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Langner M, Fröbel D, Helm J, Chavakis T, Peitzsch M, Bechmann N. Accurate redox state indication by in situ derivatization with N-ethylmaleimide - Profiling of transsulfuration and glutathione pathway metabolites by UPLC-MS/MS. J Chromatogr B Analyt Technol Biomed Life Sci 2024; 1236:124062. [PMID: 38432191 DOI: 10.1016/j.jchromb.2024.124062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 02/08/2024] [Accepted: 02/19/2024] [Indexed: 03/05/2024]
Abstract
BACKGROUND Reduced and oxidized glutathione play an important role for the intracellular detoxification of reactive oxygen species. The iron-dependent formation of such reactive oxygen species in conjunction with the inhibition of the redox-balancing enzyme glutathione peroxidase 4 underlie an imbalance in the cellular redox state, thereby resulting in a non-apoptotic form of cell death, defined as ferroptosis, which is relevant in several pathologies. METHODS Here we present a rapid ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) based method providing the accurate quantification of 12 glutathione pathway metabolites after in situ derivatization with N-Ethylmaleimide (NEM). The method was validated regards linearity, recovery and accuracy as well as precision. The assay includes glutathione and its oxidized form glutathione disulfide. Furthermore, the related precursors cysteine, cystine, glutamic acid, γ-glutamylcysteine and cysteinylglycine, biomarkers of protein crosslinking such as cystathionine and lanthionine, as well as metabolites of the transsulfuration pathway, methionine, homocysteine and serine are simultaneously determined. RESULTS Twelve glutathione pathway metabolites were simultaneously analyzed in four different human cell line extracts within a total LC run time of 5.5 min. Interday coefficients of variation (1.7 % to 12.0 %), the mean observed accuracy (100.0 % ± 5.2 %), linear quantification ranges over three orders of magnitude for all analytes and sufficient metabolite stability after NEM-derivatization demonstrate method reliability. Immediate derivatization with NEM at cell harvesting prevents autooxidation of glutathione, ensures accurate results for the GSH/GSSG redox ratio and thereby allows interpretation of cellular redox state. CONCLUSION The described UPLC-MS/MS method provides a sensitive and selective tool for a fast and simultaneous analysis of glutathione pathway metabolites, its direct precursors and related compounds. Assay performance characteristics demonstrate the suitability of the method for applications in different cell cultures. Therefore, by providing glutathione related functional metabolic readouts, the method enables investigations in mechanisms of ferroptosis and alterations in oxidative stress levels in several pathophysiologies.
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Affiliation(s)
- Mathias Langner
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital and Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Fetscherstraße 74, 01307 Dresden, Germany
| | - Dennis Fröbel
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital and Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Fetscherstraße 74, 01307 Dresden, Germany
| | - Jana Helm
- Department of Medicine III, University Hospital and Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Fetscherstraße 74, 01307 Dresden, Germany
| | - Triantafyllos Chavakis
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital and Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Fetscherstraße 74, 01307 Dresden, Germany
| | - Mirko Peitzsch
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital and Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Fetscherstraße 74, 01307 Dresden, Germany.
| | - Nicole Bechmann
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital and Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Fetscherstraße 74, 01307 Dresden, Germany
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2
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Metabolic profiling workflow for cell extracts by targeted hydrophilic interaction liquid chromatography-tandem mass spectrometry. J Chromatogr A 2022; 1684:463556. [DOI: 10.1016/j.chroma.2022.463556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 10/04/2022] [Accepted: 10/07/2022] [Indexed: 11/22/2022]
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3
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El Abiead Y, Bueschl C, Panzenboeck L, Wang M, Doppler M, Seidl B, Zanghellini J, Dorrestein PC, Koellensperger G. Heterogeneous multimeric metabolite ion species observed in LC-MS based metabolomics data sets. Anal Chim Acta 2022; 1229:340352. [PMID: 36156231 DOI: 10.1016/j.aca.2022.340352] [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: 04/10/2022] [Revised: 08/08/2022] [Accepted: 09/01/2022] [Indexed: 11/30/2022]
Abstract
Covalent or non-covalent heterogeneous multimerization of molecules associated with extracts from biological samples analyzed via LC-MS are quite difficult to recognize/annotate and therefore the prevalence of multimerization remains largely unknown. In this study, we utilized 13C labeled and unlabeled Pichia pastoris extracts to recognize heterogeneous multimers. More specifically, between 0.8% and 1.5% of the biologically-derived features detected in our experiments were confirmed to be heteromers, about half of which we could successfully annotate with monomeric partners. Interestingly, we found specific chemical classes such as nucleotides to disproportionately contribute to heteroadducts. Furthermore, we compiled these compounds into the first MS/MS library that included data from heteromultimers to provide a starting point for other labs to improve the annotation of such ions in other metabolomics data sets. Then, the detected heteromers were also searched in publicly accessible LC-MS datasets available in Metabolights, Metabolomics WB and GNPS/MassIVE to demonstrate that these newly annotated ions are also relevant to other public datasets. Furthermore, in additional datasets (Triticum aestivum, Fusarium graminearum, and Trichoderma reesei) our developed workflow also detected 0.5%-4.9% of metabolite features to originate from heterodimers, demonstrating heteroadducts to be present in metabolomics studies at a low percentage.
