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Ma F, Chen K, Zhou C, Li X, Fan J, Yan X, Ruan R, Cheng P. Effect of phytohormone on proliferation and accumulation of cellular metabolites of microalgae Isochrysis zhanjiangensis. BIORESOURCE TECHNOLOGY 2024; 410:131299. [PMID: 39153691 DOI: 10.1016/j.biortech.2024.131299] [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: 05/20/2024] [Revised: 08/12/2024] [Accepted: 08/14/2024] [Indexed: 08/19/2024]
Abstract
Phytohormones play a role in regulating microalgae cells tolerance to adversity. This paper examines the effects of different temperatures (20 °C, 25 °C, 30 °C and 35 °C) on the physiological characteristics and endogenous phytohormones of the Isochrysis Zhanjiangensis (IZ) and its mutagenic strain (3005). The results showed that the endogenous phytohormones indole acetic acid (IAA) and jasmonic acid (JA) exhibited significant differences (P<0.05) between the two strains. The addition of 0.5 mg·L-1 exogenous JA inhibitor ibuprofen (IBU) improved cell growth of IZ, and was extremely effective in the accumulation of polysaccharides, which accounted for 33.25 %. Transcriptomic analyses revealed that genes involved in photosynthesis, such as PetC and PsbO, exhibited significantly elevated expression of the strain IZ, while the pathways related to JA synthesis may be the factor affecting microalgae temperature tolerance. This study provides a theoretical foundation for elucidating the underlying mechanisms and potential applications for high temperature tolerance in IZ.
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Affiliation(s)
- Feifei Ma
- College of Food Science and Engineering, Ningbo University, Ningbo, Zhejiang 315211, PR China
| | - Kang Chen
- College of Food Science and Engineering, Ningbo University, Ningbo, Zhejiang 315211, PR China
| | - Chengxu Zhou
- College of Food Science and Engineering, Ningbo University, Ningbo, Zhejiang 315211, PR China
| | - Xiaohui Li
- College of Food Science and Engineering, Ningbo University, Ningbo, Zhejiang 315211, PR China
| | - Jianhua Fan
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, PR China
| | - Xiaojun Yan
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang 315211, PR China
| | - Roger Ruan
- Center for Biorefining, and Department of Bioproducts and Biosystems Engineering, University of Minnesota-Twin Cities, Saint Paul, MN 55108, USA.
| | - Pengfei Cheng
- College of Food Science and Engineering, Ningbo University, Ningbo, Zhejiang 315211, PR China; Center for Biorefining, and Department of Bioproducts and Biosystems Engineering, University of Minnesota-Twin Cities, Saint Paul, MN 55108, USA.
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Bulbule S, Gottschalk CG, Drosen ME, Peterson D, Arnold LA, Roy A. Dysregulation of tetrahydrobiopterin metabolism in myalgic encephalomyelitis/chronic fatigue syndrome by pentose phosphate pathway. J Cent Nerv Syst Dis 2024; 16:11795735241271675. [PMID: 39161795 PMCID: PMC11331476 DOI: 10.1177/11795735241271675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 06/24/2024] [Indexed: 08/21/2024] Open
Abstract
Background Tetrahydrobiopterin (BH4) and its oxidized derivative dihydrobiopterin (BH2) were found to be strongly elevated in ME/CFS patients with orthostatic intolerance (ME + OI). Objective However, the molecular mechanism of biopterin biogenesis is poorly understood in ME + OI subjects. Here, we report that the activation of the non-oxidative pentose phosphate pathway (PPP) plays a critical role in the biogenesis of biopterins (BH4 and BH2) in ME + OI subjects. Research Design and Results Microarray-based gene screening followed by real-time PCR-based validation, ELISA assay, and finally enzyme kinetic studies of glucose-6-phosphate dehydrogenase (G6PDH), transaldolase (TALDO1), and transketolase (TK) enzymes revealed that the augmentation of anaerobic PPP is critical in the regulations of biopterins. To further investigate, we devised a novel cell culture strategy to induce non-oxidative PPP by treating human microglial cells with ribose-5-phosphate (R5P) under a hypoxic condition of 85%N2/10%CO2/5%O2 followed by the analysis of biopterin metabolism via ELISA, immunoblot, and dual immunocytochemical analyses. Moreover, the siRNA knocking down of the taldo1 gene strongly inhibited the bioavailability of phosphoribosyl pyrophosphate (PRPP), reduced the expressions of purine biosynthetic enzymes, attenuated GTP cyclohydrolase 1 (GTPCH1), and suppressed subsequent production of BH4 and its metabolic conversion to BH2 in R5P-treated and hypoxia-induced C20 human microglia cells. These results confirmed that the activation of non-oxidative PPP is indeed required for the upregulation of both BH4 and BH2 via the purine biosynthetic pathway. To test the functional role of ME + OI plasma-derived biopterins, exogenously added plasma samples of ME + OI plasma with high BH4 upregulated inducible nitric oxide synthase (iNOS) and nitric oxide (NO) in human microglial cells indicating that the non-oxidative PPP-induced-biopterins could stimulate inflammatory response in ME + OI patients. Conclusion Taken together, our current research highlights that the induction of non-oxidative PPP regulates the biogenesis of biopterins contributing to ME/CFS pathogenesis.
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Affiliation(s)
- Sarojini Bulbule
- Research and Development Laboratory, Simmaron Research Institute, Milwaukee, WI, USA
| | - Carl Gunnar Gottschalk
- Research and Development Laboratory, Simmaron Research Institute, Milwaukee, WI, USA
- Simmaron Research Institute, Incline Village, NV, USA
| | - Molly E. Drosen
- Research and Development Laboratory, Simmaron Research Institute, Milwaukee, WI, USA
| | | | - Leggy A. Arnold
- Department of Chemistry and Biochemistry and the Milwaukee Institute for Drug Discovery, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Avik Roy
- Research and Development Laboratory, Simmaron Research Institute, Milwaukee, WI, USA
- Simmaron Research Institute, Incline Village, NV, USA
- Department of Chemistry and Biochemistry and the Milwaukee Institute for Drug Discovery, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
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House RRJ, Soper-Hopper MT, Vincent MP, Ellis AE, Capan CD, Madaj ZB, Wolfrum E, Isaguirre CN, Castello CD, Johnson AB, Escobar Galvis ML, Williams KS, Lee H, Sheldon RD. A diverse proteome is present and enzymatically active in metabolite extracts. Nat Commun 2024; 15:5796. [PMID: 38987243 PMCID: PMC11237058 DOI: 10.1038/s41467-024-50128-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 07/02/2024] [Indexed: 07/12/2024] Open
Abstract
Metabolite extraction is the critical first-step in metabolomics experiments, where it is generally regarded to inactivate and remove proteins. Here, arising from efforts to improve extraction conditions for polar metabolomics, we discover a proteomic landscape of over 1000 proteins within metabolite extracts. This is a ubiquitous feature across several common extraction and sample types. By combining post-resuspension stable isotope addition and enzyme inhibitors, we demonstrate in-extract metabolite interconversions due to residual transaminase activity. We extend these findings with untargeted metabolomics where we observe extensive protein-mediated metabolite changes, including in-extract formation of glutamate dipeptide and depletion of total glutathione. Finally, we present a simple extraction workflow that integrates 3 kDa filtration for protein removal as a superior method for polar metabolomics. In this work, we uncover a previously unrecognized, protein-mediated source of observer effects in metabolomics experiments with broad-reaching implications across all research fields using metabolomics and molecular metabolism.
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Affiliation(s)
- Rachel Rae J House
- Department of Cell Biology, Van Andel Institute, Grand Rapids, MI, USA
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI, USA
- Mass Spectrometry Core, Van Andel Institute, Grand Rapids, MI, USA
| | | | | | - Abigail E Ellis
- Mass Spectrometry Core, Van Andel Institute, Grand Rapids, MI, USA
| | - Colt D Capan
- Mass Spectrometry Core, Van Andel Institute, Grand Rapids, MI, USA
| | - Zachary B Madaj
- Bioinformatics and Biostatistics Core, Van Andel Institute, Grand Rapids, MI, USA
| | - Emily Wolfrum
- Bioinformatics and Biostatistics Core, Van Andel Institute, Grand Rapids, MI, USA
| | | | | | - Amy B Johnson
- Mass Spectrometry Core, Van Andel Institute, Grand Rapids, MI, USA
| | - Martha L Escobar Galvis
- Office of the Cores, Core Technologies and Services, Van Andel Institute, Grand Rapids, MI, USA
| | - Kelsey S Williams
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI, USA
| | - Hyoungjoo Lee
- Mass Spectrometry Core, Van Andel Institute, Grand Rapids, MI, USA
| | - Ryan D Sheldon
- Mass Spectrometry Core, Van Andel Institute, Grand Rapids, MI, USA.
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Papp LA, Imre S, Bálint I, Lungu AI, Mărcutiu PE, Papp J, Ion V. Is it Time to Migrate to Liquid Chromatography Automated Platforms in the Clinical Laboratory? A Brief Point of View. J Chromatogr Sci 2024; 62:191-200. [PMID: 36715315 DOI: 10.1093/chromsci/bmad002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 11/28/2022] [Indexed: 01/31/2023]
Abstract
Liquid chromatography coupled to mass spectrometry already started to surpass the major drawbacks in terms of sensitivity, specificity and cross-reactivity that some analytical methods used in the clinical laboratory exhibit. This hyphenated technique is already preferred for specific applications while finding its own place in the clinical laboratory setting. However, large-scale usage, high-throughput analysis and lack of automation emerge as shortcomings that liquid chromatography coupled to mass spectrometry still has to overrun in order to be used on a larger scale in the clinical laboratory. The aim of this review article is to point out the present-day position of the liquid chromatography coupled to mass spectrometry technique while trying to understand how this analytical method relates to the basic working framework of the clinical laboratory. This paper offers insights about the main regulation and traceability criteria that this coupling method has to align and comply to, automation and standardization issues and finally the critical steps in sample preparation workflows all related to the high-throughput analysis framework. Further steps are to be made toward automation, speed and easy-to-use concept; however, the current technological and quality premises are favorable for chromatographic coupled to mass spectral methods.
