SE159:/S1

Sample Set Information

ID	TSE1316
Title	Comprehensive flavonol profiling and transcriptome coexpression analysis leading to decoding gene-metabolite correlations in Arabidopsis.
Description	To complete the metabolic map for an entire class of compounds, it is essential to identify gene-metabolite correlations of a metabolic pathway. We used liquid chromatography-mass spectrometry (LC-MS) to identify the flavonoids produced by Arabidopsis thaliana wild-type and flavonoid biosynthetic mutant lines. The structures of 15 newly identified and eight known flavonols were deduced by LC-MS profiling of these mutants. Candidate genes presumably involved in the flavonoid pathway were delimited by transcriptome coexpression network analysis using public databases, leading to the detailed analysis of two flavonoid pathway genes, UGT78D3 (At5g17030) and RHM1 (At1g78570). The levels of flavonol 3-O-arabinosides were reduced in ugt78d3 knockdown mutants, suggesting that UGT78D3 is a flavonol arabinosyltransferase. Recombinant UGT78D3 protein could convert quercetin to quercetin 3-O-arabinoside. The strict substrate specificity of UGT78D3 for flavonol aglycones and UDP-arabinose indicate that UGT78D3 is a flavonol arabinosyltransferase. A comparison of flavonol profile in RHM knockout mutants indicated that RHM1 plays a major role in supplying UDP-rhamnose for flavonol modification. The rate of flavonol 3-O-glycosylation is more affected than those of 7-O-glycosylation by the supply of UDP-rhamnose. The precise identification of flavonoids in conjunction with transcriptomics thus led to the identification of a gene function and a more complete understanding of a plant metabolic network.
Authors	Yonekura-Sakakibara K, Tohge T, Matsuda F, Nakabayashi R, Takayama H, Niida R, Watanabe-Takahashi A, Inoue E, Saito K.
Reference	Plant Cell. 2008 Aug;20(8):2160-76. doi: 10.1105/tpc.108.058040. Epub 2008 Aug 29.
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PubMed

Sample Information

ID	S1
Title	Arabidopsis thaliana (accession Columbia-0; Lehle Seeds)
Organism - Scientific Name	Arabidopsis thaliana
Organism - ID	NCBI taxonomy:3702
Compound - ID
Compound - Source
Preparation	Arabidopsis thaliana (accession Columbia-0; Lehle Seeds) was used as the wild type in this study. The mutants ugt75c1, ugt78d1, ugt78d2, ugt89c1, rol1-1, rol1-2, and rhm2-1 were described previously (Jones et al., 2003; Usadel et al., 2004; Tohge et al., 2005; Diet et al., 2006; Yonekura-Sakakibara et al., 2007). The T-DNA–inserted knockout mutants of omt1 (CS25167) and tt7 (CS6509) were obtained from the ABRC. The tt4 (C1) mutant was obtained from tt mutant lines induced by ion beam irradiation of Arabidopsis (Shikazono et al., 2003). The T-DNA–inserted mutant of Arabidopsis, lines SALK_114099 for UGT78D3 and SALK_085051 (rhm2-3, a homozygous knockout line) for RHM2, were obtained from the Salk Institute. T-DNA insertion lines were screened by PCR using specific primers for UGT78D3, RHM2 ,and T-DNA: UGT78D3f, UGT78D3r, RHM2f, RHM2r, LBa1, and RBa1 (see Supplemental Table 1 online). PCR products were sequenced to determine the exact insertion points. Plants were cultured on Murashige and Skoog–agar medium containing 1% sucrose (Valvekens et al., 1988) in a growth chamber at 22°C with 16 h/ 8 h light and dark cycles for 18 d or in a greenhouse at 22°C with 16 h/ 8 h light/dark for 4 weeks. Plants were harvested, immediately frozen with liquid nitrogen, and stored at −30°C until use. Five biological replicates were used for flavonoid profiling.
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