1
|
Tian B, Chen M, Liu L, Rui B, Deng Z, Zhang Z, Shen T. 13C metabolic flux analysis: Classification and characterization from the perspective of mathematical modeling and application in physiological research of neural cell. Front Mol Neurosci 2022; 15:883466. [PMID: 36157075 PMCID: PMC9493264 DOI: 10.3389/fnmol.2022.883466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 08/15/2022] [Indexed: 11/17/2022] Open
Abstract
13C metabolic flux analysis (13C-MFA) has emerged as a forceful tool for quantifying in vivo metabolic pathway activity of different biological systems. This technology plays an important role in understanding intracellular metabolism and revealing patho-physiology mechanism. Recently, it has evolved into a method family with great diversity in experiments, analytics, and mathematics. In this review, we classify and characterize the various branch of 13C-MFA from a unified perspective of mathematical modeling. By linking different parts in the model to each step of its workflow, the specific technologies of 13C-MFA are put into discussion, including the isotope labeling model (ILM), isotope pattern measuring technique, optimization algorithm and statistical method. Its application in physiological research in neural cell has also been reviewed.
Collapse
Affiliation(s)
- Birui Tian
- Key Laboratory of Information and Computing Science Guizhou Province, Guizhou Normal University, Guiyang, China
| | - Meifeng Chen
- Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China, Key Laboratory of Plant Physiology and Development Regulation, School of Life Science, Guizhou Normal University, Guiyang, China
| | - Lunxian Liu
- Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China, Key Laboratory of Plant Physiology and Development Regulation, School of Life Science, Guizhou Normal University, Guiyang, China
| | - Bin Rui
- Eurofins Lancaster Laboratories Professional Scientific Services, Lancaster, PA, United States
| | - Zhouhui Deng
- China Guizhou Science Data Center Gui’an Supercomputing Center, Guiyang, China
| | - Zhengdong Zhang
- College of Mathematics and Information Science, Guiyang University, Guiyang, China
- *Correspondence: Zhengdong Zhang,
| | - Tie Shen
- Key Laboratory of Information and Computing Science Guizhou Province, Guizhou Normal University, Guiyang, China
- Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China, Key Laboratory of Plant Physiology and Development Regulation, School of Life Science, Guizhou Normal University, Guiyang, China
- Tie Shen,
| |
Collapse
|
2
|
Liu Z, Pan X, Wang C, Yun F, Huang D, Yao Y, Gao R, Ye F, Liu X, Liao W. Genome-wide identification and expression analysis of serine hydroxymethyltransferase ( SHMT) gene family in tomato ( Solanum lycopersicum). PeerJ 2022; 10:e12943. [PMID: 35186505 PMCID: PMC8841039 DOI: 10.7717/peerj.12943] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 01/24/2022] [Indexed: 01/11/2023] Open
Abstract
Serine hydroxymethyltransferase (SHMT) is one of the most important enzyme families in one-carbon metabolic pathway and photorespiration within plant cells. Recently studies reported the active roles of plant SHMTs in defending abiotic stresses. However, genome-scale analysis of SHMT in tomato is currently unknown. In this study, seven SHMT genes were identified in the tomato genome using a genome-wide search approach. In addition, their physicochemical properties, protein secondary structure, subcellular localization, gene structure, conserved motifs, phylogenetic and collinear relationships were analyzed. Our results demonstrated that tomato SHMT members were divided into two group and four subgroups, and they were conserved with the orthologs of other plants. Analysis of cis-acting elements showed that each of the SlSHMT genes contained different kinds of hormones and stress-related cis-acting elements in their promoter regions. Finally, qRT-PCR analysis indicated that SlSHMTs were expressed at different levels in different tissues, and they responded to UV, cold, heat, NaCl, H2O2, ABA and PEG treatments. These results provided definite evidence that SlSHMTs might involve in growth, development and stress responses in tomato, which laid a foundation for future functional studies of SlSHMTs.
