Genomic insights into the evolution of flavonoid biosynthesis and O-methyltransferase and glucosyltransferase in Chrysanthemum indicum

Molecular characterization and structural basis of a promiscuous glycosyltransferase for β-(1,6) oligoglucoside chain glycosides biosynthesis

Sugar building blocks are crucial for the chemical diversity and biological activity of secondary metabolites. UDP-dependent glycosyltransferases (UGTs) play a pivotal role in the biosynthesis of glycosides in plants by catalysing the attachment of sugar moieties to various bioactive natural products. However, the biosynthesis of oligosaccharide-chain glycosides is often limited by the narrow substrate specificity of UGTs. In this study, we identify a regio-specific β-(1,6) glycosyltransferase, UGT94BY1, from Platycodon grandiflorum. UGT94BY1 exhibits broad substrate promiscuity and can transfer up to three sugar moieties to the C6-OH position of the glucosyl group in various triterpenoids and phenolic glycosides, thereby forming β-(1,6) oligoglucoside chains. To elucidate the mechanism underlying its substrate selectivity, we determined the crystal structure of the UGT94BY1 complex with UDP at a resolution of 2.0 Å. Molecular simulations revealed that a critical structural motif, comprising residues N84-M91, S141-L155 and R179-E186, plays a key role in recognizing sugar acceptors and facilitating chain elongation. Our study unveils a powerful glycosyltransferase for β-(1,6) oligoglucoside chain biosynthesis and highlights key regions involved in substrate recognition and sugar chain extension, providing valuable insights for designing UGTs with customized substrate specificities for biotechnological applications.

A natural variation of flavone synthase II gene enhances flavone accumulation and confers drought adaptation in chrysanthemum

Flavones, a key group of flavonoids, play a significant role in plant adaptation to ecological niches and are valuable medicinal resources. However, the genetic basis underlying their contribution to ecological adaptation remains largely unknown. Here, using metabolite-based genome-wide association study, we report that the natural variation of flavone contents in Chrysanthemum indicum, a wild chrysanthemum and medicinal herb, is mainly determined by a recently duplicated flavone synthase II gene CiFNSII-1.2. Enzymatic assays and molecular dynamics simulations reveal that the key amino acid residues 246th and 261th confer the higher enzymatic activity of CiFNSII-1.2 compared with its ancestral form. These residues act as critical modulators, regulating the flexibility of the external entrance and contributing to the enzyme's improved functionality. Transgenic evaluation demonstrate that CiFNSII-1.2 contributes to flavone accumulation and drought adaptation. Our findings provide insights into the biochemical and evolutionary role of flavones in facilitating adaptation to drought-prone habitats in chrysanthemum.

Genome-wide identification and expression analyses of CYP450 genes in Chrysanthemum indicum

BACKGROUND

The cytochrome P450 superfamily comprises a large group of enzymes crucial for the biosynthesis and metabolism of diverse endogenous and exogenous secondary metabolites in plants. Chrysanthemum, an ornamental genus with considerable medicinal value, is one of the most economically important floricultural crops in the world. The characteristics and functions of CYP450 genes in Chrysanthemum species, however, remain largely unknown.

RESULTS

In this study, we identified 371 CYP450 genes in the Chrysanthemum indicum genome, and categorized them into 8 clans and 44 families through phylogenetic analysis. Gene duplication analysis revealed 111 genes in 47 tandem duplicated clusters and 28 genes in 15 syntenic blocks, suggesting that extensive duplication events may account for the rapid expansion of CiCYP450 superfamily. Additionally, extensive variations in gene structure, motif composition, and cis-regulatory element likely enhance the functional diversity of CiCYP450 proteins. Volatile metabolomic analysis detected a total of 53 distinct volatile organic compounds across the leaves, stems, and roots of C. indicum, with 19 and 16 compounds being exclusive to leaves and stems, respectively. Transcriptomic analysis identified 248 expressed CiCYP450 genes, with 31, 40, and 88 specifically or preferentially expressed in leaves, stems, and roots, respectively. Further correlation analyses between gene expression levels and compound contents highlighted 36 candidate CiCYP450 genes potentially responsible for the biosynthesis of 47 volatile organic compounds.

CONCLUSIONS

The genome-wide analyses of cytochrome P450 superfamily offers essential genomic resources for functional studies of CiCYP450 genes, and is significant for the molecular breeding of Chrysanthemum.

