Top-down phenomics of Arabidopsis thaliana: Metabolic profiling by one- and two-dimensional nuclear magnetic resonance spectroscopy and transcriptome analysis of albino mutants

Journal of Biological Chemistry

Volumn 282, Issue 25, 2007, Pages 18532-18541

  Tian, Chunjie ^a,b   Chikayama, Eisuke ^c   Tsuboi, Yuuri ^a,b   Kuromori, Takashi ^c   Shinozaki, Kazuo ^c   Kikuchi, Jun ^c,d,e,f   Hirayama, Takashi ^a,b,d,f  

^a Japan Science and Technology Agency   (Japan)

^b YOKOHAMA CITY UNIVERSITY   (Japan)

^c RIKEN Center for Sustainable Resource Science   (Japan)

^d JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

^e NAGOYA UNIVERSITY   (Japan)

^f RIKEN YOKOHAMA INSTITUTE   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ENZYME KINETICS; METABOLISM; METABOLITES; MUTAGENESIS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PLANTS (BOTANY);

ARABIDOPSIS THALIANA; METABOLIC ANALYSIS; METABOLIC FINGERPRINTING; TRANSCRIPTOME ANALYSIS;

GENE ENCODING;

ALIPHATIC COMPOUND; AMINO ACID; AROMATIC COMPOUND; ASPARAGINE; CARBON; CARBON 13; ENZYME; GLUCOSE; GLUTAMINE; NITROGEN;

ALBINISM; ARABIDOPSIS; ARTICLE; CARBON NUCLEAR MAGNETIC RESONANCE; CHLOROPLAST; CONTROLLED STUDY; DNA FINGERPRINTING; FEEDING; GENE DISRUPTION; GENE EXPRESSION PROFILING; ISOTOPE LABELING; METABOLIC REGULATION; METABOLITE; METABOLOMICS; MICROARRAY ANALYSIS; MUTANT; NONHUMAN; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PHOTOSYNTHESIS; PLANT GENETICS; PLANT METABOLISM; PRIORITY JOURNAL; PROTON NUCLEAR MAGNETIC RESONANCE;

ARABIDOPSIS; ARABIDOPSIS PROTEINS; CHLOROPLASTS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; GENE REGULATORY NETWORKS; GENES, PLANT; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, BIOLOGICAL; MUTATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PLANT PHYSIOLOGY; PLANT PROTEINS; PLANTS; TRANSCRIPTION, GENETIC;

ARABIDOPSIS; ARABIDOPSIS THALIANA;

EID: 34547123115     PISSN: 00219258     EISSN: 1083351X     Source Type: Journal    
DOI: 10.1074/jbc.M700549200     Document Type: Article

References (69)

