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Ubierna N, Holloway-Phillips MM, Wingate L, Ogée J, Busch FA, Farquhar GD. Using Carbon Stable Isotopes to Study C 3 and C 4 Photosynthesis: Models and Calculations. Methods Mol Biol 2024; 2790:163-211. [PMID: 38649572 DOI: 10.1007/978-1-0716-3790-6_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
Stable carbon isotopes are a powerful tool to study photosynthesis. Initial applications consisted of determining isotope ratios of plant biomass using mass spectrometry. Subsequently, theoretical models relating C isotope values to gas exchange characteristics were introduced and tested against instantaneous online measurements of 13C photosynthetic discrimination. Beginning in the twenty-first century, laser absorption spectroscopes with sufficient precision for determining isotope mixing ratios became commercially available. This has allowed collection of large data sets at lower cost and with unprecedented temporal resolution. More data and accompanying knowledge have permitted refinement of 13C discrimination model equations, but often at the expense of increased model complexity and difficult parametrization. This chapter describes instantaneous online measurements of 13C photosynthetic discrimination, provides recommendations for experimental setup, and presents a thorough compilation of equations available to researchers. We update our previous 2018 version of this chapter by including recently improved descriptions of (photo)respiratory processes and associated fractionations. We discuss the capabilities and limitations of the diverse 13C discrimination model equations and provide guidance for selecting the model complexity needed for different applications.
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Affiliation(s)
- Nerea Ubierna
- Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), Unité Mixte de Recherche (UMR)1391 ISPA, Villenave D'Ornon, France
| | - Meisha-Marika Holloway-Phillips
- Research Unit of Forest Dynamics, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmendsorf, Switzerland
| | - Lisa Wingate
- Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), Unité Mixte de Recherche (UMR)1391 ISPA, Villenave D'Ornon, France
| | - Jérôme Ogée
- Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), Unité Mixte de Recherche (UMR)1391 ISPA, Villenave D'Ornon, France
| | - Florian A Busch
- School of Biosciences and The Birmingham Institute of Forest Research, University of Birmingham, Birmingham, UK
| | - Graham D Farquhar
- Research School of Biology, Australian National University, Canberra, ACT, Australia
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2
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Lloyd MK, Stein RA, Ibarra DE, Barclay RS, Wing SL, Stahle DW, Dawson TE, Stolper DA. Isotopic clumping in wood as a proxy for photorespiration in trees. Proc Natl Acad Sci U S A 2023; 120:e2306736120. [PMID: 37931112 PMCID: PMC10655223 DOI: 10.1073/pnas.2306736120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 09/22/2023] [Indexed: 11/08/2023] Open
Abstract
Photorespiration can limit gross primary productivity in terrestrial plants. The rate of photorespiration relative to carbon fixation increases with temperature and decreases with atmospheric [CO2]. However, the extent to which this rate varies in the environment is unclear. Here, we introduce a proxy for relative photorespiration rate based on the clumped isotopic composition of methoxyl groups (R-O-CH3) in wood. Most methoxyl C-H bonds are formed either during photorespiration or the Calvin cycle and thus their isotopic composition may be sensitive to the mixing ratio of these pathways. In water-replete growing conditions, we find that the abundance of the clumped isotopologue 13CH2D correlates with temperature (18-28 °C) and atmospheric [CO2] (280-1000 ppm), consistent with a common dependence on relative photorespiration rate. When applied to a global dataset of wood, we observe global trends of isotopic clumping with climate and water availability. Clumped isotopic compositions are similar across environments with temperatures below ~18 °C. Above ~18 °C, clumped isotopic compositions in water-limited and water-replete trees increasingly diverge. We propose that trees from hotter climates photorespire substantially more than trees from cooler climates. How increased photorespiration is managed depends on water availability: water-replete trees export more photorespiratory metabolites to lignin whereas water-limited trees either export fewer overall or direct more to other sinks that mitigate water stress. These disparate trends indicate contrasting responses of photorespiration rate (and thus gross primary productivity) to a future high-[CO2] world. This work enables reconstructing photorespiration rates in the geologic past using fossil wood.
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Affiliation(s)
- Max K. Lloyd
- Department of Earth and Planetary Science, University of California, Berkeley, CA94720
- Department of Geosciences, The Pennsylvania State University, University Park, PA16802
| | - Rebekah A. Stein
- Department of Earth and Planetary Science, University of California, Berkeley, CA94720
- Department of Chemistry and Physical Sciences, Quinnipiac University, Hamden, CT06518
| | - Daniel E. Ibarra
- Department of Earth and Planetary Science, University of California, Berkeley, CA94720
- Department of Earth, Environmental, and Planetary Sciences, Brown University, Providence, RI02912
| | - Richard S. Barclay
- Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington, DC20560
| | - Scott L. Wing
- Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington, DC20560
| | - David W. Stahle
- Department of Geosciences, University of Arkansas, Fayetteville, AR72701
| | - Todd E. Dawson
- Department of Integrative Biology, University of California, Berkeley, CA94720
| | - Daniel A. Stolper
- Department of Earth and Planetary Science, University of California, Berkeley, CA94720
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3
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Salomón RL, Rodríguez-Calcerrada J, De Roo L, Miranda JC, Bodé S, Boeckx P, Steppe K. Carbon isotope composition of respired CO2 in woody stems and leafy shoots of three tree species along the growing season: physiological drivers for respiratory fractionation. TREE PHYSIOLOGY 2023; 43:1731-1744. [PMID: 37471648 DOI: 10.1093/treephys/tpad091] [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: 05/30/2023] [Revised: 07/10/2023] [Accepted: 07/17/2023] [Indexed: 07/22/2023]
Abstract
The carbon isotope composition of respired CO2 (δ13CR) and bulk organic matter (δ13CB) of various plant compartments informs about the isotopic fractionation and substrate of respiratory processes, which are crucial to advance the understanding of carbon allocation in plants. Nevertheless, the variation across organs, species and seasons remains poorly understood. Cavity Ring-Down Laser Spectroscopy was applied to measure δ13CR in leafy shoots and woody stems of maple (Acer platanoides L.), oak (Quercus robur L.) and cedar (Thuja occidentalis L.) trees during spring and late summer. Photosynthesis, respiration, growth and non-structural carbohydrates were measured in parallel to evaluate potential drivers for respiratory fractionation. The CO2 respired by maple and oak shoots was 13C-enriched relative to δ13CB during spring, but not late summer or in the stem. In cedar, δ13CR did not vary significantly throughout organs and seasons, with respired CO2 being 13C-depleted relative to δ13CB. Shoot δ13CR was positively related to leaf starch concentration in maple, while stem δ13CR was inversely related to stem growth. These relations were not significant for oak or cedar. The variability in δ13CR suggests (i) different contributions of respiratory pathways between organs and (ii) seasonality in the respiratory substrate and constitutive compounds for wood formation in deciduous species, less apparent in evergreen cedar, whose respiratory metabolism might be less variable.
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Affiliation(s)
- Roberto L Salomón
- Department of Plants and Crops, Faculty of Bioscience Engineering, Laboratory of Plant Ecology, Ghent University, Coupure links 653, Ghent 9000, Belgium
- Departamento de Sistemas y Recursos Naturales, Research Group FORESCENT, Universidad Politécnica de Madrid, Jose Antonio Novais 10, 28040, Madrid, Spain
| | - Jesús Rodríguez-Calcerrada
- Departamento de Sistemas y Recursos Naturales, Research Group FORESCENT, Universidad Politécnica de Madrid, Jose Antonio Novais 10, 28040, Madrid, Spain
| | - Linus De Roo
- Department of Plants and Crops, Faculty of Bioscience Engineering, Laboratory of Plant Ecology, Ghent University, Coupure links 653, Ghent 9000, Belgium
| | - José Carlos Miranda
- Departamento de Sistemas y Recursos Naturales, Research Group FORESCENT, Universidad Politécnica de Madrid, Jose Antonio Novais 10, 28040, Madrid, Spain
| | - Samuel Bodé
- Department of Green Chemistry and Technology, Faculty of Bioscience Engineering, Isotope Bioscience Laboratory - ISOFYS, Ghent University, Coupure links 653, Gent 9000, Belgium
| | - Pascal Boeckx
- Department of Green Chemistry and Technology, Faculty of Bioscience Engineering, Isotope Bioscience Laboratory - ISOFYS, Ghent University, Coupure links 653, Gent 9000, Belgium
| | - Kathy Steppe
- Department of Plants and Crops, Faculty of Bioscience Engineering, Laboratory of Plant Ecology, Ghent University, Coupure links 653, Ghent 9000, Belgium
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4
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Fry B, Carter JF, O'Mara K. Fingerprinting eukaryotic metabolism across the animal kingdom using position-specific isotope analysis (PSIA) 13C/ 12C measurements. SCIENCE ADVANCES 2023; 9:eadg1549. [PMID: 37406114 DOI: 10.1126/sciadv.adg1549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 06/01/2023] [Indexed: 07/07/2023]
Abstract
Despite differences in their overall metabolism, eukaryotes share a common mitochondrial biochemistry. We investigated how this fundamental biochemistry supports overall metabolism using a high-resolution carbon isotope approach, position-specific isotope analysis. We measured carbon isotope 13C/12C cycling in animals, focusing on amino acids that are formed in mitochondrial reactions and are most metabolically active. Carboxyl isotope determinations for amino acids showed strong signals related to common biochemical pathways. Contrasting isotope patterns were measured for metabolism associated with major life history patterns, including growth and reproduction. Turnover of proteins and lipids as well as gluoconeogensis dynamics could be estimated for these metabolic life histories. The high-resolution isotomics measurements fingerprinted metabolism and metabolic strategies across the eukaryotic animal kingdom, yielding results for humans, ungulates, whales, and diverse fish and invertebrates in a nearshore marine food web.
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Affiliation(s)
- Brian Fry
- Australian Rivers Institute, Griffith University, Nathan, Queensland 4111, Australia
| | - James F Carter
- Queensland Health, Forensic and Scientific Services, Coopers Plains, Queensland 4108, Australia
| | - Kaitlyn O'Mara
- Australian Rivers Institute, Griffith University, Nathan, Queensland 4111, Australia
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5
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Trevisan F, Tiziani R, Hall RD, Cesco S, Mimmo T. δ 13C as a tool for iron and phosphorus deficiency prediction in crops. PLANT DIRECT 2023; 7:e487. [PMID: 36950260 PMCID: PMC10027435 DOI: 10.1002/pld3.487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 01/27/2023] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
Many studies proposed the use of stable carbon isotope ratio (δ13C) as a predictor of abiotic stresses in plants, considering only drought and nitrogen deficiency without further investigating the impact of other nutrient deficiencies, that is, phosphorus (P) and/or iron (Fe) deficiencies. To fill this knowledge gap, we assessed the δ13C of barley (Hordeum vulgare L.), cucumber (Cucumis sativus L.), maize (Zea mays L.), and tomato (Solanum lycopersicon L.) plants suffering from P, Fe, and combined P/Fe deficiencies during a two-week period using an isotope-ratio mass spectrometer. Simultaneously, plant physiological status was monitored with an infra-red gas analyzer. Results show clear contrasting time-, treatment-, species-, and tissue-specific variations. Furthermore, physiological parameters showed limited correlation with δ13C shifts, highlighting that the plants' δ13C, does not depend solely on photosynthetic carbon isotope fractionation/discrimination (Δ). Hence, the use of δ13C as a predictor is highly discouraged due to its inability to detect and discern different nutrient stresses, especially when combined stresses are present.
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Affiliation(s)
- Fabio Trevisan
- Faculty of Science and TechnologyFree University of BolzanoBolzanoItaly
| | - Raphael Tiziani
- Faculty of Science and TechnologyFree University of BolzanoBolzanoItaly
| | - Robert D. Hall
- Laboratory of Plant PhysiologyWageningen University & ResearchWageningenThe Netherlands
- Business Unit BioscienceWageningen University & ResearchWageningenThe Netherlands
| | - Stefano Cesco
- Faculty of Science and TechnologyFree University of BolzanoBolzanoItaly
| | - Tanja Mimmo
- Faculty of Science and TechnologyFree University of BolzanoBolzanoItaly
- Competence Centre of Plant HealthFree University of Bozen‐BolzanoBolzanoItaly
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6
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Carbon dioxide isotopic compositions during tundra ecosystem respiration and photosynthesis in relation to environmental variables in maritime Antarctica. Polar Biol 2021. [DOI: 10.1007/s00300-021-02829-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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7
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Iron MA, Gropp J. Cost-effective density functional theory (DFT) calculations of equilibrium isotopic fractionation in large organic molecules. Phys Chem Chem Phys 2019; 21:17555-17570. [PMID: 31342034 DOI: 10.1039/c9cp02975c] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The application of stable isotopes to address a wide range of biochemical, microbiological and environmental problems is hindered by the experimental difficulty and the computational cost of determining equilibrium isotopic fractionations (EIF) of large organic molecules. Here, we evaluate the factors that impact the accuracy of computed EIFs and develop a framework for cost-effective and accurate computation of EIFs by density functional theory (DFT). We generated two benchmark databases of experimentally determined EIFs, one for H isotopes and another for the isotopes of the heavy atoms C, N and O. The accuracy of several DFT exchange-correlation functionals in calculating EIFs was then evaluated by comparing the computational results to these experimental datasets. We find that with the def2-TZVP basis set, O3LYP had the lowest mean absolute deviation (21‰ and 3.9‰ for the isotopic fractionation of H and the heavier atoms, respectively), but the GGA/meta-GGA functionals τHCTHD3BJ, τHCTH and HCTH have similar performances (22‰ and 4.1‰, respectively, for τHCTHD3BJ). Leveraging the good performance of computationally efficient functionals, we provide a robust, practical, experimentally validated framework for using DFT to accurately predict EIFs of large organic molecules, including uncertainty estimates.