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Affiliation(s)
- Lajos-Attila Papp
- Faculty of Pharmacy, George Emil Palade University of Medicine, Pharmacy, Science, and Technology from Targu Mures, Gheorghe Marinescu street 38, 540142 Targu Mures, Romania
- Public Health Department Mures, Gheorghe Marinescu street 40, 540136 Targu Mures, Romania
| | - Silvia Imre
- Faculty of Pharmacy, George Emil Palade University of Medicine, Pharmacy, Science, and Technology from Targu Mures, Gheorghe Marinescu street 38, 540142 Targu Mures, Romania
- Center for Advanced Medical and Pharmaceutical Research, George Emil Palade University of Medicine, Pharmacy, Science, and Technology from Targu Mures, Gheorghe Marinescu street 38, 540142 Targu Mures, Romania
| | - István Bálint
- Faculty of Pharmacy, George Emil Palade University of Medicine, Pharmacy, Science, and Technology from Targu Mures, Gheorghe Marinescu street 38, 540142 Targu Mures, Romania
- Public Health Department Mures, Gheorghe Marinescu street 40, 540136 Targu Mures, Romania
| | - Andreea-Ioana Lungu
- Faculty of Pharmacy, George Emil Palade University of Medicine, Pharmacy, Science, and Technology from Targu Mures, Gheorghe Marinescu street 38, 540142 Targu Mures, Romania
- Public Health Department Mures, Gheorghe Marinescu street 40, 540136 Targu Mures, Romania
| | - Petra-Edina Mărcutiu
- Faculty of Pharmacy, George Emil Palade University of Medicine, Pharmacy, Science, and Technology from Targu Mures, Gheorghe Marinescu street 38, 540142 Targu Mures, Romania
- Public Health Department Mures, Gheorghe Marinescu street 40, 540136 Targu Mures, Romania
| | - Júlia Papp
- Faculty of Pharmacy, George Emil Palade University of Medicine, Pharmacy, Science, and Technology from Targu Mures, Gheorghe Marinescu street 38, 540142 Targu Mures, Romania
- Public Health Department Mures, Gheorghe Marinescu street 40, 540136 Targu Mures, Romania
| | - Valentin Ion
- Faculty of Pharmacy, George Emil Palade University of Medicine, Pharmacy, Science, and Technology from Targu Mures, Gheorghe Marinescu street 38, 540142 Targu Mures, Romania
- Center for Advanced Medical and Pharmaceutical Research, George Emil Palade University of Medicine, Pharmacy, Science, and Technology from Targu Mures, Gheorghe Marinescu street 38, 540142 Targu Mures, Romania
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Wang T, Wang X, Zhuang Y, Wang G. A systematic evaluation of quenching and extraction procedures for quantitative metabolome profiling of HeLa carcinoma cell under 2D and 3D cell culture conditions. Biotechnol J 2023; 18:e2200444. [PMID: 36796787 DOI: 10.1002/biot.202200444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 01/13/2023] [Accepted: 02/10/2023] [Indexed: 02/18/2023]
Abstract
Metabolic reprogramming has been coined as a hallmark of cancer, accompanied by which the alterations in metabolite levels have profound effects on gene expression, cellular differentiation, and the tumor environment. Yet a systematic evaluation of quenching and extraction procedures for quantitative metabolome profiling of tumor cells is currently lacking. To achieve this, this study is aimed at establishing an unbiased and leakage-free metabolome preparation protocol for HeLa carcinoma cell. We evaluated 12 combinations of quenching and extraction methods from three quenchers (liquid nitrogen, -40°C 50% methanol, 0.5°C normal saline) and four extractants (-80°C 80% methanol, 0.5°C methanol/chloroform/water [1:1:1 v/v/v], 0.5°C 50% acetonitrile, 75°C 70% ethanol) for global metabolite profiling of adherent HeLa carcinoma cells. Based on the isotope dilution mass spectrometry (IDMS) method, gas/liquid chromatography in tandem with mass spectrometry was used to quantitatively determine 43 metabolites including sugar phosphates, organic acids, amino acids (AAs), adenosine nucleotides, and coenzymes involved in central carbon metabolism. The results showed that the total amount of the intracellular metabolites in cell extracts obtained using different sample preparation procedures with the IDMS method ranged from 21.51 to 295.33 nmol per million cells. Among 12 combinations, cells that washed twice with phosphate buffered saline (PBS), quenched with liquid nitrogen, and then extracted with 50% acetonitrile were found to be the most optimal method to acquire intracellular metabolites with high efficiency of metabolic arrest and minimal loss during sample preparation. In addition, the same conclusion was drawn as these 12 combinations were applied to obtain quantitative metabolome data from three-dimensional (3D) tumor spheroids. Furthermore, a case study was carried out to evaluate the effect of doxorubicin (DOX) on both adherent cells and 3D tumor spheroids using quantitative metabolite profiling. Pathway enrichment analysis using targeted metabolomics data showed that DOX exposure would significantly affect AA metabolism-related pathways, which might be related to the mitigation of redox stress. Strikingly, our data suggested that compared to two-dimensional (2D) cells the increased intracellular glutamine level in 3D cells benefited replenishing the tricarboxylic acid (TCA) cycle when the glycolysis was limited after dosing with DOX. Taken together, this study provides a well-established quenching and extraction protocol for quantitative metabolome profiling of HeLa carcinoma cell under 2D and 3D cell culture conditions. Based on this, quantitative time-resolved metabolite data can serve to the generation of hypotheses on metabolic reprogramming to reveal its important role in tumor development and treatment.
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Affiliation(s)
- Tong Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology (ECUST), Shanghai, People's Republic of China
| | - Xueting Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology (ECUST), Shanghai, People's Republic of China
| | - Yingping Zhuang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology (ECUST), Shanghai, People's Republic of China.,Qingdao Innovation Institute of East China University of Science and Technology, Shanghai, People's Republic of China
| | - Guan Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology (ECUST), Shanghai, People's Republic of China.,Qingdao Innovation Institute of East China University of Science and Technology, Shanghai, People's Republic of China
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Su M, Serafimov K, Li P, Knappe C, Lämmerhofer M. Isomer selectivity of one- and two-dimensional approaches of mixed-mode and hydrophilic interaction liquid chromatography coupled to tandem mass spectrometry for sugar phosphates of glycolysis and pentose phosphate pathways. J Chromatogr A 2023; 1688:463727. [PMID: 36566570 DOI: 10.1016/j.chroma.2022.463727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 12/16/2022] [Accepted: 12/17/2022] [Indexed: 12/23/2022]
Abstract
In this study, the chromatographic behavior of mixed-mode and hydrophilic interaction liquid chromatography (HILIC) with the mixed-mode HILIC/strong anion-exchange (SAX) column HILICpak VT-50 2D and the two HILIC columns Atlantis Premier BEH Z-HILIC and Acquity Premier BEH Amide was assessed with regard to their separation capability of the metabolites from the glycolysis and pentose phosphate pathways. Chromatographic conditions were evaluated with the aim of achieving separation of the isomeric glycolytic phosphorylated carbohydrate metabolites free from isomeric interferences and thus allowing for selective targeted analysis by liquid chromatography with tandem mass spectrometry (MS/MS) using multiple reaction monitoring acquisition. The effects of pH values (8.0/9.0/10.0) of the ammonium bicarbonate buffer and gradient time were investigated during HILIC-MS/MS analysis, with the optimal conditions found at pH = 10.0. Separation of the pentose phosphate isomers (ribose 5- and 1-phosphate, xylulose 5-phosphate and ribulose 5-phosphate) was achieved on the mixed-mode HILIC/SAX (HILICpak VT-50 2D) column and HILIC BEH Amide column. Column performance was evaluated based on the direct comparison of chromatographic parameters, i.e. peak width at 50% and peak tailing factors of the individual metabolites. Parity plots were generated allowing a direct comparison between the normalized retention times and assessment of orthogonality of all 3 stationary phases evaluated. Separation of 7 biologically relevant hexose monophosphates metabolites turned out to be challenging by HILIC-MS/MS, with the BEH Amide providing the best individual results for such a separation. However, fructose 6-phosphate and glucose 1-phosphate co-eluted. Therefore, an on-line heart-cutting HILIC-Mixed Mode 2D-LC-QToF experiment was conducted, allowing the separation of this critical isomer pair. In this setup, the BEH Amide column in the 1D separated the majority of target metabolites, while a heart-cut of the peak from totally coeluted fructose 6-phosphate and glucose 1-phosphate was separated in the 2D with HILICpak VT50-2D column, thus allowing undisturbed determination of the glycolytic phosphorylated carbohydrate metabolites due to their chromatographic separation from hexose monophosphate metabolites. The assay specificity towards 7 common hexose monophosphates was characterized (glucose 1- and 6-phosphate, galactose 1- and 6-phosphate, fructose 6-phosphate, mannose 1- and 6-phosphate). The selectivity of some rare hexose monophosphates (allose 6-phosphate, tagatose 6-phosphate, sorbose 1-phosphate) was also tested.
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Affiliation(s)
- Min Su
- Pharmaceutical (Bio-)Analysis, Institute of Pharmaceutical Sciences, University of Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany
| | - Kristian Serafimov
- Pharmaceutical (Bio-)Analysis, Institute of Pharmaceutical Sciences, University of Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany
| | - Peng Li
- Pharmaceutical (Bio-)Analysis, Institute of Pharmaceutical Sciences, University of Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany
| | - Cornelius Knappe
- Pharmaceutical (Bio-)Analysis, Institute of Pharmaceutical Sciences, University of Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany
| | - Michael Lämmerhofer
- Pharmaceutical (Bio-)Analysis, Institute of Pharmaceutical Sciences, University of Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany.
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Li S, Zhang Z, Liu FL, Yuan BF, Liu TG, Feng YQ. Comprehensive Profiling of Phosphomonoester Metabolites in Saccharomyces cerevisiae by the Chemical Isotope Labeling-LC-MS Method. J Proteome Res 2023; 22:114-122. [PMID: 36484485 DOI: 10.1021/acs.jproteome.2c00507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Phosphomonoesters are important biosynthetic and energy metabolism intermediates in microorganisms. A comprehensive analysis of phosphomonoester metabolites is of great significance for the understanding of their metabolic phosphorylation process and inner mechanism. In this study, we established a pair of isotope reagent d0/d5-2-diazomethyl-N-methyl-phenyl benzamide-labeling-based LC-MS method for the comprehensive analysis of phosphomonoester metabolites. By this method, the labeled phosphomonoester metabolites specifically produced characteristic isotope paired peaks with an m/z difference of 5.0314 in the MS1 spectra and a pair of diagnostic ions (m/z 320.0693/325.1077) in the MS2 spectra. Based on this, a diagnostic ion-based strategy was established for the rapid screening, identification, and relative quantification of phosphomonoester metabolites. Using this strategy, 42 phosphomonoester metabolites were highly accurately identified fromSaccharomyces cerevisiae (S. cerevisiae). Notably, two phosphomonoesters were first detected fromS. cerevisiae. The relative quantification results indicated that the contents of nine phosphomonoester metabolites including two intermediates (Ru5P and S7P) in the pentose phosphate pathway (PPP) were significantly different between lycopene-producible and wild-type S. cerevisiae. A further enzyme assay indicated that the activity of the PPP was closely related to the production of lycopene. Our findings provide new perspectives for the related mechanism study and valuable references for making informed microbial engineering decisions.
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Affiliation(s)
- Sha Li
- Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Zheng Zhang
- Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Fei-Long Liu
- Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Bi-Feng Yuan
- School of Public Health, Wuhan University, Wuhan 430071, China
| | - Tian-Gang Liu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Yu-Qi Feng
- Department of Chemistry, Wuhan University, Wuhan 430072, China.,School of Public Health, Wuhan University, Wuhan 430071, China
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Piedrafita G, Varma SJ, Castro C, Messner CB, Szyrwiel L, Griffin JL, Ralser M. Cysteine and iron accelerate the formation of ribose-5-phosphate, providing insights into the evolutionary origins of the metabolic network structure. PLoS Biol 2021; 19:e3001468. [PMID: 34860829 PMCID: PMC8673631 DOI: 10.1371/journal.pbio.3001468] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 12/15/2021] [Accepted: 11/04/2021] [Indexed: 12/21/2022] Open
Abstract
The structure of the metabolic network is highly conserved, but we know little about its evolutionary origins. Key for explaining the early evolution of metabolism is solving a chicken–egg dilemma, which describes that enzymes are made from the very same molecules they produce. The recent discovery of several nonenzymatic reaction sequences that topologically resemble central metabolism has provided experimental support for a “metabolism first” theory, in which at least part of the extant metabolic network emerged on the basis of nonenzymatic reactions. But how could evolution kick-start on the basis of a metal catalyzed reaction sequence, and how could the structure of nonenzymatic reaction sequences be imprinted on the metabolic network to remain conserved for billions of years? We performed an in vitro screening where we add the simplest components of metabolic enzymes, proteinogenic amino acids, to a nonenzymatic, iron-driven reaction network that resembles glycolysis and the pentose phosphate pathway (PPP). We observe that the presence of the amino acids enhanced several of the nonenzymatic reactions. Particular attention was triggered by a reaction that resembles a rate-limiting step in the oxidative PPP. A prebiotically available, proteinogenic amino acid cysteine accelerated the formation of RNA nucleoside precursor ribose-5-phosphate from 6-phosphogluconate. We report that iron and cysteine interact and have additive effects on the reaction rate so that ribose-5-phosphate forms at high specificity under mild, metabolism typical temperature and environmental conditions. We speculate that accelerating effects of amino acids on rate-limiting nonenzymatic reactions could have facilitated a stepwise enzymatization of nonenzymatic reaction sequences, imprinting their structure on the evolving metabolic network. The evolutionary origins of metabolism are largely unknown. This study shows that the prebiotically available proteinogenic amino acid cysteine can promote the metabolism-like rate-limiting formation of ribose-5-phosphate, suggesting that early metabolic pathways could have emerged thought the stepwise enzymatization of non-enzymatic reaction sequences.
