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A network model was constructed to illustrate the potential regulatory mechanism through which LED influences postharvest ripening and senescence of apricot fruits based on the comprehensive analysis of transcriptome, metabolome and ATAC-Seq. [Display omitted] • LED treatment effectively maintained the quality of apricot fruit during postharvest storage. • LED treatment activated pathways involved in ascorbate and aldarate metabolism, flavonoid biosynthesis. • LED treatment activated pathways involved in ascorbate and aldarate metabolism, flavonoid biosynthesis.LED treatment can promote phenylpropanoid and anthocyanin biosynthesis. • LED treatment influenced the expression of genes associated with plant hormone signal transduction, fruit texture and color transformation, and plant antioxidant activity. Apricot (Prunus armeniaca L.) fruits are highly perishable and prone to quality deterioration during storage and transportation. To investigate the effects of LED white light treatment on postharvest ripening of fruits using metabolomics, transcriptomics, and ATAC-Seq analysis. Fruits were exposed to 5 μmol m−2 s−1 LED white light for 12 h followed by 12 h of darkness at 20 °C daily for 12 days. The effects of the treatments on the physiological and nutritional quality of the fruits were evaluated. These data were combined with transcriptomic, metabolomic, and ATAC-Seq data from fruits taken on 8 d of treatment to provide insight into the potential mechanism by which LED treatment delays ripening. LED treatment activated pathways involved in ascorbate and aldarate metabolism and flavonoid and phenylpropanoid biosynthesis. Specifically, LED treatment increased the expression of UDP-sugar pyrophosphorylase (USP) , L-ascorbate peroxidase (AO) , dihydroflavonol 4-reductase (DFR) , chalcone synthase (CHS) , and caffeoyl-CoA O-methyltransferase (CCOAOMT1) , leading to the accumulation of caffeoyl quinic acid, epigallocatechin, and dihydroquercetin and the activation of anthocyanin biosynthesis. LED treatment also affected the expression of genes associated with plant hormone signal transduction, fruit texture and color transformation, and antioxidant activity. The notable genes affected by LED treatment included 1-aminocyclopropane-1-carboxylate synthase (ACS) , 1-aminocyclopropane-1-carboxylate oxidase (ACO) , hexokinase (HK) , lipoxygenase (LOX) , malate dehydrogenase (MDH) , endoglucanase (CEL) , various transcription factors (TCP, MYB, EFR) , and peroxidase (POD). ATAC-Seq analysis further revealed that LED treatment primarily regulated phenylpropanoid biosynthesis. The results obtained in this study provide insights into the effects of LED light exposure on apricot fruits ripening. LEDs offer a promising approach for extending the shelf life of other fruits and vegetables. [ABSTRACT FROM AUTHOR]

• In silico methods are used to examine the characteristics of GbPAL, GbCHS, GbDFR, and GbANS structural genes in Gynura bicolor. • Detailed prediction of the physico-chemical properties, protein classifications and models, gene ontologies associated with GbPAL, GbCHS, GbDFR, and GbANS have been provided and verified in silico. • GbPAL showed a secondary structure dominated by helix (mainly alpha), GbCHS and GbDFR (Alpha-beta), and GbANS (mainly beta). • Phylogenetic tree was constructed to evaluate the relationship of GbPAL, GbCHS, GbDFR, and GbANS with other Asteraceae plants. • GbPAL, GbCHS, GbDFR, and GbANS enzymes have been modelled and accurately docked with their appropriate substrates. Gynura bicolor is a member of the Asteraceae family, possessing important pharmaceutical compounds such as flavonoids, anthocyanins, and terpenoids. Genetic and molecular studies focusing on the biosynthesis of flavonoids are indispensable to determining their regulation. GbPAL, GbCHS, GbDFR , and GbANS are genes encoding Phenylalanine ammonia lyase, Chalcone synthase, Dihydroflavonol reductase, and Anthocyanidin synthase enzymes, resepectively and are involved in the biosynthesis of flavonoids in G. bicolor, resepectively. There are still a few studies concerning the characterization of these genes. In this study, the structural enzyme sequences were selected to be characterized in silico using bioinformatics software. The phylogenetic analysis demonstrated that the genes in question were closely related to several species of the Asteraceae family. Our data revealed that the G. bicolor PAL, CHS, DFR and ANS genes are closely related to the sequence of genes found in Chrysanthemum morifolium. Furthermore, the CHS, DFR and ANS of G. bicolor also tightly correlated with sequence from Callistephus chinensis. Further analysis also demonstrated that all conserved motifs contain active functional and catalytic domain supporting the flavonoid-related enzyme functions. All physicochemical parameters used in this study also meet the prediction criteria. The investigation of secondary structure prediction using two instruments (PSIPRED and SOPMA) revealed that all enzymes tested possess similar α-helix (H), β-sheet (E), and coil (C) composition. GbPAL showed a secondary structure dominated by helix (mainly alpha), GbCHS and GbDFR (Alpha-beta), and GbANS (mainly beta). Each enzyme was modeled, with RMSD values superimposed on the template: 0.125 Å (GbPAL), 0.061 Å (GbCHS), 0.065 Å (GbDFR), and 0.089 Å (GbANS). The 3D model evaluation was checked using four parameters, including PROCHECK, Verify3D, ERRAT, and QMEAN-Z score. All the parameters verified that the model showed a high quality (more than 90 % of the favored region), high ressemblence of the 3D and 1D amino acid sequence, the 3D modeles were acceptable since they possesed high resolution of the protein structure (2.5 – 3 Å), and the enzyme models have Z-Score values in the permissible range. The accuracy and reliability of the generated models met Ramachandran value in comparison to experimentally resolved protein templates. The molecular docking analysis showed that each substrate compound docked at the real binding site in every tested enzyme. Furthermore, they also showed similar results compared to other experimentally observed proteins. The overall findings provide an insight into the molecular characteristics of flavonoid-related genes, which might enrich our understanding for further genomic application of the Gynura bicolor. [ABSTRACT FROM AUTHOR]

Chalcone isomerase-like (CHIL) protein is a noncatalytic protein that enhances flavonoid content in green plants by serving as a metabolite binder and a rectifier of chalcone synthase (CHS). Rectification of CHS catalysis occurs through direct protein-protein interactions between CHIL and CHS, which alter CHS kinetics and product profiles, favoring naringenin chalcone (NC) production. These discoveries raise questions about how CHIL proteins interact structurally with metabolites and how CHIL-ligand interactions affect interactions with CHS. Using differential scanning fluorimetry on a CHIL protein from Vitis vinifera (VvCHIL), we report that positive thermostability effects are induced by the binding of NC, and negative thermostability effects are induced by the binding of naringenin. NC further causes positive changes to CHIL-CHS binding, whereas naringenin causes negative changes to VvCHIL-CHS binding. These results suggest that CHILs may act as sensors for ligand-mediated pathway feedback by influencing CHS function. The protein X-ray crystal structure of VvCHIL compared with the protein X-ray crystal structure of a CHIL from Physcomitrella patens reveals key amino acid differences at a ligand-binding site of VvCHIL that can be substituted to nullify the destabilizing effect caused by naringenin. Together, these results support a role for CHIL proteins as metabolite sensors that modulate the committed step of the flavonoid pathway. [ABSTRACT FROM AUTHOR]

Chromium (Cr) toxicity impairs essential morphological and metabolic activities in plants. The present investigation was carried out to evaluate the beneficial role of plant growth promoting rhizobacterial strains namely Pseudomonas aeruginosa (M1), Burkholderia gladioli (M2) and earthworms (Eisenia fetida) in alleviating Cr toxicity in 10 days old Brassica juncea L. The findings delineated that addition of earthworms and PGPR restored growth, boosted Cr uptake and showed upregulation of metal transporter genes (SULTR 1–4). Supplementation of rhizospheric amendments reinstated Cr induced impairment in photosynthetic attributes. Gaseous exchange attributes, the efficiency of PS II, the content of total phenols, anthocyanin and flavonoids was enhanced with application of earthworms along with PGPR. Confocal imaging of primary photosynthetic pigment (chlorophyll), accessory photosynthetic pigment (carotenoids) and total phenols showed maximum fluorescence with combined inoculation of earthworms and both microbial strains (M1M2). The gene expression analysis revealed that Phyotene synthase (PSY), Photosystem II core protein psb A , psb B were down regulated in Cr stressed seedlings which upon supplementation with earthworms and PGPR were upregulated. Further, Phenylalanine ammonialyase (PAL), chalcone synthase (CHS) were upregulated with addition of earthworms and PGPR. Increased nitric oxide content, enhanced activity and upregulation of nitrate reductase (NR) gene was observed with addition of PGPR and earthworms [Display omitted] • Chromium (Cr) toxicity affects photosynthesis and physio-biochemical attributes. • PGPR and earthworm enhanced the expression of genes related to photosynthesis. • PGPR and earthworms enhanced the expression of metal transporters in B. juncea. • PGPR and earthworms enhanced expression of PAL, CHS and secondary metabolites. • Nitrate reductase gene expression was upregulated with PGPR and earthworms. [ABSTRACT FROM AUTHOR]

Soil salinity represents a significant threat to agricultural productivity. The identification of salt response genes from halophytes is of great significance for improving the resistance of glycophytic crops to salt stress. Iris halophila Pall. is an important ornamental and medicinal halophyte that exhibits strong resistance to salt stress and is rich in flavonoids. Previously, transcriptome analysis revealed that chalcone synthase (CHS)-catalyzed flavonoid biosynthesis is involved in the response of I. halophila to high salt stress. However, the regulatory mechanism of CHS on plant metabolome under salt stress remains unclear. In this study, the function of IhCHS1 gene in regulating plant salt tolerance and metabolism was investigated. The results demonstrated that IhCHS1 was upregulated in I. halophila under salt stress. Transgenic Arabidopsis overexpressing IhCHS1 exhibited enhanced salt tolerance at both the seedling and mature stages. Physiological and metabolomic analysis indicated that the overexpression of IhCHS1 resulted in a reduction in the degree of membrane lipid peroxidation and an increase in proline content, antioxidant enzyme activities, and the abundance of several flavonoids and other phenylpropanoid compounds. Interestingly, IhCHS1 overexpression also significantly stimulated the accumulation of JA and IAA biosynthesis and signal transduction-related compounds, and altered the profiles of oligopeptides and nucleotide metabolites under salt stress. Our findings will provide new insight into the molecular mechanism of IhCHS1 -mediated salt tolerance in plants and contribute to the development of strategies for cultivation of crop species with high salt tolerance and high metabolite accumulation on saline-alkali soil. [Display omitted] • IhCHS1 enhanced salt tolerance of Arabidopsis at both the seedling and mature stages. • This study provides an overview of CHS-mediated metabolic changes in plant under salt stress. • IhCHS1 upregulated the accumulation of JA and IAA-related signaling molecules under salt stress. • IhCHS1 altered the abundance of oligopeptides and nucleotide metabolites under salt stress. [ABSTRACT FROM AUTHOR]

