Analysis of T-DNA alleles of flavonoid biosynthesis genes in Arabidopsis ecotype Columbia

Generation and characterisation of an Arabidopsis thaliana f3h/fls1/ans triple mutant that accumulates eriodictyol derivatives

BACKGROUND

Flavonoids are plant specialised metabolites, which derive from phenylalanine and acetate metabolism. They possess a variety of beneficial characteristics for plants and humans. Several modification steps in the synthesis of tricyclic flavonoids cause for the amazing diversity of flavonoids in plants. The 2-oxoglutarate-dependent dioxygenases (2-ODDs) flavanone 3-hydroxylase (F3H, synonym FHT), flavonol synthase (FLS) and anthocyanidin synthase (ANS, synonym leucoanthocyanidin dioxygenase (LDOX)), catalyse oxidative modifications to the central C ring. They are highly similar and have been shown to catalyse, at least in part, each other's reactions. FLS and ANS have been identified as bifunctional enzymes in many species, including Arabidopsis thaliana, stressing the capability of plants to bypass missing or mutated reaction steps on the way to flavonoid production. However, little is known about such bypass reactions and the flavonoid composition of plants lacking all three central flavonoid 2-ODDs.

RESULTS

To address this issue, we generated a f3h/fls1/ans mutant, as well as the corresponding double mutants and investigated the flavonoid composition of this mutant collection. The f3h/fls1/ans mutant was further characterised at the genomic level by analysis of a nanopore DNA sequencing generated genome sequence assembly and at the transcriptomic level by RNA-Seq analysis. The mutant collection established, including the novel double mutants f3h/fls1 and f3h/ans, was used to validate and analyse the multifunctionalities of F3H, FLS1, and ANS in planta. Metabolite analyses revealed the accumulation of eriodictyol and additional glycosylated derivatives in mutants carrying the f3h mutant allele, resulting from the conversion of naringenin to eriodictyol by flavonoid 3'-hydroxylase (F3'H) activity.

CONCLUSIONS

We describe the in planta multifunctionality of the three central flavonoid 2-ODDs from A. thaliana and identify a bypass in the f3h/fls1/ans triple mutant that leads to the formation of eriodictyol derivatives. As (homo-)eriodictyols are known as bitter taste maskers, the annotated eriodictyol (derivatives) and in particular the observations made on their in planta production, could provide valuable insights for the creation of novel food supplements.

Genome-wide identification of grape ANS gene family and expression analysis at different fruit coloration stages

BACKGROUND

Anthocyanin synthase (ANS) is the enzyme downstream of the anthocyanins synthesis pathway and the rate-limiting enzyme of the synthesis pathway. It catalyzes the conversion of colorless anthocyanins to anthocyanins and plays an important role in plant color presentation and stress resistance. However, ANS gene is rarely studied in grapes.

RESULTS

In this study, 121 VvANS genes were identified and distributed on 18 chromosomes, VvANS family members were divided into 8 subgroups. Secondary structure prediction showed mainly irregular coils and α-helices, and subcellular localization indicated that VvANS gene family is mainly located in chloroplast, cytoplasm and nucleus. The promoter region of the VvANS gene family contains multiple cis-acting elements that are associated with light, abiotic stress, and hormones. Intraspecific collinearity analysis showed that there were 13 pairs of collinearity between VvANS genes. Interspecific collinearity analysis showed that there was more collinearity between grape, apple and Arabidopsis, but less collinearity between grape and rice. Microarray data analysis showed that VvANS17, VvANS23 and VvANS75 had higher expression levels in flesh and peel, while VvANS25, VvANS64 and VvANS106 had higher expression levels in flower. The results of qRT-PCR analysis showed that VvANS genes were expressed throughout the whole process of fruit coloring, such as VvANS47 and VvANS55 in the green fruit stage, VvANS3, VvANS64 and VvANS90 in the initial fruit color turning stage. The expression levels of VvANS21, VvANS79 and VvANS108 were higher at 50% coloring stage, indicating that these genes play an important role in the fruit coloring process. VvANS4, VvANS66 and VvANS113 had the highest expression levels in the full maturity stage.

CONCLUSIONS

These results indicated that different members of VvANS gene family played a role in different coloring stages, and this study laid a foundation for further research on the function of ANS gene family.

Kaempferol-3-rhamnoside overaccumulation in flavonoid 3'-hydroxylase tt7 mutants compromises seed coat outer integument differentiation and seed longevity

Seeds slowly accumulate damage during storage, which ultimately results in germination failure. The seed coat protects the embryo from the external environment, and its composition is critical for seed longevity. Flavonols accumulate in the outer integument. The link between flavonol composition and outer integument development has not been explored. Genetic, molecular and ultrastructural assays on loss-of-function mutants of the flavonoid biosynthesis pathway were used to study the effect of altered flavonoid composition on seed coat development and seed longevity. Controlled deterioration assays indicate that loss of function of the flavonoid 3' hydroxylase gene TT7 dramatically affects seed longevity and seed coat development. Outer integument differentiation is compromised from 9 d after pollination in tt7 developing seeds, resulting in a defective suberin layer and incomplete degradation of seed coat starch. These distinctive phenotypes are not shared by other mutants showing abnormal flavonoid composition. Genetic analysis indicates that overaccumulation of kaempferol-3-rhamnoside is mainly responsible for the observed phenotypes. Expression profiling suggests that multiple cellular processes are altered in the tt7 mutant. Overaccumulation of kaempferol-3-rhamnoside in the seed coat compromises normal seed coat development. This observation positions TRANSPARENT TESTA 7 and the UGT78D1 glycosyltransferase, catalysing flavonol 3-O-rhamnosylation, as essential players in the modulation of seed longevity.