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Affiliation(s)
- Gabriel Piedrafita
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, United Kingdom
| | - Sreejith J. Varma
- Department of Biochemistry, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Cecilia Castro
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, United Kingdom
| | - Christoph B. Messner
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Lukasz Szyrwiel
- Department of Biochemistry, Charité Universitätsmedizin Berlin, Berlin, Germany
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Julian L. Griffin
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, United Kingdom
- The Rowett Institute, The University of Aberdeen, Aberdeen, United Kingdom
| | - Markus Ralser
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, United Kingdom
- Department of Biochemistry, Charité Universitätsmedizin Berlin, Berlin, Germany
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, United Kingdom
- * E-mail:
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Coupling Mixed Mode Chromatography/ESI Negative MS Detection with Message-Passing Neural Network Modeling for Enhanced Metabolome Coverage and Structural Identification. Metabolites 2021; 11:metabo11110772. [PMID: 34822429 PMCID: PMC8620857 DOI: 10.3390/metabo11110772] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/28/2021] [Accepted: 11/08/2021] [Indexed: 11/16/2022] Open
Abstract
A key unmet need in metabolomics continues to be the specific, selective, accurate detection of traditionally difficult to retain molecules including simple sugars, sugar phosphates, carboxylic acids, and related amino acids. Designed to retain the metabolites of central carbon metabolism, this Mixed Mode (MM) chromatography applies varied pH, salt concentration and organic content to a positively charged quaternary amine polyvinyl alcohol stationary phase. This MM method is capable of separating glucose from fructose, and four hexose monophosphates a single chromatographic run. Coupled to a QExactive Orbitrap Mass Spectrometer with negative ESI, linearity, LLOD, %CV, and mass accuracy were assessed using 33 metabolite standards. The standards were linear on average >3 orders of magnitude (R2 > 0.98 for 30/33) with LLOD < 1 pmole (26/33), median CV of 12% over two weeks, and median mass accuracy of 0.49 ppm. To assess the breadth of metabolome coverage and better define the structural elements dictating elution, we injected 607 unique metabolites and determined that 398 are well retained. We then split the dataset of 398 documented RTs into training and test sets and trained a message-passing neural network (MPNN) to predict RT from a featurized heavy atom connectivity graph. Unlike traditional QSAR methods that utilize hand-crafted descriptors or pre-defined structural keys, the MPNN aggregates atomic features across the molecular graph and learns to identify molecular subgraphs that are correlated with variations in RTs. For sugars, sugar phosphates, carboxylic acids, and isomers, the model achieves a predictive RT error of <2 min on 91%, 50%, 77%, and 72% of held-out compounds from these subsets, with overall root mean square errors of 0.11, 0.34, 0.18, and 0.53 min, respectively. The model was then applied to rank order metabolite IDs for molecular features altered by GLS2 knockout in mouse primary hepatocytes.
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11
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Wang C, Zhang B, Song L, Li P, Hao Y, Zhang J. Assessment of different blanching strategies on quality characteristics and bioactive constituents of Toona sinensis. Lebensm Wiss Technol 2020. [DOI: 10.1016/j.lwt.2020.109549] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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12
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Akram M, Ali Shah SM, Munir N, Daniyal M, Tahir IM, Mahmood Z, Irshad M, Akhlaq M, Sultana S, Zainab R. Hexose monophosphate shunt, the role of its metabolites and associated disorders: A review. J Cell Physiol 2019; 234:14473-14482. [PMID: 30697723 DOI: 10.1002/jcp.28228] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 01/15/2019] [Accepted: 01/15/2019] [Indexed: 01/24/2023]
Abstract
The hexose monophosphate (HMP) shunt acts as an essential component of cellular metabolism in maintaining carbon homeostasis. The HMP shunt comprises two phases viz. oxidative and nonoxidative, which provide different intermediates for the synthesis of biomolecules like nucleotides, DNA, RNA, amino acids, and so forth; reducing molecules for anabolism and detoxifying the reactive oxygen species during oxidative stress. The HMP shunt is significantly important in the liver, adipose tissue, erythrocytes, adrenal glands, lactating mammary glands and testes. We have researched the articles related to the HMP pathway, its metabolites and disorders related to its metabolic abnormalities. The literature for this paper was taken typically from a personal database, the Cochrane database of systemic reviews, PubMed publications, biochemistry textbooks, and electronic journals uptil date on the hexose monophosphate shunt. The HMP shunt is a tightly controlled metabolic pathway, which is also interconnected with other metabolic pathways in the body like glycolysis, gluconeogenesis, and glucuronic acid depending upon the metabolic needs of the body and depending upon the biochemical demand. The HMP shunt plays a significant role in NADPH2 formation and in pentose sugars that are biosynthetic precursors of nucleic acids and amino acids. Cells can be protected from highly reactive oxygen species by NADPH 2 . Deficiency in the hexose monophosphate pathway is linked to numerous disorders. Furthermore, it was also reported that this metabolic pathway could act as a therapeutic target to treat different types of cancers, so treatments at the molecular level could be planned by limiting the synthesis of biomolecules required for proliferating cells provided by the HMP shunt, hence, more experiments still could be carried out to find additional discoveries.
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Affiliation(s)
- Muhammad Akram
- Department of Eastern Medicine, Directorate of Medical Sciences, Government College University, Faisalabad, Pakistan
| | - Syed Muhammad Ali Shah
- Department of Eastern Medicine, Directorate of Medical Sciences, Government College University, Faisalabad, Pakistan
| | - Naveed Munir
- College of Allied Health Professional, Directorate of Medical Sciences, Government College University, Faisalabad, Pakistan.,Department of Biochemistry, Government College University, Faisalabad, Pakistan
| | - Muhammad Daniyal
- TCM and Ethnomedicine Innovation & Development International Laboratory, School of Pharmacy, Hunan University of Chinese Medicine, Changsha, China
| | - Imtiaz Mahmood Tahir
- College of Allied Health Professional, Directorate of Medical Sciences, Government College University, Faisalabad, Pakistan
| | - Zahed Mahmood
- Department of Biochemistry, Government College University, Faisalabad, Pakistan
| | - Muhammad Irshad
- Department of Chemistry, University of Kotli, Azad Jammu & Kashmir (UoKAJK), Pakistan
| | - Muhammad Akhlaq
- Department of Pharmaceutics, Faculty of Pharmacy, Gomal University, DIK, KP, Pakistan
| | - Sabira Sultana
- Department of Eastern Medicine, Directorate of Medical Sciences, Government College University, Faisalabad, Pakistan
| | - Rida Zainab
- Department of Eastern Medicine, Directorate of Medical Sciences, Government College University, Faisalabad, Pakistan
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13
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Abstract
Mass spectrometry is a sensitive and selective analytical technique that enables detection and quantitation of low abundance compounds in a complex sample matrix. Targeted metabolomics allows for quantitative analysis of metabolites, providing kinetic information of production and consumption rates, an essential step to investigate microbial metabolism. Here, we describe a targeted metabolomics protocol for yeast samples, from sample preparation to mass spectrometry analysis, which enables the identification of metabolic fluxes after xylose consumption. Sample preparation methods were optimized for quenching of yeast metabolism followed by intracellular metabolite extraction, using cold methanol and boiling ethanol protocols. Ultrahigh performance liquid chromatography tandem mass spectrometry (UHPLC-MS/MS) methods using ion pair chromatography (IPC) and hydrophilic interaction liquid chromatography (HILIC) allowed for the quantitation of 18 metabolites involved in central carbon metabolism (glycolysis, pentose phosphate pathway, and tricarboxylic acid cycle). The protocol here described was successfully applied to quantify metabolites in Scheffersomyces stipitis, Spathaspora passalidarum, Spathaspora arborariae, and Candida tenuis samples after xylose consumption.
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14
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Cheng J, Lu H, Li K, Zhu Y, Zhou J. Enhancing growth-relevant metabolic pathways of Arthrospira platensis (CYA-1) with gamma irradiation from 60Co. RSC Adv 2018; 8:16824-16833. [PMID: 35540541 PMCID: PMC9080328 DOI: 10.1039/c8ra01626g] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 05/01/2018] [Indexed: 11/21/2022] Open
Abstract
The biomass yield of Arthrospira mutant ZJU9000 was 176% higher than that of wild type on day 4, and the results of transcriptome sequencing showed that processes related to cell growth were synergistically enhanced in this mutant. The amount of energy for biomass accumulation increased because the efficiency of the photoreaction was enhanced by the elevated levels of chlorophyll a and carotene. The increased biosynthesis rates of ribose phosphate, nucleotides and multiple vitamins increased the production of genetic materials for cell proliferation. Furthermore, the carbon concentration mechanism in mutant ZJU9000 was enhanced, indicating the increased utilization efficiency of CO2 at low concentration (0.04 vol% in air). The enhancement of these growth-relevant metabolic pathways contributed to the robust growth of Arthrospira mutant ZJU9000. Growth-relevant metabolic pathways of Arthrospira enhanced after gamma irradiation.![]()
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Affiliation(s)
- Jun Cheng
- State Key Laboratory of Clean Energy Utilization
- Zhejiang University
- Hangzhou 310027
- China
| | - Hongxiang Lu
- State Key Laboratory of Clean Energy Utilization
- Zhejiang University
- Hangzhou 310027
- China
| | - Ke Li
- State Key Laboratory of Clean Energy Utilization
- Zhejiang University
- Hangzhou 310027
- China
| | - Yanxia Zhu
- State Key Laboratory of Clean Energy Utilization
- Zhejiang University
- Hangzhou 310027
- China
| | - Junhu Zhou
- State Key Laboratory of Clean Energy Utilization
- Zhejiang University
- Hangzhou 310027
- China
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15
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Campos CG, Veras HCT, de Aquino Ribeiro JA, Costa PPKG, Araújo KP, Rodrigues CM, de Almeida JRM, Abdelnur PV. New Protocol Based on UHPLC-MS/MS for Quantitation of Metabolites in Xylose-Fermenting Yeasts. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:2646-2657. [PMID: 28879550 DOI: 10.1007/s13361-017-1786-9] [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: 06/08/2017] [Accepted: 08/14/2017] [Indexed: 06/07/2023]
Abstract
Xylose fermentation is a bottleneck in second-generation ethanol production. As such, a comprehensive understanding of xylose metabolism in naturally xylose-fermenting yeasts is essential for prospection and construction of recombinant yeast strains. The objective of the current study was to establish a reliable metabolomics protocol for quantification of key metabolites of xylose catabolism pathways in yeast, and to apply this protocol to Spathaspora arborariae. Ultra-high performance liquid chromatography coupled to tandem mass spectrometry (UHPLC-MS/MS) was used to quantify metabolites, and afterwards, sample preparation was optimized to examine yeast intracellular metabolites. S. arborariae was cultivated using xylose as a carbon source under aerobic and oxygen-limited conditions. Ion pair chromatography (IPC) and hydrophilic interaction liquid chromatography-tandem mass spectrometry (HILIC-MS/MS) were shown to efficiently quantify 14 and 5 metabolites, respectively, in a more rapid chromatographic protocol than previously described. Thirteen and eleven metabolites were quantified in S. arborariae under aerobic and oxygen-limited conditions, respectively. This targeted metabolomics protocol is shown here to quantify a total of 19 metabolites, including sugars, phosphates, coenzymes, monosaccharides, and alcohols, from xylose catabolism pathways (glycolysis, pentose phosphate pathway, and tricarboxylic acid cycle) in yeast. Furthermore, to our knowledge, this is the first time that intracellular metabolites have been quantified in S. arborariae after xylose consumption. The results indicated that fine control of oxygen levels during fermentation is necessary to optimize ethanol production by S. arborariae. The protocol presented here may be applied to other yeast species and could support yeast genetic engineering to improve second generation ethanol production. Graphical Abstract ᅟ.
