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Han SY, Kim WY, Kim JS, Hwang I. Comparative transcriptomics reveals the role of altered energy metabolism in the establishment of single-cell C 4 photosynthesis in Bienertia sinuspersici. FRONTIERS IN PLANT SCIENCE 2023; 14:1202521. [PMID: 37476170 PMCID: PMC10354284 DOI: 10.3389/fpls.2023.1202521] [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: 04/08/2023] [Accepted: 05/31/2023] [Indexed: 07/22/2023]
Abstract
Single-cell C4 photosynthesis (SCC4) in terrestrial plants without Kranz anatomy involves three steps: initial CO2 fixation in the cytosol, CO2 release in mitochondria, and a second CO2 fixation in central chloroplasts. Here, we investigated how the large number of mechanisms underlying these processes, which occur in three different compartments, are orchestrated in a coordinated manner to establish the C4 pathway in Bienertia sinuspersici, a SCC4 plant. Leaves were subjected to transcriptome analysis at three different developmental stages. Functional enrichment analysis revealed that SCC4 cycle genes are coexpressed with genes regulating cyclic electron flow and amino/organic acid metabolism, two key processes required for the production of energy molecules in C3 plants. Comparative gene expression profiling of B. sinuspersici and three other species (Suaeda aralocaspica, Amaranthus hypochondriacus, and Arabidopsis thaliana) showed that the direction of metabolic flux was determined via an alteration in energy supply in peripheral chloroplasts and mitochondria via regulation of gene expression in the direction of the C4 cycle. Based on these results, we propose that the redox homeostasis of energy molecules via energy metabolism regulation is key to the establishment of the SCC4 pathway in B. sinuspersici.
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Affiliation(s)
- Sang-Yun Han
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Woe-Yeon Kim
- Division of Applied Life Science (BK21+) and Research Institute of Life Science, Institute of Agriculture and Life Sciences, Gyeongsang National University, Jinju, Republic of Korea
| | - Jung Sun Kim
- Genomic Division, Department of Agricultural Bio-Resources, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, Republic of Korea
| | - Inhwan Hwang
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
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2
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Wieloch T, Sharkey TD, Werner RA, Schleucher J. Intramolecular carbon isotope signals reflect metabolite allocation in plants. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:2558-2575. [PMID: 35084456 PMCID: PMC9015809 DOI: 10.1093/jxb/erac028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 01/24/2022] [Indexed: 05/26/2023]
Abstract
Stable isotopes at natural abundance are key tools to study physiological processes occurring outside the temporal scope of manipulation and monitoring experiments. Whole-molecule carbon isotope ratios (13C/12C) enable assessments of plant carbon uptake yet conceal information about carbon allocation. Here, we identify an intramolecular 13C/12C signal at tree-ring glucose C-5 and C-6 and develop experimentally testable theories on its origin. More specifically, we assess the potential of processes within C3 metabolism for signal introduction based (inter alia) on constraints on signal propagation posed by metabolic networks. We propose that the intramolecular signal reports carbon allocation into major metabolic pathways in actively photosynthesizing leaf cells including the anaplerotic, shikimate, and non-mevalonate pathway. We support our theoretical framework by linking it to previously reported whole-molecule 13C/12C increases in cellulose of ozone-treated Betula pendula and a highly significant relationship between the intramolecular signal and tropospheric ozone concentration. Our theory postulates a pronounced preference for leaf cytosolic triose-phosphate isomerase to catalyse the forward reaction in vivo (dihydroxyacetone phosphate to glyceraldehyde 3-phosphate). In conclusion, intramolecular 13C/12C analysis resolves information about carbon uptake and allocation enabling more comprehensive assessments of carbon metabolism than whole-molecule 13C/12C analysis.
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Affiliation(s)
- Thomas Wieloch
- Department of Medical Biochemistry and Biophysics, Umeå University, 901 87 Umeå, Sweden
| | - Thomas David Sharkey
- MSU-DOE Plant Research Laboratory, Plant Resilience Institute, and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Roland Anton Werner
- Department of Environmental Systems Science, ETH Zürich, Universitätstrasse 2, 8092 Zürich, Switzerland
| | - Jürgen Schleucher
- Department of Medical Biochemistry and Biophysics, Umeå University, 901 87 Umeå, Sweden
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3
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Kreuzwieser J, Meischner M, Grün M, Yáñez-Serrano AM, Fasbender L, Werner C. Drought affects carbon partitioning into volatile organic compound biosynthesis in Scots pine needles. THE NEW PHYTOLOGIST 2021; 232:1930-1943. [PMID: 34523149 DOI: 10.1111/nph.17736] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 09/03/2021] [Indexed: 06/13/2023]
Abstract
The effect of drought on the interplay of processes controlling carbon partitioning into plant primary and secondary metabolisms, such as respiratory CO2 release and volatile organic compound (VOC) biosynthesis, is not fully understood. To elucidate the effect of drought on the fate of cellular C sources into VOCs vs CO2 , we conducted tracer experiments with 13 CO2 and position-specific 13 C-labelled pyruvate, a key metabolite between primary and secondary metabolisms, in Scots pine seedlings. We determined the stable carbon isotope composition of leaf exchanged CO2 and VOC. Drought reduced the emission of the sesquiterpenes α-farnesene and β-farnesene but did not affect 13 C-incorporation from 13 C-pyruvate. The labelling patterns suggest that farnesene biosynthesis partially depends on isopentenyl diphosphate crosstalk between chloroplasts and cytosol, and that drought inhibits this process. Contrary to sesquiterpenes, drought did not affect emission of isoprene, monoterpenes and some oxygenated compounds. During the day, pyruvate was used in the TCA cycle to a minor degree but was mainly consumed in pathways of secondary metabolism. Drought partly inhibited such pathways, while allocation into the TCA cycle increased. Drought caused a re-direction of pyruvate consuming pathways, which contributed to maintenance of isoprene and monoterpene production despite strongly inhibited photosynthesis. This underlines the importance of these volatiles for stress tolerance.
