The importance of anatomy and physiology in plant metabolomics

Topics in Current Genetics

Volumn 18, Issue , 2007, Pages 253-278

  Roessner, Ute ^a   Pettolino, Filomena ^a  

^a UNIVERSITY OF MELBOURNE   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 34548850061     PISSN: 16102096     EISSN: 16106970     Source Type: Book Series    
DOI: 10.1007/4735_2007_0218     Document Type: Article

References (65)

1. Arabidospis genome initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796-815
2. Baldwin TC, Handford MG, Yuseff M-I, Orellana A, Dupree P. (2001) Identification and characterization of GONST1, a Golgi-localised GDP-mannose transporter in Arabidopsis. Plant Cell 13:2283-2295
3. Baur A, Reski R, Gorr G (2005) Enhanced recovery of a secreted recombinant human growth factor using stabilizing additives and by co-expression of human serum albumin in the moss Physcomitrella patens. Plant Biotech J 3:331-340
4. Colebatch G, Desbrosses G, Ott T, Krusell L, Montanari O, Kloska S, Kopka J,
5. Udvardi MK (2004) Global changes in transcription orchestrate metabolic differentiation during symbiotic nitrogen fixation in Lotus japonicus Plant J 39:487-512
6. Cook D, Fowler S, Fiehn O, Thomashow MF (2004) A prominent role for the CBF cold response pathway in configuring the low-temperature metabolome of Arabidopsis. Proc Natl Acad Sci USA 101:15243-15248
7. Cosgrove DJ (2001) Wall Structure and Wall Loosening. A Look Backwards and Forwards. Plant Physiol 125:131-134
8. Decker EL, Reski R (2004) The moss bioreactor. Curr Opin Plant Biol 7:166-170
9. DeLuca V and St Pierre B 2000. The cell and developmental biology of alkaloid biosynthesis. Trends Plant Sci 5:168-173
10. Delmer DP, Amor Y (1995) Cellulose biosynthesis. Plant Cell 7:987-100
11. Desbrosses GG, Kopka J, Udvardi MK. (2005) Lotus japonicus metabolic profiling. Development of gas chromatography-mass spectrometry resources for the study of plantmicrobe interactions. Plant Physiol. 137:1302-1318
12. Farré EM, Tiessen A, Roessner U, Geigenberger P, Trethewey RN, Willmitzer L (2001) Analysis of the compartmentation of glycolytic intermediates, nucleotides, sugars, organic acids, amino acids and sugar alcohols in potato tubers using a non-aqueous fractionation method. Plant Physiol. 127:685-700
13. Fehr M, Ehrhardt DW, Lalonde S, Frommer WB. (2004) Minimally invasive dynamic imaging of ions and metabolites in living cells. Curr Opin Plant Biol. 7:345-351
14. Galili G, Sengupta-Gopalan C, Ceriotti A (1998) The endoplasmic reticulum of plant cells and its role in protein maturation and biogenesis of oil bodies. Plant Mol Biol 38:1-29
15. Gibeaut DM, Carpita NC (1994) Biosynthesis of plant cell wall polysaccharides. FASEB J 8:904-915
16. Gong Q, Li P, Ma S, Indu Rupassara S, Bohnert HJ. (2005) Salinity stress adaptation competence in the extremophile Thellungiella halophila in comparison with its relative Arabidopsis thaliana. Plant J 44:826-839
17. Hall RD. (2006) Plant metabolomics: From holistic hope, to hype, to hot topic. New Phytol 169:453-68
18. Hellwig S, Drossard J, Twyman RM, Fischer R (2004) Plant cell cultures for the production of recombinant proteins. Nature Biotech 22:1415-1422
19. Hirai MY, Klein M, Fujikawa Y, Yano M, Goodenowe DB, Yamazaki Y, Kanaya S, Nakamura Y, Kitayama M, Suzuki H, Sakurai N, Shibata D, Tokuhisa J, Reichelt M, Gershenzon J, Papenbrock J, Saito K. (2005) Elucidation of gene-to-gene and metabolite to-gene networks in Arabidopsis by integration of metabolomics and transcriptomics. J Biol Chem 280:25590-25595
20. James C (2005) Executive Summary of Global Status of Commercialized Biotech/GM Crops: 2005. ISAAA Briefs No 34 ISAAA: Ithaca, NY
21. Kaplan F, Kopka J, Haskell DW, Zhao W, Schiller KC, Gatzke N, Sung DY, Guy CL (2004) Exploring the temperature-stress metabolome of Arabidopsis. Plant Physiol 136:4159-4168
22. Ketchum, REB, DM Gibson (1996) Paclitaxel production in suspension cell cultures of Taxus. Plant Cell Tiss Org Cult 46:9-16