Characterization and Engineering of Multifunctional Glycosyltransferase HtUGT73EW3 for the Highly Efficient Synthesis of Flavonoid Mono/di-O-glycosides

Glycosylation modification is an effective way to improve the solubility, stability, and bioavailability of flavonoids. In this study, a multifunctional flavonoid glycosyltransferase HtUGT73EW3 was identified from Helleborus thibetanus. HtUGT73EW3 exhibited multisite selectivity for 3-, 6-, 7-, 2'-, 3'-, and 4'-OH of flavonoids and showed potent 3/3'-, 3/4'-, and 7/4'-di-O-glycosylation activity. HtUGT73EW3 was able to glycosylate structurally diverse flavonoid aglycones and monoglycosides, and showed efficient glycosylation capacity toward flavonoid structures modified with functional groups at the C-3, C-7, C-8, and C-4' positions. Notably, the mutation of Gln85 to Leu greatly enhanced its catalytic activity, enabling not only the conversion of steroids and terpenoids, but also the improved utilization of UDP-sugars. Furthermore, the Q85L and I94A variants were found to catalyze specific 7,4'- and 3,4'-di-O-glycosylation, respectively. A cost-effective one-pot synthetic reaction was established by coupling AtSuSy and HtUGT73EW3, and the gram-scale synthesis of flavonoid 4'-O-glucoside and 3,4'-/7,4'-di-O-glucoside was achieved by a fed-batch strategy.

Identification and Evaluation of Colour Change in Rosemary and Biluochun Tea Infusions

BACKGROUND

The colour of tea beverages during processing and storage significantly influences their visual quality. However, natural pink tea products are rare. This study investigated the mechanism behind the pink colouration in the mixed infusion of Biluochun (a green tea) and rosemary.

METHODS

Infusions of Biluochun (B), rosemary (R), and their mixture (BR), brewed with boiling water for 10 min, were analysed using liquid chromatography-mass spectrometry (LC-MS). Additionally, the pH value and tea pigment content were measured.

RESULTS

A total of 134 differential metabolites (DEMs) were detected. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that phenylalanine metabolism and tyrosine metabolism pathways were enriched with abundant DEMs. Some amino acids in BR showed degradation. The content of pelargonin, a compound in the anthocyanin biosynthetic pathway, was significantly elevated in BR compared to that in B and R. DEMs related to fatty acid metabolism were at low levels in BR. Other compounds, such as quercetin, caffeate, rosmarinic acid, and isoferulic acid, were also more abundant in BR. No significant differences in pH value and tea pigment content were found among the three infusions.

CONCLUSIONS

A model of pink colouration formation in BR was proposed based on the results of this study. Some substances in Biluochun and rosemary were released during the brewing process. Tyrosine was converted into p-coumaric acid, which further reacted to form pelargonin. Pelargonin, an orange-red (pH ≈ 5.0) anthocyanin, was the primary contributor to the pink colouration in BR. Additionally, p-coumaric acid formed co-pigments such as quercetin, caffeic acid, rosmarinic acid, and isovaleric acid. These co-pigments stabilised or enhanced the colour of pelargonin through co-pigmentation. The findings provide a theoretical basis for optimising tea processing techniques and improving quality control in beverage production.

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

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

Engineering Nicotiana benthamiana for chrysoeriol production using synthetic biology approaches

Flavonoids are prevalent plant secondary metabolites with a broad range of biological activities. Their antioxidant, anti-inflammatory, and anti-cancer activities make flavonoids widely useful in a variety of industries, including the pharmaceutical and health food industries. However, many flavonoids occur at only low concentrations in plants, and they are difficult to synthesize chemically due to their structural complexity. To address these difficulties, new technologies have been employed to enhance the production of flavonoids in vivo. In this study, we used synthetic biology techniques to produce the methylated flavone chrysoeriol in Nicotiana benthamiana leaves. The chrysoeriol biosynthetic pathway consists of eight catalytic steps. However, using an Agrobacterium-mediated transient expression assay to examine the in planta activities of genes of interest, we shortened this pathway to four steps catalyzed by five enzymes. Co-expression of these five enzymes in N. benthamiana leaves resulted in de novo chrysoeriol production. Chrysoeriol production was unaffected by the Agrobacterium cell density used for agroinfiltration and increased over time, peaking at 10 days after infiltration. Chrysoeriol accumulation in agroinfiltrated N. benthamiana leaves was associated with increased antioxidant activity, a typical property of flavones. Taken together, our results demonstrate that synthetic biology represents a practical method for engineering plants to produce substantial amounts of flavonoids and flavonoid derivatives without the need for exogenous substrates.