Collapse
Affiliation(s)
- Zesheng Liu
- Gansu Agricultural University, College of Horticulture, Lanzhou, Gansu, China
| | - Xuejuan Pan
- Gansu Agricultural University, College of Horticulture, Lanzhou, Gansu, China
| | - Chunlei Wang
- Gansu Agricultural University, College of Horticulture, Lanzhou, Gansu, China
| | - Fahong Yun
- Gansu Agricultural University, College of Horticulture, Lanzhou, Gansu, China
| | - Dengjing Huang
- Gansu Agricultural University, College of Horticulture, Lanzhou, Gansu, China
| | - Yandong Yao
- Gansu Agricultural University, College of Horticulture, Lanzhou, Gansu, China
| | - Rong Gao
- Gansu Agricultural University, College of Horticulture, Lanzhou, Gansu, China
| | - Fujin Ye
- Gansu Agricultural University, College of Horticulture, Lanzhou, Gansu, China
| | - Xingjuan Liu
- Gansu Agricultural University, College of Horticulture, Lanzhou, Gansu, China
| | - Weibiao Liao
- Gansu Agricultural University, College of Horticulture, Lanzhou, Gansu, China
| |
Collapse
|
3
|
Leiva LE, Pincheira A, Elgamal S, Kienast SD, Bravo V, Leufken J, Gutiérrez D, Leidel SA, Ibba M, Katz A. Modulation of Escherichia coli Translation by the Specific Inactivation of tRNA Gly Under Oxidative Stress. Front Genet 2020; 11:856. [PMID: 33014012 PMCID: PMC7461829 DOI: 10.3389/fgene.2020.00856] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 07/14/2020] [Indexed: 11/17/2022] Open
Abstract
Bacterial oxidative stress responses are generally controlled by transcription factors that modulate the synthesis of RNAs with the aid of some sRNAs that control the stability, and in some cases the translation, of specific mRNAs. Here, we report that oxidative stress additionally leads to inactivation of tRNAGly in Escherichia coli, inducing a series of physiological changes. The observed inactivation of tRNAGly correlated with altered efficiency of translation of Gly codons, suggesting a possible mechanism of translational control of gene expression under oxidative stress. Changes in translation also depended on the availability of glycine, revealing a mechanism whereby bacteria modulate the response to oxidative stress according to the prevailing metabolic state of the cells.
Collapse
Affiliation(s)
- Lorenzo Eugenio Leiva
- Programa de Biología Celular y Molecular, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Andrea Pincheira
- Programa de Biología Celular y Molecular, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Sara Elgamal
- Department of Microbiology and The Center for RNA Biology, The Ohio State University, Columbus, OH, United States
| | - Sandra D Kienast
- Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany.,Cells-in-Motion Cluster of Excellence and Faculty of Medicine, University of Münster, Münster, Germany.,Research Group for RNA Biochemistry, Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
| | - Verónica Bravo
- Unidad de Microbiología, Escuela de Medicina, Facultad de Ciencias Médicas, Universidad de Santiago de Chile, Santiago, Chile
| | - Johannes Leufken
- Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany.,Cells-in-Motion Cluster of Excellence and Faculty of Medicine, University of Münster, Münster, Germany.,Research Group for RNA Biochemistry, Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
| | - Daniela Gutiérrez
- Programa de Biología Celular y Molecular, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Sebastian A Leidel
- Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany.,Cells-in-Motion Cluster of Excellence and Faculty of Medicine, University of Münster, Münster, Germany.,Research Group for RNA Biochemistry, Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
| | - Michael Ibba
- Department of Microbiology and The Center for RNA Biology, The Ohio State University, Columbus, OH, United States
| | - Assaf Katz
- Programa de Biología Celular y Molecular, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| |
Collapse
|
4
|
Omidbakhshfard MA, Sujeeth N, Gupta S, Omranian N, Guinan KJ, Brotman Y, Nikoloski Z, Fernie AR, Mueller-Roeber B, Gechev TS. A Biostimulant Obtained from the Seaweed Ascophyllum nodosum Protects Arabidopsis thaliana from Severe Oxidative Stress. Int J Mol Sci 2020; 21:E474. [PMID: 31940839 PMCID: PMC7013732 DOI: 10.3390/ijms21020474] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 12/26/2019] [Accepted: 01/09/2020] [Indexed: 11/16/2022] Open
Abstract
Abiotic stresses cause oxidative damage in plants. Here, we demonstrate that foliar application of an extract from the seaweed Ascophyllum nodosum, SuperFifty (SF), largely prevents paraquat (PQ)-induced oxidative stress in Arabidopsis thaliana. While PQ-stressed plants develop necrotic lesions, plants pre-treated with SF (i.e., primed plants) were unaffected by PQ. Transcriptome analysis revealed induction of reactive oxygen species (ROS) marker genes, genes involved in ROS-induced programmed cell death, and autophagy-related genes after PQ treatment. These changes did not occur in PQ-stressed plants primed with SF. In contrast, upregulation of several carbohydrate metabolism genes, growth, and hormone signaling as well as antioxidant-related genes were specific to SF-primed plants. Metabolomic analyses revealed accumulation of the stress-protective metabolite maltose and the tricarboxylic acid cycle intermediates fumarate and malate in SF-primed plants. Lipidome analysis indicated that those lipids associated with oxidative stress-induced cell death and chloroplast degradation, such as triacylglycerols (TAGs), declined upon SF priming. Our study demonstrated that SF confers tolerance to PQ-induced oxidative stress in A. thaliana, an effect achieved by modulating a range of processes at the transcriptomic, metabolic, and lipid levels.
