pUGTdb: A comprehensive database of plant UDP-dependent glycosyltransferases

Glycosyltransferases: Pioneering roles in agriculture and medicine

Glycosyltransferases (GTs) belong to a diverse family of enzymes that catalyze the transfer of sugar moieties from activated donor sugars to specific acceptors, thus playing a crucial roles in various biological processes. This review explores the pioneering roles of uridine diphosphate-dependent GTs (UGTs), which use uridine diphosphate glucose as donors. UGTs have also been extensively studied in agricultural and medical fields, emphasizing their potential to revolutionize these sectors. In the agricultural sector, the genetic engineering of UGTs has demonstrate potential in developing crops with enhanced stress tolerance, regulated plant development, and increased resistance to pests and diseases. These advancements not only contribute to sustainable farming practices but also address global food security challenges by facilitating the production of more resilient plant varieties. Furthermore, UGTs facilitate the synthesis of complex carbohydrates and glycoconjugates in plants, which are critical for developing drugs and therapeutic strategies targeting various ailments, including cancer and infectious diseases. Thus, this review explored the functions and synthesis methods of flavonoid glycosides, terpenoid glycosides, and polyketosides in detail. Moreover, owing to the functional diversity of UGTs, numerous research methods were reviewed, and novel, more valuable UGTs will be obtained. In summary, this study synthesizes the current research findings and discusses future perspectives to underscore the transgenic technology and synthetic biological impact of UGTs on agriculture and medicine and bridge the gap between fundamental science and practical applications.

An Effective Computational Strategy for UGTs Catalytic Function Prediction

The GT-B type glycosyltransferases play a crucial post-modification role in synthesizing natural products, such as triterpenoid and steroidal saponins, renowned for their diverse pharmacological activities. Despite phylogenetic analysis aiding in enzyme family classification, distinguishing substrate specificity between triterpenoid and steroidal saponins, with their highly similar cyclic scaffolds, remains a formidable challenge. Our studies unveil the potential transport tunnels for the glycosyl donor and acceptor in PpUGT73CR1, by molecular dynamics simulations. This revelation leads to a plausible substrate transport mechanism, highlighting the regulatory role of the N-terminal domain (NTD) in glycosyl acceptor binding and transport. Inspired by these structural and mechanistic insights, we further analyze the binding pockets of 44 plant-derived UGTs known to glycosylate triterpenes and sterols. Notably, sterol UGTs are found to harbor aromatic and hydrophobic residues with polar residues typically present at the bottom of the active pocket. Drawing inspiration from the substrate binding and product release mechanism revealed through structure-based molecular modeling, we devised a fast sequence-based method for classifying UGTs using the pre-trained ESM2 protein model. This method involved extracting the NTD features of UGTs and performing PCA clustering analysis, enabling accurate identification of enzyme function, and even differentiation of substrate specificity/promiscuity between structurally similar triterpenoid and steroidal substrates, which is further validated by experiments. This work not only deepens our understanding of substrate binding mechanisms but also provides an effective computational protocol for predicting the catalytic function of unknown UGTs.

Research Progress of Genomics Applications in Secondary Metabolites of Medicinal Plants: A Case Study in Safflower

Medicinal plants, recognized as significant natural resources, have gained prominence in response to the increasing global demand for herbal medicines, necessitating the large-scale production of these plants and their derivatives. Medicinal plants are exposed to a variety of internal and external factors that interact to influence the biosynthesis and accumulation of secondary metabolites. With the rapid development of omics technologies such as genomics, transcriptomics, proteomics, and metabolomics, multi-omics technologies have become important tools for revealing the complexity and functionality of organisms. They are conducive to further uncovering the biological activities of secondary metabolites in medicinal plants and clarifying the molecular mechanisms underlying the production of secondary metabolites. Also, artificial intelligence (AI) technology accelerates the comprehensive utilization of high-dimensional datasets and offers transformative potential for multi-omics analysis. However, there is currently no systematic review summarizing the genomic mechanisms of secondary metabolite biosynthesis in medicinal plants. Safflower (Carthamus tinctorius L.) has rich and diverse bioactive flavonoids, among of which Hydroxysafflor yellow A (HSYA) is specific to safflower and emerging as a potential medication for treating a wide range of diseases. Hence, significant progress has been made in the study of safflower as an excellent example for the regulation of secondary metabolites in medicinal plants in recent years. Here, we review the progress on the understanding of the regulation of main secondary metabolites at the multi-omics level, and summarize the influence of various factors on their types and contents, with a particular focus on safflower flavonoids. This review aims to provide a comprehensive insight into the regulatory mechanisms of secondary metabolite biosynthesis from the perspective of genomics.

