SE192:/S1

Sample Set Information

ID	TSE1351
Title	Functional genomics by integrated analysis of metabolome and transcriptome of Arabidopsis plants over-expressing an MYB transcription factor.
Description	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.
Authors	Tohge, T., Nishiyama, Y., Hirai, M.Y., Yano, M., Nakajima, J., Awazuhara, M., Inoue, E., Takahashi, H., Goodenowe, D.B., Kitayama, M., Noji, M., Yamazaki, M., and Saito, K.
Reference	Plant J. 2005 Apr;42(2):218-35
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PubMed

Sample Information

ID	S1
Title	Arabidopsis thaliana
Organism - Scientific Name	Arabidopsis thaliana
Organism - ID	NCBI taxonomy:3702
Compound - ID
Compound - Source
Preparation	Arabidopsis thaliana (ecotype Columbia) plants were used as the wild‐type plant in this study. The pap1‐D mutant was described previously (Borevitz et al., 2000). The PAP1 cDNA over‐expressing transformant was obtained by transformation of A. thaliana with the engineered Ti plasmid carrying cauliflower mosaic virus 35S promoter linked with the coding sequence of PAP1 cDNA. The plants were cultured on GM‐agar medium containing 1% sucrose (Valvekens et al., 1988) in a growth chamber at 22°C in 16/8 h light and dark cycles for 3 weeks, or in a standard greenhouse at 22°C in 16/8 h light for 4 weeks. Samples from wild‐type plant and PAP1over‐expressing lines were used, namely: WLA (wild‐type leaves grown on GM agar medium); PLA (pap1‐D mutant leaves grown on GM agar medium); OLA (PAP1‐over‐expressed transgenic leaves grown on GM agar medium); WLV (wild‐type leaves grown on vermiculite); PLV (pap1‐D mutant leaves grown on vermiculite); WRA (wild‐type roots grown on GM medium); and PRA (pap1‐D mutant roots grown on GM medium). The leaves and roots of plants were harvested, immediately frozen with liquid nitrogen and stored at −30°C until use.
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