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Affiliation(s)
- Yasin El Abiead
- Department of Analytical Chemistry, University of Vienna, 1090, Vienna, Austria.
| | - Christoph Bueschl
- Department of Analytical Chemistry, University of Vienna, 1090, Vienna, Austria; Institute of Bioanalytics and Agro-Metabolomics, Department of Agrobiotechnology IFA-Tulln, University of Natural Resources and Life Sciences, Vienna, 3430, Tulln, Austria
| | - Lisa Panzenboeck
- Department of Analytical Chemistry, University of Vienna, 1090, Vienna, Austria
| | - Mingxun Wang
- Department of Computer Science and Engineering, University of California Riverside, 900 University Ave, Riverside, CA, 92521, USA
| | - Maria Doppler
- Institute of Bioanalytics and Agro-Metabolomics, Department of Agrobiotechnology IFA-Tulln, University of Natural Resources and Life Sciences, Vienna, 3430, Tulln, Austria; Core Facility Bioactive Molecules: Screening and Analysis, University of Natural Resources and Life Sciences, Vienna, 3430, Tulln, Austria
| | - Bernhard Seidl
- Institute of Bioanalytics and Agro-Metabolomics, Department of Agrobiotechnology IFA-Tulln, University of Natural Resources and Life Sciences, Vienna, 3430, Tulln, Austria
| | - Jürgen Zanghellini
- Department of Analytical Chemistry, University of Vienna, 1090, Vienna, Austria
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA; Department of Pharmacology, School of Medicine, University of California San Diego, La Jolla, CA, USA; Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA; Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Gunda Koellensperger
- Department of Analytical Chemistry, University of Vienna, 1090, Vienna, Austria.
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Direct Derivatization in Dried Blood Spots for Oxidized and Reduced Glutathione Quantification in Newborns. Antioxidants (Basel) 2022; 11:antiox11061165. [PMID: 35740062 PMCID: PMC9219658 DOI: 10.3390/antiox11061165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/06/2022] [Accepted: 06/09/2022] [Indexed: 11/29/2022] Open
Abstract
The glutathione (GSH)-to-glutathione disulfide (GSSG) ratio is an essential node contributing to intracellular redox status. GSH/GSSG determination in whole blood can be accomplished by liquid chromatography–mass spectrometry (LC-MS) after the derivatization of GSH with N-ethylmaleimide (NEM). While this is feasible in a laboratory environment, its application in the clinical scenario is cumbersome and therefore ranges reported in similar populations differ noticeably. In this work, an LC-MS procedure for the determination of GSH and GSSG in dried blood spot (DBS) samples based on direct in situ GSH derivatization with NEM of only 10 µL of blood was developed. This novel method was applied to 73 cord blood samples and 88 residual blood volumes from routine newborn screening performed at discharge from healthy term infants. Two clinical scenarios simulating conditions of sampling and storage relevant for routine clinical analysis and clinical trials were assessed. Levels of GSH-NEM and GSSG measured in DBS samples were comparable to those obtained by liquid blood samples. GSH-NEM and GSSG median values for cord blood samples were significantly lower than those for samples at discharge. However, the GSH-NEM-to-GSSG ratios were not statistically different between both groups. With DBS testing, the immediate manipulation of samples by clinical staff is reduced. We therefore expect that this method will pave the way in providing an accurate and more robust determination of the GSH/GSSG values and trends reported in clinical trials.
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Bustos C, Quezada J, Veas R, Altamirano C, Braun-Galleani S, Fickers P, Berrios J. Advances in Cell Engineering of the Komagataella phaffii Platform for Recombinant Protein Production. Metabolites 2022; 12:metabo12040346. [PMID: 35448535 PMCID: PMC9027633 DOI: 10.3390/metabo12040346] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 04/01/2022] [Accepted: 04/06/2022] [Indexed: 12/11/2022] Open
Abstract
Komagataella phaffii (formerly known as Pichia pastoris) has become an increasingly important microorganism for recombinant protein production. This yeast species has gained high interest in an industrial setting for the production of a wide range of proteins, including enzymes and biopharmaceuticals. During the last decades, relevant bioprocess progress has been achieved in order to increase recombinant protein productivity and to reduce production costs. More recently, the improvement of cell features and performance has also been considered for this aim, and promising strategies with a direct and substantial impact on protein productivity have been reported. In this review, cell engineering approaches including metabolic engineering and energy supply, transcription factor modulation, and manipulation of routes involved in folding and secretion of recombinant protein are discussed. A lack of studies performed at the higher-scale bioreactor involving optimisation of cultivation parameters is also evidenced, which highlights new research aims to be considered.
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Affiliation(s)
- Cristina Bustos
- School of Biochemical Engineering, Pontificia Universidad Católica de Valparaíso, Av. Brasil 2085, Valparaíso 2362803, Chile; (C.B.); (J.Q.); (R.V.); (C.A.); (S.B.-G.)
- Microbial Processes and Interactions, TERRA Teaching and Research Centre, Gembloux Agro-Bio Tech, University of Liège, Av. de la Faculté 2B, 5030 Gembloux, Belgium;
| | - Johan Quezada
- School of Biochemical Engineering, Pontificia Universidad Católica de Valparaíso, Av. Brasil 2085, Valparaíso 2362803, Chile; (C.B.); (J.Q.); (R.V.); (C.A.); (S.B.-G.)
| | - Rhonda Veas
- School of Biochemical Engineering, Pontificia Universidad Católica de Valparaíso, Av. Brasil 2085, Valparaíso 2362803, Chile; (C.B.); (J.Q.); (R.V.); (C.A.); (S.B.-G.)
| | - Claudia Altamirano
- School of Biochemical Engineering, Pontificia Universidad Católica de Valparaíso, Av. Brasil 2085, Valparaíso 2362803, Chile; (C.B.); (J.Q.); (R.V.); (C.A.); (S.B.-G.)