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Affiliation(s)
- Christiane Gonçalves Campos
- Brazilian Agricultural Research Corporation, Embrapa Agroenergy, W3 Norte, PqEB, Brasília, DF, 70770-901, Brazil
- Chemistry Institute, Federal University of Goiás, Campus Samambaia, Goiânia, GO, 74690-900, Brazil
| | - Henrique César Teixeira Veras
- Brazilian Agricultural Research Corporation, Embrapa Agroenergy, W3 Norte, PqEB, Brasília, DF, 70770-901, Brazil
- Postgraduate Program in Molecular Biology, Department of Cellular Biology, University of Brasília, Campus Darcy Ribeiro, Brasília, DF, Brazil
| | | | | | - Katiúscia Pereira Araújo
- Brazilian Agricultural Research Corporation, Embrapa Agroenergy, W3 Norte, PqEB, Brasília, DF, 70770-901, Brazil
| | - Clenilson Martins Rodrigues
- Brazilian Agricultural Research Corporation, Embrapa Agroenergy, W3 Norte, PqEB, Brasília, DF, 70770-901, Brazil
| | - João Ricardo Moreira de Almeida
- Brazilian Agricultural Research Corporation, Embrapa Agroenergy, W3 Norte, PqEB, Brasília, DF, 70770-901, Brazil
- Postgraduate Program in Chemical and Biological Technologies, Institute of Chemistry, University of Brasília, Campus Darcy Ribeiro, Brasília, DF, Brazil
| | - Patrícia Verardi Abdelnur
- Brazilian Agricultural Research Corporation, Embrapa Agroenergy, W3 Norte, PqEB, Brasília, DF, 70770-901, Brazil.
- Chemistry Institute, Federal University of Goiás, Campus Samambaia, Goiânia, GO, 74690-900, Brazil.
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16
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Qin Q, Wang B, Chang M, Zhou Z, Shi X, Xu G. Highly efficient solid-phase derivatization of sugar phosphates with titanium-immobilized hydrophilic polydopamine-coated silica. J Chromatogr A 2016; 1457:125-33. [PMID: 27371021 DOI: 10.1016/j.chroma.2016.06.046] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 06/11/2016] [Accepted: 06/15/2016] [Indexed: 10/21/2022]
Abstract
Sugar phosphates are a type of key metabolic intermediates of glycolysis, gluconeogenesis and pentose phosphate pathway, which can regulate tumor energetic metabolism. Due to their low endogenous concentrations, poor chromatographic retention properties as well as ionization suppression from complex matrix interference, the determination of sugar phosphates in biological samples is very difficult. In this study, titanium-immobilized hydrophilic polydopamine-coated silica microspheres (SiO2@PD-Ti(4+)) were synthesized for highly efficient solid-phase derivatization of sugar phosphates. Sugar phosphates were selectively captured onto the surface of the SiO2@PD-Ti(4+) microspheres by chelating with phosphate groups, and then reacted with 3-amino-9-ethylcarbazole via reductive amination based on solid-phase derivatization, which could not only increase the retention and resolution of sugar phosphates on reversed-phase liquid chromatography (RPLC), but also improve the mass spectrometry (MS) sensitivity of sugar phosphates. The adsorption capacity of SiO2@PD-Ti(4+) microspheres towards glucose-6-phosphate is 0.76mg/g, which is much larger than that of commercial TiO2. Compared with the traditional liquid-phase derivatization, the solid-phase derivatization based on the SiO2@PD-Ti(4+) microspheres displayed several superiorities including shorter derivatization time (within 10min), higher product purity and much lower limit of detection (up to 38pmol/L). In addition, good linearity (R(2)≥0.99), excellent recovery (80.6-118%) and high precision (RSDs with 2.8-7.8%) were obtained when the developed method was used for quantitative analysis of sugar phosphates. Finally, the SiO2@PD-Ti(4+) microspheres combined with RPLC-MS were successfully applied to the determination of sugar phosphates from hepatocarcinoma cell lines and could even detect the trace sugar phosphates in thousands of cells.
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Affiliation(s)
- Qian Qin
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bohong Wang
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mengmeng Chang
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhihui Zhou
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xianzhe Shi
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
| | - Guowang Xu
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
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17
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Allen DK. Assessing compartmentalized flux in lipid metabolism with isotopes. Biochim Biophys Acta Mol Cell Biol Lipids 2016; 1861:1226-1242. [PMID: 27003250 DOI: 10.1016/j.bbalip.2016.03.017] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2016] [Revised: 03/13/2016] [Accepted: 03/14/2016] [Indexed: 12/28/2022]
Abstract
Metabolism in plants takes place across multiple cell types and within distinct organelles. The distributions equate to spatial heterogeneity; though the limited means to experimentally assess metabolism frequently involve homogenizing tissues and mixing metabolites from different locations. Most current isotope investigations of metabolism therefore lack the ability to resolve spatially distinct events. Recognition of this limitation has resulted in inspired efforts to advance metabolic flux analysis and isotopic labeling techniques. Though a number of these efforts have been applied to studies in central metabolism; recent advances in instrumentation and techniques present an untapped opportunity to make similar progress in lipid metabolism where the use of stable isotopes has been more limited. These efforts will benefit from sophisticated radiolabeling reports that continue to enrich our knowledge on lipid biosynthetic pathways and provide some direction for stable isotope experimental design and extension of MFA. Evidence for this assertion is presented through the review of several elegant stable isotope studies and by taking stock of what has been learned from radioisotope investigations when spatial aspects of metabolism were considered. The studies emphasize that glycerolipid production occurs across several locations with assembly of lipids in the ER or plastid, fatty acid biosynthesis occurring in the plastid, and the generation of acetyl-CoA and glycerol-3-phosphate taking place at multiple sites. Considering metabolism in this context underscores the cellular and subcellular organization that is important to enhanced production of glycerolipids in plants. An attempt is made to unify salient features from a number of reports into a diagrammatic model of lipid metabolism and propose where stable isotope labeling experiments and further flux analysis may help address questions in the field. This article is part of a Special Issue entitled: Plant Lipid Biology edited by Kent D. Chapman and Ivo Feussner.
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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.
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18
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Keller MA, Zylstra A, Castro C, Turchyn AV, Griffin JL, Ralser M. Conditional iron and pH-dependent activity of a non-enzymatic glycolysis and pentose phosphate pathway. SCIENCE ADVANCES 2016; 2:e1501235. [PMID: 26824074 PMCID: PMC4730858 DOI: 10.1126/sciadv.1501235] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 11/18/2015] [Indexed: 06/05/2023]
Abstract
Little is known about the evolutionary origins of metabolism. However, key biochemical reactions of glycolysis and the pentose phosphate pathway (PPP), ancient metabolic pathways central to the metabolic network, have non-enzymatic pendants that occur in a prebiotically plausible reaction milieu reconstituted to contain Archean sediment metal components. These non-enzymatic reactions could have given rise to the origin of glycolysis and the PPP during early evolution. Using nuclear magnetic resonance spectroscopy and high-content metabolomics that allowed us to measure several thousand reaction mixtures, we experimentally address the chemical logic of a metabolism-like network constituted from these non-enzymatic reactions. Fe(II), the dominant transition metal component of Archean oceanic sediments, has binding affinity toward metabolic sugar phosphates and drives metabolism-like reactivity acting as both catalyst and cosubstrate. Iron and pH dependencies determine a metabolism-like network topology and comediate reaction rates over several orders of magnitude so that the network adopts conditional activity. Alkaline pH triggered the activity of the non-enzymatic PPP pendant, whereas gentle acidic or neutral conditions favored non-enzymatic glycolytic reactions. Fe(II)-sensitive glycolytic and PPP-like reactions thus form a chemical network mimicking structural features of extant carbon metabolism, including topology, pH dependency, and conditional reactivity. Chemical networks that obtain structure and catalysis on the basis of transition metals found in Archean sediments are hence plausible direct precursors of cellular metabolic networks.
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Affiliation(s)
- Markus A. Keller
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Andre Zylstra
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Cecilia Castro
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Alexandra V. Turchyn
- Department of Earth Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EQ, UK
| | - Julian L. Griffin
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
- MRC Human Nutrition Research, Elsie Widdowson Laboratory, 120 Fulbourn Road, Cambridge CB1 9NL, UK
| | - Markus Ralser
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London NW7 1AA, UK
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19
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Wamelink MMC, Ramos RJJF, van den Elzen APM, Ruijter GJG, Bonte R, Diogo L, Garcia P, Neves N, Nota B, Haschemi A, Tavares de Almeida I, Salomons GS. First two unrelated cases of isolated sedoheptulokinase deficiency: A benign disorder? J Inherit Metab Dis 2015; 38:889-94. [PMID: 25647543 PMCID: PMC4551550 DOI: 10.1007/s10545-014-9809-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2014] [Revised: 12/29/2014] [Accepted: 12/30/2014] [Indexed: 12/13/2022]
Abstract
We present the first two reported unrelated patients with an isolated sedoheptulokinase (SHPK) deficiency. The first patient presented with neonatal cholestasis, hypoglycemia, and anemia, while the second patient presented with congenital arthrogryposis multiplex, multiple contractures, and dysmorphisms. Both patients had elevated excretion of erythritol and sedoheptulose, and each had a homozygous nonsense mutation in SHPK. SHPK is an enzyme that phosphorylates sedoheptulose to sedoheptulose-7-phosphate, which is an important intermediate of the pentose phosphate pathway. It is questionable whether SHPK deficiency is a causal factor for the clinical phenotypes of our patients. This study illustrates the necessity of extensive functional and clinical workup for interpreting a novel variant, including nonsense variants.
