Plant metabolomics: towards biological function and mechanism

Trends in Plant Science

Volumn 11, Issue 10, 2006, Pages 508-516

  Schauer, Nicolas ^a   Fernie, Alisdair R ^a  

^a MAX PLANCK INSTITUTE OF MOLECULAR PLANT PHYSIOLOGY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

VEGETABLE PROTEIN;

BOTANY; CHEMISTRY; CLASSIFICATION; GENE; GENETICS; GENOMICS; METABOLISM; METHODOLOGY; PLANT; PLANT GENE; QUANTITATIVE TRAIT LOCUS; REVIEW;

BOTANY; GENES, PLANT; GENOMICS; PLANT PROTEINS; PLANTS; QUANTITATIVE TRAIT LOCI;

EID: 33947307759     PISSN: 13601385     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tplants.2006.08.007     Document Type: Review

References (109)

1. Stitt M., and Fernie A.R. From measurements of metabolites to metabolomics: an 'on the fly' perspective illustrated by recent studies of carbon-nitrogen interactions. Curr. Opin. Biotechnol. 14 (2003) 136-144
2. Kopka J., et al. Metabolite profiling in plant biology: platforms and destinations. Genome Biol. 5 (2004) 109
3. Fiehn O., et al. Identification of uncommon plant metabolites based on calculation of elemental compositions using gas chromatography and quadrupole mass spectrometry. Anal. Chem. 72 (2000) 3573-3580
4. Kaplan F., et al. Exploring the temperature-stress metabolome of Arabidopsis. Plant Physiol. 136 (2004) 4159-4168
5. Schauer N., et al. Metabolic profiling of leaves and fruit of wild species tomato: a survey of the Solanum lycopersicum complex. J. Exp. Bot. 56 (2005) 297-307
6. Roessner-Tunali U., et al. Metabolic profiling of transgenic tomato plants overexpressing hexokinase reveals that the influence of hexose phosphorylation diminishes during fruit development. Plant Physiol. 133 (2003) 84-99
7. Roessner U., et al. Metabolic profiling allows comprehensive phenotyping of genetically or environmentally modified plant systems. Plant Cell 13 (2001) 11-29
8. Roessner U., et al. Simultaneous analysis of metabolites in potato tuber by gas chromatography-mass spectrometry. Plant J. 23 (2000) 131-142
9. Sato S., et al. Simultaneous determination of the main metabolites in rice leaves using capillary electrophoresis mass spectrometry and capillary electrophoresis diode array detection. Plant J. 40 (2004) 151-163
10. Hamzehzarghani H., et al. Metabolic profiling and factor analysis to discriminate quantitative resistance in wheat cultivars against fusarium head blight. Physiol. Mol. Plant Pathol. 66 (2005) 119-133
11. Aharoni A., et al. Nontargeted metabolome analysis by use of Fourier Transform Ion Cyclotron Mass Spectrometry. OMICS 6 (2002) 217-234
12. Chen F., et al. Profiling phenolic metabolites in transgenic alfalfa modified in lignin biosynthesis. Phytochemistry 64 (2003) 1013-1021
13. Tagashira N., et al. The metabolic profiles of transgenic cucumber lines vary with different chromosomal locations of the transgene. Cell. Mol. Biol. Lett. 10 (2005) 697-710
14. Garratt L.C., et al. Metabolite fingerprinting in transgenic lettuce. Plant Biotechnol. J. 3 (2005) 165-174
15. Blount J.W., et al. Over-expression of cinnamate 4-hydroxylase leads to increased accumulation of acetosyringone in elicited tobacco cell-suspension cultures. Planta 214 (2002) 902-910
16. Robinson A.R., et al. The potential of metabolite profiling as a selection tool for genotype discrimination in Populus. J. Exp. Bot. 56 (2005) 2807-2819
17. Brosche M., et al. Gene expression and metabolite profiling of Populus euphratica growing in the Negev desert. Genome Biol. 6 (2005) R101
18. Merchant A., et al. Targeted metabolite profiling provides a functional link among eucalypt taxonomy, physiology and evolution. Phytochemistry 67 (2006) 402-408
19. Sauter H., et al. Metabolic profiling of plants - a new diagnostic-technique. Abstr. Pap. Am. Chem. S. 195 (1988) 129
