximately doubled in the engineered strain in response to the roughly two-fold increase in fatty acid biosynthesis, while the flux through malic enzyme does not differ significantly between the two strains. Moreover, the estimated rate of NADPH production in the oxidative Pentose Phosphate Pathway is in good agreement with the estimated rate of NADPH consumption in fatty acid biosynthesis in both strains. These results suggest the oxidative Pentose Phosphate Pathway is the primary source of lipogenic NADPH in Y. lipolytica.
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Affiliation(s)
- Thomas M Wasylenko
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Woo Suk Ahn
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Gregory Stephanopoulos
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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16
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Wasylenko TM, Stephanopoulos G. Metabolomic and (13)C-metabolic flux analysis of a xylose-consuming Saccharomyces cerevisiae strain expressing xylose isomerase. Biotechnol Bioeng 2014; 112:470-83. [PMID: 25311863 DOI: 10.1002/bit.25447] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 08/11/2014] [Accepted: 08/27/2014] [Indexed: 11/09/2022]
Abstract
Over the past two decades, significant progress has been made in the engineering of xylose-consuming Saccharomyces cerevisiae strains for production of lignocellulosic biofuels. However, the ethanol productivities achieved on xylose are still significantly lower than those observed on glucose for reasons that are not well understood. We have undertaken an analysis of central carbon metabolite pool sizes and metabolic fluxes on glucose and on xylose under aerobic and anaerobic conditions in a strain capable of rapid xylose assimilation via xylose isomerase in order to investigate factors that may limit the rate of xylose fermentation. We find that during xylose utilization the flux through the non-oxidative Pentose Phosphate Pathway (PPP) is high but the flux through the oxidative PPP is low, highlighting an advantage of the strain employed in this study. Furthermore, xylose fails to elicit the full carbon catabolite repression response that is characteristic of glucose fermentation in S. cerevisiae. We present indirect evidence that the incomplete activation of the fermentation program on xylose results in a bottleneck in lower glycolysis, leading to inefficient re-oxidation of NADH produced in glycolysis.
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Affiliation(s)
- Thomas M Wasylenko
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, 02139, Massachussetts
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17
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Shupletsov MS, Golubeva LI, Rubina SS, Podvyaznikov DA, Iwatani S, Mashko SV. OpenFLUX2: (13)C-MFA modeling software package adjusted for the comprehensive analysis of single and parallel labeling experiments. Microb Cell Fact 2014; 13:152. [PMID: 25408234 PMCID: PMC4263107 DOI: 10.1186/s12934-014-0152-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Accepted: 10/18/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Steady-state (13)C-based metabolic flux analysis ((13)C-MFA) is the most powerful method available for the quantification of intracellular fluxes. These analyses include concertedly linked experimental and computational stages: (i) assuming the metabolic model and optimizing the experimental design; (ii) feeding the investigated organism using a chosen (13)C-labeled substrate (tracer); (iii) measuring the extracellular effluxes and detecting the (13)C-patterns of intracellular metabolites; and (iv) computing flux parameters that minimize the differences between observed and simulated measurements, followed by evaluating flux statistics. In its early stages, (13)C-MFA was performed on the basis of data obtained in a single labeling experiment (SLE) followed by exploiting the developed high-performance computational software. Recently, the advantages of parallel labeling experiments (PLEs), where several LEs are conducted under the conditions differing only by the tracer(s) choice, were demonstrated, particularly with regard to improving flux precision due to the synergy of complementary information. The availability of an open-source software adjusted for PLE-based (13)C-MFA is an important factor for PLE implementation. RESULTS The open-source software OpenFLUX, initially developed for the analysis of SLEs, was extended for the computation of PLE data. Using the OpenFLUX2, in silico simulation confirmed that flux precision is improved when (13)C-MFA is implemented by fitting PLE data to the common model compared with SLE-based analysis. Efficient flux resolution could be achieved in the PLE-mediated analysis when the choice of tracer was based on an experimental design computed to minimize the flux variances from different parts of the metabolic network. The analysis provided by OpenFLUX2 mainly includes (i) the optimization of the experimental design, (ii) the computation of the flux parameters from LEs data, (iii) goodness-of-fit testing of the model's adequacy, (iv) drawing conclusions concerning the identifiability of fluxes and construction of a contribution matrix reflecting the relative contribution of the measurement variances to the flux variances, and (v) precise determination of flux confidence intervals using a fine-tunable and convergence-controlled Monte Carlo-based method. CONCLUSIONS The developed open-source OpenFLUX2 provides a friendly software environment that facilitates beginners and existing OpenFLUX users to implement LEs for steady-state (13)C-MFA including experimental design, quantitative evaluation of flux parameters and statistics.