Collapse
Affiliation(s)
- Mohammad Amin Omidbakhshfard
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; (M.A.O.); (S.G.); (N.O.); (Y.B.); (A.R.F.); (B.M.-R.)
| | - Neerakkal Sujeeth
- BioAtlantis Ltd., Clash Industrial Estate, Tralee, V92 RWV5 Co. Kerry, Ireland;
| | - Saurabh Gupta
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; (M.A.O.); (S.G.); (N.O.); (Y.B.); (A.R.F.); (B.M.-R.)
- Molecular Biology, Institute of Biochemistry and Biology, University of Potsdam, Karl Liebknecht Str. 24-25, 14476 Potsdam-Golm, Germany
| | - Nooshin Omranian
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; (M.A.O.); (S.G.); (N.O.); (Y.B.); (A.R.F.); (B.M.-R.)
- Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, Karl Liebknecht Str. 24-25, 14476 Potsdam-Golm, Germany;
| | - Kieran J. Guinan
- BioAtlantis Ltd., Clash Industrial Estate, Tralee, V92 RWV5 Co. Kerry, Ireland;
| | - Yariv Brotman
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; (M.A.O.); (S.G.); (N.O.); (Y.B.); (A.R.F.); (B.M.-R.)
| | - Zoran Nikoloski
- Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, Karl Liebknecht Str. 24-25, 14476 Potsdam-Golm, Germany;
- Department of Molecular Stress Physiology, Center of Plant Systems Biology and Biotechnology, 139 Ruski blvd., 4000 Plovdiv, Bulgaria;
| | - Alisdair R. Fernie
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; (M.A.O.); (S.G.); (N.O.); (Y.B.); (A.R.F.); (B.M.-R.)
- Department of Molecular Stress Physiology, Center of Plant Systems Biology and Biotechnology, 139 Ruski blvd., 4000 Plovdiv, Bulgaria;
| | - Bernd Mueller-Roeber
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; (M.A.O.); (S.G.); (N.O.); (Y.B.); (A.R.F.); (B.M.-R.)
