Top-down phenomics of Arabidopsis thaliana: metabolic profiling by one- and two-dimensional nuclear magnetic resonance spectroscopy and transcriptome analysis of albino mutants.
Elucidating the function of each gene in a genome is important for understanding the whole organism. We previously constructed 4000 disruptant mutants of Arabidopsis by insertion of Ds transposons. Here, we describe a top-down phenomics approach based on metabolic profiling that uses one-dimensional 1H and two-dimensional 1H,13C NMR analyses and transcriptome analysis of albino mutant lines of Arabidopsis. One-dimensional 1H NMR metabolic fingerprinting revealed global metabolic changes in the albino mutants, notably a decrease in aromatic metabolites and changes in aliphatic metabolites. NMR measurements of plants fed with 13C6-glucose showed that the albino lines had dramatically different 13C-labeling patterns and increased levels of several amino acids, especially Asn and Gln. Microarray analysis of one of the albino lines revealed a unique expression profile and showed that changes in the expression of genes encoding metabolic enzymes did not correspond with changes in the levels of metabolites. Collectively, these results suggest that albino mutants lose the normal carbon/nitrogen balance, presumably mainly through lack of photosynthesis. Our study offers an idea of how much the metabolite network is affected by chloroplast function in plants and shows the effectiveness of NMR-based metabolic analysis for metabolite profiling. On the basis of these findings, we propose that future investigations of plant systems biology combine transcriptomic, metabolomic, and phenomic analyses of gene disruptant lines.
Tian
Chunjie
C
Laboratory of Environmental Molecular Biology, RIKEN Wako Institute, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; Graduate School of Integrated Science, Yokohama City University, 1-7-29 Suehiro, Tsurumi, Yokohama 230-0045, Japan.
Chikayama
Eisuke
E
Metabolomics Research Group, RIKEN Plant Science Center, 1-7-22 Tsurumi, Yokohama 230-0045, Japan.
Tsuboi
Yuuri
Y
Laboratory of Environmental Molecular Biology, RIKEN Wako Institute, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; Graduate School of Integrated Science, Yokohama City University, 1-7-29 Suehiro, Tsurumi, Yokohama 230-0045, Japan.
Kuromori
Takashi
T
Gene Discovery Research Group, RIKEN Plant Science Center, 1-7-22 Tsurumi, Yokohama 230-0045, Japan.
Shinozaki
Kazuo
K
Gene Discovery Research Group, RIKEN Plant Science Center, 1-7-22 Tsurumi, Yokohama 230-0045, Japan.
Kikuchi
Jun
J
Metabolomics Research Group, RIKEN Plant Science Center, 1-7-22 Tsurumi, Yokohama 230-0045, Japan; CREST, Japan Science and Technology Agency, 4-1-8 Hon-cho, Kawaguchi 332-0012, Japan; Graduate School of Bioagriculture Science, Nagoya University, 1 Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan. Electronic address: kikuchi@psc.riken.jp.
Hirayama
Takashi
T
Laboratory of Environmental Molecular Biology, RIKEN Wako Institute, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; Graduate School of Integrated Science, Yokohama City University, 1-7-29 Suehiro, Tsurumi, Yokohama 230-0045, Japan; CREST, Japan Science and Technology Agency, 4-1-8 Hon-cho, Kawaguchi 332-0012, Japan. Electronic address: hirayama@gsc.riken.jp.
D017360:Arabidopsis / Q000378:metabolism*; D029681:Arabidopsis Proteins / Q000737:chemistry / Q000502:physiology*; D002736:Chloroplasts / Q000378:metabolism; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D053263:Gene Regulatory Networks; D017343:Genes, Plant; D009682:Magnetic Resonance Spectroscopy / Q000379:methods*; D008954:Models, Biological; D009154:Mutation; D020411:Oligonucleotide Array Sequence Analysis; D018521:Plant Physiological Phenomena; D010940:Plant Proteins / Q000737:chemistry; D010944:Plants / Q000378:metabolism; D014158:Transcription, Genetic
D029681:Arabidopsis Proteins; D010940:Plant Proteins