20. Ott K.H., et al. Metabolomics classifies pathways affected by bioactive compounds. Artificial neural network classification of NMR spectra of plant extracts. Phytochemistry 62 (2003) 971-985
21. Catchpole G.S., et al. Hierarchical metabolomics demonstrates substantial compositional similarity between genetically modified and conventional potato crops. Proc. Natl. Acad. Sci. U. S. A. 102 (2005) 14458-14462
22. Defernez M., et al. NMR and HPLC-UV profiling of potatoes with genetic modifications to metabolic pathways. J. Agric. Food Chem. 52 (2004) 6075-6085
23. Fiehn O., et al. Metabolite profiling for plant functional genomics. Nat. Biotechnol. 18 (2000) 1157-1161
24. Roessner U., et al. High-resolution metabolic phenotyping of genetically and environmentally diverse potato tuber systems. Identification of phenocopies. Plant Physiol. 127 (2001) 749-764
25. Tikunov Y., et al. A novel approach for nontargeted data analysis for metabolomics. Large-scale profiling of tomato fruit volatiles. Plant Physiol. 139 (2005) 1125-1137
26. Cook D., et al. A prominent role for the CBF cold response pathway in configuring the low-temperature metabolome of Arabidopsis. Proc. Natl. Acad. Sci. U. S. A. 101 (2004) 15243-15248
27. Urbanczyk-Wochniak E., and Fernie A.R. Metabolic profiling reveals altered nitrogen nutrient regimes have diverse effects on the metabolism of hydroponically-grown tomato (Solanum lycopersicum) plants. J. Exp. Bot. 56 (2005) 309-321
28. Nikiforova V.J., et al. Systems rebalancing of metabolism in response to sulfur deprivation, as revealed by metabolome analysis of Arabidopsis plants. Plant Physiol. 138 (2005) 304-318
29. Hirai M.Y., and Saito K. Post-genomics approaches for the elucidation of plant adaptive mechanisms to sulphur deficiency. J. Exp. Bot. 55 (2004) 1871-1879
30. Hirai M.Y., et al. Elucidation of gene-to-gene and metabolite-to-gene networks in Arabidopsis by integration of metabolomics and transcriptomics. J. Biol. Chem. 280 (2005) 25590-25595
31. Morikawa T., et al. Cytochrome P450 CYP710A encodes the sterol C-22 desaturase in Arabidopsis and tomato. Plant Cell 18 (2006) 1008-1022
32. Goossens A., et al. A functional genomics approach toward the understanding of secondary metabolism in plant cells. Proc. Natl. Acad. Sci. U. S. A. 100 (2003) 8595-8600
33. Hirai M.Y., et al. Integration of transcriptomics and metabolomics for understanding of global responses to nutritional stresses in Arabidopsis thaliana. Proc. Natl. Acad. Sci. U. S. A. 101 (2004) 10205-10210
34. Suzuki H., et al. Methyl jasmonate and yeast elicitor induce differential transcriptional and metabolic re-programming in cell suspension cultures of the model legume Medicago truncatula. Planta 220 (2005) 696-707
35. Morino K., et al. Metabolic profiling of tryptophan-overproducing rice calli that express a feedback-insensitive alpha subunit of anthranilate synthase. Plant Cell Physiol. 46 (2005) 514-521
36. Junker B.H., et al. Temporally regulated expression of a yeast invertase in potato tubers allows dissection of the complex metabolic phenotype obtained following its constitutive expression. Plant Mol. Biol. 56 (2004) 91-110
37. Sweetlove L.J., and Fernie A.R. Regulation of metabolic networks: understanding metabolic complexity in the systems biology era. New Phytol. 168 (2005) 9-23
38. Schauer N., et al. Comprehensive metabolic profiling and phenotyping of interspecific introgression lines for tomato improvement. Nat. Biotechnol. 24 (2006) 447-454
39. Hall R.D. Plant metabolomics: from holistic hope, to hype, to hot topic. New Phytol. 169 (2006) 453-468
40. Fernie A.R., et al. Natural genetic variation for improving crop quality. Curr. Opin. Plant Biol. 9 (2006) 196-202
41. Harrigan G.G., and Goodacre R. Metabolic Profiling: Its Role in Biomarker Discovery and Gene Function Analysis (2003), Springer Verlag
