Metabolomics of Arabidopsis Thaliana

Annual Plant Reviews Volume 43: Biology of Plant Metabolomics

Volumn 43, Issue , 2011, Pages 157-180

  Beale, Michael H ^a   Sussman, Michael R ^b  

^a ROTHAMSTED RESEARCH   (United Kingdom)

^b UNIVERSITY OF WISCONSIN MADISON   (United States)

Author keywords

Arabidopsis; Functional genomics; Isotope labelling; Metabolomics; QTL analysis

Indexed keywords

EID: 84872554512     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9781444339956.ch6     Document Type: Chapter

References (108)

1. Aharoni, A., de Vos, C.H., Verhoeven, H.A. et al. (2002) Non-targeted metabolome analysis by use of Fourier transform ion cyclotron mass spectrometry. OMICS 6, 217-234.
2. Alonso-Blanco, C. and Koorneef, M. (2000) Naturally occurring variation in Arabidopsis: an underexploited resource for plant genetics. Trends in Plant Science 5, 22-29.
3. Armengaud, P., Sulpice, R., Miller, A.J. et al. (2009) Multilevel analysis of primary metabolism provides new insights into the role of potassium nutrition for glycolysis and nitrogen assimilation in Arabidopsis roots. Plant Physiology 150, 772-785.
4. Arrivault, S., Guenther, M., Ivakov, A. et al. (2009) Use of reverse-phase liquid chromatography, linked to tandem mass spectrometry, to profile the Calvin cycle and other metabolic intermediates in Arabidopsis rosettes at different carbon dioxide concentrations. Plant Journal 59, 824-839.
5. Aubourg S., Lechamy, A. and Bohlmann J (2002) Genomic analysis of the terpenoid synthase (AtTPS) gene family of Arabidopsis thaliana. MolecularGenetics and Genomics 267, 730-745.
6. Bais, P., Moon, S.M., He, K. et al. (2010) Plantmetabolomics.org: A web portal for plant metabolomics experiments. Plant Physiology, 152, 1807-816.
7. Baxter, I., Ouzzani, M., Orcun, S. et al. (2007) Purdue ionomics information management system. An integrated functional genomics platform. Plant Physiology 143, 600-611.
8. Bedair, M. and Sumner, L.W. (2008) Current and emerging mass-spectrometry technologies for metabolomics. Trends in Analytical Chemistry 27, 238-250.
9. Bindschedler, L.V., Palmblad, M. and Cramer, R. (2008) Hydroponic isotope labelling of entire plants (HILEP) for quantitative plant proteomics: an oxidative stress case study. Phytochemistry 69, 1962-1972.
10. Bino, R.J., Hall, R.D., Fiehn, O. et al. (2004) Potential of metabolomics as a functional genomics tool. Trends in Plant Science 9, 418-425.
11. Bläsing, O.E., Gibon, Y., Gunther, M. et al. (2005) Sugars and circadian regulation make major contributions to the global regulation of diurnal gene expression in Arabidopsis. Plant Cell 17, 3257-3281.
12. Bloor, S.J. and Abrahams S. (2002) The structure of the major anthocyanin in Arabidopsis thaliana. Phytochemistry 59, 343-346.
13. Böttcher, C., von Roepenack-Lahaye, E., Schmidt, J. et al. (2008) Metabolome analysis of biosynthetic mutants reveals a diversity of metabolic changes and allows identification of a large number of new compounds in Arabidopsis. Plant Physiology 147, 2107-2120.
14. Bradbury, L.M.T., Gillies, S.A., Brushett, D.J. et al. (2008) Inactivation of an aminoaldehyde dehydrogenase is responsible for fragrance in rice. Plant Molecular Biology 68, 439-449.
15. Bringmann, G., Kajahn, I., Neusüß, C. et al. (2005) Analysis of the glucosinolate pattern of Arabidopsis seeds by capillary zone electrophoresis coupled to electrospray ionisation-mass spectrometry. Electrophoresis 26, 1513-1522.
