Transcriptional regulation of flavonol biosynthesis in plants

Enhancing the terpenoid and flavonoid profiles and fruit quality in an elite Chinese bayberry line through hybridization

Chinese bayberry fruit is rich in bioactive compounds which are beneficial to health. Fruit hybridization can improve quality and metabolite content, but this has yet to be explored in bayberry. Here, we investigated the effects of hybridization on fruit quality and the metabolomic profile of a newly developed hybrid 'BD-107' compared to the parent 'Biqi' and 'Dongkui', the main cultivars in China. Physiochemical evaluations indicated that 'BD-107' outperformed both parental cultivars in crucial quality attributes such as firmness, sugar content, and vitamin C. Metabolomic analysis revealed that hybridization positively influenced the overall metabolite content, with the highest alterations in terpenoids (21.4 %) and flavonoids (12.2 %). Notably, the novel hybrid 'BD-107' contains seven unique metabolites that are not in either parent; Safranal, Myrcenon, p-Menth-3-en-1-ol, Balanophonin B, Swertisin, Genistein-8-C-glucoside, and Ethanone, 1-(1,4-dimethyl-3-cyclohexen-1-yl), linked to antioxidant and health-promoting properties. Our findings provide valuable insights into the influence of bayberry heterosis on terpenoid and flavonoid biosynthesis, enhancing bioactive metabolites and fruit quality, which meet the demand for health-promoting fruit.

CPK27 enhances cold tolerance by promoting flavonoid biosynthesis through phosphorylating HY5 in tomato

Cold stress is a major environmental challenge affecting the production of crops. Calcium-dependent protein kinases (CDPKs/CPKs) are crucial regulators relaying calcium (Ca2+) signals into cellular stress responses. However, the specific mechanisms of CPKs in regulating cold stress signaling are not well understood. In this study, through genetic, physiological and molecular biology assays, we characterized the function of CPK27 in enhancing tomato cold tolerance. We found that CPK27 stimulates flavonoid biosynthesis in a Ca2+-dependent manner, which in turn boosts the plant's tolerance. Tomato plants lacking CPK27 (cpk27) showed decreased flavonoid levels under cold stress, accompanied by the increased sensitivity to cold. Activated by cold stress, CPK27 accumulates within the nucleus, where it physically interacts and phosphorylates ELONGATED HYPOCOTYL 5 (HY5) protein at serine23 (S23) and S57 residues, contributing to the cold-induced accumulation of HY5 protein. HY5 directly binds to the promoter regions and stimulates the transcription of flavonoid biosynthesis genes. Further genetic analysis showed that CPK27 acts upstream of HY5, and the flavonoid biosynthesis pathway activated by CPK27 is HY5-dependent. Our study elucidates the regulatory mechanism whereby the CPK27-HY5 molecule integrates cold-triggered Ca2+ signals with flavonoid biosynthesis pathways to confer cold stress tolerance, thereby uncovering the key strategy for cold signal transduction.

RNA signaling in medicinal plants: An overlooked mechanism for phytochemical regulation

Background/objective

Medicinal plants are invaluable sources of bioactive phytochemicals critical for global health. This mini review explores the role of RNA signaling in regulating phytochemical production in medicinal plants, highlighting its potential for optimizing their therapeutic potential.

Methods

This mini review integrates insights from recent studies published in Scopus and Web of Science (2019-2025) on RNA-mediated signaling, including small RNAs (sRNAs), long non-coding RNAs (lncRNAs), and messenger RNAs (mRNAs).

Results

RNA signaling is revealed as a pivotal mechanism in secondary metabolite regulation, mediating stress-induced compound synthesis and environmental interactions. Notable findings include the role of siRNAs in activating alkaloid pathways and lncRNAs in regulating phenolic compound biosynthesis. RNA-directed DNA methylation and systemic RNA signaling further highlight its versatility in phytochemical regulation.

Conclusion

RNA signaling enhances medicinal plant research, unlocking therapeutic potential through bioactive compound production. The study calls for focused research to bridge knowledge gaps and translate laboratory findings into field applications.

