1
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Tcherkez G, Abadie C, Dourmap C, Lalande J, Limami AM. Leaf day respiration: More than just catabolic CO 2 production in the light. PLANT, CELL & ENVIRONMENT 2024; 47:2631-2639. [PMID: 38528759 DOI: 10.1111/pce.14904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 02/08/2024] [Accepted: 03/18/2024] [Indexed: 03/27/2024]
Abstract
Summary statementDay respiration is a net flux resulting from several CO2‐generating and CO2‐fixing reactions, not only related to catabolism but also to anabolism. We review pieces of evidence that decarboxylating reactions are partly fed by carbon sources disconnected from current photosynthesis and how they reflect various metabolic pathways.
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Affiliation(s)
- Guillaume Tcherkez
- Institut de recherche en horticulture et semences, Université d'Angers, INRAe, Beaucouzé, France
- Research school of biology, ANU College of Science, Australian National University, Canberra, Australia
| | - Cyril Abadie
- Institut de recherche en horticulture et semences, Université d'Angers, INRAe, Beaucouzé, France
- Ecophysiologie et génomique fonctionnelle de la vigne, Institut des Sciences de la Vigne et du Vin, INRAe, Université de Bordeaux, Villenave-d'Ornon, France
| | - Corentin Dourmap
- Institut de recherche en horticulture et semences, Université d'Angers, INRAe, Beaucouzé, France
| | - Julie Lalande
- Institut de recherche en horticulture et semences, Université d'Angers, INRAe, Beaucouzé, France
| | - Anis M Limami
- Institut de recherche en horticulture et semences, Université d'Angers, INRAe, Beaucouzé, France
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2
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Sharkey TD. The end game(s) of photosynthetic carbon metabolism. PLANT PHYSIOLOGY 2024; 195:67-78. [PMID: 38163636 PMCID: PMC11060661 DOI: 10.1093/plphys/kiad601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 10/27/2023] [Indexed: 01/03/2024]
Abstract
The year 2024 marks 70 years since the general outline of the carbon pathway in photosynthesis was published. Although several alternative pathways are now known, it is remarkable how many organisms use the reaction sequence described 70 yrs ago, which is now known as the Calvin-Benson cycle or variants such as the Calvin-Benson-Bassham cycle or Benson-Calvin cycle. However, once the carbon has entered the Calvin-Benson cycle and is converted to a 3-carbon sugar, it has many potential fates. This review will examine the last stages of photosynthetic metabolism in leaves. In land plants, this process mostly involves the production of sucrose provided by an endosymbiont (the chloroplast) to its host for use and transport to the rest of the plant. Photosynthetic metabolism also usually involves the synthesis of starch, which helps maintain respiration in the dark and enables the symbiont to supply sugars during both the day and night. Other end products made in the chloroplast are closely tied to photosynthetic CO2 assimilation. These include serine from photorespiration and various amino acids, fatty acids, isoprenoids, and shikimate pathway products. I also describe 2 pathways that can short circuit parts of the Calvin-Benson cycle. These final processes of photosynthetic metabolism play many important roles in plants.
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Affiliation(s)
- Thomas D Sharkey
- MSU-DOE Plant Research Laboratory, Plant Resilience Institute, and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
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3
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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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4
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Ma L, Wang Y, Wang X, Lü X. Solid-State Fermentation Improves Tobacco Leaves Quality via the Screened Bacillus subtilis of Simultaneously Degrading Starch and Protein Ability. Appl Biochem Biotechnol 2024; 196:506-521. [PMID: 37148443 DOI: 10.1007/s12010-023-04486-x] [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] [Accepted: 04/11/2023] [Indexed: 05/08/2023]
Abstract
The process of tobacco aging plays a significant role in enhancing the smoking experience by improving the flavor and quality of tobacco leaves. During natural aging, the metabolic activity of the microbes on the surface of tobacco leaves will be greatly changed. Besides, starch and protein are two of the main macromolecular compounds causing the poor smoking quality of tobacco leaves which to be degraded for better tobacco quality. In this study, a bacterium with the simultaneously degrading ability of starch (degradation rate of 33.87%) and protein (degradation rate of 20%) has been screened out from high-class tobacco leaf and then inoculated into low-class tobacco leaf by solid-state fermentation for quality improvement. The changes in components related to carbon and nitrogen showed that the strain had an obvious effect on the quality improvement of tobacco leaves. After that, GC-MS analyses displayed the volatile flavor compounds which become rich and the flavor has been improved. It has been proved that inoculation solid-state fermentation by dominant strain could improve tobacco quality, as well as instead of the traditional natural aging process which greatly shortens the aging process. The work also offers a helpful strategy for solid-state products for deep fermentation.