Trigonella persica Boiss., is renowned for its rich phytochemical profile, particularly the presence of the flavonol quercetin. This study explored the effects of various light treatments, including blue, red, blue-red (1:1) radiation (BRR), and pink fluorescent light (PFL), on the biochemical and molecular mechanisms governing quercetin and flavonoid biosynthesis in T. persica at different growth stages. Our results showed that light treatments significantly influenced the activity of key enzymes phenylalanine ammonia-lyase (PAL) and tyrosine ammonia-lyase (TAL) during germination and vegetative growth, with blue light inducing higher PAL and TAL activities compared to control conditions. High-performance liquid chromatography (HPLC) and liquid chromatography-mass spectrometry (LC-MS) analyses revealed that 48-h-old sprouts grown under red light exhibited the highest levels of flavonoid components and phenolic acids, with catechin as the predominant flavonoid. Notably, BRR treatment led to elevated concentrations of the bioavailable quercetin-3-rhamnoside in 48-h-old sprouts, while 15-day-old plants grown under PFL conditions showed a significant accumulation of the sulfated quercetin-3-sulfate. Real-time PCR analysis demonstrated that BRR upregulated the expression of flavonoid biosynthesis genes PAL , chalcone synthase (CHS), and chalcone isomerase (CHI) in sprouts, whereas PFL treatment induced higher expression of these genes, as well as cinnamate 4-hydroxylase (C4H), in aerial parts. These findings suggest that targeted light treatments, particularly blue and red LED light, can enhance the accumulation of bioavailable quercetin-3-rhamnoside during T. persica germination and sprouts exhibit higher levels of flavonoids and phenolic acids than aerial parts during different vegetative growth stages. • Controlled spectral lighting affects flavonoid biosynthesis in Trigonella persica. • Blue light boosts PAL and TAL enzyme activity during germination and growth. • Red light boosts flavonoids and phenolic acids in sprouts. • Blue-red radiation enhances quercetin-3-rhamnoside in sprouts. • Pink fluorescent light induces quercetin-3-sulfate in plants. [ABSTRACT FROM AUTHOR]

Methyl jasmonate (MeJA) is widely involved in the life processes of plants, especially playing an active role in regulating the synthesis and accumulation of metabolites. Prickly ash (Zanthoxylum bungeanum), as a species of spice tree, is rich in flavonoids throughout its entire plant, showing enormous potential for development into functional foods. Flavonoids play crucial roles in signal transduction and defense mechanisms between plants and their environment, influencing the ecological adaptability of plants. Analyzing the regulatory relationship between methyl jasmonate and flavonoid metabolites will help understand the self-protection mechanism of Zanthoxylum bungeanum under adverse stress. Research results show that the upstream promoter of CHSs (Chalcone synthase), a key gene for flavonoid synthesis, contains multiple methyl jasmonate response elements. Exogenous MeJA induction experiments proved that MeJA can significantly increase the expression levels of ZbCHS71 , ZbCHS43 and ZbCHS26 in different tissues of Zanthoxylum bungeanum and directly promote the synthesis and accumulation of flavonoid metabolites. The research results help analyze the regulatory relationship between methyl jasmonate and flavonoids, and provide a reference for research on the accumulation of protective substances under stress conditions in Zanthoxylum bungeanum. [Display omitted] • Specific CHS genes play central role in the synthesis of flavonoids in prickly ash. • CHSs upstream promoter contains multiple methyl jasmonate response elements. • Methyl jasmonate can induce the accumulation of flavonoids. [ABSTRACT FROM AUTHOR]

B-box zinc-finger transcription factor (BBX) plays important regulatory roles in plant secondary metabolism. Here, we identified 21 BBXs that could be further categorized into five subfamilies from Cerasus humilis. Two segmentally duplicated Subfamily IV members, ChBBX6 and ChBBX18 , were found to share high homology with reported anthocyanin-related BBXs and express highly in fruits with high anthocyanins but low carotenoids contents. Their transient overexpression in apple and C. humilis fruits both led to significantly increased anthocyanins accumulation and significantly upregulated expression of anthocyanins-related genes. However, their overexpression resulted in decreased carotenoids accumulation and greatly upregulated the expression of carotenoids-related genes especially degradation-related genes. Additionally, their overexpression both greatly improved the ABA content in C. humilis fruits. Through yeast one-hybrid and dual-luciferase reporter assays, we found that both ChBBX6 and ChBBX18 could bind to and activate the promoters of chalcone synthase (ChCHS), flavanone 3-hydroxylase (ChF3H), and 9-cis-epoxycarotenoid dioxygenase 5 (ChNCED5). Our study demonstrates that ChBBX6 and ChBBX18 are positive regulators of anthocyanins biosynthesis and carotenoids degradation and can provide basis for understanding the roles of BBX genes in C. humilis. [ABSTRACT FROM AUTHOR]

Aluminum (Al) toxicity is a significant limiting factor for crop production in acid soils. The functions and regulatory mechanisms of transcription factor STOP1 (Sensitive to Proton Rhizotoxicity 1) family genes in Al-tolerance have been widely studied in many plant species, except for soybean. Here, expression of GmSTOP1–3 was significantly enhanced by Al stress in soybean roots. Overexpression of GmSTOP1–3 resulted in enhanced root elongation and decreased Al content, which was accompanied by increased antioxidant capacity under Al treatment. Furthermore, RNA-seq identified 498 downstream genes of GmSTOP1–3 , including genes involved in flavonoid biosynthesis. Among them, the expression of chalcone synthase (GmCHS) and isoflavone synthase (GmIFS) were highly enhanced by GmSTOP1–3 overexpression. Further quantitative flavonoid metabolome analysis showed that overexpression of GmSTOP1–3 significantly increased the content of naringenin chalcone, naringenin, and genistein in soybean roots under Al treatment, which positively correlated with the expression level of the genes relative to flavonoid biosynthesis. Notably, genistein had a significant positive correlation with the expression levels of GmIFS. Combination of Dual Luciferase Complementation (LUC) and Electrophoretic Mobility Shift Assays (EMSA) revealed that GmSTOP1–3 directly bound to the promoters of GmCHS / GmIFS and activated both genes' transcription. Taken together, these results suggest that GmSTOP1–3 enhances soybean Al tolerance partially through regulating the flavonoid synthesis. [Display omitted] • Application of genistein is able to reduce ROS accumulation, thus improve soybean Al tolerance. • Expression of GmSTOP1-3 is up-regulated by Al in soybean roots. • GmSTOP1-3 confers soybean Al tolerance by regulating flavonoids biosynthesis. [ABSTRACT FROM AUTHOR]

• The accumulation of cell wall components reduces the tenderness of young tea plant shoots. • Lignin and flavonoid metabolism balance affects the quality of young tea plant shoots. • HCT and CHS are key factors dominating lignin and flavonoid metabolism balance. • MYBs regulate the balance between lignin and flavonoid metabolism. Tenderness is a core index for evaluating the quality of young tea plant shoots and ultimately influences the quality and yield of tea products in terms of bioactive components, processing adaptability, tenderness-keeping ability, and other factors. In this study, we describe the underlying regulatory mechanism of tenderness changes in young shoots of tea plants, combined with biochemical composition determination and transcriptome analysis. The high accumulation of lignin, cellulose, hemicellulose, and pectin is a direct factor leading to a decrease in the tenderness of young shoots, which is dependent on the upregulated expression of genes encoding enzymes related to their biosynthesis. The accumulation of lignin during tenderness decrease in young shoots was accompanied by a decrease in the major flavonoid catechins and anthocyanins, and the upregulated expression of lignin biosynthesis-related genes was also accompanied by the downregulated expression of flavonoid biosynthesis-related genes, implying that the competition between the lignin and flavonoid biosynthesis pathways influences tenderness and bioactive component changes in young tea plant shoots. In addition, as core factors, hydroxycinnamoyl-CoA: shikimate/quinate hydroxycinnamoyl transferase (HCT) and chalcone synthase (CHS) synergize with downstream enzymes to maintain the balance between lignin and flavonoid metabolism. MYB transcription factors in the G10 and G11 groups regulated the expression of genes related to lignin and flavonoid biosynthesis pathways, respectively, and other transcription factors may also play roles in regulating this balance. This study elucidates the regulatory mechanisms of quality changes in young tea plant shoots from the perspective of tenderness. [ABSTRACT FROM AUTHOR]

• Studies apigenin biosynthesis in Houttuynia cordata for industrial use. • Applies LC-MS and RNA-Seq to analyze tissue profiles. • Detects 314 metabolites, 1893 genes showing tissue variation. • Details key enzymes, TFs like HcMYB_45 for apigenin boost. Houttuynia cordata (H. cordata) , known as "yuxingcao" and distinguished by its unique aroma, is primarily cultivated in various Chinese provinces for its rich contents of biologically active compounds such as flavonoids, including apigenin. This study investigated the tissue-specific biosynthesis and regulatory mechanisms of apigenin in H. cordata using integrated metabolomic and transcriptomic approaches. Through integrated metabolomic and transcriptomic analyses, our results revealed that the rhizomes have a higher polysaccharide content (32.32 mg g-1) than that of the leaves (8.41 mg g-1), while the leaves contain more flavonoids (2.47 mg g-1) compared to rhizomes (1.45 mg g-1). We identified 314 differentially accumulated metabolites (DAMs) in rhizomes and leaves, including 70 flavonoids. Correspondingly, 1,894 differentially expressed genes (DEGs) were identified, with significant correlations between gene expression and metabolite accumulation. In the apigenin biosynthesis pathway, 15 enzyme-coding candidate genes were enriched in rhizomes, including phenylalanine ammonia-lyase (PAL1–7), chalcone synthase (CHS2), and flavone synthase II (FNSII). The study also uncovered the role of 23 MYB transcription factors in regulating flavonoid biosynthesis, particularly the central role of HcMYB_45, which showed significant positive correlations with key enzyme genes. Further analysis demonstrated that HcMYB_45 localized to the nucleus and was highly expressed in rhizomes, suggesting its involvement in apigenin biosynthesis regulation. These findings deepen our understanding of the metabolic and genetic networks influencing apigenin production in H. cordata and provide a basis for future genetic engineering strategies optimizing the production of bioactive flavonoids. [Display omitted] [ABSTRACT FROM AUTHOR]

Banana Fusarium Wilt (BFW), caused by Fusarium oxysporum f. sp. cubense (Foc), threatens banana crops globally, with the pathogen's virulence partially regulated by the Sge1 transcription factor, which enhances disease severity. Certain Musa species display resistance to Foc, suggesting inherent genetic traits that confer immunity against Sge1Foc. This study utilized bioinformatics tools to investigate the mechanisms underlying this resistance in Musa accuminata subsp. a alaccensis. Through in silico analyses, we explored interactions between Musa spp. and Foc, focusing on the Sge1 protein. Tools such as Anti-SMASH, AutoDockVina 4.0, STRING, and Phoenix facilitated the profiling of secondary metabolites in Musa spp. and the identification of biosynthetic gene clusters involved in defense. Our results indicate that secondary metabolites, including saccharides, terpenes, and polyketides, are crucial to the plant's immune response. Molecular docking studies of selected Musa metabolites, such as 3-Phenylphenol, Catechin, and Epicatechin, revealed 3-Phenylphenol as having the highest binding affinity to the Sge1Foc protein (-6.7 kcal/mol).Further analysis of gene clusters associated with secondary metabolite biosynthesis in Musa spp. identified key domains like Chalcone synthase, Phenylalanine ammonia-lyase, Aminotran 1–2, and CoA-ligase, which are integral to phenylpropanoid production—a critical pathway for secondary metabolites. The study highlights that the phenylpropanoid pathway and secondary metabolite biosynthesis are vital for Musa spp. resistance to Foc. Flavonoids and lignin may inhibit Sge1 protein formation, potentially disrupting Foc's cellular processes. These findings emphasize the role of phenylpropanoid pathways and secondary metabolites in combating BFW and suggest that targeting these pathways could offer innovative strategies for enhancing resistance and controlling BFW in banana crops. This research lays the groundwork for developing sustainable methods to protect banana cultivation and ensure food security. [Display omitted] • key SMs such as saccharides, terpenes, and polyketides. • Docking between SMs and Sge1Foc protein. • Phenylpropanoid pathways. [ABSTRACT FROM AUTHOR]

