Seed-coat protective neolignans are produced by the dirigent protein AtDP1 and the laccase AtLAC5 in Arabidopsis.

Lignans/neolignans are generally synthesized from coniferyl alcohol (CA) in the cinnamate/monolignol pathway by oxidation to generate the corresponding radicals with subsequent stereoselective dimerization aided by dirigent proteins (DIRs). Genes encoding oxidases and DIRs for neolignan biosynthesis have not been identified previously. In Arabidopsis thaliana, the DIR AtDP1/AtDIR12 plays an essential role in the 8-O-4' coupling in neolignan biosynthesis by unequivocal structural determination of the compound missing in the atdp1 mutant as a sinapoylcholine (SC)-conjugated neolignan, erythro-3-{4-[2-hydroxy-2-(4-hydroxy-3-methoxyphenyl)-1-hydroxymethylethoxy]-3,5-dimethoxyphenyl}acryloylcholine.

A conserved strategy of chalcone isomerase-like protein to rectify promiscuous chalcone synthase specificity.

Land plants produce diverse flavonoids for growth, survival, and reproduction. Chalcone synthase is the first committed enzyme of the flavonoid biosynthetic pathway and catalyzes the production of 2',4,4',6'-tetrahydroxychalcone (THC). However, it also produces other polyketides, including p-coumaroyltriacetic acid lactone (CTAL), because of the derailment of the chalcone-producing pathway.

The Origin and Evolution of Plant Flavonoid Metabolism.

During their evolution, plants have acquired the ability to produce a huge variety of compounds. Unlike the specialized metabolites that accumulate in limited numbers of species, flavonoids are widely distributed in the plant kingdom. Therefore, a detailed analysis of flavonoid metabolism in genomics and metabolomics is an ideal way to investigate how plants have developed their unique metabolic pathways during the process of evolution.

UGT79B31 is responsible for the final modification step of pollen-specific flavonoid biosynthesis in Petunia hybrida.

UGT79B31 encodes flavonol 3- O -glycoside: 2″- O -glucosyltransferase, an enzyme responsible for the terminal modification of pollen-specific flavonols in Petunia hybrida. Flavonoids are known to be involved in pollen fertility in petunia (P. hybrida) and maize (Zea mays).

Cloning and characterization of soybean gene Fg1 encoding flavonol 3-O-glucoside/galactoside (1→6) glucosyltransferase.

Flavonoids are important secondary metabolites in plants. Sugar-sugar glycosyltransferases are involved in the final step of flavonoid biosynthesis and contribute to the structural diversity of flavonoids. This manuscript describes the first cloning of a sugar-sugar glucosyltransferase gene in the UGT family that attaches glucose to the 6″-position of sugar bound to a flavonol.

Linkage mapping, molecular cloning and functional analysis of soybean gene Fg3 encoding flavonol 3-O-glucoside/galactoside (1 → 2) glucosyltransferase.

Background: Flavonol glycosides (FGs) are major components of soybean leaves and there are substantial differences in FG composition among genotypes. The first objective of this study was to identify genes responsible for FG biosynthesis and to locate them in the soybean genome. The second objective was to clone the candidate genes and to verify their function.

A flavonoid 3-O-glucoside:2"-O-glucosyltransferase responsible for terminal modification of pollen-specific flavonols in Arabidopsis thaliana.

Flavonol 3-O-diglucosides with a 1→2 inter-glycosidic linkage are representative pollen-specific flavonols that are widely distributed in plants, but their biosynthetic genes and physiological roles are not well understood. Flavonoid analysis of four Arabidopsis floral organs (pistils, stamens, petals and calyxes) and flowers of wild-type and male sterility 1 (ms1) mutants, which are defective in normal development of pollen and tapetum, showed that kaempferol/quercetin 3-O-β-d-glucopyranosyl-(1→2)-β-d-glucopyranosides accumulated in Arabidopsis pollen. Microarray data using wild-type and ms1 mutants, gene expression patterns in various organs, and phylogenetic analysis of UDP-glycosyltransferases (UGTs) suggest that UGT79B6 (At5g54010) is a key modification enzyme for determining pollen-specific flavonol structure.

Enhancement of oxidative and drought tolerance in Arabidopsis by overaccumulation of antioxidant flavonoids.