Flavonols modulate plant development, signaling, and stress responses

Flavonols are plant-specialized metabolites with important functions in plant growth and development. Isolation and characterization of mutants with reduced flavonol levels, especially the transparent testa mutants in Arabidopsis thaliana, have contributed to our understanding of the flavonol biosynthetic pathway. These mutants have also uncovered the roles of flavonols in controlling development in above- and below-ground tissues, notably in the regulation of root architecture, guard cell signaling, and pollen development. In this review, we present recent progress made towards a mechanistic understanding of flavonol function in plant growth and development. Specifically, we highlight findings that flavonols act as reactive oxygen species (ROS) scavengers and inhibitors of auxin transport in diverse tissues and cell types to modulate plant growth and development and responses to abiotic stresses.

The complexities of proanthocyanidin biosynthesis and its regulation in plants

Proanthocyanidins (PAs) are natural flavan-3-ol polymers that contribute protection to plants under biotic and abiotic stress, benefits to human health, and bitterness and astringency to food products. They are also potential targets for carbon sequestration for climate mitigation. In recent years, from model species to commercial crops, research has moved closer to elucidating the flux control and channeling, subunit biosynthesis and polymerization, transport mechanisms, and regulatory networks involved in plant PA metabolism. This review extends the conventional understanding with recent findings that provide new insights to address lingering questions and focus strategies for manipulating PA traits in plants.

Maternal control of triploid seed development by the TRANSPARENT TESTA 8 (TT8) transcription factor in Arabidopsis thaliana

The balance between parental genome dosage is critical to offspring development in both animals and plants. In some angiosperm species, despite the imbalance between maternally and paternally inherited chromosome sets, crosses between parental lines of different ploidy may result in viable offspring. However, many plant species, like Arabidopsis thaliana, present a post-zygotic reproductive barrier, known as triploid block which results in the inability of crosses between individuals of different ploidy to generate viable seeds but also, in defective development of the seed. Several paternal regulators have been proposed as active players in establishing the triploid block. Maternal regulators known to be involved in this process are some flavonoid biosynthetic (FB) genes, expressed in the innermost layer of the seed coat. Here we explore the role of selected flavonoid pathway genes in triploid block, including TRANSPARENT TESTA 4 (TT4), TRANSPARENT TESTA 7 (TT7), SEEDSTICK (STK), TRANSPARENT TESTA 16 (TT16), TT8 and TRANSPARENT TESTA 13 (TT13). This approach allowed us to detect that TT8, a bHLH transcription factor, member of this FB pathway is required for the paternal genome dosage, as loss of function tt8, leads to complete rescue of the triploid block to seed development.

Two independent loss-of-function mutations in anthocyanidin synthase homeologous genes are responsible for the all-green phenotype of sweet basil

Sweet basil, Ocimum basilicum L., is an important culinary herb grown worldwide. Although basil is green, many landraces, breeding lines, and exotic cultivars have purple stems and flowers. This anthocyanin pigmentation is unacceptable in traditional Italian basil used for Pesto sauce production. In the current study, we aimed to resolve the genetics that underlines the different colors. We used the recently published sweet basil genome to map quantitative trait loci (QTL) for flower and stem color in a bi-parental F₂ population. It was found that the pigmentation is governed by a single QTL, harboring an anthocyanidin synthase (ANS) gene (EC 1.14.20.4). Further analysis revealed that the basil genome harbors two homeologous ANS genes, each carrying a loss-of-function mutation. ObANS1 carries a single base pair insertion resulting in a frameshift, and ObANS2 carries a missense mutation within the active site. In the purple-flower parent, ANS1 is functional, and ANS2 carries a nonsense mutation. The functionality of the ObANS1 active allele was validated by complementation assay in an Arabidopsis ANS mutant. Moreover, we have restored the functionality of the missense-mutated ObANS2 using site-directed activation. We found that the non-functional alleles were expressed to similar levels as the functional allele, suggesting polyploids invest futile effort in expressing non-functional genes, offsetting their advantageous redundancy. This work demonstrated the usefulness of the genomics and genetics of basil to understand the basic mechanism of metabolic traits and raise fundamental questions in polyploid plant biology.

PtoWRKY40 interacts with PtoPHR1-LIKE3 while regulating the phosphate starvation response in poplar

Plants usually suffer from phosphorus starvation because of the low inorganic phosphate (Pi) status of most soils. To cope with this, plants have evolved an adaptive phosphate starvation response (PSR) which involves both developmental and metabolic changes regulated mainly by PHOSPHATE STARVATION RESPONSE1 (PHR1) and its homologs. Here, we elucidated how perennial woody plants, such as poplars (Populus spp.), respond to low-Pi stress. We first performed RNA-seq analysis of low-Pi-treated poplars and identified PtoWRKY40 is rapidly downregulated and protein degraded after stress. Overexpressing and knocking-down PtoWRKY40 downregulated and upregulated the expression of Pi starvation signaling genes, respectively, such as PHOSPHATE TRANSPORTER1 (PHT1)-type genes and PURPLE ACID PHOSPHATASE genes. PtoWRKY40 bound to the W box in the promoter of several PtoPHT1s and repressed their expression. Moreover, PtoWRKY40 interacted with PtoPHR1-LIKE3 (PtoPHL3), a PHR1 homolog in poplar, to inhibit the latter binding to the P1BS element and thus reduced PtoPHT1s' transcription under Pi-sufficient conditions. However, Pi deficiency decreased PtoWRKY40 abundance and therefore released its inhibition on PHT1s. In conclusion, we have uncovered a PSR mechanism mediated by PtoWRKY40 and PtoPHL3 which regulates Pi content in poplars, deepening our understanding of how poplars adapt to diverse Pi conditions and regulate appropriate responses to maintain Pi homeostasis.

