1
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Westhoff P, Weber APM. The role of metabolomics in informing strategies for improving photosynthesis. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:1696-1713. [PMID: 38158893 DOI: 10.1093/jxb/erad508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 12/29/2023] [Indexed: 01/03/2024]
Abstract
Photosynthesis plays a vital role in acclimating to and mitigating climate change, providing food and energy security for a population that is constantly growing, and achieving an economy with zero carbon emissions. A thorough comprehension of the dynamics of photosynthesis, including its molecular regulatory network and limitations, is essential for utilizing it as a tool to boost plant growth, enhance crop yields, and support the production of plant biomass for carbon storage. Photorespiration constrains photosynthetic efficiency and contributes significantly to carbon loss. Therefore, modulating or circumventing photorespiration presents opportunities to enhance photosynthetic efficiency. Over the past eight decades, substantial progress has been made in elucidating the molecular basis of photosynthesis, photorespiration, and the key regulatory mechanisms involved, beginning with the discovery of the canonical Calvin-Benson-Bassham cycle. Advanced chromatographic and mass spectrometric technologies have allowed a comprehensive analysis of the metabolite patterns associated with photosynthesis, contributing to a deeper understanding of its regulation. In this review, we summarize the results of metabolomics studies that shed light on the molecular intricacies of photosynthetic metabolism. We also discuss the methodological requirements essential for effective analysis of photosynthetic metabolism, highlighting the value of this technology in supporting strategies aimed at enhancing photosynthesis.
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Affiliation(s)
- Philipp Westhoff
- CEPLAS Plant Metabolomics and Metabolism Laboratory, Heinrich-Heine-University, Universitätsstrasse 1, D-40225 Düsseldorf, Germany
| | - Andreas P M Weber
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Science (CEPLAS), Heinrich-Heine-University, Universitätsstrasse 1, D-40225 Düsseldorf, Germany
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2
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Kambhampati S, Hubbard AH, Koley S, Gomez JD, Marsolais F, Evans BS, Young JD, Allen DK. SIMPEL: using stable isotopes to elucidate dynamics of context specific metabolism. Commun Biol 2024; 7:172. [PMID: 38347116 PMCID: PMC10861564 DOI: 10.1038/s42003-024-05844-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: 08/03/2022] [Accepted: 01/23/2024] [Indexed: 02/15/2024] Open
Abstract
The capacity to leverage high resolution mass spectrometry (HRMS) with transient isotope labeling experiments is an untapped opportunity to derive insights on context-specific metabolism, that is difficult to assess quantitatively. Tools are needed to comprehensively mine isotopologue information in an automated, high-throughput way without errors. We describe a tool, Stable Isotope-assisted Metabolomics for Pathway Elucidation (SIMPEL), to simplify analysis and interpretation of isotope-enriched HRMS datasets. The efficacy of SIMPEL is demonstrated through examples of central carbon and lipid metabolism. In the first description, a dual-isotope labeling experiment is paired with SIMPEL and isotopically nonstationary metabolic flux analysis (INST-MFA) to resolve fluxes in central metabolism that would be otherwise challenging to quantify. In the second example, SIMPEL was paired with HRMS-based lipidomics data to describe lipid metabolism based on a single labeling experiment. Available as an R package, SIMPEL extends metabolomics analyses to include isotopologue signatures necessary to quantify metabolic flux.
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Affiliation(s)
- Shrikaar Kambhampati
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA.
- Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA.
| | - Allen H Hubbard
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | - Somnath Koley
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | - Javier D Gomez
- Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, 37235, USA
| | - Frédéric Marsolais
- London Research and Development Center, London, ON, N5V 4T3, Canada
- Department of Biology, University of Western Ontario, London, ON, N6A 5B7, Canada
| | - Bradley S Evans
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | - Jamey D Young
- Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, 37235, USA
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37235, USA
| | - Doug K Allen
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA.
- Agricultural Research Service, US Department of Agriculture, St. Louis, MO, 63132, USA.
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3
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Puzanskiy RK, Romanyuk DA, Kirpichnikova AA, Yemelyanov VV, Shishova MF. Plant Heterotrophic Cultures: No Food, No Growth. PLANTS (BASEL, SWITZERLAND) 2024; 13:277. [PMID: 38256830 PMCID: PMC10821431 DOI: 10.3390/plants13020277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 01/10/2024] [Accepted: 01/15/2024] [Indexed: 01/24/2024]
Abstract
Plant cells are capable of uptaking exogenous organic substances. This inherited trait allows the development of heterotrophic cell cultures in various plants. The most common of them are Nicotiana tabacum and Arabidopsis thaliana. Plant cells are widely used in academic studies and as factories for valuable substance production. The repertoire of compounds supporting the heterotrophic growth of plant cells is limited. The best growth of cultures is ensured by oligosaccharides and their cleavage products. Primarily, these are sucrose, raffinose, glucose and fructose. Other molecules such as glycerol, carbonic acids, starch, and mannitol have the ability to support growth occasionally, or in combination with another substrate. Culture growth is accompanied by processes of specialization, such as elongation growth. This determines the pattern of the carbon budget. Culture ageing is closely linked to substrate depletion, changes in medium composition, and cell physiological rearrangements. A lack of substrate leads to starvation, which results in a decrease in physiological activity and the mobilization of resources, and finally in the loss of viability. The cause of the instability of cultivated cells may be the non-optimal metabolism under cultural conditions or the insufficiency of internal regulation.
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Affiliation(s)
- Roman K. Puzanskiy
- Laboratory of Analytical Phytochemistry, Komarov Botanical Institute of the Russian Academy of Sciences, 197022 St. Petersburg, Russia;
| | - Daria A. Romanyuk
- Laboratory of Genetics of Plant-Microbe Interactions, All-Russia Research Institute for Agricultural Microbiology, 196608 St. Petersburg, Russia;
| | | | - Vladislav V. Yemelyanov
- Faculty of Biology, St. Petersburg State University, 199034 St. Petersburg, Russia; (A.A.K.); (V.V.Y.)
| | - Maria F. Shishova
- Faculty of Biology, St. Petersburg State University, 199034 St. Petersburg, Russia; (A.A.K.); (V.V.Y.)
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4
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Huß S, Nikoloski Z. Systematic comparison of local approaches for isotopically nonstationary metabolic flux analysis. FRONTIERS IN PLANT SCIENCE 2023; 14:1178239. [PMID: 37346134 PMCID: PMC10280729 DOI: 10.3389/fpls.2023.1178239] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 05/04/2023] [Indexed: 06/23/2023]
Abstract
Quantification of reaction fluxes of metabolic networks can help us understand how the integration of different metabolic pathways determine cellular functions. Yet, intracellular fluxes cannot be measured directly but are estimated with metabolic flux analysis (MFA) that relies on the patterns of isotope labeling of metabolites in the network. For metabolic systems, typical for plants, where all potentially labeled atoms effectively have only one source atom pool, only isotopically nonstationary MFA can provide information about intracellular fluxes. There are several global approaches that implement MFA for an entire metabolic network and estimate, at once, a steady-state flux distribution for all reactions with identifiable fluxes in the network. In contrast, local approaches deal with estimation of fluxes for a subset of reactions, with smaller data demand for flux estimation. Here we present a systematic comparative review and benchmarking of the existing local approaches for isotopically nonstationary MFA. The comparison is conducted with respect to the required data and underlying computational problems solved on a synthetic network example. Furthermore, we benchmark the performance of these approaches in estimating fluxes for a subset of reactions using data obtained from the simulation of nitrogen fluxes in the Arabidopsis thaliana core metabolism. The findings pinpoint practical aspects that need to be considered when applying local approaches for flux estimation in large-scale plant metabolic networks.
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Affiliation(s)
- Sebastian Huß
- Systems Biology and Mathematical Modelling Group, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
- Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Zoran Nikoloski
- Systems Biology and Mathematical Modelling Group, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
- Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
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5
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Smith EN, Ratcliffe RG, Kruger NJ. Isotopically non-stationary metabolic flux analysis of heterotrophic Arabidopsis thaliana cell cultures. FRONTIERS IN PLANT SCIENCE 2023; 13:1049559. [PMID: 36699846 PMCID: PMC9868915 DOI: 10.3389/fpls.2022.1049559] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
Fluxes are the ultimate phenotype of metabolism and their accurate quantification is fundamental to any understanding of metabolic networks. Steady state metabolic flux analysis has been the method of choice for quantifying fluxes in heterotrophic cells, but it is unable to measure fluxes during short-lived metabolic states, such as a transient oxidative load. Isotopically non-stationary metabolic flux analysis (INST-MFA) can be performed over shorter timescales (minutes - hours) and might overcome this limitation. INST-MFA has recently been applied to photosynthesising leaves, but agriculturally important tissues such as roots and storage organs, or plants during the night are heterotrophic. Here we outline the application of INST-MFA to heterotrophic plant cells. Using INST-MFA we were able to identify changes in the fluxes supported by phosphoenolpyruvate carboxylase and malic enzyme under oxidative load, highlighting the potential of INST-MFA to measure fluxes during short-lived metabolic states. We discuss the challenges in applying INST-MFA, and highlight further development required before it can be routinely used to quantify fluxes in heterotrophic plant cells.
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Affiliation(s)
- Edward N. Smith
- Molecular Plant Biology, Department of Biology, University of Oxford, Oxford, United Kingdom
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - R. George Ratcliffe
- Molecular Plant Biology, Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Nicholas J. Kruger
- Molecular Plant Biology, Department of Biology, University of Oxford, Oxford, United Kingdom
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6
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Porto NP, Bret RSC, Souza PVL, Cândido-Sobrinho SA, Medeiros DB, Fernie AR, Daloso DM. Thioredoxins regulate the metabolic fluxes throughout the tricarboxylic acid cycle and associated pathways in a light-independent manner. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 193:36-49. [PMID: 36323196 DOI: 10.1016/j.plaphy.2022.10.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 10/11/2022] [Accepted: 10/19/2022] [Indexed: 06/16/2023]
Abstract
The metabolic fluxes throughout the tricarboxylic acid cycle (TCAC) are inhibited in the light by the mitochondrial thioredoxin (TRX) system. However, it is unclear how this system orchestrates the fluxes throughout the TCAC and associated pathways in the dark. Here we carried out a13C-HCO3 labelling experiment in Arabidopsis leaves from wild type (WT) and mutants lacking TRX o1 (trxo1), TRX h2 (trxh2), or both NADPH-dependent TRX reductase A and B (ntra ntrb) exposed to 0, 30 and 60 min of dark or light conditions. No 13C-enrichment in TCAC metabolites in illuminated WT leaves was observed. However, increased succinate content was found in parallel to reductions in Ala in the light, suggesting the latter operates as an alternative carbon source for succinate synthesis. By contrast to WT, all mutants showed substantial changes in the content and 13C-enrichment in TCAC metabolites under both dark and light conditions. Increased 13C-enrichment in glutamine in illuminated trxo1 leaves was also observed, strengthening the idea that TRX o1 restricts in vivo carbon fluxes from glycolysis and the TCAC to glutamine. We further demonstrated that both photosynthetic and gluconeogenic fluxes toward glucose are increased in trxo1 and that the phosphoenolpyruvate carboxylase (PEPc)-mediated 13C-incorporation into malate is higher in trxh2 mutants, as compared to WT. Our results collectively provide evidence that TRX h2 and the mitochondrial NTR/TRX system regulate the metabolic fluxes throughout the TCAC and associated pathways, including glycolysis, gluconeogenesis and the synthesis of glutamine in a light-independent manner.
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Affiliation(s)
- Nicole P Porto
- LabPlant, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, 60451-970, Fortaleza, Ceará, Brazil
| | - Raissa S C Bret
- LabPlant, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, 60451-970, Fortaleza, Ceará, Brazil
| | - Paulo V L Souza
- LabPlant, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, 60451-970, Fortaleza, Ceará, Brazil
| | - Silvio A Cândido-Sobrinho
- LabPlant, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, 60451-970, Fortaleza, Ceará, Brazil
| | - David B Medeiros
- Max-Planck-Institute of Molecular Plant Physiology, 14476, Potsdam-Golm, Germany
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, 14476, Potsdam-Golm, Germany
| | - Danilo M Daloso
- LabPlant, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, 60451-970, Fortaleza, Ceará, Brazil.
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7
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Huß S, Judd RS, Koper K, Maeda HA, Nikoloski Z. An automated workflow that generates atom mappings for large-scale metabolic models and its application to Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:1486-1500. [PMID: 35819300 DOI: 10.1111/tpj.15903] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 07/01/2022] [Accepted: 07/06/2022] [Indexed: 06/15/2023]
Abstract
Quantification of reaction fluxes of metabolic networks can help us understand how the integration of different metabolic pathways determines cellular functions. Yet, intracellular fluxes cannot be measured directly but are estimated with metabolic flux analysis (MFA), which relies on the patterns of isotope labeling of metabolites in the network. The application of MFA also requires a stoichiometric model with atom mappings that are currently not available for the majority of large-scale metabolic network models, particularly of plants. While automated approaches such as the Reaction Decoder Toolkit (RDT) can produce atom mappings for individual reactions, tracing the flow of individual atoms of the entire reactions across a metabolic model remains challenging. Here we establish an automated workflow to obtain reliable atom mappings for large-scale metabolic models by refining the outcome of RDT, and apply the workflow to metabolic models of Arabidopsis thaliana. We demonstrate the accuracy of RDT through a comparative analysis with atom mappings from a large database of biochemical reactions, MetaCyc. We further show the utility of our automated workflow by simulating 15 N isotope enrichment and identifying nitrogen (N)-containing metabolites which show enrichment patterns that are informative for flux estimation in future 15 N-MFA studies of A. thaliana. The automated workflow established in this study can be readily expanded to other species for which metabolic models have been established and the resulting atom mappings will facilitate MFA and graph-theoretic structural analyses with large-scale metabolic networks.
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Affiliation(s)
- Sebastian Huß
- Systems Biology and Mathematical Modelling Group, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany
- Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24- 25, 14476, Potsdam, Germany
| | - Rika Siedah Judd
- Department of Botany, University of Wisconsin-Madison, 430, Lincoln, Dr. Madison, Wisconsin, 53706, USA
| | - Kaan Koper
- Department of Botany, University of Wisconsin-Madison, 430, Lincoln, Dr. Madison, Wisconsin, 53706, USA
| | - Hiroshi A Maeda
- Department of Botany, University of Wisconsin-Madison, 430, Lincoln, Dr. Madison, Wisconsin, 53706, USA
| | - Zoran Nikoloski
- Systems Biology and Mathematical Modelling Group, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany
- Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24- 25, 14476, Potsdam, Germany
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8
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Lima VF, Erban A, Daubermann AG, Freire FBS, Porto NP, Cândido-Sobrinho SA, Medeiros DB, Schwarzländer M, Fernie AR, Dos Anjos L, Kopka J, Daloso DM. Establishment of a GC-MS-based 13 C-positional isotopomer approach suitable for investigating metabolic fluxes in plant primary metabolism. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:1213-1233. [PMID: 34486764 DOI: 10.1111/tpj.15484] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/20/2021] [Accepted: 08/30/2021] [Indexed: 06/13/2023]
Abstract
13 C-Metabolic flux analysis (13 C-MFA) has greatly contributed to our understanding of plant metabolic regulation. However, the generation of detailed in vivo flux maps remains a major challenge. Flux investigations based on nuclear magnetic resonance have resolved small networks with high accuracy. Mass spectrometry (MS) approaches have broader potential, but have hitherto been limited in their power to deduce flux information due to lack of atomic level position information. Herein we established a gas chromatography (GC) coupled to MS-based approach that provides 13 C-positional labelling information in glucose, malate and glutamate (Glu). A map of electron impact (EI)-mediated MS fragmentation was created and validated by 13 C-positionally labelled references via GC-EI-MS and GC-atmospheric pressure chemical ionization-MS technologies. The power of the approach was revealed by analysing previous 13 C-MFA data from leaves and guard cells, and 13 C-HCO3 labelling of guard cells harvested in the dark and after the dark-to-light transition. We demonstrated that the approach is applicable to established GC-EI-MS-based 13 C-MFA without the need for experimental adjustment, but will benefit in the future from paired analyses by the two GC-MS platforms. We identified specific glucose carbon atoms that are preferentially labelled by photosynthesis and gluconeogenesis, and provide an approach to investigate the phosphoenolpyruvate carboxylase (PEPc)-derived 13 C-incorporation into malate and Glu. Our results suggest that gluconeogenesis and the PEPc-mediated CO2 assimilation into malate are activated in a light-independent manner in guard cells. We further highlight that the fluxes from glycolysis and PEPc toward Glu are restricted by the mitochondrial thioredoxin system in illuminated leaves.
