1
|
Abadie C, Lalande J, Dourmap C, Limami AM, Tcherkez G. Leaf day respiration involves multiple carbon sources and depends on previous dark metabolism. PLANT, CELL & ENVIRONMENT 2024; 47:2146-2162. [PMID: 38444114 DOI: 10.1111/pce.14871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 02/06/2024] [Accepted: 02/20/2024] [Indexed: 03/07/2024]
Abstract
Day respiration (Rd) is the metabolic, nonphotorespiratory process by which illuminated leaves liberate CO2 during photosynthesis. Rd is used routinely in photosynthetic models and is thus critical for calculations. However, metabolic details associated with Rd are poorly known, and this can be problematic to predict how Rd changes with environmental conditions and relates to night respiration. It is often assumed that day respiratory CO2 release just reflects 'ordinary' catabolism (glycolysis and Krebs 'cycle'). Here, we carried out a pulse-chase experiment, whereby a 13CO2 pulse in the light was followed by a chase period in darkness and then in the light. We took advantage of nontargeted, isotope-assisted metabolomics to determine non-'ordinary' metabolism, detect carbon remobilisation and compare light and dark 13C utilisation. We found that several concurrent metabolic pathways ('ordinary' catabolism, oxidative pentose phosphates pathway, amino acid production, nucleotide biosynthesis and secondary metabolism) took place in the light and participated in net CO2 efflux associated with day respiration. Flux reconstruction from metabolomics leads to an underestimation of Rd, further suggesting the contribution of a variety of CO2-evolving processes. Also, the cornerstone of the Krebs 'cycle', citrate, is synthetised de novo from photosynthates mostly in darkness, and remobilised or synthesised from stored material in the light. Collectively, our data provides direct evidence that leaf day respiration (i) involves several CO2-producing reactions and (ii) is fed by different carbon sources, including stored carbon disconnected from current photosynthates.
Collapse
Affiliation(s)
- Cyril Abadie
- Institut de recherche en horticulture et semences, INRAe, Université d'Angers, 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
| | - Julie Lalande
- Institut de recherche en horticulture et semences, INRAe, Université d'Angers, Beaucouzé, France
| | - Corentin Dourmap
- Institut de recherche en horticulture et semences, INRAe, Université d'Angers, Beaucouzé, France
| | - Anis M Limami
- Institut de recherche en horticulture et semences, INRAe, Université d'Angers, Beaucouzé, France
| | - Guillaume Tcherkez
- Institut de recherche en horticulture et semences, INRAe, Université d'Angers, Beaucouzé, France
- Research School of Biology, ANU College of Science, Australian National University, Canberra, Australia
| |
Collapse
|
3
|
Kato Y, Inabe K, Hidese R, Kondo A, Hasunuma T. Metabolomics-based engineering for biofuel and bio-based chemical production in microalgae and cyanobacteria: A review. BIORESOURCE TECHNOLOGY 2022; 344:126196. [PMID: 34710610 DOI: 10.1016/j.biortech.2021.126196] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/18/2021] [Accepted: 10/19/2021] [Indexed: 06/13/2023]
Abstract
Metabolomics, an essential tool in modern synthetic biology based on the design-build-test-learn platform, is useful for obtaining a detailed understanding of cellular metabolic mechanisms through comprehensive analyses of the metabolite pool size and its dynamic changes. Metabolomics is critical to the design of a rational metabolic engineering strategy by determining the rate-limiting reaction and assimilated carbon distribution in a biosynthetic pathway of interest. Microalgae and cyanobacteria are promising photosynthetic producers of biofuels and bio-based chemicals, with high potential for developing a bioeconomic society through bio-based carbon neutral manufacturing. Metabolomics technologies optimized for photosynthetic organisms have been developed and utilized in various microalgal and cyanobacterial species. This review provides a concise overview of recent achievements in photosynthetic metabolomics, emphasizing the importance of microalgal and cyanobacterial cell factories that satisfy industrial requirements.
