Temporally resolved GC-MS-based metabolic profiling of herbicide treated plants treated reveals that changes in polar primary metabolites alone can distinguish herbicides of differing mode of action

Metabolomics

Volumn 5, Issue 3, 2009, Pages 277-291

  Trenkamp, Sandra ^a   Eckes, Peter ^b   Busch, Marco ^b   Fernie, Alisdair R ^a  

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

^b BAYER CROPSCIENCE AG   (Germany)

Author keywords

GC MS; Herbicide; Metabolic profiling; Mode of action

Indexed keywords

ARABIDOPSIS; ARABIDOPSIS THALIANA;

EID: 70149116999     PISSN: 15733882     EISSN: 15733890     Source Type: Journal    
DOI: 10.1007/s11306-008-0149-8     Document Type: Article

References (38)

1. Aharoni, A., de Vos, R. C. H., Verhoeven, H. A., Maliepaard, C. A., Kruppa, G., Bino, R., et al. (2002). Non-targeted metabolome analysis by use of Fourier Transform Ion Cyclotron Mass Spectrometry. OMICS, 6, 217-234. doi: 10.1089/15362310260256882.
2. Amrhein, N., Schab, J., & Steinrucken, H. C. (1980). The mode of action of glyphosate. Naturwissenschaft, 67, 356-357. doi: 10.1007/ BF01106593.
3. Aranibar, N., Singh, B. K., Stockton, G. W., & Ott, K. H. (2001). Automated mode of action detection by metabolic profiling. Biochemical and Biophysical Research Communications, 286, 150-155. doi: 10.1006/ bbrc.2001.5350.
4. Barsch, A., Carvalho, H. G., Cullimore, J. V., & Niehaus, K. (2006). GC-MS profiling implies three independent ways of ammonium assimilation in Medicago truncatula root nodules. Journal of Biotechnology, 127, 79-83. doi: 10.1016/j.jbiotec.2006.06.007.
5. Böttcher, C., Centeno, D., Freitag, J., Höfgen, R., Köhl, K., Kopka, J., et al. (2008). Teaching (and learning from) metabolomics: The 2006 PlantMetaNet ETNA Metabolomics research school. Physiologia Plantarum, 132, 136-144.
6. Brindle, J. T., Antti, H., Holmes, E., Tranter, G., Nicholson, J. K., Bethell, H. W. L., et al. (2002). Rapid and non-invasive diagnosis of the presence and severity of coronary heart disease using H-1-NMR-based metabonomics. Nature Medicine, 8, 1439-1444. doi: 10.1038/nm802.
7. Catchpole, G. S., Beckmann, M., Enot, D. P., Mondhe, M., Zywicki, B., Taylor, J., et al. (2005). Hierarchical metabolomics demonstrates substantial composition similarity between genetically modified and conventional potato crops. Proceedings of the National Academy of Sciences of the United States of America, 102, 14458-14462. doi: 10.1073/ pnas.0503955102.
8. DeMaria, N., Becerril, J. M., Garcia-Plazaola, J. I., Hernandez, A., De Felipe, M. R., & Fernandez-Pascual, M. (2006). New insights on glyphosate mode of action in nodular metabolism: Role of shikimate accumulation. Journal of Agricultural and Food Chemistry, 54, 2621-2628. doi: 10.1021/jf058166c.
9. Eckes, P., & Busch, M. (2007). Fast identification of the mode of action of herbicides by DNA chips. In W. Krämer & U. Schirmer (Eds.), Modern crop protection compounds (pp. 1161-1174). Weinheim, Germany: Wiley.
10. Fernie, A. R., Trethewey, R. N., Krotzky, A., & Willmitzer, L. (2004). Metabolite profiling: From diagnostics to systems biology. Nature Reviews. Molecular Cell Biology, 5, 763-769. doi: 10.1038/nrm1451.