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Affiliation(s)
- Mirjam M C Wamelink
- Department of Clinical Chemistry, Neuroscience Campus Amsterdam, VU University Medical Center, De Boelelaan 1117, 1081HV, Amsterdam, The Netherlands,
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20
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Michel S, Keller MA, Wamelink MMC, Ralser M. A haploproficient interaction of the transaldolase paralogue NQM1 with the transcription factor VHR1 affects stationary phase survival and oxidative stress resistance. BMC Genet 2015; 16:13. [PMID: 25887987 PMCID: PMC4331311 DOI: 10.1186/s12863-015-0171-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 01/21/2015] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Studying the survival of yeast in stationary phase, known as chronological lifespan, led to the identification of molecular ageing factors conserved from yeast to higher organisms. To identify functional interactions among yeast chronological ageing genes, we conducted a haploproficiency screen on the basis of previously identified long-living mutants. For this, we created a library of heterozygous Saccharomyces cerevisiae double deletion strains and aged them in a competitive manner. RESULTS Stationary phase survival was prolonged in a double heterozygous mutant of the metabolic enzyme non-quiescent mutant 1 (NQM1), a paralogue to the pentose phosphate pathway enzyme transaldolase (TAL1), and the transcription factor vitamin H response transcription factor 1 (VHR1). We find that cells deleted for the two genes possess increased clonogenicity at late stages of stationary phase survival, but find no indication that the mutations delay initial mortality upon reaching stationary phase, canonically defined as an extension of chronological lifespan. We show that both genes influence the concentration of metabolites of glycolysis and the pentose phosphate pathway, central metabolic players in the ageing process, and affect osmolality of growth media in stationary phase cultures. Moreover, NQM1 is glucose repressed and induced in a VHR1 dependent manner upon caloric restriction, on non-fermentable carbon sources, as well as under osmotic and oxidative stress. Finally, deletion of NQM1 is shown to confer resistance to oxidizing substances. CONCLUSIONS The transaldolase paralogue NQM1 and the transcription factor VHR1 interact haploproficiently and affect yeast stationary phase survival. The glucose repressed NQM1 gene is induced under various stress conditions, affects stress resistance and this process is dependent on VHR1. While NQM1 appears not to function in the pentose phosphate pathway, the interplay of NQM1 with VHR1 influences the yeast metabolic homeostasis and stress tolerance during stationary phase, processes associated with yeast ageing.
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Affiliation(s)
- Steve Michel
- Max Planck Institute for Molecular Genetics, Ihnestr 73, Berlin, 14195, Germany.
| | - Markus A Keller
- Department of Biochemistry and Cambridge Systems Biology Center, University of Cambridge, 80, Tennis, Court Road, Cambridge, CB2 1GA, UK.
| | - Mirjam M C Wamelink
- Metabolic Unit, Department of Clinical Chemistry, VU University Medical Centre Amsterdam, Amsterdam, The Netherlands.
| | - Markus Ralser
- Department of Biochemistry and Cambridge Systems Biology Center, University of Cambridge, 80, Tennis, Court Road, Cambridge, CB2 1GA, UK.
- MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London, UK.
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21
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Stincone A, Prigione A, Cramer T, Wamelink MMC, Campbell K, Cheung E, Olin-Sandoval V, Grüning NM, Krüger A, Tauqeer Alam M, Keller MA, Breitenbach M, Brindle KM, Rabinowitz JD, Ralser M. The return of metabolism: biochemistry and physiology of the pentose phosphate pathway. Biol Rev Camb Philos Soc 2014; 90:927-63. [PMID: 25243985 PMCID: PMC4470864 DOI: 10.1111/brv.12140] [Citation(s) in RCA: 823] [Impact Index Per Article: 82.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 07/07/2014] [Accepted: 07/16/2014] [Indexed: 12/13/2022]
Abstract
The pentose phosphate pathway (PPP) is a fundamental component of cellular metabolism. The PPP is important to maintain carbon homoeostasis, to provide precursors for nucleotide and amino acid biosynthesis, to provide reducing molecules for anabolism, and to defeat oxidative stress. The PPP shares reactions with the Entner–Doudoroff pathway and Calvin cycle and divides into an oxidative and non-oxidative branch. The oxidative branch is highly active in most eukaryotes and converts glucose 6-phosphate into carbon dioxide, ribulose 5-phosphate and NADPH. The latter function is critical to maintain redox balance under stress situations, when cells proliferate rapidly, in ageing, and for the ‘Warburg effect’ of cancer cells. The non-oxidative branch instead is virtually ubiquitous, and metabolizes the glycolytic intermediates fructose 6-phosphate and glyceraldehyde 3-phosphate as well as sedoheptulose sugars, yielding ribose 5-phosphate for the synthesis of nucleic acids and sugar phosphate precursors for the synthesis of amino acids. Whereas the oxidative PPP is considered unidirectional, the non-oxidative branch can supply glycolysis with intermediates derived from ribose 5-phosphate and vice versa, depending on the biochemical demand. These functions require dynamic regulation of the PPP pathway that is achieved through hierarchical interactions between transcriptome, proteome and metabolome. Consequently, the biochemistry and regulation of this pathway, while still unresolved in many cases, are archetypal for the dynamics of the metabolic network of the cell. In this comprehensive article we review seminal work that led to the discovery and description of the pathway that date back now for 80 years, and address recent results about genetic and metabolic mechanisms that regulate its activity. These biochemical principles are discussed in the context of PPP deficiencies causing metabolic disease and the role of this pathway in biotechnology, bacterial and parasite infections, neurons, stem cell potency and cancer metabolism.
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Affiliation(s)
- Anna Stincone
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, U.K.,Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, U.K
| | - Alessandro Prigione
- Max Delbrueck Centre for Molecular Medicine, Robert-Rössle-Str. 10, 13092 Berlin, Germany
| | - Thorsten Cramer
- Department of Gastroenterology and Hepatology, Molekulares Krebsforschungszentrum (MKFZ), Charité - Universitätsmedizin Berlin, Campus Virchow-Klinikum, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Mirjam M C Wamelink
- Metabolic Unit, Department of Clinical Chemistry, VU University Medical Centre Amsterdam, De Boelelaaan 1117, 1081 HV Amsterdam, The Netherlands
| | - Kate Campbell
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, U.K.,Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, U.K
| | - Eric Cheung
- Cancer Research UK, Beatson Institute, Switchback Road, Glasgow G61 1BD, U.K
| | - Viridiana Olin-Sandoval
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, U.K.,Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, U.K
| | - Nana-Maria Grüning
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, U.K.,Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, U.K
| | - Antje Krüger
- Max Planck Institute for Molecular Genetics, Ihnestr 73, 14195 Berlin, Germany
| | - Mohammad Tauqeer Alam
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, U.K.,Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, U.K
| | - Markus A Keller
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, U.K.,Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, U.K
| | - Michael Breitenbach
- Department of Cell Biology, University of Salzburg, Hellbrunnerstrasse 34, A-5020 Salzburg, Austria
| | - Kevin M Brindle
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, U.K.,Cancer Research UK Cambridge Research Institute (CRI), Li Ka Shing Centre, University of Cambridge, Robinson Way, Cambridge CB2 0RE, U.K
| | - Joshua D Rabinowitz
- Department of Chemistry, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, 08544 NJ, U.S.A
| | - Markus Ralser
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, U.K.,Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, U.K.,Division of Physiology and Metabolism, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7, U.K
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22
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Ravi G, Venkatesh YP. Recognition of flavin mononucleotide, Haemophilus influenzae type b and its capsular polysaccharide vaccines by antibodies specific to D-ribitol-5-phosphate. Glycoconj J 2014; 31:573-85. [PMID: 25108762 DOI: 10.1007/s10719-014-9539-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Revised: 07/22/2014] [Accepted: 07/22/2014] [Indexed: 11/25/2022]
Abstract
D-Ribitol-5-phosphate (Rbt-5-P) is an important metabolite in the pentose phosphate pathway and an integral part of bacterial cell wall polysaccharides, specifically as polyribosyl ribitol phosphate (PRP) in Haemophilus influenzae type b (Hib). The major objective of this study was to investigate whether an antibody specific to Rbt-5-P can recognize the PRP of Hib. D-Ribose-5-phosphate was reacted with proteins in the presence of sodium cyanoborohydride to obtain Rbt-5-P epitopes; 120 h reaction resulted in conjugation of ~30 and ~17 moles of Rbt-5-P/mole of BSA and OVA, respectively, based on decrease in amino groups, MALDI-TOF analyses, an increase in apparent molecular weight (SDS-PAGE) and glycoprotein staining. Immunization of rabbits with Rbt-5-P-BSA conjugate generated antibodies to Rbt-5-P as demonstrated by dot immunoblot and non-competitive ELISA. Homogeneous Rbt-5-P-specific antibody was purified from Rbt-5-P-BSA antiserum subjected to caprylic acid precipitation followed by hapten-affinity chromatography; its affinity constant is 7.1 × 10(8) M(-1). Rbt-5-P antibody showed 100 % specificity to Rbt-5-P, ~230 %, 10 % and 3.4 % cross-reactivity to FMN, riboflavin and FAD, respectively; the antibody showed ~4 % cross-reactivity to D-ribitol and <3 % to other sugars/sugar alcohols. Rbt-5-P-specific antibody recognized Hib conjugate vaccines containing PRP which was inhibited specifically by Rbt-5-P, and also detected Hib cell-surface capsular polysaccharides by immunofluorescence. In conclusion, Rbt-5-P-protein conjugate used as an immunogen elicited antibodies binding to an epitope also present in PRP and Hib bacteria. Rbt-5-P-specific antibody has potential applications in the detection and quantification of free/bound Rbt-5-P and FMN as well as immunological recognition of Hib bacteria and its capsular polysaccharide.
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Affiliation(s)
- G Ravi
- Department of Biochemistry and Nutrition, CSIR-Central Food Technological Research Institute (CFTRI), 'Chaluvamba Vilas', KRS Road, Mysore, 570020, Karnataka State, India
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Keller MA, Turchyn AV, Ralser M. Non-enzymatic glycolysis and pentose phosphate pathway-like reactions in a plausible Archean ocean. Mol Syst Biol 2014; 10:725. [PMID: 24771084 PMCID: PMC4023395 DOI: 10.1002/msb.20145228] [Citation(s) in RCA: 141] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 03/11/2014] [Accepted: 03/18/2014] [Indexed: 11/30/2022] Open
Abstract
The reaction sequences of central metabolism, glycolysis and the pentose phosphate pathway provide essential precursors for nucleic acids, amino acids and lipids. However, their evolutionary origins are not yet understood. Here, we provide evidence that their structure could have been fundamentally shaped by the general chemical environments in earth's earliest oceans. We reconstructed potential scenarios for oceans of the prebiotic Archean based on the composition of early sediments. We report that the resultant reaction milieu catalyses the interconversion of metabolites that in modern organisms constitute glycolysis and the pentose phosphate pathway. The 29 observed reactions include the formation and/or interconversion of glucose, pyruvate, the nucleic acid precursor ribose-5-phosphate and the amino acid precursor erythrose-4-phosphate, antedating reactions sequences similar to that used by the metabolic pathways. Moreover, the Archean ocean mimetic increased the stability of the phosphorylated intermediates and accelerated the rate of intermediate reactions and pyruvate production. The catalytic capacity of the reconstructed ocean milieu was attributable to its metal content. The reactions were particularly sensitive to ferrous iron Fe(II), which is understood to have had high concentrations in the Archean oceans. These observations reveal that reaction sequences that constitute central carbon metabolism could have been constrained by the iron-rich oceanic environment of the early Archean. The origin of metabolism could thus date back to the prebiotic world.