Identification and Functional Characterization of Two UDP-Glycosyltransferases Involved in Narcissoside Biosynthesis in Anoectochilus roxburghii

Flavonoid rutinosides, a group of bioactive compounds in Anoectochilus roxburghii, contribute greatly to the plant's beneficial effects on human health. However, the glycosylation mechanism of flavonoid rutinosides in A. roxburghii remains unclear. In this study, two efficient and selective glycosyltransferases, AUTG25 and AUTG23, involved in the biosynthesis of narcissoside, a major flavonoid rutinoside in A. roxburghii, were identified through transcriptome analysis and functional validation. AUTG25 could regioselectively catalyze 3-O-glucosylation of isorhamnetin to produce isorhamnetin 3-O-glucoside, while AUTG23 could further catalyze 6"-O-rhamnosylation to generate narcissoside. Both AUTG25 and AUTG23 exhibited high positional and sugar donor selectivities in the catalytic reaction. Homology modeling and site-directed mutagenesis showed that H20, E83, E385, and F143 in AUTG25 and E280, E89, D188, W327, D369, and Y191 in AUTG23 may be critical for their catalytic functions. Transient expression in Nicotiana benthamiana finally confirmed that AUTG25 possesses flavonol-3-O-glucosyltransferase activity and AUTG23 has flavonol-3-O-glucoside (1→6) rhamnosyltransferase activity. This study clarified and provided candidate UDP-dependent glycosyltransferase genes for narcissoside biosynthesis in A. roxburghii.

Recent Advancements in the Biomanufacturing of Crocetin and Crocins: Key Enzymes and Metabolic Engineering

Crocetin and crocins are high-value apocarotenoids recognized for their role as food colorants as well as for their numerous industrial and therapeutic applications. Biotechnological platforms have the potential to replace traditional plant-based extraction of these compounds with a more sustainable approach. This review first introduced the catalytic characteristics of key enzymes involved in the biosynthetic pathway of crocetin and crocins, including carotenoid cleavage dioxygenases, aldehyde dehydrogenases, and uridine diphosphate glycosyltransferases. Next, we highlighted advanced metabolic engineering strategies aimed at enhancing crocetin and crocin production, such as increasing the pool of precursors and cofactors, protein mining and engineering, tuning protein expression, biosensor, genomic integration, and process optimization. Finally, the paper proposed potential strategies and tools associated with further boosting the heterologous production of crocetin and crocins to meet commercial-scale demands.

Biosynthesis of triterpenoids in plants: Pathways, regulation, and biological functions

Plant triterpenoids, a vast and diverse group of natural compounds derived from six isoprene units, exhibit an extensive array of structural diversity and remarkable biological activities. In this review, we update the recent research progress in the catalytic mechanisms underlying triterpene synthesis and summarize the current insights into the biosynthetic pathways and regulatory mechanisms of triterpenoids. We emphasize the biosynthesis of pharmacologically active triterpenoids and the role of triterpenoid synthesis in plant growth, development, defense mechanisms, and plant-microbe interactions. This insight review offers a comprehensive perspective on the applications and future avenues of triterpenoid research.

Insights into functional divergence, catalytic versatility and specificity of small molecule glycosyltransferases

Glycosylation is one of the most fundamental biochemical processes in cells. It plays crucial roles in diversifying plant natural products for structures, bioavailability and bioactivity, and thus, renders the glycosylated compounds valuable as food additives, nutraceuticals and pharmaceuticals. Moreover, glycosylated compounds impact plant growth, development and stress response. Therefore, understanding the biochemical function of the glycosyltransferases (GTs) is crucial to the elucidation of natural product biosynthetic pathways, improving plant traits and development of processes for industrially-important compounds. UDP-dependent glycosyltransferases (UGTs) that belong to the glycosyltransferase family-1 (GT1) and catalyze the transfer of glycosyl moieties from UDP-sugars to various small molecules, are the key players in natural product glycosylation. Recent studies also found the involvement of non-canonical cellulose synthase-like (CesAs) and glycosyl hydrolase (GH) family enzymes in the glycosylation of plant specialized metabolites. Decades of research on GTs provided critical insights into catalytic mechanism, substrate/product specificity and catalytic promiscuity, but biochemical function and physiological roles of GTs in majority of the natural product biosynthetic pathways remain to be understood. It is also important to redefine high-throughput strategies of GT mining to uncover novel biochemical function, considering that GTs are the large superfamily members in plants and other organisms. This review underscores the roles of GTs in small molecule glycosylation, plant development and stress responses, highlighting the catalytic versatility and substrate/product specificity of GTs in shaping plant metabolic diversity, and discusses the emerging strategies for mining of uncharacterized GTs to unravel biochemical and physiological functions and to elucidate natural product biosynthetic pathways.