- Molecular Biology, Institute of Biochemistry and Biology, University of Potsdam, Karl Liebknecht Str. 24-25, 14476 Potsdam-Golm, Germany
- Department of Molecular Stress Physiology, Center of Plant Systems Biology and Biotechnology, 139 Ruski blvd., 4000 Plovdiv, Bulgaria;
| | - Tsanko S. Gechev
- Department of Molecular Stress Physiology, Center of Plant Systems Biology and Biotechnology, 139 Ruski blvd., 4000 Plovdiv, Bulgaria;
- Department of Plant Physiology and Molecular Biology, University of Plovdiv, 24 Tsar Assen Str., 4000 Plovdiv, Bulgaria
| |
Collapse
|
5
|
Noster J, Persicke M, Chao TC, Krone L, Heppner B, Hensel M, Hansmeier N. Impact of ROS-Induced Damage of TCA Cycle Enzymes on Metabolism and Virulence of Salmonella enterica serovar Typhimurium. Front Microbiol 2019; 10:762. [PMID: 31105651 PMCID: PMC6491894 DOI: 10.3389/fmicb.2019.00762] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Accepted: 03/26/2019] [Indexed: 01/10/2023] Open
Abstract
Salmonella enterica serovar Typhimurium (STM) is exposed to reactive oxygen species (ROS) originating from aerobic respiration, antibiotic treatment, and the oxidative burst occurring inside the Salmonella-containing vacuole (SCV) within host cells. ROS damage cellular compounds, thereby impairing bacterial viability and inducing cell death. Proteins containing iron–sulfur (Fe–S) clusters are particularly sensitive and become non-functional upon oxidation. Comprising five enzymes with Fe–S clusters, the TCA cycle is a pathway most sensitive toward ROS. To test the impact of ROS-mediated metabolic perturbations on bacterial physiology, we analyzed the proteomic and metabolic profile of STM deficient in both cytosolic superoxide dismutases (ΔsodAB). Incapable of detoxifying superoxide anions (SOA), endogenously generated SOA accumulate during growth. ΔsodAB showed reduced abundance of aconitases, leading to a metabolic profile similar to that of an aconitase-deficient strain (ΔacnAB). Furthermore, we determined a decreased expression of acnA in STM ΔsodAB. While intracellular proliferation in RAW264.7 macrophages and survival of methyl viologen treatment were not reduced for STM ΔacnAB, proteomic profiling revealed enhanced stress response. We conclude that ROS-mediated reduced expression and damage of aconitase does not impair bacterial viability or virulence, but might increase ROS amounts in STM, which reinforces the bactericidal effects of antibiotic treatment and immune responses of the host.
Collapse
Affiliation(s)
- Janina Noster
- Abteilung Mikrobiologie, Universität Osnabrück, Osnabrück, Germany
| | - Marcus Persicke
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Tzu-Chiao Chao
- Institute of Environmental Change and Society, University of Regina, Regina, SK, Canada
| | - Lena Krone
- Abteilung Mikrobiologie, Universität Osnabrück, Osnabrück, Germany
| | - Bianca Heppner
- Abteilung Mikrobiologie, Universität Osnabrück, Osnabrück, Germany
| | - Michael Hensel
- Abteilung Mikrobiologie, Universität Osnabrück, Osnabrück, Germany
| | - Nicole Hansmeier
- Abteilung Mikrobiologie, Universität Osnabrück, Osnabrück, Germany.,Institute of Environmental Change and Society, University of Regina, Regina, SK, Canada.,Luther College, University of Regina, Regina, SK, Canada
| |
Collapse
|
6
|
Mao X, Liu T, Bi J, Luo L, Tian D, Li H. The synthesis of pillar[5]arene functionalized graphene as a fluorescent probe for paraquat in living cells and mice. Chem Commun (Camb) 2016; 52:4385-8. [DOI: 10.1039/c6cc00949b] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
As complex organisms vary in vivo, it remains a challenging task to get fluorescence ‘turn on’ imaging for special targets.
