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Functional genomics by integrated analysis of metabolome and transcriptome of Arabidopsis plants over-expressing an MYB transcription factor
Article first published online: 2 MAR 2005
DOI: 10.1111/j.1365-313X.2005.02371.x
Additional Information
How to Cite
Tohge, T., Nishiyama, Y., Hirai, M. Y., Yano, M., Nakajima, J.-i., Awazuhara, M., Inoue, E., Takahashi, H., Goodenowe, D. B., Kitayama, M., Noji, M., Yamazaki, M. and Saito, K. (2005), Functional genomics by integrated analysis of metabolome and transcriptome of Arabidopsis plants over-expressing an MYB transcription factor. The Plant Journal, 42: 218–235. doi: 10.1111/j.1365-313X.2005.02371.x
Publication History
- Issue published online: 7 MAR 2005
- Article first published online: 2 MAR 2005
- Received 8 October 2004; revised 24 December 2004; accepted 7 January 2005.
Keywords:
- metabolome;
- transcriptome;
- MYB factor;
- anthocyanins;
- glycosyltransferase;
- Arabidopsis thaliana
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.