| | - Stephanie Braun-Galleani
- School of Biochemical Engineering, Pontificia Universidad Católica de Valparaíso, Av. Brasil 2085, Valparaíso 2362803, Chile; (C.B.); (J.Q.); (R.V.); (C.A.); (S.B.-G.)
| | - Patrick Fickers
- Microbial Processes and Interactions, TERRA Teaching and Research Centre, Gembloux Agro-Bio Tech, University of Liège, Av. de la Faculté 2B, 5030 Gembloux, Belgium;
| | - Julio Berrios
- School of Biochemical Engineering, Pontificia Universidad Católica de Valparaíso, Av. Brasil 2085, Valparaíso 2362803, Chile; (C.B.); (J.Q.); (R.V.); (C.A.); (S.B.-G.)
- Correspondence: ; Tel.: +56-32-237-2012
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Zhang Y, Fang YC, Cui LX, Jiang YT, Luo YS, Zhang W, Yu DX, Wen J, Zhou TT. Zhi-Zi-Chi Decoction Reverses Depressive Behaviors in CUMS Rats by Reducing Oxidative Stress Injury Via Regulating GSH/GSSG Pathway. Front Pharmacol 2022; 13:887890. [PMID: 35462900 PMCID: PMC9021728 DOI: 10.3389/fphar.2022.887890] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 03/21/2022] [Indexed: 12/27/2022] Open
Abstract
Depression is one of the main diseases that lead to disability and loss of ability to work. As a traditional Chinese medicine, Zhi-zi-chi decoction is utilized to regulate and improve depression. However, the research on the antidepressant mechanism and efficacy material basis of Zhi-zi-chi decoction has not been reported yet. Our previous research has found that Zhi-Zi-chi decoction can reduce glutamate-induced oxidative stress damage to PC 12 cells, which can exert a neuroprotective effect, and the antidepressant effect of Zhi-Zi-chi decoction was verified in CUMS rat models. In this study, the animal model of depression was established by chronic unpredictable mild stimulation combined with feeding alone. The brain metabolic profile of depressed rats was analyzed by the method of metabolomics based on ultra-performance liquid chromatography-quadrupole/time-of-flight mass. 26 differential metabolites and six metabolic pathways related to the antidepressant of Zhi-zi-chi decoction were screened and analyzed. The targeted metabolism of the glutathione metabolic pathway was analyzed. At the same time, the levels of reactive oxygen species, superoxide dismutase, glutathione reductase, glutathione peroxidase in the brain of depressed rats were measured. Combined with our previous study, the antioxidant effect of the glutathione pathway in the antidepressant effect of Zhi-zi-chi decoction was verified from the cellular and animal levels respectively. These results indicated that Zhi-zi-chi decoction exerted a potential antidepressive effect associated with reversing the imbalance of glutathione and oxidative stress in the brain of depressed rats.
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Affiliation(s)
- Yin Zhang
- School of Pharmacy, Second Military Medical University, Shanghai, China
- Shanghai Key Laboratory for Pharmaceutical Metabolite Research, School of Pharmacy, Second Military Medical University, Shanghai, China
- Chengdu Institute for Drug Control, Chengdu, China
| | - Yi-Chao Fang
- School of Pharmacy, Second Military Medical University, Shanghai, China
- Shanghai Key Laboratory for Pharmaceutical Metabolite Research, School of Pharmacy, Second Military Medical University, Shanghai, China
| | - Li-Xun Cui
- School of Pharmacy, Second Military Medical University, Shanghai, China
- Shanghai Key Laboratory for Pharmaceutical Metabolite Research, School of Pharmacy, Second Military Medical University, Shanghai, China
| | - Yue-Tong Jiang
- School of Pharmacy, Second Military Medical University, Shanghai, China
- Shanghai Key Laboratory for Pharmaceutical Metabolite Research, School of Pharmacy, Second Military Medical University, Shanghai, China
| | - Yu-Sha Luo
- School of Pharmacy, Second Military Medical University, Shanghai, China
- Shanghai Key Laboratory for Pharmaceutical Metabolite Research, School of Pharmacy, Second Military Medical University, Shanghai, China
| | - Wen Zhang
- School of Pharmacy, Second Military Medical University, Shanghai, China
- Shanghai Key Laboratory for Pharmaceutical Metabolite Research, School of Pharmacy, Second Military Medical University, Shanghai, China
| | - De-Xun Yu
- School of Pharmacy, Second Military Medical University, Shanghai, China
- Shanghai Key Laboratory for Pharmaceutical Metabolite Research, School of Pharmacy, Second Military Medical University, Shanghai, China
| | - Jun Wen
- School of Pharmacy, Second Military Medical University, Shanghai, China
- Shanghai Key Laboratory for Pharmaceutical Metabolite Research, School of Pharmacy, Second Military Medical University, Shanghai, China
- *Correspondence: Jun Wen, ; Ting-Ting Zhou,
| | - Ting-Ting Zhou
- School of Pharmacy, Second Military Medical University, Shanghai, China
- Shanghai Key Laboratory for Pharmaceutical Metabolite Research, School of Pharmacy, Second Military Medical University, Shanghai, China
- *Correspondence: Jun Wen, ; Ting-Ting Zhou,
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7
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Abstract
Oxidative stress and reactive oxygen species (ROS) are central to many physiological and pathophysiological processes. However, due to multiple technical challenges, it is hard to capture a comprehensive readout of the cell, involving both biochemical and functional status. We addressed this problem by developing a fully parallelized workflow for metabolomics (providing absolute quantities for > 100 metabolites including TCA cycle, pentose phosphate pathway, purine metabolism, glutathione metabolism, cysteine and methionine metabolism, glycolysis and gluconeogenesis) and live cell imaging microscopy. The correlative imaging strategy was applied to study morphological and metabolic adaptation of cancer cells upon short-term hydrogen peroxide (H2O2) exposure in vitro. The combination provided rich metabolic information at the endpoint of exposure together with imaging of mitochondrial effects. As a response, superoxide concentrations were elevated with a strong mitochondrial localization, and multi-parametric image analysis revealed a shift towards fragmentation. In line with this, metabolism reflected both the impaired mitochondrial function and shifts to support the first-line cellular defense and compensate for energy loss. The presented workflow combining high-end technologies demonstrates the applicability for the study of short-term oxidative stress, but it can be suitable for the in-depth study of various short-term oxidative and other cellular stress-related phenomena.
