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PMID: 21423574 Published · epublish English Journal Article Research Support, Non-U.S. Gov't

A topological map of the compartmentalized Arabidopsis thaliana leaf metabolome.

PloS one ·Vol. 6 ·No. 3 ·2011-03-15 ·Pages e17806

Krueger S, Giavalisco P, Krall L, Steinhauser MC, Büssis D, Usadel B, Flügge UI, Fernie AR, Willmitzer L, Steinhauser D

Abstract

The extensive subcellular compartmentalization of metabolites and metabolism in eukaryotic cells is widely acknowledged and represents a key factor of metabolic activity and functionality. In striking contrast, the knowledge of actual compartmental distribution of metabolites from experimental studies is surprisingly low. However, a precise knowledge of, possibly all, metabolites and their subcellular distributions remains a key prerequisite for the understanding of any cellular function. Here we describe results for the subcellular distribution of 1,117 polar and 2,804 lipophilic mass spectrometric features associated to known and unknown compounds from leaves of the model plant Arabidopsis thaliana. Using an optimized non-aqueous fractionation protocol in conjunction with GC/MS- and LC/MS-based metabolite profiling, 81.5% of the metabolic data could be associated to one of three subcellular compartments: the cytosol (including the mitochondria), vacuole, or plastids. Statistical analysis using a marker-'free' approach revealed that 18.5% of these metabolites show intermediate distributions, which can either be explained by transport processes or by additional subcellular compartments. Next to a functional and conceptual workflow for the efficient, highly resolved metabolite analysis of the fractionated Arabidopsis thaliana leaf metabolome, a detailed survey of the subcellular distribution of several compounds, in the graphical format of a topological map, is provided. This complex data set therefore does not only contain a rich repository of metabolic information, but due to thorough validation and testing by statistical methods, represents an initial step in the analysis of metabolite dynamics and fluxes within and between subcellular compartments.

MeSH Terms
Arabidopsis/cytology,metabolism Biomarkers/metabolism Cell Compartmentation Cell Fractionation Cluster Analysis Metabolome Models, Biological Models, Statistical Plant Leaves/cytology,metabolism Principal Component Analysis Reproducibility of Results Subcellular Fractions/metabolism
Chemicals
Biomarkers
Authors & Affiliations
10 authors, click to expand affiliations / ORCID
Krueger Stephan
Botanical Institute, University of Cologne, Cologne, Germany.
Giavalisco Patrick
Krall Leonard
Steinhauser Marie-Caroline
Büssis Dirk
Usadel Bjoern
Flügge Ulf-Ingo
Fernie Alisdair R
Willmitzer Lothar
Steinhauser Dirk
References (78)
78 references, click to expand
  1. The Arabidopsis MATE transporter TT12 acts as a vacuolar flavonoid/H+ -antiporter active in proanthocyanidin-accumulating cells of the seed coat.
    Plant Cell. 2007 Jun;19(6):2023-38 PMID: 17601828
  2. Arabidopsis thaliana GLN2-encoded glutamine synthetase is dual targeted to leaf mitochondria and chloroplasts.
    Plant Cell. 2004 Aug;16(8):2048-58 PMID: 15273293
  3. Functional and physiological characterization of Arabidopsis INOSITOL TRANSPORTER1, a novel tonoplast-localized transporter for myo-inositol.
    Plant Cell. 2008 Apr;20(4):1073-87 PMID: 18441213
  4. Evidence for p-hydroxybenzoate formation involving enzymatic phenylpropanoid side-chain cleavage in hairy roots of Daucus carota.
    J Plant Physiol. 2008 Mar 13;165(4):407-14 PMID: 17658659
  5. Mass spectrometry-based proteomics.
    Nature. 2003 Mar 13;422(6928):198-207 PMID: 12634793
  6. Engineering of ubiquinone biosynthesis using the yeast coq2 gene confers oxidative stress tolerance in transgenic tobacco.
    Plant J. 2004 Dec;40(5):734-43 PMID: 15546356
  7. Assessment of sampling strategies for gas chromatography-mass spectrometry (GC-MS) based metabolomics of cyanobacteria.
    J Chromatogr B Analyt Technol Biomed Life Sci. 2009 Oct 1;877(27):2952-60 PMID: 19631594
  8. The aspartate aminotransferase gene family of Arabidopsis encodes isoenzymes localized to three distinct subcellular compartments.
    Plant J. 1995 Jan;7(1):61-75 PMID: 7894512
  9. Analysis of subcellular metabolite levels of potato tubers (Solanum tuberosum) displaying alterations in cellular or extracellular sucrose metabolism.