11. Fiehn, O., Kopka, J., Dörmann, P., Altmann, T., Trethewey, R. N., & Willmitzer, L. (2000). Metabolic profiling for plant functional genomics. Nature Biotechnology, 18, 1157-1161. doi: 10.1038/81137.
12. Gaston, S., Ribas-Carbo, M., Busquets, S., Berry, J. A., Zabalaza, A., & Royuela, M. (2003). Changes in mitochondrial electron partitioning in response to herbicides inhibiting branched chain amino acid biosynthesis in soybean. Plant Physiology, 133, 1351-1359. doi: 10.1104/ pp.103.027805.
13. Hacker, E., Bieringer, H., Willms, L., Schnabel, G., Koecher, H., Hagenteister, H., et al. (2002). Foramsulfuron plus safener - a new technology for weed control in maize. Journal of Plant Diseases and Protection, 18(Special Issue), 747-756.
14. Iijima, Y., Nakamura, Y., Ogata, Y., Tanaka, K., Sakurai, N., Suda, K., et al. (2008). Metabolite annotations based on the integration of mass spectral information. The Plant Journal, 54, 949-962. doi: 10.1111/ j.1365-313X.2008.03434.x.
15. Kiedaisch, B. M., Blanton, R. L., & Haigler, C. H. (2003). Characterisation of a novel cellulose synthesis inhibitor. Planta, 217, 922-930. doi: 10.1007/s00425-003-1071-y.
16. Kopka, J., Schauer, N., Krueger, S., Birkmeyer, C., Usadel, B., Bergmuller, E., et al. (2005). GMDΓSB.DB: The Golm Metabolome Database. Bioinformatics (Oxford, England), 21, 1635-1638. doi: 10.1093/ bioinformatics/bti236.
17. Lechelt-Kunze, C., Meissner, R. C., Drewes, M., & Tietjen, K. (2003). Flufenacet herbicide treatment phenocopies the fiddlehead mutant in Arabidopsis thaliana. Pest Management Science, 59, 847-856. doi: 10.1002/ps.714.
18. Lein, W., Bornke, F., Reindl, A., Erhardt, T., Stitt, M., & Sonnewald, U. (2004). Target-based discovery of novel herbicides. Current Opinion in Plant Biology, 7, 219-225. doi: 10.1016/ j.pbi.2004.01.001.
19. Lisec, J., Schauer, N., Kopka, J., Willmitzer, L., & Fernie, A. R. (2006). Gas chromatrography mass spectrometry-based metabolite profiling in plants. Nature Protocols, 1, 387-396. doi: 10.1038/nprot.2006.59.
20. Menne, H., & Köcher, H. (2007). HRAC classification of herbicides and resistance development. In W. Krämer & U. Schirmer (Eds.), Modern crop protection compounds (pp. 5-26). NY: Wiley.
21. Oikawa, A., Nakamura, Y., Ogura, T., Kimura, A., Suzuki, H., Sakarai, N., 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. doi: 10.1104/pp.106.080317.
22. Ott, K. H., Aranibar, N., Singh, B. J., & Stockton, G. W. (2003). Metabononics classifies pathways affected by bioactive compounds. Artificial neural network classification of NMR spectra of plant extracts. Phytochemistry, 62, 971-985. doi: 10.1016/ S0031-9422(02)00717-3.
23. Pallett, K. E. (2000). Mode of action of isoxaflutole - a case study of an emerging target site. In A. H. Cobb & R. C. Kirkwood (Eds.), Herbicides and their mechanisms of action (pp. 215-238). Sheffield: Sheffield Academic Press.
24. Petroff, O. A. C. (1988). Biological 1HNMR spectroscopy. Comparative Biochemistry and Physiology, 90B, 249-260.
25. Raghavan, C., Ong, E. K., Dalling, M. J., & Stevenson, T. W. (2006). Regulation of genes associated with auxin, ethylene and ABA pathways by 2-4-dichlorophenoxyacetic acid in Arabidopsis. Functional and Integrative Genomics, 6, 60-70. doi: 10.1007/s10142-005-0012-1.