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Affiliation(s)
- Lingling Ma
- Laboratory of Bioresources, College of Food Science and Engineering, Northwest A&F University, Shaanxi Province, 712100, Yangling, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu Province, 214122, China
| | - Ying Wang
- Laboratory of Bioresources, College of Food Science and Engineering, Northwest A&F University, Shaanxi Province, 712100, Yangling, China
- Technology Center, China Tobacco Shaanxi Industrial Co., Ltd., Baoji, 721013, Shaanxi Province, China
| | - Xin Wang
- Laboratory of Bioresources, College of Food Science and Engineering, Northwest A&F University, Shaanxi Province, 712100, Yangling, China
| | - Xin Lü
- Laboratory of Bioresources, College of Food Science and Engineering, Northwest A&F University, Shaanxi Province, 712100, Yangling, China.
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5
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Dellero Y, Berardocco S, Bouchereau A. U- 13C-glucose incorporation into source leaves of Brassica napus highlights light-dependent regulations of metabolic fluxes within central carbon metabolism. JOURNAL OF PLANT PHYSIOLOGY 2024; 292:154162. [PMID: 38103478 DOI: 10.1016/j.jplph.2023.154162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 11/07/2023] [Accepted: 12/08/2023] [Indexed: 12/19/2023]
Abstract
Plant central carbon metabolism comprises several important metabolic pathways acting together to support plant growth and yield establishment. Despite the emergence of 13C-based dynamic approaches, the regulation of metabolic fluxes between light and dark conditions has not yet received sufficient attention for agronomically relevant plants. Here, we investigated the impact of light/dark conditions on carbon allocation processes within central carbon metabolism of Brassica napus after U-13C-glucose incorporation into leaf discs. Leaf gas-exchanges and metabolite contents were weakly impacted by the leaf disc method and the incorporation of glucose. 13C-analysis by GC-MS showed that U-13C-glucose was converted to fructose for de novo biosynthesis of sucrose at similar rates in both light and dark conditions. However, light conditions led to a reduced commitment of glycolytic carbons towards respiratory substrates (pyruvate, alanine, malate) and TCA cycle intermediates compared to dark conditions. Analysis of 13C-enrichment at the isotopologue level and metabolic pathway isotopic tracing reconstructions identified the contribution of multiple pathways to serine biosynthesis in light and dark conditions. However, the direct contribution of the glucose-6-phosphate shunt to serine biosynthesis was not observed. Our results also provided isotopic evidences for an active metabolic connection between the TCA cycle, glycolysis and photorespiration in light conditions through a rapid reallocation of TCA cycle decarboxylations back to the TCA cycle through photorespiration and glycolysis. Altogether, these results suggest the active coordination of core metabolic pathways across multiple compartments to reorganize C-flux modes.
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Affiliation(s)
- Younès Dellero
- INRAE, Université Rennes, Institut Agro, IGEPP-UMR1349, P2M2-MetaboHUB, Le Rheu, 35653, France.
| | - Solenne Berardocco
- INRAE, Université Rennes, Institut Agro, IGEPP-UMR1349, P2M2-MetaboHUB, Le Rheu, 35653, France
| | - Alain Bouchereau
- INRAE, Université Rennes, Institut Agro, IGEPP-UMR1349, P2M2-MetaboHUB, Le Rheu, 35653, France
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6
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Burgess AJ, Degen GE. The long and the short of it: Adaptation of carbon uptake and metabolic flux to different daylengths. PLANT PHYSIOLOGY 2023; 194:317-318. [PMID: 37812729 PMCID: PMC10756749 DOI: 10.1093/plphys/kiad523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 09/27/2023] [Accepted: 09/27/2023] [Indexed: 10/11/2023]
Affiliation(s)
- Alexandra J Burgess
- Assistant Features Editor, Plant Physiology, American Society of Plant Biologists
- Agriculture and Environmental Sciences, School of Biosciences, University of Nottingham Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - Gustaf E Degen
- Assistant Features Editor, Plant Physiology, American Society of Plant Biologists
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
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7
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Xu Y, Koroma AA, Weise SE, Fu X, Sharkey TD, Shachar-Hill Y. Daylength variation affects growth, photosynthesis, leaf metabolism, partitioning, and metabolic fluxes. PLANT PHYSIOLOGY 2023; 194:475-490. [PMID: 37726946 PMCID: PMC10756764 DOI: 10.1093/plphys/kiad507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 09/01/2023] [Accepted: 09/01/2023] [Indexed: 09/21/2023]
Abstract
Daylength, a seasonal and latitudinal variable, exerts a substantial impact on plant growth. However, the relationship between daylength and growth is nonproportional, suggesting the existence of adaptive mechanisms. Thus, our study aimed to comprehensively investigate the adaptive strategies employed by plants in response to daylength variation. We grew false flax (Camelina sativa) plants, a model oilseed crop, under long-day (LD) and short-day (SD) conditions and used growth measurements, gas exchange measurements, and isotopic labeling techniques, including 13C, 14C, and 2H2O, to determine responses to different daylengths. Our findings revealed that daylength influences various growth parameters, photosynthetic physiology, carbon partitioning, metabolic fluxes, and metabolite levels. SD plants employed diverse mechanisms to compensate for reduced CO2 fixation in the shorter photoperiod. These mechanisms included enhanced photosynthetic rates and reduced respiration in the light (RL), leading to increased shoot investment. Additionally, SD plants exhibited reduced rates of the glucose 6-phosphate (G6P) shunt and greater partitioning of sugars into starch, thereby sustaining carbon availability during the longer night. Isotopic labeling results further demonstrated substantial alterations in the partitioning of amino acids and TCA cycle intermediates between rapidly and slowly turning over pools. Overall, the results point to multiple developmental, physiological, and metabolic ways in which plants adapt to different daylengths to maintain growth.