Metabolic signatures of rhizobacteria-induced plant growth promotion

Various root-colonizing bacterial species can promote plant growth and trigger systemic resistance against aboveground leaf pathogens and herbivore insects. To date, the underlying metabolic signatures of these rhizobacteria-induced plant phenotypes are poorly understood. To identify core metabolic pathways that are targeted by growth-promoting rhizobacteria, we used combinations of three plant species and three rhizobacterial species and interrogated plant shoot chemistry by untargeted metabolomics. A substantial part (50%-64%) of the metabolites detected in plant shoot tissue was differentially affected by the rhizobacteria. Among others, the phenylpropanoid pathway was targeted by the rhizobacteria in each of the three plant species. Differential regulation of the various branches of the phenylpropanoid pathways showed an association with either plant growth promotion or growth reduction. Overall, suppression of flavonoid biosynthesis was associated with growth promotion, while growth reduction showed elevated levels of flavonoids. Subsequent assays with 12 Arabidopsis flavonoid biosynthetic mutants revealed that the proanthocyanidin branch plays an essential role in rhizobacteria-mediated growth promotion. Our study also showed that a number of pharmaceutically and nutritionally relevant metabolites in the plant shoot were significantly increased by rhizobacterial treatment, providing new avenues to use rhizobacteria to tilt plant metabolism towards the biosynthesis of valuable natural plant products.

Mutations that alter Arabidopsis flavonoid metabolism affect the circadian clock

Flavonoids are a well-known class of specialized metabolites that play key roles in plant development, reproduction, and survival. Flavonoids are also of considerable interest from the perspective of human health, as both phytonutrients and pharmaceuticals. RNA sequencing analysis of an Arabidopsis null allele for chalcone synthase (CHS), which catalyzes the first step in flavonoid metabolism, has uncovered evidence that these compounds influence the expression of genes associated with the plant circadian clock. Analysis of promoter-luciferase constructs further showed that the transcriptional activity of CCA1 and TOC1, two key clock genes, is altered in CHS-deficient seedlings across the day/night cycle. Similar findings for a mutant line lacking flavonoid 3'-hydroxylase (F3'H) activity, and thus able to synthesize mono- but not dihydroxylated B-ring flavonoids, suggests that the latter are at least partially responsible; this was further supported by the ability of quercetin to enhance CCA1 promoter activity in wild-type and CHS-deficient seedlings. The effects of flavonoids on circadian function were also reflected in photosynthetic activity, with chlorophyll cycling abolished in CHS- and F3'H-deficient plants. Remarkably, the same phenotype was exhibited by plants with artificially high flavonoid levels, indicating that neither the antioxidant potential nor the light-screening properties of flavonoids contribute to optimal clock function, as has recently also been demonstrated in animal systems. Collectively, the current experiments point to a previously unknown connection between flavonoids and circadian cycling in plants and open the way to better understanding of the molecular basis of flavonoid action.

Isolating an active and inactive CACTA transposon from lettuce color mutants and characterizing their family

Dietary flavonoids play an important role in human nutrition and health. Flavonoid biosynthesis genes have recently been identified in lettuce (Lactuca sativa); however, few mutants have been characterized. We now report the causative mutations in Green Super Lettuce (GSL), a natural light green mutant derived from red cultivar NAR; and GSL-Dark Green (GSL-DG), an olive-green natural derivative of GSL. GSL harbors CACTA 1 (LsC1), a 3.9-kb active nonautonomous CACTA superfamily transposon inserted in the 5' untranslated region of anthocyanidin synthase (ANS), a gene coding for a key enzyme in anthocyanin biosynthesis. Both terminal inverted repeats (TIRs) of this transposon were intact, enabling somatic excision of the mobile element, which led to the restoration of ANS expression and the accumulation of red anthocyanins in sectors on otherwise green leaves. GSL-DG harbors CACTA 2 (LsC2), a 1.1-kb truncated copy of LsC1 that lacks one of the TIRs, rendering the transposon inactive. RNA-sequencing and reverse transcription quantitative PCR of NAR, GSL, and GSL-DG indicated the relative expression level of ANS was strongly influenced by the transposon insertions. Analysis of flavonoid content indicated leaf cyanidin levels correlated positively with ANS expression. Bioinformatic analysis of the cv Salinas lettuce reference genome led to the discovery and characterization of an LsC1 transposon family with a putative transposon copy number greater than 1,700. Homologs of tnpA and tnpD, the genes encoding two proteins necessary for activation of transposition of CACTA elements, were also identified in the lettuce genome.

Variation in Seed Metabolites between Two Indica Rice Accessions Differing in Seed Longevity

For a better understanding of germination after seed storage, metabolite profiling was conducted using hybrid triple quadrupole time-of-flight (QTOF) mass spectrometry. After moisture content (MC) equilibration, seeds of "WAS170" (short-lived) and "IR65483" (long-lived) were stored at 10.9% MC and 45 °C. Samples for metabolite analysis were taken after 0 and 20 days of storage. Among 288 metabolites, two flavonoids (kaempferide and quercetin-3-arabinoside), one amino acid (S-sulfocysteine) and one sugar (D-glucose) increased in "IR65483" seeds after storage but were not detected in "WAS170" seeds. Based on the genome sequence database, we identified clear allelic differences with non-synonymous mutations on the six flavonol synthase genes regulating the accumulation of kaempferol- and quercetin-metabolites. On the other hand, two metabolites (thiamine monophosphate and harmaline) increased in short-lived seeds after storage; these metabolites could be potential biochemical indicators of seed deterioration.

