Differential metabolomics unraveling light/dark regulation of metabolic activities in Arabidopsis cell culture.
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.
Nakamura
Yukiko
Y
Graduate School of Information Science, Nara Institute of Science and Technology, Takayama 8916-5, Ikoma, Nara, Japan.
Kimura
Atsuko
A
Saga
Hirohisa
H
Oikawa
Akira
A
Shinbo
Yoko
Y
Kai
Kosuke
K
Sakurai
Nozomu
N
Suzuki
Hideyuki
H
Kitayama
Masahiko
M
Shibata
Daisuke
D
Kanaya
Shigehiko
S
Ohta
Daisaku
D
D017360:Arabidopsis / Q000166:cytology / Q000235:genetics* / Q000378:metabolism*; D029681:Arabidopsis Proteins / Q000235:genetics* / Q000378:metabolism*; D002478:Cells, Cultured; D018506:Gene Expression Regulation, Plant / Q000528:radiation effects; D008027:Light; D013058:Mass Spectrometry; D008954:Models, Biological; D020411:Oligonucleotide Array Sequence Analysis; D020133:Reverse Transcriptase Polymerase Chain Reaction; D053719:Tandem Mass Spectrometry
D029681:Arabidopsis Proteins
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