The purpose of research was to study in detail the dynamics of the anthocyanin pathway during the ripening of olives, comprising the relative gene expression of nine enzymes and the contents of twelve phenolic compounds. The analyses were conducted on cv. 'Istrska belica' at seven maturity stages, separately in the pulp and the skin. Most phenolic compounds showed a higher content in the skin than in the pulp. Results showed that the accumulation of dihidroquercetin and dihydromyricetin started at the latest maturity stages. The most abundant phenolics evaluated in the current study present in both tissues were cyanidin-3- O -rutinoside and delphinidin-3- O -glucoside, both presented at all maturity stages, even when colour was not yet visible in the skin or pulp. Gene expression of enzymes revealed tissue-specific regulation during ripening. Genes expressions for phenylalanine ammonia lyase, chalcone synthase, chalcone isomerase, flavonoid 3-hydroxylase and flavonoid 3′-hydroxylase showed higher levels in the skin than in the pulp, and an upregulation during ripening in both tissues. Anthocyanidin synthase was the only gene with the highest expression at the beginning of ripening, with extreme decrease between second and third maturity stage, which suggests that the enzyme is mainly synthesized at the beginning of ripening and that enzyme activation starts at latest maturity stages. Our research contributes to a better understanding of the dynamics of phenolic accumulation and the relative gene expression of enzymes involved in the anthocyanin pathway in reveals tissue-specific changes during olive fruit ripening. The previous results are also supported by physical changes, which are reflected in a statistical increase in fruit weight, a decrease in fruit firmness and also by changes in appearance observed during ripening. Understanding the accumulation of anthocyanins could, through further study, help to improve the quality of the fruit and therefore the quality of olive products. • Gene expression and phenolics showed tissue-specific changes during ripening. • Phenolic content was higher in the skin than the pulp, except p -coumaric acid. • The most of genes were upregulated and had higher relative expressions in the skin. • During ripening, ANS gene expression was downregulated in both tissues. • PAL, CHS, CHI, F3H, and F3′H gene expression were upregulated in both tissues.. [ABSTRACT FROM AUTHOR]

Drought is an important threat worldwide, therefore, it is vital to create workable solutions to mitigate the negative effects of drought stress. To this end, we investigated the interactive effect of compost (Comp), arbuscular mycorrhizal fungi (AMF) and carbon nanoparticles (CNPs) on maize plant crops under drought stress. The combined treatments were more effective at increasing soil fertility and promoting the growth of maize plants under both control and drought stress conditions by 20.1% and 39.4%, respectively. The interactions between treatments, especially the effects of Comp-AMF-CNPs mixture, reduce the activity of photorespiration induced H 2 O 2 production that consequently reduces drought-related oxidative damages (lipid peroxidation and protein oxidation). Plants treated with Comp-AMF or Comp-AMF-CNPs showed an increase in their antioxidant defense system. Comp-AMF-CNPs increased enzyme activities by 50.3%, 30.1%, and 71% for ascorbate peroxidase (APX), dehydro-ASC reductase (DHAR), and monodehydro-ASC reductase (MDHAR), respectively. Comp-AMF-CNPs also induced the highest increase in anthocyanins (69.5%) compared to the control treatment. This increase was explained by increased anthocyanin percussor, by 37% and 13% under control and drought, respectively. While the increases in biosynthetic key enzymes, phenylalanine aminolayse (PAL) and chalcone synthase (CHS) were 77% and 5% under control and 69% and 89% under drought, respectively. This work advanced our understanding on how Comp-AMF-CNPs improve growth, physiology, and biochemistry of maize plants under drought stress conditions. Overall, this study suggests the effectiveness of Comp-AMF-CNPs as a promising approach to enhance the growth of maize plants in dry areas. • The study highlight the combination of carbon nanoparticles, AMF, and compost in agriculture. • The Mixture increase Maize productivity under control and drought. • The mixture reduces H 2 O 2 stress and boosts antioxidant enzyme activity. • The combination of nanoparticles, AMF, and compost could be a novel strategy to combat drought stress. [ABSTRACT FROM AUTHOR]

Jujube (Ziziphus jujuba Mill.) is a popular fruit with health benefits ascribed to its various metabolites. These metabolites determine the flavors and bioactivities of the fruit, as well as their desirability. However, the dynamics of the metabolite composition and the underlying gene expression that modulate the overall flavor and accumulation of active ingredients during fruit development remain largely unknown. Therefore, we conducted an integrated metabolomic and transcriptomic investigation covering various developmental stages in the jujube cultivar Z. jujuba cv. Jinsixiaozao, which is famous for its nutritional and bioactive properties. A total of 407 metabolites were detected by non-targeted metabolomics. Metabolite accumulation during different jujube developmental stages was examined. Most nucleotides and amino acids and their derivatives accumulated during development, with cAMP increasing notably during ripening. Triterpenes gradually accumulated and were maintained at high concentrations during ripening. Many flavonoids were maintained at relatively high levels in early development, but then rapidly decreased later. Transcriptomic and metabolomic analyses revealed that chalcone synthase (CHS), chalcone isomerase (CHI), flavonol synthase (FLS), and dihydroflavonol 4-reductase (DFR) were mainly responsible for regulating the accumulation of flavonoids. Therefore, the extensive downregulation of these genes was probably responsible for the decreases in flavonoid content during fruit ripening. This study provide an overview of changes of active components in 'Jinsixiaozao' during development and ripening. These findings enhance our understanding of flavor formation and will facilitate jujube breeding for improving both nutrition and function. • Transcriptome and metabolome analyses of 'Jinsixiaozao' were completed throughout development. • The content of most active compounds decreased gradually with the jujube fruit maturity. • Many flavonoids were maintained high levels in the early stage, but then rapidly decreased. • The decrease in flavonoid content was probably caused by the downregulation of CHS , CHI , and FLS. [ABSTRACT FROM AUTHOR]

Drought stress poses a significant threat to global agricultural production, including the cultivation of medicinal plants. Plant growth-promoting bacteria (PGPB) and the eco-friendly element silicon (Si) are known to alleviate the adverse effects of drought stress. This study examines how inoculation with Bacillus pumilus G5 or/and Si influences plant hormone signaling and flavonoid biosynthesis pathways in drought-stressed Glycyrrhiza uralensis Fisch. (G. uralensis), focusing on genetic and metabolic aspects. The results indicate that the combined application of G5 and Si (G5+Si) may regulate the crosstalk among jasmonate (JA), gibberellin (GA), and ethylene (ET) signaling pathways, thereby up-regulating key flavonoid biosynthesis genes, including phenylalanine ammonia-lyase (PAL), cinnamate 4-hydroxylase (C4H), 4-coumarate-CoA ligase (4CL), and chalcone synthase (CHS), leading to the accumulation of isoliquiritigenin, liquiritigenin, liquiritin, and licochalcone A, thereby enhancing the drought tolerance of G. uralensis seedlings. The findings provide new insights into the synergistic role of PGPB and Si in improving plant resilience to drought stress, offering theoretical reference for further studies on plant drought tolerance mechanisms. [Display omitted] • G5 and Si alleviate oxidative stress in drought-stressed G. uralensis. • G5 and Si activate flavonoid synthesis in drought-stressed G. uralensis. • G5 and Si promote flavonoid synthesis in G. uralensis by regulating hormone crosstalk. [ABSTRACT FROM AUTHOR]

Lagerstroemia excelsa is a unique plant species from China, holds a significant aesthetic and economic value, and plays a crucial role in landscape architecture and horticulture. Thus far, there is little genetic and genomic information available about this species, which limits its use in development of new cultivars. In this study, a high-quality genome map of L. excelsa was obtained via whole-genome sequencing. Results showed that its genome size is about 330.4 Mb and a scaffold mapping rate is approximately 97.20%, resulting in 24 pseudochromosomes. L. excelsa might have undergone a recent whole-genome triplication event and diverged from the pomegranate about 32.3 million years ago (MYA). Subsequently, the divergence time between L. indica and L. excelsa was around 5.9 MYA. The transcriptomic and metabolomic analyses of L. excelsa and L. indica indicated that the chalcone synthase pathway may play a key role in regulating flower color differentiation between the two species. Additionally, a transcription factor LeMYB103 may be involved in regulating anthocyanin synthesis by interacting with LeMYB66, resulting in the accumulation of anthocyanins in the stem bark. This study is the first step toward genomic analysis of L. excelsa , which may provide a foundation for further molecular investigation of this species and offer valuable insights into the molecular mechanisms underlying the flower and stem bark colors in L. excelsa, two important ornamental traits in Lagerstroemia breeding. • Whole genome sequence of Lagerstroemia excelsa was analyzed. • Its genome size is about 330.4 Mb. • The divergence time between L. excelsa and L. indica was around 5.9 MYA. • Carotenoid biosynthesis pathway plays an important role in regulating flower colors. • Stem bark colors are associated with the accumulation of flavonoid metabolites. [ABSTRACT FROM AUTHOR]

The phytotoxic effect of cosmetics such as galaxolide (HHCB) has been investigated, however, their metabolic basis of this impact is still obscure. Thus, we investigated the effect of HHCB on the biomass accumulation, photosynthesis, primary and secondary metabolites in two species from different functional groups i.e. , barley (C3) and maize (C4). In addition, the metabolic bases of HHCB stress mitigating impact of the bioactive Rhodospirillum sp. JY3 were investigated. HHCB toxicity on plant growth and physiology was significantly reduced in PGPB treated plants. At metabolism level, sugars levels and metabolic enzymes (e.g. , invertase, sucrose synthase, starch synthase) were increased. Consequentially, this provided a route for organic, amino and fatty acids biosynthesis. PGPB further mitigated the phytotoxic impact of HHCB upon the levels of organic acids (e.g. , oxalic, citric, succinic, malic and isobutyric acids), amino acids, particularly proline, in addition to unsaturated fatty acids. Furthermore, plant growth-promoting bacteria (PGPB) treatment reduced HHCB toxicity through increasing antioxidant metabolites (e.g. , polyamines and anthocyanin), their precursors (e.g. , phenylalanine, naringenin, cinnamic and coumaric acids) and their related biosynthetic enzymes such as chalcone synthase and cinnamate-4-hydroxylase. Overall, this study, for the first time, significantly contributes to quenching the environmental hazards and maintaining agriculture sustainability using eco-friendly tools. • Barley and maize were differently responded to galaxolide toxicity. • Rhodospirillum sp. counteracts galaxolide-induced growth and photosynthesis inhibition. • R hodospirillum sp. enhances primary metabolite accumulation to reduce galaxolide toxicity. • Rhodospirillum sp. boosts anthocyanin and polyamine levels in galaxolide-treated plants. • Rhodospirillum sp. presents an innovative approach to reducing galaxolide toxicity. [ABSTRACT FROM AUTHOR]

Polysaccharides and various secondary metabolites are the major bioactive ingredients in Bletilla striata tubers and their biosynthesis and accumulation are influenced by light intensity. However, the mechanisms underlying shading effects remain largely unknown. In the present study, we used a combined analysis of the physiology, metabolome, and transcriptome to investigate the physiological activities and bioactive component accumulation of B. striata under different shading treatments (S0, S50, S70, and S90). The dry weight of shoots and tubers, net photosynthetic rate, and polysaccharide content were highest in S50 and lowest in S90. The content of precursors (sucrose, Glucose-6P, and Mannose-6P) for polysaccharide synthesis significantly increased in S50. However, the expression levels of genes involved in starch biosynthesis decreased in S50. Several structural genes involved in secondary metabolism, including cinnamic acid 4-hydroxylase (C4H), chalcone synthase (CHS), and 1 - Deoxy - D - xylulose - 5 - phosphate synthase (DXS), showed decreased expression in S50. However, the shading effect on the biosynthesis of secondary metabolites (phenylpropanoids, flavonoids, and terpenoids) was inconsistent. Our study provides the molecular mechanisms underlying the effects of shading on the biosynthesis of polysaccharides and secondary metabolites in B. striata and offers a theoretical basis for the artificial cultivation and industrial production of bioactive ingredients. • The biomass and net photosynthetic rate were highest in S50. • The contents of BSP and precursors for BSP synthesis were highest in S50. • The shading effect on the biosynthesis of secondary metabolites was inconsistent. • Several structural genes (such as C4H , CHS , and DXS) were downregulated in S50. [ABSTRACT FROM AUTHOR]