Collapse
Affiliation(s)
- Xiaowei Mao
- Key Laboratory of Pesticide and Chemical Biology (CCNU)
- Ministry of Education
- College of Chemistry
- Central China Normal University
- Wuhan 430079
| | - Ting Liu
- Key Laboratory of Pesticide and Chemical Biology (CCNU)
- Ministry of Education
- College of Chemistry
- Central China Normal University
- Wuhan 430079
| | - Jiahai Bi
- Key Laboratory of Pesticide and Chemical Biology (CCNU)
- Ministry of Education
- College of Chemistry
- Central China Normal University
- Wuhan 430079
| | - Li Luo
- Key Laboratory of Pesticide and Chemical Biology (CCNU)
- Ministry of Education
- College of Chemistry
- Central China Normal University
- Wuhan 430079
| | - Demei Tian
- Key Laboratory of Pesticide and Chemical Biology (CCNU)
- Ministry of Education
- College of Chemistry
- Central China Normal University
- Wuhan 430079
| | - Haibing Li
- Key Laboratory of Pesticide and Chemical Biology (CCNU)
- Ministry of Education
- College of Chemistry
- Central China Normal University
- Wuhan 430079
| |
Collapse
|
7
|
Elementary Flux Mode Analysis Revealed Cyclization Pathway as a Powerful Way for NADPH Regeneration of Central Carbon Metabolism. PLoS One 2015; 10:e0129837. [PMID: 26086807 PMCID: PMC4472234 DOI: 10.1371/journal.pone.0129837] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 05/13/2015] [Indexed: 01/18/2023] Open
Abstract
NADPH regeneration capacity is attracting growing research attention due to its important role in resisting oxidative stress. Besides, NADPH availability has been regarded as a limiting factor in production of industrially valuable compounds. The central carbon metabolism carries the carbon skeleton flux supporting the operation of NADPH-regenerating enzyme and offers flexibility in coping with NADPH demand for varied intracellular environment. To acquire an insightful understanding of its NADPH regeneration capacity, the elementary mode method was employed to compute all elementary flux modes (EFMs) of a network representative of central carbon metabolism. Based on the metabolic flux distributions of these modes, a cluster analysis of EFMs with high NADPH regeneration rate was conducted using the self-organizing map clustering algorithm. The clustering results were used to study the relationship between the flux of total NADPH regeneration and the flux in each NADPH producing enzyme. The results identified several reaction combinations supporting high NADPH regeneration, which are proven to be feasible in cells via thermodynamic analysis and coincident with a great deal of previous experimental report. Meanwhile, the reaction combinations showed some common characteristics: there were one or two decarboxylation oxidation reactions in the combinations that produced NADPH and the combination constitution included certain gluconeogenesis pathways. These findings suggested cyclization pathways as a powerful way for NADPH regeneration capacity of bacterial central carbon metabolism.
Collapse
|
8
|
Hesketh A, Deery MJ, Hong HJ. High-Resolution Mass Spectrometry Based Proteomic Analysis of the Response to Vancomycin-Induced Cell Wall Stress in Streptomyces coelicolor A3(2). J Proteome Res 2015; 14:2915-28. [PMID: 25965010 DOI: 10.1021/acs.jproteome.5b00242] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Understanding how bacteria survive periods of cell wall stress is of fundamental interest and can help generate ideas for improved antibacterial treatments. In this study we use tandem mass tagging to characterize the proteomic response of vancomycin resistant Streptomyces coelicolor to the exposure to sublethal levels of the antibiotic. A common set of 804 proteins were identified in triplicate experiments. Contrasting changes in the abundance of proteins closely associated with the cytoplasmic membrane with those taking place in the cytosol identified aspects of protein spatial localization that are associated with the response to vancomycin. Enzymes for peptidoglycan precursor, mycothiol, ectoine and menaquinone biosynthesis together with a multisubunit nitrate reductase were recruited to the membrane following vancomycin treatment. Many proteins with regulatory functions (including sensor protein kinases) also exhibited significant changes in abundance exclusively in the membrane-associated protein fraction. Several enzymes predicted to be involved in extracellular peptidoglycan crossbridge formation became significantly depleted from the membrane. A comparison with data previously acquired on the changes in gene transcription following vancomycin treatment identified a common high-confidence set of changes in gene expression. Generalized changes in protein abundance indicate roles for proteolysis, the pentose phosphate pathway and a reorganization of amino acid biosynthesis in the stress response.
