Skip to main content
SpringerLink
Log in

The importance of anatomy and physiology in plant metabolomics

  • Chapter
  • First Online:
Metabolomics

Part of the book series: Topics in Current Genetics ((TCG,volume 18))

Abstract

Plant metabolomics offers some unique opportunities in the assignment of biochemical pathways.The genetics of model plants is well-characterized which enables functional genomic approaches, qualitativetrait loci identification and genetic engineering. Metabolomics has successfully supported the identificationof gene function. As a specialized system, a number of key features of plants create challenges insample preparation and interpretation of metabolomic data. Significantly, most plant tissues arecomposed of multiple cell types which are difficult to isolate, often resulting in limited numbersper cell type. This hinders spatial resolution of the analysis of metabolites. Secondly, cells aresurrounded by a dynamic cell wall which is in constant turnover, interfering with the metabolome.Thirdly, green plant cells are capable of fixing carbon through photosynthesis producing metabolite-capturedenergy. This also implies a strong light-dependency in plant metabolism. Finally, plants are characterizedby a diversity of secondary metabolites produced in response to environmental stimuli.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 219.00
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 279.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 279.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Arabidospis genome initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796–815

    Article  Google Scholar 

  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

    PubMed  CAS  Google Scholar 

  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

    Article  CAS  Google Scholar 

  4. Colebatch G, Desbrosses G, Ott T, Krusell L, Montanari O, Kloska S, Kopka J, Udvardi MK (2004) Global changes in transcription orchestrate metabolic differentiation during symbiotic nitrogen fixation in Lotus japonicus. Plant J 39:487–512

    Article  PubMed  Google Scholar 

  5. 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

    Article  PubMed  CAS  Google Scholar 

  6. Cosgrove DJ (2001) Wall Structure and Wall Loosening. A Look Backwards and Forwards. Plant Physiol 125:131–134

    Article  PubMed  CAS  Google Scholar 

  7. Decker EL, Reski R (2004) The moss bioreactor. Curr Opin Plant Biol 7:166–170

    Article  PubMed  CAS  Google Scholar 

  8. DeLuca V, St Pierre B (2000) The cell and developmental biology of alkaloid biosynthesis. Trends Plant Sci 5:168–173

    Article  CAS  Google Scholar 

  9. Delmer DP, Amor Y (1995) Cellulose biosynthesis. Plant Cell 7:987–100

    PubMed  CAS  Google Scholar 

  10. Desbrosses GG, Kopka J, Udvardi MK (2005) Lotus japonicus metabolic profiling. Development of gas chromatography-mass spectrometry resources for the study of plant-microbe interactions. Plant Physiol 137:1302–1318

    Article  PubMed  CAS  Google Scholar 

  11. 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

    Article  PubMed  Google Scholar 

  12. 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

    Article  PubMed  CAS  Google Scholar 

  13. 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

    Article  PubMed  CAS  Google Scholar 

  14. Gibeaut DM, Carpita NC (1994) Biosynthesis of plant cell wall polysaccharides. FASEB J 8:904–915

    PubMed  CAS  Google Scholar 

  15. 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

    Article  PubMed  CAS  Google Scholar 

  16. Hall RD (2006) Plant metabolomics: from holistic hope, to hype, to hot topic. New Phytol 169:453–68

    Article  PubMed  CAS  Google Scholar 

  17. Hellwig S, Drossard J, Twyman RM, Fischer R (2004) Plant cell cultures for the production of recombinant proteins. Nature Biotech 22:1415–1422

    Article  CAS  Google Scholar 

  18. 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

    Article  PubMed  CAS  Google Scholar 

  19. James C (2005) Executive Summary of Global Status of Commercialized Biotech/GM Crops: 2005. ISAAA Briefs No 34 ISAAA: Ithaca, NY

    Google Scholar 

  20. 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

    Article  PubMed  CAS  Google Scholar 

  21. Ketchum REB, Gibson DM (1996) Paclitaxel production in suspension cell cultures of Taxus. Plant Cell Tiss Org Cult 46:9–16

    Article  CAS  Google Scholar 

  22. 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

    Article  PubMed  CAS  Google Scholar 

  23. 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

    Article  PubMed  CAS  Google Scholar 

  24. Marty F (1999) Plant vacuoles. Plant Cell 11:587–599

    PubMed  CAS  Google Scholar 

  25. McGarvey DJ, Croteau R (1995) Terpenoid metabolism. Plant Cell 7:1015–1026

    PubMed  CAS  Google Scholar 

  26. McLean BG, Hempel FD, Zambryski PC (1997) Plant intercellular communication via plasmodesmata. Plant Cell 9:1043–1054

    Article  PubMed  CAS  Google Scholar 

  27. 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

    Article  CAS  Google Scholar 

  28. Nebenführ A, Staehelin LA (2001) Mobile factories: Golgi dynamics in plant cells. Trends Plant Sci 6:160–167

    Article  PubMed  Google Scholar 

  29. 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

    Article  PubMed  CAS  Google Scholar 

  30. 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

    Article  PubMed  CAS  Google Scholar 

  31. Orellana A (2005) Biosynthesis of non-cellulosic polysaccharides in the Golgi apparatus. Topological considerations. Plant Biosystems 139:42–45