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Affiliation(s)
- Mikhail S Shupletsov
- Ajinomoto-Genetika Research Institute, 117545, Moscow, Russian Federation. .,Computational Mathematics and Cybernetics Department, Lomonosov Moscow State University, 119991, Moscow, Russian Federation.
| | - Lyubov I Golubeva
- Ajinomoto-Genetika Research Institute, 117545, Moscow, Russian Federation.
| | - Svetlana S Rubina
- Ajinomoto-Genetika Research Institute, 117545, Moscow, Russian Federation.
| | - Dmitry A Podvyaznikov
- Ajinomoto-Genetika Research Institute, 117545, Moscow, Russian Federation. .,Department of Theoretical and Experimental Physics, Moscow Physical Engineering Institute (Technical University), 115409, Moscow, Russian Federation.
| | - Shintaro Iwatani
- Ajinomoto-Genetika Research Institute, 117545, Moscow, Russian Federation. .,Present address: Fermentation Group, Process Industrialization Section, Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., 840-2193, SAGA, Saga-shi, Morodomi-cho, 450 Morodomitsu, Japan.
| | - Sergey V Mashko
- Ajinomoto-Genetika Research Institute, 117545, Moscow, Russian Federation. .,Department of Theoretical and Experimental Physics, Moscow Physical Engineering Institute (Technical University), 115409, Moscow, Russian Federation. .,Biological Department, Lomonosov Moscow State University, 119991, Moscow, Russian Federation.
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18
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Mattanovich D, Hatzimanikatis V. Editorial: metabolic modeling in biotechnology and medical research. Biotechnol J 2014; 8:962-3. [PMID: 24031032 DOI: 10.1002/biot.201300378] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Metabolic Modeling and Simulation: This special issue of Biotechnology Journal is edited by Diethard Mattanovich and Vassily Hatzimanikatis and covers the state-of-the-art in metabolic modeling, including the major themes of methods in metabolic modeling, modeling of human and microbial metabolism, and modeling of bioprocesses.
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Affiliation(s)
- Diethard Mattanovich
- Department of Biotechnology, University of Natural Resources and Life Sciences Vienna, Austria; Austrian Centre of Industrial Biotechnology, Vienna, Austria.