In this study, we created a schematic diagram explaining the accumulation of flavonoids and anthocyanins in currant fruits leading to changes in fruit color. MYB, bHLH, bZIP and WRKY TFs may act on structural genes to cooperatively regulate the accumulation of anthocyanins and flavonoids. Upregulated structural genes enhance the expression of anthocyanin and flavonoid pathways, promoting coloration in black and red currants. In contrast, in white currant, TFs are not activated throughout the ripening process to act on structural genes, thereby failing to enhance the accumulation of anthocyanins and flavonoids, resulting in uncolored fruits. [Display omitted] • Investigated the mechanism of anthocyanin accumulation throughout the three currants using transcriptomics and metabolomics. • Identified 23 structural genes with differential expression, along with 11 transcription factors in anthocyanin biosynthesis. • Summarized the regulatory dynamics within the flavonoid biosynthesis pathway. Anthocyanins are natural plant metabolites that are beneficial for human health. In order to study the fruit coloring mechanism mediated by anthocyanin biosynthesis in three currant varieties (white currant, red currant and black currant), we used a combination of transcriptomics and metabolomics analyses. Our comprehensive examination revealed that anthocyanins play a pivotal role in regulating the red and purple hues of black currant and red currant fruits. Specifically, Delphinidin-3-O-rutinoside, Pelargonidin-3-O-rutinoside, Cyanidin-3-O-rutinoside, Cyanidin-3,5-O-diglucoside, Cyanidin-3-O-rutinoside-5-O-glucoside and Petunidin-3-O-glucoside emerged as key anthocyanins in black currant, while Cyanidin-3-O-rutinoside (Keracyanin), Cyanidin-3-O-sambubioside[Cyanidin-3-O-(2″-O-xylosyl)glucoside], Cyanidin-3-O-glucoside (Kuromanin) and Cyanidin-3-O-(2″-O-xylosyl)rutinoside were identified as crucial anthocyanins in red currant. Transcriptomic data showed that the upregulation of dihydroflavonol 4-reductase (DFR), anthocyanin synthase (ANS), and UDP-glucose-flavonoid-3-O-glucosyltransferase (UFGT) genes significantly promoted the purple coloration of black currant fruit, while increased expression of Chalcone synthase (CHS) and flavonoid 3'-hydroxylase (F3′H) genes significantly intensified the red hue of red currant fruit. Furthermore, through weighted gene co-expression network analysis (WGCNA), we identified 11 transcription factors, including 3 bHLH , 2 MYB , 3 bZIP and 3 WRKY genes, which may serve as key regulators of anthocyanin biosynthesis. These findings provide a foundational understanding of the color dynamics in different currant varieties fruits throughout their developmental stages. [ABSTRACT FROM AUTHOR]

Postharvest low-temperature storage is the main strategy for extending the shelf life of peach fruit, but unsuitable low temperatures are susceptible to induced chilling injury for peaches. In this study, postharvest calcium chloride (CaCl 2) treatment effectively mitigated cold damage in nectarines during long-term low-temperature storage. CaCl 2 treatment influences plenty of genes participated in secondary metabolite biosynthesis and primarily affects the phenylpropanoid pathway. The total phenolic and flavonoid contents significantly increased by 12.5 % and 80.6 % in CaCl 2 -treated fruit, respectively. This increase was caused by the elevated expression of phenylpropanoid metabolism enzymes, including phenylalanine ammonia-lyase (PAL), 4-coumarate-CoA ligase (4CL), and chalcone synthase (CHS). PAL activity, located upstream of the phenylpropanoid pathway, was enhanced by the CaCl 2 treatment. Additionally, CaCl 2 significantly enhanced the ROS-scavenging capacity of nectarines, with a significant reduction in ROS content and a significant increase in the activity of several antioxidant enzymes in the CaCl 2 -treated fruit. Furthermore, CaCl 2 promoted the expression of several genes involved in auxin, gibberellin, and abscisic acid metabolism and signaling to mitigate chilling injury. And CaCl 2 treatment reduced fruit decay by enhancing the expression of pathogen resistance genes. Overall, our study revealed that CaCl 2 treatment enhances chilling injury resistance in nectarines through both non-enzymatic and enzymatic antioxidant systems, and demonstrated that postharvest CaCl 2 treatment is an effective strategy to extend the cold storage of peaches. • CaCl 2 treatment alleviates postharvest chilling injury in nectarines. • CaCl 2 enhances phenylpropanoid pathway and elevates total phenolic and flavonoid. • CaCl 2 reduces ROS production and improves activities of antioxidant enzymes. • CaCl 2 activates auxin, gibberellin, abscisic acid metabolism or signaling genes. [ABSTRACT FROM AUTHOR]

• ABA improved the alkali tolerance of grapevines. • ABA mediated photosynthesis, antioxidant defense, and ion homeostasis in grapevines under alkali stress. • ABA was involved in flavonoids biosynthesis in grapevines. • ABA participated in regulating in signaling transduction, key biological pathways, gene expression in grapevines under alkali stress. Abscisic acid (ABA) is a crucial signaling regulator governing plant growth and survival during adverse conditions. However, the mechanism by which ABA mediates grapevine tolerance to alkali stress has not yet been elucidated. Here, we investigated the role of ABA in regulating physiological characteristics and transcriptome of grapevines under alkali stress through the application of exogenous ABA and fluridone (an ABA biosynthesis inhibitor). The results revealed that alkali stress led to significant reductions in the net photosynthetic rate (Pn), stomatal conductance (Gs), intercellular CO 2 concentration (Ci), transpiration rate (Tr), chlorophyll content, the maximum quantum yields of primary photochemistry of PSII (Fv/Fm), nonphotochemical quenching (NPQ), which were greatly alleviated by exogenous ABA (50 and 100 μM) application. Specifically, the application of exogenous ABA (50 μM) increased Pn, chlorophyll content and Fv/Fm by 28.39 %, 30.45 % and 17.29 %, respectively, compared with alkali stress alone. Furthermore, exogenous ABA treatment reduced alkali stress-induced superoxide anions (O 2 ∙−) and hydrogen peroxide (H 2 O 2), malondialdehyde (MDA), and electrolyte leakage, as well as higher proline content and activities of superoxide dismutase (SOD), catalase (CAT), and ascorbate peroxidase (APX). Additionally, exogenous ABA (50 μM) decreased O 2 ∙−, H 2 O 2 , MDA, electrolyte leakage by 38.64 %, 28.16 %, 39.29 % and 39.42 %, respectively, respect to alkali stress alone. Moreover, exogenous ABA reduced the Na+, increased K + and K +/Na+ ratio, as well as the phenylalanine ammonia-lyase (PAL), chalcone synthase (CHS), chalcone isomerase (CHI) activities and flavonoid content, and increased zeaxanthin epoxidase (ZEP) and 9-cis-epoxy carotenoid dioxygenase (NCED) activities and endogenous ABA levels in alkali stress-treated grapevines. Exogenous ABA (50 μM) increased flavonoid content and endogenous ABA content by 74.03 % and 20.84 %, compared with alkali stress alone, respectively. Conversely, exogenous fluridone exacerbated alkali stress-induced physiological damage in grapevine plants. Transcriptome analysis revealed that exogenous ABA (50 μM) and fluridone significantly induced the 'Plant hormone signal transduction (ko04075)', the 'MAPK signaling pathway-plant (ko04016)', 'ABC transporters (ko02010)', 'Photosynthesis-antenna proteins (ko00196)', 'Flavonoid biosynthesis (ko00941)', 'Phenylpropanoid biosynthesis (ko00940)' and other biological pathways and key gene involved in chlorophyll metabolism and ion transport. In conclusion, ABA markedly enhanced grapevines tolerance to alkali stress by modulating key biological pathways and physiological characteristics. [ABSTRACT FROM AUTHOR]

Previous studies have confirmed the stimulating effect of blue light on phenolic compound accumulation and emphasized that sufficient dose of blue light is essential for biosynthesis of B-dihydroxylated flavonoids with enhanced antioxidant properties (under UV-lacking conditions). This study investigates the importance of blue light and complex role of phenolic compounds in plant tolerance against acute photooxidative stress. Hordeum vulgare (L. Cv. Bojos) seedlings were acclimated to different light spectra (blue, green:red 1:1, and white composed of blue:green:red 1:1:1) at total irradiance 400 µmol.m−2.s−1. Subsequently, they were subjected to a 3-hour combined stress induced by high photosynthetically active (850–950 µmol.m−2.s−1) and UV-B (2.0–2.5 W.m−2) radiation. Content of flavonoids, expression of genes involved in their biosynthesis (phenylalanine ammonia-lyase, chalcone synthase, flavonoid 3′-hydroxylase), and antioxidant activity of plant extracts were significantly highest in plants acclimated to blue light. As an indicator of reactive oxygen species interaction with biomolecules, the content of lipid hydroperoxides was estimated. It was demonstrated that plants acclimated to blue light revealed significantly lower extent of lipid peroxidation compared to those acclimated to white or green:red light. Plants exposed to combined light-induced stress for 3 hours exhibited pronounced disruption of PSII function: F V /F M tended to decrease proportionally with decreasing amount of blue photons in the treatments. Additionally, stress exposure upregulated the expression of genes related to phenolic compounds but not genes encoding antioxidant enzymes. We confirmed higher resistance of plants acclimated to blue light and presume that phenolic compounds are significantly involved in protection during the acute phase of stress. • High PAR + UV-B stress upregulates genes for phenolic compound biosynthesis. • Blue light enhances content of specific protective B-dihydroxylated flavonoids. • Plants acclimated to blue light are less susceptible to lipid peroxidation. • Blue light improves PSII stability and enhances recovery after excessive light stress. [ABSTRACT FROM AUTHOR]

Docking domains (DDs) located at the C- and N-termini of polypeptides play a crucial role in directing the assembly of polyketide synthases (PKSs), which are multienzyme complexes. Here, we determined the crystal structure of a complex comprising the C-terminal DD (CDD MlnB) and N-terminal DD (NDD MlnC) of macrolactin trans -acyltransferase (AT) PKS that were fused to a functional enzyme, AmpC EC2 β-lactamase. Interface analyses of the CDD MlnB /NDD MlnC complex revealed the molecular intricacies in the core section underpinning the precise DD assembly. Additionally, circular dichroism and steady-state kinetics demonstrated that the formation of the CDD MlnB /NDD MlnC complex had no influence on the structural and functional fidelity of the fusion partner, AmpC EC2. This inspired us to apply the CDD MlnB /NDD MlnC assembly to metabolon engineering. Indeed, DD assembly induced the formation of a complex between 4-coumarate-CoA ligase and chalcone synthase both involved in flavonoid biosynthesis, leading to a remarkable increase in naringenin production in vitro. [Display omitted] • Crystal structure of a docking domain (DD) complex fused to a functional enzyme • Structural determinants for the specificity between the cognate DD pairs revealed • K d value for DDs fused to two distinct metabolic enzymes was determined • DD assembly yielded an approx. 2-fold increased production of naringenin Son et al. determined the crystal structure of the docking domains (DDs) complex from macrolactin trans -AT PKS, fused to a functional enzyme. The authors measured the K d value for DDs fused to two distinct metabolic enzymes. DD-mediated substrate channeling was demonstrated by an increased naringenin production in flavonoid biosynthesis. [ABSTRACT FROM AUTHOR]

