title: Functional genomics by integrated analysis of metabolome and transcriptome of Arabidopsis plants over-expressing an MYB transcription factor.
abstract: 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.affiliation: Department of Molecular Biology and Biotechnology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 263-8522, Japan.
authors.forename: Takayuki
authors.initials: T
authors.lastname: Tohge
authors.forename: Yasutaka
authors.initials: Y
authors.lastname: Nishiyama
authors.forename: Masami Yokota
authors.initials: MY
authors.lastname: Hirai
authors.forename: Mitsuru
authors.initials: M
authors.lastname: Yano
authors.forename: Jun-ichiro
authors.initials: J
authors.lastname: Nakajima
authors.forename: Motoko
authors.initials: M
authors.lastname: Awazuhara
authors.forename: Eri
authors.initials: E
authors.lastname: Inoue
authors.forename: Hideki
authors.initials: H
authors.lastname: Takahashi
authors.forename: Dayan B
authors.initials: DB
authors.lastname: Goodenowe
authors.forename: Masahiko
authors.initials: M
authors.lastname: Kitayama
authors.forename: Masaaki
authors.initials: M
authors.lastname: Noji
authors.forename: Mami
authors.initials: M
authors.lastname: Yamazaki
authors.forename: Kazuki
authors.initials: K
authors.lastname: Saito
mesh_terms: D017360:Arabidopsis / Q000235:genetics / Q000378:metabolism*; D029681:Arabidopsis Proteins / Q000378:metabolism; D002874:Chromosome Mapping; D032461:Chromosomes, Plant; D015536:Down-Regulation; D044948:Flavonols / Q000096:biosynthesis*; D015870:Gene Expression / Q000502:physiology*; D020869:Gene Expression Profiling; D023281:Genomics; D000073718:Pancreatitis-Associated Proteins; D010802:Phylogeny; D018515:Plant Leaves / Q000502:physiology; D014157:Transcription Factors / Q000235:genetics*; D015854:Up-Regulation
chemical_list: D029681:Arabidopsis Proteins; D044948:Flavonols; D000073718:Pancreatitis-Associated Proteins; D014157:Transcription Factors; C502612:AT1G56650 protein, Arabidopsis; C000612141:REG3A protein, human