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Affiliation(s)
- Mark A Iron
- Computational Chemistry Unit, Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, 7610001, Israel.
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8
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Sonawane BV, Cousins AB. Uncertainties and limitations of using carbon-13 and oxygen-18 leaf isotope exchange to estimate the temperature response of mesophyll CO 2 conductance in C 3 plants. THE NEW PHYTOLOGIST 2019; 222:122-131. [PMID: 30394538 DOI: 10.1111/nph.15585] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 10/28/2018] [Indexed: 06/08/2023]
Abstract
The internal CO2 gradient imposed by mesophyll conductance (gm ) reduces substrate availability for C3 photosynthesis. With several assumptions, estimates of gm can be made from coupled leaf gas exchange with isoflux analysis of carbon ∆13 C-gm and oxygen in CO2 , coupled with transpired water (H2 O) ∆18 O-gm to partition gm into its biochemical and anatomical components. However, these assumptions require validation under changing leaf temperatures. To test these assumptions, we measured and modeled the temperature response (15-40°C) of ∆13 C-gm and ∆18 O-gm along with leaf biochemistry in the C3 grass Panicum bisulcatum, which has naturally low carbonic anhydrase activity. Our study suggests that assumptions regarding the extent of isotopic equilibrium (θ) between CO2 and H2 O at the site of exchange, and that the isotopic composition of the H2 O at the sites of evaporation ( δw-e18 ) and at the site of exchange ( δw-ce18 ) are similar, may lead to errors in estimating the ∆18 O-gm temperature response. The input parameters for ∆13 C-gm appear to be less sensitive to temperature. However, this needs to be tested in species with diverse carbonic anhydrase activity. Additional information on the temperature dependency of cytosolic and chloroplastic pH may clarify uncertainties used for ∆18 O-gm under changing leaf temperatures.
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Affiliation(s)
- Balasaheb V Sonawane
- School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Asaph B Cousins
- School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA
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9
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Smith MR, Merchant A. Limitations to using phloem sap to assess tree water and nutrient status. TREE PHYSIOLOGY 2019; 39:332-339. [PMID: 30551158 DOI: 10.1093/treephys/tpy132] [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: 05/31/2018] [Revised: 11/05/2018] [Accepted: 11/09/2018] [Indexed: 06/09/2023]
Abstract
Rapid, reliable tools are needed to infer physiological and nutritional health for managing forest systems. Understanding the processes governing tree health is central to the development of these tools. Non-foliar approaches such as the collection of phloem sap reflect processes governing both the use and acquisition of plant water and nutrients at a wide range of temporal (diurnal to seasonal) and spatial (canopy) scales. Despite this, phloem sap is not commonly employed due to an incomplete understanding of transport and post-photosynthetic processes and their effects on chemical concentrations and carbon isotope discrimination. We highlight the need to characterize the influences of storage, remobilization and transport on the concentrations of metabolites to address the time and spatial decoupling of phloem contents to that of environmental stimuli. A conceptual framework is suggested to focus research on key phenomena regarding metabolite transport and highlight significant advantages, misconceptions and limitations to its application.
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Affiliation(s)
- Millicent R Smith
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney NSW, Australia
| | - A Merchant
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney NSW, Australia
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10
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Ubierna N, Holloway-Phillips MM, Farquhar GD. Using Stable Carbon Isotopes to Study C 3 and C 4 Photosynthesis: Models and Calculations. Methods Mol Biol 2018; 1770:155-196. [PMID: 29978402 DOI: 10.1007/978-1-4939-7786-4_10] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Stable carbon isotopes are a powerful tool to study photosynthesis. Initial applications consisted of determining isotope ratios of plant biomass using mass spectrometry. Subsequently, theoretical models relating C-isotope values to gas exchange characteristics were introduced and tested against instantaneous online measurements of 13C photosynthetic discrimination. Beginning in the twenty-first century, tunable diode laser spectroscopes with sufficient precision for determining isotope mixing ratios became commercially available. This has allowed collection of large data sets, at low cost and with unprecedented temporal resolution. With more data and accompanying knowledge, it has become apparent that there is a need for increased complexity in models and calculations. This chapter describes instantaneous online measurements of 13C photosynthetic discrimination, provides recommendations for experimental setup, and presents a thorough compilation of equations needed for different applications.
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Affiliation(s)
- Nerea Ubierna
- School of Biological Sciences, Molecular Plant Sciences, Washington State University, Pullman, WA, USA.
| | | | - Graham D Farquhar
- Research School of Biology, Australian National University, Canberra, ACT, Australia
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11
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Zhong S, Chai H, Xu Y, Li Y, Ma JY, Sun W. Drought Sensitivity of the Carbon Isotope Composition of Leaf Dark-Respired CO 2 in C 3 ( Leymus chinensis) and C 4 ( Chloris virgata and Hemarthria altissima) Grasses in Northeast China. FRONTIERS IN PLANT SCIENCE 2017; 8:1996. [PMID: 29375587 PMCID: PMC5770615 DOI: 10.3389/fpls.2017.01996] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 11/07/2017] [Indexed: 05/13/2023]
Abstract
Whether photosynthetic pathway differences exist in the amplitude of nighttime variations in the carbon isotope composition of leaf dark-respired CO2 (δ13Cl) and respiratory apparent isotope fractionation relative to biomass (ΔR,biomass) in response to drought stress is unclear. These differences, if present, would be important for the partitioning of C3-C4 mixed ecosystem C fluxes. We measured δ13Cl, the δ13C of biomass and of potential respiratory substrates and leaf gas exchange in one C3 (Leymus chinensis) and two C4 (Chloris virgata and Hemarthria altissima) grasses during a manipulated drought period. For all studied grasses, δ13Cl decreased from 21:00 to 03:00 h. The magnitude of the nighttime shift in δ13Cl decreased with increasing drought stress. The δ13Cl values were correlated with the δ13C of respiratory substrates, whereas the magnitude of the nighttime shift in δ13Cl strongly depended on the daytime carbon assimilation rate and the range of nighttime variations in the respiratory substrate content. The ΔR,biomass in the C3 and C4 grasses varied in opposite directions with the intensification of the drought stress. The contribution of C4 plant-associated carbon flux is likely to be overestimated if carbon isotope signatures are used for the partitioning of ecosystem carbon exchange and the δ13C of biomass is used as a substitute for leaf dark-respired CO2. The detected drought sensitivities in δ13Cl and differences in respiratory apparent isotope fractionation between C3 and C4 grasses have marked implications for isotope partitioning studies at the ecosystem level.
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Affiliation(s)
- Shangzhi Zhong
- Key Laboratory of Vegetation Ecology, Ministry of Education, Institute of Grassland Science, Northeast Normal University, Changchun, China
| | - Hua Chai
- Key Laboratory of Vegetation Ecology, Ministry of Education, Institute of Grassland Science, Northeast Normal University, Changchun, China
| | - Yueqiao Xu
- Key Laboratory of Vegetation Ecology, Ministry of Education, Institute of Grassland Science, Northeast Normal University, Changchun, China
| | - Yan Li
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Jian-Ying Ma
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Wei Sun
- Key Laboratory of Vegetation Ecology, Ministry of Education, Institute of Grassland Science, Northeast Normal University, Changchun, China
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12
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Ellsworth PZ, Ellsworth PV, Cousins AB. Relationship of leaf oxygen and carbon isotopic composition with transpiration efficiency in the C4 grasses Setaria viridis and Setaria italica. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:3513-3528. [PMID: 28859378 PMCID: PMC5853516 DOI: 10.1093/jxb/erx185] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 05/26/2017] [Indexed: 05/20/2023]
Abstract
Leaf carbon and oxygen isotope ratios can potentially provide a time-integrated proxy for stomatal conductance (gs) and transpiration rate (E), and can be used to estimate transpiration efficiency (TE). In this study, we found significant relationships of bulk leaf carbon isotopic signature (δ13CBL) and bulk leaf oxygen enrichment above source water (Δ18OBL) with gas exchange and TE in the model C4 grasses Setaria viridis and S. italica. Leaf δ13C had strong relationships with E, gs, water use, biomass, and TE. Additionally, the consistent difference in δ13CBL between well-watered and water-limited plants suggests that δ13CBL is effective in separating C4 plants with different availability of water. Alternatively, the use of Δ18OBL as a proxy for E and TE in S. viridis and S. italica was problematic. First, the oxygen isotopic composition of source water, used to calculate leaf water enrichment (Δ18OLW), was variable with time and differed across water treatments. Second, water limitations changed leaf size and masked the relationship of Δ18OLW and Δ18OBL with E. Therefore, the data collected here suggest that δ13CBL but not Δ18OBL may be an effective proxy for TE in C4 grasses.
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Affiliation(s)
- Patrick Z Ellsworth
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | | | - Asaph B Cousins
- School of Biological Sciences, Washington State University, Pullman, WA, USA
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13
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Tcherkez G. The mechanism of Rubisco-catalysed oxygenation. PLANT, CELL & ENVIRONMENT 2016; 39:983-997. [PMID: 26286702 DOI: 10.1111/pce.12629] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 07/28/2015] [Accepted: 08/09/2015] [Indexed: 06/04/2023]
Abstract
Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) is the cornerstone of photosynthetic carbon assimilation because it catalyses the fixation of CO2 onto ribulose-1,5-bisphosphate (RuBP). The enzyme also catalyses RuBP oxygenation, thereby evolving phosphoglycolate which is recycled along the photorespiratory pathway. Oxygenation is quantitatively important, because under ordinary gaseous conditions, more than one third of RuBP molecules are oxygenated rather than carboxylated. However, contrary to carboxylation, the chemical mechanism of oxygenation is not well known, and little progress has been made since the early 80s. Here, I review recent experimental data that provide some new insights into the reaction mechanism, and carry out simple calculations of kinetic parameters. Isotope effects suggest that oxygenation is less likely initiated by a redox phenomenon (such as superoxide production) and more likely involves concerted chemical events that imply interactions with protons. A possible energy profile of the reaction is drawn which suggests that the generation of the oxygenated reaction intermediate (peroxide) is irreversible. Possible changes in oxygenation-associated rate constants between Rubisco forms are discussed.
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Affiliation(s)
- Guillaume Tcherkez
- Research School of Biology, ANU College of Medicine, Biology and Environment, Australian National University, Canberra, 2601, ACT, Australia
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14
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Romek KM, Nun P, Remaud GS, Silvestre V, Taïwe GS, Lecerf-Schmidt F, Boumendjel A, De Waard M, Robins RJ. A retro-biosynthetic approach to the prediction of biosynthetic pathways from position-specific isotope analysis as shown for tramadol. Proc Natl Acad Sci U S A 2015; 112:8296-301. [PMID: 26106160 PMCID: PMC4500278 DOI: 10.1073/pnas.1506011112] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Tramadol, previously only known as a synthetic analgesic, has now been found in the bark and wood of roots of the African medicinal tree Nauclea latifolia. At present, no direct evidence is available as to the biosynthetic pathway of its unusual skeleton. To provide guidance as to possible biosynthetic precursors, we have adopted a novel approach of retro-biosynthesis based on the position-specific distribution of isotopes in the extracted compound. Relatively recent developments in isotope ratio monitoring by (13)C NMR spectrometry make possible the measurement of the nonstatistical position-specific natural abundance distribution of (13)C (δ(13)Ci) within the molecule with better than 1‰ precision. Very substantial variation in the (13)C positional distribution is found: between δ(13)Ci = -11 and -53‰. Distribution is not random and it is argued that the pattern observed can substantially be interpreted in relation to known causes of isotope fractionation in natural products. Thus, a plausible biosynthetic scheme based on sound biosynthetic principals of precursor-substrate relationships can be proposed. In addition, data obtained from the (18)O/(16)O ratios in the oxygen atoms of the compound add support to the deductions made from the carbon isotope analysis. This paper shows how the use of (13)C NMR at natural abundance can help with proposing a biosynthetic route to compounds newly found in nature or those difficult to tackle by conventional means.