The notion that plants use specialized metabolism to protect against environmental stresses needs to be experimentally proven by addressing the question of whether stress tolerance by specialized metabolism is directly due to metabolites such as flavonoids. We report that flavonoids with radical scavenging activity mitigate against oxidative and drought stress in Arabidopsis thaliana. Metabolome and transcriptome profiling and experiments with oxidative and drought stress in wild-type, single overexpressors of MYB12/PFG1 (PRODUCTION OF FLAVONOL GLYCOSIDES1) or MYB75/PAP1 (PRODUCTION OF ANTHOCYANIN PIGMENT1), double overexpressors of MYB12 and PAP1, transparent testa4 (tt4) as a flavonoid-deficient mutant, and flavonoid-deficient MYB12 or PAP1 overexpressing lines (obtained by crossing tt4 and the individual MYB overexpressor) demonstrated that flavonoid overaccumulation was key to enhanced tolerance to such stresses.

Linkage mapping, molecular cloning and functional analysis of soybean gene Fg2 encoding flavonol 3-O-glucoside (1 → 6) rhamnosyltransferase.

There are substantial genotypic differences in the levels of flavonol glycosides (FGs) in soybean leaves. The first objective of this study was to identify and locate genes responsible for FG biosynthesis in the soybean genome. The second objective was to clone and verify the function of these candidate genes.

Transcriptome coexpression analysis using ATTED-II for integrated transcriptomic/metabolomic analysis.

Transcriptome coexpression analysis is an excellent tool for predicting the physiological functions of genes. It is based on the "guilt-by-association" principle. Generally, genes involved in certain metabolic processes are coordinately regulated.

Medicago glucosyltransferase UGT72L1: potential roles in proanthocyanidin biosynthesis.

In the first reaction specific for proanthocyanidin (PA) biosynthesis in Arabidopsis thaliana and Medicago truncatula, anthocyanidin reductase (ANR) converts cyanidin to (-)-epicatechin. The glucosyltransferase UGT72L1 catalyzes formation of epicatechin 3'-O-glucoside (E3'OG), the preferred substrate for MATE transporters implicated in PA biosynthesis in both species. The mechanism of PA polymerization is still unclear, but may involve the laccase-like polyphenol oxidase TRANSPARENT TESTA 10 (TT10).

The flavonoid biosynthetic pathway in Arabidopsis: structural and genetic diversity.

Flavonoids are representative plant secondary products. In the model plant Arabidopsis thaliana, at least 54 flavonoid molecules (35 flavonols, 11 anthocyanins and 8 proanthocyanidins) are found. Scaffold structures of flavonoids in Arabidopsis are relatively simple.

Transcriptome data modeling for targeted plant metabolic engineering.

The massive data generated by omics technologies require the power of bioinformatics, especially network analysis, for data mining and doing data-driven biology. Gene coexpression analysis, a network approach based on comprehensive gene expression data using microarrays, is becoming a standard tool for predicting gene function and elucidating the relationship between metabolic pathways. Differential and comparative gene coexpression analyses suggest a change in coexpression relationships and regulators controlling common and/or specific biological processes.

Tissue-specific transcriptome analysis reveals cell wall metabolism, flavonol biosynthesis and defense responses are activated in the endosperm of germinating Arabidopsis thaliana seeds.

Seed germination is a result of the competition of embryonic growth potential and mechanical constraint by surrounding tissues such as the endosperm. To understand the processes occurring in the endosperm during germination, we analyzed tiling array expression data on dissected endosperm and embryo from 6 and 24 h-imbibed Arabidopsis seeds. The genes preferentially expressed in the endosperm of both 6 and 24 h-imbibed seeds were enriched for those related to cell wall biosynthesis/modifications, flavonol biosynthesis, defense responses and cellular transport.

Two glycosyltransferases involved in anthocyanin modification delineated by transcriptome independent component analysis in Arabidopsis thaliana.

To identify candidate genes involved in Arabidopsis flavonoid biosynthesis, we applied transcriptome coexpression analysis and independent component analyses with 1388 microarray data from publicly available databases. Two glycosyltransferases, UGT79B1 and UGT84A2 were found to cluster with anthocyanin biosynthetic genes. Anthocyanin was drastically reduced in ugt79b1 knockout mutants.

Ligand-binding properties and subcellular localization of maize cytokinin receptors.

The ligand-binding properties of the maize (Zea mays L.) cytokinin receptors ZmHK1, ZmHK2, and ZmHK3a have been characterized using cytokinin binding assays with living cells or membrane fractions. According to affinity measurements, ZmHK1 preferred N(6)-(Δ(2)-isopentenyl)adenine (iP) and had nearly equal affinities to trans-zeatin (tZ) and cis-zeatin (cZ).