Anthocyanins are major flavonoid compounds with established health benefits. Although the molecular mechanisms of MYB transcription factors (TFs) within the MYB–basic helix-loop-helix (bHLH)–WD-repeat protein (MBW) complex in anthocyanin biosynthesis have been revealed, the functions of other MYB TFs that are unable to form the MBW complex in this process remain unclear. In this study, we uncovered and extensively characterized an R2R3-MYB TF in onion (Allium cepa L.), named AcMYB96, which was identified as a potential anthocyanin activator. AcMYB96 was classified into subgroup 1 of the R2R3-MYB TF family and lacked the conserved sequences required for interactions with bHLH IIIf TFs. Consistently, yeast two-hybrid assays showed that AcMYB96 did not interact with any bHLH IIIf TFs examined, including AcB2 and AtTT8. The transcription pattern of AcMYB96 correlated with the level of anthocyanin accumulation, and its role in activating anthocyanin biosynthesis was confirmed through overexpression in the epithelial cells of onion bulbs and Arabidopsis. Yeast one-hybrid, electrophoretic mobility shift, and promoter transactivation assays further demonstrated that AcMYB96 promoted anthocyanin biosynthesis by binding to the promoters of the chalcone synthase (AcCHS1), anthocyanidin synthase (AcANS), and UDP-glucose-flavonoid 3- O -glucosyltransferase (AcUFGT) genes, thereby activating their expression independent of bHLH IIIf TFs. These results demonstrate that AcMYB96 activates anthocyanin biosynthesis without forming the MBW complex, providing a theoretical foundation to further enrich the gene resources for promoting anthocyanin accumulation and breeding red onions with high anthocyanin content. • The expression level of AcMYB96 is positively related to anthocyanin accumulation. • AcMYB96 lacks conserved sequences for bHLH IIIf interaction to form the MBW complex. • AcMYB96 activates structural genes to stimulate anthocyanin biosynthesis. [ABSTRACT FROM AUTHOR]

Soybean germination under ultraviolet-B (UV–B) radiation stress is a common and effective way to enrich the isoflavone content of sprouts. However, the growth and biomass of germinated soybeans are significantly suppressed using this method. Melatonin (MT), a novel plant biostimulant, not only plays a vital protective role in responses to various abiotic stresses but also regulates the accumulation of secondary metabolites. In the present study, the effects of exogenous MT on the growth and isoflavone metabolism of germinating soybeans exposed to UV-B stress were investigated. Compared to UV-B stress, the application of exogenous MT (25 μM) significantly increased sprout length, fresh weight, Ca2+ influx, and peroxidase activity; markedly decreased the content of malondialdehyde and H 2 O 2 and the fluorescence intensity of H 2 O 2 and O 2 •-; but had no noticeable effect on the activity of superoxide dismutase and catalase during germination. Moreover, the content of total flavonoids and isoflavone monomers (including daidzein, genistein, daidzin, glycitin and genistin) in 4-day-old germinated soybeans was significantly enhanced by MT application under UV-B stress and was not only companied by dramatically increased phenylalanine ammonia lyase activity, but also by markedly increased relative expression levels of phenylalanine ammonia lyase 1, chalcone synthase , isoflavone reductase and flavanone 3-hydroxylase that are involved in the isoflavone biosynthesis pathway. The inhibitory effects of UV-B stress on the growth and biomass of germinated soybeans were alleviated with exogenous MT. MT enhanced the content of total flavonoids and isoflavone monomers under UV-B stress by increasing the activity and relative gene expression level of critical isoflavone biosynthesis-related enzymes. • Melatonin plus UV-B treatment promoted the isoflavone biosynthesis of soybeans. • Negative effects of UV-B stress was removed by exogenous melatonin (25 μM). • Melatonin plus UV-B stimulated gene expression and activities of key enzymes. • Change of PAL activity was inconsistent with its gene expression. [ABSTRACT FROM AUTHOR]

• 29 CHS members in common bean genome grouped into 5 subgroups, with tissue-specific expression. • PvCHS01, 05, 14, 25 up-regulated under alkaline salt stress, suggesting involvement in abiotic stress response. • PvCHSs expression linked to CHS activity, flavonoid content; exogenous flavonoids reduce ROS, alleviate salt stress damage. Secondary metabolites such as flavonoids, produced by plants, could help plants cope with external stress. Flavonoid synthesis is catalyzed by chalcone synthase (CHS). CHS plays a broad role in the growth, development, and physiological activities of plants. However, studies of the CHS gene family in Phaseolus vulgaris are limited. In this study, the HMMER search tool was used to identify 29 CHS members in the reference genome of P. vulgaris. These PvCHS members were divided into 5 subgroups. Notably, subfamilies with close genetic relationships exhibited similarities in motifs and gene structures of PvCHSs. Additionally, analysis of the cis-element indicated the involvement of PvCHSs in response to abiotic stress. Furthermore, quantitative real-time PCR (qRT-PCR) analysis under various abiotic stress conditions revealed that the majority of PvCHSs were associated with the response to salt stress (NaCl), alkaline salt stress (NaHCO 3), and heavy metal stress (CdCl 2). Particularly, PvCHS01, PvCHS05, PvCHS14 , and PvCHS25 were significantly up-regulated under alkaline salt stress. PvCHSs were also correlated with CHS activity and flavonoid content. In addition, exogenous flavonoids were observed to significantly decrease accumulation of ROS in P. vulgaris under alkaline salt stress. This study provides a basis for further analysis of the mechanisms underlying the response of PvCHSs to abiotic stress. [ABSTRACT FROM AUTHOR]

• EGC, caffeine, catechin, EC, EGCG, and ECG were isolated using HPLC at UPASI 3 and UPASI 17. • Phytochemical levels were relatively higher in UPASI 17 than in UPASI 3. • CHS, F3′5′H, ANS, DFR , and LAR expressions were upregulated in UPASI 17 compared with UPASI 3. • UPASI 17 treated cancer cells elevated the activation of caspase 3 enzyme more effectively than UPASI 3 for apoptosis. Genetically superior tea clones United Planters Association of Southern India (UPASI) 3 and UPASI 17 have been identified as prime candidates for chemo-profiling, assessment of antioxidant activity, and evaluation of anticancer properties against the human adenocarcinoma A549 cancer cell line. High-performance liquid chromatography (HPLC) analysis of UPASI 3 and UPASI 17 revealed the presence of caffeine and five catechins, including epicatechin-3-gallate, catechin, epicatechin, epigallocatechin gallate, and epicatechin gallate, with UPASI 17 exhibiting a higher total catechin content than UPASI 3. Comparative assays of antioxidant capacity and tea quality enzymes, such as total polyphenols, polyphenol oxidase (PPO), superoxide dismutase (SOD), catalase (CAT), phenylalanine ammonia-lyase (PAL), and peroxidase (POD), showed higher levels in UPASI 17 than in UPASI 3. Additionally, transcriptional analysis revealed upregulated expression of key flavonoid biosynthesis genes such as chalcone synthase (CHS), flavonoid 3′,5′-hydroxylase (F3′5′H), anthocyanidin synthase (ANS) dihydroflavonol 4-reductase (DFR) and leucoanthocyanidin 4-reductase (LAR) in UPASI 17 compared with UPASI 3. The anticancer potential of the methanolic extracts of these tea clones against the A549 cancer cell line was evaluated using MTT cytotoxicity assays, along with cell cycle, caspase activation, and mitochondrial membrane potential analyses. Notably, UPASI 17 significantly inhibited cancer cell viability at a concentration of 0.5 µg/ml within 36 h, induced cell cycle arrest in the S phase, and more effectively activated the caspase 3 enzyme to promote apoptosis than UPASI 3. Furthermore, exposure to UPASI 3 and UPASI 17 extracts triggered apoptosis in A549 cells through modulation of the PI3K-Akt-mTOR signalling pathway. The enhanced anticancer activity of UPASI 17 was attributed to its high concentration of phytocompounds and its antioxidant activities. These findings underscore the potential for further molecular-level research and animal studies to develop novel anticancer drugs that target lethal diseases. [Display omitted] [ABSTRACT FROM AUTHOR]

• The expression pattern of 40 DzMYB s in durian pulp at five stages was profiled and the most expressed DzMYB during postharvest ripening was characterized. • Transient expression of DzMYB1 raised flavonoids in tomato. • DzMYB1 binds promoters of early flavonoid genes: pCHS, pCHI, and pF3H. • DzMYB1 forms a homodimer and binds DzbHLH1's homodimer. Flavonoids are phenolic substances and exhibit strong antioxidant properties. The biosynthesis of flavonoids is regulated by various transcription factors (TFs), with MYB TFs playing a key role in controlling essential genes within this pathway. In this study, we identified candidate MYB TFs from our pulp transcriptome database of durian 'Monthong' cultivar. MYBs exhibiting upregulation during the ripe stage were considered transcriptional activators, due to their positive correlation with flavonoid gene expression and flavonoid accumulation in ripe durian pulps. One candidate MYB activator, DzMYB1, which was highly expressed at the ripe stage, was selected for functional characterization. Studies involving transient expression of DzMYB1 in Solanum lycopersicum cv. Micro-Tom fruit demonstrated increased flavonoid content, as analyzed by LC–MS/MS, compared with the GFP control. Moreover, we showed that DzMYB1 controls flavonoid biosynthesis by interacting with the promoters of various flavonoid biosynthetic genes, including chalcone synthase, chalcone isomerase, and flavanone 3-hydroxylase, resulting in their transcriptional activation. Additionally, we found that DzMYB1 functions as a homodimer and binds to a homodimerized DzbHLH1 in the intricate regulation of flavonoid biosynthesis. These findings provide comprehensive insights into the functional roles of MYB protein in the regulation of the flavonoid pathway within durian pulps. [ABSTRACT FROM AUTHOR]

The development of quinoa-based functional foods with cost-effective methods has gained considerable attention. In this study, the effects of magnetic field pretreatment on the germination characteristics, phenolic synthesis, and antioxidant system of quinoa (Chenopodium quinoa Willd.) were investigated. The results showed that the parameters of magnetic field pretreatment had different effects on the germination properties of five quinoa varieties, in which Sanjiang-1 (SJ-1) was more sensitive to magnetic field pretreatment. The content of total phenolics and phenolic acids in 24-h germinated seeds increased by 20.48% and 26.54%, respectively, under the pretreatment of 10 mT magnetic fields for 10 min compared with the control. This was closely related to the activation of the phenylpropanoid pathway by increasing enzyme activities and gene expression. In addition, magnetic field improved 1,1-diphenyl-2-picrylhydrazyl (DPPH) and 2,2′-Azinobis-(3-ethylbenzthiazoline-6-sulphonate) (ABTS) free radicals scavenging capacities and increased peroxidase (POD), catalase (CAT), superoxide dismutase (SOD), ascorbate peroxidase (APX) and glutathione peroxidase (GSH-Px) activities. This study suggests that magnetic field pretreatment enhanced gene expression of phenylalanine ammonia lyase (PAL), 4-coumarate-CoA ligase (4CL), chalcone synthase (CHS) and chalcone isomerase (CHI), increased antioxidant enzyme activity and phenolics content. Thereby lead to an increase in the antioxidative capacity of quinoa. • Magnetic field pretreatment promoted the germination of five quinoa species. • Magnetic field enhanced the nutritional and functional profiles of quinoa. • Magnetic fields (10 mT and 10 min) had the greatest enrichment effect on phenolics • Phenolics enrichment is associated with phenylpropanoid pathway activation. • Magnetic field improved scavenging capacities and antioxidant enzyme activities. [ABSTRACT FROM AUTHOR]