    Metabolomics. 2008 Jun;4(2):161-170 PMID: 19816536
  10. Plant cells contain two functionally distinct vacuolar compartments.
    Cell. 1996 May 17;85(4):563-72 PMID: 8653791
  11. Identification of a new glucosinolate-rich cell type in Arabidopsis flower stalk.
    Plant Physiol. 2000 Oct;124(2):599-608 PMID: 11027710
  12. Determination of subcellular concentrations of soluble carbohydrates in rose petals during opening by nonaqueous fractionation method combined with infiltration-centrifugation method.
    Planta. 2009 Nov;230(6):1115-27 PMID: 20183924
  13. The TRANSPARENT TESTA12 gene of Arabidopsis encodes a multidrug secondary transporter-like protein required for flavonoid sequestration in vacuoles of the seed coat endothelium.
    Plant Cell. 2001 Apr;13(4):853-71 PMID: 11283341
  14. ADP-glucose pyrophosphorylase is activated by posttranslational redox-modification in response to light and to sugars in leaves of Arabidopsis and other plant species.
    Plant Physiol. 2003 Oct;133(2):838-49 PMID: 12972664
  15. Proline metabolism and transport in plant development.
    Amino Acids. 2010 Oct;39(4):949-62 PMID: 20204435
  16. Duplicated P5CS genes of Arabidopsis play distinct roles in stress regulation and developmental control of proline biosynthesis.
    Plant J. 2008 Jan;53(1):11-28 PMID: 17971042
  17. Metabolite profiling: from diagnostics to systems biology.
    Nat Rev Mol Cell Biol. 2004 Sep;5(9):763-9 PMID: 15340383
  18. Regulation of Sucrose Synthesis by Cytoplasmic Fructosebisphosphatase and Sucrose Phosphate Synthase during Photosynthesis in Varying Light and Carbon Dioxide.
    Plant Physiol. 1983 Jul;72(3):767-74 PMID: 16663083
  19. Subcellular Metabolite Levels in Spinach Leaves : Regulation of Sucrose Synthesis during Diurnal Alterations in Photosynthetic Partitioning.
    Plant Physiol. 1987 Feb;83(2):399-407 PMID: 16665257
  20. Measurement of the ATP/ADP ratio in mitochondria and in the extramitochondrial compartment by fractionation of freeze-stopped liver tissue in non-aqueous media.
    Hoppe Seylers Z Physiol Chem. 1974 Mar;355(3):378-93 PMID: 4154892
  21. Geranyl diphosphate:4-hydroxybenzoate geranyltransferase from Lithospermum erythrorhizon. Cloning and characterization of a ket enzyme in shikonin biosynthesis.
    J Biol Chem. 2002 Feb 22;277(8):6240-6 PMID: 11744717
  22. Amino Acid and sucrose content determined in the cytosolic, chloroplastic, and vacuolar compartments and in the Phloem sap of spinach leaves.
    Plant Physiol. 1991 Sep;97(1):227-33 PMID: 16668375
  23. Combining genomics, metabolome analysis, and biochemical modelling to understand metabolic networks.
    Comp Funct Genomics. 2001;2(3):155-68 PMID: 18628911
  24. Identification, subcellular localization and biochemical characterization of water-soluble heteroglycans (SHG) in leaves of Arabidopsis thaliana L.: distinct SHG reside in the cytosol and in the apoplast.
    Plant J. 2005 Aug;43(4):568-85 PMID: 16098110
  25. Galactolipids rule in seed plants.
    Trends Plant Sci. 2002 Mar;7(3):112-8 PMID: 11906834
  26. Mitochondrial and cytosolic ATP/ADP ratios in isolated hepatocytes. A comparison of the digitonin method and the non-aqueous fractionation procedure.
    Biochem J. 1980 Dec 15;192(3):951-4 PMID: 7236247
  27. Alteration of the cytosolic-mitochondrial distribution of high-energy phosphates during global myocardial ischemia may contribute to early contractile failure.
    Circ Res. 1994 Oct;75(4):760-9 PMID: 7923621
  28. A salvage pathway for phytol metabolism in Arabidopsis.
    J Biol Chem. 2006 Feb 3;281(5):2470-7 PMID: 16306049
  29. Real-time imaging of the intracellular glutathione redox potential.
    Nat Methods. 2008 Jun;5(6):553-9 PMID: 18469822
  30. Desorption electrospray ionization mass spectrometry: Imaging drugs and metabolites in tissues.
    Proc Natl Acad Sci U S A. 2008 Nov 25;105(47):18120-5 PMID: 18697929
  31. Methyl-beta-D-glucopyranoside in higher plants: accumulation and intracellular localization in Geum montanum L. leaves and in model systems studied by 13C nuclear magnetic resonance.