1. Hirai, M. Y., Yano, M., Goodenowe, D. B., Kanaya, S., Kimura, T., Awazuhara, M., Arita, M., Fujiwara, T., and Saito, K. (2004) Proc. Natl. Acad. Sci. U. S. A. 101, 10205-10210
2. Stitt, M., Muller, C., Matt, P., Gibon, Y., Carillo, P., Morcuende, R., Scheible, W. R., and Krapp, A. (2002) J. Exp. Bot. 53, 959-970
3. Kolbe, A., Oliver, S. N., Fernie, A. R., Stitt, M., van Dongen, J. T., and Geigenberger, P. (2006) Plant Physiol. 141, 412-422
4. Mori, H. (2004) J. Biochem. Mol. Biol. 37, 83-92
5. Hughes, T. R., Robinson, M. D., Mitsakakis, N., and Johnston, M. (2004) Curr. Opin. Microbiol. 7, 546-554
6. Oliver, S. G. (2006) Philos. Trans. R. Soc. Lond. B Biol. Sci. 361, 477-482
7. Raamsdonk, L. M., Teusink, B., Broadhurst, D., Zhang, N., Hayes, A., Walsh, M. C., Berden, J. A., Brindle, K. M., Kell, D. B., Rowland, J. J., Westerhoff, H. V., van Dam, K., and Oliver, S. G. (2001) Nat. Biotechnol. 19, 45-50
8. Giaever, G., Chu, A. M., Ni, L., Connelly, C., Riles, L., Veronneau, S., Dow, S., Lucau-Danila, A., Anderson, K., Andre, B., Arkin, A. P., Astromoff, A., El-Bakkoury, M., Bangham, R., Benito, R., Brachat, S., Campanaro, S., Curtiss, M., Davis, K., Deutschbauer, A., Entian, K. D., Flaherty, P., Foury, F., Garfinkel, D. J., Gerstein, M., Gotte, D., Guldener, U., Hegemann, J. H., Hempel, S., Herman, Z., Jaramillo, D. F., Kelly, D. E., Kelly, S. L., Kotter, P., LaBonte, D., Lamb, D. C., Lan, N., Liang, H., Liao, H., Liu, L., Luo, C., Lussier, M., Mao, R., Menard, P., Ooi, S. L., Revuelta, J. L., Roberts, C. J., Rose, M., Ross-Macdonald, P., Scherens, B., Schimmack, G., Shafer, B., Shoemaker, D. D., Sookhai-Mahadeo, S., Storms, R. K., Strathern, J. N., Valle, G., Voet, M., Volckaert, G., Wang, C. Y., Ward, T. R., Wilhelmy, J., Winzeler, E. A., Yang, Y., Yen, G., Youngman, E., Yu, K., Bussey, H., Boeke, J. D., Snyder, M., Philippsen, P., Davis, R. W., and Johnston, M. (2002) Nature 418, 387-391
9. Ishii, N., Soga, T., Nishioka, T., and Tomita, M. (2005) Metabolomics 1, 29-37
10. Fong, S. S., and Palsson, B. O. (2004) Nat. Genet. 36, 1056-1058
11. Ibarra, R. U., Edwards, J. S., and Palsson, B. O. (2002) Nature 420, 186-189
12. Thiele, I., Price, N. D., Vo, T. D., and Palsson, B. O. (2005) J. Biol. Chem. 280, 11683-11695
13. Thiele, I., Vo, T. D., Price, N. D., and Palsson, B. O. (2005) J. Bacteriol. 187, 5818-5830
14. Arabidopsis Genome Initiative (2000) Nature 408, 796-815
15. Goff, S. A., Ricke, D., Lan, T. H., Presting, G., Wang, R., Dunn, M., Glazebrook, J., Sessions, A., Oeller, P., and Varma, H. (2002) Science 296, 92-100
16. Yu, J., Hu, S., Wang, J., Wong, G. K., Li, S., Liu, B., Deng, Y., Dai, L., Zhou, Y., Zhang, X., Cao, M., Liu, J., Sun, J., Tang, J., Chen, Y., Huang, X., Lin, W., Ye, C., Tong, W., Cong, L., Geng, J., Han, Y., Li, L., Li, W., Hu, G., Huang, X., Li, W., Li, J., Liu, Z., Li, L., Liu, J., Qi, Q., Liu, J., Li, L., Li, T., Wang, X., Lu, H., Wu, T., Zhu, M., Ni, P., Han, H., Dong, W., Ren, X., Feng, X., Cui, P., Li, X., Wang, H., Xu, X., Zhai, W., Xu, Z., Zhang, J., He, S., Zhang, J., Xu, J., Zhang, K., Zheng, X., Dong, J., Zeng, W., Tao, L., Ye, J., Tan, J., Ren, X., Chen, X., He, J., Liu, D., Tian, W., Tian, C., Xia, H., Bao, Q., Li, G., Gao, H., Cao, T., Wang, J., Zhao, W., Li, P., Chen, W., Wang, X., Zhang, Y., Hu, J., Wang, J., Liu, S., Yang, J., Zhang, G., Xiong, Y., Li, Z., Mao, L., Zhou, C., Zhu, Z., Chen, R., Hao, B., Zheng, W., Chen, S., Guo, W., Li, G., Liu, S., Tao, M., Wang, J., Zhu, L., Yuan, L., and Yang, H. (2002) Science 296, 79-92