16. Brown, P.D., Tokuhisa, J.G., Reichelt, M. et al. (2003) Variation of glucosinolate accumulation among different organs and developmental stages of Arabidopsis thaliana. Phytochemistry 62, 471-481.
17. Chen, F., Tholl, D., D'Auria, J.C. et al. (2003) Biosynthesis and emission of terpenoid volatiles from Arabidopsis flowers. Plant Cell 15, 481-494.
18. Chia, D.W., Yoder, T.J., Reiter, W-D. et al. (2000) Fumaric acid: an overlooked form of fixed carbon in Arabidopsis and other plant species. Planta 211, 743-751.
19. D'Auria, J.C. and Gershenzon, J. (2005) The secondary metabolism of Arabidopsis thaliana: growing like a weed. Current Opinion in Plant Biology 8, 308-316.
20. Dixon, R.A. and Strack, D. (2003) Phytochemistrymeets genome analysis, and beyond. Phytochemistry 62, 815-816.
21. Draper, J., Rasmussen, S. and Zubair, H. (2010) Metabolite analysis andmetabolomics in the study of biotrophic interactions between plants and microbes. In: Hall, R.D. (ed.) Annual Plant Reviews, Biology of PlantMetabolomics. Blackwell Publishing Ltd., Oxford, UK.
22. Dunn, W.B. and Ellis, D.I (2005) Metabolomics: current analytical platforms and methodologies. Trends in Analytical Chemistry 24, 285-294.
23. Facchini, P.J., Bird, D.A. and St-Pierre, B. (2004) Can Arabidopsis make complex alkaloids? Trends in Plant Science 9, 116-122.
24. Fahnenstich, H., Saigo, M., Andreo, C. et al. (2008) Malate and fumarate emerge as key players in primary metabolism: Arabidopsis thaliana overexpressing C4-NADP-ME offer a way to manipulate the levels of malate and to analyse the physiological consequences. In: Allen, J.F. et al. (eds.) Photosynthesis. Energy from the Sun: 14th International Congress on Photosynthesis, pp. 971-975. Springer.
25. Fellenberg, C., Bottcher, C. and Vogt, T. (2009) Phenylpropanoid polyamine conjugate biosynthesis in Arabidopsis thaliana flower buds. Phytochemistry 70, 1392-1400.
26. Fernie, A.R. Trethewey, R.N., Krotzky, A.J. et al. (2004) Metabolite profiling: from diagnostics to systems biology. Nature Reviews, Molecular Cell Biology 5, 1-7.
27. Fiehn, O. (2002) Metabolomics - the link between genotypes and phenotypes. Plant Molecular Biology 48, 155-171.
28. Fiehn, O. (2006) Metabolite profiling in Arabidopsis. In: Salinas, J. and Sanchez-Serrano, J.J (eds.) Arabidopsis Protocols. Methods in Molecular Biology, 2nd edn, pp. 439-477. Humana Press, NJ.
29. Fiehn, O. (2008) Extending the breadth of' metabolite profiling by gas chromatography coupled to mass spectrometry. Trends in Analytical Chemistry 27, 261-269.
30. Fiehn, O., Kopka, J., Dormann, P. et al. (2000) Metabolite profiling for plant functional genomics. Nature Biotechnology 18, 1157-1161.
31. Fiehn, O., Kind, T., Kumar Barupal, D.K. (2010) Data processing, metgabolomics databases and pathway analysis. In: Hall, R.D. (ed.) Annual Plant Reviews, Biology of Plant Metabolomics. Blackwell Publishing Ltd.
32. Fu, J., Keurentjes, J.J.B., Bouwmeester, H. et al. (2009) System-widemolecular evidence for phenotypic buffering in Arabidopsis. Nature Genetics 41, 166-167.
33. Fukushima, A., Kusano, M., Redestig, H. et al. (2009). Integrated omics approaches in plant systems biology. Current Opinion in Chemical Biology 13, 1-7.
34. Garcia-Hernandez M., Berardini T.Z., Chen G. et al. (2002) TAIR: a resource for integrated Arabidopsis data. Functional and Integrated Genomics 2, 239-253.
35. Ghassemian, M., Lutes, J., Teppermann, J.M. et al. (2006) Integrative analysis of transcript and metabolite profiling data sets to evaluate the regulation of biochemical pathways during photomorphogenesis. Archives, Biochemistry Biophysics 448, 45-49.