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Affiliation(s)
- Valéria F Lima
- LabPLant, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza-CE, 60451-970, Brazil
| | - Alexander Erban
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, D-14476, Germany
| | - André G Daubermann
- Departamento de Biologia, Setor de Fisiologia Vegetal, Universidade Federal de Lavras, Lavras-MG, 37200-900, Brazil
| | - Francisco Bruno S Freire
- LabPLant, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza-CE, 60451-970, Brazil
| | - Nicole P Porto
- LabPLant, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza-CE, 60451-970, Brazil
| | - Silvio A Cândido-Sobrinho
- LabPLant, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza-CE, 60451-970, Brazil
| | - David B Medeiros
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, D-14476, Germany
| | - Markus Schwarzländer
- Institute of Plant Biology and Biotechnology, Westfälische-Wilhelms-Universität Münster, Münster, D-48143, Germany
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, D-14476, Germany
| | - Leticia Dos Anjos
- Departamento de Biologia, Setor de Fisiologia Vegetal, Universidade Federal de Lavras, Lavras-MG, 37200-900, Brazil
| | - Joachim Kopka
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, D-14476, Germany
| | - Danilo M Daloso
- LabPLant, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza-CE, 60451-970, Brazil
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9
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Takagi D, Ishiyama K, Suganami M, Ushijima T, Fujii T, Tazoe Y, Kawasaki M, Noguchi K, Makino A. Manganese toxicity disrupts indole acetic acid homeostasis and suppresses the CO 2 assimilation reaction in rice leaves. Sci Rep 2021; 11:20922. [PMID: 34686733 PMCID: PMC8536708 DOI: 10.1038/s41598-021-00370-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 10/11/2021] [Indexed: 11/21/2022] Open
Abstract
Despite the essentiality of Mn in terrestrial plants, its excessive accumulation in plant tissues can cause growth defects, known as Mn toxicity. Mn toxicity can be classified into apoplastic and symplastic types depending on its onset. Symplastic Mn toxicity is hypothesised to be more critical for growth defects. However, details of the relationship between growth defects and symplastic Mn toxicity remain elusive. In this study, we aimed to elucidate the molecular mechanisms underlying symplastic Mn toxicity in rice plants. We found that under excess Mn conditions, CO2 assimilation was inhibited by stomatal closure, and both carbon anabolic and catabolic activities were decreased. In addition to stomatal dysfunction, stomatal and leaf anatomical development were also altered by excess Mn accumulation. Furthermore, indole acetic acid (IAA) concentration was decreased, and auxin-responsive gene expression analyses showed IAA-deficient symptoms in leaves due to excess Mn accumulation. These results suggest that excessive Mn accumulation causes IAA deficiency, and low IAA concentrations suppress plant growth by suppressing stomatal opening and leaf anatomical development for efficient CO2 assimilation in leaves.
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Affiliation(s)
- Daisuke Takagi
- grid.412493.90000 0001 0454 7765Faculty of Agriculture, Setsunan University, Hirakata, Osaka 573-0101 Japan ,grid.69566.3a0000 0001 2248 6943Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi 980-8572 Japan
| | - Keiki Ishiyama
- grid.69566.3a0000 0001 2248 6943Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi 980-8572 Japan
| | - Mao Suganami
- grid.69566.3a0000 0001 2248 6943Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi 980-8572 Japan ,grid.443549.b0000 0001 0603 1148Present Address: Faculty of Food and Agricultural Sciences, Fukushima University, Kanayagawa, Fukushima 960-1296 Japan
| | - Tomokazu Ushijima
- grid.412493.90000 0001 0454 7765Faculty of Agriculture, Setsunan University, Hirakata, Osaka 573-0101 Japan
| | - Takeshi Fujii
- grid.412493.90000 0001 0454 7765Faculty of Agriculture, Setsunan University, Hirakata, Osaka 573-0101 Japan
| | - Youshi Tazoe
- grid.69566.3a0000 0001 2248 6943Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi 980-8572 Japan ,grid.505732.60000 0004 6417 4827Present Address: Faculty of Agro-Food Science, Niigata Agro-Food University, Tainai, Niigata 959-2702 Japan
| | - Michio Kawasaki
- grid.412493.90000 0001 0454 7765Faculty of Agriculture, Setsunan University, Hirakata, Osaka 573-0101 Japan
| | - Ko Noguchi
- grid.410785.f0000 0001 0659 6325Department of Applied Life Science, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392 Japan
| | - Amane Makino
- grid.69566.3a0000 0001 2248 6943Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi 980-8572 Japan
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10
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Herrmann HA, Rusz M, Baier D, Jakupec MA, Keppler BK, Berger W, Koellensperger G, Zanghellini J. Thermodynamic Genome-Scale Metabolic Modeling of Metallodrug Resistance in Colorectal Cancer. Cancers (Basel) 2021; 13:4130. [PMID: 34439283 PMCID: PMC8391396 DOI: 10.3390/cancers13164130] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 07/23/2021] [Accepted: 08/03/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Mass spectrometry-based metabolomics approaches provide an immense opportunity to enhance our understanding of the mechanisms that underpin the cellular reprogramming of cancers. Accurate comparative metabolic profiling of heterogeneous conditions, however, is still a challenge. METHODS Measuring both intracellular and extracellular metabolite concentrations, we constrain four instances of a thermodynamic genome-scale metabolic model of the HCT116 colorectal carcinoma cell line to compare the metabolic flux profiles of cells that are either sensitive or resistant to ruthenium- or platinum-based treatments with BOLD-100/KP1339 and oxaliplatin, respectively. RESULTS Normalizing according to growth rate and normalizing resistant cells according to their respective sensitive controls, we are able to dissect metabolic responses specific to the drug and to the resistance states. We find the normalization steps to be crucial in the interpretation of the metabolomics data and show that the metabolic reprogramming in resistant cells is limited to a select number of pathways. CONCLUSIONS Here, we elucidate the key importance of normalization steps in the interpretation of metabolomics data, allowing us to uncover drug-specific metabolic reprogramming during acquired metal-drug resistance.
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Affiliation(s)
- Helena A. Herrmann
- Department of Analytical Chemistry, University of Vienna, 1090 Vienna, Austria; (H.A.H.); (M.R.)
| | - Mate Rusz
- Department of Analytical Chemistry, University of Vienna, 1090 Vienna, Austria; (H.A.H.); (M.R.)
- Institute of Inorganic Chemistry, University of Vienna, 1090 Vienna, Austria; (D.B.); (M.A.J.); (B.K.K.)
| | - Dina Baier
- Institute of Inorganic Chemistry, University of Vienna, 1090 Vienna, Austria; (D.B.); (M.A.J.); (B.K.K.)
| | - Michael A. Jakupec
- Institute of Inorganic Chemistry, University of Vienna, 1090 Vienna, Austria; (D.B.); (M.A.J.); (B.K.K.)
- Research Cluster Translational Cancer Therapy Research, University of Vienna and Medical University of Vienna, 1090 Vienna, Austria;
| | - Bernhard K. Keppler
- Institute of Inorganic Chemistry, University of Vienna, 1090 Vienna, Austria; (D.B.); (M.A.J.); (B.K.K.)
- Research Cluster Translational Cancer Therapy Research, University of Vienna and Medical University of Vienna, 1090 Vienna, Austria;
| | - Walter Berger
- Research Cluster Translational Cancer Therapy Research, University of Vienna and Medical University of Vienna, 1090 Vienna, Austria;
- Institute of Cancer Research and Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
| | - Gunda Koellensperger
- Department of Analytical Chemistry, University of Vienna, 1090 Vienna, Austria; (H.A.H.); (M.R.)
- Vienna Metabolomics Center (VIME), University of Vienna, 1090 Vienna, Austria
- Research Network Chemistry Meets Microbiology, University of Vienna, 1090 Vienna, Austria
| | - Jürgen Zanghellini
- Department of Analytical Chemistry, University of Vienna, 1090 Vienna, Austria; (H.A.H.); (M.R.)
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11
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Daloso DDM, Williams TCR. Current Challenges in Plant Systems Biology. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1346:155-170. [DOI: 10.1007/978-3-030-80352-0_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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12
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Correa SM, Alseekh S, Atehortúa L, Brotman Y, Ríos-Estepa R, Fernie AR, Nikoloski Z. Model-assisted identification of metabolic engineering strategies for Jatropha curcas lipid pathways. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:76-95. [PMID: 33001507 DOI: 10.1111/tpj.14906] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 06/03/2020] [Accepted: 06/12/2020] [Indexed: 06/11/2023]
Abstract
Efficient approaches to increase plant lipid production are necessary to meet current industrial demands for this important resource. While Jatropha curcas cell culture can be used for in vitro lipid production, scaling up the system for industrial applications requires an understanding of how growth conditions affect lipid metabolism and yield. Here we present a bottom-up metabolic reconstruction of J. curcas supported with labeling experiments and biomass characterization under three growth conditions. We show that the metabolic model can accurately predict growth and distribution of fluxes in cell cultures and use these findings to pinpoint energy expenditures that affect lipid biosynthesis and metabolism. In addition, by using constraint-based modeling approaches we identify network reactions whose joint manipulation optimizes lipid production. The proposed model and computational analyses provide a stepping stone for future rational optimization of other agronomically relevant traits in J. curcas.
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Affiliation(s)
- Sandra M Correa
- Genetics of Metabolic Traits Group, Max Planck Institute of Molecular Plant Physiology, Potsdam, 14476, Germany
- Grupo de Biotecnología, Departamento de Ciencias Exactas y Naturales, Universidad de Antioquia, Medellín, 050010, Colombia
| | - Saleh Alseekh
- Central Metabolism Group, Max Planck Institute of Molecular Plant Physiology, Potsdam, 14476, Germany
- Centre for Plant Systems Biology and Biotechnology, Plovdiv, 4000, Bulgaria
| | - Lucía Atehortúa
- Grupo de Biotecnología, Departamento de Ciencias Exactas y Naturales, Universidad de Antioquia, Medellín, 050010, Colombia
| | - Yariv Brotman
- Genetics of Metabolic Traits Group, Max Planck Institute of Molecular Plant Physiology, Potsdam, 14476, Germany
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, 8410501, Israel
| | - Rigoberto Ríos-Estepa
- Grupo de Bioprocesos, Departamento de Ingeniería Química, Universidad de Antioquia, Medellín, 050010, Colombia
| | - Alisdair R Fernie
- Central Metabolism Group, Max Planck Institute of Molecular Plant Physiology, Potsdam, 14476, Germany
- Centre for Plant Systems Biology and Biotechnology, Plovdiv, 4000, Bulgaria
| | - Zoran Nikoloski
- Centre for Plant Systems Biology and Biotechnology, Plovdiv, 4000, Bulgaria
- Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, 14476, Germany
- Systems Biology and Mathematical Modelling Group, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
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Correa SM, Fernie AR, Nikoloski Z, Brotman Y. Towards model-driven characterization and manipulation of plant lipid metabolism. Prog Lipid Res 2020; 80:101051. [PMID: 32640289 DOI: 10.1016/j.plipres.2020.101051] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 06/20/2020] [Accepted: 06/21/2020] [Indexed: 01/09/2023]
Abstract
Plant lipids have versatile applications and provide essential fatty acids in human diet. Therefore, there has been a growing interest to better characterize the genetic basis, regulatory networks, and metabolic pathways that shape lipid quantity and composition. Addressing these issues is challenging due to context-specificity of lipid metabolism integrating environmental, developmental, and tissue-specific cues. Here we systematically review the known metabolic pathways and regulatory interactions that modulate the levels of storage lipids in oilseeds. We argue that the current understanding of lipid metabolism provides the basis for its study in the context of genome-wide plant metabolic networks with the help of approaches from constraint-based modeling and metabolic flux analysis. The focus is on providing a comprehensive summary of the state-of-the-art of modeling plant lipid metabolic pathways, which we then contrast with the existing modeling efforts in yeast and microalgae. We then point out the gaps in knowledge of lipid metabolism, and enumerate the recent advances of using genome-wide association and quantitative trait loci mapping studies to unravel the genetic regulations of lipid metabolism. Finally, we offer a perspective on how advances in the constraint-based modeling framework can propel further characterization of plant lipid metabolism and its rational manipulation.
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Affiliation(s)
- Sandra M Correa
- Genetics of Metabolic Traits Group, Max Planck Institute for Molecular Plant Physiology, Potsdam 14476, Germany; Department of Life Sciences, Ben-Gurion University of the Negev, 8410501 Beer-Sheva, Israel; Departamento de Ciencias Exactas y Naturales, Universidad de Antioquia, Medellín 050010, Colombia.
| | - Alisdair R Fernie
- Central Metabolism Group, Max Planck Institute for Molecular Plant Physiology, Potsdam 14476, Germany; Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria
| | - Zoran Nikoloski
- Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria; Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany; Systems Biology and Mathematical Modelling Group, Max Planck Institute for Molecular Plant Physiology, Potsdam-Golm 14476, Germany.
| | - Yariv Brotman
- Genetics of Metabolic Traits Group, Max Planck Institute for Molecular Plant Physiology, Potsdam 14476, Germany; Department of Life Sciences, Ben-Gurion University of the Negev, 8410501 Beer-Sheva, Israel
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14
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Cocuron JC, Koubaa M, Kimmelfield R, Ross Z, Alonso AP. A Combined Metabolomics and Fluxomics Analysis Identifies Steps Limiting Oil Synthesis in Maize Embryos. PLANT PHYSIOLOGY 2019; 181:961-975. [PMID: 31530627 PMCID: PMC6836839 DOI: 10.1104/pp.19.00920] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 09/06/2019] [Indexed: 05/21/2023]
Abstract
Enhancing fatty acid synthesis (FAS) in maize (Zea mays) has tremendous potential nutritional and economic benefits due to the rapidly growing demand for vegetable oil. In maize kernels, the endosperm and the embryo are the main sites for synthesis and accumulation of starch and oil, respectively. So far, breeding efforts to achieve elevated oil content in maize have resulted in smaller endosperms and therefore lower yield. Directly changing their carbon metabolism may be the key to increasing oil content in maize kernels without affecting yield. To test this hypothesis, the intracellular metabolite levels were compared in maize embryos from two different maize lines, ALEXHO S K SYNTHETIC (Alex) and LH59, which accumulate 48% and 34% of oil, respectively. Comparative metabolomics highlighted the metabolites and pathways that were active in the embryos and important for oil production. The contribution of each pathway to FAS in terms of carbon, reductant, and energy provision was assessed by measuring the carbon flow through the metabolic network (13C-metabolic flux analysis) in developing Alex embryos to build a map of carbon flow through the central metabolism. This approach combined mathematical modeling with biochemical quantification to identify metabolic bottlenecks in FAS in maize embryos. This study describes a combination of innovative tools that will pave the way for controlling seed composition in important food crops.