Multi-omics analysis reveals the role of UGT72 family genes in arbutin biosynthesis in Pyrus and evolution driven by whole genome duplication

The UGT72 gene family encodes proteins that glycosylate phenylpropanoids, and thus contribute to the synthesis of various phenolic substances. However, their functional role and evolutionary history in Pyrus spp. remains poorly understood. Here we explored the evolution, amplification, coding region structural variation, and functional divergence of the UGT72 gene family and its subfamilies. Further, we identified functional genes involved in arbutin synthesis and functionally validated the key genes. 15 UGT72 genes were identified in the complete genome sequence and classified into two subfamilies of Pyrus betulifolia. Significant expansion of the UGT72 gene family occurred after genome duplication in P. betulifolia. 53.33 % of all UGT72 family genes were found to have undergone expansion via WGD/segmental duplication. A noteworthy discovery was that the amplification of functional genes such as PbUGT72B1714 during polyploidization, combined with the loss of vital motifs and variations at important sites within these genes, significantly impacted the diversification of arbutin metabolism. These findings offer novel insights into how gene gains and losses caused by WGDs have contributed to metabolic diversification and evolutionary adaptation in Pyrus, as well as a groundwork for more detailed investigations into the mechanisms of arbutin metabolism.

Multi-omics analysis reveals promiscuous O-glycosyltransferases involved in the diversity of flavonoid glycosides in Periploca forrestii (Apocynaceae)

Flavonoid glycosides are widespread in plants, and are of great interest owing to their diverse biological activities and effectiveness in preventing chronic diseases. Periploca forrestii, a renowned medicinal plant of the Apocynaceae family, contains diverse flavonoid glycosides and is clinically used to treat rheumatoid arthritis and traumatic injuries. However, the mechanisms underlying the biosynthesis of these flavonoid glycosides have not yet been elucidated. In this study, we used widely targeted metabolomics and full-length transcriptome sequencing to identify flavonoid diversity and biosynthetic genes in P. forrestii. A total of 120 flavonoid glycosides, including 21 C-, 96 O-, and 3 C/O-glycosides, were identified and annotated. Based on 24,123 full-length coding sequences, 99 uridine diphosphate sugar-utilizing glycosyltransferases (UGTs) were identified and classified into 14 groups. Biochemical assays revealed that four UGTs exhibited O-glycosyltransferase activity toward apigenin and luteolin. Among them, PfUGT74B4 and PfUGT92A8 were highly promiscuous and exhibited multisite O-glycosylation or consecutive glycosylation activities toward various flavonoid aglycones. These four glycosyltransferases may significantly contribute to the diversity of flavonoid glycosides in P. forrestii. Our findings provide a valuable genetic resource for further studies on P. forrestii and insights into the metabolic engineering of bioactive flavonoid glycosides.

The biosynthesis of asiaticoside and madecassoside reveals tandem duplication-directed evolution of glycoside glycosyltransferases in the Apiales

Certain plant species within the Apiales order accumulate triterpenoid saponins that feature a distinctive glucose-glucose-rhamnose (G-G-R) sugar chain attached at the C-28 position of the pentacyclic triterpene skeleton. Until recently, the genomic basis underlying the biosynthesis and evolution of this sugar chain has remained elusive. In this study, we identified two novel glycoside glycosyltransferases (GGTs) that can sequentially install the sugar chain's second D-glucose and third L-rhamnose during the biosynthesis of asiaticoside and madecassoside, two representative G-G-R sugar chain-containing triterpenoid saponins produced by Centella asiatica. Enzymatic assays revealed the remarkable substrate promiscuity of the two GGTs and the key residues crucial for sugar-donor selectivity of the glucosyltransferase and rhamnosyltransferase. We further identified syntenic tandem gene duplicates of the two GGTs in the Apiaceae and Araliaceae families, suggesting a well-conserved genomic basis underlying sugar chain assembly that likely has evolved in the early ancestors of the Apiales order. Moreover, expression patterns of the two GGTs in pierced leaves of C. asiatica were found to be correlated with the production of asiaticoside and madecassoside, implying their involvement in host defense against herbivores and pathogens. Our work sheds light on the biosynthesis and evolution of complex saponin sugars, paving the way for future engineering of diverse bioactive triterpenoids with unique glycoforms.