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Affiliation(s)
- Markus A Keller
- Department of Biochemistry and Cambridge Systems Biology CentreUniversity of CambridgeCambridgeUK
| | | | - Markus Ralser
- Department of Biochemistry and Cambridge Systems Biology CentreUniversity of CambridgeCambridgeUK
- Division of Physiology and MetabolismMRC National Institute for Medical ResearchMill HillLondonUK
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Grüning NM, Du D, Keller MA, Luisi BF, Ralser M. Inhibition of triosephosphate isomerase by phosphoenolpyruvate in the feedback-regulation of glycolysis. Open Biol 2014; 4:130232. [PMID: 24598263 PMCID: PMC3971408 DOI: 10.1098/rsob.130232] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The inhibition of triosephosphate isomerase (TPI) in glycolysis by the pyruvate kinase (PK) substrate phosphoenolpyruvate (PEP) results in a newly discovered feedback loop that counters oxidative stress in cancer and actively respiring cells. The mechanism underlying this inhibition is illuminated by the co-crystal structure of TPI with bound PEP at 1.6 Å resolution, and by mutational studies guided by the crystallographic results. PEP is bound to the catalytic pocket of TPI and occludes substrate, which accounts for the observation that PEP competitively inhibits the interconversion of glyceraldehyde-3-phosphate and dihydroxyacetone phosphate. Replacing an isoleucine residue located in the catalytic pocket of TPI with valine or threonine altered binding of substrates and PEP, reducing TPI activity in vitro and in vivo. Confirming a TPI-mediated activation of the pentose phosphate pathway (PPP), transgenic yeast cells expressing these TPI mutations accumulate greater levels of PPP intermediates and have altered stress resistance, mimicking the activation of the PK-TPI feedback loop. These results support a model in which glycolytic regulation requires direct catalytic inhibition of TPI by the pyruvate kinase substrate PEP, mediating a protective metabolic self-reconfiguration of central metabolism under conditions of oxidative stress.
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Affiliation(s)
- Nana-Maria Grüning
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
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25
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Novel association of early onset hepatocellular carcinoma with transaldolase deficiency. JIMD Rep 2013; 12:121-7. [PMID: 24097415 PMCID: PMC3897795 DOI: 10.1007/8904_2013_254] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Revised: 07/15/2013] [Accepted: 07/22/2013] [Indexed: 01/20/2023] Open
Abstract
We evaluated a family with a 16-month-old boy with cirrhosis and hepatocellular carcinoma and his 30-month-old brother with cirrhosis. After failing to identify a diagnosis after routine metabolic evaluation, we utilized a combination of RNA-Seq and whole exome sequencing to identify a novel homozygous p.Ser171Phe Transaldolase (TALDO1) variant in the proband, his brother with cirrhosis, as well as a clinically asymptomatic older 8-year-old brother. Metabolite analysis and enzymatic testing of TALDO1 demonstrated elevated ribitol, sedoheptitol, and sedoheptulose-7P, and lack of activity of TALDO1 in the three children homozygous for the p.Ser171Phe mutation. Our findings expand the phenotype of transaldolase deficiency to include early onset hepatocellular carcinoma in humans and demonstrate that, even within the same family, individuals with the same homozygous mutation demonstrate a wide range of phenotypes.
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Xia M, Huang D, Li S, Wen J, Jia X, Chen Y. Enhanced FK506 production inStreptomyces tsukubaensisby rational feeding strategies based on comparative metabolic profiling analysis. Biotechnol Bioeng 2013; 110:2717-30. [DOI: 10.1002/bit.24941] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Revised: 03/22/2013] [Accepted: 04/17/2013] [Indexed: 11/11/2022]
Affiliation(s)
- Menglei Xia
- Department of Biological Engineering, School of Chemical Engineering and Technology; Tianjin University; Tianjin; 300072; People's Republic of China
| | - Di Huang
- Department of Biological Engineering, School of Chemical Engineering and Technology; Tianjin University; Tianjin; 300072; People's Republic of China
| | - Shanshan Li
- Department of Biological Engineering, School of Chemical Engineering and Technology; Tianjin University; Tianjin; 300072; People's Republic of China
| | | | | | - Yunlin Chen
- School of Science; Beijing Jiaotong University; Beijing; People's Republic of China
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Sedoheptulose kinase regulates cellular carbohydrate metabolism by sedoheptulose 7-phosphate supply. Biochem Soc Trans 2013; 41:674-80. [DOI: 10.1042/bst20120354] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Dynamic carbon re-routing between catabolic and anabolic metabolism is an essential element of cellular transformation associated with tumour formation and immune cell activation. Such bioenergetic adaptations are important for cellular function and therefore require tight control. Carbohydrate phosphorylation has been proposed as a rate-limiting step of several metabolic networks. The recent identification of a sedoheptulose kinase indicated that free sedoheptulose is a relevant and accessible carbon source in humans. Furthermore, the bioavailability of its phosphorylated form, sedoheptulose 7-phosphate, appears to function as a rheostat for carbon-flux at the interface of glycolysis and the pentose phosphate pathway. In the present paper, we review reports of sedoheptulose metabolism, compare it with glucose metabolism, and discuss the regulation of sedoheptulose kinase as mechanism to achieve bioenergetic reprogramming in cells.
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Becker S, Kortz L, Helmschrodt C, Thiery J, Ceglarek U. LC–MS-based metabolomics in the clinical laboratory. J Chromatogr B Analyt Technol Biomed Life Sci 2012; 883-884:68-75. [DOI: 10.1016/j.jchromb.2011.10.018] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2011] [Revised: 10/13/2011] [Accepted: 10/14/2011] [Indexed: 10/16/2022]
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Varum S, Rodrigues AS, Moura MB, Momcilovic O, Easley CA, Ramalho-Santos J, Van Houten B, Schatten G. Energy metabolism in human pluripotent stem cells and their differentiated counterparts. PLoS One 2011; 6:e20914. [PMID: 21698063 PMCID: PMC3117868 DOI: 10.1371/journal.pone.0020914] [Citation(s) in RCA: 516] [Impact Index Per Article: 39.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Accepted: 05/16/2011] [Indexed: 12/11/2022] Open
Abstract
Background Human pluripotent stem cells have the ability to generate all cell types present in the adult organism, therefore harboring great potential for the in vitro study of differentiation and for the development of cell-based therapies. Nonetheless their use may prove challenging as incomplete differentiation of these cells might lead to tumoregenicity. Interestingly, many cancer types have been reported to display metabolic modifications with features that might be similar to stem cells. Understanding the metabolic properties of human pluripotent stem cells when compared to their differentiated counterparts can thus be of crucial importance. Furthermore recent data has stressed distinct features of different human pluripotent cells lines, namely when comparing embryo-derived human embryonic stem cells (hESCs) and induced pluripotent stem cells (IPSCs) reprogrammed from somatic cells. Methodology/Principal Findings We compared the energy metabolism of hESCs, IPSCs, and their somatic counterparts. Focusing on mitochondria, we tracked organelle localization and morphology. Furthermore we performed gene expression analysis of several pathways related to the glucose metabolism, including glycolysis, the pentose phosphate pathway and the tricarboxylic acid (TCA) cycle. In addition we determined oxygen consumption rates (OCR) using a metabolic extracellular flux analyzer, as well as total intracellular ATP levels by high performance liquid chromatography (HPLC). Finally we explored the expression of key proteins involved in the regulation of glucose metabolism. Conclusions/Findings Our results demonstrate that, although the metabolic signature of IPSCs is not identical to that of hESCs, nonetheless they cluster with hESCs rather than with their somatic counterparts. ATP levels, lactate production and OCR revealed that human pluripotent cells rely mostly on glycolysis to meet their energy demands. Furthermore, our work points to some of the strategies which human pluripotent stem cells may use to maintain high glycolytic rates, such as high levels of hexokinase II and inactive pyruvate dehydrogenase (PDH).
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Affiliation(s)
- Sandra Varum
- Pittsburgh Development Center, Magee Womens Research Institute, Pittsburgh, Pennsylvania, United States of America
- Center for Neuroscience and Cell Biology and Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Ana S. Rodrigues
- Pittsburgh Development Center, Magee Womens Research Institute, Pittsburgh, Pennsylvania, United States of America
- Center for Neuroscience and Cell Biology and Department of Life Sciences, University of Coimbra, Coimbra, Portugal
- PhD Programme in Experimental Biology and Biomedicine (PDBEB), Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Michelle B. Moura
- Department of Pharmacology and Chemical Biology, University of Pittsburgh Cancer Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Olga Momcilovic
- Pittsburgh Development Center, Magee Womens Research Institute, Pittsburgh, Pennsylvania, United States of America
| | - Charles A. Easley
- Pittsburgh Development Center, Magee Womens Research Institute, Pittsburgh, Pennsylvania, United States of America
| | - João Ramalho-Santos
- Center for Neuroscience and Cell Biology and Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Bennett Van Houten
- Department of Pharmacology and Chemical Biology, University of Pittsburgh Cancer Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Gerald Schatten
- Pittsburgh Development Center, Magee Womens Research Institute, Pittsburgh, Pennsylvania, United States of America
- Department of Obstetrics, Gynecology & Reproductive Sciences, and Cell Biology-Physiology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
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Schutz PW, Struys EA, Sinclair G, Stockler S. Protective effects of d-3-hydroxybutyrate and propionate during hypoglycemic coma: clinical and biochemical insights from infant rats. Mol Genet Metab 2011; 103:179-84. [PMID: 21439874 DOI: 10.1016/j.ymgme.2011.02.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2011] [Accepted: 02/20/2011] [Indexed: 10/18/2022]
Abstract
BACKGROUND d-3-hydroxybutyrate (3OHB) is an alternative energy substrate for the brain during hypoglycemia, especially during infancy. Supplementation of 3OHB during sustained hypoglycemia in rat pups delays onset of burst suppression coma, but is associated with white matter injury and increased mortality. The biochemical basis for this ambivalent effect is not known. It may be related to an anaplerotic or gluconeogenetic deficit of 3OHB. METHODS AND RESULTS We studied clinical alertness, EEG and brain metabolites (acyl-carnitines, amino acids, glycolytic and pentose phosphate intermediates) in 13 day-old rat pups during insulin induced hypoglycemic coma and after treatment with 3OHB alone or in combination with the anaplerotic substrate propionate. Clinically, treatment with 3OHB and propionate resulted in an alert state and EEG improvement, while treatment with 3OHB alone resulted in an improved EEG but animals remained clinically comatose. Biochemically, both treatments resulted in correction of cerebral glutamate and ammonia levels but not of gluconeogenetic substrates and pentose phosphate metabolites. CONCLUSION 3OHB treatment restores glutamate metabolism but cannot restore a glycolytic or pentose phosphate pathway deficit. Additional treatment with propionate significantly improved the clinical protective effect of 3OHB in hypoglycemic coma.