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Affiliation(s)
- Yuan Xu
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
| | - Abubakarr A Koroma
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
- Department of Microbiology and Immunology, Emory University, Atlanta, GA 30329, USA
| | - Sean E Weise
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Xinyu Fu
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
| | - Thomas D Sharkey
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
- Plant Resilience Institute, Michigan State University, East Lansing, MI 48824, USA
| | - Yair Shachar-Hill
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
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8
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Geffen O, Achaintre D, Treves H. 13CO 2-labelling and Sampling in Algae for Flux Analysis of Photosynthetic and Central Carbon Metabolism. Bio Protoc 2023; 13:e4808. [PMID: 37719071 PMCID: PMC10501915 DOI: 10.21769/bioprotoc.4808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 06/09/2023] [Accepted: 06/14/2023] [Indexed: 09/19/2023] Open
Abstract
The flux in photosynthesis can be studied by performing 13CO2 pulse labelling and analysing the temporal labelling kinetics of metabolic intermediates using gas or liquid chromatography linked to mass spectrometry. Metabolic flux analysis (MFA) is the primary approach for analysing metabolic network function and quantifying intracellular metabolic fluxes. Different MFA approaches differ based on the metabolic state (steady vs. non-steady state) and the use of stable isotope tracers. The main methodology used to investigate metabolic systems is metabolite steady state associated with stable isotope labelling experiments. Specifically, in biological systems like photoautotrophic organisms, isotopic non-stationary 113C metabolic flux analysis at metabolic steady state with transient isotopic labelling (13C-INST-MFA) is required. The common requirement for metabolic steady state, alongside its very short half-timed reactions, complicates robust MFA of photosynthetic metabolism. While custom gas chambers design has addressed these challenges in various model plants, no similar tools were developed for liquid photosynthetic cultures (e.g., algae, cyanobacteria), where diffusion and equilibration of inorganic carbon species in the medium entails a new dimension of complexity. Recently, a novel tailor-made microfluidics labelling system has been introduced, supplying short 13CO2 pulses at steady state, and resolving fluxes across most photosynthetic metabolic pathways in algae. The system involves injecting algal cultures and medium containing pre-equilibrated inorganic 13C into a microfluidic mixer, followed by rapid metabolic quenching, enabling precise seconds-level label pulses. This was complemented by a 13CO2-bubbling-based open labelling system (photobioreactor), allowing long pulses (minutes-hours) required for investigating fluxes into central C metabolism and major products. This combined labelling procedure provides a comprehensive fluxome cover for most algal photosynthetic and central C metabolism pathways, thus allowing comparative flux analyses across algae and plants.
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Affiliation(s)
- Or Geffen
- School of Plant Sciences and Food Security, Faculty of Biology, Tel-Aviv University, Tel Aviv-Yafo, Israel
| | - David Achaintre
- School of Plant Sciences and Food Security, Faculty of Biology, Tel-Aviv University, Tel Aviv-Yafo, Israel
| | - Haim Treves
- School of Plant Sciences and Food Security, Faculty of Biology, Tel-Aviv University, Tel Aviv-Yafo, Israel
- Plant Metabolism Group, Faculty of Biology, Rhineland-Palatinate Technical University of Kaiserslautern-Landau, Kaiserslautern, Germany
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9
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Apriyanto A, Compart J, Fettke J. Transcriptomic analysis of mesocarp tissue during fruit development of the oil palm revealed specific isozymes related to starch metabolism that control oil yield. FRONTIERS IN PLANT SCIENCE 2023; 14:1220237. [PMID: 37554560 PMCID: PMC10405827 DOI: 10.3389/fpls.2023.1220237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 07/05/2023] [Indexed: 08/10/2023]
Abstract
The oil palm (Elaeis guineensis Jacq.) produces a large amount of oil from the fruit. However, increasing the oil production in this fruit is still challenging. A recent study has shown that starch metabolism is essential for oil synthesis in fruit-producing species. Therefore, the transcriptomic analysis by RNA-seq was performed to observe gene expression alteration related to starch metabolism genes throughout the maturity stages of oil palm fruit with different oil yields. Gene expression profiles were examined with three different oil yields group (low, medium, and high) at six fruit development phases (4, 8, 12, 16, 20, and 22 weeks after pollination). We successfully identified and analyzed differentially expressed genes in oil palm mesocarps during development. The results showed that the transcriptome profile for each developmental phase was unique. Sucrose flux to the mesocarp tissue, rapid starch turnover, and high glycolytic activity have been identified as critical factors for oil production in oil palms. For starch metabolism and the glycolytic pathway, we identified specific gene expressions of enzyme isoforms (isozymes) that correlated with oil production, which may determine the oil content. This study provides valuable information for creating new high-oil-yielding palm varieties via breeding programs or genome editing approaches.