    J Exp Bot. 2004 Oct;55(406):2179-89 PMID: 15361539
  32. A COMPARISON OF WATER CULTURE AND SOIL AS MEDIA FOR CROP PRODUCTION.
    Science. 1939 Jun 2;89(2318):512-4 PMID: 17776587
  33. Variation of glucosinolate accumulation among different organs and developmental stages of Arabidopsis thaliana.
    Phytochemistry. 2003 Feb;62(3):471-81 PMID: 12620360
  34. Rapid metabolism of glucose detected with FRET glucose nanosensors in epidermal cells and intact roots of Arabidopsis RNA-silencing mutants.
    Plant Cell. 2006 Sep;18(9):2314-25 PMID: 16935985
  35. Lipid biosynthesis.
    Plant Cell. 1995 Jul;7(7):957-70 PMID: 7640528
  36. Mass spectrometry-based metabolomics.
    Mass Spectrom Rev. 2007 Jan-Feb;26(1):51-78 PMID: 16921475
  37. Knocking on the heaven's wall: pathogenesis of and resistance to biotrophic fungi at the cell wall.
    Curr Opin Plant Biol. 2004 Aug;7(4):377-83 PMID: 15231259
  38. A glutathione S-transferase involved in vacuolar transfer encoded by the maize gene Bronze-2.
    Nature. 1995 Jun 1;375(6530):397-400 PMID: 7760932
  39. Sucrose synthase catalyses a readily reversible reaction in vivo in developing potato tubers and other plant tissues.
    Planta. 1993 Mar;189(3):329-39 PMID: 24178489
  40. Pheophytin pheophorbide hydrolase (pheophytinase) is involved in chlorophyll breakdown during leaf senescence in Arabidopsis.
    Plant Cell. 2009 Mar;21(3):767-85 PMID: 19304936
  41. Intracellular metabolite transporters in plants.
    Mol Plant. 2010 Jan;3(1):21-53 PMID: 20038549
  42. Analysis of the expression of potato uridinediphosphate-glucose pyrophosphorylase and its inhibition by antisense RNA.
    Planta. 1993;190(2):247-52 PMID: 7763665
  43. Vacuolar transporters and their essential role in plant metabolism.
    J Exp Bot. 2007;58(1):83-102 PMID: 17110589
  44. Advances of high-resolution NMR techniques in the structural and metabolic analysis of plant biochemistry.
    Phytochemistry. 2007 Nov-Dec;68(22-24):2799-815 PMID: 18023829
  45. Brittle-1, an adenylate translocator, facilitates transfer of extraplastidial synthesized ADP--glucose into amyloplasts of maize endosperms.
    Plant Physiol. 1998 Aug;117(4):1235-52 PMID: 9701580
  46. Analysis of cytosolic and plastidic serine acetyltransferase mutants and subcellular metabolite distributions suggests interplay of the cellular compartments for cysteine biosynthesis in Arabidopsis.
    Plant Cell Environ. 2009 Apr;32(4):349-67 PMID: 19143986
  47. Sub-cellular immunolocalization of the glucosinolate sinigrin in seedlings of Brassica juncea.
    Planta. 1998 Oct;206(3):370-7 PMID: 9763706
  48. Mass spectrometry-based metabolomics: accelerating the characterization of discriminating signals by combining statistical correlations and ultrahigh resolution.
    Anal Chem. 2008 Jul 1;80(13):4918-32 PMID: 18512947
  49. Redox Transfer across the Inner Chloroplast Envelope Membrane.
    Plant Physiol. 1991 Apr;95(4):1131-7 PMID: 16668101
  50. Making the connections--the crucial role of metabolite transporters at the interface between chloroplast and cytosol.
    FEBS Lett. 2007 May 25;581(12):2215-22 PMID: 17316618
  51. Comparing and combining NMR spectroscopy and mass spectrometry in metabolomics.
    Anal Bioanal Chem. 2007 Jan;387(2):525-7 PMID: 16955259
  52. Mitochondrial redox biology and homeostasis in plants.
    Trends Plant Sci. 2007 Mar;12(3):125-34 PMID: 17293156
  53. Different myrosinase and idioblast distribution in Arabidopsis and Brassica napus.
    Plant Physiol. 2001 Dec;127(4):1750-63 PMID: 11743118
  54. Mitochondrial fusion, division and positioning in plants.
    Biochem Soc Trans. 2010 Jun;38(3):789-95 PMID: 20491666
  55. Vesicle-mediated solute transport between the vacuole and the plasma membrane.
    Plant Physiol. 2000 Aug;123(4):1217-26 PMID: 10938341
  56. Variation of enzyme activities and metabolite levels in 24 Arabidopsis accessions growing in carbon-limited conditions.