42. Sumner L.W., et al. Plant metabolomics: large-scale phytochemistry in the functional genomics era. Phytochemistry 62 (2003) 817-836
43. Fernie A.R., et al. Innovation - metabolite profiling: from diagnostics to systems biology. Nat. Rev. Mol. Cell Biol. 5 (2004) 763-769
44. Saito K., et al. Plant Metabolomics (2006), Springer Verlag
45. Schauer N., et al. GC-MS libraries for the rapid identification of metabolites in complex biological samples. FEBS Lett. 579 (2005) 1332-1337
46. Kopka J., et al. GMD@CSB DB: the Golm Metabolome Database. Bioinformatics 21 (2005) 1635-1638
47. Bino R.J., et al. Potential of metabolomics as a functional genomics tool. Trends Plant Sci. 9 (2004) 418-425
48. Jenkins H., et al. A proposed framework for the description of plant metabolomics experiments and their results. Nat. Biotechnol. 22 (2004) 1601-1606
49. Brazma A., et al. Minimum information about a microarray experiment (MIAME) - toward standards for microarray data. Nat. Genet. 29 (2001) 365-371
50. Taylor C.F., et al. A systematic approach to modeling, capturing, and disseminating proteomics experimental data. Nat. Biotechnol. 21 (2003) 247-254
51. Moing A., et al. Quantitative metabolic profiling by 1-dimensional H-1-NMR analyses: application to plant genetics and functional genomics. Funct. Plant Biol. 31 (2004) 889-902
52. Nunes-Nesi A., et al. Enhanced photosynthetic performance and growth as a consequence of decreasing mitochondrial malate dehydrogenase activity in transgenic tomato plants. Plant Physiol. 137 (2005) 611-622
53. Tarpley L., et al. Biomarker metabolites capturing the metabolite variance present in a rice plant developmental period. BMC Plant Biol. 5 (2005) 8
54. Taylor J., et al. Application of metabolomics to plant genotype discrimination using statistics and machine learning. Bioinformatics 18 (2002) S241-S248
55. Choi Y.H., et al. Metabolic discrimination of Catharanthus roseus leaves infected by phytoplasma using 1H-NMR spectroscopy and multivariate data analysis. Plant Physiol. 135 (2004) 2398-2410
56. Allwood J.W., et al. Metabolomic approaches reveal that phosphatidic and phosphatidyl glycerol phospholipids are major discriminatory non-polar metabolites in responses by Brachypodium distachyon to challenge by Magnaporthe grisea. Plant J. 46 (2006) 351-368
57. Petro-Turza M. Flavor of tomato and tomato products. Food Rev. Int. 2 (1986) 309-352
58. Broeckling C.D., et al. Metabolic profiling of Medicago truncatula cell cultures reveals the effects of biotic and abiotic elicitors on metabolism. J. Exp. Bot. 56 (2005) 323-336
59. Desbrosses G.G., et al. Lotus japonicus metabolic profiling. Development of gas chromatography-mass spectrometry resources for the study of plant-microbe interactions. Plant Physiol. 137 (2005) 1302-1318
60. Ishizaki K., et al. The critical role of Arabidopsis electron-transfer flavoprotein: ubiquinone oxidoreductase during dark-induced starvation. Plant Cell 17 (2005) 2587-2600
61. Ishizaki K., et al. The mitochondrial electron transfer flavoprotein complex is essential for survival of Arabidopsis in extended darkness. Plant J. 47 (2006) 751-760
62. Bohnert H.J., et al. Unraveling abiotic stress tolerance mechanisms - getting genomics going. Curr. Opin. Plant Biol. 9 (2006) 180-188
63. Fernie A.R. Metabolome characterisation in plant system analysis. Funct. Plant Biol. 30 (2003) 111-120
64. Holmstrom K.O., et al. Improved tolerance to salinity and low temperature in transgenic tobacco producing glycine betaine. J. Exp. Bot. 51 (2000) 177-185
65. Nikiforova V.J., et al. Towards dissecting nutrient metabolism in plants: a systems biology case study on sulphur metabolism. J. Exp. Bot. 55 (2004) 1861-1870
66. Daskalchuk T., et al. The use of non-targeted metabolomics in plant science. In: Saito K., et al. (Ed). Plant Metabolomics (2006), Springer Verlag 311-326