Understanding the proteins and metabolites produced by plants aids in developing superior planting materials. Gymnema sylvestre , a significant medicinal plant containing beneficial compounds such as oleanane, dammarane, flavonoids and gymnemic acids, exhibiting antioxidant and antidiabetic properties, making it a promising alternative treatment for Type 2 diabetes with minimal side effects. Transcriptomics in G. sylvestre yielded Coding DNA Sequences (CDS) for 12 key genes of flavonoid biosynthesis. Translated protein sequences of those 12 genes underwent characterization using protPARAM and i-TASSER. In silico protein modelling found similarities to validated enzymes, suggesting functional potential of the studied proteins. The study enlightens the first comprehensive insight into key proteins involved in G. sylvestre 's flavonoid biosynthesis pathway. GsCHS (G. sylvestre chalcone synthase), a key enzyme in flavonoid biosynthesis, corroborated its phylogenetic proximity to Vincetoxicum mongolicum 's CHS. Protein docking analysis delineated the distinctive features of GsCHS from cpCHS1 of Cyclosorus parasiticus , particularly in its substrate binding pockets and interactive sites crucial for synthesizing essential flavonoids. • In silico characterization of translated proteins of flavonoid biosynthesis genes. • Predicted proteins compared with publicly available validated enzymes. • Interaction sites of G. sylvestre CHS enzyme with Naringenin and CoA identified. [ABSTRACT FROM AUTHOR]

At specific vibration frequencies like ones generated by insects such as caterpillar chewing and bee's buzz-pollination turn on the plants secondary metabolism and their respective pathways gets activated. Thus, studies report that vibrations and sound waves applied to plants improves their fitness performance. Commonly, acoustic treatments for plants have used arbitrarily random frequencies. In this work, a group of signals obtained from hydric-stressed plants was recorded as vibrational patterns using a laser vibrometer. These vibration-signals were classified as representative of each condition and then externally applied as Acoustic Emission Patterns (AEP). The present research hypothesized that specific vibration frequencies could "emulate" a plant signal through mechanical energy based on tplant's ability to recognize vibration pattern similarity to a hydric status. This investigation aimed to apply the AEP's as characteristic vibrations classified as Low hydric stress (LHS), medium hydric stress (MHS), and high hydric stress (HHS) to evaluate their effect on healthy-well watered plants at two developmental stages. In the vegetative stage, the gene expression related to antioxidant and hydric stress responses was assessed. The LHS, MHS, and HHS acoustic treatments up-regulated the peroxidase (Pod) (~2.8, 1.9, and 3.6-fold change, respectively). The superoxide dismutase (Mn-sod) and phenylalanine ammonia-lyase (Pal) genes were up-regulated by HHS (~0.23 and ~0.55-fold change, respectively) and, the chalcone synthase (Chs) gene was induced by MHS (~0.63-fold-change). At the fructification stage, the MHS treatment induced a significant increase in Capsaicin content (5.88-fold change), probably through the at3 and kas gene activation. Findings are correlated for a better understanding of plant responses to different multi frequency-signals tones from vibrations with potential for agricultural applications. [Display omitted] • Plants change their vibrational frequency pattern according to their hydric stress level. • Acoustic emission patterns (AEP) have the potential to emulate hydric-stress signals on healthy plants.. • AEP externally applied can trigger transcriptional changes in antioxidant responses. • AEP has the possible recreate self-adjustment on osmoregulation in plants through aquaporin and proline. • AEP induces an increase in the capsaicinoids synthesis and at3 and kas up-regulation pathway.. [ABSTRACT FROM AUTHOR]

Quantitative RT- PCR is one of the most common methods to study gene expression in response to stress. Therefore, it is crucial to have suitable reference genes (RGs) for result normalization. Although several reports describe UV-B-modulated gene expression in Solanum lycopersicum , there are no suitable RGs identified until now. The aim of this work was to evaluate the suitability of seven traditional genes: actin (ACT), tubulin (TUB), ubiquitin (UBI), glyceraldehyde- 3 phosphate dehydrogenase (GAPDH), elongation factor 1α (EF1α), phosphatase 2A catalytic subunit (PP2A) and GAGA binding transcriptional activator (GAGA); and two non-traditional genes: thioredoxin h1 (TRX h1) and UV-B RESISTANCE LOCUS 8 (UVR8), as candidate RGs for their potential use as reliable internal controls in leaves, stems and roots of tomato seedlings exposed to acute and chronic UV-B. The stability of these genes expression was evaluated using five statistical algorithms: geNorm, NormFinder, BestKeeper, Delta Ct and ANOVA. Considering the comprehensive stability ranking, we recommend ACT + TUB as the best pair of RGs for leaves, PP2A + GAPDH + TRX h1 for stems and TUB + UVR8 for roots. The reliability of the selected RGs for each tissue was verified amplifying tomato chalcone synthase 1 (CHS1) and cyclobutane pyrimidine dimer (CPD) photolyase (PHR1-LIKE). Under UV-B treatment, CHS1 was upregulated in leaves, stems and roots whereas PHR1-LIKE was only upregulated in leaves and stems. This interpretation differs when the most and least stable RGs are chosen. This is the first report regarding suitable RGs selection for accurate normalization of gene expression in tomato seedlings exposed to UV-B irradiation. • Nine candidate reference genes (RGs) were validated in tomato seedlings exposed to UV-B • Four conditions and three tissues were analysed with five statistical algorithms. • ACT +(TUB/PP2A/TRX h1) were the suggested RG in leaves, PP2A + GAPDH + TRX h1 in stems and TUB + UVR8 in roots. • UV-B induced CHS1 and PHR1-LIKE mRNA in leaves and stems whereas CHS1 in roots. • This work will facilitate RT-qPCR studies of UV-B exposed tomato seedlings. [ABSTRACT FROM AUTHOR]

• The successful Rhizobium (Agrobacterium)mediated hairy root (HR) induction in Ficus carica L. was confirmed by the presence of rol B gene in the HR lines. • The effects of cell extract and medium culture filtrate (two elicitors) derived from axenic culture of Piriformospora indica on some phenolic compounds and expression level of some genes in F. carica HR cultures was investigated in this study. • Depending on concentration and treatment time, P. indica elicitation induced to change biomass, phenolic compounds accumulation and antioxidant activity of HRs. • P. indica elicitation improved the expression rate of PAL, CHS, UFGT, MYB3 genes and increased the synthesis of apigenin, quercetin, rutin and phenolic acids (gallic, caffeic, chlorogenic, coumaric, rosmarinic and cinnamic acids) in F. carica elicited-HRs. Ficus carica L. is an important source of phenolic and flavonoid compounds with valuable pharmaceutical application across various diseases. The current study was carried out to investigate the influence of Piriformospora indica elicitation on growth, production of phenolic compounds, antioxidant capacity, and expression level of flavonoid biosynthetic pathway genes in hairy root (HR) cultures of F. carica. The maximum improvement in accumulation of phenolic compounds was observed when HR culture of Ficus carica L. was exposed to 2% culture filtrate of P. indica for 72 h: gallic acid (80.5- fold), caffeic acid (26.2-fold), coumaric acid (4.5-fold), and cinnamic acid (60.1-fold), apigenin (27.6-fold) and rutin (5.7-fold). While the highest levels of chlorogenic acid (4.9-fold) and quercetin flavonoid (8.8-fold) were obtained after 48 h elicitation with culture filtrate and cell extract of P. indica at 6% (v/v), respectively. The analysis of biosynthetic genes revealed that the exposure to fungal elicitors resulted in up-regulation of phenylalanine ammonia-lyase (PAL), chalcone synthase (CHS), UDP-glucose flavonoid 3-O-glucosyltransferase (UFGT) and MYB3 transcription factor. This study shows the potential of P. indica as an efficacious elicitor for enhancing the secondary metabolites production by F. carica HRs. [ABSTRACT FROM AUTHOR]

Quercetin is one of the main flavonoids in the human diet and mainly found in different plant tissues, including seeds, flowers, leaves, stems, and roots. However, its biological function in plant tissues, especially in seeds, is unknown. In this study, the seed germination and subsequent seedling growth of Apocynum pictum and A. venetum under osmotic stress (400 mmol L−1 mannitol) supplemented with 5 μmol L−1 quercetin were evaluated after 7, 14, and 21 days of germination. Results showed that quercetin improved the germination percentage and seed vigor, as indicated by the higher germination energy, shoot length, root length, dry weight, fresh weight, and chlorophyll content in A. pictum and A. venetum seedlings under the mannitol compared with those under the mannitol alone. Quercetin decreased H 2 O 2 and O 2 − production and cell membrane damage, and mostly increased the gene expression of superoxide dismutase, peroxidase, catalase, chalcone synthase and flavonol synthase in A. pictum and A. venetum seedlings under the mannitol compared with those under the mannitol alone. In addition, the germination energy of A. pictum was 21.57% higher than that of A. venetum , and the gene expression of key enzymes in quercetin biosynthesis in A. pictum was mostly higher than that in A. venetum after 1 and 7 days of germination. These results indicated that quercetin was an effective anti-osmotic agent that alleviated the adverse effect of mannitol-induced osmotic stress on seed germination and seed vigor, and A. pictum seeds were more osmotic resistant than A. venetum seeds. Quercetin supplement alleviated the adverse impact of osmotic stress on seed germination and seed vigor in A. pictum and A. venetum by decreasing ROS production and cell membrane damage, and enhancing antioxidant enzyme activity, photosynthesis, and quercetin biosynthesis. Image 1 • Quercetin enhanced the seed germination and seed vigor under osmotic stress. • A. pictum seeds were more osmotic resistant than A. venetum seeds. [ABSTRACT FROM AUTHOR]

We investigated the bi-colored dahlia cultivar 'Seattle', which exhibits bright yellow petals with white tips, for its potential use as a model system for studies of the anthochlor biosynthesis. The yellow base contained high amounts of the 6′-deoxychalcones and the structurally related 4-deoxyaurones, as well as flavones. In contrast, only traces of anthochlors and flavones were detected in the white tips. No anthocyanins, flavonols, flavanones or dihydroflavonols were found in the petals. Gene expression studies indicated that the absence of anthocyanins in the petals is caused by a lack of flavanone 3-hydroxylase (FHT) expression, which is accompanied by a lack of expression of the bHLH transcription factor IVS. Expression of other genes involved in anthocyanidin biosynthesis such as dihydroflavonol 4-reductase (DFR) and anthocyanidin synthase (ANS) was not affected. The yellow and white petal parts showed significant differences in the expression of chalcone synthase 2 (CHS2), which is sufficient to explain the absence of yellow pigments in the white tips. Transcriptomes of both petal parts were de novo assembled and three candidate genes for chalcone reductase (CHR) were identified. None of them showed a significantly higher expression in the yellow base compared to the white tips. In summary, it was shown that the bicolouration is most likely caused by a bottleneck in chalcone formation in the white tip. The relative prevalence of flavones compared to the anthochlors in the white tips could be an indication for the presence of a so far unknown differentially expressed CHR. Image 1 • In-depth chemical, molecular and transcriptome analysis of a yellow-white dahlia • In contrast to white tips, the yellow base contains high anthochlor and flavonoid contents • Significant differences in the expression of DvCHS2, DvFHT and transcription factor DvIVS • Bicolouration is explained by a bottleneck in chalcone formation in the white tip • cv. 'Seattle' is a suitable model system for studying anthochlor biosynthesis [ABSTRACT FROM AUTHOR]