A high-quality sponge gourd (Luffa cylindrica) genome

Sponge gourd (Luffa cylindrica) is an important cultivated vegetable and medicinal plant in the family Cucurbitaceae. In this study, a draft genome sequence of the sponge gourd inbred line P93075 was analyzed. Using Illumina, PacBio, and 10× Genomics sequencing techniques as well as new assembly techniques such as FALCON and chromatin interaction mapping (Hi-C), a chromosome-scale genome of approximately 656.19 Mb, with an N50 scaffold length of 48.76 Mb, was generated. From this assembly, 25,508 protein-coding gene loci were identified, and 63.81% of the whole-genome consisted of transposable elements, which are major contributors to the expansion of the sponge gourd genome. According to a phylogenetic analysis of conserved genes, the sponge gourd lineage diverged from the bitter gourd lineage approximately 41.6 million years ago. Additionally, many genes that respond to biotic and abiotic stresses were found to be lineage specific or expanded in the sponge gourd genome, as demonstrated by the presence of 462 NBS-LRR genes, a much greater number than are found in the genomes of other cucurbit species; these results are consistent with the high stress resistance of sponge gourd. Collectively, our study provides insights into genome evolution and serves as a valuable reference for the genetic improvement of sponge gourd.

Combining transcriptomics and genetic linkage based information to identify candidate genes associated with Heterobasidion-resistance in Norway spruce

The Heterobasidion annosum s.l species complex comprises the most damaging forest pathogens to Norway spruce. We revisited previously identified Quantitative Trait Loci (QTLs) related to Heterobasidion-resistance in Norway spruce to identify candidate genes associated with these QTLs. We identified 329 candidate genes associated with the resistance QTLs using a gene-based composite map for Pinaceae. To evaluate the transcriptional responses of these candidate genes to H. parviporum, we inoculated Norway spruce plants and sequenced the transcriptome of the interaction at 3 and 7 days post inoculation. Out of 298 expressed candidate genes 124 were differentially expressed between inoculation and wounding control treatment. Interestingly, PaNAC04 and two of its paralogs in the subgroup III-3 of the NAC family transcription factors were found to be associated with one of the QTLs and was also highly induced in response to H. parviporum. These genes are possibly involved in the regulation of biosynthesis of flavonoid compounds. Furthermore, several of the differentially expressed candidate genes were associated with the phenylpropanoid pathway including a phenylalanine ammonia-lyase, a cinnamoyl-CoA reductase, a caffeoyl-CoA O-methyltransferase and a PgMYB11-like transcription factor gene. Combining transcriptome and genetic linkage analyses can help identifying candidate genes for functional studies and molecular breeding in non-model species.

Synergy between the anthocyanin and RDR6/SGS3/DCL4 siRNA pathways expose hidden features of Arabidopsis carbon metabolism

Anthocyanin pigments furnish a powerful visual output of the stress and metabolic status of Arabidopsis thaliana plants. Essential for pigment accumulation is TRANSPARENT TESTA19 (TT19), a glutathione S-transferase proposed to bind and stabilize anthocyanins, participating in their vacuolar sequestration, a function conserved across the flowering plants. Here, we report the identification of genetic suppressors that result in anthocyanin accumulation in the absence of TT19. We show that mutations in RDR6, SGS3, or DCL4 suppress the anthocyanin defect of tt19 by pushing carbon towards flavonoid biosynthesis. This effect is not unique to tt19 and extends to at least one other anthocyanin pathway gene mutant. This synergy between mutations in components of the RDR6-SGS3-DCL4 siRNA system and the flavonoid pathway reveals genetic/epigenetic mechanisms regulating metabolic fluxes.

TRANSPARENT TESTA19 (TT19) encodes a glutathione S-transferase which functions in anthocyanin stabilization and vacuolar transport. Here, by tt19 suppressor screening, the authors show that RDR6/SGS3/DCL4 siRNA pathway constituents synergistically interact with components of the flavonoid pathway to control carbon metabolism.

Arg-type dihydroflavonol 4-reductase genes from the fern Dryopteris erythrosora play important roles in the biosynthesis of anthocyanins

Dihydroflavonol 4-reductase (DFR), a key enzyme involved in the biosynthesis of anthocyanins, has been cloned from various species. However, little research has been conducted on this enzyme in ferns, which occupy a unique evolutionary position. In this study, we isolated two novel DFR genes from the fern Dryopteris erythrosora. In vitro enzymatic analysis revealed that DeDFR1 and DeDFR2 enzymes can catalyze dihydrokaempferol and dihydroquercetin but cannot catalyze dihydromyricetin. Amino acid sequence analysis showed that DeDFR1 and DeDFR2 have an arginine at the same substrate-specificity-determining site as that in the ferns Salvinia cucullata and Azolla filiculoides. Thus, we speculate that the Arg-type DFR is a new DFR functional type. To further verify the substrate preferences of the Arg-type DFR, an amino acid substitution assay was conducted. When N133 was mutated to R133, Arabidopsis DFR protein completely lost its catalytic activity for dihydromyricetin, as observed for DeDFR1 and DeDFR2. Additionally, heterologous expression of DeDFR2 in the Arabidopsis tt3-1 mutant resulted in increasing anthocyanin accumulation. In summary, DeDFR1 and DeDFR2 are considered to be a new type of DFR with unique structures and functions. The discovery of the Arg-type DFR provides new insights into the anthocyanin biosynthesis pathway in ferns.