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8
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Herzog K, IJlst L, van Cruchten AG, van Roermund CWT, Kulik W, Wanders RJA, Waterham HR. An UPLC-MS/MS Assay to Measure Glutathione as Marker for Oxidative Stress in Cultured Cells. Metabolites 2019; 9:metabo9030045. [PMID: 30841653 PMCID: PMC6468779 DOI: 10.3390/metabo9030045] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 02/15/2019] [Accepted: 02/28/2019] [Indexed: 11/16/2022] Open
Abstract
Oxidative stress plays a role in the onset and progression of a number of diseases, such as Alzheimer’s disease, diabetes and cancer, as well as ageing. Oxidative stress is caused by an increased production of reactive oxygen species and reduced antioxidant activity, resulting in the oxidation of glutathione. The ratio of reduced to oxidised glutathione is often used as a marker of the redox state in the cell. Whereas a variety of methods have been developed to measure glutathione in blood samples, methods to measure glutathione in cultured cells are scarce. Here we present a protocol to measure glutathione levels in cultured human and yeast cells using ultra-performance liquid chromatography-tandem mass spectrometry (UPLC–MS/MS).
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Affiliation(s)
- Katharina Herzog
- Centre for Analysis and Synthesis, Department of Chemistry, Lund University, 223 62 Lund, Sweden.
- Laboratory Genetic Metabolic Diseases, Department of Clinical Chemistry, Amsterdam UMC, Location AMC, University of Amsterdam, 1105 Amsterdam, The Netherlands.
| | - Lodewijk IJlst
- Laboratory Genetic Metabolic Diseases, Department of Clinical Chemistry, Amsterdam UMC, Location AMC, University of Amsterdam, 1105 Amsterdam, The Netherlands.
| | - Arno G van Cruchten
- Laboratory Genetic Metabolic Diseases, Department of Clinical Chemistry, Amsterdam UMC, Location AMC, University of Amsterdam, 1105 Amsterdam, The Netherlands.
| | - Carlo W T van Roermund
- Laboratory Genetic Metabolic Diseases, Department of Clinical Chemistry, Amsterdam UMC, Location AMC, University of Amsterdam, 1105 Amsterdam, The Netherlands.
| | - Wim Kulik
- Laboratory Genetic Metabolic Diseases, Department of Clinical Chemistry, Amsterdam UMC, Location AMC, University of Amsterdam, 1105 Amsterdam, The Netherlands.
| | - Ronald J A Wanders
- Laboratory Genetic Metabolic Diseases, Department of Clinical Chemistry, Amsterdam UMC, Location AMC, University of Amsterdam, 1105 Amsterdam, The Netherlands.
| | - Hans R Waterham
- Laboratory Genetic Metabolic Diseases, Department of Clinical Chemistry, Amsterdam UMC, Location AMC, University of Amsterdam, 1105 Amsterdam, The Netherlands.
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Gil A, van der Pol A, van der Meer P, Bischoff R. LC-MS analysis of key components of the glutathione cycle in tissues and body fluids from mice with myocardial infarction. J Pharm Biomed Anal 2018; 160:289-296. [DOI: 10.1016/j.jpba.2018.08.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 07/31/2018] [Accepted: 08/01/2018] [Indexed: 12/11/2022]
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10
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Rampler E, Criscuolo A, Zeller M, El Abiead Y, Schoeny H, Hermann G, Sokol E, Cook K, Peake DA, Delanghe B, Koellensperger G. A Novel Lipidomics Workflow for Improved Human Plasma Identification and Quantification Using RPLC-MSn Methods and Isotope Dilution Strategies. Anal Chem 2018; 90:6494-6501. [PMID: 29708737 DOI: 10.1021/acs.analchem.7b05382] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Lipid identification and quantification are essential objectives in comprehensive lipidomics studies challenged by the high number of lipids, their chemical diversity, and their dynamic range. In this work, we developed a tailored method for profiling and quantification combining (1) isotope dilution, (2) enhanced isomer separation by C30 fused-core reversed-phase material, and (3) parallel Orbitrap and ion trap detection by the Orbitrap Fusion Lumos Tribid mass spectrometer. The combination of parallelizable ion analysis without time loss together with different fragmentation techniques (HCD/CID) and an inclusion list led to higher quality in lipid identifications exemplified in human plasma and yeast samples. Moreover, we used lipidome isotope-labeling of yeast (LILY)-a fast and efficient in vivo labeling strategy in Pichia pastoris-to produce (nonradioactive) isotopically labeled eukaryotic lipid standards in yeast. We integrated the 13C lipids in the LC-MS workflow to enable relative and absolute compound-specific quantification in yeast and human plasma samples by isotope dilution. Label-free and compound-specific quantification was validated by comparison against a recent international interlaboratory study on human plasma SRM 1950. In this way, we were able to prove that LILY enabled quantification leads to accurate results, even in complex matrices. Excellent analytical figures of merit with enhanced trueness, precision and linearity over 4-5 orders of magnitude were observed applying compound-specific quantification with 13C-labeled lipids. We strongly believe that lipidomics studies will benefit from incorporating isotope dilution and LC-MSn strategies.