• The difference between Ar and Af leaf samples was first characterized applying transcriptome and metabolome analysis. • Correlation analysis between metabolites and metabolic enzyme gene expression revealed flavonoid metabolic differences between Ar and Af. • This study screened and obtained key genes potentially involved in the differentially accumulation of flavonoids between Ar leaves and Af leaves. • This study provides an in-depth understanding of differentially flavonoid accumulation between Ar leaves and Af leaves. Anoectochilus roxburghii (Wall.) Lindl (Ar) and Anoectochilus formosanus Hayata (Af) are two species of valuable Chinese herbal medicines that belong to the genus Anoectochilus in Orchidaceae and have often been applied as the Chinese herbal medicine "Jin Xian Lian". However, these species exhibit obvious differences in leaf color, and the difference in their medicinal value remains unclear. In this study, the metabolomes of leaf samples of Ar and Af were analyzed by high-performance liquid chromatography-mass spectrometry (LC–MS) in the positive and negative ion modes. The analysis of the leaves of both species in the positive ion mode identified 4013 metabolites enriched in 106 metabolic pathways, and the analysis in the negative ion mode found 1530 metabolites enriched in 98 metabolic pathways. A differential metabolic profiling analysis of the results obtained in positive ion mode found that 816 differentially accumulated metabolites were enriched in 80 metabolic pathways, whereas 297 differentially accumulated metabolites enriched in 55 metabolic pathways were obtained from the analysis in the negative ion mode. The number of flavonoids was higher than those of alkaloids and terpenoids. A quantitative analysis of the differentially accumulated metabolites showed that the most highly upregulated metabolites (Af/Ar) among the top 20 differentially accumulated metabolites in Af were mainly related to amino acid-related metabolic pathways, whereas the most highly downregulated metabolites (Af/Ar) in Af were mainly associated with flavonoid-related metabolic pathways. In addition, the transcriptome sequencing of Ar and Af leaf samples yielded 40.12 Gb of transcriptomic data. The analysis of differentially expressed genes (DEGs) classified 555 metabolism-related DEGs into 23 metabolism-related KEGG pathways, and the top DEGs were involved in the phenylpropanoid biosynthetic pathways, which included up to 138 DEGs associated with the flavonoid metabolism pathway. In addition, significant differences in the flavonoid-related KEGG pathways were found. A comprehensive analysis of the metabolomes and transcriptomes showed that the genes annotated as chalcone synthase (CHS), chalcone isomerase (CHI), flavonol synthase (FLS), caffeoyl-CoA O -methyltransferase (CCOAOMT) and anthocyanidin synthase (ANS) were downregulated in Af leaves compared with Ar leaves, which might account for the downregulation of flavonoid-related metabolites in Af. In summary, both the metabolomic and transcriptomic analyses showed significant differences in flavonoid metabolism between the Ar and Af leaves, and the mechanisms underlying the molecular regulation of these differences were preliminarily analyzed. [ABSTRACT FROM AUTHOR]

Chalcone synthase (CHS) is a key enzyme and producing flavonoid derivatives as well play a vital roles in sustaining plant growth and development. However, the systematic and comprehensive analysis of CHS genes in island cotton (G. barbadense) has not been reported yet especially response to cytoplasmic male sterility (CMS). To fill this knowledge gap, a genome-wide investigation of CHS genes were studied in island cotton. A total of 20 GbCHS genes were identified and grouped into five GbCHSs. The gene structure analysis revealed that most of GbCHS genes consisted of two exons and one intron, and 20 motifs were identified. Twenty five pairs duplicated events (12 GbCHS genes) were identified including 23 segmental duplication pairs and two tandem duplication events, representing that GbCHS gene family amplification mainly owned to segmental duplication events and evolving slowly. Gene expression analysis exhibited that the GbCHS family genes presented a diversity expression patterns in various organs of cotton. Coupled with functional predictions and gene expression, the abnormal expression of GbCHS06 , 10 , 16 and 19 might be associated with pollen abortion of CMS line in island cotton. Conclusively, GbCHS genes exhibited diversity and conservation in many aspects, which will help to better understand functional studies and a reference for CHS research in island cotton and other plants. [ABSTRACT FROM AUTHOR]

Plants belonging to the genus Artemisia L. have been used for medicinal purposes since ancient times. These aromatic plants produce and accumulate a wide range of potent secondary metabolites, many of which have shown antioxidant, antiparasitic, antimicrobial, anti-inflammatory, and even anticancer activities. Enhanced biosynthesis of these compounds is a prerequisite for comprehensive studies of their therapeutic properties and cost-efficient use. Transformation of plants with Agrobacterium rhizogenes native root locus (rol) genes is a promising approach to increase the biosynthesis of plant secondary metabolites. The aim of the present study was to evaluate the effects of A. rhizogenes -mediated transformation on the flavonoid contents in hairy roots of medicinal herb A. tilesii Ledeb. Transgenic A. tilesii hairy root lines were analyzed for stable integration of the rolB and rolC transgenes into the plant genome, total flavonoid contents, antioxidant activities of extracts, and the spatiotemporal expression of two flavonoid biosynthetic genes, phenylalanine ammonialyase (PAL) and chalcone synthase (CHS). The flavonoid contents of A. tilesii directly correlated with the antiradical activity and reducing power of their respective lines, with the greatest antioxidant activity found in the plants with the highest level of total flavonoids. Furthermore, all hairy root lines demonstrated altered expression of plant native PAL and CHS genes. Most importantly, A. rhizogenes -mediated transformation enhanced the biosynthesis of natural antioxidants in A. tilesii , producing almost twice the amount of flavonoids than controls. These findings provide an opportunity for the identification of the bioactive molecules in A. tilesii extracts and their potential health benefits. • Agrobacterium rol genes enhance flavonoid biosynthesis in Artemisia tilesii Ledeb. • Flavonoid contents of A. tilesii directly correlate with antioxidant activity. • Development of A. tilesii hairy roots affects expression of native PAL and CHS genes. [ABSTRACT FROM AUTHOR]

• Characterization and validation of two CHSs functional in E. ferox. • EfCHS2 occupied a more important position in flavonoid biosynthesis. • EfGATA8, a novel transcription factor capable of regulating CHS expression. • EfGATA8 inhibits EfCHS2 expression to negatively regulate flavonoid biosynthesis. Chalcone synthase is a crucial rate-limiting enzyme for flavonoid biosynthesis in plants. Despite the abundance of flavonoid resources in Euryale ferox , resolving their biosynthesis and regulatory pathways is remained scarce. Five putative CHS genes were obtained in E. ferox through genome-wide characterization. Phylogenetic, structural analysis and sequence alignment were performed to determine EfCHS1 and EfCHS2 as candidate genes for flavonoid biosynthesis. Enzyme activity assays and transient overexpression demonstrated that EfCHS1 and EfCHS2 exhibited potent activities. Interestingly, it was found that there was strong expression of EfCHS1 in the seed shells and EfCHS2 in the leaves. Moreover, the transcription factor EfGATA8 was screened in the E. ferox yeast library using a yeast one-hybrid system. Subcellular localization analysis displayed that EfGATA8 only existed fluorescent signals in the nucleus. It was revealed that EfGATA8 binds directly to the promoter of EfCHS2 and represses its expression according to further Y1H assay and luciferase (LUC) activity analysis. EfGATA8 transient transformation into tobacco leaves resulted in significantly reduced accumulation of flavonoids. Taken together, these findings clarify the position of EfCHS1 and EfCHS2 as key genes for flavonoid biosynthesis in E. ferox , while perfecting the regulatory network for flavonoid biosynthesis in plants. [ABSTRACT FROM AUTHOR]

• Proper shading could reduce the content of TPC and TFC in in Juglans sigillata Dode pellicle, and promote the accumulation of total flavonoids in extreme darkness. • Shading could reduce the accumulation of flavonoids in Juglans sigillata Dode pellicle. • Shading could increase of PAL enzyme activity and JsPAL expression level indicated that it played an important role in the accumulation of TPC and TFC. • Shading decreased activity of key enzymes (C4H, 4CL, CHS, CHI, F3H, FLS) in the phenylpropane-flavonoid pathway and the down-regulated expression of key structural genes (JsC4H, Js4CL, JsCHS, JsCHI, JsF3H, JsFLS) after shading. Polyphenols, abundant in the pellicle of walnuts, confer health benefits to the human body. The intricate relationship between light and phenolic compounds underscores the impact of shading, which can effectively diminish phenolic content and enhance the palatability of food. In this study, we delved into the connection between polyphenol accumulation, related enzyme activities, and gene expression in the pellicle of Juglans sigillata Dode under varying degrees of shading. The results show that different shade intensities can change polyphenols' content and affect the activity of key polyphenols anabolism enzymes and their gene expression. With the increase of the shading intensity, the total phenolics content (TPC) and total flavonoids content (TFC) were lower than the nomal light. In the mature stage, shading 60 % was lowest. 7 individual phenolics were identified in the pellicle, and the content of each varied significantly with the decrease of light intensity. Except for p -coumaric acid and ferulic acid, which were higher than the control at mature stage, all phenolics were lower than the control, but the overall trend was the same as that of the control. The activity of key enzymes in the anabolism of polyphenols was significantly affected after shading. In complete darkness phenylalanine ammonia lyase (PAL) was highest at the kernel-filling stage, shading 20 % of chalcone synthase (CHS) and shading 60 % of flavonol synthase (FLS) responded most strongly at the hard-core stage, while flavanone 3-hydroxylase (F3H) was most active at shading 60 % of kernel-filling stage, which was 2.03, 1.38, 4.67, and 2.08 times that of the control, respectively. The expression levels of key genes showed that the expression level of JsPAL was significantly increased at hard-core stage and mature stage, and the expression of JsPAL was 3.85 times higher than that of the control at the mature stage with 60 % shading. Correlation analysis showed that PAL enzyme activity was highly correlated with TPC, TFC and various individual phenolics with the increase of shading intensity. The content of p -coumaric acid was positively correlated with the activities of 4-coumarate coenzyme A ligase (4CL), F3H and FLS. The increase of shading intensity enhanced the correlation between total phenolics content, total flavonoids content, individual phenolics substances and JsPAL, JsC4H, JsCHS, JsCHI and JsFLS. Overall, PAL was a key enzyme affecting polyphenol accumulation under different shading levels, while at the genetic level, JsPAL, JsC4H, JsCHS, JsCHI and JsFLS were the key genes affecting them. This study will potentially provide more information for light management and polyphenol regulation in walnut cultivation. [ABSTRACT FROM AUTHOR]

Flavonoids are plant pigments that play a major role in plant defense and have significant health benefits to humans. Chalcone synthase (CHS) is an important enzyme in flavonoid biosynthesis and investigation transcription factors (TFs) regulating its expression and downstream targets is critical to understanding its mechanism. Here, a novel TF, PbWRKY18, was isolated from the pear Pyrus betulaefolia. Its expression was evaluated in various tissues by RT-PCR, particularly in response to Alternaria alternata , the pathogen responsible for black spot disease, and exogenous hormone administration. The PbWRKY18 protein was primarily found in the nucleus where it regulated transcriptional activity. Yeast one-hybrid and dual-luciferase reporter assays showed a strong association between PbWRKY18 and the PbCHS3 promoter, which drives PbCHS3 expression. It was also found that PbCHS3 was critical for the development of resistance against black spot disease. In addition, PbWRKY18 was found to significantly increase the expression of PbCHS3 and salicylic acid-related genes, as well as defense enzyme activity and tolerance to black spot disease. PbWRKY18 or PbCHS3 knockdown in pear attenuates resistance to Alternaria alternata. In summary, the study identified a novel WRKY18-CHS3 axis involved in resistance against black spot disease in pear. • PbWRKY18 and PbCHS3 were critical for the black spot disease resistance. • PbWRKY18 can bind to the PbCHS3 promoter to enhance the transcripts level and the activity of PbCHS3. • The study identified a novel PbWRKY18-PbCHS3 axis involved in black spot disease resistance. [ABSTRACT FROM AUTHOR]

