Functional genomics by integrated analysis of metabolome and transcriptome of Arabidopsis plants over-expressing an MYB transcription factor.
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.
Tohge
Takayuki
T
Department of Molecular Biology and Biotechnology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 263-8522, Japan.
Nishiyama
Yasutaka
Y
Hirai
Masami Yokota
MY
Yano
Mitsuru
M
Nakajima
Jun-ichiro
J
Awazuhara
Motoko
M
Inoue
Eri
E
Takahashi
Hideki
H
Goodenowe
Dayan B
DB
Kitayama
Masahiko
M
Noji
Masaaki
M
Yamazaki
Mami
M
Saito
Kazuki
K
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
D029681:Arabidopsis Proteins; D044948:Flavonols; D000073718:Pancreatitis-Associated Proteins; D014157:Transcription Factors; C502612:AT1G56650 protein, Arabidopsis; C000612141:REG3A protein, human