    Plant Physiol. 2006 Dec;142(4):1574-88 PMID: 17085515
  57. Gas chromatography mass spectrometry-based metabolite profiling in plants.
    Nat Protoc. 2006;1(1):387-96 PMID: 17406261
  58. A key role for vesicles in fungal secondary metabolism.
    Proc Natl Acad Sci U S A. 2009 Nov 17;106(46):19533-8 PMID: 19889978
  59. Immunoelectron microscopy for locating calvin cycle enzymes in the thylakoids of synechocystis 6803.
    Mol Plant. 2009 Jan;2(1):32-42 PMID: 19529819
  60. The Arabidopsis epithiospecifier protein promotes the hydrolysis of glucosinolates to nitriles and influences Trichoplusia ni herbivory.
    Plant Cell. 2001 Dec;13(12):2793-807 PMID: 11752388
  61. Transporters of secondary metabolites.
    Curr Opin Plant Biol. 2005 Jun;8(3):301-7 PMID: 15860427
  62. Pvclust: an R package for assessing the uncertainty in hierarchical clustering.
    Bioinformatics. 2006 Jun 15;22(12):1540-2 PMID: 16595560
  63. Analysis of the compartmentation of glycolytic intermediates, nucleotides, sugars, organic acids, amino acids, and sugar alcohols in potato tubers using a nonaqueous fractionation method.
    Plant Physiol. 2001 Oct;127(2):685-700 PMID: 11598242
  64. Metabolomics-oriented isolation and structure elucidation of 37 compounds including two anthocyanins from Arabidopsis thaliana.
    Phytochemistry. 2009 May;70(8):1017-29 PMID: 19497599
  65. KEGG: kyoto encyclopedia of genes and genomes.
    Nucleic Acids Res. 2000 Jan 1;28(1):27-30 PMID: 10592173
  66. Adenine nucleotide levels in the cytosol, chloroplasts, and mitochondria of wheat leaf protoplasts.
    Plant Physiol. 1982 Oct;70(4):971-7 PMID: 16662653
  67. Measurement of subcellular metabolite levels in leaves by fractionation of freeze-stopped material in nonaqueous media.
    Plant Physiol. 1984 Jul;75(3):542-7 PMID: 16663663
  68. The 'ins' and 'outs' of flavonoid transport.
    Trends Plant Sci. 2010 Feb;15(2):72-80 PMID: 20006535
  69. Metabolic profiling allows comprehensive phenotyping of genetically or environmentally modified plant systems.
    Plant Cell. 2001 Jan;13(1):11-29 PMID: 11158526
  70. From measurements of metabolites to metabolomics: an 'on the fly' perspective illustrated by recent studies of carbon-nitrogen interactions.
    Curr Opin Biotechnol. 2003 Apr;14(2):136-44 PMID: 12732314
  71. pcaMethods--a bioconductor package providing PCA methods for incomplete data.
    Bioinformatics. 2007 May 1;23(9):1164-7 PMID: 17344241
  72. Phloem Transport of Amino Acids in Relation to their Cytosolic Levels in Barley Leaves.
    Plant Physiol. 1992 Jul;99(3):996-1004 PMID: 16669030
  73. Localization of a flavonoid biosynthetic polyphenol oxidase in vacuoles.
    Plant J. 2006 Jan;45(2):133-43 PMID: 16367960
  74. Starch: its metabolism, evolution, and biotechnological modification in plants.
    Annu Rev Plant Biol. 2010;61:209-34 PMID: 20192737
  75. λ-Glutamylcysteine synthetase in higher plants: catalytic properties and subcellular localization.
    Planta. 1990 Mar;180(4):603-12 PMID: 24202107
  76. Calvin cycle multienzyme complexes are bound to chloroplast thylakoid membranes of higher plants in situ.
    Proc Natl Acad Sci U S A. 1993 Jun 15;90(12):5514-8 PMID: 11607406
  77. Biosynthesis of ubiquinone and plastoquinone in the endoplasmic reticulum-Golgi membranes of spinach leaves.
    J Biol Chem. 1993 Jan 15;268(2):1494-9 PMID: 8419349
  78. Cell- and tissue-specific localization and regulation of the epithiospecifier protein in Arabidopsis thaliana.
    Plant Mol Biol. 2007 May;64(1-2):173-85 PMID: 17390109
Article Info
Journal
PloS one
Abbr.
PLoS One
ISSN
1932-6203
DOI
10.1371/journal.pone.0017806
Published
2011-03-15
Epub
2011-00-15
Pages
e17806
Language
English
Region
United States
NLM ID
101285081
PMCID
PMC3058050
Subset
IM
External Links
PubMed source DOI: 10.1371/journal.pone.0017806 PMC Full Text View journal details
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