Functional genomics by integrated analysis of metabolome and transcriptome of Arabidopsis plants over-expressing an MYB transcription factor

Authors

  • Takayuki Tohge,

    1. Department of Molecular Biology and Biotechnology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 263-8522, Japan,
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  • Yasutaka Nishiyama,

    1. Department of Molecular Biology and Biotechnology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 263-8522, Japan,
    2. Institute of Life Science, Ehime Women's College, 421 Ibuki-cho Baba, Uwajima-shi, Ehime, 798-0025, Japan,
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  • Masami Yokota Hirai,

    1. Department of Molecular Biology and Biotechnology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 263-8522, Japan,
    2. CREST, JST (Japan Science and Technology Agency), Yayoi-cho 1-33, Inage-ku, Chiba-shi, Chiba 263-8522, Japan,
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  • Mitsuru Yano,

    1. Department of Molecular Biology and Biotechnology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 263-8522, Japan,
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  • Jun-ichiro Nakajima,

    1. Department of Molecular Biology and Biotechnology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 263-8522, Japan,
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  • Motoko Awazuhara,

    1. Department of Molecular Biology and Biotechnology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 263-8522, Japan,
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  • Eri Inoue,

    1. RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan, and
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  • Hideki Takahashi,

    1. RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan, and
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  • Dayan B. Goodenowe,

    1. Phenomenome Discoveries Inc., 204-407 Downey Road, Saskatoon, SK S7N 4L8, Canada
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  • Masahiko Kitayama,

    1. Institute of Life Science, Ehime Women's College, 421 Ibuki-cho Baba, Uwajima-shi, Ehime, 798-0025, Japan,
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  • Masaaki Noji,

    1. Department of Molecular Biology and Biotechnology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 263-8522, Japan,
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  • Mami Yamazaki,

    1. Department of Molecular Biology and Biotechnology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 263-8522, Japan,
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  • Kazuki Saito

    Corresponding author
    1. Department of Molecular Biology and Biotechnology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 263-8522, Japan,
    2. CREST, JST (Japan Science and Technology Agency), Yayoi-cho 1-33, Inage-ku, Chiba-shi, Chiba 263-8522, Japan,
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(fax +81 43 290 2905; e-mail ksaito@faculty.chiba-u.jp).

Summary

The integration of metabolomics and transcriptomics can provide precise information on gene-to-metabolite networks for identifying the function of unknown genes unless there has been a post-transcriptional modification. Here, we report a comprehensive analysis of the metabolome and transcriptome of Arabidopsis thaliana over-expressing the PAP1 gene encoding an MYB transcription factor, for the identification of novel gene functions involved in flavonoid biosynthesis. For metabolome analysis, we performed flavonoid-targeted analysis by high-performance liquid chromatography-mass spectrometry and non-targeted analysis by Fourier-transform ion-cyclotron mass spectrometry with an ultrahigh-resolution capacity. This combined analysis revealed the specific accumulation of cyanidin and quercetin derivatives, and identified eight novel anthocyanins from an array of putative 1800 metabolites in PAP1 over-expressing plants. The transcriptome analysis of 22 810 genes on a DNA microarray revealed the induction of 38 genes by ectopic PAP1 over-expression. In addition to well-known genes involved in anthocyanin production, several genes with unidentified functions or annotated with putative functions, encoding putative glycosyltransferase, acyltransferase, glutathione S-transferase, sugar transporters and transcription factors, were induced by PAP1. Two putative glycosyltransferase genes (At5g17050 and At4g14090) induced by PAP1 expression were confirmed to encode flavonoid 3-O-glucosyltransferase and anthocyanin 5-O-glucosyltransferase, respectively, from the enzymatic activity of their recombinant proteins in vitro and results of the analysis of anthocyanins in the respective T-DNA-inserted mutants. The functional genomics approach through the integration of metabolomics and transcriptomics presented here provides an innovative means of identifying novel gene functions involved in plant metabolism.

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