23. Keurentjes JJ, Fu J, de Vos CH, Lommen A, Hall RD, Bino RJ, van der Plas LH, Jansen RC, Vreugdenhil D, Koornneef M (2006) The genetics of plant metabolism. Nature Genet 38:842-849
24. Kong Q, Richter L, Yang YF, Arntzen CJ, Mason HS, Thanavala Y (2001) Oral immunization with hepatitis B surface antigen expressed in transgenic plants. Proc Natl Acad Sci USA 98:11539-11544
25. Marty F (1999) Plant vacuoles. Plant Cell 11:587-599
26. McGarvey DJ, Croteau R (1995) Terpenoid metabolism. Plant Cell 7:1015-1026
27. McLean BG, Hempel FD, Zambryski PC (1997) Plant intercellular communication via plasmodesmata. Plant Cell 9:1043-1054
28. Moore PJ, Staehelin LA (1988) Immunogold localization of the cell-wall-matrix polysaccharides rhamnogalacturonan I and xyloglucan during cell expansion and cytokinesis in Trifolium prantese L.; implication for secretory pathways. Planta 174:433-445
29. Nebenführ A, Staehelin LA (2001) Mobile factories: Golgi dynamics in plant cells. Trends Plant Sci 6:160-167
30. Nikiforova VJ, Kopka J, Tolstikov V, Fiehn O, Hopkins L, Hawkesford MJ, Hesse H, Hoefgen R. (2005) Systems rebalancing of metabolism in response to sulphur deprivation, as revealed by metabolome analysis of Arabidopsis plants. Plant Physiol 138:304-318
31. Oksman-Caldentey K-M, Inze D (2004) Plant cell factories in the post-genomic era: New ways to produce designer secondary metabolites. Trends Plant Sci 9:433-440
32. Orellana A (2005) Biosynthesis of non-cellulosic polysaccharides in the Golgi apparatus. Topological considerations. Plant Biosystems 139:42-45
33. Oxley D, Currie G, Bacic A (2004) In: Purifying Proteins for Proteomics. A laboratory manual. Pp 579-637. R.J. Simpson (Ed) Cold Spring Harbour Laboratory Press New York
34. Palacpac NQ, Yoshida S, Sakai H, Kimura Y, Fujiyama K, Yoshida T, Seki T (1999) Stable expression of human β1,4-galactosyltransferase in plant cells modifies N-linked glycosylation patterns. Proc Natl Acad Sci USA 96:4692-4697
35. Pauly M, Scheller HV (2000) O-Acetylation of plant cell wall polysaccharides: Identification and partial characterization of a rhamnogalacturonan O-acetyl-transferase from potato suspension-cultured cells. Planta 210:659-667
36. Peng L, Kawagoe Y, Hogan P, Delmer D (2002) Sitosterol-β-glucoside as primer for cellulose synthesis in plants. Sci 295:147-150
37. Prance GT (2001) Discovering the plant world. Taxon 50:345-359
38. Ramm M, Wolfender J-L, Queiroz EF, Hostettmann K, Hamburger M (2004) Rapid analysis of nucleotide-activated sugars by high-performance liquid chromatography coupled with diode-array detection, electrospray ionization mass spectrometry and nuclear magnetic resonance. J Chromatogr A 1034:139-148
39. Rayon C, Lerouge P, Faye L (1998) The protein N-glycosylation in plants. J Exp Bot 49:1463-1472
40. Reiter W-D, Vanzin GF (2001) Molecular genetics of nucleotide sugar interconversion pathways in plants. Plant Mol Biol 47:95-113
41. Reski R and Frank W (2005) Moss (Physcomitrella patens) functional genomics - Gene discovery and tool development, with implications for crop plants and human health. Briefings in Functional Genomics and Proteomics 4:48-57
42. Rischer H, Oksman-Caldentey KM. (2006) Unintended effects in genetically modified crops: Revealed by metabolomics? Trends Biotech 24:102-104
43. Roessner-Tunali U, Urbanczyk-Wochniak E, Czechowski T, Kolbe A, Willmitzer., Fernie AR (2003a) De novo amino acid biosynthesis in plant storage tissues is regulated by sucrose levels. Plant Physiol 133:683-692
44. Roessner-Tunali U, Hegemann B, Lytovchenko A, Carrari F, Bruedigam C, Granot D, Fernie AR (2003b) Metabolic profiling of transgenic tomato plants overexpressing hexokinase reveals that the influence of hexose phosphorylation diminishes during fruit development. Plant Physiol 133:84-99
45. Roessner U, Patterson J, Forbes MG, Fincher G, Langridge P, Bacic A. (2006) An investigation of boron toxicity in barley using metabolomics. Plant Physiol 142:1087-101