Flavonols regulate root hair development by modulating accumulation of reactive oxygen species in the root epidermis

Reactive oxygen species (ROS) are signaling molecules produced by tissue-specific respiratory burst oxidase homolog (RBOH) enzymes to drive development. In Arabidopsis thaliana, ROS produced by RBOHC was previously reported to drive root hair elongation. We identified a specific role for one ROS, H₂O₂, in driving root hair initiation and demonstrated that localized synthesis of flavonol antioxidants control the level of H₂O₂ and root hair formation. Root hairs form from trichoblast cells that express RBOHC and have elevated H₂O₂ compared with adjacent atrichoblast cells that do not form root hairs. The flavonol-deficient tt4 mutant has elevated ROS in trichoblasts and elevated frequency of root hair formation compared with the wild type. The increases in ROS and root hairs in tt4 are reversed by genetic or chemical complementation. Auxin-induced root hair initiation and ROS accumulation were reduced in an rbohc mutant and increased in tt4, consistent with flavonols modulating ROS and auxin transport. These results support a model in which localized synthesis of RBOHC and flavonol antioxidants establish patterns of ROS accumulation that drive root hair formation.

Diversity of genetic lesions characterizes new Arabidopsis flavonoid pigment mutant alleles from T-DNA collections

The visual phenotypes afforded by flavonoid pigments have provided invaluable tools for modern genetics. Many Arabidopsis transparent testa (tt) mutants lacking the characteristic proanthocyanidin (PA) seed coat pigmentation and often failing to accumulate anthocyanins in vegetative tissues have been characterized. These mutants have significantly contributed to our understanding of flavonoid biosynthesis, regulation, and transport. A comprehensive screening for tt mutants in available large T-DNA collection lines resulted in the identification of 16 independent lines lacking PAs and anthocyanins, or with seed coat pigmentation clearly distinct from wild type. Segregation analyses and the characterization of second alleles in the genes disrupted by the indexed T-DNA insertions demonstrated that all the lines contained at least one additional mutation responsible for the tt phenotypes. Using a combination of RNA-Seq and whole genome re-sequencing and confirmed through complementation, we show here that these mutations correspond to novel alleles of ttg1 (two alleles), tt3 (two alleles), tt5 (two alleles), ban (two alleles), tt1 (two alleles), and tt8 (six alleles), which harbored additional T-DNA insertions, indels, missense mutations, and large genomic deletion. Several of the identified alleles offer interesting perspectives on flavonoid biosynthesis and regulation.

Comparative Genomics of Spatholobus suberectus and Insight Into Flavonoid Biosynthesis

Spatholobus suberectus Dunn (S. suberectus), has been widely used in traditional medicines plant source of the Leguminosae family. Its vine stem of which plays an important role in the prevention and treatment of various diseases because it contains various flavonoids. Comparative genome analysis suggested well-conserved genomic components and genetic collinearity between the genome of S. suberectus and other genera of Leguminosae such as Glycine max. We discovered two whole genome duplications (WGD) events in S. suberectus and G. max lineage underwent a WGD after speciation from S. suberectus. The determination of expansion and contractions of orthologous gene families revealed 1,001 expanded gene families and 3,649 contracted gene families in the S. suberectus lineage. Comparing to the model plants, many novel flavonoid biosynthesis-related genes were predicted in the genome of S. suberectus, and the expression patterns of these genes in the roots are similar to those in the stems [such as the isoflavone synthase (IFS) genes]. The expansion of IFS from a single copy in the Leguminosae ancestor to four copies in S. suberectus, will accelerate the biosynthesis of flavonoids. MYB genes are widely involved in plant flavonoid biosynthesis and the most abundant member of the TF family in S. suberectus. Activated retrotransponson positive regulates the accumulation of flavonoid in S. suberectus by introducing the cis-elements of tissue-specific expressed MYBs. Our study not only provides significant insight into the evolution of specific flavonoid biosynthetic pathways in S. suberectus, but also would facilitate the development of tools for enhancing bioactive productivity by metabolic engineering in microbes or by molecular breeding for alleviating resource shortage of S. suberectus.

Genetic and Phytochemical Characterization of Lettuce Flavonoid Biosynthesis Mutants

We previously developed red lettuce (Lactuca sativa L.) cultivars with high flavonoid and phenolic acid content and demonstrated their anti-diabetic effect. Here we report on developing three fertile and true-breeding lettuce lines enriched with flavonoids with reported beneficial health effects. These lines were identified in a segregating population of EMS-mutagenized red lettuce and characterized biochemically and genetically. Change in red coloration was used as a visual indicator of a mutation in a flavonoid pathway gene, leading to accumulation of flavonoid precursors of red anthocyanins. Pink-green kaempferol overproducing kfoA and kfoB mutants accumulated kaempferol to 0.6-1% of their dry weight, higher than in any vegetable reported. The yellow-green naringenin chalcone overproducing mutant (nco) accumulated naringenin chalcone, not previously reported in lettuce, to 1% dry weight, a level only observed in tomato peel. Kfo plants carried a mutation in the FLAVONOID-3' HYDROXYLASE (F3'H) gene, nco in CHALCONE ISOMERASE (CHI). This work demonstrates how non-GMO approaches can transform a common crop plant into a functional food with possible health benefits.

Identification of MOS9 as an interaction partner for chalcone synthase in the nucleus

Plant flavonoid metabolism has served as a platform for understanding a range of fundamental biological phenomena, including providing some of the early insights into the subcellular organization of metabolism. Evidence assembled over the past three decades points to the organization of the component enzymes as a membrane-associated complex centered on the entry-point enzyme, chalcone synthase (CHS), with flux into branch pathways controlled by competitive protein interactions. Flavonoid enzymes have also been found in the nucleus in a variety of plant species, raising the possibility of alternative, or moonlighting functions for these proteins in this compartment. Here, we present evidence that CHS interacts with MOS9, a nuclear-localized protein that has been linked to epigenetic control of R genes that mediate effector-triggered immunity. Overexpression of MOS9 results in a reduction of CHS transcript levels and a metabolite profile that substantially intersects with the effects of a null mutation in CHS. These results suggest that the MOS9-CHS interaction may point to a previously-unknown mechanism for controlling the expression of the highly dynamic flavonoid pathway.