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Affiliation(s)
- Katarzyna M Romek
- Elucidation of Biosynthesis by Isotopic Spectrometry Group, Interdisciplinary Chemistry: Synthesis, Analysis, Modeling, CNRS-University of Nantes Unité Mixte de Recherche 6230, F-44322 Nantes, France; Laboratory for Isotope Effects Studies, Department of Chemistry, Institute of Applied Radiation Chemistry, Lodz University of Technology, 90-924 Lodz, Poland
| | - Pierrick Nun
- Elucidation of Biosynthesis by Isotopic Spectrometry Group, Interdisciplinary Chemistry: Synthesis, Analysis, Modeling, CNRS-University of Nantes Unité Mixte de Recherche 6230, F-44322 Nantes, France
| | - Gérald S Remaud
- Elucidation of Biosynthesis by Isotopic Spectrometry Group, Interdisciplinary Chemistry: Synthesis, Analysis, Modeling, CNRS-University of Nantes Unité Mixte de Recherche 6230, F-44322 Nantes, France
| | - Virginie Silvestre
- Elucidation of Biosynthesis by Isotopic Spectrometry Group, Interdisciplinary Chemistry: Synthesis, Analysis, Modeling, CNRS-University of Nantes Unité Mixte de Recherche 6230, F-44322 Nantes, France
| | | | - Florine Lecerf-Schmidt
- Department of Medicinal Chemistry, University Grenoble Alpes-CNRS Unité Mixte de Recherche 5063, F-38041 Grenoble, France
| | - Ahcène Boumendjel
- Department of Medicinal Chemistry, University Grenoble Alpes-CNRS Unité Mixte de Recherche 5063, F-38041 Grenoble, France
| | - Michel De Waard
- Grenoble Institute of Neuroscience, Unit Inserm U836, F-38700 La Tronche, France; University Joseph Fourier, F-38041 Grenoble, France
| | - Richard J Robins
- Elucidation of Biosynthesis by Isotopic Spectrometry Group, Interdisciplinary Chemistry: Synthesis, Analysis, Modeling, CNRS-University of Nantes Unité Mixte de Recherche 6230, F-44322 Nantes, France;
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15
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Diomande DG, Martineau E, Gilbert A, Nun P, Murata A, Yamada K, Watanabe N, Tea I, Robins RJ, Yoshida N, Remaud GS. Position-Specific Isotope Analysis of Xanthines: A 13C Nuclear Magnetic Resonance Method to Determine the 13C Intramolecular Composition at Natural Abundance. Anal Chem 2015; 87:6600-6. [DOI: 10.1021/acs.analchem.5b00559] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Didier G. Diomande
- EBSI
team, Interdisciplinary Chemistry: Synthesis, Analysis, Modelling
(CEISAM), University of Nantes, CNRS UMR 6230, 2 rue de la Houssinière, BP 92208, F-44322 cedex 3 Nantes, France
| | - Estelle Martineau
- EBSI
team, Interdisciplinary Chemistry: Synthesis, Analysis, Modelling
(CEISAM), University of Nantes, CNRS UMR 6230, 2 rue de la Houssinière, BP 92208, F-44322 cedex 3 Nantes, France
- Spectromaitrise, CAPACITÉS SAS, 26 boulevard Vincent Gâche, 44200 Nantes, France
| | - Alexis Gilbert
- Earth-Life
Science Institute, Tokyo Institute of Technology, Meguro, Tokyo 152-8551, Japan
| | - Pierrick Nun
- EBSI
team, Interdisciplinary Chemistry: Synthesis, Analysis, Modelling
(CEISAM), University of Nantes, CNRS UMR 6230, 2 rue de la Houssinière, BP 92208, F-44322 cedex 3 Nantes, France
| | - Ariaki Murata
- Institute
of Food Chemistry, Braunschweig University of Technology, Schleinitzstrasse
20, DE-38106 Braunschweig, Germany
| | - Keita Yamada
- Department
of Environmental Chemistry and Engineering, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8503, Japan
| | - Naoharu Watanabe
- Graduate
School of Engineering, Shizuoka University, 3-5-1 Johoku, Naka-ku, Hamamatsu 432-8561, Japan
| | - Illa Tea
- EBSI
team, Interdisciplinary Chemistry: Synthesis, Analysis, Modelling
(CEISAM), University of Nantes, CNRS UMR 6230, 2 rue de la Houssinière, BP 92208, F-44322 cedex 3 Nantes, France
| | - Richard J. Robins
- EBSI
team, Interdisciplinary Chemistry: Synthesis, Analysis, Modelling
(CEISAM), University of Nantes, CNRS UMR 6230, 2 rue de la Houssinière, BP 92208, F-44322 cedex 3 Nantes, France
| | - Naohiro Yoshida
- Earth-Life
Science Institute, Tokyo Institute of Technology, Meguro, Tokyo 152-8551, Japan
- Department
of Environmental Chemistry and Engineering, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8503, Japan
| | - Gérald S. Remaud
- EBSI
team, Interdisciplinary Chemistry: Synthesis, Analysis, Modelling
(CEISAM), University of Nantes, CNRS UMR 6230, 2 rue de la Houssinière, BP 92208, F-44322 cedex 3 Nantes, France
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16
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Bayle K, Akoka S, Remaud GS, Robins RJ. Nonstatistical 13C distribution during carbon transfer from glucose to ethanol during fermentation is determined by the catabolic pathway exploited. J Biol Chem 2015; 290:4118-28. [PMID: 25538251 PMCID: PMC4326821 DOI: 10.1074/jbc.m114.621441] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Revised: 12/22/2014] [Indexed: 11/06/2022] Open
Abstract
During the anaerobic fermentation of glucose to ethanol, the three micro-organisms Saccharomyces cerevisiae, Zymomonas mobilis, and Leuconostoc mesenteroides exploit, respectively, the Embden-Meyerhof-Parnas, the Entner-Doudoroff, and the reductive pentose phosphate pathways. Thus, the atoms incorporated into ethanol do not have the same affiliation to the atomic positions in glucose. The isotopic fractionation occurring in each pathway at both the methylene and methyl positions of ethanol has been investigated by isotopic quantitative (13)C NMR spectrometry with the aim of observing whether an isotope redistribution characteristic of the enzymes active in each pathway can be measured. First, it is found that each pathway has a unique isotope redistribution signature. Second, for the methylene group, a significant apparent kinetic isotope effect is only found in the reductive pentose phosphate pathway. Third, the apparent kinetic isotope effects related to the methyl group are more pronounced than for the methylene group. These findings can (i) be related to known kinetic isotope effects of some of the enzymes concerned and (ii) give indicators as to which steps in the pathways are likely to be influencing the final isotopic composition in the ethanol.
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Affiliation(s)
- Kevin Bayle
- From the Elucidation of Biosynthesis by Isotopic Spectrometry Group, CEISAM, UMR 6230, CNRS-University of Nantes, BP 99208, F-44322 Nantes, France
| | - Serge Akoka
- From the Elucidation of Biosynthesis by Isotopic Spectrometry Group, CEISAM, UMR 6230, CNRS-University of Nantes, BP 99208, F-44322 Nantes, France
| | - Gérald S Remaud
- From the Elucidation of Biosynthesis by Isotopic Spectrometry Group, CEISAM, UMR 6230, CNRS-University of Nantes, BP 99208, F-44322 Nantes, France
| | - Richard J Robins
- From the Elucidation of Biosynthesis by Isotopic Spectrometry Group, CEISAM, UMR 6230, CNRS-University of Nantes, BP 99208, F-44322 Nantes, France
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17
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Durão P, Aigner H, Nagy P, Mueller-Cajar O, Hartl FU, Hayer-Hartl M. Opposing effects of folding and assembly chaperones on evolvability of Rubisco. Nat Chem Biol 2015; 11:148-55. [PMID: 25558973 DOI: 10.1038/nchembio.1715] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 10/27/2014] [Indexed: 12/29/2022]
Abstract
Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) catalyzes the fixation of CO2 in photosynthesis. Despite its pivotal role, Rubisco is an inefficient enzyme and thus is a key target for directed evolution. Rubisco biogenesis depends on auxiliary factors, including the GroEL/ES-type chaperonin for folding and the chaperone RbcX for assembly. Here we performed directed evolution of cyanobacterial form I Rubisco using a Rubisco-dependent Escherichia coli strain. Overexpression of GroEL/ES enhanced Rubisco solubility and tended to expand the range of permissible mutations. In contrast, the specific assembly chaperone RbcX had a negative effect on evolvability by preventing a subset of mutants from forming holoenzyme. Mutation F140I in the large Rubisco subunit, isolated in the absence of RbcX, increased carboxylation efficiency approximately threefold without reducing CO2 specificity. The F140I mutant resulted in a ∼55% improved photosynthesis rate in Synechocystis PCC6803. The requirement of specific biogenesis factors downstream of chaperonin may have retarded the natural evolution of Rubisco.
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Affiliation(s)
- Paulo Durão
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Harald Aigner
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Péter Nagy
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Oliver Mueller-Cajar
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - F Ulrich Hartl
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Manajit Hayer-Hartl
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany
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18
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Schmidt HL, Robins RJ, Werner RA. Multi-factorial in vivo stable isotope fractionation: causes, correlations, consequences and applications. ISOTOPES IN ENVIRONMENTAL AND HEALTH STUDIES 2015; 51:155-199. [PMID: 25894429 DOI: 10.1080/10256016.2015.1014355] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Many physical and chemical processes in living systems are accompanied by isotope fractionation on H, C, N, O and S. Although kinetic or thermodynamic isotope effects are always the basis, their in vivo manifestation is often modulated by secondary influences. These include metabolic branching events or metabolite channeling, metabolite pool sizes, reaction mechanisms, anatomical properties and compartmentation of plants and animals, and climatological or environmental conditions. In the present contribution, the fundamentals of isotope effects and their manifestation under in vivo conditions are outlined. The knowledge about and the understanding of these interferences provide a potent tool for the reconstruction of physiological events in plants and animals, their geographical origin, the history of bulk biomass and the biosynthesis of defined representatives. It allows the use of isotope characteristics of biomass for the elucidation of biochemical pathways and reaction mechanisms and for the reconstruction of climatic, physiological, ecological and environmental conditions during biosynthesis. Thus, it can be used for the origin and authenticity control of food, the study of ecosystems and animal physiology, the reconstruction of present and prehistoric nutrition chains and paleaoclimatological conditions. This is demonstrated by the outline of fundamental and application-orientated examples for all bio-elements. The aim of the review is to inform (advanced) students from various disciplines about the whole potential and the scope of stable isotope characteristics and fractionations and to provide them with a comprehensive introduction to the literature on fundamental aspects and applications.
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Affiliation(s)
- Hanns-Ludwig Schmidt
- a Lehrstuhl für Biologische Chemie , Technische Universität München , Freising-Weihenstephan, Germany
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19
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von Caemmerer S, Ghannoum O, Pengelly JJL, Cousins AB. Carbon isotope discrimination as a tool to explore C4 photosynthesis. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:3459-70. [PMID: 24711615 DOI: 10.1093/jxb/eru127] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Photosynthetic carbon isotope discrimination is a non-destructive tool for investigating C4 metabolism. Tuneable diode laser absorption spectroscopy provides new opportunities for making rapid, concurrent measurements of carbon isotope discrimination and CO2 assimilation over a range of environmental conditions, and this has facilitated the use of carbon isotope discrimination as a probe of C4 metabolism. In spite of the significant progress made in recent years, understanding how photosynthetic carbon isotope discrimination measured concurrently with gas exchange relates to carbon isotope composition of leaf and plant dry matter remains a challenge that requires resolution if this technique is to be successfully applied as a screening tool in crop breeding and phylogenetic research. In this review, we update our understanding of the factors and assumptions that underlie variations in photosynthetic carbon isotope discrimination in C4 leaves. Closing the main gaps in our understanding of carbon isotope discrimination during C4 photosynthesis may help advance research aimed at developing higher productivity and efficiency in key C4 food, feed, and biofuel crops.