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Affiliation(s)
- Evelyn Rampler
- Department of Analytical Chemistry, Faculty of Chemistry , University of Vienna , Währingerstrasse 38 , 1090 Vienna , Austria.,Vienna Metabolomics Center (VIME) , University of Vienna , Althanstraße 14 , 1090 Vienna , Austria.,Chemistry Meets Microbiology , Althanstraße 14 , 1090 Vienna , Austria
| | - Angela Criscuolo
- Thermo Fisher Scientific (Bremen GmbH) , Hanna-Kunath-Str. 11 , 28199 Bremen , Germany.,Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy , Universität Leipzig , Leipzig , Germany
| | - Martin Zeller
- Thermo Fisher Scientific (Bremen GmbH) , Hanna-Kunath-Str. 11 , 28199 Bremen , Germany
| | - Yasin El Abiead
- Department of Analytical Chemistry, Faculty of Chemistry , University of Vienna , Währingerstrasse 38 , 1090 Vienna , Austria
| | - Harald Schoeny
- Department of Analytical Chemistry, Faculty of Chemistry , University of Vienna , Währingerstrasse 38 , 1090 Vienna , Austria
| | - Gerrit Hermann
- Department of Analytical Chemistry, Faculty of Chemistry , University of Vienna , Währingerstrasse 38 , 1090 Vienna , Austria.,ISOtopic solutions , Währingerstrasse 38 , 1090 Vienna , Austria
| | - Elena Sokol
- Thermo Fisher Scientific , 1 Boundary Park , Hemel Hempstead HP2 7GE , United Kingdom
| | - Ken Cook
- Thermo Fisher Scientific , 1 Boundary Park , Hemel Hempstead HP2 7GE , United Kingdom
| | - David A Peake
- Thermo Fisher Scientific , 355 River Oaks Parkway , 95134 San Jose , California United States
| | - Bernard Delanghe
- Thermo Fisher Scientific (Bremen GmbH) , Hanna-Kunath-Str. 11 , 28199 Bremen , Germany
| | - Gunda Koellensperger
- Department of Analytical Chemistry, Faculty of Chemistry , University of Vienna , Währingerstrasse 38 , 1090 Vienna , Austria.,Vienna Metabolomics Center (VIME) , University of Vienna , Althanstraße 14 , 1090 Vienna , Austria.,Chemistry Meets Microbiology , Althanstraße 14 , 1090 Vienna , Austria
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Zahrl RJ, Peña DA, Mattanovich D, Gasser B. Systems biotechnology for protein production in Pichia pastoris. FEMS Yeast Res 2017; 17:4093073. [DOI: 10.1093/femsyr/fox068] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2017] [Accepted: 08/22/2017] [Indexed: 12/31/2022] Open
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Rampler E, Coman C, Hermann G, Sickmann A, Ahrends R, Koellensperger G. LILY-lipidome isotope labeling of yeast: in vivo synthesis of 13C labeled reference lipids for quantification by mass spectrometry. Analyst 2017; 142:1891-1899. [PMID: 28475182 DOI: 10.1039/c7an00107j] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Quantification is an essential task in comprehensive lipidomics studies challenged by the high number of lipids, their chemical diversity and their dynamic range of the lipidome. In this work, we introduce lipidome isotope labeling of yeast (LILY) in order to produce (non-radioactive) isotopically labeled eukaryotic lipid standards in yeast for normalization and quantification in mass spectrometric assays. More specifically, LILY is a fast and efficient in vivo labeling strategy in Pichia pastoris for the production of 13C labeled lipid library further paving the way to comprehensive compound-specific internal standardization in quantitative mass spectrometry based assays. More than 200 lipid species (from PA, PC, PE, PG, PI, PS, LysoGP, CL, DAG, TAG, DMPE, Cer, HexCer, IPC, MIPC) were obtained from yeast extracts with an excellent 13C enrichment >99.5%, as determined by complementary high resolution mass spectrometry based shotgun and high resolution LC-MS/MS analysis. In a first proof of principle study we tested the relative and absolute quantification capabilities of the 13C enriched lipids obtained by LILY using a parallel reaction monitoring based LC-MS approach. In relative quantification it could be shown that compound specific internal standardization was essential for the accuracy extending the linear dynamic range to four orders of magnitude. Excellent analytical figures of merit were observed for absolute quantification for a selected panel of 5 investigated glycerophospholipids (e.g. LOQs around 5 fmol absolute; typical concentrations ranging between 1 to 10 nmol per 108 yeast cell starting material; RSDs <10% (N = 4)).
