Systematic NMR analysis of stable isotope labeled metabolite mixtures in plant and animal systems: Coarse grained views of metabolic pathways

Eisuke Chikayama, Michitaka Suto, Takashi Nishihara, Kazuo Shinozaki, Takashi Hirayama, Jun Kikuchi

Research output: Contribution to journalArticle

65 Citations (Scopus)

Abstract

Background: Metabolic phenotyping has become an important 'bird's-eye-view' technology which can be applied to higher organisms, such as model plant and animal systems in the post-genomics and proteomics era. Although genotyping technology has expanded greatly over the past decade, metabolic phenotyping has languished due to the difficulty of 'topdown' chemical analyses. Here, we describe a systematic NMR methodology for stable isotope-labeling and analysis of metabolite mixtures in plant and animal systems. Methodology/Principal Findings: The analysis method includes a stable isotope labeling technique for use in living organisms; a systematic method for simultaneously identifying a large number of metabolites by using a newly developed HSQC-based metabolite chemical shift database combined with heteronuclear multidimensional NMR spectroscopy; Principal Components Analysis; and a visualization method using a coarse-grained overview of the metabolic system. The database contains more than 1000 1H and 13C chemical shifts corresponding to 142 metabolites measured under identical physicochemical conditions. Using the stable isotope labeling technique in Arabidopsis T87 cultured cells and Bombyx mori, we systematically detected >450 HSQC peaks in each 13C-HSQC spectrum derived from model plant, Arabidopsis T87 cultured cells and the invertebrate animal model Bombyx mori. Furthermore, for the first time, efficient 13C labeling has allowed reliable signal assignment using analytical separation techniques such as 3D HCCH-COSY spectra in higher organism extracts. Conclusions/Significance: Overall physiological changes could be detected and categorized in relation to a critical developmental phase change in B. mori by coarse-grained representations in which the organization of metabolic pathways related to a specific developmental phase was visualized on the basis of constituent changes of 56 identified metabolites. Based on the observed intensities of 13C atoms of given metabolites on development-dependent changes in the 56 identified 13C-HSQC signals, we have determined the changes in metabolic networks that are associated with energy and nitrogen metabolism.

Original languageEnglish
Article numbere3805
JournalPLoS One
Volume3
Issue number11
DOIs
Publication statusPublished - Nov 25 2008
Externally publishedYes

Fingerprint

Isotope Labeling
Bombyx
Metabolites
Metabolic Networks and Pathways
Isotopes
stable isotopes
biochemical pathways
Animals
Nuclear magnetic resonance
metabolites
Arabidopsis
isotope labeling
Labeling
Cultured Cells
Bombyx mori
Animal Models
Chemical Databases
Biomolecular Nuclear Magnetic Resonance
Technology
labeling techniques

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Systematic NMR analysis of stable isotope labeled metabolite mixtures in plant and animal systems : Coarse grained views of metabolic pathways. / Chikayama, Eisuke; Suto, Michitaka; Nishihara, Takashi; Shinozaki, Kazuo; Hirayama, Takashi; Kikuchi, Jun.

In: PLoS One, Vol. 3, No. 11, e3805, 25.11.2008.

Research output: Contribution to journalArticle

Chikayama, Eisuke ; Suto, Michitaka ; Nishihara, Takashi ; Shinozaki, Kazuo ; Hirayama, Takashi ; Kikuchi, Jun. / Systematic NMR analysis of stable isotope labeled metabolite mixtures in plant and animal systems : Coarse grained views of metabolic pathways. In: PLoS One. 2008 ; Vol. 3, No. 11.
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