    Article  Google Scholar 

  32. Oxley D, Currie G, Bacic A (2004) In: Purifying Proteins for Proteomics. A laboratory manual. In: Simpson RJ (ed) Cold Spring Harbour Laboratory, Press, New York, p 579–637

    Google Scholar 

  33. 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

    Article  PubMed  CAS  Google Scholar 

  34. 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

    Article  PubMed  CAS  Google Scholar 

  35. Peng L, Kawagoe Y, Hogan P, Delmer D (2002) Sitosterol-β-glucoside as primer for cellulose synthesis in plants. Sci 295:147–150

    Article  CAS  Google Scholar 

  36. Prance GT (2001) Discovering the plant world. Taxon 50:345–359

    Article  Google Scholar 

  37. 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

    Article  PubMed  CAS  Google Scholar 

  38. Rayon C, Lerouge P, Faye L (1998) The protein N-glycosylation in plants. J Exp Bot 49:1463–1472

    CAS  Google Scholar 

  39. Reiter W-D, Vanzin GF (2001) Molecular genetics of nucleotide sugar interconversion pathways in plants. Plant Mol Biol 47:95–113

    Article  PubMed  CAS  Google Scholar 

  40. Reski R, 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

    Article  PubMed  CAS  Google Scholar 

  41. Rischer H, Oksman-Caldentey KM (2006) Unintended effects in genetically modified crops: revealed by metabolomics? Trends Biotech 24:102–104

    Article  CAS  Google Scholar 

  42. 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

    Article  PubMed  CAS  Google Scholar 

  43. 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

    Article  PubMed  CAS  Google Scholar 

  44. 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

    Article  PubMed  CAS  Google Scholar 

  45. 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

    Article  PubMed  Google Scholar 

  46. Saito K, Dixon RA, Willmitzer L (eds) (2006) Plant Metabolomics. Vol. 57 of the series Biotechnology in agriculture and forestry. In: Nagata T, Lörz H, Widholm JM (eds) Publ. Springer, Berlin Heidelberg, Germany

    Google Scholar 

  47. 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

    Article  PubMed  CAS  Google Scholar 

  48. Schad M, Mungur R, Fiehn O, Kehr J (2005) Metabolic profiling of laser microdissected vascular bundles of Arabidopsis thaliana. Plant Methods 1:2

    Article  PubMed  Google Scholar 

  49. 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

    Article  CAS  Google Scholar 

  50. Scheible W-R, Pauly M (2004) Glycosyltransferases and cell wall biosynthesis: novel players and insights. Curr Opin Plant Biol 7:285–295

    Article  PubMed  CAS  Google Scholar 

  51. Schena M, Shalon D, Davis RW, Brown PO (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270:467–470

    Article  PubMed  CAS  Google Scholar 

  52. Somerville C, Somerville S (1999) Plant functional genomics. Science 285:380–383

    Article  PubMed  CAS  Google Scholar 

  53. Staehelin AL, Newcomb EH (2000) Membrane structure and membranous organelles. In: B Buchanan B, Gruissem W, Jones R (eds) Biochemistry and Molecular Biology of Plants. American Society of Plant Physiologists, USA

    Google Scholar 

  54. Sturm A (1995) N-glycosylation of plant proteins. New Compr Biochem 29a:521–542

    Google Scholar 

  55. Sumner LW, Mendes P, Dixon RA (2003) Plant metabolomics: large-scale phytochemistry in the functional genomics era. Phytochem 62:817–836

    Article  CAS  Google Scholar 

  56. 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

    Article  CAS  Google Scholar 

  57. 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

    Article  PubMed  Google Scholar 

  58. 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

    Article  PubMed  CAS  Google Scholar 

  59. 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

    Article  PubMed  CAS  Google Scholar 

  60. 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

    Article  PubMed  CAS  Google Scholar 

  61. Willats WGT, Orfila C, Limberg G, Buchholti HC, van Alebeek G-JWM, Voragen AG J, 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

    Article  PubMed  CAS  Google Scholar 

  62. Villas-Boas SG, Roessner U, Hansen M, Smedsgaard J, Nielsen J (2006) Metabolome Analysis. Wiley, New Jersey, NJ, USA (in press)

    Google Scholar 

  63. 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

    Article  Google Scholar 

  64. 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

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Australian Centre for Plant Functional Genomics, School of Botany, The University of Melbourne, 3010, Victoria, Australia

    Ute Roessner

  2. School of Botany, The University of Melbourne, 3010, Victoria, Australia

    Filomena Pettolino

Authors
  1. Ute Roessner
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Filomena Pettolino
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Ute Roessner .

Editor information

Jens Nielsen Michael C. Jewett

Rights and permissions

Reprints and permissions

Copyright information

© 2007 Springer-Verlag Berlin Heidelberg

About this chapter

Cite this chapter

Roessner, U., Pettolino, F. (2007). The importance of anatomy and physiology in plant metabolomics. In: Nielsen, J., Jewett, M.C. (eds) Metabolomics. Topics in Current Genetics, vol 18. Springer, Berlin, Heidelberg. https://doi.org/10.1007/4735_2007_0218

Download citation

Publish with us

Policies and ethics

Search

Navigation