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Affiliation(s)
- Jean-Christophe Cocuron
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, Texas 76203
| | - Mohamed Koubaa
- Laboratoire Transformations Intégrées de la Matière Renouvelable (Université de Technologie de Compiègne/École Supérieure de Chimie Organique et Minérale, Équipe d'Accueil 4297 Transformations Integrées de la Matière Renouvelable), Centre de Recherche de Royallieu, Université de Technologie de Compiègne, course spéciale 60319, F-60203 Compiègne cedex, France
| | - Rebecca Kimmelfield
- Center for Applied Plant Sciences, The Ohio State University, Columbus, Ohio 43210
| | - Zacchary Ross
- Ohio University Heritage College of Osteopathic Medicine, Dublin, Ohio 43016
| | - Ana Paula Alonso
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, Texas 76203
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Limitations of Deuterium-Labelled Substrates for Quantifying NADPH Metabolism in Heterotrophic Arabidopsis Cell Cultures. Metabolites 2019; 9:metabo9100205. [PMID: 31569392 PMCID: PMC6835633 DOI: 10.3390/metabo9100205] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 09/19/2019] [Accepted: 09/26/2019] [Indexed: 01/21/2023] Open
Abstract
NADPH is the primary source of cellular reductant for biosynthesis, and strategies for increasing productivity via metabolic engineering need to take account of the requirement for reducing power. In plants, while the oxidative pentose phosphate pathway is the most direct route for NADPH production in heterotrophic tissues, there is increasing evidence that other pathways make significant contributions to redox balance. Deuterium-based isotopic labelling strategies have recently been developed to quantify the relative production of NADPH from different pathways in mammalian cells, but the application of these methods to plants has not been critically evaluated. In this study, LC-MS was used to measure deuterium incorporation into metabolites extracted from heterotrophic Arabidopsis cell cultures grown on [1-2H]glucose or D2O. The results show that a high rate of flavin-enzyme-catalysed water exchange obscures labelling of NADPH from deuterated substrates and that this exchange cannot be accurately accounted for due to exchange between triose- and hexose-phosphates. In addition, the duplication of NADPH generating reactions between subcellular compartments can confound analysis based on whole cell extracts. Understanding how the structure of the metabolic network affects the applicability of deuterium labelling methods is a prerequisite for development of more effective flux determination strategies, ensuring data are both quantitative and representative of endogenous biological processes.
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Thomas SC, Tamadonfar KO, Seymour CO, Lai D, Dodsworth JA, Murugapiran SK, Eloe-Fadrosh EA, Dijkstra P, Hedlund BP. Position-Specific Metabolic Probing and Metagenomics of Microbial Communities Reveal Conserved Central Carbon Metabolic Network Activities at High Temperatures. Front Microbiol 2019; 10:1427. [PMID: 31333598 PMCID: PMC6624737 DOI: 10.3389/fmicb.2019.01427] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Accepted: 06/05/2019] [Indexed: 12/02/2022] Open
Abstract
Temperature is a primary driver of microbial community composition and taxonomic diversity; however, it is unclear to what extent temperature affects characteristics of central carbon metabolic pathways (CCMPs) at the community level. In this study, 16S rRNA gene amplicon and metagenome sequencing were combined with 13C-labeled metabolite probing of the CCMPs to assess community carbon metabolism along a temperature gradient (60–95°C) in Great Boiling Spring, NV. 16S rRNA gene amplicon diversity was inversely proportional to temperature, and Archaea were dominant at higher temperatures. KO richness and diversity were also inversely proportional to temperature, yet CCMP genes were similarly represented across the temperature gradient and many individual metagenome-assembled genomes had complete pathways. In contrast, genes encoding cellulosomes and many genes involved in plant matter degradation and photosynthesis were absent at higher temperatures. In situ13C-CO2 production from labeled isotopomer pairs of glucose, pyruvate, and acetate suggested lower relative oxidative pentose phosphate pathway activity and/or fermentation at 60°C, and a stable or decreased maintenance energy demand at higher temperatures. Catabolism of 13C-labeled citrate, succinate, L-alanine, L-serine, and L-cysteine was observed at 85°C, demonstrating broad heterotrophic activity and confirming functioning of the TCA cycle. Together, these results suggest that temperature-driven losses in biodiversity and gene content in geothermal systems may not alter CCMP function or maintenance energy demands at a community level.
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Affiliation(s)
- Scott C Thomas
- School of Life Sciences, University of Nevada, Las Vegas, NV, United States
| | - Kevin O Tamadonfar
- School of Life Sciences, University of Nevada, Las Vegas, NV, United States
| | - Cale O Seymour
- School of Life Sciences, University of Nevada, Las Vegas, NV, United States
| | - Dengxun Lai
- School of Life Sciences, University of Nevada, Las Vegas, NV, United States
| | - Jeremy A Dodsworth
- Department of Biology, California State University, San Bernardino, CA, United States
| | | | - Emiley A Eloe-Fadrosh
- Department of Energy Joint Genome Institute, Joint Genome Institute, Walnut Creek, CA, United States
| | - Paul Dijkstra
- Department of Biological Sciences, Center of Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, United States
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, NV, United States.,Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, NV, United States
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17
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Zakhartsev M. Using a Multi-compartmental Metabolic Model to Predict Carbon Allocation in Arabidopsis thaliana. Methods Mol Biol 2019; 2014:345-369. [PMID: 31197808 DOI: 10.1007/978-1-4939-9562-2_27] [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] [Indexed: 06/09/2023]
Abstract
The molecular mechanism of loading/unloading of sucrose into/from the phloem plays an important role in sucrose translocation among plant tissues. Perturbation of this mechanism results in growth phenotypes of a plant. In order to better understand the coupling of sucrose translocation with metabolic processes a multi-compartmental metabolic network of Arabidopsis thaliana was reconstructed and optimized with respect to biomass growth, both in light and in dark conditions. The model can be used to perform flux balance analysis of metabolic fluxes through the central carbon metabolism and catabolic and anabolic pathways. Balances and turnover of energy (ATP/ADP) and redox metabolites (NAD(P)H/NAD(P)) as well as proton concentrations in different compartments can be estimated. Importantly, the model can be used to quantify the translocation of sucrose from source to sink tissues through phloem in association with an integral balance of protons, which in turn is defined by the operational modes of the energy metabolism (light and dark conditions). This chapter describes how a multi-compartmental model to predict carbon allocation is constructed and used.
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Affiliation(s)
- Maksim Zakhartsev
- Centre for Integrative Genetics, Norwegian University of Life Sciences, Ås, Norway.
- Plant Systems Biology, University of Hohenheim, Stuttgart, Germany.
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18
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Pfau T, Christian N, Masakapalli SK, Sweetlove LJ, Poolman MG, Ebenhöh O. The intertwined metabolism during symbiotic nitrogen fixation elucidated by metabolic modelling. Sci Rep 2018; 8:12504. [PMID: 30131500 PMCID: PMC6104047 DOI: 10.1038/s41598-018-30884-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 08/07/2018] [Indexed: 11/09/2022] Open
Abstract
Genome-scale metabolic network models can be used for various analyses including the prediction of metabolic responses to changes in the environment. Legumes are well known for their rhizobial symbiosis that introduces nitrogen into the global nutrient cycle. Here, we describe a fully compartmentalised, mass and charge-balanced, genome-scale model of the clover Medicago truncatula, which has been adopted as a model organism for legumes. We employed flux balance analysis to demonstrate that the network is capable of producing biomass components in experimentally observed proportions, during day and night. By connecting the plant model to a model of its rhizobial symbiont, Sinorhizobium meliloti, we were able to investigate the effects of the symbiosis on metabolic fluxes and plant growth and could demonstrate how oxygen availability influences metabolic exchanges between plant and symbiont, thus elucidating potential benefits of inter organism amino acid cycling. We thus provide a modelling framework, in which the interlinked metabolism of plants and nodules can be studied from a theoretical perspective.
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Affiliation(s)
- Thomas Pfau
- Institute of Complex Systems and Mathematical Biology, University of Aberdeen, Aberdeen, UK
- Life Sciences Research Unit, University of Luxembourg, Belvaux, Luxembourg
| | - Nils Christian
- Institute of Complex Systems and Mathematical Biology, University of Aberdeen, Aberdeen, UK
| | - Shyam K Masakapalli
- School of Basic Sciences, Indian Institute of Technology Mandi, Mandi, India
| | - Lee J Sweetlove
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | - Mark G Poolman
- Department Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
| | - Oliver Ebenhöh
- Institute of Quantitative and Theoretical Biology, Cluster of Excellence on Plant Sciences CEPLAS, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany.
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19
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Medeiros DB, Perez Souza L, Antunes WC, Araújo WL, Daloso DM, Fernie AR. Sucrose breakdown within guard cells provides substrates for glycolysis and glutamine biosynthesis during light-induced stomatal opening. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018. [PMID: 29543357 DOI: 10.1111/tpj.13889] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Sucrose has long been thought to play an osmolytic role in stomatal opening. However, recent evidence supports the idea that the role of sucrose in this process is primarily energetic. Here we used a combination of stomatal aperture assays and kinetic [U-13 C]-sucrose isotope labelling experiments to confirm that sucrose is degraded during light-induced stomatal opening and to define the fate of the C released from sucrose breakdown. We additionally show that addition of sucrose to the medium did not enhance light-induced stomatal opening. The isotope experiment showed a consistent 13 C enrichment in fructose and glucose, indicating that during light-induced stomatal opening sucrose is indeed degraded. We also observed a clear 13 C enrichment in glutamate and glutamine (Gln), suggesting a concerted activation of sucrose degradation, glycolysis and the tricarboxylic acid cycle. This is in contrast to the situation for Gln biosynthesis in leaves under light, which has been demonstrated to rely on previously stored C. Our results thus collectively allow us to redraw current models concerning the influence of sucrose during light-induced stomatal opening, in which, instead of being accumulated, sucrose is degraded providing C skeletons for Gln biosynthesis.
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Affiliation(s)
- David B Medeiros
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, Potsdam-Golm, 14476, Germany
- Max-Planck Partner Group, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil
| | - Leonardo Perez Souza
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, Potsdam-Golm, 14476, Germany
| | - Werner C Antunes
- Departamento de Biologia, Universidade Estadual de Maringá, Maringá, Paraná, 87020-900, Brazil
| | - Wagner L Araújo
- Max-Planck Partner Group, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil
| | - Danilo M Daloso
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza, Ceará, 60440-970, Brazil
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, Potsdam-Golm, 14476, Germany
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Acket S, Degournay A, Gosset M, Merlier F, Troncoso-Ponce MA, Thomasset B. Analysis of 13C labeling amino acids by capillary electrophoresis – High resolution mass spectrometry in developing flaxseed. Anal Biochem 2018; 547:14-18. [DOI: 10.1016/j.ab.2018.02.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 02/07/2018] [Accepted: 02/08/2018] [Indexed: 12/27/2022]
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Lima VF, de Souza LP, Williams TCR, Fernie AR, Daloso DM. Gas Chromatography-Mass Spectrometry-Based 13C-Labeling Studies in Plant Metabolomics. Methods Mol Biol 2018; 1778:47-58. [PMID: 29761430 DOI: 10.1007/978-1-4939-7819-9_4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Abstract
Stable-isotope labeling analysis has been used to discover new metabolic pathways and their key regulatory points in a wide range of organisms. Given the complexity of the plant metabolic network, this analysis provides information complementary to that obtained from metabolite profiling that can be used to understand how plants cope with adverse conditions, and how metabolism varies between different cells, tissues, and organs. Here we describe the experimental procedures from sample harvesting and extraction to mass spectral analysis and interpretation that allow the researcher to perform 13C-labeling experiments. A wide range of plant material, from single cells to whole plants, can be used to investigate the metabolic fate of the 13C from a predefined tracer. Thus, a key point of this analysis is to choose the correct biological system, the substrate and the condition to be investigated; all of which implicitly relies on the biological question to be investigated. Rapid sample quenching and a careful data analysis are also critical points in such studies. By contrast to other metabolomic approaches, stable-isotope labeling can provide information concerning the fluxes through metabolic networks, which is essential for understanding and manipulating metabolic phenotypes and therefore of pivotal importance for both systems biology and plant metabolic engineering.
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Affiliation(s)
- Valéria F Lima
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza, CE, Brazil
| | | | | | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Danilo M Daloso
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza, CE, Brazil.
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22
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Deborde C, Moing A, Roch L, Jacob D, Rolin D, Giraudeau P. Plant metabolism as studied by NMR spectroscopy. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2017; 102-103:61-97. [PMID: 29157494 DOI: 10.1016/j.pnmrs.2017.05.001] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 05/19/2017] [Accepted: 05/22/2017] [Indexed: 05/07/2023]
Abstract
The study of plant metabolism impacts a broad range of domains such as plant cultural practices, plant breeding, human or animal nutrition, phytochemistry and green biotechnologies. Plant metabolites are extremely diverse in terms of structure or compound families as well as concentrations. This review attempts to illustrate how NMR spectroscopy, with its broad variety of experimental approaches, has contributed widely to the study of plant primary or specialized metabolism in very diverse ways. The review presents recent developments of one-dimensional and multi-dimensional NMR methods to study various aspects of plant metabolism. Through recent examples, it highlights how NMR has proved to be an invaluable tool for the global characterization of sample composition within metabolomic studies, and shows some examples of use for targeted phytochemistry, with a special focus on compound identification and quantitation. In such cases, NMR approaches are often used to provide snapshots of the plant sample composition. The review also covers dynamic aspects of metabolism, with a description of NMR techniques to measure metabolic fluxes - in most cases after stable isotope labelling. It is mainly intended for NMR specialists who would be interested to learn more about the potential of their favourite technique in plant sciences and about specific details of NMR approaches in this field. Therefore, as a practical guide, a paragraph on the specific precautions that should be taken for sample preparation is also included. In addition, since the quality of NMR metabolic studies is highly dependent on approaches to data processing and data sharing, a specific part is dedicated to these aspects. The review concludes with perspectives on the emerging methods that could change significantly the role of NMR in the field of plant metabolism by boosting its sensitivity. The review is illustrated throughout with examples of studies selected to represent diverse applications of liquid-state or HR-MAS NMR.
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Affiliation(s)
- Catherine Deborde
- INRA, UMR 1332 Biologie du Fruit et Pathologie, Centre INRA Bordeaux, F-33140 Villenave d'Ornon, France; Plateforme Métabolome Bordeaux - MetaboHUB, Centre de Génomique Fonctionnelle Bordeaux, IBVM, Centre INRA Bordeaux, F-33140 Villenave d'Ornon, France
| | - Annick Moing
- INRA, UMR 1332 Biologie du Fruit et Pathologie, Centre INRA Bordeaux, F-33140 Villenave d'Ornon, France; Plateforme Métabolome Bordeaux - MetaboHUB, Centre de Génomique Fonctionnelle Bordeaux, IBVM, Centre INRA Bordeaux, F-33140 Villenave d'Ornon, France
| | - Léa Roch
- INRA, UMR 1332 Biologie du Fruit et Pathologie, Centre INRA Bordeaux, F-33140 Villenave d'Ornon, France; Plateforme Métabolome Bordeaux - MetaboHUB, Centre de Génomique Fonctionnelle Bordeaux, IBVM, Centre INRA Bordeaux, F-33140 Villenave d'Ornon, France
| | - Daniel Jacob
- INRA, UMR 1332 Biologie du Fruit et Pathologie, Centre INRA Bordeaux, F-33140 Villenave d'Ornon, France; Plateforme Métabolome Bordeaux - MetaboHUB, Centre de Génomique Fonctionnelle Bordeaux, IBVM, Centre INRA Bordeaux, F-33140 Villenave d'Ornon, France
| | - Dominique Rolin
- Plateforme Métabolome Bordeaux - MetaboHUB, Centre de Génomique Fonctionnelle Bordeaux, IBVM, Centre INRA Bordeaux, F-33140 Villenave d'Ornon, France; Univ. Bordeaux, UMR1332, Biologie du Fruit et Pathologie, 71 av Edouard Bourlaux, 33140 Villenave d'Ornon, France
| | - Patrick Giraudeau
- Chimie et Interdisciplinarité: Synthèse, Analyse, Modélisation (CEISAM), UMR 6230, CNRS, Université de Nantes, Faculté des Sciences, BP 92208, 2 rue de la Houssinière, F-44322 Nantes Cedex 03, France; Institut Universitaire de France, 1 rue Descartes, 75005 Paris, France.