67. Thimm O., et al. MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. Plant J. 37 (2004) 914-939
68. Rohde P., et al. Heterosis in the freezing tolerance of crosses between two Arabidopsis thaliana accessions (Columbia-0 and C24) that show differences in non-acclimated and acclimated freezing tolerance. Plant J. 38 (2004) 790-799
69. Ferrario-Mery S., et al. Diurnal changes in ammonia assimilation in transformed tobacco plants expressing ferredoxin-dependent glutamate synthase mRNA in the antisense orientation. Plant Science (Shannon) 163 (2002) 59-67
70. Noctor G., et al. Interactions between biosynthesis, compartmentation and transport in the control of glutathione homeostasis and signalling. J. Exp. Bot. 53 (2002) 1283-1304
71. Stitt M., et al. Steps towards an integrated view of nitrogen metabolism. J. Exp. Bot. 53 (2002) 959-970
72. Wang R., et al. Genomic analysis of the nitrate response using a nitrate reductase-null mutant of Arabidopsis. Plant Physiol. 136 (2004) 2512-2522
73. Dutilleul C., et al. Mitochondria-driven changes in leaf NAD status exert a crucial influence on the control of nitrate assimilation and the integration of carbon and nitrogen metabolism. Plant Physiol. 139 (2005) 64-78
74. Bolling C., and Fiehn O. Metabolite profiling of Chlamydomonas reinhardtii under nutrient deprivation. Plant Physiol. 139 (2005) 1995-2005
75. Blasing O.E., et al. Sugars and circadian regulation make major contributions to the global regulation of diurnal gene expression in Arabidopsis. Plant Cell 17 (2005) 3257-3281
76. Buchanan-Wollaston V., et al. Comparative transcriptome analysis reveals significant differences in gene expression and signalling pathways between developmental and dark/starvation-induced senescence in Arabidopsis. Plant J. 42 (2005) 567-585
77. Manzanares-Dauleux M.J., et al. Development of a pathotype specific SCAR marker in Plasmodiophora brassicae. Eur. J. Plant Pathol. 106 (2000) 781-787
78. Ott P.G., et al. Novel extracellular chitinases rapidly and specifically induced by general bacterial elicitors and suppressed by virulent bacteria as a marker of early basal resistance in tobacco. Mol. Plant Microbe Interact. 19 (2006) 161-172
79. Olszak B., et al. A putative flavin-containing mono-oxygenase as a marker for certain defense and cell death pathways. Plant Sci. 170 (2006) 614-623
80. Schnee C., et al. The products of a single maize sesquiterpene synthase form a volatile defense signal that attracts natural enemies of maize herbivores. Proc. Natl. Acad. Sci. U. S. A. 103 (2006) 1129-1134
81. Kappers I.F., et al. Genetic engineering of terpenoid metabolism attracts bodyguards to Arabidopsis. Science 309 (2005) 2070-2072
82. Bednarek P., et al. Structural complexity, differential response to infection, and tissue specificity of indolic and phenylpropanoid secondary metabolism in Arabidopsis roots. Plant Physiol. 138 (2005) 1058-1070
83. Zimmermann P., et al. GENEVESTIGATOR. Arabidopsis microarray database and analysis toolbox. Plant Physiol. 136 (2004) 2621-2632
84. Steinhauser D., et al. CSB.DB: a comprehensive systems-biology database. Bioinformatics 20 (2004) 3647-3651
85. Achnine L., et al. Genomics-based selection and functional characterization of triterpene glycosyltransferases from the model legume Medicago truncatula. Plant J. 41 (2005) 875-887
86. Mercke P., et al. Combined transcript and metabolite analysis reveals genes involved in spider mite induced volatile formation in cucumber plants. Plant Physiol. 135 (2004) 2012-2024
87. Tohge T., et al. Functional genomics by integrated analysis of metabolome and transcriptome of Arabidopsis plants over-expressing an MYB transcription factor. Plant J. 42 (2005) 218-235