36. Giavalisco, P., Hummel, J., Lisec, J. et al. (2008) High-resolution direct infusion-based mass spectrometry in combination with whole 13C metabolome isotope labelling allows unambiguous assignment of chemical sum formulas. Analytical Chemistry 80, 9417-9425.
37. Gibon, Y., Usadel, B., Blaesing, O.E. et al. (2006) Integration of metabolite with transcript and enzyme activity profiling during diurnal cycles in Arabidopsis rosettes. Genome Biology 7, R76.
38. Griffiths J., Murase K., Rieu I. et al. (2006) Genetic Characterization and Functional Analysis of the GID1 Gibberellin Receptors in Arabidopsis. Plant Cell 18, 3399-3414.
39. Gu, L., Jones, A.D. and Last, R.L. (2010) Broad connections in the Arabidopsis seed metabolic network revealed by metabolite profiling of an amino acid catabolism mutant. Plant Journal 61, 579-590.
40. Gullberg, J., Jonsson, P., Nordstrom, A. et al. (2004) Design of experiments: an efficient strategy to identify factors influencing extraction and derivitisation of Arabidospis thaliana samples inmetabolomic studies with gas chromatography/mass spectrometry. Analytical Biochemistry 331, 283-295.
41. Hall, R.D. (2006) Plant metabolomics: from holistic hope, to hype, to hot topic. New Phytologist 169, 453.
42. Hegeman, A.D., Schulte, C.F., Cui, Q. et al. (2007) Stable isotope assisted assignment of elemental compositions for metabolomics. Analytical Chemistry 79, 6912-6921.
43. Hendrawati, O., Yao, Q., Kim, H.K. et al. (2006) Metabolic differentiation of Arabidopsis treated with methyl jasmonate using nuclear magnetic resonance spectroscopy. Plant Science 170, 1118-1124.
44. Hirai, M.Y., Yano, M., Goodenowe, D.B. et al. (2004) Integration of transcriptomics and metbolomics for understanding of global responses to nutritional stresses in Arabidopsis thaliana. Proceedings National Academy Sciences USA. 101, 10205-10210.
45. Hirai, M.Y., Klein, M., Fujikawa, Y. et al. (2005) Elucidation of gene-to-gene and metabolite-to-gene networks in Arabidopsis by integration of metabolomics and transcriptomics. Journal Biological Chemistry 280, 25590-25595.
46. Hirai, M.Y., Sugiyama, K., Sawada, Y. et al. (2007) Omics-based identification of Arabidopsis Myb transcription factors regulating aliphatic glucosinolate biosynthesis. Proceedings National Academy Sciences USA 104, 6478-6483.
47. Kai, K., Shimizu, B, Mizutani, M. et al. (2006) Accumulation of coumarins inArabidopsis thaliana. Phytochemistry 67, 379-386.
48. Kerhoas, L., Aouak, D., Cingoz, A. et al. (2006) Structural characterisation of the major flavonoid glycosides from Arabidopsis thaliana seeds. Journal Agricultural Food Chemistry 54, 6603-6612.
49. Keurentjes, J.J.B. (2009) Genetical metabolomics: closing in on phenotypes. Current Opinion in Plant Biology 12, 223-230.
50. Keurentjes, J.J.B., Fu, J., de Vos, C.H.R. et al. (2006) The genetics of plant metabolism. Nature Genetics 7, 842-849.
51. Kikuchi, J., Shinozaki, K., Hirayama, T. (2004) Stable isotope labelling of Arabidopsis thaliana for an NMR based metabolomics approach. Plant Cell Physiology 45, 1099-1104.
52. Kirch, H-H., Bartels, D., Wei, L. et al. (2004) The ALDH gene superfamily of Arabidopsis. Trends in Plant Science 9, 371-377.
53. Kliebenstein, D.J., Kroymann, J., Brown, P. et al. (2001) Genetic control of natural variation in Arabidopsis glucosinolate accumulation. Plant Physiology 126, 811-825.