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23
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24
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Koch I, Nöthen J, Schleiff E. Modeling the Metabolism of Arabidopsis thaliana: Application of Network Decomposition and Network Reduction in the Context of Petri Nets. Front Genet 2017; 8:85. [PMID: 28713420 PMCID: PMC5491931 DOI: 10.3389/fgene.2017.00085] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 06/06/2017] [Indexed: 12/16/2022] Open
Abstract
Motivation:Arabidopsis thaliana is a well-established model system for the analysis of the basic physiological and metabolic pathways of plants. Nevertheless, the system is not yet fully understood, although many mechanisms are described, and information for many processes exists. However, the combination and interpretation of the large amount of biological data remain a big challenge, not only because data sets for metabolic paths are still incomplete. Moreover, they are often inconsistent, because they are coming from different experiments of various scales, regarding, for example, accuracy and/or significance. Here, theoretical modeling is powerful to formulate hypotheses for pathways and the dynamics of the metabolism, even if the biological data are incomplete. To develop reliable mathematical models they have to be proven for consistency. This is still a challenging task because many verification techniques fail already for middle-sized models. Consequently, new methods, like decomposition methods or reduction approaches, are developed to circumvent this problem. Methods: We present a new semi-quantitative mathematical model of the metabolism of Arabidopsis thaliana. We used the Petri net formalism to express the complex reaction system in a mathematically unique manner. To verify the model for correctness and consistency we applied concepts of network decomposition and network reduction such as transition invariants, common transition pairs, and invariant transition pairs. Results: We formulated the core metabolism of Arabidopsis thaliana based on recent knowledge from literature, including the Calvin cycle, glycolysis and citric acid cycle, glyoxylate cycle, urea cycle, sucrose synthesis, and the starch metabolism. By applying network decomposition and reduction techniques at steady-state conditions, we suggest a straightforward mathematical modeling process. We demonstrate that potential steady-state pathways exist, which provide the fixed carbon to nearly all parts of the network, especially to the citric acid cycle. There is a close cooperation of important metabolic pathways, e.g., the de novo synthesis of uridine-5-monophosphate, the γ-aminobutyric acid shunt, and the urea cycle. The presented approach extends the established methods for a feasible interpretation of biological network models, in particular of large and complex models.
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Affiliation(s)
- Ina Koch
- Department of Molecular Bioinformatics, Institute of Computer Science, Cluster of Excellence “Macromolecular Complexes”, Goethe-University FrankfurtFrankfurt am Main, Germany
| | - Joachim Nöthen
- Department of Molecular Bioinformatics, Institute of Computer Science, Cluster of Excellence “Macromolecular Complexes”, Goethe-University FrankfurtFrankfurt am Main, Germany
| | - Enrico Schleiff
- Department of Biosciences, Institute of Molecular Biosciences, Molecular Cell Biology of Plants, Cluster of Excellence “Macromolecular Complexes”, Goethe-University FrankfurtFrankfurt am Main, Germany
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Salon C, Avice JC, Colombié S, Dieuaide-Noubhani M, Gallardo K, Jeudy C, Ourry A, Prudent M, Voisin AS, Rolin D. Fluxomics links cellular functional analyses to whole-plant phenotyping. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:2083-2098. [PMID: 28444347 DOI: 10.1093/jxb/erx126] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Fluxes through metabolic pathways reflect the integration of genetic and metabolic regulations. While it is attractive to measure all the mRNAs (transcriptome), all the proteins (proteome), and a large number of the metabolites (metabolome) in a given cellular system, linking and integrating this information remains difficult. Measurement of metabolome-wide fluxes (termed the fluxome) provides an integrated functional output of the cell machinery and a better tool to link functional analyses to plant phenotyping. This review presents and discusses sets of methodologies that have been developed to measure the fluxome. First, the principles of metabolic flux analysis (MFA), its 'short time interval' version Inst-MFA, and of constraints-based methods, such as flux balance analysis and kinetic analysis, are briefly described. The use of these powerful methods for flux characterization at the cellular scale up to the organ (fruits, seeds) and whole-plant level is illustrated. The added value given by fluxomics methods for unravelling how the abiotic environment affects flux, the process, and key metabolic steps are also described. Challenges associated with the development of fluxomics and its integration with 'omics' for thorough plant and organ functional phenotyping are discussed. Taken together, these will ultimately provide crucial clues for identifying appropriate target plant phenotypes for breeding.
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Affiliation(s)
- Christophe Salon
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, 17 Rue Sully, BP 86510, 21065 Dijon Cedex, France
| | - Jean-Christophe Avice
- UNICAEN, UMR INRA 950 Ecophysiologie Végétale, Agronomie et nutritions N, C, S, Esplanade de la Paix, Université Caen Normandie, 14032 Caen Cedex 5, France
| | - Sophie Colombié
- UMR 1332 Biologie du Fruit et Pathologie, INRA, Université de Bordeaux, 33882 Villenave d'Ornon, France
| | - Martine Dieuaide-Noubhani
- UMR 1332 Biologie du Fruit et Pathologie, INRA, Université de Bordeaux, 33882 Villenave d'Ornon, France
| | - Karine Gallardo
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, 17 Rue Sully, BP 86510, 21065 Dijon Cedex, France
| | - Christian Jeudy
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, 17 Rue Sully, BP 86510, 21065 Dijon Cedex, France
| | - Alain Ourry
- UNICAEN, UMR INRA 950 Ecophysiologie Végétale, Agronomie et nutritions N, C, S, Esplanade de la Paix, Université Caen Normandie, 14032 Caen Cedex 5, France
| | - Marion Prudent
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, 17 Rue Sully, BP 86510, 21065 Dijon Cedex, France
| | - Anne-Sophie Voisin
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, 17 Rue Sully, BP 86510, 21065 Dijon Cedex, France
| | - Dominique Rolin
- UMR 1332 Biologie du Fruit et Pathologie, INRA, Université de Bordeaux, 33882 Villenave d'Ornon, France
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Dethloff F, Orf I, Kopka J. Rapid in situ 13C tracing of sucrose utilization in Arabidopsis sink and source leaves. PLANT METHODS 2017; 13:87. [PMID: 29075313 PMCID: PMC5648436 DOI: 10.1186/s13007-017-0239-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 10/10/2017] [Indexed: 05/08/2023]
Abstract
BACKGROUND Conventional metabolomics approaches face the problem of hidden metabolic phenotypes where only fluxes are altered but pool sizes stay constant. Metabolic flux experiments are used to detect such hidden flux phenotypes. These experiments are, however, time consuming, may be cost intensive, and involve specialists for modeling. We fill the gap between conventional metabolomics and flux modeling. We present rapid stable isotope tracing assays and analysis strategies of 13C labeling data. For this purpose, we combine the conventional metabolomics approach that detects significant relative changes of metabolite pool sizes with analyses of differential utilization of 13C labeled carbon. As a test case, we use uniformly labeled 13C-sucrose. RESULTS We present petiole and hypocotyl feeding assays for the rapid in situ feeding (≤ 4 h) of isotopically labeled metabolic precursor to whole Arabidopsis thaliana rosettes. The assays are assessed by conventional gas chromatography-mass spectrometry based metabolite profiling that was extended by joined differential analysis of 13C-labeled sub-pools and of 13C enrichment of metabolites relative to the enrichment of 13C-sucrose within each sample. We apply these analyses to the sink to source transition continuum of leaves from single A. thaliana rosettes and characterize the associated relative changes of metabolite pools, as well as previously hidden changes of sucrose-derived carbon partitioning. We compared the contribution of sucrose as a carbon source in predominantly sink to predominantly source leaves and identified a set of primary metabolites with differential carbon utilization during sink to source transition. CONCLUSION The presented feeding assays and data evaluation strategies represent a rapid and easy-to-use tool box for enhanced metabolomics studies that combine differential pool size analysis with screening for differential carbon utilization from defined stable isotope labeled metabolic precursors.
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Affiliation(s)
- Frederik Dethloff
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Kraepelinstr. 2-10, 80804 Munich, Germany
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Isabel Orf
- French Associates Institute for Agriculture and Biotechnology of Drylands, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer, Israel
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Joachim Kopka
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
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Zakhartsev M, Medvedeva I, Orlov Y, Akberdin I, Krebs O, Schulze WX. Metabolic model of central carbon and energy metabolisms of growing Arabidopsis thaliana in relation to sucrose translocation. BMC PLANT BIOLOGY 2016; 16:262. [PMID: 28031032 PMCID: PMC5192601 DOI: 10.1186/s12870-016-0868-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 08/05/2016] [Indexed: 05/12/2023]
Abstract
BACKGROUND Sucrose translocation between plant tissues is crucial for growth, development and reproduction of plants. Systemic analysis of these metabolic and underlying regulatory processes allow a detailed understanding of carbon distribution within the plant and the formation of associated phenotypic traits. Sucrose translocation from 'source' tissues (e.g. mesophyll) to 'sink' tissues (e.g. root) is tightly bound to the proton gradient across the membranes. The plant sucrose transporters are grouped into efflux exporters (SWEET family) and proton-symport importers (SUC, STP families). To better understand regulation of sucrose export from source tissues and sucrose import into sink tissues, there is a need for a metabolic model that takes in account the tissue organisation of Arabidopsis thaliana with corresponding metabolic specificities of respective tissues in terms of sucrose and proton production/utilization. An ability of the model to operate under different light modes ('light' and 'dark') and correspondingly in different energy producing modes is particularly important in understanding regulatory modules. RESULTS Here, we describe a multi-compartmental model consisting of a mesophyll cell with plastid and mitochondrion, a phloem cell, as well as a root cell with mitochondrion. In this model, the phloem was considered as a non-growing transport compartment, the mesophyll compartment was considered as both autotrophic (growing on CO2 under light) and heterotrophic (growing on starch in darkness), and the root was always considered as heterotrophic tissue dependent on sucrose supply from the mesophyll compartment. In total, the model includes 413 balanced compounds interconnected by 400 transformers. The structured metabolic model accounts for central carbon metabolism, photosynthesis, photorespiration, carbohydrate metabolism, energy and redox metabolisms, proton metabolism, biomass growth, nutrients uptake, proton gradient generation and sucrose translocation between tissues. Biochemical processes in the model were associated with gene-products (742 ORFs). Flux Balance Analysis (FBA) of the model resulted in balanced carbon, nitrogen, proton, energy and redox states under both light and dark conditions. The main H+-fluxes were reconstructed and their directions matched with proton-dependent sucrose translocation from 'source' to 'sink' under any light condition. CONCLUSIONS The model quantified the translocation of sucrose between plant tissues in association with an integral balance of protons, which in turn is defined by operational modes of the energy metabolism.
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Affiliation(s)
- Maksim Zakhartsev
- Department of Plant Systems Biology, University of Hohenheim, Fruwirthstraße 12, 70599 Stuttgart, Germany
| | - Irina Medvedeva
- Novosibirsk State University, Pirogova 2, 630090 Novosibirsk, Russia
| | - Yury Orlov
- The Federal Research Center Institute of Cytology and Genetics, Russian Academy of Sciences, Lavrentyeva 10, 630090 Novosibirsk, Russia
| | - Ilya Akberdin
- The Federal Research Center Institute of Cytology and Genetics, Russian Academy of Sciences, Lavrentyeva 10, 630090 Novosibirsk, Russia
- Biology Department, San Diego State University, San Diego, CA 92182-4614 USA
| | - Olga Krebs
- Heidelberg Institute of Theoretical Sciences, Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany
| | - Waltraud X. Schulze
- Department of Plant Systems Biology, University of Hohenheim, Fruwirthstraße 12, 70599 Stuttgart, Germany
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Dersch LM, Beckers V, Rasch D, Melzer G, Bolten C, Kiep K, Becker H, Bläsing OE, Fuchs R, Ehrhardt T, Wittmann C. Novel Approach for High-Throughput Metabolic Screening of Whole Plants by Stable Isotopes. PLANT PHYSIOLOGY 2016; 171:25-41. [PMID: 26966172 PMCID: PMC4854671 DOI: 10.1104/pp.15.01217] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 03/09/2016] [Indexed: 05/21/2023]
Abstract
Here, we demonstrate whole-plant metabolic profiling by stable isotope labeling and combustion isotope-ratio mass spectrometry for precise quantification of assimilation, translocation, and molecular reallocation of (13)CO2 and (15)NH4NO3 The technology was applied to rice (Oryza sativa) plants at different growth stages. For adult plants, (13)CO2 labeling revealed enhanced carbon assimilation of the flag leaf from flowering to late grain-filling stage, linked to efficient translocation into the panicle. Simultaneous (13)CO2 and (15)NH4NO3 labeling with hydroponically grown seedlings was used to quantify the relative distribution of carbon and nitrogen. Two hours after labeling, assimilated carbon was mainly retained in the shoot (69%), whereas 7% entered the root and 24% was respired. Nitrogen, taken up via the root, was largely translocated into the shoot (85%). Salt-stressed seedlings showed decreased uptake and translocation of nitrogen (69%), whereas carbon metabolism was unaffected. Coupled to a gas chromatograph, labeling analysis provided enrichment of proteinogenic amino acids. This revealed significant protein synthesis in the panicle of adult plants, whereas protein biosynthesis in adult leaves was 8-fold lower than that in seedling shoots. Generally, amino acid enrichment was similar among biosynthetic families and allowed us to infer labeling dynamics of their precursors. On this basis, early and strong (13)C enrichment of Embden-Meyerhof-Parnas pathway and pentose phosphate pathway intermediates indicated high activity of these routes. Applied to mode-of-action analysis of herbicides, the approach showed severe disturbance in the synthesis of branched-chain amino acids upon treatment with imazapyr. The established technology displays a breakthrough for quantitative high-throughput plant metabolic phenotyping.