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Affiliation(s)
- Ardha Apriyanto
- Biopolymer Analytics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam-Golm, Germany
- Research and Development, PT. Astra Agro Lestari Tbk, Jakarta Timur, Indonesia
| | - Julia Compart
- Biopolymer Analytics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam-Golm, Germany
| | - Joerg Fettke
- Biopolymer Analytics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam-Golm, Germany
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10
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Dellero Y, Filangi O, Bouchereau A. Evaluation of GC/MS-Based 13C-Positional Approaches for TMS Derivatives of Organic and Amino Acids and Application to Plant 13C-Labeled Experiments. Metabolites 2023; 13:metabo13040466. [PMID: 37110124 PMCID: PMC10142191 DOI: 10.3390/metabo13040466] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/20/2023] [Accepted: 03/20/2023] [Indexed: 04/29/2023] Open
Abstract
Analysis of plant metabolite 13C-enrichments with gas-chromatography mass spectrometry (GC/MS) has gained interest recently. By combining multiple fragments of a trimethylsilyl (TMS) derivative, 13C-positional enrichments can be calculated. However, this new approach may suffer from analytical biases depending on the fragments selected for calculation leading to significant errors in the final results. The goal of this study was to provide a framework for the validation of 13C-positional approaches and their application to plants based on some key metabolites (glycine, serine, glutamate, proline, α-alanine and malate). For this purpose, we used tailor-made 13C-PT standards, harboring known carbon isotopologue distributions and 13C-positional enrichments, to evaluate the reliability of GC-MS measurements and positional calculations. Overall, we showed that some mass fragments of proline_2TMS, glutamate_3TMS, malate_3TMS and α-alanine_2TMS had important biases for 13C measurements resulting in significant errors in the computational estimation of 13C-positional enrichments. Nevertheless, we validated a GC/MS-based 13C-positional approach for the following atomic positions: (i) C1 and C2 of glycine_3TMS, (ii) C1, C2 and C3 of serine_3TMS, and (iii) C1 of malate_3TMS and glutamate_3TMS. We successfully applied this approach to plant 13C-labeled experiments for investigating key metabolic fluxes of plant primary metabolism (photorespiration, tricarboxylic acid cycle and phosphoenolpyruvate carboxylase activity).
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Affiliation(s)
- Younès Dellero
- Institute for Genetics, Environment and Plant Protection (IGEPP), National Research Institute for Agriculture, Food and Environment (INRAE), Institut Agro, Université Rennes, 35650 Le Rheu, France
- Metabolic Profiling and Metabolomic Platform (P2M2), Biopolymers Interactions Assemblies, Institute for Genetics, Environment and Plant Protection, 35650 Le Rheu, France
- MetaboHUB, National Infrastructure of Metabolomics and Fluxomics, 35650 Le Rheu, France
| | - Olivier Filangi
- Institute for Genetics, Environment and Plant Protection (IGEPP), National Research Institute for Agriculture, Food and Environment (INRAE), Institut Agro, Université Rennes, 35650 Le Rheu, France
- Metabolic Profiling and Metabolomic Platform (P2M2), Biopolymers Interactions Assemblies, Institute for Genetics, Environment and Plant Protection, 35650 Le Rheu, France
- MetaboHUB, National Infrastructure of Metabolomics and Fluxomics, 35650 Le Rheu, France
| | - Alain Bouchereau
- Institute for Genetics, Environment and Plant Protection (IGEPP), National Research Institute for Agriculture, Food and Environment (INRAE), Institut Agro, Université Rennes, 35650 Le Rheu, France
- Metabolic Profiling and Metabolomic Platform (P2M2), Biopolymers Interactions Assemblies, Institute for Genetics, Environment and Plant Protection, 35650 Le Rheu, France
- MetaboHUB, National Infrastructure of Metabolomics and Fluxomics, 35650 Le Rheu, France
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11
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Morley SA, Ma F, Alazem M, Frankfater C, Yi H, Burch-Smith T, Clemente TE, Veena V, Nguyen H, Allen DK. Expression of malic enzyme reveals subcellular carbon partitioning for storage reserve production in soybeans. THE NEW PHYTOLOGIST 2023. [PMID: 36829298 DOI: 10.1111/nph.18835] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 02/09/2023] [Indexed: 06/18/2023]
Abstract