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19
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Nargund S, Misra A, Zhang X, Coleman GD, Sriram G. Flux and reflux: metabolite reflux in plant suspension cells and its implications for isotope-assisted metabolic flux analysis. MOLECULAR BIOSYSTEMS 2014; 10:1496-508. [PMID: 24675729 DOI: 10.1039/c3mb70348g] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Isotope-assisted metabolic flux analysis (MFA) is a powerful methodology to quantify intracellular fluxes via isotope labeling experiments (ILEs). In batch cultures, which are often convenient, inexpensive or inevitable especially for eukaryotic systems, MFA is complicated by the presence of the initially present biomass. This unlabeled biomass may either mix with the newly synthesized labeled biomass or reflux into the metabolic network, thus masking the true labeling patterns in the newly synthesized biomass. Here, we report a detailed investigation of such metabolite reflux in cell suspensions of the tree poplar. In ILEs supplying 28% or 98% U-(13)C glucose as the sole organic carbon source, biomass components exhibited lower (13)C enrichments than the supplied glucose as well as anomalous isotopomers not explainable by simple mixing of the initial and newly synthesized biomass. These anomalous labeling patterns were most prominent in a 98% U-(13)C glucose ILE. By comparing the performance of light- and dark-grown cells as well as by analyzing the isotope labeling patterns in aspartic and glutamic acids, we eliminated photosynthetic or anaplerotic fixation of extracellular (12)CO2 as explanations for the anomalous labeling patterns. We further investigated four different metabolic models for interpreting the labeling patterns and evaluating fluxes: (i) a carbon source (glucose) dilution model, (ii) an isotopomer correction model with uniform dilution for all amino acids, (iii) an isotopomer correction model with variable dilution for different amino acids, and (iv) a comprehensive metabolite reflux model. Of these, the metabolite reflux model provided a substantially better fit for the observed labeling patterns (sum of squared residues: 538) than the other three models whose sum of squared residues were (i) 4626, (ii) 4983, and (iii) 1748, respectively. We compared fluxes determined using the metabolite reflux model to those determined using an independent methodology involving an excessively long ILE to wash out initial biomass and a minimal reflux model. This comparison showed identical or similar distributions for a majority of fluxes, thus validating our comprehensive reflux model. In summary, we have demonstrated the need for quantifying interactions between initially present biomass and newly synthesized biomass in batch ILEs, especially through the use of ≈100% U-(13)C carbon sources. Our ILEs reveal a high amount of metabolite reflux in poplar cell suspensions, which is well explained by a comprehensive metabolite reflux model.
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Affiliation(s)
- Shilpa Nargund
- Department of Chemical and Biomolecular Engineering, University of Maryland, 1208D, Chemical and Nuclear Engineering Building 090, College Park, MD 20742, USA.
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20
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Abstract
Metabolic reprogramming is a key step in oncogenic transformation, and it involves alterations in both bioenergetic and anabolic metabolism. Sustained by these metabolic alterations, malignant cells acquire the ability to re-enter the cell cycle and proliferate. The so-called central carbon metabolism (CCM) is the ultimate source for energy and building blocks enabling cellular growth and proliferation. The time-resolved monitoring of the conversion of stable isotope-labeled metabolites provides profound insights into the metabolic dynamics of malignant cells and enables the tracking of individual carbon routes within the CCM. Specifically, the analysis of isotope incorporation rates within short time frames by means of pulsed stable isotope-resolved metabolomics (pSIRM) can be used to determine the dynamics of glycolysis and glutaminolysis-two metabolic circuitries that are often deregulated in malignant cells. Here, we detail a pSIRM-based method that can be applied to the study of metabolic alteration in cultured cancer cells.
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21
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Stupp GS, Clendinen CS, Ajredini R, Szewc MA, Garrett T, Menger RF, Yost RA, Beecher C, Edison AS. Isotopic ratio outlier analysis global metabolomics of Caenorhabditis elegans. Anal Chem 2013; 85:11858-11865. [PMID: 24274725 DOI: 10.1021/ac4025413] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We demonstrate the global metabolic analysis of Caenorhabditis elegans stress responses using a mass-spectrometry-based technique called isotopic ratio outlier analysis (IROA). In an IROA protocol, control and experimental samples are isotopically labeled with 95 and 5% (13)C, and the two sample populations are mixed together for uniform extraction, sample preparation, and LC-MS analysis. This labeling strategy provides several advantages over conventional approaches: (1) compounds arising from biosynthesis are easily distinguished from artifacts, (2) errors from sample extraction and preparation are minimized because the control and experiment are combined into a single sample, (3) measurement of both the molecular weight and the exact number of carbon atoms in each molecule provides extremely accurate molecular formulas, and (4) relative concentrations of all metabolites are easily determined. A heat-shock perturbation was conducted on C. elegans to demonstrate this approach. We identified many compounds that significantly changed upon heat shock, including several from the purine metabolism pathway. The metabolomic response information by IROA may be interpreted in the context of a wealth of genetic and proteomic information available for C. elegans . Furthermore, the IROA protocol can be applied to any organism that can be isotopically labeled, making it a powerful new tool in a global metabolomics pipeline.