Collapse
Affiliation(s)
- Yuichi Kato
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Kosuke Inabe
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Ryota Hidese
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan; Graduate School of Science, Innovation and Technology, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Akihiko Kondo
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan; Graduate School of Science, Innovation and Technology, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan; Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Tomohisa Hasunuma
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan; Graduate School of Science, Innovation and Technology, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan.
| |
Collapse
|
6
|
Spona-Friedl M, Braun A, Huber C, Eisenreich W, Griebler C, Kappler A, Elsner M. Substrate-dependent CO2 fixation in heterotrophic bacteria revealed by stable isotope labelling. FEMS Microbiol Ecol 2020; 96:5828077. [DOI: 10.1093/femsec/fiaa080] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 04/30/2020] [Indexed: 11/14/2022] Open
Abstract
ABSTRACTVirtually all heterotrophs incorporate carbon dioxide by anaplerotic fixation. Little explored, however, is the interdependency of pathways and rates of CO2fixation on the concurrent usage of organic substrate(s). Potentially, this could reveal which substrates out of a pool of dissolved organic carbon are utilised by environmental microorganisms. To explore this possibility, Bacillus subtilis W23 was grown in a minimal medium with normalised amounts of either glucose, lactate or malate as only organic substrates, each together with 1 g/L NaH13CO3. Incorporation of H13CO3− was traced by elemental analysis-isotope ratio mass spectrometry of biomass and gas chromatography-mass spectrometry of protein-derived amino acids. Until the late logarithmic phase, 13C incorporation into the tricarboxylic acid cycle increased with time and occurred via [4–13C]oxaloacetate formed by carboxylation of pyruvate. The levels of 13C incorporation were highest for growth on glucose and lowest on malate. Incorporation of 13C into gluconeogenesis products was mainly detected in the lactate and malate experiment, whereas glucose down-regulated this path. A proof-of-principle study with a natural groundwater community confirmed the ability to determine incorporation from H13CO3− by natural communities leading to specific labelling patterns. This underlines the potential of the labelling approach to characterise carbon sources of heterotrophic microorganisms in their natural environments.
Collapse
Affiliation(s)
- Marina Spona-Friedl
- Institute of Groundwater Ecology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
| | - Alexander Braun
- Institute of Groundwater Ecology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
| | - Claudia Huber
- Chair of Biochemistry, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany
| | - Wolfgang Eisenreich
- Chair of Biochemistry, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany
| | - Christian Griebler
- Institute of Groundwater Ecology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
- Department of Functional and Evolutionary Ecology, Universität Wien, Althanstr. 14, A-1090 Wien, Austria
| | - Andreas Kappler
- Geomicrobiology, Eberhard-Karls-University Tuebingen, Sigwartstr. 10, 72076 Tuebingen, Germany
| | - Martin Elsner
- Institute of Groundwater Ecology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
- Chair of Analytical Chemistry and Water Chemistry, Technische Universität München, Marchioninistr. 17, 81377 München, Germany
| |
Collapse
|
8
|
Ćeranić A, Doppler M, Büschl C, Parich A, Xu K, Koutnik A, Bürstmayr H, Lemmens M, Schuhmacher R. Preparation of uniformly labelled 13C- and 15N-plants using customised growth chambers. PLANT METHODS 2020; 16:46. [PMID: 32280362 PMCID: PMC7137243 DOI: 10.1186/s13007-020-00590-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 03/28/2020] [Indexed: 05/04/2023]
Abstract
BACKGROUND Stable isotopically labelled organisms have found wide application in life science research including plant physiology, plant stress and defense as well as metabolism related sciences. Therefore, the reproducible production of plant material enriched with stable isotopes such as 13C and 15N is of considerable interest. A high degree of enrichment (> 96 atom %) with a uniformly distributed isotope (global labelling) is accomplished by a continuous substrate supply during plant growth/cultivation. In the case of plants, 13C-labelling can be achieved by growth in 13CO2(g) atmosphere while global 15N-labelling needs 15N- containing salts in the watering/nutrient solution. Here, we present a method for the preparation of 13C and 15N-labelled plants by the use of closed growth chambers and hydroponic nutrient supply. The method is exemplified with durum wheat. RESULTS In total, 330 g of globally 13C- and 295 g of 15N-labelled Triticum durum wheat was produced during 87 cultivation days. For this, a total of 3.88 mol of 13CO2(g) and 58 mmol of 15N were consumed. The degree of enrichment was determined by LC-HRMS and ranged between 96 and 98 atom % for 13C and 95-99 atom % for 15N, respectively. Additionally, the isotopically labelled plant extracts were successfully used for metabolome-wide internal standardisation of native T.durum plants. Application of an isotope-assisted LC-HRMS workflow enabled the detection of 652 truly wheat-derived metabolites out of which 143 contain N. CONCLUSION A reproducible cultivation which makes use of climate chambers and hydroponics was successfully adapted to produce highly enriched, uniformly 13C- and 15N-labelled wheat. The obtained plant material is suitable to be used in all kinds of isotope-assisted research. The described technical equipment and protocol can easily be applied to other plants to produce 13C-enriched biological samples when the necessary specific adaptations e.g. temperature and light regime, as well as nutrient supply are considered. Additionally, the 15N-labelling method can also be carried out under regular glasshouse conditions without the need for customised atmosphere.