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Affiliation(s)
- Jürgen Kreuzwieser
- Chair of Ecosystem Physiology, Albert-Ludwigs-Universität Freiburg, Freiburg, 79110, Germany
| | - Mirjam Meischner
- Chair of Ecosystem Physiology, Albert-Ludwigs-Universität Freiburg, Freiburg, 79110, Germany
| | - Michel Grün
- Chair of Ecosystem Physiology, Albert-Ludwigs-Universität Freiburg, Freiburg, 79110, Germany
| | - Ana Maria Yáñez-Serrano
- Institute of Environmental Assessment and Water Research (IDAEA), Spanish Research Council (CSIC), Barcelona, 08034, Spain
- Center for Ecological Research and Forestry Applications (CREAF), Cerdanyola del Vallès, 08193, Spain
- Global Ecology Unit, CREAF-CSIC-UAB, Cerdanyola del Vallès, 08193, Spain
| | - Lukas Fasbender
- Chair of Ecosystem Physiology, Albert-Ludwigs-Universität Freiburg, Freiburg, 79110, Germany
| | - Christiane Werner
- Chair of Ecosystem Physiology, Albert-Ludwigs-Universität Freiburg, Freiburg, 79110, Germany
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4
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Igamberdiev AU. Citrate valve integrates mitochondria into photosynthetic metabolism. Mitochondrion 2020; 52:218-230. [PMID: 32278088 DOI: 10.1016/j.mito.2020.04.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 03/21/2020] [Accepted: 04/07/2020] [Indexed: 12/31/2022]
Abstract
While in heterotrophic cells and in darkness mitochondria serve as main producers of energy, during photosynthesis this function is transferred to chloroplasts and the main role of mitochondria in bioenergetics turns to be the balance of the level of phosphorylation of adenylates and of reduction of pyridine nucleotides to avoid over-energization of the cell and optimize major metabolic fluxes. This is achieved via the establishment and regulation of local equilibria of the tricarboxylic acid (TCA) cycle enzymes malate dehydrogenase and fumarase in one branch and aconitase and isocitrate dehydrogenase in another branch. In the conditions of elevation of redox level, the TCA cycle is transformed into a non-cyclic open structure (hemicycle) leading to the export of the tricarboxylic acid (citrate) to the cytosol and to the accumulation of the dicarboxylic acids (malate and fumarate). While the buildup of NADPH in chloroplasts provides operation of the malate valve leading to establishment of NADH/NAD+ ratios in different cell compartments, the production of NADH by mitochondria drives citrate export by establishing conditions for the operation of the citrate valve. The latter regulates the intercompartmental NADPH/NADP+ ratio and contributes to the biosynthesis of amino acids and other metabolic products during photosynthesis.
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Affiliation(s)
- Abir U Igamberdiev
- Department of Biology, Memorial University of Newfoundland, St. John's, NL A1B 3X9, Canada.
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5
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Shameer S, Ratcliffe RG, Sweetlove LJ. Leaf Energy Balance Requires Mitochondrial Respiration and Export of Chloroplast NADPH in the Light. PLANT PHYSIOLOGY 2019; 180:1947-1961. [PMID: 31213510 PMCID: PMC6670072 DOI: 10.1104/pp.19.00624] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 06/04/2019] [Indexed: 05/04/2023]
Abstract
Key aspects of leaf mitochondrial metabolism in the light remain unresolved. For example, there is debate about the relative importance of exporting reducing equivalents from mitochondria for the peroxisomal steps of photorespiration versus oxidation of NADH to generate ATP by oxidative phosphorylation. Here, we address this and explore energetic coupling between organelles in the light using a diel flux balance analysis model. The model included more than 600 reactions of central metabolism with full stoichiometric accounting of energy production and consumption. Different scenarios of energy availability (light intensity) and demand (source leaf versus a growing leaf) were considered, and the model was constrained by the nonlinear relationship between light and CO2 assimilation rate. The analysis demonstrated that the chloroplast can theoretically generate sufficient ATP to satisfy the energy requirements of the rest of the cell in addition to its own. However, this requires unrealistic high light use efficiency and, in practice, the availability of chloroplast-derived ATP is limited by chloroplast energy dissipation systems, such as nonphotochemical quenching, and the capacity of the chloroplast ATP export shuttles. Given these limitations, substantial mitochondrial ATP synthesis is required to fulfill cytosolic ATP requirements, with only minimal, or zero, export of mitochondrial reducing equivalents. The analysis also revealed the importance of exporting reducing equivalents from chloroplasts to sustain photorespiration. Hence, the chloroplast malate valve and triose phosphate-3-phosphoglycerate shuttle are predicted to have important metabolic roles, in addition to their more commonly discussed contribution to the avoidance of photooxidative stress.