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Affiliation(s)
- Peter W Schutz
- Department of Pediatrics, University of British Columbia, British Columbia Children's Hospital, 4480 Oak Street, Vancouver, BC, Canada V6H
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Li Y, Ptolemy AS, Harmonay L, Kellogg M, Berry GT. Ultra fast and sensitive liquid chromatography tandem mass spectrometry based assay for galactose-1-phosphate uridylyltransferase and galactokinase deficiencies. Mol Genet Metab 2011; 102:33-40. [PMID: 20863731 PMCID: PMC3743081 DOI: 10.1016/j.ymgme.2010.08.018] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2010] [Accepted: 08/26/2010] [Indexed: 11/30/2022]
Abstract
The diagnosis of transferase and galactokinase deficiency galactosemia usually involves the measurement of erythrocyte galactose-1-phosphate uridylyltransferase (GALT) and galactokinase (GALK) enzyme activity, respectively. The current gold standard assays for these enzymes are radioactive assays, which are laborious and/or incapable of measuring low enzyme activities. To further our knowledge of genotype-phenotype relationships, we had developed an assay for GALT activity alone using LC-MS/MS. In this study we generated a robust and sensitive LC-MS/MS based GALT and GALK assay using a novel normal phase chromatographic condition. We improved upon our earlier assay by drastically reducing the instrument run time and eliminating the use of an ion pairing reagent. Stable isotope labeled substrates were utilized in the GALT and GALK assays. The enzymatic products ([(13)C(6)]-uridine diphosphate galactose in GALT assay and [(13)C(6)]-galactose-1-phosphate in GALK assay) were quantified in a 3 min LC-MS/MS run. The assays were sensitive enough to allow for the quantification of enzyme activities as low as 0.2% and 0.3% of normal control values in the GALT and GALK assays, respectively. Thirty-three samples from non-galactosemic patients were assayed to have erythrocyte GALT activity of 23.4±4.2 and GALK activity of 1.8±0.47 (mean±SD) μmol⋅(g Hgb)(-1) h(-1). Erythrocyte GALT activities in a cohort of 16 patients with classic or severe galactosemia were measured: 4 patients had GALT activity less than 1% of normal control values and the remaining 12 had no detectable GALT activity. No GALK activity was detected in a GALK deficient sample we analyzed. Lastly, we tested the feasibility of adapting this LC-MS/MS based GALT/GALK assay as a newborn screening (NBS) test.
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Affiliation(s)
- Yijun Li
- The Manton Center for Orphan Disease Research, Division of Genetics, Department of Pediatrics
| | - Adam S. Ptolemy
- Department of Laboratory Medicine, Children's Hospital Boston, Harvard Medical School, Boston, MA, USA
| | - Lauren Harmonay
- The Manton Center for Orphan Disease Research, Division of Genetics, Department of Pediatrics
| | - Mark Kellogg
- Department of Laboratory Medicine, Children's Hospital Boston, Harvard Medical School, Boston, MA, USA
| | - Gerard T. Berry
- The Manton Center for Orphan Disease Research, Division of Genetics, Department of Pediatrics
- Address correspondence to: GT Berry, Children's Hospital Boston, 300 Longwood Ave, Boston, MA 02115 United States. Tel: (617) 355-4316, Fax: (617) −730-0788,
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Novel heterozygous mutations in TALDO1 gene causing transaldolase deficiency and early infantile liver failure. J Pediatr Gastroenterol Nutr 2011; 52:113-6. [PMID: 21119539 DOI: 10.1097/mpg.0b013e3181f50388] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
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Jannasch A, Sedlak M, Adamec J. Quantification of pentose phosphate pathway (PPP) metabolites by liquid chromatography-mass spectrometry (LC-MS). Methods Mol Biol 2011; 708:159-71. [PMID: 21207289 DOI: 10.1007/978-1-61737-985-7_9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The pentose phosphate pathway plays an important role in several cellular processes including biosynthesis and catabolism of five-carbon sugars and generation of reducing power through NADPH synthesis. Although the pentose phosphate metabolic reaction network has been mapped in substantial detail, the comprehensive quantitative analysis of the rates and regulation of individual reactions remains a major interest for various biofields. Here we describe a simple method for comprehensive quantitative analysis of pentose phosphate pathway intermediates. The method is based on Group Specific Internal Standard Technology (GSIST) labeling in which an experimental sample and corresponding internal standards are derivatized in vitro with isotope-coded reagents in separate reactions, then mixed and analyzed in a single LC-MS run. The use of co-eluting isotope-coded internal standards and experimental molecules eliminates potential issues with ion suppression and allows for precise quantification of individual metabolites. Derivatization also increases hydrophobicity of the metabolites enabling their effective separation using reversed-phase chromatography.
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Affiliation(s)
- Amber Jannasch
- Bindley Bioscience Center, Purdue University, West Lafayette, IN, USA.
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D'Alessandro A, Gevi F, Zolla L. A robust high resolution reversed-phase HPLC strategy to investigate various metabolic species in different biological models. MOLECULAR BIOSYSTEMS 2011; 7:1024-32. [DOI: 10.1039/c0mb00274g] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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35
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Hinterwirth H, Lämmerhofer M, Preinerstorfer B, Gargano A, Reischl R, Bicker W, Trapp O, Brecker L, Lindner W. Selectivity issues in targeted metabolomics: Separation of phosphorylated carbohydrate isomers by mixed-mode hydrophilic interaction/weak anion exchange chromatography. J Sep Sci 2010; 33:3273-82. [DOI: 10.1002/jssc.201000412] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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36
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The difference between rare and exceptionally rare: molecular characterization of ribose 5-phosphate isomerase deficiency. J Mol Med (Berl) 2010; 88:931-9. [PMID: 20499043 DOI: 10.1007/s00109-010-0634-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2010] [Revised: 05/03/2010] [Accepted: 05/04/2010] [Indexed: 12/29/2022]
Abstract
Ribose 5-phosphate isomerase (RPI) deficiency is an enzymopathy of the pentose phosphate pathway. It manifests with progressive leukoencephalopathy and peripheral neuropathy and belongs, with one sole diagnosed case, to the rarest human disorders. The single patient was found compound heterozygous for a RPI frameshift and a missense (RPI(Ala61Val)) allele. Here, we report that two patient-derived cell lines differ in RPI enzyme activity, enzyme concentration, and mRNA expression. Furthermore, we present a transgenic yeast model, which exhibits metabolite- and enzyme-activity changes that correspond to the human syndrome and show that the decrease in RPI activity in patient cells is not fully attributable to the residue exchange. Taken together, our results demonstrate that RPI deficiency is caused by the combination of a RPI null allele with an allele that encodes for a partially active enzyme which has, in addition, cell-type-dependent expression deficits. We speculate that a low probability for comparable traits accounts for the rareness of RPI deficiency.
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Bijnsdorp IV, Azijli K, Jansen EE, Wamelink MM, Jakobs C, Struys EA, Fukushima M, Kruyt FAE, Peters GJ. Accumulation of thymidine-derived sugars in thymidine phosphorylase overexpressing cells. Biochem Pharmacol 2010; 80:786-92. [PMID: 20488166 DOI: 10.1016/j.bcp.2010.05.009] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2010] [Revised: 05/10/2010] [Accepted: 05/11/2010] [Indexed: 11/30/2022]
Abstract
Thymidine phosphorylase (TP) is often overexpressed in cancer and potentially plays a role in the stimulation of angiogenesis. The exact mechanism of angiogenesis induction is unclear, but is postulated to be related to thymidine-derived sugars. TP catalyzes the conversion of thymidine (TdR) to thymine and deoxyribose-1-phosphate (dR-1-P), which can be converted to dR-5-P, glyceraldehyde-3-phosphate (G3P) or deoxyribose (dR). However, it is unclear which sugar accumulates in this reaction. Therefore, in the TP overexpressing Colo320 TP1 and RT112/TP cells we determined by LC-MS/MS which sugars accumulated, their subcellular localization (using (3)H-TdR) and whether dR was secreted from the cells. In both TP-overexpressing cell lines, dR-1-P and dR-5-P accumulated intracellularly at high levels and dR was secreted extensively by the cells. A specific inhibitor of TP completely blocked TdR conversion, and thus no sugars were formed. To examine whether these sugars may be used for the production of angiogenic factors or other products, we determined with (3)H-TdR in which subcellular location these sugars accumulated. TdR-derived sugars accumulated in the cytoskeleton and to some extent in the cell membrane, while incorporation into the DNA was responsible for trapping in the nucleus. In conclusion, various metabolic routes were entered, of which the TdR-derived sugars accumulated in the cytoskeleton and membrane. Future studies should focus on which exact metabolic pathway is involved in the induction of angiogenesis.
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Affiliation(s)
- I V Bijnsdorp
- VU University Medical Center, Department Medical Oncology, De Boelelaan 1117 CCA 1.42, 1081 HV Amsterdam, The Netherlands
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Li W, Tse FLS. Dried blood spot sampling in combination with LC-MS/MS for quantitative analysis of small molecules. Biomed Chromatogr 2010; 24:49-65. [DOI: 10.1002/bmc.1367] [Citation(s) in RCA: 456] [Impact Index Per Article: 32.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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39
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Yang WC, Sedlak M, Regnier FE, Mosier N, Ho N, Adamec J. Simultaneous quantification of metabolites involved in central carbon and energy metabolism using reversed-phase liquid chromatography-mass spectrometry and in vitro 13C labeling. Anal Chem 2009; 80:9508-16. [PMID: 19007244 DOI: 10.1021/ac801693c] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Comprehensive analysis of intracellular metabolites is a critical component of elucidating cellular processes. Although the resolution and flexibility of reversed-phase liquid chromatography-mass spectrometry (RPLC-MS) makes it one of the most powerful analytical tools for metabolite analysis, the structural diversity of even the simplest metabolome provides a formidable analytical challenge. Here we describe a robust RPLC-MS method for identification and quantification of a diverse group of metabolites ranging from sugars, phosphosugars, and carboxylic acids to phosphocarboxylics acids, nucleotides, and coenzymes. This method is based on in vitro derivatization with a (13)C-labeled tag that allows internal standard based quantification and enables separation of structural isomer pairs like glucose 6-phosphate and fructose 6-phosphate in a single chromatographic run. Calibration curves for individual metabolites showed linearity ranging over more than 2 orders of magnitude with correlation coefficients of R(2) > 0.9975. The detection limits at a signal-to-noise ratio of 3 were below 1.0 microM (20 pmol) for most compounds. Thirty common metabolites involved in glycolysis, the pentose phosphate pathway, and tricarboxylic acid cycle were identified and quantified from yeast lysate with a relative standard deviation of less than 10%.
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Affiliation(s)
- Wen-Chu Yang
- Bindley Bioscience Center, Purdue University, West Lafayette, Indiana 47907, USA
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Cipollina C, ten Pierick A, Canelas AB, Seifar RM, van Maris AJA, van Dam JC, Heijnen JJ. A comprehensive method for the quantification of the non-oxidative pentose phosphate pathway intermediates in Saccharomyces cerevisiae by GC-IDMS. J Chromatogr B Analyt Technol Biomed Life Sci 2009; 877:3231-6. [PMID: 19647496 DOI: 10.1016/j.jchromb.2009.07.019] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2009] [Revised: 07/10/2009] [Accepted: 07/15/2009] [Indexed: 11/25/2022]
Abstract
A gas chromatography isotope dilution mass spectrometry (GC-IDMS) method was developed for the quantification of the metabolites of the non-oxidative part of pentose phosphate pathway (PPP). A mid-polar GC column (Zebron ZB-AAA, 10m, film composition 50% phenyl 50% dimethyl polysiloxane) was used for the chromatographic separation of the intermediates. The optimized GC-MS procedure resulted in improved separation performances and higher sensitivities compared to previous methods. Furthermore, the use of (13)C-labeled cell extracts as internal standards improved the data quality and eliminated the need to perform a recovery check for each metabolite. The applicability of the new method was demonstrated by analyzing intracellular metabolite levels in samples derived from aerobic glucose-limited chemostat cultures of Saccharomyces cerevisiae at steady state as well as following a short-term glucose pulse. The major achievements of the proposed quantitative method are the independent quantification of the epimers ribulose-5-phosphate and xylulose-5-posphate and the measurement of compounds present at very low concentrations in biological samples such as erythrose-4-phosphate and glyceraldehyde-3-phosphate.