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Affiliation(s)
- Evelyn Rampler
- Institute of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Währingerstr. 38, 1090 Vienna, Austria. and Vienna Metabolomics Center (VIME), University of Vienna, Althanstraße 14, 1090 Vienna, Austria and Chemistry Meets Microbiolgy, Althanstraße 14, 1090 Vienna, Austria
| | - Cristina Coman
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Otto-Hahn-Str. 6b, 44227 Dortmund, Germany
| | - Gerrit Hermann
- Institute of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Währingerstr. 38, 1090 Vienna, Austria. and ISOtopic Solutions, Währingerstr. 38, 1090 Vienna, Austria
| | - Albert Sickmann
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Otto-Hahn-Str. 6b, 44227 Dortmund, Germany and College of Physical Sciences, University of Aberdeen, Department of Chemistry, AB24 3UE Aberdeen, UK and Medizinische Fakultät, Medizinische Proteom-Center (MCP), Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - Robert Ahrends
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Otto-Hahn-Str. 6b, 44227 Dortmund, Germany
| | - Gunda Koellensperger
- Institute of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Währingerstr. 38, 1090 Vienna, Austria. and Vienna Metabolomics Center (VIME), University of Vienna, Althanstraße 14, 1090 Vienna, Austria and Chemistry Meets Microbiolgy, Althanstraße 14, 1090 Vienna, Austria
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Review of sample preparation strategies for MS-based metabolomic studies in industrial biotechnology. Anal Chim Acta 2016; 938:18-32. [DOI: 10.1016/j.aca.2016.07.033] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 07/22/2016] [Accepted: 07/26/2016] [Indexed: 02/08/2023]
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14
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Correia B, Freitas R, Figueira E, Soares AMVM, Nunes B. Oxidative effects of the pharmaceutical drug paracetamol on the edible clam Ruditapes philippinarum under different salinities. Comp Biochem Physiol C Toxicol Pharmacol 2016; 179:116-24. [PMID: 26409706 DOI: 10.1016/j.cbpc.2015.09.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 08/28/2015] [Accepted: 09/15/2015] [Indexed: 01/06/2023]
Abstract
Paracetamol, a drug with analgesic and antipyretic properties, is one of the most used substances in human therapeutics, being also frequently detected in aquatic environments. Recent studies report its toxicity towards aquatic species, but the overall amount of data concerning its effects is still scarce. Global changes, likely alterations in abiotic conditions, including salinity, can modulate the interactions of contaminants with biota, conditioning the toxicological responses elicited also by pharmaceuticals. The present article describes the oxidative toxic effects posed by paracetamol on the clam species Ruditapes philippinarum under different salinity conditions. The results demonstrated the establishment of an oxidative-based effect, with significant alteration of several parameters, such as superoxide dismutase (SOD) and the ratio of reduced/oxidized glutathione (GSH/GSSG). Water salinity influenced the response of clams exposed to different paracetamol concentrations, showing the importance of studying physiological traits under realistic test conditions, which are likely to vary in great extent as a result of climate change.
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Affiliation(s)
- Bárbara Correia
- Department of Biology, Centro de Estudos do Ambiente e do MAR (CESAM), University of Aveiro, Portugal
| | - Rosa Freitas
- Department of Biology, Centro de Estudos do Ambiente e do MAR (CESAM), University of Aveiro, Portugal
| | - Etelvina Figueira
- Department of Biology, Centro de Estudos do Ambiente e do MAR (CESAM), University of Aveiro, Portugal
| | - Amadeu M V M Soares
- Department of Biology, Centro de Estudos do Ambiente e do MAR (CESAM), University of Aveiro, Portugal
| | - Bruno Nunes
- Department of Biology, Centro de Estudos do Ambiente e do MAR (CESAM), University of Aveiro, Portugal.
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15
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Ortmayr K, Hann S, Koellensperger G. Complementing reversed-phase selectivity with porous graphitized carbon to increase the metabolome coverage in an on-line two-dimensional LC-MS setup for metabolomics. Analyst 2015; 140:3465-73. [PMID: 25824707 PMCID: PMC4719141 DOI: 10.1039/c5an00206k] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Efficient and robust separation methods are indispensable in modern LC-MS based metabolomics, where high-resolution mass spectrometers are challenged by isomeric and isobaric metabolites. The optimization of chromatographic separation hence remains an invaluable tool in the comprehensive analysis of the chemically diverse intracellular metabolome. While it is widely accepted that a single method with comprehensive metabolome coverage does not exist, the potential of combining different chromatographic selectivities in two-dimensional liquid chromatography is underestimated in the field. Here, we introduce a novel separation system combining reversed-phase and porous graphitized carbon liquid chromatography in a heart-cut on-line two-dimensional setup for mass spectrometry. The proposed experimental setup can be readily implemented using standard HPLC equipment with only one additional HPLC pump and a two-position six-port valve. The method proved to be robust with excellent retention time stability (average 0.4%) even in the presence of biological matrix. Testing the presented approach on a test mixture of 82 relevant intracellular metabolites, the number of metabolites that are retained could be doubled as compared to reversed-phase liquid chromatography alone. The presented work further demonstrates how the distinct selectivity of porous graphitized carbon complements reversed-phase liquid chromatography and extends the metabolome coverage of conventional LC-MS based methods in metabolomics to biologically important, but analytically challenging compound groups such as sugar phosphates. Both metabolic profiling and metabolic fingerprinting benefit from this method's increased separation capabilities that enhance sample throughput and the biological information content of LC-MS data. An inter-platform comparison with GC- and LC-tandem MS analyses confirmed the validity of the presented two-dimensional approach in the analysis of yeast cell extracts from P. pastoris.
