Planta

, Volume 227, Issue 1, pp 57–66 | Cite as

Differential metabolomics unraveling light/dark regulation of metabolic activities in Arabidopsis cell culture

  • Yukiko Nakamura
  • Atsuko Kimura
  • Hirohisa Saga
  • Akira Oikawa
  • Yoko Shinbo
  • Kosuke Kai
  • Nozomu Sakurai
  • Hideyuki Suzuki
  • Masahiko Kitayama
  • Daisuke Shibata
  • Shigehiko Kanaya
  • Daisaku Ohta
Original Paper

Abstract

Differential metabolomics based on a non-targeted FT-ICR/MS analysis demonstrated metabolite accumulation patterns reflecting light/dark conditions in Arabidopsis T87 cell culture. First, FT-ICR/MS data sets were converted into metabolome information using the Dr.DMASS software (http://kanaya.naist.jp/DrDMASS/). A quick search of a metabolite-species database, KNApSAcK (http://kanaya.naist.jp/KNApSAcK/), was implemented to assign metabolite candidates to each accurate MS data (<1 ppm) through the prediction of molecular formulas, and the candidate structures were further studied using MS/MS analyses. Specific metabolites representing the culture conditions included sugars, phenylpropanoid derivatives, flavonol aglycons, and a plastid nonmevalonate pathway intermediate. Transcriptomics data were obtained in parallel and analyzed using a transcriptome analysis tool, KaPPA-View (http://kpv.kazusa.or.jp/kappa-view/). The specific accumulation patterns of flavonol aglycons were in good agreement with the light/dark regulation of a cytochrome P450 gene, CYP75B, and the build-up of 2-C-methyl-d-erythritol 4-phosphate, a nonmevalonate pathway intermediate, in the light grown cells was also consistent with a gene expression profile. The differential metablomics scheme based on the FT-ICR/MS metabolomics can serve as an evaluation system of metabolic activities contributing to successful identification and proper manipulation of key enzymatic steps in metabolic engineering studies.

Keywords

Cell culture Light/dark Cytochrome P450 Fourier-transform ion-cyclotron resonance mass spectrometry (FT-ICR/MS) Metabolomics 

Abbreviations

ESI

Electrospray ionization

FT-ICR

Fourier-transform ion-cyclotron resonance

MS

Mass spectrometry

Notes

Acknowledgments

This work was performed as one of the technology development projects of the “Green Biotechnology Program” supported by NEDO (New Energy and Industrial Technology Development Organization), Japan. This work was supported in part by the Ministry of Education, Culture, Sports, Science, and Technology of Japan (18380201 and 18038037 to D.O.).

Supplementary material

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Copyright information

© Springer-Verlag 2007

Authors and Affiliations

  • Yukiko Nakamura
    • 1
    • 2
    • 5
  • Atsuko Kimura
    • 3
  • Hirohisa Saga
    • 3
  • Akira Oikawa
    • 3
    • 6
  • Yoko Shinbo
    • 1
  • Kosuke Kai
    • 3
  • Nozomu Sakurai
    • 4
  • Hideyuki Suzuki
    • 4
  • Masahiko Kitayama
    • 2
  • Daisuke Shibata
    • 4
  • Shigehiko Kanaya
    • 1
  • Daisaku Ohta
    • 3
  1. 1.Graduate School of Information ScienceNara Institute of Science and TechnologyIkoma, NaraJapan
  2. 2.Ehime Women’s CollegeIbuki UwajimaJapan
  3. 3.Graduate School of Life and Environmental SciencesOsaka Prefecture UniversitySakaiJapan
  4. 4.Kazusa DNA Research InstituteKisarazuJapan
  5. 5.Kazusa DNA Research InstituteKisarazuJapan
  6. 6.Riken Plant Science CenterYamagataJapan

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