Transcriptome analysis reveals candidate genes involved in quercetin biosynthesis in Euphorbia maculata

An investigation was conducted through transcriptome sequencing in various tissues at different stages to explore the quercetin biosynthesis pathway in Euphorbia maculata. A total of 83,028 unigenes was assembled utilizing Trinity software, with an N50 length of 1721 bp and a mean length of 1004 bp. Among these unigenes, 51,822 were annotated in six public databases. The transcriptome analysis revealed 45,727 CDS sequences and 56 TF families. Candidate genes involved in quercetin biosynthesis were also revealed, including phenylalanine ammonia-lyase (17 unigenes), cinnamate 4-hydroxylase (3 unigenes), 4-coumarate-CoA ligase (16 unigenes), chalcone synthase (5 unigenes), chalcone isomerase (4 unigenes), flavanone 3-hydroxylase (1 unigene), flavonoid 3'-hydroxylase (4 unigenes), and flavonol synthase (9 unigenes). Additionally, 42 key differentially expressed genes (DEGs) related to quercetin biosynthesis were identified in the same tissues at different stages, with 35 DEGs exhibiting down-regulated expression and 7 DEGs displaying up-regulated expression. These findings not only enhance the genetic knowledge of E. maculata, but also establish a basis for further investigating the mechanism of quercetin biosynthesis, and improving the quality of E. maculata.

Functional Characterization of Grapevine VviMYC4 in Regulating Drought Tolerance by Mediating Flavonol Biosynthesis

Drought ranks among the key abiotic stresses that limit the growth and yield of grapevines (Vitis vinifera L.). Flavonols, a class of antioxidants commonly found in grapevines, play a crucial role in combating drought stress. In this study, we characterized the function and regulatory mechanism of the grapevine VviMYC4 in mediating flavonol biosynthesis in response to drought stress. VviMYC4 encodes a protein of 468 amino acids with conserved bHLH-MYC_N and bHLH domains. Phylogenetic analysis confirmed its homology with the grapevine VviMYC2 and similarity in function. The expression of VviMYC4 in 'Cabernet Sauvignon' grapevine seedling leaves increased initially and then decreased during prolonged drought stress. The homologous and heterologous transformation of VviMYC4 in grape suspension cells, Arabidopsis plants, tobacco leaves, and grapevine leaves demonstrated its ability to positively regulate flavonol biosynthesis and accumulation by promoting the expression of flavonol-related genes, thereby enhancing the drought tolerance of transgenic plants. Furthermore, VviMYC4 could bind to specific E-box sites on the promoters of VviF3H and VviFLS to improve their activities. This study highlights VviMYC4 as a pivotal positive regulator of drought tolerance in grapevines and proposes that VviMYC4 enhances the antioxidant and reactive oxygen species (ROS) scavenging abilities of grapevines in challenging environments and improves their stress resilience by mediating flavonol biosynthesis. Our findings offer crucial candidate genes and valuable insights for the molecular breeding of grapevine drought resistance.

Molecular underpinnings of EbMYBP1-mediated plant defense against UV-B radiation

MYB transcription factors play an important role in the response of plants to abiotic stress. The flavonoids found in Erigeron breviscapus have significant anti-inflammatory and cardiovascular therapeutic effects. It has been discovered that EbMYBP1, a gene cloned from E.breviscapus, positively regulates flavonoid synthesis. However, it is uncertain whether EbMYBP1-OE directly responds to ultraviolet B (UV-B) by increasing flavonoids accumulation. Here, an integrated metabolome-transcriptome analysis revealed an important role for EbMYBP1 in transgenic tobacco seeds in response to UV-B. The role of EbMYBP1 under UV-B has been examined. The results showed that a higher level of UV-B tolerance was observed in seedlings and leaves of EbMYBP1-OE lines (OE8, OE10, OE15) than in wild-type line (WT), identifying several flavonoid biosynthesis genes and metabolites. Compared with WT, a significant decrease in reactive oxygen species (ROS), an increase in antioxidant enzyme expression, and significant induction of genes involved in flavonoids synthesis, UV-B response, and ROS was observed after UV-B treatment in EbMYBP1-OE lines. Overall, EbMYBP1 modulates ROS scavengers and upregulates stress response genes to increase UV-B tolerance.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-025-01598-y.