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Affiliation(s)
- Susanne von Caemmerer
- Research School of Biology, The Australian National University, Canberra ACT 0200, Australia
| | - Oula Ghannoum
- Hawkesbury Institute for the Environment, University of Western Sydney, Hawkesbury campus, Locked Bag 1797, Penrith 2751, NSW, Australia
| | - Jasper J L Pengelly
- Research School of Biology, The Australian National University, Canberra ACT 0200, Australia
| | - Asaph B Cousins
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
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20
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Ghashghaie J, Badeck FW. Opposite carbon isotope discrimination during dark respiration in leaves versus roots - a review. THE NEW PHYTOLOGIST 2014; 201:751-769. [PMID: 24251924 DOI: 10.1111/nph.12563] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2013] [Accepted: 09/15/2013] [Indexed: 05/13/2023]
Abstract
In general, leaves are (13) C-depleted compared with all other organs (e.g. roots, stem/trunk and fruits). Different hypotheses are formulated in the literature to explain this difference. One of these states that CO2 respired by leaves in the dark is (13) C-enriched compared with leaf organic matter, while it is (13) C-depleted in the case of root respiration. The opposite respiratory fractionation between leaves and roots was invoked as an explanation for the widespread between-organ isotopic differences. After summarizing the basics of photosynthetic and post-photosynthetic discrimination, we mainly review the recent findings on the isotopic composition of CO2 respired by leaves (autotrophic organs) and roots (heterotrophic organs) compared with respective plant material (i.e. apparent respiratory fractionation) as well as its metabolic origin. The potential impact of such fractionation on the isotopic signal of organic matter (OM) is discussed. Some perspectives for future studies are also proposed .
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Affiliation(s)
- Jaleh Ghashghaie
- Laboratoire d'Ecologie, Systématique et Evolution (ESE), CNRS UMR8079, Bâtiment 362, Université de Paris-Sud (XI), F-91405, Orsay Cedex, France
| | - Franz W Badeck
- Consiglio per la Ricerca e la sperimentazione in Agricoltura, Genomics research centre (CRA - GPG), Via San Protaso, 302, 29017, Fiorenzuola d'Arda (PC), Italy
- Potsdam Institute for Climate Impact Research (PIK), PF 60 12 03, 14412, Potsdam, Germany
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21
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Tcherkez G. Modelling the reaction mechanism of ribulose-1,5-bisphosphate carboxylase/oxygenase and consequences for kinetic parameters. PLANT, CELL & ENVIRONMENT 2013; 36:1586-96. [PMID: 23305122 DOI: 10.1111/pce.12066] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Revised: 12/12/2012] [Accepted: 12/26/2012] [Indexed: 05/20/2023]
Abstract
Although ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) was discovered nearly 60 years ago, the associated chemical mechanism of the reaction is still incompletely understood. The catalytic cycle consists of four major steps: ribulose-1,5-bisphosphate binding, enolization, CO₂ or O₂ addition and hydration, and cleavage of the intermediate. The use of individual rate constants for these elemental steps yields mathematical expressions for usual kinetic constants (k(cat), K(m)), CO₂ versus O₂ specificity (S(c/o)) as well as other chemical parameters such as the ¹²C/¹³C isotope effect. That said, most of them are not simple and thus the interpretation of experimental and observed values of kcat , Km and Sc/o may be more complicated than expected. That is, Rubisco effective catalysis depends on several kinetic parameters that are influenced by both the biological origin and the cellular medium (which, in turn, can vary with environmental conditions). In this brief review, we present the basic model of Rubisco kinetics and describe how subtle biochemical changes (which may have occurred along Evolution) can easily modify Rubisco catalysis.
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Affiliation(s)
- Guillaume Tcherkez
- Institut de Biologie des Plantes, CNRS UMR 8618, Université Paris-Sud, 91405 Orsay Cedex, France.
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22
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Evans JR, von Caemmerer S. Temperature response of carbon isotope discrimination and mesophyll conductance in tobacco. PLANT, CELL & ENVIRONMENT 2013; 36:745-56. [PMID: 22882584 DOI: 10.1111/j.1365-3040.2012.02591.x] [Citation(s) in RCA: 152] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The partial pressure of CO2 at the sites of carboxylation within chloroplasts depends on the conductance to CO2 diffusion from intercellular airspace to the sites of carboxylation, termed mesophyll conductance (gm ). We investigated the temperature response of gm in tobacco (Nicotiana tabacum) by combining gas exchange in high light, ambient CO2 in either 2 or 21% O2 with carbon isotope measurements using tuneable diode laser spectroscopy. The gm increased linearly with temperature in 2 or 21% O2 . In 21% O2 , isotope discrimination associated with gm decreased from 5.0 ± 0.2 to 1.8 ± 0.2‰ as temperature increased from 15 to 40 °C, but the photorespiratory contribution to the isotopic signal is significant. While the fractionation factor for photorespiration (f = 16.2 ± 0.7‰) was independent of temperature between 20 and 35 °C, discrimination associated with photorespiration increased from 1.1 ± 0.01 to 2.7 ± 0.02‰ from 15 to 40 °C. Other mitochondrial respiration contributed around 0.2 ± 0.03‰. The drawdown in CO2 partial pressure from ambient air to intercellular airspaces was nearly independent of leaf temperature. By contrast, the increase in gm with increasing leaf temperature resulted in the drawdown in CO2 partial pressure between intercellular airspaces and the sites of carboxylation decreasing substantially at high temperature.
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Affiliation(s)
- John R Evans
- Plant Science Division, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory 0200, Australia.
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23
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Tcherkez GGB, Bathellier C, Stuart-Williams H, Whitney S, Gout E, Bligny R, Badger M, Farquhar GD. D2O Solvent Isotope Effects Suggest Uniform Energy Barriers in Ribulose-1,5-bisphosphate Carboxylase/Oxygenase Catalysis. Biochemistry 2013; 52:869-77. [DOI: 10.1021/bi300933u] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Guillaume G. B. Tcherkez
- Institut de Biologie des Plantes,
CNRS UMR 8618, Université Paris-Sud 11, 91405 Orsay cedex, France
- Institut Universitaire de France, 103 boulevard Saint-Michel, 75005 Paris,
France
| | - Camille Bathellier
- Institut de Biologie des Plantes,
CNRS UMR 8618, Université Paris-Sud 11, 91405 Orsay cedex, France
- Research School of
Biology, Australian National University, Canberra ACT 0200,
Australia
| | - Hilary Stuart-Williams
- Research School of
Biology, Australian National University, Canberra ACT 0200,
Australia
| | - Spencer Whitney
- Research School of
Biology, Australian National University, Canberra ACT 0200,
Australia
| | - Elisabeth Gout
- Laboratoire de
Physiologie Cellulaire
Végétale, CEA-Grenoble, 17
rue des Martyrs, 38009 Grenoble cedex, France
| | - Richard Bligny
- Laboratoire de
Physiologie Cellulaire
Végétale, CEA-Grenoble, 17
rue des Martyrs, 38009 Grenoble cedex, France
| | - Murray Badger
- Research School of
Biology, Australian National University, Canberra ACT 0200,
Australia
| | - Graham D. Farquhar
- Research School of
Biology, Australian National University, Canberra ACT 0200,
Australia
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24
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Sarma R, Angeles-Boza AM, Brinkley DW, Roth JP. Studies of the Di-iron(VI) Intermediate in Ferrate-Dependent Oxygen Evolution from Water. J Am Chem Soc 2012; 134:15371-86. [DOI: 10.1021/ja304786s] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Rupam Sarma
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland
21218, United States
| | - Alfredo M. Angeles-Boza
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland
21218, United States
| | - David W. Brinkley
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland
21218, United States
| | - Justine P. Roth
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland
21218, United States
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25
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Sun W, Resco V, Williams DG. Environmental and physiological controls on the carbon isotope composition of CO2 respired by leaves and roots of a C3 woody legume (Prosopis velutina) and a C4 perennial grass (Sporobolus wrightii). PLANT, CELL & ENVIRONMENT 2012; 35:567-577. [PMID: 21955347 DOI: 10.1111/j.1365-3040.2011.02436.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Accurate estimates of the δ(13) C value of CO(2) respired from roots (δ(13) C(R_root) ) and leaves (δ(13) C(R_leaf) ) are important for tracing and understanding changes in C fluxes at the ecosystem scale. Yet the mechanisms underlying temporal variation in these isotopic signals are not fully resolved. We measured δ(13) C(R_leaf) , δ(13) C(R_root) , and the δ(13) C values and concentrations of glucose and sucrose in leaves and roots in the C(4) grass Sporobolus wrightii and the C(3) tree Prosopis velutina in a savanna ecosystem in southeastern Arizona, USA. Night-time variation in δ(13) C(R_leaf) of up to 4.6 ± 0.6‰ in S. wrightii and 3.0 ± 0.6‰ in P. velutina were correlated with shifts in leaf sucrose concentration, but not with changes in δ(13) C values of these respiratory substrates. Strong positive correlations between δ(13) C(R_root) and root glucose δ(13) C values in P. velutina suggest large diel changes in δ(13) C(R_root) (were up to 3.9‰) influenced by short-term changes in δ(13) C of leaf-derived phloem C. No diel variation in δ(13) C(R_root) was observed in S. wrightii. Our findings show that short-term changes in δ(13) C(R_leaf) and δ(13) C(R_root) were both related to substrate isotope composition and concentration. Changes in substrate limitation or demand for biosynthesis may largely control short-term variation in the δ(13) C of respired CO(2) in these species.
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Affiliation(s)
- Wei Sun
- Department of Renewable Resources Department of Botany Program in Ecology, University of Wyoming, Laramie, WY 82071, USA.
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26
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27
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Offermann C, Ferrio JP, Holst J, Grote R, Siegwolf R, Kayler Z, Gessler A. The long way down--are carbon and oxygen isotope signals in the tree ring uncoupled from canopy physiological processes? TREE PHYSIOLOGY 2011; 31:1088-102. [PMID: 21957095 DOI: 10.1093/treephys/tpr093] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The carbon (δ(13)C) and oxygen (δ(18)O) stable isotope composition is widely used to obtain information on the linkages between environmental drivers and tree physiology over various time scales. The tree-ring archive can especially be exploited to reconstruct inter- and intra-annual variation of both climate and physiology. There is, however, a lack of information on the processes potentially affecting δ(13)C and δ(18)O on their way from assimilation in the leaf to the tree ring. As a consequence, the aim of this study was to trace the isotope signals in European beech (Fagus sylvatica L.) from leaf water (δ(18)O) and leaf assimilates (δ(13)C and δ(18)O) to tree-ring wood via phloem-transported compounds over a whole growing season. Phloem and leaf samples for δ(13)C and δ(18)O analyses as well as soil water, xylem water, leaf water and atmospheric water vapour samples for δ(18)O analysis were taken approximately every 2 weeks during the growing season of 2007. The δ(13)C and δ(18)O samples from the tree rings were dated intra-annually by monitoring the tree growth with dendrometers. δ(18)O in the phloem organic matter and tree-ring whole wood was not positively related to leaf water evaporative enrichment and δ(18)O of canopy organic matter pools. This finding implies a partial uncoupling of the tree-ring oxygen isotopic signal from canopy physiology. At the same time, internal carbon storage and remobilization physiology most likely prevented δ(13)C in tree-ring whole wood from being closely related to intra-annual variation in environmental drivers. Taking into account the post-photosynthetic isotope fractionation processes resulting in alterations of δ(13)C and δ(18)O not only in the tree ring but also in phloem carbohydrates, as well as the intra-annual timing of changes in the tree internal physiology, might help to better understand the meaning of the tree-ring isotope signal not only intra- but also inter-annually.
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Affiliation(s)
- Christine Offermann
- Centre for Systems Biology (ZBSA), University of Freiburg, Habsburgerstr. 49, D-79104 Freiburg, Germany
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28
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Tcherkez G, Mahé A, Hodges M. (12)C/(13)C fractionations in plant primary metabolism. TRENDS IN PLANT SCIENCE 2011; 16:499-506. [PMID: 21705262 DOI: 10.1016/j.tplants.2011.05.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2011] [Revised: 05/18/2011] [Accepted: 05/25/2011] [Indexed: 05/13/2023]
Abstract
Natural (13)C abundance is now an unavoidable tool to study ecosystem and plant carbon economies. A growing number of studies take advantage of isotopic fractionation between carbon pools or (13)C abundance in respiratory CO(2) to examine the carbon source of respiration, plant biomass production or organic matter sequestration in soils. (12)C/(13)C isotope effects associated with plant metabolism are thus essential to understand natural isotopic signals. However, isotope effects of enzymes do not influence metabolites separately, but combine to yield a (12)C/(13)C isotopologue redistribution orchestrated by metabolic flux patterns. In this review, we summarise key metabolic isotope effects and integrate them into the corpus of plant primary carbon metabolism.