Collapse
Affiliation(s)
- Asja Ćeranić
- Institute of Bioanalytics and Agro-Metabolomics, Department of Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences Vienna (BOKU), Konrad-Lorenz-Straße 20, 3430 Tulln, Austria
| | - Maria Doppler
- Institute of Bioanalytics and Agro-Metabolomics, Department of Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences Vienna (BOKU), Konrad-Lorenz-Straße 20, 3430 Tulln, Austria
| | - Christoph Büschl
- Institute of Bioanalytics and Agro-Metabolomics, Department of Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences Vienna (BOKU), Konrad-Lorenz-Straße 20, 3430 Tulln, Austria
| | - Alexandra Parich
- Institute of Bioanalytics and Agro-Metabolomics, Department of Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences Vienna (BOKU), Konrad-Lorenz-Straße 20, 3430 Tulln, Austria
| | - Kangkang Xu
- Institute of Bioanalytics and Agro-Metabolomics, Department of Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences Vienna (BOKU), Konrad-Lorenz-Straße 20, 3430 Tulln, Austria
| | - Andrea Koutnik
- Institute of Bioanalytics and Agro-Metabolomics, Department of Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences Vienna (BOKU), Konrad-Lorenz-Straße 20, 3430 Tulln, Austria
| | - Hermann Bürstmayr
- Institute of Biotechnology in Plant Production, Department of Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences Vienna (BOKU), 3430 Tulln, Austria
| | - Marc Lemmens
- Institute of Biotechnology in Plant Production, Department of Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences Vienna (BOKU), 3430 Tulln, Austria
| | - Rainer Schuhmacher
- Institute of Bioanalytics and Agro-Metabolomics, Department of Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences Vienna (BOKU), Konrad-Lorenz-Straße 20, 3430 Tulln, Austria
| |
Collapse
|
10
|
Jozwiak A, Lipko A, Kania M, Danikiewicz W, Surmacz L, Witek A, Wojcik J, Zdanowski K, Pączkowski C, Chojnacki T, Poznanski J, Swiezewska E. Modeling of Dolichol Mass Spectra Isotopic Envelopes as a Tool to Monitor Isoprenoid Biosynthesis. PLANT PHYSIOLOGY 2017; 174:857-874. [PMID: 28385729 PMCID: PMC5462023 DOI: 10.1104/pp.17.00036] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 04/05/2017] [Indexed: 05/27/2023]
Abstract
The cooperation of the mevalonate (MVA) and methylerythritol phosphate (MEP) pathways, operating in parallel in plants to generate isoprenoid precursors, has been studied extensively. Elucidation of the isoprenoid metabolic pathways is indispensable for the rational design of plant and microbial systems for the production of industrially valuable terpenoids. Here, we describe a new method, based on numerical modeling of mass spectra of metabolically labeled dolichols (Dols), designed to quantitatively follow the cooperation of MVA and MEP reprogrammed upon osmotic stress (sorbitol treatment) in Arabidopsis (Arabidopsis thaliana). The contribution of the MEP pathway increased significantly (reaching 100%) exclusively for the dominating Dols, while for long-chain Dols, the relative input of the MEP and MVA pathways remained unchanged, suggesting divergent sites of synthesis for dominating and long-chain Dols. The analysis of numerically modeled Dol mass spectra is a novel method to follow modulation of the concomitant activity of isoprenoid-generating pathways in plant cells; additionally, it suggests an exchange of isoprenoid intermediates between plastids and peroxisomes.
Collapse
Affiliation(s)
- Adam Jozwiak
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (A.J., A.L., L.S., A.W., J.W., K.Z., T.C., J.P., E.S.)