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Affiliation(s)
- Lisa Maria Dersch
- Institute of Systems Biotechnology, Saarland University, 66123 Saarbrücken, Germany (L.M.D., V.B., C.W.);Institute of Biochemical Engineering, University of Technology Braunschweig, 38106 Braunschweig, Germany (D.R., G.M., C.B., K.K.);BASF SE, 67117 Limburgerhof, Germany (H.B.); andMetanomics GmbH, 10589 Berlin, Germany (O.E.B., R.F., T.E.)
| | - Veronique Beckers
- Institute of Systems Biotechnology, Saarland University, 66123 Saarbrücken, Germany (L.M.D., V.B., C.W.);Institute of Biochemical Engineering, University of Technology Braunschweig, 38106 Braunschweig, Germany (D.R., G.M., C.B., K.K.);BASF SE, 67117 Limburgerhof, Germany (H.B.); andMetanomics GmbH, 10589 Berlin, Germany (O.E.B., R.F., T.E.)
| | - Detlev Rasch
- Institute of Systems Biotechnology, Saarland University, 66123 Saarbrücken, Germany (L.M.D., V.B., C.W.);Institute of Biochemical Engineering, University of Technology Braunschweig, 38106 Braunschweig, Germany (D.R., G.M., C.B., K.K.);BASF SE, 67117 Limburgerhof, Germany (H.B.); andMetanomics GmbH, 10589 Berlin, Germany (O.E.B., R.F., T.E.)
| | - Guido Melzer
- Institute of Systems Biotechnology, Saarland University, 66123 Saarbrücken, Germany (L.M.D., V.B., C.W.);Institute of Biochemical Engineering, University of Technology Braunschweig, 38106 Braunschweig, Germany (D.R., G.M., C.B., K.K.);BASF SE, 67117 Limburgerhof, Germany (H.B.); andMetanomics GmbH, 10589 Berlin, Germany (O.E.B., R.F., T.E.)
| | - Christoph Bolten
- Institute of Systems Biotechnology, Saarland University, 66123 Saarbrücken, Germany (L.M.D., V.B., C.W.);Institute of Biochemical Engineering, University of Technology Braunschweig, 38106 Braunschweig, Germany (D.R., G.M., C.B., K.K.);BASF SE, 67117 Limburgerhof, Germany (H.B.); andMetanomics GmbH, 10589 Berlin, Germany (O.E.B., R.F., T.E.)
| | - Katina Kiep
- Institute of Systems Biotechnology, Saarland University, 66123 Saarbrücken, Germany (L.M.D., V.B., C.W.);Institute of Biochemical Engineering, University of Technology Braunschweig, 38106 Braunschweig, Germany (D.R., G.M., C.B., K.K.);BASF SE, 67117 Limburgerhof, Germany (H.B.); andMetanomics GmbH, 10589 Berlin, Germany (O.E.B., R.F., T.E.)
| | - Horst Becker
- Institute of Systems Biotechnology, Saarland University, 66123 Saarbrücken, Germany (L.M.D., V.B., C.W.);Institute of Biochemical Engineering, University of Technology Braunschweig, 38106 Braunschweig, Germany (D.R., G.M., C.B., K.K.);BASF SE, 67117 Limburgerhof, Germany (H.B.); andMetanomics GmbH, 10589 Berlin, Germany (O.E.B., R.F., T.E.)
| | - Oliver Ernst Bläsing
- Institute of Systems Biotechnology, Saarland University, 66123 Saarbrücken, Germany (L.M.D., V.B., C.W.);Institute of Biochemical Engineering, University of Technology Braunschweig, 38106 Braunschweig, Germany (D.R., G.M., C.B., K.K.);BASF SE, 67117 Limburgerhof, Germany (H.B.); andMetanomics GmbH, 10589 Berlin, Germany (O.E.B., R.F., T.E.)
| | - Regine Fuchs
- Institute of Systems Biotechnology, Saarland University, 66123 Saarbrücken, Germany (L.M.D., V.B., C.W.);Institute of Biochemical Engineering, University of Technology Braunschweig, 38106 Braunschweig, Germany (D.R., G.M., C.B., K.K.);BASF SE, 67117 Limburgerhof, Germany (H.B.); andMetanomics GmbH, 10589 Berlin, Germany (O.E.B., R.F., T.E.)
| | - Thomas Ehrhardt
- Institute of Systems Biotechnology, Saarland University, 66123 Saarbrücken, Germany (L.M.D., V.B., C.W.);Institute of Biochemical Engineering, University of Technology Braunschweig, 38106 Braunschweig, Germany (D.R., G.M., C.B., K.K.);BASF SE, 67117 Limburgerhof, Germany (H.B.); andMetanomics GmbH, 10589 Berlin, Germany (O.E.B., R.F., T.E.)
| | - Christoph Wittmann
- Institute of Systems Biotechnology, Saarland University, 66123 Saarbrücken, Germany (L.M.D., V.B., C.W.);Institute of Biochemical Engineering, University of Technology Braunschweig, 38106 Braunschweig, Germany (D.R., G.M., C.B., K.K.);BASF SE, 67117 Limburgerhof, Germany (H.B.); andMetanomics GmbH, 10589 Berlin, Germany (O.E.B., R.F., T.E.)
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Lindén P, Keech O, Stenlund H, Gardeström P, Moritz T. Reduced mitochondrial malate dehydrogenase activity has a strong effect on photorespiratory metabolism as revealed by 13C labelling. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:3123-35. [PMID: 26889011 PMCID: PMC4867893 DOI: 10.1093/jxb/erw030] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Mitochondrial malate dehydrogenase (mMDH) catalyses the interconversion of malate and oxaloacetate (OAA) in the tricarboxylic acid (TCA) cycle. Its activity is important for redox control of the mitochondrial matrix, through which it may participate in regulation of TCA cycle turnover. In Arabidopsis, there are two isoforms of mMDH. Here, we investigated to which extent the lack of the major isoform, mMDH1 accounting for about 60% of the activity, affected leaf metabolism. In air, rosettes of mmdh1 plants were only slightly smaller than wild type plants although the fresh weight was decreased by about 50%. In low CO2 the difference was much bigger, with mutant plants accumulating only 14% of fresh weight as compared to wild type. To investigate the metabolic background to the differences in growth, we developed a (13)CO2 labelling method, using a custom-built chamber that enabled simultaneous treatment of sets of plants under controlled conditions. The metabolic profiles were analysed by gas- and liquid- chromatography coupled to mass spectrometry to investigate the metabolic adjustments between wild type and mmdh1 The genotypes responded similarly to high CO2 treatment both with respect to metabolite pools and (13)C incorporation during a 2-h treatment. However, under low CO2 several metabolites differed between the two genotypes and, interestingly most of these were closely associated with photorespiration. We found that while the glycine/serine ratio increased, a concomitant altered glutamine/glutamate/α-ketoglutarate relation occurred. Taken together, our results indicate that adequate mMDH activity is essential to shuttle reductants out from the mitochondria to support the photorespiratory flux, and strengthen the idea that photorespiration is tightly intertwined with peripheral metabolic reactions.
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Affiliation(s)
- Pernilla Lindén
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences , SE-901 83 Umeå, Sweden
| | - Olivier Keech
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-901 87 Umeå, Sweden
| | - Hans Stenlund
- Swedish Metabolomics Centre, Department of Molecular Biology, Umeå University, SE-901 87 Umeå, Sweden
| | - Per Gardeström
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-901 87 Umeå, Sweden
| | - Thomas Moritz
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences , SE-901 83 Umeå, Sweden
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Gago J, Daloso DDM, Figueroa CM, Flexas J, Fernie AR, Nikoloski Z. Relationships of Leaf Net Photosynthesis, Stomatal Conductance, and Mesophyll Conductance to Primary Metabolism: A Multispecies Meta-Analysis Approach. PLANT PHYSIOLOGY 2016; 171:265-79. [PMID: 26977088 PMCID: PMC4854675 DOI: 10.1104/pp.15.01660] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 03/10/2016] [Indexed: 05/20/2023]
Abstract
Plant metabolism drives plant development and plant-environment responses, and data readouts from this cellular level could provide insights in the underlying molecular processes. Existing studies have already related key in vivo leaf gas-exchange parameters with structural traits and nutrient components across multiple species. However, insights in the relationships of leaf gas-exchange with leaf primary metabolism are still limited. We investigated these relationships through a multispecies meta-analysis approach based on data sets from 17 published studies describing net photosynthesis (A) and stomatal (gs) and mesophyll (gm) conductances, alongside the 53 data profiles from primary metabolism of 14 species grown in different experiments. Modeling results highlighted the conserved patterns between the different species. Consideration of species-specific effects increased the explanatory power of the models for some metabolites, including Glc-6-P, Fru-6-P, malate, fumarate, Xyl, and ribose. Significant relationships of A with sugars and phosphorylated intermediates were observed. While gs was related to sugars, organic acids, myo-inositol, and shikimate, gm showed a more complex pattern in comparison to the two other traits. Some metabolites, such as malate and Man, appeared in the models for both conductances, suggesting a metabolic coregulation between gs and gm The resulting statistical models provide the first hints for coregulation patterns involving primary metabolism plus leaf water and carbon balances that are conserved across plant species, as well as species-specific trends that can be used to determine new biotechnological targets for crop improvement.
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Affiliation(s)
- Jorge Gago
- Research Group on Plant Biology under Mediterranean Conditions, Departament de Biologia, Universitat de les Illes Balears, 07122 Palma de Mallorca, Illes Balears, Spain (J.G., J.F.); Central Metabolism Group, Molecular Physiology Department, Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Golm, Germany (J.G., D.d.M.D., A.R.F.); System Regulation Group, Metabolic Networks Department, Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Golm, Germany (C.M.F.); andSystems Biology and Mathematical Modeling Group, Molecular Physiology Department, Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Golm, Germany (Z.N.)
| | - Danilo de Menezes Daloso
- Research Group on Plant Biology under Mediterranean Conditions, Departament de Biologia, Universitat de les Illes Balears, 07122 Palma de Mallorca, Illes Balears, Spain (J.G., J.F.); Central Metabolism Group, Molecular Physiology Department, Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Golm, Germany (J.G., D.d.M.D., A.R.F.); System Regulation Group, Metabolic Networks Department, Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Golm, Germany (C.M.F.); andSystems Biology and Mathematical Modeling Group, Molecular Physiology Department, Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Golm, Germany (Z.N.)
| | - Carlos María Figueroa
- Research Group on Plant Biology under Mediterranean Conditions, Departament de Biologia, Universitat de les Illes Balears, 07122 Palma de Mallorca, Illes Balears, Spain (J.G., J.F.); Central Metabolism Group, Molecular Physiology Department, Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Golm, Germany (J.G., D.d.M.D., A.R.F.); System Regulation Group, Metabolic Networks Department, Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Golm, Germany (C.M.F.); andSystems Biology and Mathematical Modeling Group, Molecular Physiology Department, Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Golm, Germany (Z.N.)
| | - Jaume Flexas
- Research Group on Plant Biology under Mediterranean Conditions, Departament de Biologia, Universitat de les Illes Balears, 07122 Palma de Mallorca, Illes Balears, Spain (J.G., J.F.); Central Metabolism Group, Molecular Physiology Department, Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Golm, Germany (J.G., D.d.M.D., A.R.F.); System Regulation Group, Metabolic Networks Department, Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Golm, Germany (C.M.F.); andSystems Biology and Mathematical Modeling Group, Molecular Physiology Department, Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Golm, Germany (Z.N.)
| | - Alisdair Robert Fernie
- Research Group on Plant Biology under Mediterranean Conditions, Departament de Biologia, Universitat de les Illes Balears, 07122 Palma de Mallorca, Illes Balears, Spain (J.G., J.F.); Central Metabolism Group, Molecular Physiology Department, Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Golm, Germany (J.G., D.d.M.D., A.R.F.); System Regulation Group, Metabolic Networks Department, Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Golm, Germany (C.M.F.); andSystems Biology and Mathematical Modeling Group, Molecular Physiology Department, Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Golm, Germany (Z.N.)
| | - Zoran Nikoloski
- Research Group on Plant Biology under Mediterranean Conditions, Departament de Biologia, Universitat de les Illes Balears, 07122 Palma de Mallorca, Illes Balears, Spain (J.G., J.F.); Central Metabolism Group, Molecular Physiology Department, Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Golm, Germany (J.G., D.d.M.D., A.R.F.); System Regulation Group, Metabolic Networks Department, Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Golm, Germany (C.M.F.); andSystems Biology and Mathematical Modeling Group, Molecular Physiology Department, Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Golm, Germany (Z.N.)
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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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32
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Dersch LM, Beckers V, Wittmann C. Green pathways: Metabolic network analysis of plant systems. Metab Eng 2016; 34:1-24. [DOI: 10.1016/j.ymben.2015.12.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 11/30/2015] [Accepted: 12/01/2015] [Indexed: 12/18/2022]
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Yuan H, Cheung CYM, Hilbers PAJ, van Riel NAW. Flux Balance Analysis of Plant Metabolism: The Effect of Biomass Composition and Model Structure on Model Predictions. FRONTIERS IN PLANT SCIENCE 2016; 7:537. [PMID: 27200014 PMCID: PMC4845513 DOI: 10.3389/fpls.2016.00537] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 04/05/2016] [Indexed: 05/22/2023]
Abstract
The biomass composition represented in constraint-based metabolic models is a key component for predicting cellular metabolism using flux balance analysis (FBA). Despite major advances in analytical technologies, it is often challenging to obtain a detailed composition of all major biomass components experimentally. Studies examining the influence of the biomass composition on the predictions of metabolic models have so far mostly been done on models of microorganisms. Little is known about the impact of varying biomass composition on flux prediction in FBA models of plants, whose metabolism is very versatile and complex because of the presence of multiple subcellular compartments. Also, the published metabolic models of plants differ in size and complexity. In this study, we examined the sensitivity of the predicted fluxes of plant metabolic models to biomass composition and model structure. These questions were addressed by evaluating the sensitivity of predictions of growth rates and central carbon metabolic fluxes to varying biomass compositions in three different genome-/large-scale metabolic models of Arabidopsis thaliana. Our results showed that fluxes through the central carbon metabolism were robust to changes in biomass composition. Nevertheless, comparisons between the predictions from three models using identical modeling constraints and objective function showed that model predictions were sensitive to the structure of the models, highlighting large discrepancies between the published models.
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Affiliation(s)
- Huili Yuan
- Department of Biomedical Engineering, Eindhoven University of TechnologyEindhoven, Netherlands
| | | | - Peter A. J. Hilbers
- Department of Biomedical Engineering, Eindhoven University of TechnologyEindhoven, Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of TechnologyEindhoven, Netherlands
| | - Natal A. W. van Riel
- Department of Biomedical Engineering, Eindhoven University of TechnologyEindhoven, Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of TechnologyEindhoven, Netherlands
- Natal A. W. van Riel
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António C, Päpke C, Rocha M, Diab H, Limami AM, Obata T, Fernie AR, van Dongen JT. Regulation of Primary Metabolism in Response to Low Oxygen Availability as Revealed by Carbon and Nitrogen Isotope Redistribution. PLANT PHYSIOLOGY 2016; 170:43-56. [PMID: 26553649 PMCID: PMC4704563 DOI: 10.1104/pp.15.00266] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 11/05/2015] [Indexed: 05/18/2023]
Abstract
Based on enzyme activity assays and metabolic responses to waterlogging of the legume Lotus japonicus, it was previously suggested that, during hypoxia, the tricarboxylic acid cycle switches to a noncyclic operation mode. Hypotheses were postulated to explain the alternative metabolic pathways involved, but as yet, a direct analysis of the relative redistribution of label through the corresponding pathways was not made. Here, we describe the use of stable isotope-labeling experiments for studying metabolism under hypoxia using wild-type roots of the crop legume soybean (Glycine max). [(13)C]Pyruvate labeling was performed to compare metabolism through the tricarboxylic acid cycle, fermentation, alanine metabolism, and the γ-aminobutyric acid shunt, while [(13)C]glutamate and [(15)N]ammonium labeling were performed to address the metabolism via glutamate to succinate. Following these labelings, the time course for the redistribution of the (13)C/(15)N label throughout the metabolic network was evaluated with gas chromatography-time of flight-mass spectrometry. Our combined labeling data suggest the inhibition of the tricarboxylic acid cycle enzyme succinate dehydrogenase, also known as complex II of the mitochondrial electron transport chain, providing support for the bifurcation of the cycle and the down-regulation of the rate of respiration measured during hypoxic stress. Moreover, up-regulation of the γ-aminobutyric acid shunt and alanine metabolism explained the accumulation of succinate and alanine during hypoxia.