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Affiliation(s)
- Guillaume Tcherkez
- Institut de Biologie des Plantes, CNRS UMR 8618, Université Paris-Sud 11, 91405 Orsay cedex, France
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29
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Gilbert A, Silvestre V, Robins RJ, Tcherkez G, Remaud GS. A 13C NMR spectrometric method for the determination of intramolecular δ13C values in fructose from plant sucrose samples. THE NEW PHYTOLOGIST 2011; 191:579-588. [PMID: 21388380 DOI: 10.1111/j.1469-8137.2011.03690.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Recent developments in (13) C NMR spectrometry have allowed the determination of intramolecular (13) C/(12) C ratios with high precision. However, the analysis of carbohydrates requires their derivatization to constrain the anomeric carbon. Fructose has proved to be particularly problematic because of a byproduct occurring during derivatization and the complexity of the NMR spectrum of the derivative. Here, we describe a method to determine the intramolecular (13) C/(12) C ratios in fructose by (13) C NMR analysis of the acetyl-isopropylidene derivative. We have applied this method to measure the intramolecular (13) C/(12) C distribution in the fructosyl moiety of sucrose and have compared this with that in the glucosyl moiety. Three prominent features stand out. First, in sucrose from both C(3) and C(4) plants, the C-1 and C-2 positions of the glucosyl and fructosyl moieties are markedly different. Second, these positions in C(3) and C(4) plants show a similar profile. Third, the glucosyl and fructosyl moieties of sucrose from Crassulacean acid metabolism (CAM) metabolism have a different profile. These contrasting values can be interpreted as a result of the isotopic selectivity of enzymes that break or make covalent bonds in glucose metabolism, whereas the distinctive (13) C pattern in CAM sucrose probably indicates a substantial contribution of gluconeogenesis to glucose synthesis.
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Affiliation(s)
- Alexis Gilbert
- Interdisciplinary Chemistry: Synthesis, Analysis, Modelling (CEISAM), University of Nantes-CNRS UMR 6230, 2 rue de la Houssinière, BP 92208, F-44322 Nantes, France
| | - Virginie Silvestre
- Interdisciplinary Chemistry: Synthesis, Analysis, Modelling (CEISAM), University of Nantes-CNRS UMR 6230, 2 rue de la Houssinière, BP 92208, F-44322 Nantes, France
| | - Richard J Robins
- Interdisciplinary Chemistry: Synthesis, Analysis, Modelling (CEISAM), University of Nantes-CNRS UMR 6230, 2 rue de la Houssinière, BP 92208, F-44322 Nantes, France
| | - Guillaume Tcherkez
- Plant Biology Institute (IBP), CNRS UMR 8618, University of Paris Sud 11, F-91405 Orsay, France
| | - Gérald S Remaud
- Interdisciplinary Chemistry: Synthesis, Analysis, Modelling (CEISAM), University of Nantes-CNRS UMR 6230, 2 rue de la Houssinière, BP 92208, F-44322 Nantes, France
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Werner RA, Buchmann N, Siegwolf RTW, Kornexl BE, Gessler A. Metabolic fluxes, carbon isotope fractionation and respiration--lessons to be learned from plant biochemistry. THE NEW PHYTOLOGIST 2011; 191:10-15. [PMID: 21521226 DOI: 10.1111/j.1469-8137.2011.03741.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Affiliation(s)
- Roland A Werner
- Institute of Agricultural Sciences, ETH Zurich, Universitaetsstrasse 2, 8092 Zurich, Switzerland
- (Author for correspondence: tel: +41 44 632 6754; email )
| | - Nina Buchmann
- Institute of Agricultural Sciences, ETH Zurich, Universitaetsstrasse 2, 8092 Zurich, Switzerland
| | - Rolf T W Siegwolf
- Lab for Atmospheric Chemistry, Stable Isotopes and Ecosystem Fluxes, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Barbara E Kornexl
- Institute of Agricultural Sciences, ETH Zurich, Universitaetsstrasse 2, 8092 Zurich, Switzerland
| | - Arthur Gessler
- Institute for Landscape Biogeochemistry, Leibniz-Centre for Agricultural Landscape Research (ZALF), Eberswalderstr. 84, 15374 Müncheberg, Germany
- Professorship for Landscape Biogeochemistry, Humboldt-University at Berlin, Lentze-Allee 75, 14195 Berlin, Germany
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Tcherkez G, Mauve C, Lamothe M, Le Bras C, Grapin A. The 13C/12C isotopic signal of day-respired CO2 in variegated leaves of Pelargonium × hortorum. PLANT, CELL & ENVIRONMENT 2011; 34:270-283. [PMID: 20955224 DOI: 10.1111/j.1365-3040.2010.02241.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
In leaves, although it is accepted that CO(2) evolved by dark respiration after illumination is naturally (13) C-enriched compared to organic matter or substrate sucrose, much uncertainty remains on whether day respiration produces (13) C-depleted or (13) C-enriched CO(2). Here, we applied equations described previously for mesocosm CO(2) exchange to investigate the carbon isotope composition of CO(2) respired by autotrophic and heterotrophic tissues of Pelargonium × hortorum leaves, taking advantage of leaf variegation. Day-respired CO(2) was slightly (13) C-depleted compared to organic matter both under 21% O(2) and 2% O(2). Furthermore, most, if not all CO(2) molecules evolved in the light came from carbon atoms that had been fixed previously before the experiments, in both variegated and green leaves. We conclude that the usual definition of day respiratory fractionation, that assumes carbon fixed by current net photosynthesis is the respiratory substrate, is not valid in Pelargonium leaves under our conditions. In variegated leaves, total organic matter was slightly (13) C-depleted in white areas and so were most primary metabolites. This small isotopic difference between white and green areas probably came from the small contribution of photosynthetic CO(2) refixation and the specific nitrogen metabolism in white leaf areas.
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Affiliation(s)
- Guillaume Tcherkez
- Plateforme Métabolisme-Métabolome IFR87, Institut de Biologie des Plantes, UMR CNRS 8618, Bâtiment 630, Université Paris-Sud 11, 91405 Orsay cedex, France.
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Gessler A. Carbon and Oxygen Isotopes in Trees: Tools to Study Assimilate Transport and Partitioning and to Assess Physiological Responses Towards the Environment. ACTA ACUST UNITED AC 2010. [DOI: 10.1007/978-3-642-13145-5_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
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Bickford CP, Hanson DT, McDowell NG. Influence of diurnal variation in mesophyll conductance on modelled 13C discrimination: results from a field study. JOURNAL OF EXPERIMENTAL BOTANY 2010; 61:3223-33. [PMID: 20501745 PMCID: PMC2905191 DOI: 10.1093/jxb/erq137] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2010] [Revised: 04/26/2010] [Accepted: 04/28/2010] [Indexed: 05/07/2023]
Abstract
Mesophyll conductance to CO(2) (g(m)) limits carbon assimilation and influences carbon isotope discrimination (Delta) under most environmental conditions. Current work is elucidating the environmental regulation of g(m), but the influence of g(m) on model predictions of Delta remains poorly understood. In this study, field measurements of Delta and g(m) were obtained using a tunable diode laser spectroscope coupled to portable photosynthesis systems. These data were used to test the importance of g(m) in predicting Delta using the comprehensive Farquhar model of Delta (Delta(comp)), where g(m) was parameterized using three methods based on: (i) mean g(m); (ii) the relationship between stomatal conductance (g(s)) and g(m); and (iii) the relationship between time of day (TOD) and g(m). Incorporating mean g(m), g(s)-based g(m), and TOD-based g(m) did not consistently improve Delta(comp) predictions of field-grown juniper compared with the simple model of Delta (Delta(simple)) that omits fractionation factors associated with g(m) and decarboxylation. Sensitivity tests suggest that b, the fractionation due to carboxylation, was lower (25 per thousand) than the value commonly used in Delta(comp) (29 per thousand) and Delta(simple) (27 per thousand). These results demonstrate the limits of all tested models in predicting observed juniper Delta, largely due to unexplained offsets between predicted and observed values that were not reconciled in sensitivity tests of variability in g(m), b, or e, the day respiratory fractionation.
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Affiliation(s)
- Christopher P Bickford
- University of New Mexico, Department of Biology, MSC03-2020, Albuquerque, NM 87131, USA.
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34
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Tcherkez G, Schäufele R, Nogués S, Piel C, Boom A, Lanigan G, Barbaroux C, Mata C, Elhani S, Hemming D, Maguas C, Yakir D, Badeck FW, Griffiths H, Schnyder H, Ghashghaie J. On the 13C/12C isotopic signal of day and night respiration at the mesocosm level. PLANT, CELL & ENVIRONMENT 2010; 33:900-913. [PMID: 20082670 DOI: 10.1111/j.1365-3040.2010.02115.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
While there is currently intense effort to examine the (13)C signal of CO(2) evolved in the dark, less is known on the isotope composition of day-respired CO(2). This lack of knowledge stems from technical difficulties to measure the pure respiratory isotopic signal: day respiration is mixed up with photorespiration, and there is no obvious way to separate photosynthetic fractionation (pure c(i)/c(a) effect) from respiratory effect (production of CO(2) with a different delta(13)C value from that of net-fixed CO(2)) at the ecosystem level. Here, we took advantage of new simple equations, and applied them to sunflower canopies grown under low and high [CO(2)]. We show that whole mesocosm-respired CO(2) is slightly (13)C depleted in the light at the mesocosm level (by 0.2-0.8 per thousand), while it is slightly (13)C enriched in darkness (by 1.5-3.2 per thousand). The turnover of the respiratory carbon pool after labelling appears similar in the light and in the dark, and accordingly, a hierarchical clustering analysis shows a close correlation between the (13)C abundance in day- and night-evolved CO(2). We conclude that the carbon source for respiration is similar in the dark and in the light, but the metabolic pathways associated with CO(2) production may change, thereby explaining the different (12)C/(13)C respiratory fractionations in the light and in the dark.
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Affiliation(s)
- Guillaume Tcherkez
- Ecologie Systématique Evolution, Bâtiment 362, Université Paris-Sud 11, 91405 Orsay cedex, Paris, France.
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35
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Sun W, Resco V, Williams DG. Nocturnal and seasonal patterns of carbon isotope composition of leaf dark-respired carbon dioxide differ among dominant species in a semiarid savanna. Oecologia 2010; 164:297-310. [DOI: 10.1007/s00442-010-1643-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2009] [Accepted: 04/13/2010] [Indexed: 10/19/2022]
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Sun W, Resco V, Williams DG. Diurnal and seasonal variation in the carbon isotope composition of leaf dark-respired CO(2) in velvet mesquite (Prosopis velutina). PLANT, CELL & ENVIRONMENT 2009; 32:1390-400. [PMID: 19558412 DOI: 10.1111/j.1365-3040.2009.02006.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
We evaluated diurnal and seasonal patterns of carbon isotope composition of leaf dark-respired CO(2) (delta(13)C(l)) in the C(3) perennial shrub velvet mesquite (Prosopis velutina) across flood plain and upland savanna ecosystems in the south-western USA. delta(13)C(l) of darkened leaves increased to maximum values late during daytime periods and declined gradually over night-time periods to minimum values at pre-dawn. The magnitude of the diurnal shift in delta(13)C(l) was strongly influenced by seasonal and habitat-related differences in soil water availability and leaf surface vapour pressure deficit. delta(13)C(l) and the cumulative flux-weighted delta(13)C value of photosynthates were positively correlated, suggesting that progressive (13)C enrichment of the CO(2) evolved by darkened leaves during the daytime mainly resulted from short-term changes in photosynthetic (13)C discrimination and associated shifts in the delta(13)C signature of primary respiratory substrates. The (13)C enrichment of dark-respired CO(2) relative to photosynthates across habitats and seasons was 4 to 6 per thousand at the end of the daytime period (1800 h), but progressively declined to 0 per thousand by pre-dawn (0300 h). The origin of night-time and daytime variations in delta(13)C(l) is discussed in terms of the carbon source(s) feeding respiration and the drought-induced changes in carbon metabolism.
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Affiliation(s)
- Wei Sun
- Department of Renewable Resources, University of Wyoming, Laramie, WY 82071, USA.
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Werner C, Wegener F, Unger S, Nogués S, Priault P. Short-term dynamics of isotopic composition of leaf-respired CO2 upon darkening: measurements and implications. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2009; 23:2428-38. [PMID: 19603472 DOI: 10.1002/rcm.4036] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Recent advances in understanding the metabolic origin and the temporal dynamics in delta(13)C of dark-respired CO(2) (delta(13)C(res)) have led to an increasing awareness of the importance of plant isotopic fractionation in respiratory processes. Pronounced dynamics in delta(13)C(res) have been observed in a number of species and three main hypotheses have been proposed: first, diurnal changes in delta(13)C of respiratory substrates; second, post-photosynthetic discrimination in respiratory pathways; and third, dynamic decarboxylation of enriched carbon pools during the post-illumination respiration period. Since different functional groups exhibit distinct diurnal patterns in delta(13)C(res) (ranging from 0 to 10 per thousand diurnal increase), we explored these hypotheses for different ecotypes and environmental (i.e. growth light) conditions. Mass balance calculations revealed that the effect of respiratory substrates on diurnal changes in delta(13)C(res) was negligible in all investigated species. Further, rapid post-illumination changes in delta(13)C(res) (30 min), which increased from 2.6 per thousand to 5 per thousand over the course of the day, were examined by positional (13)C-labelling to quantify changes in pyruvate dehydrogenase (PDH) and Krebs cycle (KC) activity. We investigated the origin of these dynamics with Rayleigh mass balance calculations based on theoretical assumptions on fractionation processes. Neither the estimated changes of PDH and KC, nor decarboxylation of a malate pool entirely explained the observed pattern in delta(13)C(res). However, a Rayleigh fractionation of (12)C-discriminating enzymes and/or a rapid decline in the decarboxylation rate of an enriched substrate pool may explain the post-illumination peak in delta(13)C(res). These results are highly relevant since delta(13)C(res) is used in large-scale carbon cycle studies.