26. Ray, T. B. (1984). Site of action of chlorsulfon. Plant Physiology, 133, 1351-1359.
27. Roessner, U., Luedemann, A., Brust, D., Fiehn, O., Linke, T., Willmitzer, L., et al. (2001). Metabolite profiling allows comprehensive phenotyping of genetically or environmentally modified plant systems. The Plant Cell, 13, 11-29.
28. Saeed, A. I., Sharov, V., White, J., Li, J., Liang, W., Bhagabati, N., et al. (2003). TM4: A free open-source system for microarray data management and analysis. BioTechniques, 34, 374-378.
29. Sauter, H., Lauer, M., & Fritsch, H. (1991). Metabolic profiling of plants - a new diagnostic technique. In D. R. Baker, J. G. Fenyes, & M. K. Moberg (Eds.), Synthesis and chemistry of Agrochemicals II. ACS Symposium Series 443(pp. 288-299). Washington, DC: American Chemical Society.
30. Schauer, N., Semel, Y., Roessner, U., Gur, A., Balbo, I., Carrari, F., et al. (2006). Comprehensive metabolic profiling and phenotyping of interspecific introgression lines for tomato improvement. Nature Biotechnology, 24, 447-454. doi: 10.1038/nbt1192.
31. Schauer, N., Steinhauser, D., Strelkov, S., Schomburg, D., Allison, G., Moritz, T., et al. (2005). GC-MS libraries for the rapid identification of metabolites in complex biological samples. FEBS Letters, 579, 1332-1337. doi: 10.1016/j.febslet.2005.01.029.
32. Scholz, M., Gatzek, S., Sterling, A., Fiehn, O., & Selbig, J. (2004). Metabolic fingerprinting: Detecting biological features by independent component analysis. Bioinformatics, 20, 2447-2454.
33. Schulz, A., Ort, O., Beyer, P., & Kleinig, H. (1993). SC-0051, a 2-benzoyl-cyclohexane-1, 3-dione bleaching herbicide, is a potent inhibitor of the enzyme 4-hydroxyphenylpyruvate dioxygenase. FEBS Letters, 319, 162-166. doi: 10.1016/0014-5793(93)80013-K.
34. Servaites, J. C., Tucci, M. A., & Geiger, D. R. (1987). Glyphosate effects on carbon assimilation, ribulose bisphosphate carboxylase activity, and metabolite levels in sugar beet leaves. Plant Physiology, 85, 370-374.
35. Stitt, M., & Fernie, A. R. (2003). From measurements of metabolites to metabolomics an "on the fly" perspective illustrated by recent studies of carbon-nitrogen interactions. Current Opinion in Biotechnology, 14, 136-144. doi: 10.1016/S0958-1669(03)00023-5.
36. Shepherd, L. V. T., McNicol, J. W., Razzo, R., Taylor, M. A., Davies, H. V., & McNicol, J. W. (2005). Assessing the potential for unintended effects in genetically modified potatoes perturbed in metabolic and developmental processes. Targeted analaysis of key nutrients and anti-nutrients. Transgenic Research, 15, 409-425. doi: 10.1007/ s11248-006-0012-5.
37. Trenkamp, S., Martin, W., & Tietjen, K. (2004). Specific and differential inhibition of very-long chain fatty acid elongases from Arabidopsis thaliana by different herbicides. Proceedings of the National Academy of Sciences of the United States of America, 101, 11903-11908. doi: 10.1073/pnas.0404600101.
38. Yip, W. K., Moore, T., & Yang, S. F. (1992). Differential accumulation of transcripts for four tomato 1-aminocyclopropane-1-carboxylate synthase homologs under various conditions. Proceedings of the National Academy of Sciences of the United States of America, 89, 2475-2479. doi: 10.1073/pnas.89.6.2475.