Despite the widespread use of dry matter content (DMC) as an indicator of kiwifruit quality, the physiological and molecular impact of DMC in fruit ripening remains unknown. Herein, the post-harvest physiological, metabolomic, and transcriptomic influence of DMC status on the pericarp and placenta tissue of 'Hayward' kiwifruit at harvest and at the onset of post-cold ripening was investigated. A segregation strategy based on DMC in commercially harvested kiwifruit was achieved with near-infrared spectroscopy for the estimation of DMC in individual fruits. Additionally, kiwifruits with distinct DMC levels were treated with 1-methylcyclopropene (1-MCP) and systematically monitored for ripening changes (20 °C) at various intervals after cold storage (0 °C). Following 90 and 120 days of cold exposure, high DMC kiwifruit generally exhibited superior physiological characteristics, such as increased pericarp and placenta firmness, and soluble solid and starch contents compared to low DMC kiwifruit, regardless of the 1-MCP application. Evidence is also presented for 1-MCP delaying the ripening of low-DMC fruit to the level of the untreated high-DMC kiwifruit. An accumulation of primary metabolites, particularly sugars and polyphenolic compounds, such as catechin, chlorogenic acid and procyanidin B1/B2 was evidenced in the high DMC group. At harvest, gene expression analysis revealed minor differences between DMC groups, with beta-amylase being the highest up-regulated gene in high DMC kiwifruit. Moreover, the gene expression patterns between DMC groups became more distinct after cold storage. Genes related to starch biosynthesis (i.e., glucose-1-phosphate adenyltransferase), water movement (i.e., aquaporin), polyphenolic biosynthesis (i.e., chalcone synthase) and lipid metabolism (i.e., diacylglycerol acyltransferase) showed strong variations between low and high DMC. Interestingly, the placenta tissue displayed almost 4 times more than DMC-affected differentially expressed genes compared to the pericarp, highlighting the key role of the placenta in kiwifruit ripening, notably following 1-MCP treatment. This study provides insights into the tissue-specific ripening response between kiwifruit with distinct DMC, as well as the gene expression influenced by an interaction of 1-MCP and DMC level, thereby helping develop postharvest programs aimed at improving kiwifruit quality traits. • 1-MCP delayed ripening in low-DMC fruit. • The placenta plays a key role in the initiation of kiwifruit ripening. • Several genes involved in DMC-affected ripening were identified. • Secondary metabolism is activated in higher DMC kiwifruit. [ABSTRACT FROM AUTHOR]

Drought stress is increasing worldwide due to global warming, which severely reduces apple (Malus domestica) yield. Clarifying the basis of drought tolerance in apple could accelerate the molecular breeding of drought-tolerant cultivars to maintain apple production. We identified a transcription factor MdWRKY50 by yeast two-hybrid (Y2H) assays as an interactor of the drought-tolerant protein MdWRKY17, and confirmed their interaction by bimolecular fluorescence complementation (BiFC) and pull-down assays. MdWRKY50 was induced by drought and when overexpressed in apple, conferred transgenic apple plants enhanced drought tolerance by directly binding to the promoter of anthocyanin synthetic gene Chalcone synthase (MdCHS) to upregulate its expression for higher anthocyanin. Increased anthocyanin relieves apple plants from oxidative damage under drought stress. MdWRKY50 RNA-interference transgenic apple plants showed opposite phenotypes. The dimerization of MdWRKY50 with mutated MdWRKY17DP mimicking drought-induced phosphorylation by the mitogen-activated protein kinase kinase 2 (MEK2)-MPK6 cascade, compared with MdWRKY17AP and MdWRKY17, further promoted anthocyanin biosynthesis, suggesting dimerization with MdWRKY17 makes MdWRKY50 more powerful in promoting anthocyanin biosynthesis under drought stress. Taken together, we isolated an entire MEK2-MAPK6-MdWRKY17-MdWRKY50-MdCHS pathway for drought tolerance and generated transgenic apple germplasm with enhanced drought tolerance and higher anthocyanin levels. • MdWRKY50 interacts with the drought positive regulator MdWRKY17. • MdWRKY50 positively regulates apple drought tolerance by promoting anthocyanin level. • MdWRKY50 directly up-regulating rate-limiting anthocyanin biosynthetic gene MdCHS. • MdWRKY50 dimerizes with phosphorylated MdWRKY17 by drought-triggered MEK2-MPK6 cascade to further promotes MdCHS expression. [ABSTRACT FROM AUTHOR]

The rising atmospheric CO 2 concentration has shown to affect plant physiology and chemistry by altering plant primary and secondary metabolisms. Nevertheless, the impacts of elevated CO 2 on plant nutrients and functional components of tea remain largely unknown, which will likely affect tea quality and taste under climate change scenario. Being sources of nutrients and secondary chemicals/metabolites for herbivorous insects, the variation in foliar soluble nutrients and functional components of tea plants resulting from CO 2 enrichment will further affect the herbivorous insects' occurrence and feeding ecology. In this study, the tea aphid, Toxoptera aurantii was selected as the phloem-feeding herbivore to study the effects of elevated CO 2 on foliar soluble nutrients and functional components of tea seedlings, and the population dynamics of T. aurantii. The results indicated that elevated CO 2 enhanced the photosynthetic ability and improved the plant growth of tea seedlings compared with ambient CO 2 , with significant increases in net photosynthetic rate (+20%), intercellular CO 2 concentration (+15.74%), leaf biomass (+15.04%) and root-to-shoot ratio (+8.08%), and significant decreases in stomatal conductance (−5.52%) and transpiration rate (−9.40%) of tea seedlings. Moreover, elevated CO 2 significantly increased the foliar content of soluble sugars (+4.74%), theanine (+3.66%) and polyphenols (+12.01%) and reduced the foliar content of free amino acids (−9.09%) and caffeine (−3.38%) of tea seedlings compared with ambient CO 2. Furthermore, the relative transcript levels of the genes of theanine synthetase (+18.64%), phenylalanine ammonia lyase (+49.50%), s'-adenosine methionine synthetase (+143.03%) and chalcone synthase (+61.86%) were up-regulated, and that of caffeine synthase (−56.91%) was down-regulated for the tea seedlings grown under elevated CO 2 relative to ambient CO 2. In addition, the foliar contents of jasmonic acid (+98.6%) and salicylic acid (+155.6%) also increased for the tea seedlings grown under elevated CO 2 in contrast to ambient CO 2. Also, significant increases in the population abundance of T. aurantii (+4.24%–41.17%) were observed when they fed on tea seedlings grown under elevated CO 2 compared to ambient CO 2. It is presumed that the tea quality and taste will be improved owing to the enhanced foliar soluble nutrients and functional components of tea seedlings under the climate change scenario, especially on account of the rising atmospheric CO 2 concentration, while the climate change may exacerbate the occurrence of tea aphid, T. aurantii, despite the enhanced secondary defensive chemicals manifested by the CO 2 enrichment. The core findings of this article are as follows： 1 Elevated CO2 enhanced the photosynthetic ability and improved the plant growth of tea seedlings compared with ambient CO2. 2 Elevated CO2 significantly affected the foliar contents of soluble nutrients and functional components of tea seedlings, with significant increases in soluble sugars, theanine and polyphenols, and significant decreases in free amino acids and caffeine compared with ambient CO2. 3 The relative transcript levels of the genes of theanine synthetase, phenylalanine ammonia lyase, s'-adenosine methionine synthetase, and chalcone synthase were up-regulated, and that of caffeine synthase was down-regulated for the tea seedlings grown under elevated CO2 relative to ambient CO2. 4 Elevated CO2 significantly affected the foliar contents of tea secondary substances. The foliar contents of jasmonic acid and salicylic acid significantly increased for the tea seedlings grown under elevated CO2 in contrast to ambient CO2. 5 Significant increase was observed in the population abundance of tea aphid on tea seedlings grown under elevated CO2 compared to ambient CO2. [ABSTRACT FROM AUTHOR]

Type III polyketide synthases (PKSs) produce an incredibly diverse group of plant specialized metabolites with medical importance despite their structural simplicity compared with the modular type I and II PKS systems. The type III PKSs use homodimeric proteins to construct the molecular scaffolds of plant polyketides by iterative condensations of starter and extender CoA thioesters. Ever since the structure of chalcone synthase (CHS) was disclosed in 1999, crystallographic and mutational studies of the type III PKSs have explored the intimate structural features of these enzyme reactions, revealing that seemingly minor alterations in the active site can drastically change the catalytic functions and product profiles. New structures described in this review further build on this knowledge, elucidating the detailed catalytic mechanism of enzymes that make curcuminoids, use extender substrates without the canonical CoA activator, and use noncanonical starter substrates, among others. These insights have been critical in identifying structural features that can serve as a platform for enzyme engineering via structure-guided and precursor-directed engineered biosynthesis of plant polyketides. In addition, we describe the unique properties of the recently discovered "second-generation" type III PKSs that catalyzes the one-pot formation of complex molecular scaffolds from three distinct CoA thioesters or from "CoA-free" substrates, which are also providing exciting new opportunities for synthetic biology approaches. Finally, we consider post-type III PKS tailoring enzymes, which can also serve as useful tools for combinatorial biosynthesis of further unnatural novel molecules. Recent progress in the field has led to an exciting time of understanding and manipulating these fascinating enzymes. [ABSTRACT FROM AUTHOR]

• Sodium nitroprusside treatment induced ROS-related protein expression. • Sodium nitroprusside treatment down-regulated proteins involved in lipid peroxidation. • Sodium nitroprusside treatment up-regulated proteins involved in flavonoid synthesis. • Sodium nitroprusside treatment modulated heat shock protein expression. In recent years, nitric oxide (NO) has been considered a plant signaling compound involved in antioxidant systems and flavonoid production enhancement. Nevertheless, its mechanism of action, from the perspective of protein expression, remains largely unknown. In this study, isobaric tags for relative and absolute quantitation (iTRAQ) was employed to investigate NO donor sodium nitroprusside treatment-induced proteomic changes in soybean sprouts. Among the 3033 proteins identified, compared with the control, sodium nitroprusside treatment up- and down-regulated 256 proteins. These proteins were involved in antioxidant system pathways, such as the thioredoxin, superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), glutathione reductase (GR), glutathione S-transferase (GST), ascorbate peroxidase (APX), monodehydroascorbate reductase (MDAR) and lipoxygenase (LOX) pathways, including allene oxide synthase and lipoxygenase. In addition, heat shock proteins (HSPs) and flavonoid biosynthetic proteins, such as cinnamate 4-hydroxylase, chalcone isomerase, chalcone synthase, isoflavone synthase and isoflavone reductase, were also modulated in response to sodium nitroprusside treatment. [ABSTRACT FROM AUTHOR]

Previous studies showed that chalcone synthase (chs) silencing in flax (Linum usitatisimum) induces a signal transduction cascade that leads to extensive modification of plant metabolism. Result presented in the current study, performed on field grown flax plants – (across the whole vegetation period) demonstrates that, in addition to its role in tannin and lignin biosynthesis, the chs gene also participates in the regulation of flavone biosynthesis during plant growth. Apigenin and luteolin glycosides constitute the flavones, the major group of flavonoids in flax. Alterations in their levels correlate with plant growth, peaking at the flower initiation stage. Suppression of chs gene expression causes significant changes in the ratio of flavone constituents at the early stage of flax growth. A significant correlation between flavonoid 3′-hydroxylase (F3′H) gene expression and accumulation of luteolin glycosides has been found, indicating that flavone biosynthesis during flax growth and development is regulated by temporal expression of this gene. The lack of such a correlation between the flavone synthase (FNS) gene and flavone accumulation in the course of plant growth suggests that the main route of flavone biosynthesis is mediated by eriodictyol. This is the first report indicating the ratio of flavone constituents as a potent marker of flax growth stages and temporal expression of F3′H, the key gene of their biosynthesis. • Dynamic changes in flavon content determinate flax development stages. • Apigenin and luteolin ratio influence plant (flax) growth and development. • The activity of flavonoid hydroxylase is crucial for flax flowering and germination. • Developmental regulation is paramount in flavonoids methabolism in flax. [ABSTRACT FROM AUTHOR]