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Affiliation(s)
- Christiane Werner
- Experimental and Systems Ecology, University of Bielefeld, Universitätsstr. 25, D-33615 Bielefeld, Germany.
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38
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Mauve C, Bleton J, Bathellier C, Lelarge-Trouverie C, Guérard F, Ghashghaie J, Tchapla A, Tcherkez G. Kinetic 12C/13C isotope fractionation by invertase: evidence for a small in vitro isotope effect and comparison of two techniques for the isotopic analysis of carbohydrates. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2009; 23:2499-2506. [PMID: 19603465 DOI: 10.1002/rcm.4068] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The natural (13)C/(12)C isotope composition (delta(13)C) of plants and organic compounds within plant organs is a powerful tool to understand carbon allocation patterns and the regulation of photosynthetic or respiratory metabolism. However, many enzymatic fractionations are currently unknown, thus impeding our understanding of carbon trafficking pathways within plant cells. One of them is the (12)C/(13)C isotope effect associated with invertases (EC 3.2.1.26) that are cornerstone enzymes for Suc metabolism and translocation in plants. Another conundrum of isotopic plant biology is the need to measure accurately the specific delta(13)C of individual carbohydrates. Here, we examined two complementary methods for measuring the delta(13)C value of sucrose, glucose and fructose, that is, off-line high-performance liquid chromatography (HPLC) purification followed by elemental analysis and isotope ratio mass spectrometry (EA-IRMS) analysis, and gas chromatography-combustion (GC-C)-IRMS. We also used these methods to determine the in vitro (12)C/(13)C isotope effect associated with the yeast invertase. Our results show that, although providing more variable values than HPLC approximately EA-IRMS, and being sensitive to derivatization conditions, the GC-C-IRMS method gives reliable results. When applied to the invertase reaction, both methods indicate that the (12)C/(13)C isotope effect is rather small and it is not affected by the use of heavy water (D(2)O).
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Affiliation(s)
- Caroline Mauve
- Plateforme Métabolisme Métabolome, IFR87 La Plante et son Environnement, Institut de Biotechnologie des Plantes, Université Paris-Sud XI, 91405 Orsay cedex, France
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Gessler A, Brandes E, Buchmann N, Helle G, Rennenberg H, Barnard RL. Tracing carbon and oxygen isotope signals from newly assimilated sugars in the leaves to the tree-ring archive. PLANT, CELL & ENVIRONMENT 2009; 32:780-795. [PMID: 19220785 DOI: 10.1111/j.1365-3040.2009.01957.x] [Citation(s) in RCA: 100] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The analysis of delta(13)C and delta(18)O in tree-ring archives offers retrospective insights into environmental conditions and ecophysiological processes. While photosynthetic carbon isotope discrimination and evaporative oxygen isotope enrichment are well understood, we lack information on how the isotope signal is altered by downstream metabolic processes. In Pinus sylvestris, we traced the isotopic signals from their origin in the leaf water (delta(18)O) or the newly assimilated carbon (delta(13)C), via phloem sugars to the tree-ring, over a time-scale that ranges from hours to a growing season. Seasonally, variable (13)C enrichment of sugars related to phloem loading and transport did lead to uncoupling between delta(13)C in the tree-ring, and the c(i)/c(a) ratio at the leaf level. In contrast, the oxygen isotope signal was transferred from the leaf water to the tree-ring with an expected enrichment of 27 per thousand, with time-lags of approximately 2 weeks and with a 40% exchange between organic oxygen and xylem water oxygen during cellulose synthesis. This integrated overview of the fate of carbon and oxygen isotope signals within the model tree species P. sylvestris provides a novel physiological basis for the interpretation of delta(13)C and delta(18)O in tree-ring ecology.
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Affiliation(s)
- Arthur Gessler
- Centre for Systems Biology (ZBSA), Albert-Ludwigs-University Freiburg, Habsburgerstr. 49, 79104 Freiburg, Germany.
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Shen T, Shen W, Xiong Y, Liu H, Zheng H, Zhou H, Rui B, Liu J, Wu J, Shi Y. Increasing the accuracy of mass isotopomer analysis through calibration curves constructed using biologically synthesized compounds. JOURNAL OF MASS SPECTROMETRY : JMS 2009; 44:1066-1080. [PMID: 19370770 DOI: 10.1002/jms.1583] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Mass isotopomer analysis is an important technique to measure the production and flow of metabolites in living cells, tissues, and organisms. This technique depends on accurate quantifications of different mass isotopomers using mass spectrometry. Constructing calibration curves using standard samples is the most universal approach to convert raw mass spectrometry measurements into quantitative distributions of mass isotopomers. Calibration curve approach has been, however, of very limited use in comprehensive analyses of biological systems, mainly suffering from the lack of extensive range of standard samples with accurately known isotopic enrichment. Here, we present a biological method capable of synthesizing specifically labeled amino acids. These amino acids have well-determined and estimable mass isotopomer distributions and thus can serve as standard samples. In this method, the bacterium strain Methylobacterium salsuginis sp. nov. was cultivated with partially 13C-labeled methanol as the only carbon source to produce 13C-enriched compounds. We show that the mass isotopomer distributions of the various biosynthesized amino acids are well determined and can be reasonably estimated based on proposed binomial approximation if the labeling state of the biomass reached an isotopic steady state. The interference of intramolecular inhomogeneity of 13C isotope abundances caused by biological isotope fractionation was eliminated by estimating average 13C isotope abundance. Further, the predictions are tested experimentally by mass spectrometry (MS) spectra of the labeled glycine, alanine, and aspartic acid. Most of the error in mass spectrometry measurements was less than 0.74 mol% in the test case, significantly reduced as compared with uncalibrated results, and this error is expected to be less than 0.4 mol% in real experiment as revealed by theoretical analysis.
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Affiliation(s)
- Tie Shen
- School of Life Science, University of Science and Technology of China, Hefei, Anhui, China.
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Gessler A, Tcherkez G, Karyanto O, Keitel C, Ferrio JP, Ghashghaie J, Kreuzwieser J, Farquhar GD. On the metabolic origin of the carbon isotope composition of CO2 evolved from darkened light-acclimated leaves in Ricinus communis. THE NEW PHYTOLOGIST 2009; 181:374-386. [PMID: 19121034 DOI: 10.1111/j.1469-8137.2008.02672.x] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The (13)C isotopic signature (delta(13)C) of CO(2) respired from plants is widely used to assess carbon fluxes and ecosystem functioning. There is, however, a lack of knowledge of the metabolic basis of the delta(13)C value of respired CO(2). To elucidate the physiological mechanisms driving (12)C/(13)C fractionation during respiration, the delta(13)C of respired CO(2) from dark-acclimated leaves during the night, from darkened leaves during the light period, and from stems and roots of Ricinus communis was analysed. The delta(13)C of potential respiratory substrates, the respiratory quotient and the activities of phosphoenolpyruvatecarboxylase (PEPc) and key respiratory enzymes were also measured. It is shown here that the CO(2) evolved from darkened light-acclimated leaves during the light period is (13)C-enriched, and that this correlates with malate accumulation in the light and rapid malate decarboxylation just after the onset of darkness. Whilst CO(2) evolved from leaves was generally (13)C-enriched (but to a lesser extent during the night), CO(2) evolved from stems and roots was depleted compared with the putative respiratory substrates; the difference was mainly caused by intensive PEPc-catalysed CO(2) refixation in stems and roots. These results provide a physiological explanation for short-term variations of delta(13)C in CO(2), illustrating the effects of variations of metabolic fluxes through different biochemical pathways.
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Affiliation(s)
- Arthur Gessler
- Environmental Biology Group; Research School of Biological Sciences, Australian National University, GPO Box 475, Canberra, ACT 2601, Australia;School of Forest and Ecosystem Science, University of Melbourne, Water Street, Creswick, VIC 3363, Australia;Institute of Forest Botany and Tree Physiology, Albert-Ludwigs Universität Freiburg, Georges-Köhler-Allee 53/54, 79110 Freiburg, Germany;Laboratoire d'Ecologie, Systématique et Evolution, Département d'Ecophysiologie Végétale, CNRS-UMR 8079, Centre scientifique d'Orsay, Bâtiment 362, Université Paris-Sud XI, 91405 Orsay Cedex, France;Plateforme Métabolisme-Métabolome IFR87, Centre scientifique d'Orsay, Bâtiment 630, Université Paris-Sud XI, 91405 Orsay Cedex, France;Present address: Core Facility Metabolomics, Centre for System Biology (ZBSA), Albert-Ludwigs Universität Freiburg, Habsburgerstr. 49, 79104 Freiburg, Germany
| | - Guillaume Tcherkez
- Environmental Biology Group; Research School of Biological Sciences, Australian National University, GPO Box 475, Canberra, ACT 2601, Australia;School of Forest and Ecosystem Science, University of Melbourne, Water Street, Creswick, VIC 3363, Australia;Institute of Forest Botany and Tree Physiology, Albert-Ludwigs Universität Freiburg, Georges-Köhler-Allee 53/54, 79110 Freiburg, Germany;Laboratoire d'Ecologie, Systématique et Evolution, Département d'Ecophysiologie Végétale, CNRS-UMR 8079, Centre scientifique d'Orsay, Bâtiment 362, Université Paris-Sud XI, 91405 Orsay Cedex, France;Plateforme Métabolisme-Métabolome IFR87, Centre scientifique d'Orsay, Bâtiment 630, Université Paris-Sud XI, 91405 Orsay Cedex, France;Present address: Core Facility Metabolomics, Centre for System Biology (ZBSA), Albert-Ludwigs Universität Freiburg, Habsburgerstr. 49, 79104 Freiburg, Germany
| | - Oka Karyanto
- Environmental Biology Group; Research School of Biological Sciences, Australian National University, GPO Box 475, Canberra, ACT 2601, Australia;School of Forest and Ecosystem Science, University of Melbourne, Water Street, Creswick, VIC 3363, Australia;Institute of Forest Botany and Tree Physiology, Albert-Ludwigs Universität Freiburg, Georges-Köhler-Allee 53/54, 79110 Freiburg, Germany;Laboratoire d'Ecologie, Systématique et Evolution, Département d'Ecophysiologie Végétale, CNRS-UMR 8079, Centre scientifique d'Orsay, Bâtiment 362, Université Paris-Sud XI, 91405 Orsay Cedex, France;Plateforme Métabolisme-Métabolome IFR87, Centre scientifique d'Orsay, Bâtiment 630, Université Paris-Sud XI, 91405 Orsay Cedex, France;Present address: Core Facility Metabolomics, Centre for System Biology (ZBSA), Albert-Ludwigs Universität Freiburg, Habsburgerstr. 49, 79104 Freiburg, Germany
| | - Claudia Keitel
- Environmental Biology Group; Research School of Biological Sciences, Australian National University, GPO Box 475, Canberra, ACT 2601, Australia;School of Forest and Ecosystem Science, University of Melbourne, Water Street, Creswick, VIC 3363, Australia;Institute of Forest Botany and Tree Physiology, Albert-Ludwigs Universität Freiburg, Georges-Köhler-Allee 53/54, 79110 Freiburg, Germany;Laboratoire d'Ecologie, Systématique et Evolution, Département d'Ecophysiologie Végétale, CNRS-UMR 8079, Centre scientifique d'Orsay, Bâtiment 362, Université Paris-Sud XI, 91405 Orsay Cedex, France;Plateforme Métabolisme-Métabolome IFR87, Centre scientifique d'Orsay, Bâtiment 630, Université Paris-Sud XI, 91405 Orsay Cedex, France;Present address: Core Facility Metabolomics, Centre for System Biology (ZBSA), Albert-Ludwigs Universität Freiburg, Habsburgerstr. 49, 79104 Freiburg, Germany
| | - Juan Pedro Ferrio
- Environmental Biology Group; Research School of Biological Sciences, Australian National University, GPO Box 475, Canberra, ACT 2601, Australia;School of Forest and Ecosystem Science, University of Melbourne, Water Street, Creswick, VIC 3363, Australia;Institute of Forest Botany and Tree Physiology, Albert-Ludwigs Universität Freiburg, Georges-Köhler-Allee 53/54, 79110 Freiburg, Germany;Laboratoire d'Ecologie, Systématique et Evolution, Département d'Ecophysiologie Végétale, CNRS-UMR 8079, Centre scientifique d'Orsay, Bâtiment 362, Université Paris-Sud XI, 91405 Orsay Cedex, France;Plateforme Métabolisme-Métabolome IFR87, Centre scientifique d'Orsay, Bâtiment 630, Université Paris-Sud XI, 91405 Orsay Cedex, France;Present address: Core Facility Metabolomics, Centre for System Biology (ZBSA), Albert-Ludwigs Universität Freiburg, Habsburgerstr. 49, 79104 Freiburg, Germany