17. Sasaki, T., Matsumoto, T., Yamamoto, K., Sakata, K., Baba, T., Katayose, Y., Wu, J., Niimura, Y., Cheng, Z., and Nagamura, Y. (2002) Nature 420, 312-316
18. Weckwerth, W. (2003) Annu. Rev. Plant Biol. 54, 669-689
19. Sweetlove, L. J., Last, R. L., and Fernie, A. R. (2003) Plant Physiol. 132, 420-425
20. Alonso, J. M., and Ecker, J. R. (2006) Nat. Rev. Genet. 7, 524-536
21. Kuromori, T., Wada, T., Kamiya, A., Yuguchi, M., Yokouchi, T., Imura, Y., Takabe, H., Sakurai, T., Akiyama, K., Hirayama, T., Okada, K., and Shinozaki, K. (2006) Plant J. 47, 640-651
22. Kuromori, T., Hirayama, T., Kiyosue, Y., Takabe, H., Mizukado, S., Sakurai, T., Akiyama, K., Kamiya, A., Ito, T., and Shinozaki, K. (2004) Plant J. 37, 897-905
23. Kikuchi, J., and Hirayama, T. (2006) Biotechnology in Agriculture and Forestry, Plant Metabolomics (Saito, K., Dixon, R. A., and Willmitzer, L., eds) Vol. 57, pp. 93-101, Springer-Verlag, Berlin
24. Kikuchi, J., and Hirayama, T. (2006) in Metabolomics: Methods and Protocols (Weckwerth, W., ed) pp. 273-286, Humana Press Inc., Totowa, NJ
25. Delaglio, F., Grzesiek, S., Vuister, G. W., Zhu, G., Pfeifer, J., and Bax, A. (1995) J. Biomol. NMR 6, 277-293
26. Kikuchi, J., Shinozaki, K., and Hirayama, T. (2004) Plant Cell Physiol. 45, 1099-1104
27. Wettenhall, J. M., Simpson, K. M., Satterley, K., and Smyth, G. K. (2006) Bioinformatics 22, 897-899
28. Thimm, O., Blasing, O., Gibon, Y., Nagel, A., Meyer, S., Kruger, P., Selbig, J., Muller, L. A., Rhee, S. Y., and Stitt, M. (2004) Plant J. 37, 914-939
29. Saeed, A. I., Sharov, V., White, J., Li, J., Liang, W., Bhagabati, N., Braisted, J., Klapa, M., Currier, T., Thiagarajan, M., Sturn, A., Snuffin, M., Rezantsev, A., Popov, D., Ryltsov, A., Kostukovich, E., Borisovsky, I., Liu, Z., Vinsavich, A., Trush, V., and Quackenbush, J. (2003) BioTechniques 34, 374-378
30. Smith, D., Yanai, Y., Liu, Y. G., Ishiguro, S., Okada, K., Shibata, D., Whittier, R. F., and Fedoroff, N. V. (1996) Plant J. 10, 721-732
31. Muskett, P. R., Clissold, L., Marocco, A., Springer, P. S., Martienssen, R., and Dean, C. (2003) Plant Physiol. 132, 506-516
32. Hsieh, M. H., and Goodman, H. M. (2006) Planta 223, 779-784
33. Fellermeier, M., Raschke, M., Sagner, S., Wungsintaweekul, J., Schuhr, C. A., Hecht, S., Kis, K., Radykewicz, T., Adam, P., Rohdich, F., Eisenreich, W., Bacher, A., Arigoni, D., and Zenk, M. H. (2001) Eur. J. Biochem. 268, 6302-6310
34. Hsieh, M. H., and Goodman, H. M. (2005) Plant Physiol. 138, 641-653
35. Pfalz, J., Liere, K., Kandlbinder, A., Dietz, K. J., and Oelmuller, R. (2006) Plant Cell 18, 176-197
36. Emanuelsson, O., Nielsen, H., Brunak, S., and von Heijne, G. (2000) J. Mol. Biol. 300, 1005-1016
37. Bi, Y. M., Zhang, Y., Signorelli, T., Zhao, R., Zhu, T., and Rothstein, S. (2005) Plant J. 44, 680-692
38. Rastogi, R., Bate, N. J., Sivasankar, S., and Rothstein, S. J. (1997) Plant Mol. Biol. 34, 465-476
39. Harmer, S. L., Hogenesch, J. B., Straume, M., Chang, H. S., Han, B., Zhu, T., Wang, X., Kreps, J. A., and Kay, S. A. (2000) Science 290, 2110-2113