Combined transcriptomic and metabolomic analyses reveal the pharmacognostic mechanism of the metabolism of flavonoids in different parts of Polygonum capitatum

The plant Polygonum capitatum (P. capitatum) contains a variety of flavonoids that are distributed differently among different parts. Nevertheless, differentially expressed genes (DEGs) associated with this heterogeneous distribution have not been identified. In this study, combined with transcriptomic and metabonomic analysis, we identified significant DEGs related to variations in flavonoid composition among different parts of P. capitatum. Subsequently, transcriptomic and nontargeted metabolomic analyses revealed that flavonoids and phenolic acids in different parts of P. capitatum were significantly enriched in the phenylpropanoid biosynthesis, shikimic acid biosynthesis, and flavonoid biosynthesis pathways. The expression levels of genes encoding enzymes, including shikimate O-hydroxycinnamoyltransferase (HCT), chalcone synthase (CHS), flavonoid 3',5'-hydroxylase (CYP75A), flavones 3-hydroxylase (F3H), flavonol synthase (FLS), leucoanthocyanidin reductase (LAR), trans-cinnamate 4-monooxygenase (CYP73A), and shikimate kinase (SK), were found to be the lowest in the leaves of P. capitatum via quantitative PCR. Interestingly, these genes are involved in the biosynthesis of quality markers such as gallic acid, quercetin, and quercitrin in P. capitatum. Finally, the targeted metabolomic results reconfirmed that the gallic acid, quercetin, and quercitrin contents were the highest in the leaves of P. capitatum. This research provides a theoretical basis for further understanding the differential regulatory mechanism of flavonoid metabolism in different parts of P. capitatum, providing novel insights into the pharmacognostic basis of P. capitatum.

The transcription factor WRKY41-FLAVONOID 3'-HYDROXYLASE module fine-tunes flavonoid metabolism and cold tolerance in potato

Cold stress adversely affects crop growth and productivity. Resolving the genetic basis of freezing tolerance is important for crop improvement. Wild potato (Solanum commersonii) exhibits excellent freezing tolerance. However, the genetic factors underlying its freezing tolerance remain poorly understood. Here, we identified flavonoid 3'-hydroxylase (F3'H), a key gene in the flavonoid biosynthesis pathway, as highly expressed in S. commersonii compared with cultivated potato (S. tuberosum L.). Loss of ScF3'H function impaired freezing tolerance in S. commersonii, while ScF3'H overexpression in cultivated potato enhanced its freezing tolerance. Metabolic analysis revealed that F3'H generates more downstream products by adding hydroxyl (-OH) groups to the flavonoid ring structures. These flavonoids enhance reactive oxygen species scavenging, thereby contributing to freezing tolerance. Furthermore, the W-box element in the F3'H promoter plays a critical role in cold responses. Cold-induced transcription factor ScWRKY41 directly binds to the ScF3'H promoter region and recruits histone acetyltransferase 1 (ScHAC1), which enhances histone acetylation at the F3'H locus and activates its transcription. Overall, we identified the cold-responsive WRKY41-F3'H module that enhances freezing tolerance by augmenting the antioxidant capacity of flavonoids. This study reveals a valuable natural gene module for breeding enhanced freezing tolerance in potato and other crops.

Repressor MrERF4 and Activator MrERF34 Synergistically Regulate High Flavonol Accumulation Under UV-B Irradiation in Morella rubra Leaves

Flavonols are important plant photoprotectants to defence UV-B irradiation, however, the underlying transcriptional regulatory mechanism of rapid flavonol accumulation in response to UV-B remains unknown. In this study, content of flavonols was significantly induced from 0.11 to 3.80 mg/g fresh weight by UV-B irradiation in leaves of Morella rubra seedlings. MrERF34 was identified as an activator that can regulate the expression of MrFLS2, and promoted flavonol biosynthesis with activator MrMYB12 under UV-B treatment. Transient overexpression of MrERF34 resulted in higher flavonol accumulation, while virus-induced gene silencing of MrERF34 reduced the content of flavonols in bayberry leaves. We further demonstrated that a repressor MrERF4 inhibited the expression of MrERF34 and MrMYB12 as well as MrFLS2 via ERF-associated-amphiphilic repression motif. Exposure to UV-B reduced the promoter activity and transcription of MrERF4, which weakened the inhibitory effect of MrERF4 on MrERF34, MrMYB12, and MrFLS2, leading to a tremendous accumulation of flavonols. Such inhibitory roles of MrERF4 in regulation of flavonol biosynthesis were further validated by transient overexpression in leaves of Nicotiana benthamiana and M. rubra. These findings enrich the synergistical regulatory mechanisms between repressor and activators in flavonol biosynthesis, and provide new insights into photoprotectants biosynthesis to mitigate UV-B stress in plants.