| | - Jaleh Ghashghaie
- Environmental Biology Group; Research School of Biological Sciences, Australian National University, GPO Box 475, Canberra, ACT 2601, Australia;School of Forest and Ecosystem Science, University of Melbourne, Water Street, Creswick, VIC 3363, Australia;Institute of Forest Botany and Tree Physiology, Albert-Ludwigs Universität Freiburg, Georges-Köhler-Allee 53/54, 79110 Freiburg, Germany;Laboratoire d'Ecologie, Systématique et Evolution, Département d'Ecophysiologie Végétale, CNRS-UMR 8079, Centre scientifique d'Orsay, Bâtiment 362, Université Paris-Sud XI, 91405 Orsay Cedex, France;Plateforme Métabolisme-Métabolome IFR87, Centre scientifique d'Orsay, Bâtiment 630, Université Paris-Sud XI, 91405 Orsay Cedex, France;Present address: Core Facility Metabolomics, Centre for System Biology (ZBSA), Albert-Ludwigs Universität Freiburg, Habsburgerstr. 49, 79104 Freiburg, Germany
| | - Jürgen Kreuzwieser
- Environmental Biology Group; Research School of Biological Sciences, Australian National University, GPO Box 475, Canberra, ACT 2601, Australia;School of Forest and Ecosystem Science, University of Melbourne, Water Street, Creswick, VIC 3363, Australia;Institute of Forest Botany and Tree Physiology, Albert-Ludwigs Universität Freiburg, Georges-Köhler-Allee 53/54, 79110 Freiburg, Germany;Laboratoire d'Ecologie, Systématique et Evolution, Département d'Ecophysiologie Végétale, CNRS-UMR 8079, Centre scientifique d'Orsay, Bâtiment 362, Université Paris-Sud XI, 91405 Orsay Cedex, France;Plateforme Métabolisme-Métabolome IFR87, Centre scientifique d'Orsay, Bâtiment 630, Université Paris-Sud XI, 91405 Orsay Cedex, France;Present address: Core Facility Metabolomics, Centre for System Biology (ZBSA), Albert-Ludwigs Universität Freiburg, Habsburgerstr. 49, 79104 Freiburg, Germany
| | - Graham D Farquhar
- Environmental Biology Group; Research School of Biological Sciences, Australian National University, GPO Box 475, Canberra, ACT 2601, Australia;School of Forest and Ecosystem Science, University of Melbourne, Water Street, Creswick, VIC 3363, Australia;Institute of Forest Botany and Tree Physiology, Albert-Ludwigs Universität Freiburg, Georges-Köhler-Allee 53/54, 79110 Freiburg, Germany;Laboratoire d'Ecologie, Systématique et Evolution, Département d'Ecophysiologie Végétale, CNRS-UMR 8079, Centre scientifique d'Orsay, Bâtiment 362, Université Paris-Sud XI, 91405 Orsay Cedex, France;Plateforme Métabolisme-Métabolome IFR87, Centre scientifique d'Orsay, Bâtiment 630, Université Paris-Sud XI, 91405 Orsay Cedex, France;Present address: Core Facility Metabolomics, Centre for System Biology (ZBSA), Albert-Ludwigs Universität Freiburg, Habsburgerstr. 49, 79104 Freiburg, Germany
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Bathellier C, Tcherkez G, Bligny R, Gout E, Cornic G, Ghashghaie J. Metabolic origin of the delta13C of respired CO2 in roots of Phaseolus vulgaris. THE NEW PHYTOLOGIST 2009; 181:387-399. [PMID: 19021866 DOI: 10.1111/j.1469-8137.2008.02679.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Root respiration is a major contributor to soil CO2 efflux, and thus an important component of ecosystem respiration. But its metabolic origin, in relation to the carbon isotope composition (delta13C), remains poorly understood. Here, 13C analysis was conducted on CO2 and metabolites under typical conditions or under continuous darkness in French bean (Phaseolus vulgaris) roots. 13C contents were measured either under natural abundance or following pulse-chase labeling with 13C-enriched glucose or pyruvate, using isotope ratio mass spectrometer (IRMS) and nuclear magnetic resonance (NMR) techniques. In contrast to leaves, no relationship was found between the respiratory quotient and the delta13C of respired CO2, which stayed constant at a low value (c. -27.5 per thousand) under continuous darkness. With labeling experiments, it is shown that such a pattern is explained by the 13C-depleting effect of the pentose phosphate pathway; and the involvement of the Krebs cycle fueled by either the glycolytic input or the lipid/protein recycling. The anaplerotic phosphoenolpyruvate carboxylase (PEPc) activity sustained glutamic acid (Glu) synthesis, with no net effect on respired CO2. These results indicate that the root delta13C signal does not depend on the availability of root respiratory substrates and it is thus plausible that, unless the 13C photosynthetic fractionation varies at the leaf level, the root delta13C signal hardly changes under a range of natural environmental conditions.
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Affiliation(s)
- Camille Bathellier
- Laboratoire d'Ecologie, Systématique et Evolution (ESE), CNRS-UMR 8079 - IFR 87, Bâtiment 362, Université Paris-Sud, 91405-Orsay Cedex, France;Plateforme Métabolisme-Métabolome, IFR87 La Plante et son Environnement, Institut de Biotechnologie des Plantes, Bâtiment 630, Université Paris-Sud, 91405-Orsay Cedex, France;Laboratoire de Physiologie Cellulaire Végétale CEA-Grenoble 17, rue des Martyrs, 38054 Grenoble Cedex 9, France
| | - Guillaume Tcherkez
- Laboratoire d'Ecologie, Systématique et Evolution (ESE), CNRS-UMR 8079 - IFR 87, Bâtiment 362, Université Paris-Sud, 91405-Orsay Cedex, France;Plateforme Métabolisme-Métabolome, IFR87 La Plante et son Environnement, Institut de Biotechnologie des Plantes, Bâtiment 630, Université Paris-Sud, 91405-Orsay Cedex, France;Laboratoire de Physiologie Cellulaire Végétale CEA-Grenoble 17, rue des Martyrs, 38054 Grenoble Cedex 9, France
| | - Richard Bligny
- Laboratoire d'Ecologie, Systématique et Evolution (ESE), CNRS-UMR 8079 - IFR 87, Bâtiment 362, Université Paris-Sud, 91405-Orsay Cedex, France;Plateforme Métabolisme-Métabolome, IFR87 La Plante et son Environnement, Institut de Biotechnologie des Plantes, Bâtiment 630, Université Paris-Sud, 91405-Orsay Cedex, France;Laboratoire de Physiologie Cellulaire Végétale CEA-Grenoble 17, rue des Martyrs, 38054 Grenoble Cedex 9, France
| | - Elizabeth Gout
- Laboratoire d'Ecologie, Systématique et Evolution (ESE), CNRS-UMR 8079 - IFR 87, Bâtiment 362, Université Paris-Sud, 91405-Orsay Cedex, France;Plateforme Métabolisme-Métabolome, IFR87 La Plante et son Environnement, Institut de Biotechnologie des Plantes, Bâtiment 630, Université Paris-Sud, 91405-Orsay Cedex, France;Laboratoire de Physiologie Cellulaire Végétale CEA-Grenoble 17, rue des Martyrs, 38054 Grenoble Cedex 9, France
| | - Gabriel Cornic
- Laboratoire d'Ecologie, Systématique et Evolution (ESE), CNRS-UMR 8079 - IFR 87, Bâtiment 362, Université Paris-Sud, 91405-Orsay Cedex, France;Plateforme Métabolisme-Métabolome, IFR87 La Plante et son Environnement, Institut de Biotechnologie des Plantes, Bâtiment 630, Université Paris-Sud, 91405-Orsay Cedex, France;Laboratoire de Physiologie Cellulaire Végétale CEA-Grenoble 17, rue des Martyrs, 38054 Grenoble Cedex 9, France
| | - Jaleh Ghashghaie
- Laboratoire d'Ecologie, Systématique et Evolution (ESE), CNRS-UMR 8079 - IFR 87, Bâtiment 362, Université Paris-Sud, 91405-Orsay Cedex, France;Plateforme Métabolisme-Métabolome, IFR87 La Plante et son Environnement, Institut de Biotechnologie des Plantes, Bâtiment 630, Université Paris-Sud, 91405-Orsay Cedex, France;Laboratoire de Physiologie Cellulaire Végétale CEA-Grenoble 17, rue des Martyrs, 38054 Grenoble Cedex 9, France
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Priault P, Wegener F, Werner C. Pronounced differences in diurnal variation of carbon isotope composition of leaf respired CO2 among functional groups. THE NEW PHYTOLOGIST 2009; 181:400-412. [PMID: 19121035 DOI: 10.1111/j.1469-8137.2008.02665.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The first broad species survey of diurnal variation in carbon (C) isotope signatures of leaf dark-respired CO(2) (delta(13)C(res)) is presented here and functional differences and diurnal dynamics are linked to fractionation in different respiratory pathways, based on (13)C-labelling experiments. delta(13)C(res) was analysed with a rapid in-tube incubation technique in 16 species. A large diurnal increase in delta(13)C(res) (4-8 per thousand) occurred in evergreen, slow-growing and aromatic species and correlated significantly with cumulative photosynthesis, whereas no variation occurred in herbaceous, fast-growing plants or temperate trees. The diurnal increase in delta(13)C(res) declined almost proportionally to reductions in cumulative light and was reduced in growing compared with mature leaves. Pyruvate positional labelling provided direct evidence that functional groups differ in C allocation between respiratory pathways owing to different metabolic demands for growth, maintenance and secondary metabolism. Diurnal increase in C flux through pyruvate dehydrogenase (for investment in, for example, isoprene or aromatic compounds) combined with consistently low Krebs cycle activity resulted in pronounced increase in delta(13)C(res) in evergreen and aromatic species. By contrast, fast growing herbs with high respiratory demand exhibited no diurnal changes since C was fully respired. Hence, diurnal delta(13)C(res) pattern may provide information for C allocation in plants.
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Affiliation(s)
- Pierrick Priault
- Experimental and Systems Ecology, University of Bielefeld, Universitätsstrasse 25, D-33615 Bielefeld, Germany;Present address: Université Henri Poincaré Nancy I, Faculté des Sciences, UMR UHP/INRA 1137 'Ecologie et Ecophysiologie Forestières'- BP 239, F-54506 Vandoeuvre-lès-Nancy cedex, France
| | - Frederik Wegener
- Experimental and Systems Ecology, University of Bielefeld, Universitätsstrasse 25, D-33615 Bielefeld, Germany;Present address: Université Henri Poincaré Nancy I, Faculté des Sciences, UMR UHP/INRA 1137 'Ecologie et Ecophysiologie Forestières'- BP 239, F-54506 Vandoeuvre-lès-Nancy cedex, France
| | - Christiane Werner
- Experimental and Systems Ecology, University of Bielefeld, Universitätsstrasse 25, D-33615 Bielefeld, Germany;Present address: Université Henri Poincaré Nancy I, Faculté des Sciences, UMR UHP/INRA 1137 'Ecologie et Ecophysiologie Forestières'- BP 239, F-54506 Vandoeuvre-lès-Nancy cedex, France
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Lanigan GJ, Betson N, Griffiths H, Seibt U. Carbon isotope fractionation during photorespiration and carboxylation in Senecio. PLANT PHYSIOLOGY 2008; 148:2013-20. [PMID: 18923019 PMCID: PMC2593675 DOI: 10.1104/pp.108.130153] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2008] [Accepted: 10/12/2008] [Indexed: 05/18/2023]
Abstract
The magnitude of fractionation during photorespiration and the effect on net photosynthetic (13)C discrimination (Delta) were investigated for three Senecio species, S. squalidus, S. cineraria, and S. greyii. We determined the contributions of different processes during photosynthesis to Delta by comparing observations (Delta(obs)) with discrimination predicted from gas-exchange measurements (Delta(pred)). Photorespiration rates were manipulated by altering the O(2) partial pressure (pO(2)) in the air surrounding the leaves. Contributions from (13)C-depleted photorespiratory CO(2) were largest at high pO(2). The parameters for photorespiratory fractionation (f), net fractionation during carboxylation by Rubisco and phosphoenolpyruvate carboxylase (b), and mesophyll conductance (g(i)) were determined simultaneously for all measurements. Instead of using Delta(obs) data to obtain g(i) and f successively, which requires that b is known, we treated b, f, and g(i) as unknowns. We propose this as an alternative approach to analyze measurements under field conditions when b and g(i) are not known or cannot be determined in separate experiments. Good agreement between modeled and observed Delta was achieved with f = 11.6 per thousand +/- 1.5 per thousand, b = 26.0 per thousand +/- 0.3 per thousand, and g(i) of 0.27 +/- 0.01, 0.25 +/- 0.01, and 0.22 +/- 0.01 mol m(-2) s(-1) for S. squalidus, S. cineraria, and S. greyii, respectively. We estimate that photorespiratory fractionation decreases Delta by about 1.2 per thousand on average under field conditions. In addition, diurnal changes in Delta are likely to reflect variations in photorespiration even at the canopy level. Our results emphasize that the effects of photorespiration must be taken into account when partitioning net CO(2) exchange of ecosystems into gross fluxes of photosynthesis and respiration.