40. Blasing, O. E., Gibon, Y., Gunther, M., Hohne, M., Morcuende, R., Osuna, D., Thimm, O., Usadel, B., Scheible, W. R., and Stitt, M. (2005) Plant Cell 17, 3257-3281
41. Coruzzi, G. M., and Zhou, L. (2001) Curr. Opin. Plant Biol. 4, 247-253
42. Lawlor, D. W. (2002) J. Exp. Bot. 53, 773-787
43. Scheible, W. R., Morcuende, R., Czechowski, T., Fritz, C., Osuna, D., Palacios-Rojas, N., Schindelasch, D., Thimm, O., Udvardi, M. K., and Stitt, M. (2004) Plant Physiol. 136, 2483-2499
44. Takei, K., Sakakibara, H., Taniguchi, M., and Sugiyama, T. (2001) Plant Cell Physiol. 42, 85-93
45. Takei, K., Ueda, N., Aoki, K., Kuromori, T., Hirayama, T., Shinozaki, K., Yamaya, T., and Sakakibara, H. (2004) Plant Cell Physiol. 45, 1053-1062
46. Sakakibara, H., Takei, K., and Hirose, N. (2006) Trends Plant Sci. 11, 440-448
47. Lam, H. M., Coschigano, K., Schultz, C., Melo-Oliveira, R., Tjaden, G., Oliveira, I., Ngai, N., Hsieh, M. H., and Coruzzi, G. (1995) Plant Cell 7, 887-898
48. Fritz, C., Mueller, C., Matt, P., Feil, R., and Stitt, M. (2006) Plant Cell Environ. 29, 2055-2076
49. Oswald, O., Martin, T., Dominy, P. J., and Graham, I. A. (2001) Proc. Natl. Acad. Sci. U. S. A. 98, 2047-2052
50. Kaiser, W. M., Kandlbinder, A., Stoimenova, M., and Glaab, J. (2000) Planta 210, 801-807
51. Sherameti, I., Sopory, S. K., Trebicka, A., Pfannschmidt, T., and Oelmuller, R. (2002) J. Biol. Chem. 277, 46594-46600
52. Ratcliffe, R. G., and Shachar-Hill, Y. (2001) Annu. Rev. Plant Physiol. Plant Mol. Biol. 52, 499-526
53. Ratcliffe, R. G., and Shachar-Hill, Y. (2006) Plant J. 45, 490-511
54. Roberts, J. K. (2000) Trends Plant Sci. 5, 30-34
55. Dixon, R. A., Gang, D. R., Charlton, A. J., Fiehn, O., Kuiper, H. A., Reynolds, T. L., Tjeerdema, R. S., Jeffery, E. H., German, J. B., Ridley, W. P., and Seiber, J. N. (2006) J. Agric. Food Chem. 54, 8984-8994
56. Emmerling, M., Dauner, M., Ponti, A., Fiaux, J., Hochuli, M., Szyperski, T., Wuthrich, K., Bailey, J. E., and Sauer, U. (2002) J. Bacteriol. 184, 152-164
57. Allen, J., Davey, H. M., Broadhurst, D., Heald, J. K., Rowland, J. J., Oliver, S. G., and Kell, D. B. (2003) Nat. Biotechnol. 21, 692-696
58. Ward, J. L., Harris, C., Lewis, J., and Beale, M. H. (2003) Phytochemistry 62, 949-957
59. Liang, Y. S., Choi, Y. H., Kim, H. K., Linthorst, H. J., and Verpoorte, R. (2006) Phytochemistry 67, 2503-2511
60. Glawischnig, E., Gierl, A., Tomas, A., Bacher, A., and Eisenreich, W. (2001) Plant Physiol. 125, 1178-1186
61. Sriram, G., Fulton, D. B., Iyer, V. V., Peterson, J. M., Zhou, R., Westgate, M. E., Spalding, M. H., and Shanks, J. V. (2004) Plant Physiol. 136, 3043-3057
62. Sekiyama, Y., and Kikuchi, J. (2007) Phytochemistry, in press
63. Verbruggen, N., Hua, X. J., May, M., and Van Montagu, M. (1996) Proc. Natl. Acad. Sci. U. S. A. 93, 8787-8791
64. Deuschle, K., Funck, D., Hellmann, H., Daschner, K., Binder, S., and Frommer, W. B. (2001) Plant J. 27, 345-356
65. Jeong, H., Tombor, B., Albert, R., Oltvai, Z. N., and Barabasi, A. L. (2000) Nature 407, 651-654
66. Albert, R., Jeong, H., and Barabasi, A. L. (2000) Nature 406, 378-382
67. Wagner, A., and Fell, D. A. (2001) Proc. Biol. Sci. 268, 1803-1810
68. Ma, H., and Zeng, A. P. (2003) Bioinformatics 19, 270-277
69. Morgenthal, K., Weckwerth, W., and Steuer, R. (2006) Biosystems 83, 108-117