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Affiliation(s)
- Sanu Shameer
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom
| | - R George Ratcliffe
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom
| | - Lee J Sweetlove
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom
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6
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de Souza VF, Niinemets Ü, Rasulov B, Vickers CE, Duvoisin Júnior S, Araújo WL, Gonçalves JFDC. Alternative Carbon Sources for Isoprene Emission. TRENDS IN PLANT SCIENCE 2018; 23:1081-1101. [PMID: 30472998 PMCID: PMC6354897 DOI: 10.1016/j.tplants.2018.09.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 09/03/2018] [Accepted: 09/25/2018] [Indexed: 05/07/2023]
Abstract
Isoprene and other plastidial isoprenoids are produced primarily from recently assimilated photosynthates via the 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway. However, when environmental conditions limit photosynthesis, a fraction of carbon for MEP pathway can come from extrachloroplastic sources. The flow of extrachloroplastic carbon depends on the species and on leaf developmental and environmental conditions. The exchange of common phosphorylated intermediates between the MEP pathway and other metabolic pathways can occur via plastidic phosphate translocators. C1 and C2 carbon intermediates can contribute to chloroplastic metabolism, including photosynthesis and isoprenoid synthesis. Integration of these metabolic processes provide an example of metabolic flexibility, and results in the synthesis of primary metabolites for plant growth and secondary metabolites for plant defense, allowing effective use of environmental resources under multiple stresses.
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Affiliation(s)
- Vinícius Fernandes de Souza
- Laboratory of Plant Physiology and Biochemistry, National Institute for Amazonian Research (INPA), Manaus, AM 69011-970, Brazil; University of Amazonas State, Manaus, AM 69050-010, Brazil
| | - Ülo Niinemets
- Department of Crop Science and Plant Biology, Estonian University of Life Sciences, Tartu 51006, Estonia; Estonian Academy of Sciences, 10130 Tallinn, Estonia
| | - Bahtijor Rasulov
- Department of Crop Science and Plant Biology, Estonian University of Life Sciences, Tartu 51006, Estonia; Institute of Technology, University of Tartu, Tartu, Estonia
| | - Claudia E Vickers
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, St Lucia, QLD 4072, Australia; Commonwealth Scientific and Industrial Research Organisation (CSIRO) Synthetic Biology Future Science Platform, EcoSciences Precinct, Brisbane, QLD 4001, Australia
| | | | - Wagner L Araújo
- Max-Planck Partner Group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900 Viçosa, MG, Brazil
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Tcherkez G, Gauthier P, Buckley TN, Busch FA, Barbour MM, Bruhn D, Heskel MA, Gong XY, Crous KY, Griffin K, Way D, Turnbull M, Adams MA, Atkin OK, Farquhar GD, Cornic G. Leaf day respiration: low CO 2 flux but high significance for metabolism and carbon balance. THE NEW PHYTOLOGIST 2017; 216:986-1001. [PMID: 28967668 DOI: 10.1111/nph.14816] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 08/13/2017] [Indexed: 05/04/2023]
Abstract
Contents 986 I. 987 II. 987 III. 988 IV. 991 V. 992 VI. 995 VII. 997 VIII. 998 References 998 SUMMARY: It has been 75 yr since leaf respiratory metabolism in the light (day respiration) was identified as a low-flux metabolic pathway that accompanies photosynthesis. In principle, it provides carbon backbones for nitrogen assimilation and evolves CO2 and thus impacts on plant carbon and nitrogen balances. However, for a long time, uncertainties have remained as to whether techniques used to measure day respiratory efflux were valid and whether day respiration responded to environmental gaseous conditions. In the past few years, significant advances have been made using carbon isotopes, 'omics' analyses and surveys of respiration rates in mesocosms or ecosystems. There is substantial evidence that day respiration should be viewed as a highly dynamic metabolic pathway that interacts with photosynthesis and photorespiration and responds to atmospheric CO2 mole fraction. The view of leaf day respiration as a constant and/or negligible parameter of net carbon exchange is now outdated and it should now be regarded as a central actor of plant carbon-use efficiency.