Central metabolism produces amino and fatty acids for protein and lipids that establish seed value. Biosynthesis of storage reserves occurs in multiple organelles that exchange central intermediates including two essential metabolites, malate, and pyruvate that are linked by malic enzyme. Malic enzyme can be active in multiple subcellular compartments, partitioning carbon and reducing equivalents for anabolic and catabolic requirements. Prior studies based on isotopic labeling and steady-state metabolic flux analyses indicated malic enzyme provides carbon for fatty acid biosynthesis in plants, though genetic evidence confirming this role is lacking. We hypothesized that increasing malic enzyme flux would alter carbon partitioning and result in increased lipid levels in soybeans. Homozygous transgenic soybean plants expressing Arabidopsis malic enzyme alleles, targeting the translational products to plastid or outside the plastid during seed development, were verified by transcript and enzyme activity analyses, organelle proteomics, and transient expression assays. Protein, oil, central metabolites, cofactors, and acyl-acyl carrier protein (ACPs) levels were quantified overdevelopment. Amino and fatty acid levels were altered resulting in an increase in lipids by 0.5-2% of seed biomass (i.e. 2-9% change in oil). Subcellular targeting of a single gene product in central metabolism impacts carbon and reducing equivalent partitioning for seed storage reserves in soybeans.
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Affiliation(s)
- Stewart A Morley
- United States Department of Agriculture, Agricultural Research Service, 975 N Warson Rd, St Louis, MO, 63132, USA
- Donald Danforth Plant Science Center, 975 N Warson Rd, St Louis, MO, 63132, USA
| | - Fangfang Ma
- Donald Danforth Plant Science Center, 975 N Warson Rd, St Louis, MO, 63132, USA
| | - Mazen Alazem
- Donald Danforth Plant Science Center, 975 N Warson Rd, St Louis, MO, 63132, USA
| | - Cheryl Frankfater
- United States Department of Agriculture, Agricultural Research Service, 975 N Warson Rd, St Louis, MO, 63132, USA
- Donald Danforth Plant Science Center, 975 N Warson Rd, St Louis, MO, 63132, USA
| | - Hochul Yi
- Donald Danforth Plant Science Center, 975 N Warson Rd, St Louis, MO, 63132, USA
| | - Tessa Burch-Smith
- Donald Danforth Plant Science Center, 975 N Warson Rd, St Louis, MO, 63132, USA
| | - Tom Elmo Clemente
- Department of Agronomy & Horticulture, University of Nebraska-Lincoln, 202 Keim Hall, Lincoln, NE, 68583, USA
| | - Veena Veena
- Donald Danforth Plant Science Center, 975 N Warson Rd, St Louis, MO, 63132, USA
| | - Hanh Nguyen
- Center for Plant Science Innovation, University of Nebraska, N300 Beadle Center, 1901 Vine St., Lincoln, NE, 68588, USA
| | - Doug K Allen
- United States Department of Agriculture, Agricultural Research Service, 975 N Warson Rd, St Louis, MO, 63132, USA
- Donald Danforth Plant Science Center, 975 N Warson Rd, St Louis, MO, 63132, USA
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12
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Doug K. Allen. THE NEW PHYTOLOGIST 2023; 237:710-713. [PMID: 36601907 DOI: 10.1111/nph.18608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
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13
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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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14
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Fu X, Gregory LM, Weise SE, Walker BJ. Integrated flux and pool size analysis in plant central metabolism reveals unique roles of glycine and serine during photorespiration. NATURE PLANTS 2023; 9:169-178. [PMID: 36536013 DOI: 10.1038/s41477-022-01294-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 10/28/2022] [Indexed: 06/17/2023]
Abstract
Photorespiration is an essential process juxtaposed between plant carbon and nitrogen metabolism that responds to dynamic environments. Photorespiration recycles inhibitory intermediates arising from oxygenation reactions catalysed by Rubisco back into the C3 cycle, but it is unclear what proportions of its nitrogen-containing intermediates (glycine and serine) are exported into other metabolisms in vivo and how these pool sizes affect net CO2 gas exchange during photorespiratory transients. Here, to address this uncertainty, we measured rates of amino acid export from photorespiration using isotopically non-stationary metabolic flux analysis. This analysis revealed that ~23-41% of the photorespiratory carbon was exported from the pathway as serine under various photorespiratory conditions. Furthermore, we determined that the build-up and relaxation of glycine pools constrained a large portion of photosynthetic acclimation during photorespiratory transients. These results reveal the unique and important roles of glycine and serine in successfully maintaining various photorespiratory fluxes that occur under environmental fluctuations in nature and providing carbon and nitrogen for metabolism.