46. Ronning CM, Stegalkina SS, Ascenzi RA, Bougri O, Hart AL, Utterbach TR, Vanaken SE, Riedmuller SB, White JA, Cho J, Pertea GM, Lee Y, Karamycheva S, Sultana R, Tsai J, Quackenbush J, Griffiths HM, Restrepo S, Smart CD., Fry WE, van der Hoeven R, Tanksley S, Zhang P, Jin H, Yamamoto ML, Baker BJ, Buell CR (2003) Comparative analyses of potato expressed sequence tag libraries. Plant Physiol 131: 419-429
47. Saito K, Dixon RA, Willmitzer L. (Eds) (2006) Plant Metabolomics. Vol. 57 of the series Biotechnology in agriculture and forestry. Eds. Nagata T., Lörz H. and Widholm JM. Publ. Springer-Verlag Berlin-Heidelberg, Germany
48. Sato S, Soga T, Nishioka T, Tomita M (2004) Simultaneous determination of the main metabolites in rice leaves using capillary electrophoresis mass spectrometry and capillary electrophoresis diode array detection. Plant J 40:151-163
49. Schad M, Mungur R, Fiehn O, Kehr J. 2005. Metabolic profiling of laser microdissected vascular bundles of Arabidopsis thaliana. Plant Methods 1:2
50. Schauer N, Semel Y, Roessner U, Gurb A, Balbo I, Carrari F, Pleban T, Perez-Melisa A, Bruedigam C, Kopka J, Willmitzer L, Zamir D, Fernie AR (2006) Quantitative genetics of metabolite accumulation in intraspecific introgressions of tomato. Nature Biotechnol 24:447-454
51. Scheible W-R, Pauly M (2004) Glycosyltransferases and cell wall biosynthesis: Novel players and insights. Curr Opin Plant Biol 7:285-295
52. Schena M, Shalon D, Davis RW, Brown PO (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270:467-470
53. Somerville C, Somerville S (1999) Plant functional genomics. Science 285:380-383
54. Staehelin AL, Newcomb EH (2000) Membrane structure and membranous organelles. In Biochemistry and Molecular Biology of Plants, B Buchanan, W Gruissem, R Jones, Eds. American Society of Plant Physiologists, USA
55. Sturm A. 1995. N-glycosylation of plant proteins. New Compr. Biochem. 29a:521-542
56. Sumner LW, Mendes P, Dixon RA. (2003) Plant metabolomics: Large-scale phytochemistry in the functional genomics era. Phytochem 62:817-836
57. Tacket CO, Mason HS, Losonsky G, Estes MK, Levine MM, Arntzen CJ (2000) Human immune responses to a novel norwalk virus vaccine delivered in transgenic potatoes. J Infect Diseases 182:302-305
58. Tarpley L, Duran AL, Kebrom TH, Sumner LW (2005) Biomarker metabolites capturing the metabolite variance present in a rice plant developmental period. BMC Plant Biol 5:8
59. Tikunov Y, Lommen A, de Vos CH, Verhoeven HA, Bino RJ, Hall RD, Bovy AG. (2005) A novel approach for nontargeted data analysis for metabolomics. Large-scale profiling of tomato fruit volatiles. Plant Physiol. 139:1125-1137
60. Tohge T, Nishiyama Y, Hirai MY, Yano M, Nakajima J, Awazuhara M, Inoue E, Takahashi H, Goodenowe DB, Kitayama M, Noji M, Yamazaki M, Saito K (2005) Functional genomics by integrated analysis of metabolome and transcriptome of Arabidopsis plants over-expressing an MYB transcription factor. Plant J 42:218-235
61. Urbanczyk-Wochniak E, Baxter C, Kolbe A, Kopka J, Sweetlove LJ, Fernie AR. (2005) Profiling of diurnal patterns of metabolite and transcript abundance in potato (Solanum tuberosum) leaves. Planta 221:891-903
62. Willats WGT, Orfila C, Limberg G, Buchholti HC, van Alebeek G-JWM, Voragen AGJ, Marcus SE,. Christensen TMIE, Mikkelsen JD, Murray BS, Knox JP (2001) Modulation of the degree and pattern of methyl-esterification of pectic homogalacturonan in plant cell walls. J Biol Chem 276:19404-19413
63. Villas-Boas S.G., Roessner U., Hansen M., Smedsgaard J., Nielsen J. (2006) Metabolome Analysis. Publ. Wiley & Sons, New Jersey, NJ, USA (in press)
64. von Roepenack-Lahaye E, Degenkolb T, Zerjeski M, Franz M, Roth U, Wessjohann L, Schmidt J, Scheel D, Clemens S (2004) Profiling of Arabidopsis secondary metabolites by capillary liquid chromatography coupled to electrospray ionization quadrupole time-of-flight mass spectrometry. Plant Physiol 134:548-559
65. Yu J, Hu S, Wang J, Wong GK-S, Li S, Liu B, Deng Y, et al (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Sci 296:79-92