Efficient CRISPR/Cas9-based genome editing in carrot cells

KEY MESSAGE

The first report presenting successful and efficient carrot genome editing using CRISPR/Cas9 system. Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated (Cas9) is a powerful genome editing tool that has been widely adopted in model organisms recently, but has not been used in carrot-a model species for in vitro culture studies and an important health-promoting crop grown worldwide. In this study, for the first time, we report application of the CRISPR/Cas9 system for efficient targeted mutagenesis of the carrot genome. Multiplexing CRISPR/Cas9 vectors expressing two single-guide RNA (gRNAs) targeting the carrot flavanone-3-hydroxylase (F3H) gene were tested for blockage of the anthocyanin biosynthesis in a model purple-colored callus using Agrobacterium-mediated genetic transformation. This approach allowed fast and visual comparison of three codon-optimized Cas9 genes and revealed that the most efficient one in generating F3H mutants was the Arabidopsis codon-optimized AteCas9 gene with up to 90% efficiency. Knockout of F3H gene resulted in the discoloration of calli, validating the functional role of this gene in the anthocyanin biosynthesis in carrot as well as providing a visual marker for screening successfully edited events. Most resulting mutations were small Indels, but long chromosome fragment deletions of 116-119 nt were also generated with simultaneous cleavage mediated by two gRNAs. The results demonstrate successful site-directed mutagenesis in carrot with CRISPR/Cas9 and the usefulness of a model callus culture to validate genome editing systems. Given that the carrot genome has been sequenced recently, our timely study sheds light on the promising application of genome editing tools for boosting basic and translational research in this important vegetable crop.

Contrasting cadmium resistance strategies in two metallicolous populations of Arabidopsis halleri

While cadmium (Cd) tolerance is a constitutive trait in the Arabidopsis halleri species, Cd accumulation is highly variable. Recent adaptation to anthropogenic metal stress has occurred independently within the genetic units of A. halleri and the evolution of different mechanisms involved in Cd tolerance and accumulation has been suggested. To gain a better understanding of the mechanisms underlying Cd tolerance and accumulation in A. halleri, ionomic inductively coupled plasma mass spectrometry (ICP-MS), transcriptomic (RNA sequencing) and metabolomic (high-performance liquid chromatography-mass spectrometry) profiles were analysed in two A. halleri metallicolous populations from different genetic units (PL22 from Poland and I16 from Italy). The PL22 and I16 populations were both hypertolerant to Cd, but PL22 hyperaccumulated Cd while I16 behaved as an excluder both in situ and when grown hydroponically. The observed hyperaccumulator vs excluder behaviours were paralleled by large differences in the expression profiles of transporter genes. Flavonoid-related transcripts and metabolites were strikingly more abundant in PL22 than in I16 shoots. The role of novel A. halleri candidate genes possibly involved in Cd hyperaccumulation or exclusion was supported by the study of corresponding A. thaliana knockout mutants. Taken together, our results are suggestive of the evolution of divergent strategies for Cd uptake, transport and detoxification in different genetic units of A. halleri.

TRANSPARENT TESTA GLABRA 1-Dependent Regulation of Flavonoid Biosynthesis

The flavonoid composition of various tissues throughout plant development is of biological relevance and particular interest for breeding. Arabidopsis thaliana TRANSPARENT TESTA GLABRA 1 (AtTTG1) is an essential regulator of late structural genes in flavonoid biosynthesis. Here, we provide a review of the regulation of the pathway's core enzymes through AtTTG1-containing R2R3-MYELOBLASTOSIS-basic HELIX-LOOP-HELIX-WD40 repeat (MBW(AtTTG1)) complexes embedded in an evolutionary context. We present a comprehensive collection of A. thalianattg1 mutants and AtTTG1 orthologs. A plethora of MBW(AtTTG1) mechanisms in regulating the five major TTG1-dependent traits is highlighted.

ROS Induces Anthocyanin Production Via Late Biosynthetic Genes and Anthocyanin Deficiency Confers the Hypersensitivity to ROS-Generating Stresses in Arabidopsis

Anthocyanins are known to have antioxidant activities. Their accumulation can be triggered by many chemical and environmental factors, including reactive oxygen species (ROS). However, the mechanism of ROS-induced anthocyanin accumulation and the role of anthocyanins in the response of Arabidopsis (Arabidopsis thaliana) to different stresses are largely unknown. Here, we study the cross-regulation between ROS and anthocyanin production. Ten Arabidopsis mutants covering the main anthocyanin regulatory and biosynthetic genes are systematically analyzed under ROS-generating stresses. We find that ROS triggers anthocyanin accumulation by up-regulating the anthocyanin late biosynthetic and the corresponding regulatory genes. The anthocyanin-deficient mutants have more endogenous ROS and are more sensitive to ROS-generating stresses while having decreased antioxidant capacity. Supplementation with cyanidin makes them less susceptible to ROS, with increased anthocyanin and reduced ROS accumulation. In contrast, pap1-D, which overaccumulates anthocyanins, shows the opposite responses. Gene expression analysis reveals that photosynthetic capacity is more impaired in anthocyanin-deficient mutants under high-light stress. Expression levels of ROS-scavenging enzyme genes are not correlated with the radical-scavenging activity in different mutants. We conclude that ROS are an important source signal to induce anthocyanin accumulation by up-regulating late biosynthetic and the corresponding regulatory genes and, as a feed-back regulation, anthocyanins modulate the ROS level and the sensitivity to ROS-generating stresses in maintaining photosynthetic capacity.