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Affiliation(s)
- Karin Ortmayr
- Department of Chemistry, University of Natural Resources and Life Sciences (BOKU) Vienna, Muthgasse 18, 1190 Vienna, Austria
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16
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Fahrenholz T, Wolle MM, Kingston HM“S, Faber S, Kern JC, Pamuku M, Miller L, Chatragadda H, Kogelnik A. Molecular Speciated Isotope Dilution Mass Spectrometric Methods for Accurate, Reproducible and Direct Quantification of Reduced, Oxidized and Total Glutathione in Biological Samples. Anal Chem 2015; 87:1232-40. [DOI: 10.1021/ac503933t] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Timothy Fahrenholz
- Department
of Chemistry and Biochemistry, Duquesne University, 600 Forbes
Avenue, Pittsburgh, Pennsylvania 15282, United States
| | - Mesay Mulugeta Wolle
- Department
of Chemistry and Biochemistry, Duquesne University, 600 Forbes
Avenue, Pittsburgh, Pennsylvania 15282, United States
| | - H. M. “Skip” Kingston
- Department
of Chemistry and Biochemistry, Duquesne University, 600 Forbes
Avenue, Pittsburgh, Pennsylvania 15282, United States
| | - Scott Faber
- Department
of Medicine, The Children’s Institute, 1405 Shady Avenue, Pittsburgh, Pennsylvania 15217, United States
| | - John C. Kern
- Department
of Mathematics and Computer Science, Duquesne University, 600 Forbes
Avenue, Pittsburgh, Pennsylvania 15282, United States
| | - Matt Pamuku
- Applied Isotope Technologies, 2403 Sidney Street, Suite 280, Pittsburgh, Pennsylvania 15203, United States
| | - Logan Miller
- Department
of Chemistry and Biochemistry, Duquesne University, 600 Forbes
Avenue, Pittsburgh, Pennsylvania 15282, United States
| | - Hemasudha Chatragadda
- Department
of Chemistry and Biochemistry, Duquesne University, 600 Forbes
Avenue, Pittsburgh, Pennsylvania 15282, United States
| | - Andreas Kogelnik
- Open Medicine Institute, 2500
Hospital Drive, Building 2, Mountain View, California 94040, United States
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17
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Ortmayr K, Schwaiger M, Hann S, Koellensperger G. An integrated metabolomics workflow for the quantification of sulfur pathway intermediates employing thiol protection with N-ethyl maleimide and hydrophilic interaction liquid chromatography tandem mass spectrometry. Analyst 2015; 140:7687-95. [DOI: 10.1039/c5an01629k] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The developed integrated thiol protection and sample preparation strategy prevents unwanted oxidation and allows accurate profiling of sulfur pathway intermediates.
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Affiliation(s)
- Karin Ortmayr
- Institute of Analytical Chemistry
- University of Vienna
- Faculty of Chemistry
- 1090 Vienna
- Austria
| | - Michaela Schwaiger
- Institute of Analytical Chemistry
- University of Vienna
- Faculty of Chemistry
- 1090 Vienna
- Austria
| | - Stephan Hann
- Department of Chemistry
- University of Natural Resources and Life Sciences (BOKU) Vienna
- 1190 Vienna
- Austria
| | - Gunda Koellensperger
- Institute of Analytical Chemistry
- University of Vienna
- Faculty of Chemistry
- 1090 Vienna
- Austria
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18
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Delic M, Graf AB, Koellensperger G, Haberhauer-Troyer C, Hann S, Mattanovich D, Gasser B. Overexpression of the transcription factor Yap1 modifies intracellular redox conditions and enhances recombinant protein secretion. MICROBIAL CELL 2014; 1:376-386. [PMID: 28357216 PMCID: PMC5349127 DOI: 10.15698/mic2014.11.173] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Oxidative folding of secretory proteins in the endoplasmic reticulum (ER) is a
redox active process, which also impacts the redox conditions in the cytosol. As
the transcription factor Yap1 is involved in the transcriptional response to
oxidative stress, we investigate its role upon the production of secretory
proteins, using the yeast Pichia pastoris as model, and report
a novel important role of Yap1 during oxidative protein folding. Yap1 is needed
for the detoxification of reactive oxygen species (ROS) caused by increased
oxidative protein folding. Constitutive co-overexpression of
PpYAP1 leads to increased levels of secreted recombinant
protein, while a lowered Yap1 function leads to accumulation of ROS and strong
flocculation. Transcriptional analysis revealed that more than 150 genes were
affected by overexpression of YAP1, in particular genes coding
for antioxidant enzymes or involved in oxidation-reduction processes. By
monitoring intracellular redox conditions within the cytosol and the ER using
redox-sensitive roGFP1 variants, we could show that overexpression of
YAP1 restores cellular redox conditions of
protein-secreting P. pastoris by reoxidizing the cytosolic
redox state to the levels of the wild type. These alterations are also reflected
by increased levels of oxidized intracellular glutathione (GSSG) in the
YAP1 co-overexpressing strain. Taken together, these data
indicate a strong impact of intracellular redox balance on the secretion of
(recombinant) proteins without affecting protein folding per se. Re-establishing
suitable redox conditions by tuning the antioxidant capacity of the cell reduces
metabolic load and cell stress caused by high oxidative protein folding load,
thereby increasing the secretion capacity.