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Affiliation(s)
- Carla António
- Energy Metabolism Group (C.A., C.P., M.R., J.T.v.D.) and Central Metabolism Group (T.O., A.R.F.), Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany;Plant Metabolomics Laboratory, Instituto de Tecnologia Química e Biológica António Xavier-Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal (C.A.);Departamento de Produção Animal e Vegetal, Faculdade de Ciências Agrárias, Universidade Federal do Amazonas, Manaus, Amazonas 69082-653, Brazil (M.R.);University of Angers (H.D., A.M.L.) and Institut National de la Recherche Agronomique (A.M.L.), Unité Mixte de Recherche 1345 IRHS, SFR 4207 QUASAV, F-49045 Angers, France; andInstitute for Biology I, RWTH Aachen University, D-52056 Aachen, Germany (J.T.v.D.)
| | - Carola Päpke
- Energy Metabolism Group (C.A., C.P., M.R., J.T.v.D.) and Central Metabolism Group (T.O., A.R.F.), Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany;Plant Metabolomics Laboratory, Instituto de Tecnologia Química e Biológica António Xavier-Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal (C.A.);Departamento de Produção Animal e Vegetal, Faculdade de Ciências Agrárias, Universidade Federal do Amazonas, Manaus, Amazonas 69082-653, Brazil (M.R.);University of Angers (H.D., A.M.L.) and Institut National de la Recherche Agronomique (A.M.L.), Unité Mixte de Recherche 1345 IRHS, SFR 4207 QUASAV, F-49045 Angers, France; andInstitute for Biology I, RWTH Aachen University, D-52056 Aachen, Germany (J.T.v.D.)
| | - Marcio Rocha
- Energy Metabolism Group (C.A., C.P., M.R., J.T.v.D.) and Central Metabolism Group (T.O., A.R.F.), Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany;Plant Metabolomics Laboratory, Instituto de Tecnologia Química e Biológica António Xavier-Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal (C.A.);Departamento de Produção Animal e Vegetal, Faculdade de Ciências Agrárias, Universidade Federal do Amazonas, Manaus, Amazonas 69082-653, Brazil (M.R.);University of Angers (H.D., A.M.L.) and Institut National de la Recherche Agronomique (A.M.L.), Unité Mixte de Recherche 1345 IRHS, SFR 4207 QUASAV, F-49045 Angers, France; andInstitute for Biology I, RWTH Aachen University, D-52056 Aachen, Germany (J.T.v.D.)
| | - Houssein Diab
- Energy Metabolism Group (C.A., C.P., M.R., J.T.v.D.) and Central Metabolism Group (T.O., A.R.F.), Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany;Plant Metabolomics Laboratory, Instituto de Tecnologia Química e Biológica António Xavier-Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal (C.A.);Departamento de Produção Animal e Vegetal, Faculdade de Ciências Agrárias, Universidade Federal do Amazonas, Manaus, Amazonas 69082-653, Brazil (M.R.);University of Angers (H.D., A.M.L.) and Institut National de la Recherche Agronomique (A.M.L.), Unité Mixte de Recherche 1345 IRHS, SFR 4207 QUASAV, F-49045 Angers, France; andInstitute for Biology I, RWTH Aachen University, D-52056 Aachen, Germany (J.T.v.D.)
| | - Anis M Limami
- Energy Metabolism Group (C.A., C.P., M.R., J.T.v.D.) and Central Metabolism Group (T.O., A.R.F.), Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany;Plant Metabolomics Laboratory, Instituto de Tecnologia Química e Biológica António Xavier-Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal (C.A.);Departamento de Produção Animal e Vegetal, Faculdade de Ciências Agrárias, Universidade Federal do Amazonas, Manaus, Amazonas 69082-653, Brazil (M.R.);University of Angers (H.D., A.M.L.) and Institut National de la Recherche Agronomique (A.M.L.), Unité Mixte de Recherche 1345 IRHS, SFR 4207 QUASAV, F-49045 Angers, France; andInstitute for Biology I, RWTH Aachen University, D-52056 Aachen, Germany (J.T.v.D.)
| | - Toshihiro Obata
- Energy Metabolism Group (C.A., C.P., M.R., J.T.v.D.) and Central Metabolism Group (T.O., A.R.F.), Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany;Plant Metabolomics Laboratory, Instituto de Tecnologia Química e Biológica António Xavier-Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal (C.A.);Departamento de Produção Animal e Vegetal, Faculdade de Ciências Agrárias, Universidade Federal do Amazonas, Manaus, Amazonas 69082-653, Brazil (M.R.);University of Angers (H.D., A.M.L.) and Institut National de la Recherche Agronomique (A.M.L.), Unité Mixte de Recherche 1345 IRHS, SFR 4207 QUASAV, F-49045 Angers, France; andInstitute for Biology I, RWTH Aachen University, D-52056 Aachen, Germany (J.T.v.D.)
| | - Alisdair R Fernie
- Energy Metabolism Group (C.A., C.P., M.R., J.T.v.D.) and Central Metabolism Group (T.O., A.R.F.), Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany;Plant Metabolomics Laboratory, Instituto de Tecnologia Química e Biológica António Xavier-Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal (C.A.);Departamento de Produção Animal e Vegetal, Faculdade de Ciências Agrárias, Universidade Federal do Amazonas, Manaus, Amazonas 69082-653, Brazil (M.R.);University of Angers (H.D., A.M.L.) and Institut National de la Recherche Agronomique (A.M.L.), Unité Mixte de Recherche 1345 IRHS, SFR 4207 QUASAV, F-49045 Angers, France; andInstitute for Biology I, RWTH Aachen University, D-52056 Aachen, Germany (J.T.v.D.)
| | - Joost T van Dongen
- Energy Metabolism Group (C.A., C.P., M.R., J.T.v.D.) and Central Metabolism Group (T.O., A.R.F.), Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany;Plant Metabolomics Laboratory, Instituto de Tecnologia Química e Biológica António Xavier-Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal (C.A.);Departamento de Produção Animal e Vegetal, Faculdade de Ciências Agrárias, Universidade Federal do Amazonas, Manaus, Amazonas 69082-653, Brazil (M.R.);University of Angers (H.D., A.M.L.) and Institut National de la Recherche Agronomique (A.M.L.), Unité Mixte de Recherche 1345 IRHS, SFR 4207 QUASAV, F-49045 Angers, France; andInstitute for Biology I, RWTH Aachen University, D-52056 Aachen, Germany (J.T.v.D.)
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Allen DK. Quantifying plant phenotypes with isotopic labeling & metabolic flux analysis. Curr Opin Biotechnol 2015; 37:45-52. [PMID: 26613198 DOI: 10.1016/j.copbio.2015.10.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 10/04/2015] [Accepted: 10/06/2015] [Indexed: 12/14/2022]
Abstract
Analyses of metabolic flux using stable isotopes in plants have traditionally been restricted to tissues with presumed homogeneous cell populations and long metabolic steady states such as developing seeds, cell suspensions, or cultured roots and root tips. It is now possible to describe these and other metabolically more dynamic tissues such as leaves in greater detail using novel methods in mass spectrometry, isotope labeling strategies, and transient labeling-based flux analyses. Such studies are necessary for a systems level description of plant function that more closely represents biological reality, and provides insights into the genes that will need to be modified as natural resources become ever more limited and environments change.
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Affiliation(s)
- Doug K Allen
- United States Department of Agriculture-Agricultural Research Service, Plant Genetics Research Unit, 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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Nikoloski Z, Perez-Storey R, Sweetlove LJ. Inference and Prediction of Metabolic Network Fluxes. PLANT PHYSIOLOGY 2015; 169:1443-55. [PMID: 26392262 PMCID: PMC4634083 DOI: 10.1104/pp.15.01082] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 09/06/2015] [Indexed: 05/18/2023]
Abstract
In this Update, we cover the basic principles of the estimation and prediction of the rates of the many interconnected biochemical reactions that constitute plant metabolic networks. This includes metabolic flux analysis approaches that utilize the rates or patterns of redistribution of stable isotopes of carbon and other atoms to estimate fluxes, as well as constraints-based optimization approaches such as flux balance analysis. Some of the major insights that have been gained from analysis of fluxes in plants are discussed, including the functioning of metabolic pathways in a network context, the robustness of the metabolic phenotype, the importance of cell maintenance costs, and the mechanisms that enable energy and redox balancing at steady state. We also discuss methodologies to exploit 'omic data sets for the construction of tissue-specific metabolic network models and to constrain the range of permissible fluxes in such models. Finally, we consider the future directions and challenges faced by the field of metabolic network flux phenotyping.
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Affiliation(s)
- Zoran Nikoloski
- Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam, Germany (Z.N.); andDepartment of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom (R.P.-S., L.J.S.)
| | - Richard Perez-Storey
- Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam, Germany (Z.N.); andDepartment of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom (R.P.-S., L.J.S.)
| | - Lee J Sweetlove
- Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam, Germany (Z.N.); andDepartment of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom (R.P.-S., L.J.S.)
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37
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Rolletschek H, Grafahrend-Belau E, Munz E, Radchuk V, Kartäusch R, Tschiersch H, Melkus G, Schreiber F, Jakob PM, Borisjuk L. Metabolic Architecture of the Cereal Grain and Its Relevance to Maximize Carbon Use Efficiency. PLANT PHYSIOLOGY 2015; 169:1698-713. [PMID: 26395842 PMCID: PMC4634074 DOI: 10.1104/pp.15.00981] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 09/20/2015] [Indexed: 05/20/2023]
Abstract
Here, we have characterized the spatial heterogeneity of the cereal grain's metabolism and demonstrated how, by integrating a distinct set of metabolic strategies, the grain has evolved to become an almost perfect entity for carbon storage. In vivo imaging revealed light-induced cycles in assimilate supply toward the ear/grain of barley (Hordeum vulgare) and wheat (Triticum aestivum). In silico modeling predicted that, in the two grain storage organs (the endosperm and embryo), the light-induced shift in solute influx does cause adjustment in metabolic flux without changes in pathway utilization patterns. The enveloping, leaf-like pericarp, in contrast, shows major shifts in flux distribution (starch metabolism, photosynthesis, remobilization, and tricarboxylic acid cycle activity) allow to refix 79% of the CO2 released by the endosperm and embryo, allowing the grain to achieve an extraordinary high carbon conversion efficiency of 95%. Shading experiments demonstrated that ears are autonomously able to raise the influx of solutes in response to light, but with little effect on the steady-state levels of metabolites or transcripts or on the pattern of sugar distribution within the grain. The finding suggests the presence of a mechanism(s) able to ensure metabolic homeostasis in the face of short-term environmental fluctuation. The proposed multicomponent modeling approach is informative for predicting the metabolic effects of either an altered level of incident light or a momentary change in the supply of sucrose. It is therefore of potential value for assessing the impact of either breeding and/or biotechnological interventions aimed at increasing grain yield.
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Affiliation(s)
- Hardy Rolletschek
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany (H.R., E.M., V.R., H.T., L.B.);Institut für Pharmazie, Martin-Luther-University of Halle, 06120 Halle, Germany (E.G.-B.);Institute of Experimental Physics 5, University of Würzburg, 97074 Würzburg, Germany (E.M., P.M.J.);Research Center Magnetic Resonance Bavaria, 97074 Wurzburg, Germany (R.K., P.M.J.);Department of Medical Imaging, University of Ottawa, Ottawa, Ontario, Canada K1Y 4E9 (G.M.); andClayton School of IT, Monash University, Melbourne, Victoria 3800, Australia (F.S.)
| | - Eva Grafahrend-Belau
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany (H.R., E.M., V.R., H.T., L.B.);Institut für Pharmazie, Martin-Luther-University of Halle, 06120 Halle, Germany (E.G.-B.);Institute of Experimental Physics 5, University of Würzburg, 97074 Würzburg, Germany (E.M., P.M.J.);Research Center Magnetic Resonance Bavaria, 97074 Wurzburg, Germany (R.K., P.M.J.);Department of Medical Imaging, University of Ottawa, Ottawa, Ontario, Canada K1Y 4E9 (G.M.); andClayton School of IT, Monash University, Melbourne, Victoria 3800, Australia (F.S.)
| | - Eberhard Munz
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany (H.R., E.M., V.R., H.T., L.B.);Institut für Pharmazie, Martin-Luther-University of Halle, 06120 Halle, Germany (E.G.-B.);Institute of Experimental Physics 5, University of Würzburg, 97074 Würzburg, Germany (E.M., P.M.J.);Research Center Magnetic Resonance Bavaria, 97074 Wurzburg, Germany (R.K., P.M.J.);Department of Medical Imaging, University of Ottawa, Ottawa, Ontario, Canada K1Y 4E9 (G.M.); andClayton School of IT, Monash University, Melbourne, Victoria 3800, Australia (F.S.)
| | - Volodymyr Radchuk
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany (H.R., E.M., V.R., H.T., L.B.);Institut für Pharmazie, Martin-Luther-University of Halle, 06120 Halle, Germany (E.G.-B.);Institute of Experimental Physics 5, University of Würzburg, 97074 Würzburg, Germany (E.M., P.M.J.);Research Center Magnetic Resonance Bavaria, 97074 Wurzburg, Germany (R.K., P.M.J.);Department of Medical Imaging, University of Ottawa, Ottawa, Ontario, Canada K1Y 4E9 (G.M.); andClayton School of IT, Monash University, Melbourne, Victoria 3800, Australia (F.S.)
| | - Ralf Kartäusch
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany (H.R., E.M., V.R., H.T., L.B.);Institut für Pharmazie, Martin-Luther-University of Halle, 06120 Halle, Germany (E.G.-B.);Institute of Experimental Physics 5, University of Würzburg, 97074 Würzburg, Germany (E.M., P.M.J.);Research Center Magnetic Resonance Bavaria, 97074 Wurzburg, Germany (R.K., P.M.J.);Department of Medical Imaging, University of Ottawa, Ottawa, Ontario, Canada K1Y 4E9 (G.M.); andClayton School of IT, Monash University, Melbourne, Victoria 3800, Australia (F.S.)
| | - Henning Tschiersch
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany (H.R., E.M., V.R., H.T., L.B.);Institut für Pharmazie, Martin-Luther-University of Halle, 06120 Halle, Germany (E.G.-B.);Institute of Experimental Physics 5, University of Würzburg, 97074 Würzburg, Germany (E.M., P.M.J.);Research Center Magnetic Resonance Bavaria, 97074 Wurzburg, Germany (R.K., P.M.J.);Department of Medical Imaging, University of Ottawa, Ottawa, Ontario, Canada K1Y 4E9 (G.M.); andClayton School of IT, Monash University, Melbourne, Victoria 3800, Australia (F.S.)
| | - Gerd Melkus
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany (H.R., E.M., V.R., H.T., L.B.);Institut für Pharmazie, Martin-Luther-University of Halle, 06120 Halle, Germany (E.G.-B.);Institute of Experimental Physics 5, University of Würzburg, 97074 Würzburg, Germany (E.M., P.M.J.);Research Center Magnetic Resonance Bavaria, 97074 Wurzburg, Germany (R.K., P.M.J.);Department of Medical Imaging, University of Ottawa, Ottawa, Ontario, Canada K1Y 4E9 (G.M.); andClayton School of IT, Monash University, Melbourne, Victoria 3800, Australia (F.S.)
| | - Falk Schreiber
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany (H.R., E.M., V.R., H.T., L.B.);Institut für Pharmazie, Martin-Luther-University of Halle, 06120 Halle, Germany (E.G.-B.);Institute of Experimental Physics 5, University of Würzburg, 97074 Würzburg, Germany (E.M., P.M.J.);Research Center Magnetic Resonance Bavaria, 97074 Wurzburg, Germany (R.K., P.M.J.);Department of Medical Imaging, University of Ottawa, Ottawa, Ontario, Canada K1Y 4E9 (G.M.); andClayton School of IT, Monash University, Melbourne, Victoria 3800, Australia (F.S.)
| | - Peter M Jakob
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany (H.R., E.M., V.R., H.T., L.B.);Institut für Pharmazie, Martin-Luther-University of Halle, 06120 Halle, Germany (E.G.-B.);Institute of Experimental Physics 5, University of Würzburg, 97074 Würzburg, Germany (E.M., P.M.J.);Research Center Magnetic Resonance Bavaria, 97074 Wurzburg, Germany (R.K., P.M.J.);Department of Medical Imaging, University of Ottawa, Ottawa, Ontario, Canada K1Y 4E9 (G.M.); andClayton School of IT, Monash University, Melbourne, Victoria 3800, Australia (F.S.)
| | - Ljudmilla Borisjuk
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany (H.R., E.M., V.R., H.T., L.B.);Institut für Pharmazie, Martin-Luther-University of Halle, 06120 Halle, Germany (E.G.-B.);Institute of Experimental Physics 5, University of Würzburg, 97074 Würzburg, Germany (E.M., P.M.J.);Research Center Magnetic Resonance Bavaria, 97074 Wurzburg, Germany (R.K., P.M.J.);Department of Medical Imaging, University of Ottawa, Ottawa, Ontario, Canada K1Y 4E9 (G.M.); andClayton School of IT, Monash University, Melbourne, Victoria 3800, Australia (F.S.)