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Affiliation(s)
- Xinyu Fu
- Michigan State University-Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI, USA
| | - Luke M Gregory
- Michigan State University-Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI, USA
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
| | - Sean E Weise
- Michigan State University-Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI, USA
| | - Berkley J Walker
- Michigan State University-Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI, USA.
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA.
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15
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Koley S, Chu KL, Mukherjee T, Morley SA, Klebanovych A, Czymmek KJ, Allen DK. Metabolic synergy in Camelina reproductive tissues for seed development. SCIENCE ADVANCES 2022; 8:eabo7683. [PMID: 36306367 PMCID: PMC9616503 DOI: 10.1126/sciadv.abo7683] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 09/14/2022] [Indexed: 06/15/2023]
Abstract
Photosynthesis in fruits is well documented, but its contribution to seed development and yield remains largely unquantified. In oilseeds, the pods are green and elevated with direct access to sunlight. With 13C labeling in planta and through an intact pod labeling system, a unique multi-tissue comprehensive flux model mechanistically described how pods assimilate up to one-half (33 to 45%) of seed carbon by proximal photosynthesis in Camelina sativa. By capturing integrated tissue metabolism, the studies reveal the contribution of plant architecture beyond leaves, to enable seed filling and maximize the number of viable seeds. The latent capacity of the pod wall in the absence of leaves contributes approximately 79% of seed biomass, supporting greater seed sink capacity and higher theoretical yields that suggest an opportunity for crop productivity gains.
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Affiliation(s)
- Somnath Koley
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Kevin L. Chu
- Donald Danforth Plant Science Center, St. Louis, MO, USA
- United States Department of Agriculture-Agricultural Research Service, Donald Danforth Plant Science Center, St. Louis, MO, USA
| | | | - Stewart A. Morley
- Donald Danforth Plant Science Center, St. Louis, MO, USA
- United States Department of Agriculture-Agricultural Research Service, Donald Danforth Plant Science Center, St. Louis, MO, USA
| | | | | | - Doug K. Allen
- Donald Danforth Plant Science Center, St. Louis, MO, USA
- United States Department of Agriculture-Agricultural Research Service, Donald Danforth Plant Science Center, St. Louis, MO, USA
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16
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Koley S, Chu KL, Gill SS, Allen DK. An efficient LC-MS method for isomer separation and detection of sugars, phosphorylated sugars, and organic acids. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:2938-2952. [PMID: 35560196 DOI: 10.1093/jxb/erac062] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Accepted: 02/15/2022] [Indexed: 06/15/2023]
Abstract
Assessing central carbon metabolism in plants can be challenging due to the dynamic range in pool sizes, with low levels of important phosphorylated sugars relative to more abundant sugars and organic acids. Here, we report a sensitive liquid chromatography-mass spectrometry method for analysing central metabolites on a hybrid column, where both anion-exchange and hydrophilic interaction chromatography (HILIC) ligands are embedded in the stationary phase. The liquid chromatography method was developed for enhanced selectivity of 27 central metabolites in a single run with sensitivity at femtomole levels observed for most phosphorylated sugars. The method resolved phosphorylated hexose, pentose, and triose isomers that are otherwise challenging. Compared with a standard HILIC approach, these metabolites had improved peak areas using our approach due to ion enhancement or low ion suppression in the biological sample matrix. The approach was applied to investigate metabolism in high lipid-producing tobacco leaves that exhibited increased levels of acetyl-CoA, a precursor for oil biosynthesis. The application of the method to isotopologue detection and quantification was considered through evaluating 13C-labeled seeds from Camelina sativa. The method provides a means to analyse intermediates more comprehensively in central metabolism of plant tissues.
