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Plant Cell, Vol. 13, 11-29, January 2001, Copyright © 2001, American Society of Plant Physiologists

GENOMICS ARTICLE

Metabolic Profiling Allows Comprehensive Phenotyping of Genetically or Environmentally Modified Plant Systems

Ute Roessnera, Alexander Luedemanna, Doreen Brustb, Oliver Fiehna, Thomas Linkeb, Lothar Willmitzera, and Alisdair R. Ferniea
a Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Golm, Germany
b Institut für Informatik, Universität Potsdam, Am Neuen Palais 10, 14469 Potsdam, Germany

Correspondence to: Alisdair R. Fernie, Fernie{at}mpimp-golm.mpg.de (E-mail), 49-331-5678408 (fax)

Metabolic profiling using gas chromatography–mass spectrometry technologies is a technique whose potential in the field of functional genomics is largely untapped. To demonstrate the general usefulness of this technique, we applied to diverse plant genotypes a recently developed profiling protocol that allows detection of a wide range of hydrophilic metabolites within a single chromatographic run. For this purpose, we chose four independent potato genotypes characterized by modifications in sucrose metabolism. Using data-mining tools, including hierarchical cluster analysis and principle component analysis, we were able to assign clusters to the individual plant systems and to determine relative distances between these clusters. Extraction analysis allowed identification of the most important components of these clusters. Furthermore, correlation analysis revealed close linkages between a broad spectrum of metabolites. In a second, complementary approach, we subjected wild-type potato tissue to environmental manipulations. The metabolic profiles from these experiments were compared with the data sets obtained for the transgenic systems, thus illustrating the potential of metabolic profiling in assessing how a genetic modification can be phenocopied by environmental conditions. In summary, these data demonstrate the use of metabolic profiling in conjunction with data-mining tools as a technique for the comprehensive characterization of a plant genotype.




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V. J. Nikiforova, B. Gakiere, S. Kempa, M. Adamik, L. Willmitzer, H. Hesse, and R. Hoefgen
Towards dissecting nutrient metabolism in plants: a systems biology case study on sulphur metabolism
J. Exp. Bot., August 1, 2004; 55(404): 1861 - 1870.
[Abstract] [Full Text] [PDF]

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 Plant Physiol.Home page
Y. H. Choi, E. C. Tapias, H. K. Kim, A. W.M. Lefeber, C. Erkelens, J. Th.J. Verhoeven, J. Brzin, J. Zel, and R. Verpoorte
Metabolic Discrimination of Catharanthus roseus Leaves Infected by Phytoplasma Using 1H-NMR Spectroscopy and Multivariate Data Analysis
Plant Physiology, August 1, 2004; 135(4): 2398 - 2410.
[Abstract] [Full Text] [PDF]

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 Proc. Natl. Acad. Sci. USAHome page
M. Y. Hirai, M. Yano, D. B. Goodenowe, S. Kanaya, T. Kimura, M. Awazuhara, M. Arita, T. Fujiwara, and K. Saito
From The Cover: Integration of transcriptomics and metabolomics for understanding of global responses to nutritional stresses in Arabidopsis thaliana
PNAS, July 6, 2004; 101(27): 10205 - 10210.
[Abstract] [Full Text] [PDF]

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 Plant Physiol.Home page
E. von Roepenack-Lahaye, T. Degenkolb, M. Zerjeski, M. Franz, U. Roth, L. Wessjohann, J. Schmidt, D. Scheel, and S. Clemens
Profiling of Arabidopsis Secondary Metabolites by Capillary Liquid Chromatography Coupled to Electrospray Ionization Quadrupole Time-of-Flight Mass Spectrometry
Plant Physiology, February 1, 2004; 134(2): 548 - 559.
[Abstract] [Full Text] [PDF]

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 Plant Cell PhysiolHome page
E. Urbanczyk-Wochniak, A. Leisse, U. Roessner-Tunali, A. Lytovchenko, J. Reismeier, L. Willmitzer, and A. R. Fernie
Expression of a Bacterial Xylose Isomerase in Potato Tubers Results in an Altered Hexose Composition and a Consequent Induction of Metabolism
Plant Cell Physiol., December 15, 2003; 44(12): 1359 - 1367.
[Abstract] [Full Text] [PDF]