88. Martzen M.R., et al. A biochemical genomics approach for identifying genes by the activity of their products. Science 286 (1999) 1153-1155
89. Raamsdonk L.M., et al. A functional genomics strategy that used metabolome data to reveal the phenotype of silent mutations. Nat. Biotechnol. 19 (2001) 45-50
90. Fridman E., et al. Metabolic, genomic, and biochemical analyses of glandular trichomes from the wild tomato species Lycopersicon hirsutum identify a key enzyme in the biosynthesis of methylketones. Plant Cell 17 (2005) 1252-1267
91. Jander G., et al. Application of a high-throughput HPLC-MS/MS assay to Arabidopsis mutant screening; evidence that threonine aldolase plays a role in seed nutritional quality. Plant J. 39 (2004) 465-475
92. Andersson-Gunneras S., et al. Biosynthesis of cellulose-enriched tension wood in Populus: global analysis of transcripts and metabolites identifies biochemical and developmental regulators in secondary wall biosynthesis. Plant J. 45 (2006) 144-165
93. Nikiforova V.J., et al. Integrative gene-metabolite network with implemented causality deciphers informational fluxes of sulphur stress response. J. Exp. Bot. 56 (2005) 1887-1896
94. Kristensen C., et al. Metabolic engineering of dhurrin in transgenic Arabidopsis plants with marginal inadvertent effects on the metabolome and transcriptome. Proc. Natl. Acad. Sci. U. S. A. 102 (2005) 1779-1784
95. Alba R., et al. Transcriptome and selected metabolite analyses reveal multiple points of ethylene control during tomato fruit development. Plant Cell 17 (2005) 2954-2965
96. Villas-Boas S.G., et al. High-throughput metabolic state analysis: the missing link in integrated functional genomics of yeasts. Biochem. J. 388 (2005) 669-677
97. Urbanczyk-Wochniak E., et al. Parallel analysis of transcript and metabolic profiles: a new approach in systems biology. EMBO Rep. 4 (2003) 989-993
98. Askenazi M., et al. Integrating transcriptional and metabolite profiles to direct the engineering of lovastatin-producing fungal strains. Nat. Biotechnol. 21 (2003) 150-156
99. Nikiforova V., et al. Transcriptome analysis of sulfur depletion in Arabidopsis thaliana: interlacing of biosynthetic pathways provides response specificity. Plant J. 33 (2003) 633-650
100. Liu Y.S., et al. There is more to tomato fruit colour than candidate carotenoid genes. Plant Biotechnol. J. 1 (2003) 195-207
101. Moose S.P., et al. Maize selection passes the century mark: a unique resource for 21st century genomics. Trends Plant Sci. 9 (2004) 358-364
102. Fernie A.R., and Willmitzer L. Carbohydrate metabolism. In: Christou P., and Klee H.K. (Eds). The Handbook of Plant Biotechnology (2004), Wiley
103. Kliebenstein D.J., et al. Genetic control of natural variation in Arabidopsis glucosinolate accumulation. Plant Physiol. 126 (2001) 811-825
104. Kliebenstein D., et al. Comparative analysis of quantitative trait loci controlling glucosinolates, myrosinase and insect resistance in Arabidopsis thaliana. Genetics 161 (2002) 325-332
105. Eshed Y., and Zamir D. A genomic library of Lycopersicon pennellii in L. esculentum: a tool for fine mapping of genes. Euphytica 79 (1994) 175-179
106. Tieman D.M., et al. Identification of loci affecting flavour volatile emissions in tomato fruits. J. Exp. Bot. 57 (2006) 887-896
107. Tieman D., et al. Tomato aromatic amino acid decarboxylases participate in synthesis of the flavor volatiles 2-phenylethanol and 2-phenylacetaldehyde. Proc. Natl. Acad. Sci. U. S. A. 103 (2006) 8287-8291
108. Roessner-Tunali U., et al. Kinetics of labelling of organic and amino acids in potato tubers by gas chromatography-mass spectrometry following incubation in (13)C labelled isotopes. Plant J. 39 (2004) 668-679
109. Fridman E., et al. Zooming in on a quantitative trait for tomato yield using interspecific introgressions. Science 305 (2004) 1786-1789