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Affiliation(s)
- Guillaume Tcherkez
- Research School of Biology, College of Science, and ARC Center of Excellence for Translational Photosynthesis, Australian National University, Canberra, ACT, 2601, Australia
| | - Paul Gauthier
- Department of Geosciences, Princeton University, Princeton, NJ, 08540, USA
| | - Thomas N Buckley
- IA Watson Grains Research Centre, University of Sydney, 12656 Newell Hwy, Narrabri, NSW, 2390, Australia
| | - Florian A Busch
- Research School of Biology, College of Science, and ARC Center of Excellence for Translational Photosynthesis, Australian National University, Canberra, ACT, 2601, Australia
| | - Margaret M Barbour
- Centre for Carbon, Water and Food, University of Sydney, 380 Werombi Rd, Brownlow Hill, NSW, 2570, Australia
| | - Dan Bruhn
- Section of Biology and Environmental Science, Department of Chemistry and Bioscience, Aalborg University, 9220, Aalborg East, Denmark
| | - Mary A Heskel
- The Ecosystems Center, Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA, 02543, USA
| | - Xiao Ying Gong
- Lehrstuhl für Grünlandlehre, Technische Universität München, Alte Akademie 12, 85354, Freising, Germany
| | - Kristine Y Crous
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW, 2751, Australia
| | - Kevin Griffin
- Department of Ecology, Evolution and Environmental Biology (E3B), Columbia University, 1200 Amsterdam Avenue, New York, NY, 10027, USA
| | - Danielle Way
- Department of Biology, University of Western Ontario, London, ON, N6A 5B7, Canada
| | - Matthew Turnbull
- Centre for Integrative Ecology, School of Biological Sciences, University of Canterbury, PB 4800, Christchurch, New Zealand
| | - Mark A Adams
- Centre for Carbon, Water and Food, University of Sydney, 380 Werombi Rd, Brownlow Hill, NSW, 2570, Australia
| | - Owen K Atkin
- ARC Centre of Excellence in Plant Energy Biology, Division of Plant Science, Research School of Biology, Australian National University, Canberra, ACT, 2601, Australia
| | - Graham D Farquhar
- Research School of Biology, College of Science, and ARC Center of Excellence for Translational Photosynthesis, Australian National University, Canberra, ACT, 2601, Australia
| | - Gabriel Cornic
- Ecologie Systématique Evolution, Université Paris-Sud, 91405, Orsay Cedex, France
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Balcke GU, Bennewitz S, Bergau N, Athmer B, Henning A, Majovsky P, Jiménez-Gómez JM, Hoehenwarter W, Tissier A. Multi-Omics of Tomato Glandular Trichomes Reveals Distinct Features of Central Carbon Metabolism Supporting High Productivity of Specialized Metabolites. THE PLANT CELL 2017; 29:960-983. [PMID: 28408661 PMCID: PMC5466034 DOI: 10.1105/tpc.17.00060] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Revised: 03/24/2017] [Accepted: 04/12/2017] [Indexed: 05/18/2023]
Abstract
Glandular trichomes are metabolic cell factories with the capacity to produce large quantities of secondary metabolites. Little is known about the connection between central carbon metabolism and metabolic productivity for secondary metabolites in glandular trichomes. To address this gap in our knowledge, we performed comparative metabolomics, transcriptomics, proteomics, and 13C-labeling of type VI glandular trichomes and leaves from a cultivated (Solanum lycopersicum LA4024) and a wild (Solanum habrochaites LA1777) tomato accession. Specific features of glandular trichomes that drive the formation of secondary metabolites could be identified. Tomato type VI trichomes are photosynthetic but acquire their carbon essentially from leaf sucrose. The energy and reducing power from photosynthesis are used to support the biosynthesis of secondary metabolites, while the comparatively reduced Calvin-Benson-Bassham cycle activity may be involved in recycling metabolic CO2 Glandular trichomes cope with oxidative stress by producing high levels of polyunsaturated fatty acids, oxylipins, and glutathione. Finally, distinct mechanisms are present in glandular trichomes to increase the supply of precursors for the isoprenoid pathways. Particularly, the citrate-malate shuttle supplies cytosolic acetyl-CoA and plastidic glycolysis and malic enzyme support the formation of plastidic pyruvate. A model is proposed on how glandular trichomes achieve high metabolic productivity.