Genome-wide identification of UDP-glycosyltransferases involved in flavonol glycosylation induced by UV-B irradiation in Eriobotrya japonica

Flavonol glycosides are secondary metabolites important for plant development and stress defense such as UV-B irradiation. UDP-glycosyltransferase (UGT) catalyzes the last step in the biosynthesis of flavonol glycosides. Eriobotrya japonica is abundant in flavonol glycosides, but UGTs responsible for accumulation of flavonol glycosides remain unknown. Here, 13 flavonol glycosides including monoglycosides and diglycosides were characterized in different tissues of loquat by LC-MS/MS. UV-B irradiation significantly increased the accumulation of four quercetin glycosides and two kaempferol glycosides in loquat fruit. Based on UGT gene family analysis, transcriptome analysis, enzyme assays of recombinant proteins as well as transient overexpression assays in Nicotiana benthamiana, three UGTs were identified, i.e. EjUGT78T4 as flavonol 3-O-galactosyltransferase, EjUGT78S3 as flavonol 3-O-glucosyltransferase, and EjUGT91AK7 as flavonol 1 → 6 rhamnosyltransferase. This work elucidates the formation of flavonol glycosides in loquat through UGT-mediated glycosylation.

Transcriptomic, metabonomic and proteomic analyses reveal that terpenoids and flavonoids are required for Pinus koraiensis early defence against Bursaphelenchus xylophilus infection

Pine wilt disease (PWD), caused by the pine wood nematode (PWN) Bursaphelenchus xylophilus, threatens Pinus seriously. Pinus koraiensis is one of the most important pine species in China and is the host for PWN. However, our understanding of the defence-regulating process following infection by B. xylophilus at the molecular level remains limited. To understand the mechanisms that P. koraiensis responds to B. xylophilus invasion, P. koraiensis was inoculated with B. xylophilus solutions and observed no obvious symptoms during the early stage; symptoms began to appear at 5 dpi. Therefore, we conducted comparative transcriptomic, metabonomic and proteomic analyses between P. koraiensis 5dpi and 0 dpi. In infected plants, 1574 genes were significantly up-regulated, including 17 terpenoid-, 41 phenylpropanoid- and 22 flavonoid-related genes. According to GO and KEGG enrichment analyses of significantly up-regulated genes, 86 GO terms and 16 KEGG pathways were significantly enriched. Most terms and pathways were associated with terpenoid-, phenylpropanoid-, flavonoid- and carbohydrate-related events. Similarly, the abundance of 36 and 30 metabolites, significantly increased in positive and negative polarity modes, respectively. Among them, naringenin and 3-methyl-2-oxovaleric acid exhibited significant toxic effects on B. xylophilus. According to functional analysis of significantly up-regulated metabolites, most terms were enriched in above pathways, in addition to alkaloid biosynthesis. Although the abundance of few proteins changed, response to stress term was significantly enriched in significant up-regulated proteins. Furthermore, plant receptor-like serine/threonine kinases, pectin methylation modulators, pinosylvin O-methyltransferase and arabinogalactan/proline-rich proteins were significantly up-regulated in the infected P. koraiensis compared to healthy plants. These proteins were not abundant in the healthy plant. Overall, these results indicate that P. koraiensis can actively response to PWN via various defense strategies, including events related to terpenoids, flavonoids, phenylpropanoids, lipids and alkaloids. Particularly, terpenoids and flavonoids are required for the early defence of P. koraiensis against B. xylophilus infection.