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Affiliation(s)
- Gregory S Stupp
- Department of Biochemistry & Molecular Biology, University of Florida, Gainesville, FL
| | - Chaevien S Clendinen
- Department of Biochemistry & Molecular Biology, University of Florida, Gainesville, FL
| | - Ramadan Ajredini
- Department of Biochemistry & Molecular Biology, University of Florida, Gainesville, FL
| | | | - Timothy Garrett
- Department of Pathology, Immunology, and Laboratory Medicine, UF.,Southeast Center for Integrated Metabolomics, UF
| | | | - Richard A Yost
- Southeast Center for Integrated Metabolomics, UF.,Department of Chemistry, UF
| | | | - Arthur S Edison
- Department of Biochemistry & Molecular Biology, University of Florida, Gainesville, FL.,Southeast Center for Integrated Metabolomics, UF
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22
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Zheng Y, Quinn AH, Sriram G. Experimental evidence and isotopomer analysis of mixotrophic glucose metabolism in the marine diatom Phaeodactylum tricornutum. Microb Cell Fact 2013; 12:109. [PMID: 24228629 PMCID: PMC3842785 DOI: 10.1186/1475-2859-12-109] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2013] [Accepted: 11/06/2013] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Heterotrophic fermentation using simple sugars such as glucose is an established and cost-effective method for synthesizing bioproducts from bacteria, yeast and algae. Organisms incapable of metabolizing glucose have limited applications as cell factories, often despite many other advantageous characteristics. Therefore, there is a clear need to investigate glucose metabolism in potential cell factories. One such organism, with a unique metabolic network and a propensity to synthesize highly reduced compounds as a large fraction of its biomass, is the marine diatom Phaeodactylum tricornutum (Pt). Although Pt has been engineered to metabolize glucose, conflicting lines of evidence leave it unresolved whether Pt can natively consume glucose. RESULTS Isotope labeling experiments in which Pt was mixotrophically grown under light on 100% U-(13)C glucose and naturally abundant (~99% (12)C) dissolved inorganic carbon resulted in proteinogenic amino acids with an average 13C-enrichment of 88%, thus providing convincing evidence of glucose uptake and metabolism. The dissolved inorganic carbon was largely incorporated through anaplerotic rather than photosynthetic fixation. Furthermore, an isotope labeling experiment utilizing 1-(13)C glucose and subsequent metabolic pathway analysis indicated that (i) the alternative Entner-Doudoroff and Phosphoketolase glycolytic pathways are active during glucose metabolism, and (ii) during mixotrophic growth, serine and glycine are largely synthesized from glyoxylate through photorespiratory reactions rather than from 3-phosphoglycerate. We validated the latter result for mixotrophic growth on glycerol by performing a 2-(13)C glycerol isotope labeling experiment. Additionally, gene expression assays showed that known, native glucose transporters in Pt are largely insensitive to glucose or light, whereas the gene encoding cytosolic fructose bisphosphate aldolase 3, an important glycolytic enzyme, is overexpressed in light but insensitive to glucose. CONCLUSION We have shown that Pt can use glucose as a primary carbon source when grown in light, but cannot use glucose to sustain growth in the dark. We further analyzed the metabolic mechanisms underlying the mixotrophic metabolism of glucose and found isotopic evidence for unusual pathways active in Pt. These insights expand the envelope of Pt cultivation methods using organic substrates. We anticipate that they will guide further engineering of Pt towards sustainable production of fuels, pharmaceuticals, and platform chemicals.
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Affiliation(s)
- Yuting Zheng
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland, MD 20742, USA
| | - Andrew H Quinn
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland, MD 20742, USA
| | - Ganesh Sriram
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland, MD 20742, USA
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