Discovery, characterization, and comparative analysis of new UGT72 and UGT84 family glycosyltransferases

Glycosylated derivatives of natural product polyphenols display a spectrum of biological activities, rendering them critical for both nutritional and pharmacological applications. Their enzymatic synthesis by glycosyltransferases is frequently constrained by the limited repertoire of characterized enzyme-catalyzed transformations. Here, we explore the glycosylation capabilities and substrate preferences of newly identified plant uridine diphosphate (UDP)-dependent glycosyltransferases (UGTs) within the UGT72 and UGT84 families, with particular focus on natural polyphenol glycosylation from UDP-glucose. Four UGTs are classified according to their phylogenetic relationships and reaction products, identifying them as biocatalysts for either glucoside (UGT72 enzymes) or glucose ester (UGT84 members) formation from selected phenylpropanoid compounds. Detailed kinetic evaluations expose the unique attributes of these enzymes, including their specific activities and regio-selectivities towards diverse polyphenolic substrates, with product characterizations validating the capacity of UGT84 family members to perform di-O-glycosylation on flavones. Sequence analysis coupled with structural predictions through AlphaFold reveal an unexpected absence of a conserved threonine residue across all four enzymes, a trait previously linked to pentosyltransferases. This comparative analysis broadens the understood substrate specificity range for UGT72 and UGT84 enzymes, enhancing our understanding of their utility in the production of natural phenolic glycosides. The findings from this in-depth characterization provide valuable insights into the functional versatility of UGT-mediated reactions.

An integrative database and its application for plant synthetic biology research

Plant synthetic biology research requires diverse bioparts that facilitate the redesign and construction of new-to-nature biological devices or systems in plants. Limited by few well-characterized bioparts for plant chassis, the development of plant synthetic biology lags behind that of its microbial counterpart. Here, we constructed a web-based Plant Synthetic BioDatabase (PSBD), which currently categorizes 1677 catalytic bioparts and 384 regulatory elements and provides information on 309 species and 850 chemicals. Online bioinformatics tools including local BLAST, chem similarity, phylogenetic analysis, and visual strength are provided to assist with the rational design of genetic circuits for manipulation of gene expression in planta. We demonstrated the utility of the PSBD by functionally characterizing taxadiene synthase 2 and its quantitative regulation in tobacco leaves. More powerful synthetic devices were then assembled to amplify the transcriptional signals, enabling enhanced expression of flavivirus non-structure 1 proteins in plants. The PSBD is expected to be an integrative and user-centered platform that provides a one-stop service for diverse applications in plant synthetic biology research.

Progress in Identification of UDP-Glycosyltransferases for Ginsenoside Biosynthesis

Ginsenosides, the primary pharmacologically active constituents of the Panax genus, have demonstrated a variety of medicinal properties, including anticardiovascular disease, cytotoxic, antiaging, and antidiabetes effects. However, the low concentration of ginsenosides in plants and the challenges associated with their extraction impede the advancement and application of ginsenosides. Heterologous biosynthesis represents a promising strategy for the targeted production of these natural active compounds. As representative triterpenoids, the biosynthetic pathway of the aglycone skeletons of ginsenosides has been successfully decoded. While the sugar moiety is vital for the structural diversity and pharmacological activity of ginsenosides, the mining of uridine diphosphate-dependent glycosyltransferases (UGTs) involved in ginsenoside biosynthesis has attracted a lot of attention and made great progress in recent years. In this paper, we summarize the identification and functional study of UGTs responsible for ginsenoside synthesis in both plants, such as Panax ginseng and Gynostemma pentaphyllum, and microorganisms including Bacillus subtilis and Saccharomyces cerevisiae. The UGT-related microbial cell factories for large-scale ginsenoside production are also mentioned. Additionally, we delve into strategies for UGT mining, particularly potential rapid screening or identification methods, providing insights and prospects. This review provides insights into the study of other unknown glycosyltransferases as candidate genetic elements for the heterologous biosynthesis of rare ginsenosides.