Integrated Metabolomic and Transcriptomic Analyses Reveal the Potential Molecular Mechanism Underlying Callus Browning in Paeonia ostii

Callus browning is a significant problem that hinders plant tissue regeneration in Paeonia ostii "Fengdan" by causing cell death and inhibiting growth. However, the molecular mechanism underlying callus browning in P. ostii remains unclear. In this study, we investigated the metabolites and potential regulatory genes involved in callus browning of P. ostii using metabolomic and transcriptomic analyses. We found a significant accumulation of phenolic compounds in the browned callus, represented by flavonoid compounds. Notably, the accumulations of luteotin and disomentin were higher in browning calli compared to non-browning calli. Transcriptomic analysis identified that candidate genes associated with flavonoid biosynthesis, including flavonoid 3-hydroxylase (PoF3H) and flavone synthase II (PoFNSII), were highly expressed in the browned callus of P. ostii "Fengdan". Weighted gene co-expression network analysis (WGCNA) further highlighted that polyphenol oxidase (PoPPO) which encoded polyphenol oxidase, together with flavonoid biosynthesis-related genes such as flavanone 3-hydroxylase (PoF3H) and flavonone Synthase II (PoFNSII), as well as cellular totipotency-related genes wuschel-related homeobox 4 (PoWOX4), were involved in callus browning. Based on these findings, we proposed the molecular mechanism by which flavonoid accumulation, polyphenol oxidation, and cellular totipotency pathways contribute to callus browning in P. ostii. Our study provides new insights into the molecular mechanism underlying callus browning and offers the foundations to facilitate the establishment of an efficient plant tissue regeneration system in P. ostii.

Harnessing the diversity of a lettuce wild relative to identify anthocyanin-related genes transcriptionally responsive to drought stress

Lettuce is a crop particularly vulnerable to drought. A transcriptomic study in the variety 'Romired' and the wild relative Lactuca homblei was conducted to understand the increase in anthocyanins (only significant in L. homblei) in response to drought previously observed. RNA-seq revealed more differentially expressed genes (DEGs), especially upregulated, in the wild species, in which the most abundant and significant GO terms were involved in regulatory processes (including response to water). Anthocyanin synthesis was triggered in L. homblei in response to drought, with 17 genes activated out of the 36 mapped in the phenylpropanoid-flavonoid pathway compared to 7 in 'Romired'. Nineteen candidate DEGs with the strongest change in expression and correlation with both anthocyanin content and drought were selected and validated by qPCR, all being differentially expressed only in the wild species with the two techniques. Their functions were related to anthocyanins and/or stress response and they harboured 404 and 11 polymorphisms in the wild and cultivated species, respectively. Some wild variants had high or moderate predicted impacts on the respective protein function: a transcription factor that responds to abiotic stresses, a heat shock protein involved in stomatal closure, and a phospholipase participating in anthocyanin accumulation under abiotic stress. These genetic variants could explain the differences in the gene expression patterns between the wild (significantly up/downregulated) and the cultivated (no significant changes) species. The diversity of this crop wild relative for anthocyanin-related genes involved in the response to drought could be exploited to improve lettuce resilience against some adverse climate effects.

A comparative study of the quality differences and seasonal dynamics of flavonoids between the aerial parts and roots of Scutellaria barbata

Introduction

Scutellaria barbata D. Don is a widely cultivated Chinese herbal medicine known for its medicinal properties. However, differences in the spatial distribution of metabolites, accumulation patterns of flavonoids, and pharmacological activities between the aerial parts and roots of S. barbata still remain unclear, posing challenges for its standardized cultivation and quality control. This study aimed to elucidate the quality differences between these plant parts and clarify their seasonal variations.

Methods

The chemical profiles were qualitatively analyzed by UPLC-QTOF-MS/MS. The accumulation patterns of total flavonoids, scutellarin and baicalin in different parts of S. barbata were quantitatively analyzed by UV and HPLC respectively. The differences of pharmacological efficacy were evaluated by antioxidant assays and CCK-8 assay.

Results

In this research, there were 46 compounds identified in S. barbata that included 44 flavonoids. The aerial parts primarily accumulate flavonoids with 4'-hydroxyl group, while the root mainly accumulate flavonoids without this group. Additionally, the accumulation and variation of flavonoid components were seasonally dependent, with the aerial parts reaching peak content in spring during vigorous vegetative growth and the roots accumulating most flavonoids in autumn. The extracts from both parts exhibited antioxidant activity and inhibitory effects on cancer cell proliferation, with notable differences between them.

Discussion

This study provides valuable insights into the quality differences and seasonal dynamics of the different parts of S. barbata, offering a reference for standardized harvesting and quality control.