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Affiliation(s)
- Gerd U Balcke
- Leibniz Institute of Plant Biochemistry, Department of Cell and Metabolic Biology, D-06120 Halle (Saale), Germany
| | - Stefan Bennewitz
- Leibniz Institute of Plant Biochemistry, Department of Cell and Metabolic Biology, D-06120 Halle (Saale), Germany
| | - Nick Bergau
- Leibniz Institute of Plant Biochemistry, Department of Cell and Metabolic Biology, D-06120 Halle (Saale), Germany
| | - Benedikt Athmer
- Leibniz Institute of Plant Biochemistry, Department of Cell and Metabolic Biology, D-06120 Halle (Saale), Germany
| | - Anja Henning
- Leibniz Institute of Plant Biochemistry, Department of Cell and Metabolic Biology, D-06120 Halle (Saale), Germany
| | - Petra Majovsky
- Leibniz Institute of Plant Biochemistry, Proteome Analytics, D-06120 Halle (Saale), Germany
| | | | - Wolfgang Hoehenwarter
- Leibniz Institute of Plant Biochemistry, Proteome Analytics, D-06120 Halle (Saale), Germany
| | - Alain Tissier
- Leibniz Institute of Plant Biochemistry, Department of Cell and Metabolic Biology, D-06120 Halle (Saale), Germany
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9
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Lee YS, Park HS, Lee DK, Jayakodi M, Kim NH, Lee SC, Kundu A, Lee DY, Kim YC, In JG, Kwon SW, Yang TJ. Comparative analysis of the transcriptomes and primary metabolite profiles of adventitious roots of five Panax ginseng cultivars. J Ginseng Res 2017; 41:60-68. [PMID: 28123323 PMCID: PMC5223079 DOI: 10.1016/j.jgr.2015.12.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 12/15/2015] [Accepted: 12/31/2015] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Various Panax ginseng cultivars exhibit a range of diversity for morphological and physiological traits. However, there are few studies on diversity of metabolic profiles and genetic background to understand the complex metabolic pathway in ginseng. METHODS To understand the complex metabolic pathway and related genes in ginseng, we tried to conduct integrated analysis of primary metabolite profiles and related gene expression using five ginseng cultivars showing different morphology. We investigated primary metabolite profiles via gas chromatography-mass spectrometry (GC-MS) and analyzed transcriptomes by Illumina sequencing using adventitious roots grown under the same conditions to elucidate the differences in metabolism underlying such genetic diversity. RESULTS GC-MS analysis revealed that primary metabolite profiling allowed us to classify the five cultivars into three independent groups and the grouping was also explained by eight major primary metabolites as biomarkers. We selected three cultivars (Chunpoong, Cheongsun, and Sunhyang) to represent each group and analyzed their transcriptomes. We inspected 100 unigenes involved in seven primary metabolite biosynthesis pathways and found that 21 unigenes encoding 15 enzymes were differentially expressed among the three cultivars. Integrated analysis of transcriptomes and metabolomes revealed that the ginseng cultivars differ in primary metabolites as well as in the putative genes involved in the complex process of primary metabolic pathways. CONCLUSION Our data derived from this integrated analysis provide insights into the underlying complexity of genes and metabolites that co-regulate flux through these pathways in ginseng.
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Affiliation(s)
- Yun Sun Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
| | - Hyun-Seung Park
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
| | - Dong-Kyu Lee
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, Korea
| | - Murukarthick Jayakodi
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
| | - Nam-Hoon Kim
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
| | - Sang-Choon Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
| | - Atreyee Kundu
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
- Department of Biological Sciences, Presidency University, Kolkata, West Bengal, India
| | - Dong-Yup Lee
- Bioprocessing Technology Institute, A*STAR (Agency for Science, Technology and Research), Centros, Singapore
- Department of Chemical and Biomolecular Engineering, Synthetic Biology Research Consortium, National University of Singapore, Singapore
| | - Young Chang Kim
- Ginseng Research Division, National Institute of Horitcultural and Herbal Science, Rural Development Administration, Eumseong, Korea
| | - Jun Gyo In
- Ginseng Resources Research Laboratory, R&D Headquarters, Korea Ginseng Corporation, Daejeon, Korea
| | - Sung Won Kwon
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, Korea
| | - Tae-Jin Yang
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
- Crop Biotechnology Institute/GreenBio Science and Technology, Seoul National University, Pyeongchang, Korea
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10
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Abadie C, Carroll A, Tcherkez G. Interactions Between Day Respiration, Photorespiration, and N and S Assimilation in Leaves. ADVANCES IN PHOTOSYNTHESIS AND RESPIRATION 2017. [DOI: 10.1007/978-3-319-68703-2_1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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11
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Rai A, Saito K. Omics data input for metabolic modeling. Curr Opin Biotechnol 2015; 37:127-134. [PMID: 26723010 DOI: 10.1016/j.copbio.2015.10.010] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 10/09/2015] [Accepted: 10/26/2015] [Indexed: 12/20/2022]
Abstract
Recent advancements in high-throughput large-scale analytical methods to sequence genomes of organisms, and to quantify gene expression, proteins, lipids and metabolites have changed the paradigm of metabolic modeling. The cost of data generation and analysis has decreased significantly, which has allowed exponential increase in the amount of omics data being generated for an organism in a very short time. Compared to progress made in microbial metabolic modeling, plant metabolic modeling still remains limited due to its complex genomes and compartmentalization of metabolic reactions. Herein, we review and discuss different omics-datasets with potential application in the functional genomics. In particular, this review focuses on the application of omics-datasets towards construction and reconstruction of plant metabolic models.
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Affiliation(s)
- Amit Rai
- Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8675, Japan.
| | - Kazuki Saito
- Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8675, Japan; RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.