An evolutionary view of functional diversity in family 1 glycosyltransferases.

Glycosyltransferases (GTs) (EC 2.4.x.

Metabolic profiling and cytological analysis of proanthocyanidins in immature seeds of Arabidopsis thaliana flavonoid accumulation mutants.

Arabidopsis TRANSPARENT TESTA19 (TT19) encodes a glutathione-S-transferase (GST)-like protein that is involved in the accumulation of proanthocyanidins (PAs) in the seed coat. PA accumulation sites in tt19 immature seeds were observed as small vacuolar-like structures, whereas those in tt12, a mutant of the tonoplast-bound transporter of PAs, and tt12 tt19 were observed at peripheral regions of small vacuoles. We found that tt19 immature seeds had small spherical structures showing unique thick morphology by differential interference contrast microscopy.

AtMetExpress development: a phytochemical atlas of Arabidopsis development.

Plants possess many metabolic genes for the production of a wide variety of phytochemicals in a tissue-specific manner. However, the metabolic systems behind the diversity and tissue-dependent regulation still remain unknown due to incomplete characterization of phytochemicals produced in a single plant species. Thus, having a metabolome dataset in addition to the genome and transcriptome information resources would enrich our knowledge of plant secondary metabolism.

Metabolomics-oriented isolation and structure elucidation of 37 compounds including two anthocyanins from Arabidopsis thaliana.

In order to conduct metabolomic studies in a model plant for genome research, such as Arabidopsis thaliana (Arabidopsis), it is a prerequisite to obtain structural information for the isolated metabolites from the plant of interest. In this study, we isolated metabolites of Arabidopsis in a relatively non-targeted way, aiming at the construction of metabolite standards and chemotaxonomic comparison. Anthocyanins (5 and 7) called A8 and A10 were isolated and their structures were elucidated as cyanidin 3-O-[2-O-(beta-D-xylopyranosyl)-6-O-(4-O-(beta-D-glucopyranosyl)-E-p-coumaroyl)-beta-D-glucopyranoside]-5-O-[6-O-(malonyl)-beta-D-glucopyranoside] and cyanidin 3-O-[2-O-(2-O-(E-sinapoyl)-beta-D-xylopyranosyl)-6-O-(4-O-(beta-D-glucopyranosyl)-E-p-coumaroyl)-beta-D-glucopyranoside]-5-O-[beta-D-glucopyranoside] from analyses of 1D NMR, 2D NMR ((1)H NMR, NOE, (13)C NMR, HMBC and HMQC), HRFABMS, FT-ESI-MS and GC-TOF-MS data.

MS/MS spectral tag-based annotation of non-targeted profile of plant secondary metabolites.

The MS/MS spectral tag (MS2T) library-based peak annotation procedure was developed for informative non-targeted metabolic profiling analysis using LC-MS. An MS2T library of Arabidopsis metabolites was created from a set of MS/MS spectra acquired using the automatic data acquisition function of the mass spectrometer. By using this library, we obtained structural information for the detected peaks in the metabolic profile data without performing additional MS/MS analysis; this was achieved by searching for the corresponding MS2T accession in the library.

Comprehensive flavonol profiling and transcriptome coexpression analysis leading to decoding gene-metabolite correlations in Arabidopsis.

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.

Decoding genes with coexpression networks and metabolomics - 'majority report by precogs'.

Following the sequencing of whole genomes of model plants, high-throughput decoding of gene function is a major challenge in modern plant biology. In view of remarkable technical advances in transcriptomics and metabolomics, integrated analysis of these 'omics' by data-mining informatics is an excellent tool for prediction and identification of gene function, particularly for genes involved in complicated metabolic pathways. The availability of Arabidopsis public transcriptome datasets containing data of >1000 microarrays reinforces the potential for prediction of gene function by transcriptome coexpression analysis.

Engineering of the rose flavonoid biosynthetic pathway successfully generated blue-hued flowers accumulating delphinidin.

Flower color is mainly determined by anthocyanins. Rosa hybrida lacks violet to blue flower varieties due to the absence of delphinidin-based anthocyanins, usually the major constituents of violet and blue flowers, because roses do not possess flavonoid 3',5'-hydoxylase (F3'5'H), a key enzyme for delphinidin biosynthesis. Other factors such as the presence of co-pigments and the vacuolar pH also affect flower color.