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38
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Tohge T, Scossa F, Fernie AR. Integrative Approaches to Enhance Understanding of Plant Metabolic Pathway Structure and Regulation. PLANT PHYSIOLOGY 2015; 169:1499-511. [PMID: 26371234 PMCID: PMC4634077 DOI: 10.1104/pp.15.01006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 09/10/2015] [Indexed: 05/05/2023]
Abstract
Huge insight into molecular mechanisms and biological network coordination have been achieved following the application of various profiling technologies. Our knowledge of how the different molecular entities of the cell interact with one another suggests that, nevertheless, integration of data from different techniques could drive a more comprehensive understanding of the data emanating from different techniques. Here, we provide an overview of how such data integration is being used to aid the understanding of metabolic pathway structure and regulation. We choose to focus on the pairwise integration of large-scale metabolite data with that of the transcriptomic, proteomics, whole-genome sequence, growth- and yield-associated phenotypes, and archival functional genomic data sets. In doing so, we attempt to provide an update on approaches that integrate data obtained at different levels to reach a better understanding of either single gene function or metabolic pathway structure and regulation within the context of a broader biological process.
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Affiliation(s)
- Takayuki Tohge
- Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany (T.T., A.R.F.); andConsiglio per la Ricerca e Analisi dell'Economia Agraria, Centro di Ricerca per la Frutticoltura, 00134 Rome, Italy (F.S.)
| | - Federico Scossa
- Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany (T.T., A.R.F.); andConsiglio per la Ricerca e Analisi dell'Economia Agraria, Centro di Ricerca per la Frutticoltura, 00134 Rome, Italy (F.S.)
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany (T.T., A.R.F.); andConsiglio per la Ricerca e Analisi dell'Economia Agraria, Centro di Ricerca per la Frutticoltura, 00134 Rome, Italy (F.S.)
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39
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Fluxes through plant metabolic networks: measurements, predictions, insights and challenges. Biochem J 2015; 465:27-38. [PMID: 25631681 DOI: 10.1042/bj20140984] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Although the flows of material through metabolic networks are central to cell function, they are not easy to measure other than at the level of inputs and outputs. This is particularly true in plant cells, where the network spans multiple subcellular compartments and where the network may function either heterotrophically or photoautotrophically. For many years, kinetic modelling of pathways provided the only method for describing the operation of fragments of the network. However, more recently, it has become possible to map the fluxes in central carbon metabolism using the stable isotope labelling techniques of metabolic flux analysis (MFA), and to predict intracellular fluxes using constraints-based modelling procedures such as flux balance analysis (FBA). These approaches were originally developed for the analysis of microbial metabolism, but over the last decade, they have been adapted for the more demanding analysis of plant metabolic networks. Here, the principal features of MFA and FBA as applied to plants are outlined, followed by a discussion of the insights that have been gained into plant metabolic networks through the application of these time-consuming and non-trivial methods. The discussion focuses on how a system-wide view of plant metabolism has increased our understanding of network structure, metabolic perturbations and the provision of reducing power and energy for cell function. Current methodological challenges that limit the scope of plant MFA are discussed and particular emphasis is placed on the importance of developing methods for cell-specific MFA.
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40
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Allen DK, Bates PD, Tjellström H. Tracking the metabolic pulse of plant lipid production with isotopic labeling and flux analyses: Past, present and future. Prog Lipid Res 2015; 58:97-120. [PMID: 25773881 DOI: 10.1016/j.plipres.2015.02.002] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 01/30/2015] [Accepted: 02/11/2015] [Indexed: 11/25/2022]
Abstract
Metabolism is comprised of networks of chemical transformations, organized into integrated biochemical pathways that are the basis of cellular operation, and function to sustain life. Metabolism, and thus life, is not static. The rate of metabolites transitioning through biochemical pathways (i.e., flux) determines cellular phenotypes, and is constantly changing in response to genetic or environmental perturbations. Each change evokes a response in metabolic pathway flow, and the quantification of fluxes under varied conditions helps to elucidate major and minor routes, and regulatory aspects of metabolism. To measure fluxes requires experimental methods that assess the movements and transformations of metabolites without creating artifacts. Isotopic labeling fills this role and is a long-standing experimental approach to identify pathways and quantify their metabolic relevance in different tissues or under different conditions. The application of labeling techniques to plant science is however far from reaching it potential. In light of advances in genetics and molecular biology that provide a means to alter metabolism, and given recent improvements in instrumentation, computational tools and available isotopes, the use of isotopic labeling to probe metabolism is becoming more and more powerful. We review the principal analytical methods for isotopic labeling with a focus on seminal studies of pathways and fluxes in lipid metabolism and carbon partitioning through central metabolism. Central carbon metabolic steps are directly linked to lipid production by serving to generate the precursors for fatty acid biosynthesis and lipid assembly. Additionally some of the ideas for labeling techniques that may be most applicable for lipid metabolism in the future were originally developed to investigate other aspects of central metabolism. We conclude by describing recent advances that will play an important future role in quantifying flux and metabolic operation in plant tissues.
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Affiliation(s)
- Doug K Allen
- United States Department of Agriculture, Agricultural Research Service, 975 North Warson Road, St. Louis, MO 63132, United States; Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO 63132, United States.
| | - Philip D Bates
- Department of Chemistry and Biochemistry, University of Southern Mississippi, Hattiesburg, MS 39406, United States
| | - Henrik Tjellström
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, United States; Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI 48824, United States
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Heise R, Fernie AR, Stitt M, Nikoloski Z. Pool size measurements facilitate the determination of fluxes at branching points in non-stationary metabolic flux analysis: the case of Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2015; 6:386. [PMID: 26082786 PMCID: PMC4451360 DOI: 10.3389/fpls.2015.00386] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 05/14/2015] [Indexed: 05/08/2023]
Abstract
Pool size measurements are important for the estimation of absolute intracellular fluxes in particular scenarios based on data from heavy carbon isotope experiments. Recently, steady-state fluxes estimates were obtained for central carbon metabolism in an intact illuminated rosette of Arabidopsis thaliana grown photoautotrophically (Szecowka et al., 2013; Heise et al., 2014). Fluxes were estimated therein by integrating mass-spectrometric data of the dynamics of the unlabeled metabolic fraction, data on metabolic pool sizes, partitioning of metabolic pools between cellular compartments and estimates of photosynthetically inactive pools, with a simplified model of plant central carbon metabolism. However, the fluxes were determined by treating the pool sizes as fixed parameters. Here we investigated whether and, if so, to what extent the treatment of pool sizes as parameters to be optimized in three scenarios may affect the flux estimates. The results are discussed in terms of benchmark values for canonical pathways and reactions, including starch and sucrose synthesis as well as the ribulose-1,5-bisphosphate carboxylation and oxygenation reactions. In addition, we discuss pathways emerging from a divergent branch point for which pool sizes are required for flux estimation, irrespective of the computational approach used for the simulation of the observable labeling pattern. Therefore, our findings indicate the necessity for development of techniques for accurate pool size measurements to improve the quality of flux estimates from non-stationary flux estimates in intact plant cells in the absence of alternative flux measurements.
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Affiliation(s)
- Robert Heise
- Systems Biology and Mathematical Modeling Group, Max Planck Institute of Molecular Plant PhysiologyPotsdam, Germany
| | - Alisdair R. Fernie
- Central Metabolism Group, Max Planck Institute of Molecular Plant PhysiologyPotsdam, Germany
| | - Mark Stitt
- System Regulation Group, Max Planck Institute of Molecular Plant PhysiologyPotsdam, Germany
| | - Zoran Nikoloski
- Systems Biology and Mathematical Modeling Group, Max Planck Institute of Molecular Plant PhysiologyPotsdam, Germany
- *Correspondence: Zoran Nikoloski, Systems Biology and Mathematical Modeling Group, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany
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42
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Wright LP, Rohwer JM, Ghirardo A, Hammerbacher A, Ortiz-Alcaide M, Raguschke B, Schnitzler JP, Gershenzon J, Phillips MA. Deoxyxylulose 5-Phosphate Synthase Controls Flux through the Methylerythritol 4-Phosphate Pathway in Arabidopsis. PLANT PHYSIOLOGY 2014; 165:1488-1504. [PMID: 24987018 PMCID: PMC4119033 DOI: 10.1104/pp.114.245191] [Citation(s) in RCA: 117] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Accepted: 06/26/2014] [Indexed: 05/18/2023]
Abstract
The 2-C-methylerythritol 4-phosphate (MEP) pathway supplies precursors for plastidial isoprenoid biosynthesis including carotenoids, redox cofactor side chains, and biogenic volatile organic compounds. We examined the first enzyme of this pathway, 1-deoxyxylulose 5-phosphate synthase (DXS), using metabolic control analysis. Multiple Arabidopsis (Arabidopsis thaliana) lines presenting a range of DXS activities were dynamically labeled with 13CO2 in an illuminated, climate-controlled, gas exchange cuvette. Carbon was rapidly assimilated into MEP pathway intermediates, but not into the mevalonate pathway. A flux control coefficient of 0.82 was calculated for DXS by correlating absolute flux to enzyme activity under photosynthetic steady-state conditions, indicating that DXS is the major controlling enzyme of the MEP pathway. DXS manipulation also revealed a second pool of a downstream metabolite, 2-C-methylerythritol-2,4-cyclodiphosphate (MEcDP), metabolically isolated from the MEP pathway. DXS overexpression led to a 3- to 4-fold increase in MEcDP pool size but to a 2-fold drop in maximal labeling. The existence of this pool was supported by residual MEcDP levels detected in dark-adapted transgenic plants. Both pools of MEcDP are closely modulated by DXS activity, as shown by the fact that the concentration control coefficient of DXS was twice as high for MEcDP (0.74) as for 1-deoxyxylulose 5-phosphate (0.35) or dimethylallyl diphosphate (0.34). Despite the high flux control coefficient for DXS, its overexpression led to only modest increases in isoprenoid end products and in the photosynthetic rate. Diversion of flux via MEcDP may partly explain these findings and suggests new opportunities to engineer the MEP pathway.
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Affiliation(s)
- Louwrance P Wright
- Department of Biochemistry, Max Plank Institute for Chemical Ecology, 07745 Jena, Germany (L.P.W., A.H., B.R., J.G.);Department of Biochemistry, Stellenbosch University, 7602 Stellenbosch, South Africa (J.M.R.);Research Unit Environmental Simulation (EUS), Institute of Biochemical Plant Pathology, Helmholtz Zentrum, 85764 Neuherberg, Germany (A.G., J.-P.S.); andPlant Metabolism and Metabolic Engineering Program, Centre for Research in Agricultural Genomics (Consorci CSIC-IRTA-UAB-UB), 08193 Bellaterra, Barcelona, Spain (M.O., M.A.P.)
| | - Johann M Rohwer
- Department of Biochemistry, Max Plank Institute for Chemical Ecology, 07745 Jena, Germany (L.P.W., A.H., B.R., J.G.);Department of Biochemistry, Stellenbosch University, 7602 Stellenbosch, South Africa (J.M.R.);Research Unit Environmental Simulation (EUS), Institute of Biochemical Plant Pathology, Helmholtz Zentrum, 85764 Neuherberg, Germany (A.G., J.-P.S.); andPlant Metabolism and Metabolic Engineering Program, Centre for Research in Agricultural Genomics (Consorci CSIC-IRTA-UAB-UB), 08193 Bellaterra, Barcelona, Spain (M.O., M.A.P.)
| | - Andrea Ghirardo
- Department of Biochemistry, Max Plank Institute for Chemical Ecology, 07745 Jena, Germany (L.P.W., A.H., B.R., J.G.);Department of Biochemistry, Stellenbosch University, 7602 Stellenbosch, South Africa (J.M.R.);Research Unit Environmental Simulation (EUS), Institute of Biochemical Plant Pathology, Helmholtz Zentrum, 85764 Neuherberg, Germany (A.G., J.-P.S.); andPlant Metabolism and Metabolic Engineering Program, Centre for Research in Agricultural Genomics (Consorci CSIC-IRTA-UAB-UB), 08193 Bellaterra, Barcelona, Spain (M.O., M.A.P.)
| | - Almuth Hammerbacher
- Department of Biochemistry, Max Plank Institute for Chemical Ecology, 07745 Jena, Germany (L.P.W., A.H., B.R., J.G.);Department of Biochemistry, Stellenbosch University, 7602 Stellenbosch, South Africa (J.M.R.);Research Unit Environmental Simulation (EUS), Institute of Biochemical Plant Pathology, Helmholtz Zentrum, 85764 Neuherberg, Germany (A.G., J.-P.S.); andPlant Metabolism and Metabolic Engineering Program, Centre for Research in Agricultural Genomics (Consorci CSIC-IRTA-UAB-UB), 08193 Bellaterra, Barcelona, Spain (M.O., M.A.P.)
| | - Miriam Ortiz-Alcaide
- Department of Biochemistry, Max Plank Institute for Chemical Ecology, 07745 Jena, Germany (L.P.W., A.H., B.R., J.G.);Department of Biochemistry, Stellenbosch University, 7602 Stellenbosch, South Africa (J.M.R.);Research Unit Environmental Simulation (EUS), Institute of Biochemical Plant Pathology, Helmholtz Zentrum, 85764 Neuherberg, Germany (A.G., J.-P.S.); andPlant Metabolism and Metabolic Engineering Program, Centre for Research in Agricultural Genomics (Consorci CSIC-IRTA-UAB-UB), 08193 Bellaterra, Barcelona, Spain (M.O., M.A.P.)
| | - Bettina Raguschke
- Department of Biochemistry, Max Plank Institute for Chemical Ecology, 07745 Jena, Germany (L.P.W., A.H., B.R., J.G.);Department of Biochemistry, Stellenbosch University, 7602 Stellenbosch, South Africa (J.M.R.);Research Unit Environmental Simulation (EUS), Institute of Biochemical Plant Pathology, Helmholtz Zentrum, 85764 Neuherberg, Germany (A.G., J.-P.S.); andPlant Metabolism and Metabolic Engineering Program, Centre for Research in Agricultural Genomics (Consorci CSIC-IRTA-UAB-UB), 08193 Bellaterra, Barcelona, Spain (M.O., M.A.P.)
| | - Jörg-Peter Schnitzler
- Department of Biochemistry, Max Plank Institute for Chemical Ecology, 07745 Jena, Germany (L.P.W., A.H., B.R., J.G.);Department of Biochemistry, Stellenbosch University, 7602 Stellenbosch, South Africa (J.M.R.);Research Unit Environmental Simulation (EUS), Institute of Biochemical Plant Pathology, Helmholtz Zentrum, 85764 Neuherberg, Germany (A.G., J.-P.S.); andPlant Metabolism and Metabolic Engineering Program, Centre for Research in Agricultural Genomics (Consorci CSIC-IRTA-UAB-UB), 08193 Bellaterra, Barcelona, Spain (M.O., M.A.P.)
| | - Jonathan Gershenzon
- Department of Biochemistry, Max Plank Institute for Chemical Ecology, 07745 Jena, Germany (L.P.W., A.H., B.R., J.G.);Department of Biochemistry, Stellenbosch University, 7602 Stellenbosch, South Africa (J.M.R.);Research Unit Environmental Simulation (EUS), Institute of Biochemical Plant Pathology, Helmholtz Zentrum, 85764 Neuherberg, Germany (A.G., J.-P.S.); andPlant Metabolism and Metabolic Engineering Program, Centre for Research in Agricultural Genomics (Consorci CSIC-IRTA-UAB-UB), 08193 Bellaterra, Barcelona, Spain (M.O., M.A.P.)
| | - Michael A Phillips
- Department of Biochemistry, Max Plank Institute for Chemical Ecology, 07745 Jena, Germany (L.P.W., A.H., B.R., J.G.);Department of Biochemistry, Stellenbosch University, 7602 Stellenbosch, South Africa (J.M.R.);Research Unit Environmental Simulation (EUS), Institute of Biochemical Plant Pathology, Helmholtz Zentrum, 85764 Neuherberg, Germany (A.G., J.-P.S.); andPlant Metabolism and Metabolic Engineering Program, Centre for Research in Agricultural Genomics (Consorci CSIC-IRTA-UAB-UB), 08193 Bellaterra, Barcelona, Spain (M.O., M.A.P.)