Compositional Analysis of Grape Berries: Mapping the Global Metabolism of Grapes

To characterize the nutrients and bioactive compounds in grape berries and to explore the real cause of the "French paradox" phenomenon, we performed metabolomic analysis of 66 grape varieties worldwide using liquid chromatography-tandem mass spectrometry (LC-MS). A nontargeted metabolomics approach detected a total of 4889 metabolite signals. From these, 964 bioactive and nutrient compounds were identified and quantified, including modified flavonoids, medicinal pentacyclic triterpenoids, vitamins, amino acids, lipids, etc. Interestingly, metabolic variations between varieties are not explained by geography or subspecies but can be significantly distinguished by grapes' color, even after excluding flavonoids and anthocyanins. In our analysis, we found that purple grape varieties had the highest levels of key bioactive components such as flavonoids, pentacyclic triterpenes, and polyphenols, which are thought to have a variety of health benefits such as antioxidant, anti-inflammatory, and antitumor properties, when compared to grapes of other colors. In addition, we found higher levels of vitamins in red and pink grapes, possibly explaining their role in preventing anemia and scurvy and protecting the skin. These findings may be a major factor in the greater health benefits of wines made from purple grapes. Our study provides comprehensive metabolic profiling data of grape berries that may contribute to future research on the French paradox.

Identification and analysis of flavonoid pathway genes in responsive to drought and salinity stress in Medicago truncatula

Flavonoid compounds are widely present in various organs and tissues of different plants, playing important roles when plants are exposed to abiotic stresses. Different types of flavonoids are biosynthesized by a series of enzymes that are encoded by a range of gene families. In this study, a total of 63 flavonoid pathway genes were identified from the genome of Medicago truncatula. Gene structure analysis revealed that they all have different gene structure, with most CHS genes containing only one intron. Additionally, analysis of promoter sequences revealed that many cis-acting elements responsive to abiotic stress are located in the promoter region of flavonoid pathway genes. Furthermore, analysis on M. truncatula gene chip data revealed significant changes in expression level of most flavonoid pathway genes under the induction of salt or drought treatment. qRT-PCR further confirmed significant increase in expression level of several flavonoid pathway genes under NaCl and mannitol treatments, with CHS1, CHS9, CHS10, F3'H4 and F3'H5 genes showing significant up-regulation, indicating they are key genes in response to abiotic stress in M. truncatula. In summary, our study identified key flavonoid pathway genes that were involved in salt and drought response, which provides important insights into possible modification of flavonoid pathway genes for molecular breeding of forage grass with improved abiotic resistance.

Integrated metabolome and transcriptome analysis provide insight into the biosynthesis of flavonoids in Panax japonicus

Panax japonicus is an important medicinal plant, and flavonoids are one of its main secondary metabolites. In this study, the main roots, fibrous roots, stems, leaves and flowers of P. japonicus were analyzed using transcriptomics and widely targeted metabolomics. Through correlation analysis of transcription and metabolism, the flavonoid biosynthesis pathway in P. japonicus was analyzed, and the accumulation of flavonoid metabolites and the expression of related genes were investigated. Metabolomics revealed a total of 209 flavonoid metabolites in P. japonicus, among which flavonoids, flavonols, flavanones and flavanonols significantly accumulated in the flowers and leaves. Transcriptome sequencing revealed that key genes in the flavonoid pathway exhibited increased expression in the flowers and leaves. The expression patterns of key genes involved in flavonoid biosynthesis, including PjC4H, Pj4CL, PjCHS, PjCHI, PjF3H, PjF3'H, PjCYP, and PjPAL, are consistent with their upstream and downstream metabolites, demonstrating a significant positive correlation among them. In addition, the PjUGT gene is highly expressed in five tissues of P. japonicus, indicating that PjUGT is one of the key factors for the diversity of flavonoid glycosides. The WGCNA results showed that WRKY transcription factors exist widely in the candidate modules, and it was possible that PjWRKY transcription factors are involved in regulating the expression of key genes involved in flavonoid biosynthesis and the biosynthesis of flavonoid metabolites. This study reveals spatial differences in the accumulation patterns of flavonoid metabolites in different tissues and provides important clues for further understanding the regulatory mechanisms of flavonoid metabolism in P. japonicus, thus contributing to the optimization of germplasm resources of P. japonicus and the promotion of genetic diversity analysis.