Collapse
Affiliation(s)
- Andy Hesketh
- †Department of Biochemistry, University of Cambridge, Cambridge, U.K.,‡Cambridge Systems Biology Centre, University of Cambridge, Cambridge, U.K
| | - Michael J Deery
- †Department of Biochemistry, University of Cambridge, Cambridge, U.K.,‡Cambridge Systems Biology Centre, University of Cambridge, Cambridge, U.K
| | - Hee-Jeon Hong
- †Department of Biochemistry, University of Cambridge, Cambridge, U.K
| |
Collapse
|
9
|
Metabolic Response of Escherichia coli upon Treatment with Hypochlorite at Sub-Lethal Concentrations. PLoS One 2015; 10:e0125823. [PMID: 25932918 PMCID: PMC4416902 DOI: 10.1371/journal.pone.0125823] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 03/25/2015] [Indexed: 01/11/2023] Open
Abstract
Hypochlorite is a reactive oxygen species that is worldwide as an antibacterial disinfectant. Hypochlorite exposure is known to cause oxidative damage to DNA and proteins. As a response to these effects, the metabolite profiles of organisms treated with sub-lethal doses of hypochlorite are assumed to be severely modified; however, the nature of these changes is hardly understood. Therefore, using nuclear magnetic resonance spectroscopy and gas chromatography-coupled mass spectrometry, we analyzed the time-dependent impact of hypochlorite exposure with a sub-lethal concentration (50 µM) on the metabolite profile of the Escherichia coli strain MG1655. Principle component analysis clearly distinguished between the metabolite profiles of bacteria treated for 0, 5,10, 20, 40, or 60 min. Major changes in the relative amounts of fatty acids, acetic acid, and formic acid occurred within the first 5 min. Comparative gas chromatography-coupled mass spectrometry analyses revealed that the amounts of free methionine and alanine were significantly decreased in the treated cells, demonstrating their susceptibility to hypochlorite exposure. The concentrations of succinate, urea, orotic acid, 2-aminobutyric acid, and 2-hydroxybutyric acid were also severely affected, indicating general changes in the metabolic network by hypochlorite. However, most metabolite levels relaxed to the reference values of untreated cells after 40–60 min, reflecting the capability of E. coli to rapidly adapt to environmental stress factors such as the presence of sub-lethal oxidant levels.
Collapse
|
10
|
Nargund S, Misra A, Zhang X, Coleman GD, Sriram G. Flux and reflux: metabolite reflux in plant suspension cells and its implications for isotope-assisted metabolic flux analysis. MOLECULAR BIOSYSTEMS 2014; 10:1496-508. [PMID: 24675729 DOI: 10.1039/c3mb70348g] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Isotope-assisted metabolic flux analysis (MFA) is a powerful methodology to quantify intracellular fluxes via isotope labeling experiments (ILEs). In batch cultures, which are often convenient, inexpensive or inevitable especially for eukaryotic systems, MFA is complicated by the presence of the initially present biomass. This unlabeled biomass may either mix with the newly synthesized labeled biomass or reflux into the metabolic network, thus masking the true labeling patterns in the newly synthesized biomass. Here, we report a detailed investigation of such metabolite reflux in cell suspensions of the tree poplar. In ILEs supplying 28% or 98% U-(13)C glucose as the sole organic carbon source, biomass components exhibited lower (13)C enrichments than the supplied glucose as well as anomalous isotopomers not explainable by simple mixing of the initial and newly synthesized biomass. These anomalous labeling patterns were most prominent in a 98% U-(13)C glucose ILE. By comparing the performance of light- and dark-grown cells as well as by analyzing the isotope labeling patterns in aspartic and glutamic acids, we eliminated photosynthetic or anaplerotic fixation of extracellular (12)CO2 as explanations for the anomalous labeling patterns. We further investigated four different metabolic models for interpreting the labeling patterns and evaluating fluxes: (i) a carbon source (glucose) dilution model, (ii) an isotopomer correction model with uniform dilution for all amino acids, (iii) an isotopomer correction model with variable dilution for different amino acids, and (iv) a comprehensive metabolite reflux model. Of these, the metabolite reflux model provided a substantially better fit for the observed labeling patterns (sum of squared residues: 538) than the other three models whose sum of squared residues were (i) 4626, (ii) 4983, and (iii) 1748, respectively. We compared fluxes determined using the metabolite reflux model to those determined using an independent methodology involving an excessively long ILE to wash out initial biomass and a minimal reflux model. This comparison showed identical or similar distributions for a majority of fluxes, thus validating our comprehensive reflux model. In summary, we have demonstrated the need for quantifying interactions between initially present biomass and newly synthesized biomass in batch ILEs, especially through the use of ≈100% U-(13)C carbon sources. Our ILEs reveal a high amount of metabolite reflux in poplar cell suspensions, which is well explained by a comprehensive metabolite reflux model.
Collapse
Affiliation(s)
- Shilpa Nargund
- Department of Chemical and Biomolecular Engineering, University of Maryland, 1208D, Chemical and Nuclear Engineering Building 090, College Park, MD 20742, USA.
| | | | | | | | | |
Collapse
|