- Institute of Organic Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland (M.K., W.D.)
- Institute of Chemistry, University of Natural Sciences and Humanities, 08-110 Siedlce, Poland (K.Z.); and
- Department of Plant Biochemistry, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland (C.P.)
| | - Agata Lipko
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (A.J., A.L., L.S., A.W., J.W., K.Z., T.C., J.P., E.S.)
- Institute of Organic Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland (M.K., W.D.)
- Institute of Chemistry, University of Natural Sciences and Humanities, 08-110 Siedlce, Poland (K.Z.); and
- Department of Plant Biochemistry, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland (C.P.)
| | - Magdalena Kania
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (A.J., A.L., L.S., A.W., J.W., K.Z., T.C., J.P., E.S.)
- Institute of Organic Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland (M.K., W.D.)
- Institute of Chemistry, University of Natural Sciences and Humanities, 08-110 Siedlce, Poland (K.Z.); and
- Department of Plant Biochemistry, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland (C.P.)
| | - Witold Danikiewicz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (A.J., A.L., L.S., A.W., J.W., K.Z., T.C., J.P., E.S.)
- Institute of Organic Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland (M.K., W.D.)
- Institute of Chemistry, University of Natural Sciences and Humanities, 08-110 Siedlce, Poland (K.Z.); and
- Department of Plant Biochemistry, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland (C.P.)
| | - Liliana Surmacz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (A.J., A.L., L.S., A.W., J.W., K.Z., T.C., J.P., E.S.)
- Institute of Organic Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland (M.K., W.D.)
- Institute of Chemistry, University of Natural Sciences and Humanities, 08-110 Siedlce, Poland (K.Z.); and
- Department of Plant Biochemistry, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland (C.P.)
| | - Agnieszka Witek
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (A.J., A.L., L.S., A.W., J.W., K.Z., T.C., J.P., E.S.)
- Institute of Organic Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland (M.K., W.D.)
- Institute of Chemistry, University of Natural Sciences and Humanities, 08-110 Siedlce, Poland (K.Z.); and
- Department of Plant Biochemistry, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland (C.P.)
| | - Jacek Wojcik
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (A.J., A.L., L.S., A.W., J.W., K.Z., T.C., J.P., E.S.)
- Institute of Organic Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland (M.K., W.D.)
- Institute of Chemistry, University of Natural Sciences and Humanities, 08-110 Siedlce, Poland (K.Z.); and
- Department of Plant Biochemistry, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland (C.P.)
| | - Konrad Zdanowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (A.J., A.L., L.S., A.W., J.W., K.Z., T.C., J.P., E.S.)
- Institute of Organic Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland (M.K., W.D.)
- Institute of Chemistry, University of Natural Sciences and Humanities, 08-110 Siedlce, Poland (K.Z.); and
- Department of Plant Biochemistry, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland (C.P.)
| | - Cezary Pączkowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (A.J., A.L., L.S., A.W., J.W., K.Z., T.C., J.P., E.S.)
- Institute of Organic Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland (M.K., W.D.)
- Institute of Chemistry, University of Natural Sciences and Humanities, 08-110 Siedlce, Poland (K.Z.); and
- Department of Plant Biochemistry, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland (C.P.)
| | - Tadeusz Chojnacki
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (A.J., A.L., L.S., A.W., J.W., K.Z., T.C., J.P., E.S.)
- Institute of Organic Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland (M.K., W.D.)
- Institute of Chemistry, University of Natural Sciences and Humanities, 08-110 Siedlce, Poland (K.Z.); and
- Department of Plant Biochemistry, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland (C.P.)
| | - Jaroslaw Poznanski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (A.J., A.L., L.S., A.W., J.W., K.Z., T.C., J.P., E.S.);
- Institute of Organic Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland (M.K., W.D.);
- Institute of Chemistry, University of Natural Sciences and Humanities, 08-110 Siedlce, Poland (K.Z.); and
- Department of Plant Biochemistry, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland (C.P.)
| | - Ewa Swiezewska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (A.J., A.L., L.S., A.W., J.W., K.Z., T.C., J.P., E.S.);
- Institute of Organic Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland (M.K., W.D.);
- Institute of Chemistry, University of Natural Sciences and Humanities, 08-110 Siedlce, Poland (K.Z.); and
- Department of Plant Biochemistry, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland (C.P.)
| |
Collapse
|