Pour some sugar on me: The diverse functions of phenylpropanoid glycosylation

The phenylpropanoid metabolism is the source of a vast array of specialized metabolites that play diverse functions in plant growth and development and contribute to all aspects of plant interactions with their surrounding environment. These compounds protect plants from damaging ultraviolet radiation and reactive oxygen species, provide mechanical support for the plants to stand upright, and mediate plant-plant and plant-microorganism communications. The enormous metabolic diversity of phenylpropanoids is further expanded by chemical modifications known as "decorative reactions", including hydroxylation, methylation, glycosylation, and acylation. Among these modifications, glycosylation is the major driving force of phenylpropanoid structural diversification, also contributing to the expansion of their properties. Phenylpropanoid glycosylation is catalyzed by regioselective uridine diphosphate (UDP)-dependent glycosyltransferases (UGTs), whereas glycosyl hydrolases known as β-glucosidases are the major players in deglycosylation. In this article, we review how the glycosylation process affects key physicochemical properties of phenylpropanoids, such as molecular stability and solubility, as well as metabolite compartmentalization/storage and biological activity/toxicity. We also summarize the recent knowledge on the functional implications of glycosylation of different classes of phenylpropanoid compounds. A balance of glycosylation/deglycosylation might represent an essential molecular mechanism to regulate phenylpropanoid homeostasis, allowing plants to dynamically respond to diverse environmental signals.

Heterologous gene expression system for the production of hydrolyzable tannin intermediates in herbaceous model plants

Aluminum toxicity is the main factor limiting the elongation of plant roots in acidic soil. The tree species Eucalyptus camaldulensis is considerably more resistant to aluminum than herbaceous model plants and crops. Hydrolyzable tannins (HTs) accumulating in E. camaldulensis roots can bind and detoxify the aluminum taken up by the roots. However, in herbaceous model plants, HTs do not accumulate and the genes involved in the HT biosynthetic pathway are largely unknown. The aim of this study was to establish a method for reconstituting the HT biosynthetic pathway in the HT non-accumulating model plant Nicotiana benthamiana. Four E. camaldulensis enzymes were transiently expressed in N. benthamiana leaves via Agrobacterium tumefaciens-mediated transformation. These enzymes included dehydroquinate dehydratase/shikimate dehydrogenases (EcDQD/SDH2 and EcDQD/SDH3), which catalyze the synthesis of gallic acid, the first intermediate of the HT biosynthetic pathway that branches off from the shikimate pathway. The others were UDP-glycosyltransferases (UGT84A25 and UGT84A26), which catalyze the conversion of gallic acid to β-glucogallin, the second intermediate. The co-expression of the EcDQD/SDHs in transgenic N. benthamiana leaf regions promoted the synthesis of gallic acid. Moreover, the co-expression of the UGT84As in addition to the EcDQD/SDHs resulted in the biosynthesis of β-glucogallin, the universal metabolic precursor of HTs. Thus, we successfully reconstituted a portion of the HT biosynthetic pathway in HT non-accumulating N. benthamiana plants. This heterologous gene expression system will be useful for co-expressing candidate genes involved in downstream reactions in the HT biosynthetic pathway and for clarifying their in planta functions.

Recent advances in triterpenoid pathway elucidation and engineering

Triterpenoids are among the most assorted class of specialized metabolites found in all the taxa of living organisms. Triterpenoids are the leading active ingredients sourced from plant species and are utilized in pharmaceutical and cosmetic industries. The triterpenoid precursor 2,3-oxidosqualene, which is biosynthesized via the mevalonate (MVA) pathway is structurally diversified by the oxidosqualene cyclases (OSCs) and other scaffold-decorating enzymes such as cytochrome P450 monooxygenases (P450s), UDP-glycosyltransferases (UGTs) and acyltransferases (ATs). A majority of the bioactive triterpenoids are harvested from the native hosts using the traditional methods of extraction and occasionally semi-synthesized. These methods of supply are time-consuming and do not often align with sustainability goals. Recent advancements in metabolic engineering and synthetic biology have shown prospects for the green routes of triterpenoid pathway reconstruction in heterologous hosts such as Escherichia coli, Saccharomyces cerevisiae and Nicotiana benthamiana, which appear to be quite promising and might lead to the development of alternative source of triterpenoids. The present review describes the biotechnological strategies used to elucidate complex biosynthetic pathways and to understand their regulation and also discusses how the advances in triterpenoid pathway engineering might aid in the scale-up of triterpenoid production in engineered hosts.