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12
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Cavalcanti JHF, Esteves-Ferreira AA, Quinhones CGS, Pereira-Lima IA, Nunes-Nesi A, Fernie AR, Araújo WL. Evolution and functional implications of the tricarboxylic acid cycle as revealed by phylogenetic analysis. Genome Biol Evol 2014; 6:2830-48. [PMID: 25274566 PMCID: PMC4224347 DOI: 10.1093/gbe/evu221] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The tricarboxylic acid (TCA) cycle, a crucial component of respiratory metabolism, is composed of a set of eight enzymes present in the mitochondrial matrix. However, most of the TCA cycle enzymes are encoded in the nucleus in higher eukaryotes. In addition, evidence has accumulated demonstrating that nuclear genes were acquired from the mitochondrial genome during the course of evolution. For this reason, we here analyzed the evolutionary history of all TCA cycle enzymes in attempt to better understand the origin of these nuclear-encoded proteins. Our results indicate that prior to endosymbiotic events the TCA cycle seemed to operate only as isolated steps in both the host (eubacterial cell) and mitochondria (alphaproteobacteria). The origin of isoforms present in different cell compartments might be associated either with gene-transfer events which did not result in proper targeting of the protein to mitochondrion or with duplication events. Further in silico analyses allow us to suggest new insights into the possible roles of TCA cycle enzymes in different tissues. Finally, we performed coexpression analysis using mitochondrial TCA cycle genes revealing close connections among these genes most likely related to the higher efficiency of oxidative phosphorylation in this specialized organelle. Moreover, these analyses allowed us to identify further candidate genes which might be used for metabolic engineering purposes given the importance of the TCA cycle during development and/or stress situations.
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Affiliation(s)
- João Henrique Frota Cavalcanti
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, MG, Brazil Max-Planck-Partner Group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, MG, Brazil
| | - Alberto A Esteves-Ferreira
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, MG, Brazil Max-Planck-Partner Group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, MG, Brazil
| | - Carla G S Quinhones
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, MG, Brazil Max-Planck-Partner Group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, MG, Brazil
| | - Italo A Pereira-Lima
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, MG, Brazil Max-Planck-Partner Group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, MG, Brazil
| | - Adriano Nunes-Nesi
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, MG, Brazil Max-Planck-Partner Group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, MG, Brazil
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Wagner L Araújo
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, MG, Brazil Max-Planck-Partner Group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, MG, Brazil
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13
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Szecowka M, Heise R, Tohge T, Nunes-Nesi A, Vosloh D, Huege J, Feil R, Lunn J, Nikoloski Z, Stitt M, Fernie AR, Arrivault S. Metabolic fluxes in an illuminated Arabidopsis rosette. THE PLANT CELL 2013; 25:694-714. [PMID: 23444331 PMCID: PMC3608787 DOI: 10.1105/tpc.112.106989] [Citation(s) in RCA: 242] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Revised: 01/25/2013] [Accepted: 02/12/2013] [Indexed: 05/18/2023]
Abstract
Photosynthesis is the basis for life, and its optimization is a key biotechnological aim given the problems of population explosion and environmental deterioration. We describe a method to resolve intracellular fluxes in intact Arabidopsis thaliana rosettes based on time-dependent labeling patterns in the metabolome. Plants photosynthesizing under limiting irradiance and ambient CO2 in a custom-built chamber were transferred into a (13)CO2-enriched environment. The isotope labeling patterns of 40 metabolites were obtained using liquid or gas chromatography coupled to mass spectrometry. Labeling kinetics revealed striking differences between metabolites. At a qualitative level, they matched expectations in terms of pathway topology and stoichiometry, but some unexpected features point to the complexity of subcellular and cellular compartmentation. To achieve quantitative insights, the data set was used for estimating fluxes in the framework of kinetic flux profiling. We benchmarked flux estimates to four classically determined flux signatures of photosynthesis and assessed the robustness of the estimates with respect to different features of the underlying metabolic model and the time-resolved data set.
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Affiliation(s)
- Marek Szecowka
- Central Metabolism Research Group, Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Robert Heise
- Systems Biology and Mathematical Modeling Research Group, Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Takayuki Tohge
- Central Metabolism Research Group, Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Adriano Nunes-Nesi
- Central Metabolism Research Group, Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Daniel Vosloh
- Metabolic Systems Research Group, Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Jan Huege
- Central Metabolism Research Group, Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Regina Feil
- Metabolic Systems Research Group, Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - John Lunn
- Metabolic Systems Research Group, Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Zoran Nikoloski
- Systems Biology and Mathematical Modeling Research Group, Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Mark Stitt
- Metabolic Systems Research Group, Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Alisdair R. Fernie
- Central Metabolism Research Group, Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
- Address correspondence to
| | - Stéphanie Arrivault
- Metabolic Systems Research Group, Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
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14
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Tcherkez G, Mahé A, Guérard F, Boex-Fontvieille ERA, Gout E, Lamothe M, Barbour MM, Bligny R. Short-term effects of CO(2) and O(2) on citrate metabolism in illuminated leaves. PLANT, CELL & ENVIRONMENT 2012; 35:2208-2220. [PMID: 22646810 DOI: 10.1111/j.1365-3040.2012.02550.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Although there is now a considerable literature on the inhibition of leaf respiration (CO(2) evolution) by light, little is known about the effect of other environmental conditions on day respiratory metabolism. In particular, CO(2) and O(2) mole fractions are assumed to cause changes in the tricarboxylic acid pathway (TCAP) but the amplitude and even the direction of such changes are still a matter of debate. Here, we took advantage of isotopic techniques, new simple equations and instant freeze sampling to follow respiratory metabolism in illuminated cocklebur leaves (Xanthium strumarium L.) under different CO(2) /O(2) conditions. Gas exchange coupled to online isotopic analysis showed that CO(2) evolved by leaves in the light came from 'old' carbon skeletons and there was a slight decrease in (13) C natural abundance when [CO(2) ] increased. This suggested the involvement of enzymatic steps fractionating more strongly against (13) C and thus increasingly limiting for the metabolic respiratory flux as [CO(2) ] increased. Isotopic labelling with (13) C(2) -2,4-citrate lead to (13) C-enriched Glu and 2-oxoglutarate (2OG), clearly demonstrating poor metabolism of citrate by the TCAP. There was a clear relationship between the ribulose-1,5-bisphosphate oxygenation-to-carboxylation ratio (v(o) /v(c) ) and the (13) C commitment to 2OG, demonstrating that 2OG and Glu synthesis via the TCAP is positively influenced by photorespiration.