54. Kolbe, A., Oliver, S.N., Fernie, A.R. et al. (2006) Combined transcript and metabolite profiling of Arabidopsis leaves reveals fundamental effects of the thiol-disulfide status on plant metabolism. Plant Physiology 141, 412-422.
55. Kover, P.X., Valder, W., Trakalo, J. et al. (2009) A multiparent advanced generation inter-cross to fine-map quantitative traits in Arabidopsis thaliana. PloS Genetics 5, e10000551.
56. Kusano, M., Fukushima, A., Arita, M. et al. (2007) Unbiased characterisation of genotype-dependent metabolic regulations by metabolomic approach in Arabidopsis thaliana. BMC Systems Biology 1, 53.
57. Laskar, D.D., Jourdes, M., Patten, A.M. et al. (2006) The Arabidopsis cinnamoyl CoA reductase irx4 mutant has a delayed but coherent (normal) program of lignification. Plant Journal 48, 674-686.
58. Lisec, J., Meyer, R.C., Steinfath, M. et al. (2008) Identificaion of metabolic and biomass QTL in Arabidopsis thaliana in a parallel analysis of RIL and IL populations. Plant Journal 53, 960-972.
59. Lisec, J., Steinfath, M., Meyer, R.C. et al. (2009) Identification of heterotic metabolite QTL in Arabidopsis thaliana RIL and IL populations. Plant Journal 59, 777-788.
60. Ljung, K., Sandberg, G. and Moritz, T., (2004) Methods of plant hormone analysis. In: Davies, P.J. (ed.) Plant Hormones, Biosynthesis, Signal Transduction and Action! Kluwer, pp. 671-694.
61. Lunn, J.E., Feil, R., Hendriks, J.H.M. et al. (2006) Sugar-induced increases in trehalose 6-phophate are correlated with redox activation ofADPglucose pyrophosphorylase and higher rates of starch synthesis in Arabidopsis thaliana. Biochemical Journal 397, 139-148.
62. Markley, J.L., Anderson, M.E., Cui, Q. et al. (2007) New bioinformatics resources for metabolomics. Pacific Symposium on Biocomputing 12, 157-168.
63. Matsuda, F., Yonekura-Sakakibara, K., Niida, R. et al. (2009) MS/MSspectral tag-based annotation of non-targeted profile of plant secondary metabolites. Plant Journal 57, 555-577.
64. Matsuda, F., Hirai, M.Y., Sasaki, E. et al. (2010) AtMetExpress development: a phytochemical atlas of Arabidopsis development. Plant Physiology 152, 566-578.
65. Maruyama, K., Takeda, M., Kidokoro, S. et al. (2009) Metabolic pathways involved in cols acclimation identified by integrated analysis of metabolites and transcripts regulated by DREB1A and DREB2A. Plant Physiology 150, 1972-1980.
66. Messerli, G., Nia, V.P., Trevisan, M. et al. (2007) Rapid classification of phenotypic mutants of Arabidopsis via metabolite fingerprinting. Plant Physiology 143, 1484-1492.
67. Nakabayashi, R., Kusano, M., Kobayashi, M. et al. (2009) Metabolomics-oriented isolation and structure elucidation of 37 compounds including two anthocyanins from Arabidopsis thaliana. Phytochemistry 70, 1017-1029.
68. Nakamura, Y., Kimura, A., Saga, H. et al. (2007) Differential metabolomics unravelling light/dark regulation of metabolic activities in Arabidopsis cell culture. Planta 227, 57-66.
69. Nikiforova, V.J., Gakiere, B., Kempa, S. et al. (2004) Towards dissecting nutrient metabolism in plants: a systems biology case study on sulfur metabolism. Journal Experimental Botany 55, 1861-1870.
70. Nikiforova, V.J., Kopka, J., Tolstikov, V. et al. (2005) Systems rebalancing of metabolism in reponse to sulfur deprivation, as revealed bymetabolome analysis of Arabidopsis plants. Plant Physiology 138, 304-318.
71. Oikawa, A., Nakamura, Y., Ogura, T. et al. (2006) Clarification of pathway-specific inhibition by fourier transform ion cyclotron resonance/mass spectrometry-based metabolic phenotyping studies. Plant Physiology 142, 398-413.