CGD: a multi-omics database for Chrysanthemum genomic and biological research

Asteraceae is the largest family of dicotyledons and includes Chrysanthemum and Helianthus, two important genera of ornamental plants. The genus Chrysanthemum consists of more than 30 species and contains many economically important ornamental, medicinal, and industrial plants. To more effectively promote Chrysanthemum research, we constructed the CGD, a Chrysanthemum genome database containing a large amount of data and useful tools. The CGD hosts well-assembled reference genome data for six Chrysanthemum species. These genomic data were fully annotated by comparison with various protein and domain data. Transcriptome data for nine different tissues, five flower developmental stages, and five treatments were subsequently added to the CGD. A fully functional 'RNA data' module was designed to provide complete and visual expression profile data. In addition, the CGD also provides many of the latest bioinformatics analysis tools, such as the efficient sgRNA search tool for Chrysanthemum. In conclusion, the CGD provides the latest, richest, and most complete multi-omics resources and powerful tools for Chrysanthemum. Collectively, the CGD will become the central gateway for Chrysanthemum genomics and genetic breeding research and will aid in the study of polyploid evolution.

Tailored biosynthesis of diosmin through reconstitution of the flavonoid pathway in Nicotiana benthamiana

The flavonoid diosmin (diosmetin 7-O-rutinoside) is used as a therapeutic agent for disorders of the blood vessels such as hemorrhoids and varicose veins. Diosmin is commercially produced using semi-synthetic methods involving the oxidation of hesperidin, the most abundant flavonoid in citrus fruits. However, this method produces byproducts that are toxic to the environment, and new sustainable methods to produce diosmin are required. Here, we used a synthetic biology approach to produce diosmin without generating toxic byproducts through reconstitution of the diosmin biosynthetic pathway in Nicotiana benthamiana. We first established that N. benthamiana leaves co-infiltrated with all seven genes in the flavonoid biosynthesis pathway produced high levels of luteolin, a precursor of diosmetin. We then compared the activity of modification enzymes such as methyltransferases, glucosyltransferases, and rhamnosyltransferases in Escherichia coli and in planta and selected genes encoding enzymes with the highest activity for producing diosmetin, diosmetin 7-O-glucoside, and diosmin, respectively. Finally, we reconstructed the entire diosmin biosynthetic pathway using three constructs containing ten genes encoding enzymes in this pathway, from phenylalanine ammonia lyase to rhamnosyltransferase. N. benthamiana leaves transiently co-expressing all these genes yielded 37.7 µg diosmin per gram fresh weight. To our knowledge, this is the first report of diosmin production in a heterologous plant system without the supply of a precursor. Successful production of diosmin in N. benthamiana opens new avenues for producing other commercially important flavonoids using similar platforms.

Asteraceae genome database: a comprehensive platform for Asteraceae genomics

Asteraceae, the largest family of angiosperms, has attracted widespread attention for its exceptional medicinal, horticultural, and ornamental value. However, researches on Asteraceae plants face challenges due to their intricate genetic background. With the continuous advancement of sequencing technology, a vast number of genomes and genetic resources from Asteraceae species have been accumulated. This has spurred a demand for comprehensive genomic analysis within this diverse plant group. To meet this need, we developed the Asteraceae Genomics Database (AGD; http://cbcb.cdutcm.edu.cn/AGD/). The AGD serves as a centralized and systematic resource, empowering researchers in various fields such as gene annotation, gene family analysis, evolutionary biology, and genetic breeding. AGD not only encompasses high-quality genomic sequences, and organelle genome data, but also provides a wide range of analytical tools, including BLAST, JBrowse, SSR Finder, HmmSearch, Heatmap, Primer3, PlantiSMASH, and CRISPRCasFinder. These tools enable users to conveniently query, analyze, and compare genomic information across various Asteraceae species. The establishment of AGD holds great significance in advancing Asteraceae genomics, promoting genetic breeding, and safeguarding biodiversity by providing researchers with a comprehensive and user-friendly genomics resource platform.