Current understanding of the pathways of flavonoid biosynthesis in model and crop plants

Flavonoids are a signature class of secondary metabolites formed from a relatively simple collection of scaffolds. They are extensively decorated by chemical reactions including glycosylation, methylation, and acylation. They are present in a wide variety of fruits and vegetables and as such in Western populations it is estimated that 20-50 mg of flavonoids are consumed daily per person. In planta they have demonstrated to contribute to both flower color and UV protection. Their consumption has been suggested to presenta wide range of health benefits. Recent technical advances allowing affordable whole genome sequencing, as well as a better inventory of species-by-species chemical diversity, have greatly advanced our understanding as to how flavonoid biosynthesis pathways vary across species. In parallel, reverse genetics combined with detailed molecular phenotyping is currently allowing us to elucidate the functional importance of individual genes and metabolites and by this means to provide further mechanistic insight into their biological roles. Here we provide an inventory of current knowledge of pathways of flavonoid biosynthesis in both the model plant Arabidopsis thaliana and a range of crop species, including tomato, maize, rice, and bean.

Integrated omics analysis of specialized metabolism in medicinal plants

Medicinal plants are a rich source of highly diverse specialized metabolites with important pharmacological properties. Until recently, plant biologists were limited in their ability to explore the biosynthetic pathways of these metabolites, mainly due to the scarcity of plant genomics resources. However, recent advances in high-throughput large-scale analytical methods have enabled plant biologists to discover biosynthetic pathways for important plant-based medicinal metabolites. The reduced cost of generating omics datasets and the development of computational tools for their analysis and integration have led to the elucidation of biosynthetic pathways of several bioactive metabolites of plant origin. These discoveries have inspired synthetic biology approaches to develop microbial systems to produce bioactive metabolites originating from plants, an alternative sustainable source of medicinally important chemicals. Since the demand for medicinal compounds are increasing with the world's population, understanding the complete biosynthesis of specialized metabolites becomes important to identify or develop reliable sources in the future. Here, we review the contributions of major omics approaches and their integration to our understanding of the biosynthetic pathways of bioactive metabolites. We briefly discuss different approaches for integrating omics datasets to extract biologically relevant knowledge and the application of omics datasets in the construction and reconstruction of metabolic models.

The Reaumuria trigyna leucoanthocyanidin dioxygenase (RtLDOX) gene complements anthocyanidin synthesis and increases the salt tolerance potential of a transgenic Arabidopsis LDOX mutant

Reaumuria trigyna is a typical, native desert halophyte that grows under extreme conditions in Inner Mongolia. In a previous transcriptomic profiling analysis, flavonoid pathway-related genes in R. trigyna showed significant differences in transcript abundance under salt stress. Leucoanthocyanidin dioxygenase (LDOX, EC 1.14.11.19) is one of three dioxygenases in the flavonoid pathway that catalyzes the formation of anthocyanidins from leucoanthocyanidins. In this study, we cloned the full-length cDNA of R. trigyna LDOX (RtLDOX), and found RtLDOX recombinant protein was able to replace flavanone-3-hydroxylase (F3H, EC 1.14.11.9), another dioxygenase in the flavonoid pathway, to convert naringenin to dihydrokaempferol in vitro. R. trigyna LDOX can complement the Arabidopsis LDOX mutant transparent testa11 (tt11-11), which has reduced proanthocyanin (PA) and anthocyanin levels in seeds, to accumulate these two compounds. Thus, RtLDOX acts as a multifunctional dioxygenase to effect the synthesis of PA and anthocyanins and can perform F3H dioxygenase activities in the flavonoid biosynthesis pathway. The RtLDOX promoter harbored many cis-acting elements that might be recognized and bound by transcription factors related to stress response. RtLDOX expression was strongly increased under salt stress, and RtLDOX transgenic Arabidopsis mutant under NaCl stress accumulated the content of flavonoids leading to an increased antioxidant activities and plant biomass. These results suggest that RtLDOX as a multifunctional dioxygenase in flavonoid biosynthesis involves in enhancing plant response to NaCl stress.

A fast and simple LC-MS-based characterization of the flavonoid biosynthesis pathway for few seed(ling)s

BACKGROUND

(Pro)anthocyanidins are synthesized by the flavonoid biosynthesis pathway with multi-layered regulatory control. Methods for the analysis of the flavonoid composition in plants are well established for different purposes. However, they typically compromise either on speed or on depth of analysis.

RESULTS

In this work we combined and optimized different protocols to enable the analysis of the flavonoid biosynthesis pathway with as little as possible biological material. We chose core substances of this metabolic pathway that serve as a fingerprint to recognize alterations in the main branches of the pathway. We used a simplified sample preparation, two deuterated internal standards, a short and efficient LC separation, highly sensitive detection with tandem MS in multiple reaction monitoring (MRM) mode and hydrolytic release of the core substances to reduce complexity. The method was optimized for Arabidopsis thaliana seeds and seedlings. We demonstrate that one Col-0 seed/seedling is sufficient to obtain a fingerprint of the core substances of the flavonoid biosynthesis pathway. For comparative analysis of different genotypes, we suggest the use of 10 seed(lings). The analysis of Arabidopsis thaliana mutants affecting steps in the pathway revealed foreseen and unexpected alterations of the pathway. For example, HY5 was found to differentially regulate kaempferol in seeds vs. seedlings. Furthermore, our results suggest that COP1 is a master regulator of flavonoid biosynthesis in seedlings but not of flavonoid deposition in seeds.