72. Okamoto, M. Hanada, A. Kamiya, Y. et al. (2009) Measurement of abscisic acid and gibberellins by gas chromatography/mass spectrometry. In: Cutler, S. and Bonetta, D. (eds.) Plant hormones, methods and protocols, Springer protocols, Methods in Molecular Biology, 495, pp. 53-60. Humana Press.
73. Okazaki, Y., Shimojima, M., Sawada, Y. et al. (2009) A chloroplastic UDP-glucose pyrophosphorylase from Arabidopsis is the committed enzyme for the first step of sulfolipid biosynthesis. Plant Cell 21, 892-909.
74. Pan, X. andWang, X. (2009) Profiling of plant hormones by mass spectrometry. Journal of Chromatography B 877, 2806-2813.
75. Paquette, S.M. Jensen, K. and Bak, S. (2009) A web-based resource for the Arabidopsis P450, cytochrome b5, NADPH-cytochrome P450 reductases, and family 1 glycosyltransferases (http://www.P450.kvl.dk). Phytochemistry 70, 1940-1947.
76. Ramautar, R, Somsen, G.W. and de Jong, G.J. (2009) CE-MS in metabolomics. Electrophoresis 30, 276-291.
77. Reichelt M., Brown, P.D., Schneider, B. et al. (2002) Benzoic acid glucosinolate esters and other glucosinolates from Arabidopsis thaliana. Phytochemistry 59, 663-671.
78. Rohde, A., Morreel, K., Ralph, J. et al. (2004) Molecular phenotyping of the pal and pal2 mutants of Arabidopsis thaliana reveals far-reaching consequences on phenylpropanoid, amino-acid ad carbohydrate metabolism. Plant Cell 16, 2749-2771.
79. Rohloff, J. and Bones, A.M. (2005) Volatile profiling of Arabidopsis thaliana - putative olfactory compounds in plant communication. Phytochemistry 66, 859-867.
80. Rosenstiel, T.N., Ebbets, A.L., Khatri, W.C. et al. (2004) Induction of Poplar leaf nitrate reductase: a test of extrachloroplastic control of isoprene emission rate. Plant Biology 6, 12-21.
81. Roessner U., Wagner, C., Kopka, J. et al. (2000) Simultaneous analysis of metabolites in ptato tuber by gas chromatography-mass spectrometry. Plant Journal 23, 131-142.
82. Rowe, H.C., Hansen, B. G., Halkier, B.A. et al. (2008) Biochemical networks and epistasis shape the Arabidopsis thaliana metabolome. Plant Cell 20, 1199-1216.
83. Saito, K., Hirai, M.Y. and Yonekura-Sakakibara, K. (2007) Decoding genes with coexpression networks and metabolomics - 'majority report by precogs'. Trends in Plant Science 13, 36-43.
84. Sato, D., Awad, A.A., Chae, S.H. et al. (2003) Analysis of strigolactones, germination stimulants for Striga and Orobanche, by high-performance liquid chromatography/tandemmass spectrometry. Journal of Agricultural and Food Chemistry 51, 1162-1168.
85. Sato, S., Soga, T., Nishioka, T. et al. (2004) Simultaneous determination of the main metabolites in rice leaves using capillary electrophoresis mass spectrometry and capillary electrophoresis diode array detection. Plant Journal 40, 151-163.
86. Sato, S., Arita, M., Soga, T. et al. (2008) Time-resolved metabolomics reveals metabolic modulation in ric foliage. BMC Systems Biology 2, 51.
87. Sawada, Y., Akiyama, K., Sakata, A. et al. (2009) Widely targeted metabolomics based on large-scale MS/MS data for elucidating metabolite accumulation patterns in plants. Plant Cell Physiology 50, 37-47.
88. Schuler, M.A. and Werck-Reichhart, D. (2003) Functional genomics of P450s. Annual Review Plant Biology 54, 629-667.
89. Sharkey, T.D., Wiberley, A.E andDonohue, A.R. (2008) Isoprene emission from plants: why and how. Annals of Botany 101, 5-18.
90. Steeghs, M., Bais, H.P., de Gouw, J. et al. (2004) Proton-transfer-reactionmass spectrometry as a new tool for real time analysis of root secreted volatile organic compounds in Arabidopsis. Plant Physiology 135, 47-58.