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Affiliation(s)
- Guillaume Tcherkez
- Institut de Biologie des Plantes, CNRS UMR8618, Université Paris-Sud, 91405 Orsay Cedex, France.
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15
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Dizengremel P, Vaultier MN, Le Thiec D, Cabané M, Bagard M, Gérant D, Gérard J, Dghim AA, Richet N, Afif D, Pireaux JC, Hasenfratz-Sauder MP, Jolivet Y. Phosphoenolpyruvate is at the crossroads of leaf metabolic responses to ozone stress. THE NEW PHYTOLOGIST 2012; 195:512-517. [PMID: 22686461 DOI: 10.1111/j.1469-8137.2012.04211.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Affiliation(s)
- Pierre Dizengremel
- Université de Lorraine, Ecologie et Ecophysiologie Forestières, UMR 1137, 54506 Vandoeuvre-lès-Nancy Cedex, France
- INRA, Ecologie et Ecophysiologie Forestières, UMR 1137, 54280 Champenoux, France
- (*Author for correspondence: tel +33 3 83 68 42 41; )
| | - Marie-Noëlle Vaultier
- Université de Lorraine, Ecologie et Ecophysiologie Forestières, UMR 1137, 54506 Vandoeuvre-lès-Nancy Cedex, France
- INRA, Ecologie et Ecophysiologie Forestières, UMR 1137, 54280 Champenoux, France
| | - Didier Le Thiec
- Université de Lorraine, Ecologie et Ecophysiologie Forestières, UMR 1137, 54506 Vandoeuvre-lès-Nancy Cedex, France
- INRA, Ecologie et Ecophysiologie Forestières, UMR 1137, 54280 Champenoux, France
| | - Mireille Cabané
- Université de Lorraine, Ecologie et Ecophysiologie Forestières, UMR 1137, 54506 Vandoeuvre-lès-Nancy Cedex, France
- INRA, Ecologie et Ecophysiologie Forestières, UMR 1137, 54280 Champenoux, France
| | - Matthieu Bagard
- Université Paris Est Créteil, Bioemco, UMR 7618, 94010 Créteil Cedex, France
| | - Dominique Gérant
- Université de Lorraine, Ecologie et Ecophysiologie Forestières, UMR 1137, 54506 Vandoeuvre-lès-Nancy Cedex, France
- INRA, Ecologie et Ecophysiologie Forestières, UMR 1137, 54280 Champenoux, France
| | - Joëlle Gérard
- Université de Lorraine, Ecologie et Ecophysiologie Forestières, UMR 1137, 54506 Vandoeuvre-lès-Nancy Cedex, France
- INRA, Ecologie et Ecophysiologie Forestières, UMR 1137, 54280 Champenoux, France
| | - Ata Allah Dghim
- Université de Lorraine, Ecologie et Ecophysiologie Forestières, UMR 1137, 54506 Vandoeuvre-lès-Nancy Cedex, France
- INRA, Ecologie et Ecophysiologie Forestières, UMR 1137, 54280 Champenoux, France
| | - Nicolas Richet
- Université de Lorraine, Ecologie et Ecophysiologie Forestières, UMR 1137, 54506 Vandoeuvre-lès-Nancy Cedex, France
- INRA, Ecologie et Ecophysiologie Forestières, UMR 1137, 54280 Champenoux, France
| | - Dany Afif
- Université de Lorraine, Ecologie et Ecophysiologie Forestières, UMR 1137, 54506 Vandoeuvre-lès-Nancy Cedex, France
- INRA, Ecologie et Ecophysiologie Forestières, UMR 1137, 54280 Champenoux, France
| | - Jean-Claude Pireaux
- Université de Lorraine, Ecologie et Ecophysiologie Forestières, UMR 1137, 54506 Vandoeuvre-lès-Nancy Cedex, France
- INRA, Ecologie et Ecophysiologie Forestières, UMR 1137, 54280 Champenoux, France
| | - Marie-Paule Hasenfratz-Sauder
- Université de Lorraine, Ecologie et Ecophysiologie Forestières, UMR 1137, 54506 Vandoeuvre-lès-Nancy Cedex, France
- INRA, Ecologie et Ecophysiologie Forestières, UMR 1137, 54280 Champenoux, France
| | - Yves Jolivet
- Université de Lorraine, Ecologie et Ecophysiologie Forestières, UMR 1137, 54506 Vandoeuvre-lès-Nancy Cedex, France
- INRA, Ecologie et Ecophysiologie Forestières, UMR 1137, 54280 Champenoux, France
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16
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Tcherkez G, Boex-Fontvieille E, Mahé A, Hodges M. Respiratory carbon fluxes in leaves. CURRENT OPINION IN PLANT BIOLOGY 2012; 15:308-14. [PMID: 22244081 DOI: 10.1016/j.pbi.2011.12.003] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2011] [Revised: 12/12/2011] [Accepted: 12/13/2011] [Indexed: 05/04/2023]
Abstract
Leaf respiration is a major metabolic process that drives energy production and growth. Earlier works in this field were focused on the measurement of respiration rates in relation to carbohydrate content, photosynthesis, enzymatic activities or nitrogen content. Recently, several studies have shed light on the mechanisms describing the regulation of respiration in the light and in the dark and on associated metabolic flux patterns. This review will highlight advances made into characterizing respiratory fluxes and provide a discussion of metabolic respiration dynamics in relation to important biological functions.