CONCLUSIONS

When sample numbers are high and the plant material is limited, this method effectively facilitates metabolic fingerprinting with one seed(ling), revealing shifts and differences in the pathway. Moreover the combination of extracted non-hydrolysed, extracted hydrolysed and non-extracted hydrolysed samples proved useful to deduce the class of derivative from which the individual flavonoids have been released.

A Genome-wide Combinatorial Strategy Dissects Complex Genetic Architecture of Seed Coat Color in Chickpea

The study identified 9045 high-quality SNPs employing both genome-wide GBS- and candidate gene-based SNP genotyping assays in 172, including 93 cultivated (desi and kabuli) and 79 wild chickpea accessions. The GWAS in a structured population of 93 sequenced accessions detected 15 major genomic loci exhibiting significant association with seed coat color. Five seed color-associated major genomic loci underlying robust QTLs mapped on a high-density intra-specific genetic linkage map were validated by QTL mapping. The integration of association and QTL mapping with gene haplotype-specific LD mapping and transcript profiling identified novel allelic variants (non-synonymous SNPs) and haplotypes in a MATE secondary transporter gene regulating light/yellow brown and beige seed coat color differentiation in chickpea. The down-regulation and decreased transcript expression of beige seed coat color-associated MATE gene haplotype was correlated with reduced proanthocyanidins accumulation in the mature seed coats of beige than light/yellow brown seed colored desi and kabuli accessions for their coloration/pigmentation. This seed color-regulating MATE gene revealed strong purifying selection pressure primarily in LB/YB seed colored desi and wild Cicer reticulatum accessions compared with the BE seed colored kabuli accessions. The functionally relevant molecular tags identified have potential to decipher the complex transcriptional regulatory gene function of seed coat coloration and for understanding the selective sweep-based seed color trait evolutionary pattern in cultivated and wild accessions during chickpea domestication. The genome-wide integrated approach employed will expedite marker-assisted genetic enhancement for developing cultivars with desirable seed coat color types in chickpea.

Arabidopsis ROOT HAIR DEFECTIVE3 is involved in nitrogen starvation-induced anthocyanin accumulation

Anthocyanin accumulation is a common phenomenon seen in plants under environmental stress. In this study, we identified a new allele of ROOT HAIR DEFECTIVE3 (RHD3) showing an anthocyanin overaccumulation phenotype under nitrogen starvation conditions. It is known that ethylene negatively regulates light- and sucrose-induced anthocyanin biosynthesis. We hypothesized that RHD3 achieves its negative effect on anthocyanin biosynthesis via an ethylene-regulating pathway. In support of this, similar to rhd3 mutants, the Arabidopsis ethylene signaling mutants etr1, ein2, and ein3/eil1 showed an anthocyanin overaccumulation phenotype under nitrogen starvation conditions. The ethylene precursor ACC strongly suppressed anthocyanin accumulation, dependent on ETR1, EIN2, EIN3/EIL1, and, partially, RHD3. In addition, inactivating RHD3 partially reversed the suppressive effect of ETO1 inactivation-evoked endogenous ethylene production on anthocyanin accumulation. The expression of nitrogen starvation-induced anthocyanin biosynthesis genes was negatively regulated by RHD3, but ethylene response genes were positively regulated by RHD3. Wild-type seedlings overexpressing RHD3 showed similar phenotypes to rhd3 mutants, indicating the existence of a fine-tuned relationship between gene expression and function. RHD3 was initially identified as a gene involved in root hair development. This study uncovered a new physiological function of RHD3 in nitrogen starvation-induced anthocyanin accumulation and ethylene homeostasis. [Correction added on 6 August 2015, after first online publication: "RND3" corrected to "RHD3".].

Update on transparent testa mutants from Arabidopsis thaliana: characterisation of new alleles from an isogenic collection

We present a comprehensive overview on flavonoid-related phenotypes of A. thaliana tt and tds mutants, provide tools for their characterisation, increase the number of available alleles and demonstrate that tds3 is allelic to tt12 and tds5 to aha10. Flavonoid biosynthesis is one of the best-studied secondary metabolite pathways in plants. In the model system Arabidopsis thaliana it leads to the synthesis of three phenolic compound classes: flavonol glycosides, anthocyanins and proanthocyanidins (PAs). PAs appear brown in their oxidised polymeric forms, and most A. thaliana mutants impaired in flavonoid accumulation were identified through screens for lack of this seed coat pigmentation. These mutants are referred to as transparent testa (tt) or tannin-deficient seed (tds). More than 20 mutants of these types have been published, probably representing most of the genes relevant for PA accumulation in A. thaliana. However, data about the genes involved in PA deposition or oxidation are still rather scarce. Also, for some of the known mutants it is unclear if they represent additional loci or if they are allelic to known genes. For the present study, we have performed a systematic phenotypic characterisation of almost all available tt and tds mutants and built a collection of mutants in the genetic background of the accession Columbia to minimise effects arising from ecotype variation. We have identified a novel tt6 allele from a forward genetic screen and demonstrated that tds3 is allelic to tt12 and tds5 to aha10.

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. These include kaempferol, quercetin and isorhamnetin for flavonols, cyanidin for anthocyanins and epicatechin for proanthocyanidins. The chemical diversity of flavonoids increases enormously by tailoring reactions which modify these scaffolds, including glycosylation, methylation and acylation. Genes responsible for the formation of flavonoid aglycone structures and their subsequent modification reactions have been extensively characterized by functional genomic efforts - mostly the integration of transcriptomics and metabolic profiling followed by reverse genetic experimentation. This review describes the state-of-art of flavonoid biosynthetic pathway in Arabidopsis regarding both structural and genetic diversity, focusing on the genes encoding enzymes for the biosynthetic reactions and vacuole translocation.