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Affiliation(s)
- Somnath Koley
- Donald Danforth Plant Science Center, St Louis, MO 63132, USA
| | - Kevin L Chu
- Donald Danforth Plant Science Center, St Louis, MO 63132, USA
- United States Department of Agriculture-Agriculture Research Service, Donald Danforth Plant Science Center, St Louis, MO 63132, USA
| | - Saba S Gill
- Donald Danforth Plant Science Center, St Louis, MO 63132, USA
- United States Department of Agriculture-Agriculture Research Service, Donald Danforth Plant Science Center, St Louis, MO 63132, USA
| | - Doug K Allen
- Donald Danforth Plant Science Center, St Louis, MO 63132, USA
- United States Department of Agriculture-Agriculture Research Service, Donald Danforth Plant Science Center, St Louis, MO 63132, USA
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17
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Joshi A, Verma KK, D Rajput V, Minkina T, Arora J. Recent advances in metabolic engineering of microorganisms for advancing lignocellulose-derived biofuels. Bioengineered 2022; 13:8135-8163. [PMID: 35297313 PMCID: PMC9161965 DOI: 10.1080/21655979.2022.2051856] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Combating climate change and ensuring energy supply to a rapidly growing global population has highlighted the need to replace petroleum fuels with clean, and sustainable renewable fuels. Biofuels offer a solution to safeguard energy security with reduced ecological footprint and process economics. Over the past years, lignocellulosic biomass has become the most preferred raw material for the production of biofuels, such as fuel, alcohol, biodiesel, and biohydrogen. However, the cost-effective conversion of lignocellulose into biofuels remains an unsolved challenge at the industrial scale. Recently, intensive efforts have been made in lignocellulose feedstock and microbial engineering to address this problem. By improving the biological pathways leading to the polysaccharide, lignin, and lipid biosynthesis, limited success has been achieved, and still needs to improve sustainable biofuel production. Impressive success is being achieved by the retouring metabolic pathways of different microbial hosts. Several robust phenotypes, mostly from bacteria and yeast domains, have been successfully constructed with improved substrate spectrum, product yield and sturdiness against hydrolysate toxins. Cyanobacteria is also being explored for metabolic advancement in recent years, however, it also remained underdeveloped to generate commercialized biofuels. The bacterium Escherichia coli and yeast Saccharomyces cerevisiae strains are also being engineered to have cell surfaces displaying hydrolytic enzymes, which holds much promise for near-term scale-up and biorefinery use. Looking forward, future advances to achieve economically feasible production of lignocellulosic-based biofuels with special focus on designing more efficient metabolic pathways coupled with screening, and engineering of novel enzymes.
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Affiliation(s)
- Abhishek Joshi
- Laboratory of Biomolecular Technology, Department of Botany, Mohanlal Sukhadia University, Udaipur313001, India
| | - Krishan K. Verma
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic improvement/Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning - 530007, China
| | - Vishnu D Rajput
- Academy of Biology and Biotechnology, Southern Federal University, 344090, Russia
| | - Tatiana Minkina
- Academy of Biology and Biotechnology, Southern Federal University, 344090, Russia
| | - Jaya Arora
- Laboratory of Biomolecular Technology, Department of Botany, Mohanlal Sukhadia University, Udaipur313001, India,CONTACT Jaya Arora Laboratory of Biomolecular Technology, Department of Botany, Mohanlal Sukhadia University, Udaipur313001, India
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18
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Clark TJ, Schwender J. Elucidation of Triacylglycerol Overproduction in the C 4 Bioenergy Crop Sorghum bicolor by Constraint-Based Analysis. FRONTIERS IN PLANT SCIENCE 2022; 13:787265. [PMID: 35251073 PMCID: PMC8892208 DOI: 10.3389/fpls.2022.787265] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 01/24/2022] [Indexed: 06/14/2023]
Abstract
Upregulation of triacylglycerols (TAGs) in vegetative plant tissues such as leaves has the potential to drastically increase the energy density and biomass yield of bioenergy crops. In this context, constraint-based analysis has the promise to improve metabolic engineering strategies. Here we present a core metabolism model for the C4 biomass crop Sorghum bicolor (iTJC1414) along with a minimal model for photosynthetic CO2 assimilation, sucrose and TAG biosynthesis in C3 plants. Extending iTJC1414 to a four-cell diel model we simulate C4 photosynthesis in mature leaves with the principal photo-assimilatory product being replaced by TAG produced at different levels. Independent of specific pathways and per unit carbon assimilated, energy content and biosynthetic demands in reducing equivalents are about 1.3 to 1.4 times higher for TAG than for sucrose. For plant generic pathways, ATP- and NADPH-demands per CO2 assimilated are higher by 1.3- and 1.5-fold, respectively. If the photosynthetic supply in ATP and NADPH in iTJC1414 is adjusted to be balanced for sucrose as the sole photo-assimilatory product, overproduction of TAG is predicted to cause a substantial surplus in photosynthetic ATP. This means that if TAG synthesis was the sole photo-assimilatory process, there could be an energy imbalance that might impede the process. Adjusting iTJC1414 to a photo-assimilatory rate that approximates field conditions, we predict possible daily rates of TAG accumulation, dependent on varying ratios of carbon partitioning between exported assimilates and accumulated oil droplets (TAG, oleosin) and in dependence of activation of futile cycles of TAG synthesis and degradation. We find that, based on the capacity of leaves for photosynthetic synthesis of exported assimilates, mature leaves should be able to reach a 20% level of TAG per dry weight within one month if only 5% of the photosynthetic net assimilation can be allocated into oil droplets. From this we conclude that high TAG levels should be achievable if TAG synthesis is induced only during a final phase of the plant life cycle.