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Affiliation(s)
- Gary J Lanigan
- Physiological Ecology Group, Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
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Barabás B, Caglioti L, Micskei K, Zucchi C, Pályi G. Isotope chirality and asymmetric autocatalysis: a possible entry to biological chirality. ORIGINS LIFE EVOL B 2008; 38:317-27. [PMID: 18521719 DOI: 10.1007/s11084-008-9138-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2008] [Accepted: 05/05/2008] [Indexed: 10/22/2022]
Abstract
Natural-abundance isotopic substitution in isotopically prochiral groups of otherwise achiral molecules can provide stochastically formed enantiomeric excesses which exceed the sensitivity threshold of sensitive asymmetric autocatalytic (Soai-type) reactions. This kind of induction of chirality should be taken into consideration in in vitro model experiments and offer a new kind of entry into primary prebiotic or early biotic enantioselection in the earliest stages of molecular evolution.
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Affiliation(s)
- Béla Barabás
- Institute of Stochastics, University of Technology and Economics, Muegyetem rkp. 3 H ép., Budapest, Hungary
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46
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Gessler A, Tcherkez G, Peuke AD, Ghashghaie J, Farquhar GD. Experimental evidence for diel variations of the carbon isotope composition in leaf, stem and phloem sap organic matter in Ricinus communis. PLANT, CELL & ENVIRONMENT 2008; 31:941-953. [PMID: 18331588 DOI: 10.1111/j.1365-3040.2008.01806.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Carbon isotope fractionation in metabolic processes following carboxylation of ribulose-1,5-bisphosphate (RuBP) is not as well described as the discrimination during photosynthetic CO(2) fixation. However, post-carboxylation fractionation can influence the diel variation of delta(13)C of leaf-exported organic matter and can cause inter-organ differences in delta(13)C. To obtain a more mechanistic understanding of post-carboxylation modification of the isotopic signal as governed by physiological and environmental controls, we combined the modelling approach of Tcherkez et al., which describes the isotopic fractionation in primary metabolism with the experimental determination of delta(13)C in leaf and phloem sap and root carbon pools during a full diel course. There was a strong diel variation of leaf water-soluble organic matter and phloem sap sugars with relatively (13)C depleted carbon produced and exported during the day and enriched carbon during the night. The isotopic modelling approach reproduces the experimentally determined day-night differences in delta(13)C of leaf-exported carbon in Ricinus communis. These findings support the idea that patterns of transitory starch accumulation and remobilization govern the diel rhythm of delta(13)C in organic matter exported by leaves. Integrated over the whole 24 h day, leaf-exported carbon was enriched in (13)C as compared with the primary assimilates. This may contribute to the well-known--yet poorly explained--relative (13)C depletion of autotrophic organs compared with other plant parts. We thus emphasize the need to consider post-carboxylation fractionations for studies that use delta(13)C for assessing environmental effects like water availability on ratio of mole fractions of CO(2) inside and outside the leaf (e.g. tree ring studies), or for partitioning of CO(2) fluxes at the ecosystem level.
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Affiliation(s)
- Arthur Gessler
- Environmental Biology Group, Research School of Biological Sciences, Australian National University, GPO Box 475, Canberra, ACT 2601, Australia.
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47
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Aranjuelo I, Irigoyen JJ, Sánchez-Díaz M, Nogués S. Carbon partitioning in N 2 fixing Medicago sativa plants exposed to different CO 2 and temperature conditions. FUNCTIONAL PLANT BIOLOGY : FPB 2008; 35:306-317. [PMID: 32688786 DOI: 10.1071/fp07296] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2007] [Accepted: 04/22/2008] [Indexed: 05/17/2023]
Abstract
Many of the studies analysing the CO2 effect on plant development have been conducted in optimal growth conditions. Furthermore, although some of those studies suggest that legumes might show a steady productivity increase with rising CO2, the role of nodule activity on the plant responsiveness to predicted atmospheric CO2 enhancement is not well understood. In this study, C (metabolism and allocation) and N (nodule activity) interaction between the plant and the bacterial symbiont during the photosynthetic acclimation of N2-fixing alfalfa (Medicago sativa L. cv. Aragón) plants exposed to elevated CO2 and temperature conditions was analysed. The plants were grown in temperature gradient greenhouses (TGG) where, in the case of elevated CO2 treatments, the isotopic 13C/12C composition (δ13C) inside the TGG was modified. Compared with the corresponding temperature treatment, exposure to 700 μmol mol-1 CO2 enhanced dry mass (DM) of plants in elevated temperature treatments (26%), whereas no significant effect was detected in ambient temperature treatments. The δ13C data revealed that although all the carbon corresponding to leaf total organic matter (TOM) came from newly assimilated C, plants exposed to elevated CO2 did not develop strong sink activity (especially in ambient temperature conditions). Leaf carbohydrate build-up induced reduction in the Rubisco (E.C. 4.1.1.39) carboxylation capacity of plants. Despite this reduction in Rubisco content, plants exposed to elevated CO2 conditions maintained (at ambient temperature) or increased (at elevated temperature) photosynthetic rates (measured at growth conditions) by increasing N use efficiency. The larger C sink strength of nodules in plants grown at elevated CO2 and temperature conditions did not contribute towards overcoming photosynthetic acclimation. Further, the inhibitory effect of CO2 on nodule total activity was caused by a large depletion in total soluble protein (TSP) of nodules. Depletion of leaf N demand, together with the reduction in nodule carbohydrate availability (as reflected by the nodule starch concentration), negatively affected the nodule TSP content and enzymatic activity.
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Affiliation(s)
- Iker Aranjuelo
- Unitat de Fisologia Vegetal, Facultat de Biologia, Universitat de Barcelona, Diagonal 645, 08028, Barcelona, Spain
| | - Juan J Irigoyen
- Departamento de Biología Vegetal, Sección Fisiología Vegetal (Assoicated Unit with the Spanish National Research Council, CSIC, EEAD, Zaragoza), Facultades de Ciencias y Farmacia, Universidad de Navarra, Irunlarrea s/n, 31008, Pamplona, Navarra, Spain
| | - Manuel Sánchez-Díaz
- Departamento de Biología Vegetal, Sección Fisiología Vegetal (Assoicated Unit with the Spanish National Research Council, CSIC, EEAD, Zaragoza), Facultades de Ciencias y Farmacia, Universidad de Navarra, Irunlarrea s/n, 31008, Pamplona, Navarra, Spain
| | - Salvador Nogués
- Unitat de Fisologia Vegetal, Facultat de Biologia, Universitat de Barcelona, Diagonal 645, 08028, Barcelona, Spain
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Tcherkez G, Farquhar GD. On the effect of heavy water (D 2O) on carbon isotope fractionation in photosynthesis. FUNCTIONAL PLANT BIOLOGY : FPB 2008; 35:201-212. [PMID: 32688774 DOI: 10.1071/fp07282] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2007] [Accepted: 02/18/2008] [Indexed: 06/11/2023]
Abstract
Internal conductance to carbon dioxide is a key aspect of leaf photosynthesis although is still not well understood. It is thought that it comprises two components, namely, a gas phase component (diffusion from intercellular spaces to cell walls) and a liquid phase component (dissolution, diffusion in water, hydration equilibrium). Here we use heavy water (D2O), which is known to slow down CO2 hydration by a factor of nearly three. Using 12C/13C stable isotope techniques and Xanthium strumarium L. leaves, we show that the on-line carbon isotope discrimination (Δ13C, or Δobs) associated with photosynthesis is not significantly decreased by heavy water, and that the internal conductance, estimated with relationships involving the deviation of Δ13C, decreased by 8-40% in 21% O2. It is concluded that in typical conditions, the CO2-hydration equilibrium does not exert an effect on CO2 assimilation larger than 9%. The carbon isotope discrimination associated with CO2 addition to ribulose-1,5,bisphosphate by Rubisco is slightly decreased by heavy water. This effect is proposed to originate from the use of solvent-derived proton/deuteron during the last step of the catalytic cycle of the enzyme (hydration/cleavage).
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Affiliation(s)
- Guillaume Tcherkez
- Plateforme Métabolisme-Métabolome, IFR87, Université Paris-Sud XI, 91405 Orsay, France
| | - Graham D Farquhar
- Environmental Biology Group, Research School of Biological Sciences, Australian National University, Canberra, ACT 2601, Australia
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Nogués S, Aranjuelo I, Pardo A, Azcón-Bieto J. Assessing the stable carbon isotopic composition of intercellular CO2 in a CAM plant using gas chromatography-combustion-isotope ratio mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2008; 22:1017-1022. [PMID: 18320540 DOI: 10.1002/rcm.3460] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Most of the literature focused on internal CO(2) (Ci) determinations in plants has used indirect methods based on gas-exchange estimations. We have developed a new method based on the capture of internal air gas samples and their analysis by gas chromatography-combustion-isotope ratio mass spectrometry (GC-C-IRMS). This method provided a direct measure of intercellular CO(2) concentrations combined with stable carbon isotopic composition in O. ficus-indica plants. Plants were grown at both ambient and elevated CO(2) concentration. During the day period, when the stomata are closed, the Ci was high and was very (13)C-enriched in both ambient and elevated CO(2)-grown plants, reflecting Rubisco's fractionation (this plant enzyme has been shown to discriminate by 29 per thousand, in vitro, against (13)CO(2)). Other enzyme fractionations involved in C metabolism in plants, such as carbonic anhydrase, could also be playing an important role in the diurnal delta(13)C enrichment of the Ci. During the night, when stomata are open, Ci concentrations were higher in elevated (and the corresponding delta(13)C values were more (13)C-depleted) than in ambient CO(2)-grown plants.
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Affiliation(s)
- Salvador Nogués
- Unitat de Fisiologia Vegetal, Departament de Biologia Vegetal, Facultat de Biologia, Universitat de Barcelona, Av. Diagonal, 645, Barcelona, Spain.
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Bowling DR, Pataki DE, Randerson JT. Carbon isotopes in terrestrial ecosystem pools and CO2 fluxes. THE NEW PHYTOLOGIST 2008; 178:24-40. [PMID: 18179603 DOI: 10.1111/j.1469-8137.2007.02342.x] [Citation(s) in RCA: 180] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Stable carbon isotopes are used extensively to examine physiological, ecological, and biogeochemical processes related to ecosystem, regional, and global carbon cycles and provide information at a variety of temporal and spatial scales. Much is known about the processes that regulate the carbon isotopic composition (delta(13)C) of leaf, plant, and ecosystem carbon pools and of photosynthetic and respiratory carbon dioxide (CO(2)) fluxes. In this review, systematic patterns and mechanisms underlying variation in delta(13)C of plant and ecosystem carbon pools and fluxes are described. We examine the hypothesis that the delta(13)C of leaf biomass can be used as a reference point for other carbon pools and fluxes, which differ from the leaf in delta(13)C in a systematic fashion. Plant organs are typically enriched in (13)C relative to leaves, and most ecosystem pools and respiratory fluxes are enriched relative to sun leaves of dominant plants, with the notable exception of root respiration. Analysis of the chemical and isotopic composition of leaves and leaf respiration suggests that growth respiration has the potential to contribute substantially to the observed offset between the delta(13)C values of ecosystem respiration and the bulk leaf. We discuss the implications of systematic variations in delta(13)C of ecosystem pools and CO(2) fluxes for studies of carbon cycling within ecosystems, as well as for studies that use the delta(13)C of atmospheric CO(2) to diagnose changes in the terrestrial biosphere over annual to millennial time scales.
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Affiliation(s)
- David R Bowling
- Department of Biology, 257 South, 1400 East, University of Utah, Salt Lake City, UT 84112-0820, USA
| | - Diane E Pataki
- Department of Earth System Science and
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA
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