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Affiliation(s)
- Marizela Delic
- Department of Biotechnology, BOKU University of Natural Resources and Life Sciences Vienna, Vienna, Austria. ; Austrian Centre of Industrial Biotechnology (ACIB), Vienna, Austria
| | - Alexandra B Graf
- Austrian Centre of Industrial Biotechnology (ACIB), Vienna, Austria. ; School of Bioengineering, University of Applied Sciences FH Campus Wien, Vienna, Austria
| | - Gunda Koellensperger
- Department of Biotechnology, BOKU University of Natural Resources and Life Sciences Vienna, Vienna, Austria. ; Department of Chemistry, BOKU University of Natural Resources and Life Sciences Vienna, Vienna, Austria
| | - Christina Haberhauer-Troyer
- Department of Biotechnology, BOKU University of Natural Resources and Life Sciences Vienna, Vienna, Austria. ; Department of Chemistry, BOKU University of Natural Resources and Life Sciences Vienna, Vienna, Austria
| | - Stephan Hann
- Department of Biotechnology, BOKU University of Natural Resources and Life Sciences Vienna, Vienna, Austria. ; Department of Chemistry, BOKU University of Natural Resources and Life Sciences Vienna, Vienna, Austria
| | - Diethard Mattanovich
- Department of Biotechnology, BOKU University of Natural Resources and Life Sciences Vienna, Vienna, Austria. ; Austrian Centre of Industrial Biotechnology (ACIB), Vienna, Austria
| | - Brigitte Gasser
- Department of Biotechnology, BOKU University of Natural Resources and Life Sciences Vienna, Vienna, Austria. ; Austrian Centre of Industrial Biotechnology (ACIB), Vienna, Austria
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19
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Profiling thiol metabolites and quantification of cellular glutathione using FT-ICR-MS spectrometry. Anal Bioanal Chem 2014; 406:4371-9. [PMID: 24858467 DOI: 10.1007/s00216-014-7810-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Revised: 03/31/2014] [Accepted: 04/03/2014] [Indexed: 10/25/2022]
Abstract
We describe preparation and use of the quaternary ammonium-based α-iodoacetamide QDE and its isotopologue *QDE as reagents for chemoselective derivatization of cellular thiols. Direct addition of the reagents to live cells followed by adduct extraction into n-butanol and analysis by FT-ICR-MS provided a registry of matched isotope peaks from which molecular formulae of thiol metabolites were derived. Acidification to pH 4 during cell lysis and adduct formation further improves the chemoselectivity for thiol derivatization. Examination of A549 human lung adenocarcinoma cells using this approach revealed cysteine, cysteinylglycine, glutathione, and homocysteine as principal thiol metabolites as well as the sulfinic acid hypotaurine. The method is also readily applied to quantify the thiol metabolites, as demonstrated here by the quantification of both glutathione and glutathione disulfide in A549 cells at concentrations of 34.4 ± 11.5 and 10.1 ± 4.0 nmol/mg protein, respectively.
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20
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Reinbold J, Koehler P, Rychlik M. Quantitation of glutathione and its oxidation products in erythrocytes by multiple-label stable-isotope dilution. Anal Biochem 2014; 445:41-8. [DOI: 10.1016/j.ab.2013.09.029] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Revised: 08/30/2013] [Accepted: 09/27/2013] [Indexed: 12/14/2022]
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21
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Abstract
Overexpression of a foreign protein may negatively affect several cell growth parameters, as well as cause cellular stress. Central (or core) metabolism plays a crucial role since it supplies energy, reduction equivalents, and precursor molecules for the recombinant product, cell's maintenance, and growth needs. However, the number of quantitative physiology studies of the impact of recombinant protein production on the central metabolic pathways of yeast cell factories has been traditionally rather limited, thereby hampering the application of rational strain engineering strategies targeting central metabolism.The development and application of quantitative physiology and modelling tools and methodologies is allowing for a systems-level understanding of the effect of bioprocess parameters such as growth rate, temperature, oxygen availability, and substrate(s) choice on metabolism, and its subsequent interactions with recombinant protein synthesis, folding, and secretion.Here, we review the recent developments and applications of (13)C-based metabolic flux analysis ((13)C-MFA) of Pichia pastoris and the gained understanding of the metabolic behavior of this yeast in recombinant protein production bioprocesses. We also discuss the potential of multilevel studies integrating (13)C-MFA with other omics analyses, as well as future perspectives on the metabolic modelling approaches to study and design metabolic engineering strategies for improved protein production.
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Affiliation(s)
- Pau Ferrer
- Escola d'Enginyeria, Edifici Q, Universitat Autònoma de Barcelona, Campus de Bellaterra, 08193, Bellaterra (Cerdanyola del Vallès), Catalonia, Spain,
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22
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Karakosta TD, Tzanavaras PD, Themelis DG. Determination of glutathione and cysteine in yeasts by hydrophilic interaction liquid chromatography followed by on-line postcolumn derivatization. J Sep Sci 2013; 36:1877-82. [DOI: 10.1002/jssc.201300202] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2013] [Revised: 03/24/2013] [Accepted: 03/24/2013] [Indexed: 11/09/2022]
Affiliation(s)
- Theano D. Karakosta
- Laboratory of Analytical Chemistry, Department of Chemistry; Aristotelian University of Thessaloniki; Thessaloniki; Greece
| | - Paraskevas D. Tzanavaras
- Laboratory of Analytical Chemistry, Department of Chemistry; Aristotelian University of Thessaloniki; Thessaloniki; Greece
| | - Demetrius G. Themelis
- Laboratory of Analytical Chemistry, Department of Chemistry; Aristotelian University of Thessaloniki; Thessaloniki; Greece
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23
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Hermann G, Heffeter P, Falta T, Berger W, Hann S, Koellensperger G. In vitro studies on cisplatin focusing on kinetic aspects of intracellular chemistry by LC-ICP-MS. Metallomics 2013; 5:636-47. [DOI: 10.1039/c3mt20251h] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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