SE46:/MS01
Sample Set Information
| ID | SE46 |
|---|---|
| Title | Unbiased characterization of genotype-dependent metabolic regulations by metabolomic approach in Arabidopsis thaliana |
| Description | Metabolites are not only the catalytic products of enzymatic reactions but also the active regulators or the ultimate phenotype of metabolic homeostasis in highly complex cellular processes. The modes of regulation at the metabolome level can be revealed by metabolic networks. We investigated the metabolic network between wild-type and 2 mutant (methionine-over accumulation 1 [mto1] and transparent testa4 [tt4]) plants regarding the alteration of metabolite accumulation in Arabidopsis thaliana. In the GC-TOF/MS analysis, we acquired quantitative information regarding over 170 metabolites, which has been analyzed by a novel score (ZMC, z-score of metabolite correlation) describing a characteristic metabolite in terms of correlation. Although the 2 mutants revealed no apparent morphological abnormalities, the overall correlation values in mto1 were much lower than those of the wild-type and tt4 plants, indicating the loss of overall network stability due to the uncontrolled accumulation of methionine. In the tt4 mutant, a new correlation between malate and sinapate was observed although the levels of malate, sinapate, and sinapoylmalate remain unchanged, suggesting an adaptive reconfiguration of the network. Gene-expression correlations presumably responsible for these metabolic networks were determined using the metabolite correlations as clues. Two Arabidopsis mutants, mto1 and tt4, exhibited the following changes in entire metabolome networks: the overall loss of metabolic stability (mto1) or the generation of a metabolic network of a backup pathway for the lost physiological functions (tt4). The expansion of metabolite correlation to gene-expression correlation provides detailed insights into the systemic understanding of the plant cellular process regarding metabolome and transcriptome. |
| Authors | Miyako Kusano, Atsushi Fukushima, Masanori Arita, Par Jonsson, Thomas Moritz, Makoto Kobayashi, Naomi Hayashi, Takayuki Tohge, Kazuki Saito, RIKEN PSC |
| Reference | Kusano, Fukushima et al. (2007) BMC Syst Biol 1:53 (PMID: 18028551) |
| Comment |
Related data are deposited in MetaboLights.
Analytical Method Details Information
| ID | MS01 |
|---|---|
| Title | GC-TOF/MS |
| Instrument | GC Agilent 6890N gas chromatograph / MS Pegasus III TOF mass spectrometer |
| Instrument Type | |
| Ionization | EI |
| Ion Mode | positive |
| Description | Among these harvested plants, the plants that had fresh weight over 13 mg were used for GC-TOF/MS analysis (WT, n = 17; mto1, n = 13; and tt4, n = 20). For liquid chromatography-quadrupole-time-of-flight/mass spectrometry (LC-Q-TOF/MS) analysis, 3 biological replicates were prepared. All the plant materials were frozen immediately in liquid nitrogen to quench the enzymatic activity. Extraction and sample preparation for GC-TOF/MS analysis For methoximation, 20 μl of methoxyamine hydrochloride (20 mg/ml in pyridine) was added to the sample. After 30 h of derivatization at room temperature, the sample was trimethylsilylated for 1 h using 20 μl of MSTFA with 1% TMCS at 37°C with shaking. Twenty μl of n-heptane was added following silylation. All the derivatization steps were performed in the vacuum glove box VSC-100 (Sanplatec, Japan) filled with 99.9995% (G3 grade) of dry nitrogen. The analysis of metabolites by GC-TOF/MS was performed as described previously. |
| Comment_of_details |