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Pianelli K, Monier A, Andrieu MH, Beauvoit B, Dieuaide-Noubhani M. ¹⁴C pulse labeling to estimate external fluxes and turnovers in primary metabolism. Methods Mol Biol 2014; 1090:41-52. [PMID: 24222408 DOI: 10.1007/978-1-62703-688-7_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Steady state (13)C-MFA is classically used to measure fluxes in complex metabolic networks. However, the modeling of steady state labeling allows the quantification of internal fluxes only and requires the estimation, by other methods, of the external fluxes, corresponding to substrate uptake (carbon input into the network) and to the production rate of compounds that accumulate within plant cells (network output). Additionally, it is not always possible to discriminate between different pathways that lead to the same label distribution. Methods to measure fluxes, based on direct measurements of pool size and on (14)C short-time labeling experiments, are described in this chapter. To illustrate this approach, we focus on the quantification of sucrose and starch turnovers.
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Affiliation(s)
- Katia Pianelli
- UMR 1332 de Biologie du Fruit et Pathologie, INRA, Villenave d'Ornon, France
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44
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Arnold A, Nikoloski Z. Bottom-up Metabolic Reconstruction of Arabidopsis and Its Application to Determining the Metabolic Costs of Enzyme Production. PLANT PHYSIOLOGY 2014; 165:1380-1391. [PMID: 24808102 PMCID: PMC4081344 DOI: 10.1104/pp.114.235358] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 04/12/2014] [Indexed: 05/07/2023]
Abstract
Large-scale modeling of plant metabolism provides the possibility to compare and contrast different cellular and environmental scenarios with the ultimate aim of identifying the components underlying the respective plant behavior. The existing models of Arabidopsis (Arabidopsis thaliana) are top-down assembled, whereby the starting point is the annotated genome, in particular, the metabolic genes. Hence, dead-end metabolites and blocked reactions can arise that are subsequently addressed by using gap-filling algorithms in combination with species-unspecific genes. Here, we present a bottom-up-assembled, large-scale model that relies solely on Arabidopsis-specific annotations and results in the inclusion of only manually curated reactions. While the existing models are largely condition unspecific by employing a single biomass reaction, we provide three biomass compositions that pertain to realistic and frequently examined scenarios: carbon-limiting, nitrogen-limiting, and optimal growth conditions. The comparative analysis indicates that the proposed Arabidopsis core model exhibits comparable efficiency in carbon utilization and flexibility to the existing network alternatives. Moreover, the model is utilized to quantify the energy demand of amino acid and enzyme de novo synthesis in photoautotrophic growth conditions. Illustrated by the case of the most abundant protein in the world, Rubisco, we determine its synthesis cost in terms of ATP requirements. This, in turn, allows us to explore the tradeoff between protein synthesis and growth in Arabidopsis. Altogether, the model provides a solid basis for completely species-specific integration of high-throughput data, such as gene expression levels, and for condition-specific investigations of in silico metabolic engineering strategies.
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Affiliation(s)
- Anne Arnold
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
| | - Zoran Nikoloski
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
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45
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Töpfer N, Scossa F, Fernie A, Nikoloski Z. Variability of metabolite levels is linked to differential metabolic pathways in Arabidopsis's responses to abiotic stresses. PLoS Comput Biol 2014; 10:e1003656. [PMID: 24946036 PMCID: PMC4063599 DOI: 10.1371/journal.pcbi.1003656] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2014] [Accepted: 04/16/2014] [Indexed: 11/19/2022] Open
Abstract
Constraint-based approaches have been used for integrating data in large-scale metabolic networks to obtain insights into metabolism of various organisms. Due to the underlying steady-state assumption, these approaches are usually not suited for making predictions about metabolite levels. Here, we ask whether we can make inferences about the variability of metabolite levels from a constraint-based analysis based on the integration of transcriptomics data. To this end, we analyze time-resolved transcriptomics and metabolomics data from Arabidopsis thaliana under a set of eight different light and temperature conditions. In a previous study, the gene expression data have already been integrated in a genome-scale metabolic network to predict pathways, termed modulators and sustainers, which are differentially regulated with respect to a biochemically meaningful data-driven null model. Here, we present a follow-up analysis which bridges the gap between flux- and metabolite-centric methods. One of our main findings demonstrates that under certain environmental conditions, the levels of metabolites acting as substrates in modulators or sustainers show significantly lower temporal variations with respect to the remaining measured metabolites. This observation is discussed within the context of a systems-view of plasticity and robustness of metabolite contents and pathway fluxes. Our study paves the way for investigating the existence of similar principles in other species for which both genome-scale networks and high-throughput metabolomics data of high quality are becoming increasingly available.
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Affiliation(s)
- Nadine Töpfer
- Systems Biology and Mathematical Modeling Group, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Federico Scossa
- Central Metabolism Group, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
- Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Centro di ricerca per l'Orticoltura, Pontecagnano (Salerno), Italy
| | - Alisdair Fernie
- Central Metabolism Group, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Zoran Nikoloski
- Systems Biology and Mathematical Modeling Group, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
- * E-mail:
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46
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Masakapalli SK, Bryant FM, Kruger NJ, Ratcliffe RG. The metabolic flux phenotype of heterotrophic Arabidopsis cells reveals a flexible balance between the cytosolic and plastidic contributions to carbohydrate oxidation in response to phosphate limitation. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 78:964-977. [PMID: 24674596 DOI: 10.1111/tpj.12522] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Revised: 03/17/2014] [Accepted: 03/24/2014] [Indexed: 05/29/2023]
Abstract
Understanding the mechanisms that allow plants to respond to variable and reduced availability of inorganic phosphate is of increasing agricultural importance because of the continuing depletion of the rock phosphate reserves that are used to combat inadequate phosphate levels in the soil. Changes in gene expression, protein levels, enzyme activities and metabolite levels all point to a reconfiguration of the central metabolic network in response to reduced availability of inorganic phosphate, but the metabolic significance of these changes can only be assessed in terms of the fluxes supported by the network. Steady-state metabolic flux analysis was used to define the metabolic phenotype of a heterotrophic Arabidopsis thaliana cell culture grown on a Murashige and Skoog medium containing 0, 1.25 or 5 mm inorganic phosphate. Fluxes through the central metabolic network were deduced from the redistribution of (13) C into metabolic intermediates and end products when cells were labelled with [1-(13) C], [2-(13) C], or [(13) C6 ]glucose, in combination with (14) C measurements of the rates of biomass accumulation. Analysis of the flux maps showed that reduced levels of phosphate in the growth medium stimulated flux through phosphoenolpyruvate carboxylase and malic enzyme, altered the balance between cytosolic and plastidic carbohydrate oxidation in favour of the plastid, and increased cell maintenance costs. We argue that plant cells respond to phosphate deprivation by reconfiguring the flux distribution through the pathways of carbohydrate oxidation to take advantage of better phosphate homeostasis in the plastid.
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Affiliation(s)
- Shyam K Masakapalli
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
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47
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Ampofo-Asiama J, Baiye VMM, Hertog MLATM, Waelkens E, Geeraerd AH, Nicolai BM. The metabolic response of cultured tomato cells to low oxygen stress. PLANT BIOLOGY (STUTTGART, GERMANY) 2014; 16:594-606. [PMID: 24119171 DOI: 10.1111/plb.12094] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Accepted: 07/17/2013] [Indexed: 05/10/2023]
Abstract
The storage of fruits and vegetables under a controlled atmosphere can induce low oxygen stress, which can lead to post-harvest losses through the induction of disorders such as core breakdown and browning. To gain better understanding of the metabolic response of plant organs to low oxygen, cultured tomato cells (Lycopersicum esculentum) were used as a model system to study the metabolic stress response to low oxygen (0 and 1 kPa O2). By adding 13C labelled glucose, changes in the levels of polar metabolites and their 13C label accumulation were quantified. Low oxygen stress altered the metabolite profile of tomato cells, with the accumulation of the intermediates of glycolysis in addition to increases in lactate and sugar alcohols. 13C label data showed reduced label accumulation in almost all metabolites except lactate and some sugar alcohols. The results showed that low oxygen stress in tomato cell culture activated fermentative metabolism and sugar alcohol synthesis while inhibiting the activity of the TCA cycle and the biosynthesis of metabolites whose precursors are derived from central metabolism, including fluxes to most organic acids, amino acids and sugars.
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Affiliation(s)
- J Ampofo-Asiama
- Division of Mechatronics, Department of Biosystems (BIOSYST), Biostatistics and Sensors (MeBioS), KU Leuven, Leuven, Belgium
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Masakapalli SK, Ritala A, Dong L, van der Krol AR, Oksman-Caldentey KM, Ratcliffe RG, Sweetlove LJ. Metabolic flux phenotype of tobacco hairy roots engineered for increased geraniol production. PHYTOCHEMISTRY 2014; 99:73-85. [PMID: 24472392 DOI: 10.1016/j.phytochem.2013.12.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Revised: 12/04/2013] [Accepted: 12/09/2013] [Indexed: 05/09/2023]
Abstract
The goal of this study was to characterise the metabolic flux phenotype of transgenic tobacco (Nicotiana tabacum) hairy roots engineered for increased biosynthesis of geraniol, an intermediate of the terpenoid indole alkaloid pathway. Steady state, stable isotope labelling was used to determine flux maps of central carbon metabolism for transgenic lines over-expressing (i) plastid-targeted geraniol synthase (pGES) from Valeriana officinalis, and (ii) pGES in combination with plastid-targeted geranyl pyrophosphate synthase from Arabidopsis thaliana (pGES+pGPPS), as well as for wild type and control-vector-transformed roots. Fluxes were constrained by the redistribution of label from [1-¹³C]-, [2-¹³C]- or [¹³C6]glucose into amino acids, sugars and organic acids at isotopic steady state, and by biomass output fluxes determined from the fractionation of [U-¹⁴C]glucose into insoluble polymers. No significant differences in growth and biomass composition were observed between the lines. The pGES line accumulated significant amounts of geraniol/geraniol glycosides (151±24 ng/mg dry weight) and the de novo synthesis of geraniol in pGES was confirmed by ¹³C labelling analysis. The pGES+pGPPS also accumulated geraniol and geraniol glycosides, but to lower levels than the pGES line. Although there was a distinct impact of the transgenes at the level of geraniol synthesis, other network fluxes were unaffected, reflecting the capacity of central metabolism to meet the relatively modest demand for increased precursors in the transgenic lines. It is concluded that re-engineering of the terpenoid indole alkaloid pathway will only require simultaneous manipulation of the steps producing the pathway precursors that originate in central metabolism in tissues engineered to produce at least an order of magnitude more geraniol than has been achieved so far.
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Affiliation(s)
- Shyam K Masakapalli
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
| | - Anneli Ritala
- VTT Technical Research Centre of Finland, P.O. Box 1000, 02044 VTT (Espoo), Finland
| | - Lemeng Dong
- Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Alexander R van der Krol
- Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | | | - R George Ratcliffe
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
| | - Lee J Sweetlove
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK.
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Poskar CH, Huege J, Krach C, Shachar-Hill Y, Junker BH. High-throughput data pipelines for metabolic flux analysis in plants. Methods Mol Biol 2014; 1090:223-246. [PMID: 24222419 DOI: 10.1007/978-1-62703-688-7_14] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
In this chapter we illustrate the methodology for high-throughput metabolic flux analysis. Central to this is developing an end to end data pipeline, crucial for integrating the wet lab experiments and analytics, combining hardware and software automation, and standardizing data representation providing importers and exporters to support third party tools. The use of existing software at the start, data extraction from the chromatogram, and the end, MFA analysis, allows for the most flexibility in this workflow. Developing iMS2Flux provided a standard, extensible, platform independent tool to act as the "glue" between these end points. Most importantly this tool can be easily adapted to support different data formats, data verification and data correction steps allowing it to be central to managing the data necessary for high-throughput MFA. An additional tool was needed to automate the MFA software and in particular to take advantage of the course grained parallel nature of high-throughput analysis and available high performance computing facilities.In combination these methods show the development of high-throughput pipelines that allow metabolic flux analysis to join as a full member of the omics family.
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Affiliation(s)
- C Hart Poskar
- Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
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50
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Schwender J, König C, Klapperstück M, Heinzel N, Munz E, Hebbelmann I, Hay JO, Denolf P, De Bodt S, Redestig H, Caestecker E, Jakob PM, Borisjuk L, Rolletschek H. Transcript abundance on its own cannot be used to infer fluxes in central metabolism. FRONTIERS IN PLANT SCIENCE 2014; 5:668. [PMID: 25506350 PMCID: PMC4246676 DOI: 10.3389/fpls.2014.00668] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 11/10/2014] [Indexed: 05/18/2023]
Abstract
An attempt has been made to define the extent to which metabolic flux in central plant metabolism is reflected by changes in the transcriptome and metabolome, based on an analysis of in vitro cultured immature embryos of two oilseed rape (Brassica napus) accessions which contrast for seed lipid accumulation. Metabolic flux analysis (MFA) was used to constrain a flux balance metabolic model which included 671 biochemical and transport reactions within the central metabolism. This highly confident flux information was eventually used for comparative analysis of flux vs. transcript (metabolite). Metabolite profiling succeeded in identifying 79 intermediates within the central metabolism, some of which differed quantitatively between the two accessions and displayed a significant shift corresponding to flux. An RNA-Seq based transcriptome analysis revealed a large number of genes which were differentially transcribed in the two accessions, including some enzymes/proteins active in major metabolic pathways. With a few exceptions, differential activity in the major pathways (glycolysis, TCA cycle, amino acid, and fatty acid synthesis) was not reflected in contrasting abundances of the relevant transcripts. The conclusion was that transcript abundance on its own cannot be used to infer metabolic activity/fluxes in central plant metabolism. This limitation needs to be borne in mind in evaluating transcriptome data and designing metabolic engineering experiments.
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Affiliation(s)
- Jörg Schwender
- Brookhaven National Laboratory, Department of Biological, Environmental and Climate SciencesUpton, NY, USA
| | - Christina König
- Leibniz-Institut für Pflanzengenetik und KulturpflanzenforschungGatersleben, Germany
| | - Matthias Klapperstück
- Leibniz-Institut für Pflanzengenetik und KulturpflanzenforschungGatersleben, Germany
| | - Nicolas Heinzel
- Leibniz-Institut für Pflanzengenetik und KulturpflanzenforschungGatersleben, Germany
| | - Eberhard Munz
- Leibniz-Institut für Pflanzengenetik und KulturpflanzenforschungGatersleben, Germany
- University of Würzburg, Institute of Experimental Physics 5Würzburg, Germany
| | - Inga Hebbelmann
- Brookhaven National Laboratory, Department of Biological, Environmental and Climate SciencesUpton, NY, USA
| | - Jordan O. Hay
- Brookhaven National Laboratory, Department of Biological, Environmental and Climate SciencesUpton, NY, USA
| | - Peter Denolf
- Bayer CropScience NV, Trait ResearchZwijnaarde, Belgium
| | | | | | | | - Peter M. Jakob
- University of Würzburg, Institute of Experimental Physics 5Würzburg, Germany
| | - Ljudmilla Borisjuk
- Leibniz-Institut für Pflanzengenetik und KulturpflanzenforschungGatersleben, Germany
| | - Hardy Rolletschek
- Leibniz-Institut für Pflanzengenetik und KulturpflanzenforschungGatersleben, Germany
- *Correspondence: Hardy Rolletschek, Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung, Corrensstrasse 3, 06466 Gatersleben, Germany e-mail:
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