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Affiliation(s)
- Guillaume Tcherkez
- Institut de Biologie des Plantes, CNRS UMR 8618, Université Paris-Sud, Orsay Cedex, France.
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17
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Araújo WL, Tohge T, Nunes-Nesi A, Daloso DM, Nimick M, Krahnert I, Bunik VI, Moorhead GBG, Fernie AR. Phosphonate analogs of 2-oxoglutarate perturb metabolism and gene expression in illuminated Arabidopsis leaves. FRONTIERS IN PLANT SCIENCE 2012; 3:114. [PMID: 22876250 PMCID: PMC3410613 DOI: 10.3389/fpls.2012.00114] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2012] [Accepted: 05/14/2012] [Indexed: 05/19/2023]
Abstract
Although the role of the 2-oxoglutarate dehydrogenase complex (2-OGDHC) has previously been demonstrated in plant heterotrophic tissues its role in photosynthetically active tissues remains poorly understood. By using a combination of metabolite and transcript profiles we here investigated the function of 2-OGDHC in leaves of Arabidopsis thaliana via use of specific phosphonate inhibitors of the enzyme. Incubation of leaf disks with the inhibitors revealed that they produced the anticipated effects on the in situ enzyme activity. In vitro experiments revealed that succinyl phosphonate (SP) and a carboxy ethyl ester of SP are slow-binding inhibitors of the 2-OGDHC. Our results indicate that the reduced respiration rates are associated with changes in the regulation of metabolic and signaling pathways leading to an imbalance in carbon-nitrogen metabolism and cell homeostasis. The inducible alteration of primary metabolism was associated with altered expression of genes belonging to networks of amino acids, plant respiration, and sugar metabolism. In addition, by using isothermal titration calorimetry we excluded the possibility that the changes in gene expression resulted from an effect on 2-oxoglutarate (2OG) binding to the carbon/ATP sensing protein PII. We also demonstrated that the 2OG degradation by the 2-oxoglutarate dehydrogenase strongly influences the distribution of intermediates of the tricarboxylic acid (TCA) cycle and the GABA shunt. Our results indicate that the TCA cycle activity is clearly working in a non-cyclic manner upon 2-OGDHC inhibition during the light period.
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Affiliation(s)
- Wagner L. Araújo
- Max-Planck-Institut für Molekulare PflanzenphysiologiePotsdam-Golm, Germany
- Departamento de Biologia Vegetal, Universidade Federal de ViçosaViçosa, Minas Gerais, Brazil
| | - Takayuki Tohge
- Max-Planck-Institut für Molekulare PflanzenphysiologiePotsdam-Golm, Germany
| | - Adriano Nunes-Nesi
- Max-Planck Partner Group, Departamento de Biologia Vegetal, Universidade Federal de ViçosaViçosa, Minas Gerais, Brazil
| | - Danilo M. Daloso
- Max-Planck-Institut für Molekulare PflanzenphysiologiePotsdam-Golm, Germany
- Departamento de Biologia Vegetal, Universidade Federal de ViçosaViçosa, Minas Gerais, Brazil
| | - Mhairi Nimick
- Department of Biological Sciences, University of CalgaryCalgary, AB, Canada
| | - Ina Krahnert
- Max-Planck-Institut für Molekulare PflanzenphysiologiePotsdam-Golm, Germany
| | - Victoria I. Bunik
- A.N. Belozersly Institute of Physico-Chemical Biology, Moscow State UniversityMoscow, Russia
| | | | - Alisdair R. Fernie
- Max-Planck-Institut für Molekulare PflanzenphysiologiePotsdam-Golm, Germany
- *Correspondence: Alisdair R. Fernie, Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany. e-mail:
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