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Affiliation(s)
- Teresa J. Clark
- Biology Department, Brookhaven National Laboratory, Upton, NY, United States
| | - Jorg Schwender
- Biology Department, Brookhaven National Laboratory, Upton, NY, United States
- Department of Energy Center for Advanced Bioenergy and Bioproducts Innovation, Upton, NY, United States
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19
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Dellero Y, Berardocco S, Berges C, Filangi O, Bouchereau A. Validation of carbon isotopologue distribution measurements by GC-MS and application to 13C-metabolic flux analysis of the tricarboxylic acid cycle in Brassica napus leaves. FRONTIERS IN PLANT SCIENCE 2022; 13:885051. [PMID: 36704152 PMCID: PMC9871494 DOI: 10.3389/fpls.2022.885051] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 11/28/2022] [Indexed: 05/14/2023]
Abstract
The estimation of metabolic fluxes in photosynthetic organisms represents an important challenge that has gained interest over the last decade with the development of 13C-Metabolic Flux Analysis at isotopically non-stationary steady-state. This approach requires a high level of accuracy for the measurement of Carbon Isotopologue Distribution in plant metabolites. But this accuracy has still not been evaluated at the isotopologue level for GC-MS, leading to uncertainties for the metabolic fluxes calculated based on these fragments. Here, we developed a workflow to validate the measurements of CIDs from plant metabolites with GC-MS by producing tailor-made E. coli standard extracts harboring a predictable binomial CID for some organic and amino acids. Overall, most of our TMS-derivatives mass fragments were validated with these standards and at natural isotope abundance in plant matrices. Then, we applied this validated MS method to investigate the light/dark regulation of plant TCA cycle by incorporating U-13C-pyruvate to Brassica napus leaf discs. We took advantage of pathway-specific isotopologues/isotopomers observed between two and six hours of labeling to show that the TCA cycle can operate in a cyclic manner under both light and dark conditions. Interestingly, this forward cyclic flux mode has a nearly four-fold higher contribution for pyruvate-to-citrate and pyruvate-to-malate fluxes than the phosphoenolpyruvate carboxylase (PEPc) flux reassimilating carbon derived from some mitochondrial enzymes. The contribution of stored citrate to the mitochondrial TCA cycle activity was also questioned based on dynamics of 13C-enrichment in citrate, glutamate and succinate and variations of citrate total amounts under light and dark conditions. Interestingly, there was a light-dependent 13C-incorporation into glycine and serine showing that decarboxylations from pyruvate dehydrogenase complex and TCA cycle enzymes were actively reassimilated and could represent up to 5% to net photosynthesis.
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Affiliation(s)
- Younès Dellero
- Institute for Genetics, Environment and Plant Protection (IGEPP), National Research Institute for Agriculture, Food and Environment (INRAE), Université Rennes, Institut Agro, Le Rheu, France
- Metabolic Profiling and Metabolomics platform (P2M2), Institute for Genetics, Environment and Plant Protection (IGEPP), Biopolymers Interactions Assemblies (BIA), Le Rheu, France
- MetaboHUB, National Infrastructure of Metabolomics and Fluxomics, Toulouse, France
- *Correspondence: Younès Dellero,
| | - Solenne Berardocco
- Institute for Genetics, Environment and Plant Protection (IGEPP), National Research Institute for Agriculture, Food and Environment (INRAE), Université Rennes, Institut Agro, Le Rheu, France
- Metabolic Profiling and Metabolomics platform (P2M2), Institute for Genetics, Environment and Plant Protection (IGEPP), Biopolymers Interactions Assemblies (BIA), Le Rheu, France
| | - Cécilia Berges
- MetaboHUB, National Infrastructure of Metabolomics and Fluxomics, Toulouse, France
- Toulouse Biotechnology Institute, Université de Toulouse, National center for Scientific Research (CNRS), National Institute for Research for Agriculture, Food and Environment (INRAE), National Institute of Applied Sciences (INSA), Toulouse, France
| | - Olivier Filangi
- Institute for Genetics, Environment and Plant Protection (IGEPP), National Research Institute for Agriculture, Food and Environment (INRAE), Université Rennes, Institut Agro, Le Rheu, France
- Metabolic Profiling and Metabolomics platform (P2M2), Institute for Genetics, Environment and Plant Protection (IGEPP), Biopolymers Interactions Assemblies (BIA), Le Rheu, France
- MetaboHUB, National Infrastructure of Metabolomics and Fluxomics, Toulouse, France
| | - Alain Bouchereau
- Institute for Genetics, Environment and Plant Protection (IGEPP), National Research Institute for Agriculture, Food and Environment (INRAE), Université Rennes, Institut Agro, Le Rheu, France
- Metabolic Profiling and Metabolomics platform (P2M2), Institute for Genetics, Environment and Plant Protection (IGEPP), Biopolymers Interactions Assemblies (BIA), Le Rheu, France
- MetaboHUB, National Infrastructure of Metabolomics and Fluxomics, Toulouse, France
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