91. Sun, X., Zhang, J., Zhang, H. et al. (2010) The responses of Arabidopsis thaliana to cadmium exposure via metabolite profiling. Chemosphere 78, 840-845.
92. Tian, C., Chikayama, E. Tsuboi, Y. et al. (2007) Top-down phenomics of Arabidopsis thaliana. Journal of Biological Chemistry 282, 18532-18541.
93. Tohge, T., Nishiyama, Y., Hirai, M.Y. et al. (2005) Functional genomics by integrated analysis of metabolome and transcriptome of Arabidopsis plants over-expressing an MYB transcription factor. Plant Journal 42, 218-235.
94. Tohge, T., Yonekura-Sakiakibara, K., Niida, R. et al. (2007) Phytochemical genomics in Arabidopsis thaliana: A case study for functional identification of flavonoid biosynthesis genes. Pure and Applied Chemistry 79, 811-823.
95. Trethewey, R.N. (2001) Gene discovery via metabolic profiling. Current Opinion in Biotechnology 12, 135-138.
96. Urano, K., Maruyama, K., Ogata, Y. et al. (2009) Characterisation of the ABA-regulated global responses to dehydration in Arabidopsis by metabolomics. Plant Journal 57, 1065-1078.
97. vanDongen, J.T., Frohlich, A., Ramirez-Aguilar, S.J. et al. (2009) Transcript and metabolite profiling of the adaptive response to mild decreases in oxygen concentration in the roots of Arabidopsis plants. Annals of Botany 103, 269-280.
98. Veit M. and Pauli, G.F. (1999) Major flavonoids from Arabidopsis thaliana leaves. Journal of Natural Products 62, 1301-1303.
99. Viant, M. (2003) Improved methods for the acquisition and interpretation of NMR metabolomic data. Biochemistry Biophysics Research Communications 310, 943-948.
100. von Roepenack-Lahaye, E., Degenkolb, T., Zerjeski, M. et al. (2004) Profiling of Arabidopsis secondary metabolites by capillary liquid chromatography coupled to electrospray ionisation quadrupole time-of-flight mass spectrometry. Plant Physiology 134, 548-559.
101. Ward, J.L., Harris, C., Lewis, J. et al. (2003) Assessment of 1H-NMR spectroscopy and multivariate analysis as a technique for metabolite fingerprinting of Arabidopsis thaliana. Phytochemistry 62, 949-957.
102. Ward, J.L., Baker, J.M. and Beale, M.H. (2007) Recent applications of NMR Spectroscopy in plant metabolomics. FEBS Journal 274, 1126-1131.
103. Ward, J.L., Baker, J.M., Miller, S.J., et al.. (2010) Aninter-laboratory comparison demonstrates that [1H]-NMR metabolite fingerprinting is a robust technique for collaborative plant metabolomic data collection. Metabolomics, 6, 263-273.
104. Weckwerth, W., Wenzel, K. and Fiehn, O. (2004a) Process for the integrated extrcation, identification and quantitification of metabolites, proteins and RNA to reveal their co-regulation in biochemical networks. Proteomics 4, 78-83.
105. Weckwerth, W., Loureiro, M.E., Wenzel, K. et al. (2004b) Differential metabolic networks unravel the effects of silent plant phenotypes. Proceedings National Academy Sciences USA 101, 7809-7814.
106. Welti, R., Shah, J., Li, W. et al. (2007) Plant lipidomics: discerning biological function by profiling plant complex lipids using mass spectrometry. Frontiers in Bioscience 12, 2494-2506.
107. Wittstock U. and Halkier, B.A. (2002) Glucosinolate research in the Arabidopsis era. Trends Plant Science 7, 263-270.
108. Yonekura-Sakakibara, K., Tohge, T., Matsuda, F. et al. (2008) Comprehensive flavonol profiling and transcriptome coexpression analysis leading to decoding genemetabolite correlations in Arabidopsis. Plant Cell 20, 2160-2176.