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 Plant Physiol.Home page
F. Carrari, A. Nunes-Nesi, Y. Gibon, A. Lytovchenko, M. E. Loureiro, and A. R. Fernie
Reduced Expression of Aconitase Results in an Enhanced Rate of Photosynthesis and Marked Shifts in Carbon Partitioning in Illuminated Leaves of Wild Species Tomato
Plant Physiology, November 1, 2003; 133(3): 1322 - 1335.
[Abstract] [Full Text] [PDF]

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 Plant Physiol.Home page
U. Roessner-Tunali, E. Urbanczyk-Wochniak, T. Czechowski, A. Kolbe, L. Willmitzer, and A. R. Fernie
De Novo Amino Acid Biosynthesis in Potato Tubers Is Regulated by Sucrose Levels
Plant Physiology, October 1, 2003; 133(2): 683 - 692.
[Abstract] [Full Text] [PDF]

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 Plant CellHome page
P. Giege, J. L. Heazlewood, U. Roessner-Tunali, A. H. Millar, A. R. Fernie, C. J. Leaver, and L. J. Sweetlove
Enzymes of Glycolysis Are Functionally Associated with the Mitochondrion in Arabidopsis Cells
PLANT CELL, September 1, 2003; 15(9): 2140 - 2151.
[Abstract] [Full Text] [PDF]

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 Plant Physiol.Home page
U. Roessner-Tunali, B. Hegemann, A. Lytovchenko, F. Carrari, C. Bruedigam, D. Granot, and A. R. Fernie
Metabolic Profiling of Transgenic Tomato Plants Overexpressing Hexokinase Reveals That the Influence of Hexose Phosphorylation Diminishes during Fruit Development
Plant Physiology, September 1, 2003; 133(1): 84 - 99.
[Abstract] [Full Text] [PDF]

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 Plant Physiol.Home page
K. L. Bologa, A. R. Fernie, A. Leisse, M. Ehlers Loureiro, and P. Geigenberger
A Bypass of Sucrose Synthase Leads to Low Internal Oxygen and Impaired Metabolic Performance in Growing Potato Tubers
Plant Physiology, August 1, 2003; 132(4): 2058 - 2072.
[Abstract] [Full Text] [PDF]

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 Plant Physiol.Home page
L. J. Sweetlove, R. L. Last, and A. R. Fernie
Predictive Metabolic Engineering: A Goal for Systems Biology
Plant Physiology, June 1, 2003; 132(2): 420 - 425.
[Full Text] [PDF]

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 Plant Physiol.Home page
O. Kreft, R. Hoefgen, and H. Hesse
Functional Analysis of Cystathionine gamma -Synthase in Genetically Engineered Potato Plants
Plant Physiology, April 1, 2003; 131(4): 1843 - 1854.
[Abstract] [Full Text] [PDF]

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 Plant Physiol.Home page
C. Kuhn, M.-R. Hajirezaei, A. R. Fernie, U. Roessner-Tunali, T. Czechowski, B. Hirner, and W. B. Frommer
The Sucrose Transporter StSUT1 Localizes to Sieve Elements in Potato Tuber Phloem and Influences Tuber Physiology and Development
Plant Physiology, January 1, 2003; 131(1): 102 - 113.
[Abstract] [Full Text] [PDF]

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 J Exp BotHome page
G. Noctor, L. Novitskaya, P. J. Lea, and C. H. Foyer
Co-ordination of leaf minor amino acid contents in crop species: significance and interpretation
J. Exp. Bot., April 15, 2002; 53(370): 939 - 945.
[Abstract] [Full Text] [PDF]

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 Plant Physiol.Home page
A. R. Fernie and L. Willmitzer
Molecular and Biochemical Triggers of Potato Tuber Development
Plant Physiology, December 1, 2001; 127(4): 1459 - 1465.
[Full Text] [PDF]

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 Plant Physiol.Home page
U. Roessner, L. Willmitzer, and A. R. Fernie
High-Resolution Metabolic Phenotyping of Genetically and Environmentally Diverse Potato Tuber Systems. Identification of Phenocopies
Plant Physiology, November 1, 2001; 127(3): 749 - 764.
[Abstract] [Full Text] [PDF]

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 Plant Physiol.Home page
M. Zeh, A. P. Casazza, O. Kreft, U. Roessner, K. Bieberich, L. Willmitzer, R. Hoefgen, and H. Hesse
Antisense Inhibition of Threonine Synthase Leads to High Methionine Content in Transgenic Potato Plants
Plant Physiology, November 1, 2001; 127(3): 792 - 802.
[Abstract] [Full Text] [PDF]


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