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Affiliation(s)
- Chiara Cipollina
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
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41
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Ross KL, Dalluge JJ. Liquid chromatography/tandem mass spectrometry of glycolytic intermediates: deconvolution of coeluting structural isomers based on unique product ion ratios. Anal Chem 2009; 81:4021-6. [PMID: 19354282 DOI: 10.1021/ac9004698] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A method has been developed for rapid quantification of nine glycolytic intermediates using ultraperformance liquid chromatography/electrospray-tandem mass spectrometry (UPLC/ESI-MS/MS) to monitor the metabolism of glucose during microbial fermentation. Because comprehensive chromatographic separation is not required, analysis time is significantly less than traditional ion exchange liquid chromatography assays or enzymatic assays. Complete glycolytic intermediate analysis by LC/MS/MS can be achieved in less than 7 min per sample. Quantification is accomplished using isotopically labeled glucose, glucose-6-phosphate, and pyruvate as internal standards. In addition, a method to deconvolute peak areas of coeluting structural isomers based on unique product ion ratios has been developed to allow accurate quantification of the individual isomers 2-phosphoglycerate and 3-phosphoglycerate, as well as glucose-6-phosphate and fructose-6-phosphate. Intrasample precisions for glycolytic intermediate measurements in cell-free extracts using this method vary between 0.9% and 11.8%, averaging 3.5% (RSD). Calibration curves are linear over the range 0.1-100 microg/mL, and detection limits are estimated at 2-49 ng/mL. Spike recoveries in cell extracts vary from 53% to 127% averaging 91%. This method has the potential to demonstrate correlation of glycolytic intermediate flux to microbial production profiles toward acceleration of the bioprocess development cycle.
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Affiliation(s)
- Keri Lyn Ross
- Cargill Global Food Technology Group, Cargill Incorporated, P.O. Box 5702, Minneapolis, Minnesota 55440-5702, USA
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Tylki-Szymańska A, Stradomska TJ, Wamelink MMC, Salomons GS, Taybert J, Pawłowska J, Jakobs C. Transaldolase deficiency in two new patients with a relative mild phenotype. Mol Genet Metab 2009; 97:15-7. [PMID: 19299175 DOI: 10.1016/j.ymgme.2009.01.016] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2008] [Revised: 01/30/2009] [Accepted: 01/30/2009] [Indexed: 11/18/2022]
Abstract
Transaldolase (TALDO) deficiency is a recently described inborn error of metabolism of the pentose phosphate pathway that so far has been diagnosed in only eight patients. In this article, we report the clinical course and biochemical findings of two newly identified patients with TALDO deficiency-two sons of consanguineous parents from Polish origin, presenting with neonatal onset of bleeding diathesis, haemolytic anemia, thrombocytopenia and hepatosplenomegaly. Subsequently the patients had persistent thrombocytopenia, a bleeding tendency, impaired liver function and fibrosis. Their physical and psychomotor development progressed normally.
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Affiliation(s)
- Anna Tylki-Szymańska
- Clinic of Metabolic Diseases, Endocrinology and Diabetology, The Children's Memorial Health Institute, Al. Dzieci Polskich 20, 04-730 Warsaw, Poland. ,
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43
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Wamelink MMC, Struys EA, Jakobs C. The biochemistry, metabolism and inherited defects of the pentose phosphate pathway: a review. J Inherit Metab Dis 2008; 31:703-17. [PMID: 18987987 DOI: 10.1007/s10545-008-1015-6] [Citation(s) in RCA: 208] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2008] [Revised: 09/09/2008] [Accepted: 09/17/2008] [Indexed: 11/27/2022]
Abstract
The recent discovery of two defects (ribose-5-phosphate isomerase deficiency and transaldolase deficiency) in the reversible part of the pentose phosphate pathway (PPP) has stimulated interest in this pathway. In this review we describe the functions of the PPP, its relation to other pathways of carbohydrate metabolism and an overview of the metabolic defects in the reversible part of the PPP.
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Affiliation(s)
- M M C Wamelink
- Metabolic Unit, Department of Clinical Chemistry, VU University Medical Center, De Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands.
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A catabolic block does not sufficiently explain how 2-deoxy-D-glucose inhibits cell growth. Proc Natl Acad Sci U S A 2008; 105:17807-11. [PMID: 19004802 DOI: 10.1073/pnas.0803090105] [Citation(s) in RCA: 125] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The glucose analogue 2-deoxy-D-glucose (2-DG) restrains growth of normal and malignant cells, prolongs the lifespan of C. elegans, and is widely used as a glycolytic inhibitor to study metabolic activity with regard to cancer, neurodegeneration, calorie restriction, and aging. Here, we report that separating glycolysis and the pentose phosphate pathway highly increases cellular tolerance to 2-DG. This finding indicates that 2-DG does not block cell growth solely by preventing glucose catabolism. In addition, 2-DG provoked similar concentration changes of sugar-phosphate intermediates in wild-type and 2-DG-resistant yeast strains and in human primary fibroblasts. Finally, a genome-wide analysis revealed 19 2-DG-resistant yeast knockouts of genes implicated in carbohydrate metabolism and mitochondrial homeostasis, as well as ribosome biogenesis, mRNA decay, transcriptional regulation, and cell cycle. Thus, processes beyond the metabolic block are essential for the biological properties of 2-DG.
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Wamelink MMC, Struys EA, Jansen EEW, Levtchenko EN, Zijlstra FSM, Engelke U, Blom HJ, Jakobs C, Wevers RA. Sedoheptulokinase deficiency due to a 57-kb deletion in cystinosis patients causes urinary accumulation of sedoheptulose: elucidation of the CARKL gene. Hum Mutat 2008; 29:532-6. [PMID: 18186520 DOI: 10.1002/humu.20685] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The most common mutation in the nephropathic cystinosis (CTNS) gene is a homozygous 57-kb deletion that also includes an adjacent gene carbohydrate kinase-like (CARKL). The latter gene encodes a protein that is predicted to function as a carbohydrate kinase. Cystinosis patients with the common 57-kb deletion had strongly elevated urinary concentrations of sedoheptulose (28-451 mmol/mol creatinine; controls and other cystinosis patients <9) and erythritol (234-1110 mmol/mol creatinine; controls and other cystinosis patients <148). Enzyme studies performed on fibroblast homogenates derived from patients carrying the 57-kb deletion revealed 80% reduction in their sedoheptulose phosphorylating activity compared to cystinosis patients with other mutations and controls. This indicates that the CARKL-encoded protein, sedoheptulokinase (SHK), is responsible for the reaction: sedoheptulose + ATP --> sedoheptulose-7-phosphate + ADP and that deletion of CARKL causes urinary accumulation of sedoheptulose and erythritol.
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Affiliation(s)
- Mirjam M C Wamelink
- Department of Clinical Chemistry, Metabolic Unit, VU University Medical Center, Amsterdam, The Netherlands.
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46
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Hyphenated mass spectrometry in the analysis of the central carbon metabolism. Anal Bioanal Chem 2008; 391:895-8. [PMID: 18414831 DOI: 10.1007/s00216-008-2084-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2008] [Revised: 03/19/2008] [Accepted: 03/19/2008] [Indexed: 10/22/2022]
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47
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Wamelink MMC, Struys EA, Valayannopoulos V, Gonzales M, Saudubray JM, Jakobs C. Retrospective detection of transaldolase deficiency in amniotic fluid: implications for prenatal diagnosis. Prenat Diagn 2008; 28:460-2. [DOI: 10.1002/pd.2002] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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48
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Ralser M, Wamelink MM, Kowald A, Gerisch B, Heeren G, Struys EA, Klipp E, Jakobs C, Breitenbach M, Lehrach H, Krobitsch S. Dynamic rerouting of the carbohydrate flux is key to counteracting oxidative stress. J Biol 2007; 6:10. [PMID: 18154684 PMCID: PMC2373902 DOI: 10.1186/jbiol61] [Citation(s) in RCA: 410] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2007] [Revised: 08/07/2007] [Accepted: 10/12/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Eukaryotic cells have evolved various response mechanisms to counteract the deleterious consequences of oxidative stress. Among these processes, metabolic alterations seem to play an important role. RESULTS We recently discovered that yeast cells with reduced activity of the key glycolytic enzyme triosephosphate isomerase exhibit an increased resistance to the thiol-oxidizing reagent diamide. Here we show that this phenotype is conserved in Caenorhabditis elegans and that the underlying mechanism is based on a redirection of the metabolic flux from glycolysis to the pentose phosphate pathway, altering the redox equilibrium of the cytoplasmic NADP(H) pool. Remarkably, another key glycolytic enzyme, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), is known to be inactivated in response to various oxidant treatments, and we show that this provokes a similar redirection of the metabolic flux. CONCLUSION The naturally occurring inactivation of GAPDH functions as a metabolic switch for rerouting the carbohydrate flux to counteract oxidative stress. As a consequence, altering the homoeostasis of cytoplasmic metabolites is a fundamental mechanism for balancing the redox state of eukaryotic cells under stress conditions.
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Affiliation(s)
- Markus Ralser
- Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany.
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Ritter JB, Genzel Y, Reichl U. Simultaneous extraction of several metabolites of energy metabolism and related substances in mammalian cells: optimization using experimental design. Anal Biochem 2007; 373:349-69. [PMID: 18036549 DOI: 10.1016/j.ab.2007.10.037] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2007] [Revised: 10/13/2007] [Accepted: 10/24/2007] [Indexed: 10/22/2022]
Abstract
As a basis for the development of predictive mathematical models in systems biology and a quantitative understanding of cellular metabolism, reliable experimental data sets of intracellular metabolites are indispensable. A prerequisite for the acquisition of such data is the identification of a suitable sample preparation method. In this work, the extraction procedure for the simultaneous measurement of a wide range of intracellular metabolites from adherent mammalian cells in culture was optimized. A screening of several commonly used extraction protocols with Madin-Darby canine kidney (MDCK) cells found the methanol/chloroform (MeOH/CHCl(3)) and MeOH/Boil methods to be promising candidates for further analysis by anion-exchange chromatography. Both methods were optimized based on experimental design techniques with four response variables: Nucleotide Content, Energy Charge, Fructose 1,6-Bisphosphate content (F16bP), and Absorption at 280 nm. After data evaluation and with the help of desirability functions, an overall optimum for the extraction conditions was found. Using optimal settings, the extraction performances for MDCK and Vero cell cultivations of both methods were compared. Both methods extracted nearly the same absolute amounts of intracellular metabolites, suggesting that these methods are equal. However, recoveries for nucleotide diphosphates were significantly above 100% for both methods. This most likely was due to remaining nucleotide kinase activity during extraction. After combining individual steps of both methods, recoveries close to 100% for all metabolites could be reached. Absolute values of intracellular metabolites extracted with this modified method are comparable to the results of the two previously optimized methods, indicating a good extraction procedure according to the chosen response variables.
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Affiliation(s)
- Joachim B Ritter
- Max Planck Institute for Dynamics of Complex Technical Systems, 39106 Magdeburg, Germany.
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Rodrigues J, Antonio C, Robinson S, Thomas-Oates J. Mass Spectrometry in Glycobiology. METABOLOMICS, METABONOMICS AND METABOLITE PROFILING 2007. [DOI: 10.1039/9781847558107-00210] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- João Rodrigues
- Department of Chemistry, University of York Heslington York YO10 5DD UK
| | - Carla Antonio
- Department of Chemistry, University of York Heslington York YO10 5DD UK
| | - Sarah Robinson
- Department of Chemistry, University of York Heslington York YO10 5DD UK
| | - Jane Thomas-Oates
- Department of Chemistry, University of York Heslington York YO10 5DD UK
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