Insights into the missing apiosylation step in flavonoid apiosides biosynthesis of Leguminosae plants

Apiose is a natural pentose containing an unusual branched-chain structure. Apiosides are bioactive natural products widely present in the plant kingdom. However, little is known on the key apiosylation reaction in the biosynthetic pathways of apiosides. In this work, we discover an apiosyltransferase GuApiGT from Glycyrrhiza uralensis. GuApiGT could efficiently catalyze 2″-O-apiosylation of flavonoid glycosides, and exhibits strict selectivity towards UDP-apiose. We further solve the crystal structure of GuApiGT, determine a key sugar-binding motif (RLGSDH) through structural analysis and theoretical calculations, and obtain mutants with altered sugar selectivity through protein engineering. Moreover, we discover 121 candidate apiosyltransferase genes from Leguminosae plants, and identify the functions of 4 enzymes. Finally, we introduce GuApiGT and its upstream genes into Nicotiana benthamiana, and complete de novo biosynthesis of a series of flavonoid apiosides. This work reports an efficient phenolic apiosyltransferase, and reveals mechanisms for its sugar donor selectivity.

Functional characterization of two efficient glycosyltransferases catalysing the formation of rutin from Sophora japonica L

Two efficient and selective glycosyltransferases were identified from Sophora japonica L. Sj3GT could regio-selectively catalyse 3-O-glucosylation of quercetin to produce isoquercitrin, and Sj6''RhaT could further catalyse its 6''-O-rhamnosylation to generate rutin. It is particularly noteworthy that Sj6''RhaT shows high sugar donor selectivity towards UDP-rhamnose.

Proteomics Identified UDP-Glycosyltransferase Family Members as Pro-Viral Factors for Turnip Mosaic Virus Infection in Nicotiana benthamiana

Viruses encounter numerous host factors that facilitate or suppress viral infection. Although some host factors manipulated by viruses were uncovered, we have limited knowledge of the pathways hijacked to promote viral replication and activate host defense responses. Turnip mosaic virus (TuMV) is one of the most prevalent viral pathogens in many regions of the world. Here, we employed an isobaric tag for relative and absolute quantitation (iTRAQ)-based proteomics approach to characterize cellular protein changes in the early stages of infection of Nicotiana benthamiana by wild type and replication-defective TuMV. A total of 225 differentially accumulated proteins (DAPs) were identified (182 increased and 43 decreased). Bioinformatics analysis showed that a few biological pathways were associated with TuMV infection. Four upregulated DAPs belonging to uridine diphosphate-glycosyltransferase (UGT) family members were validated by their mRNA expression profiles and their effects on TuMV infection. NbUGT91C1 or NbUGT74F1 knockdown impaired TuMV replication and increased reactive oxygen species production, whereas overexpression of either promoted TuMV replication. Overall, this comparative proteomics analysis delineates the cellular protein changes during early TuMV infection and provides new insights into the role of UGTs in the context of plant viral infection.

Functional characterization of a Flavonol 3-O-rhamnosyltransferase and two UDP-rhamnose synthases from Hypericum monogynum

Rhamnosyltransferase (RT) and rhamnose synthase (Rhs) are the key enzymes that are responsible for the biosynthesis of rhamnosides and UDP-l-rhamnose (UDP-Rha) in plants, respectively. How to discover such enzymes efficiently for use is still a problem to be solved. Here, we identified HmF3RT, HmRhs1, and HmRhs2 from Hypericum monogynum, which is abundant in flavonol rhamnosides, with the help of a full-length and high throughput transcriptome sequencing platform. HmF3RT could regiospecifically transfer the rhamnose moiety of UDP-Rha onto the 3-OH position of flavonols and has weakly catalytic for UDP-xylose (UDP-Xyl) and UDP-glucose (UDP-Glc). HmF3RT showed well quercetin substrate affinity and high catalytic efficiency with K_m of 5.14 μM and k_cat/K_m of 2.21 × 10⁵ S^-1 M^-1, respectively. Docking, dynamic simulation, and mutagenesis studies revealed that V129, D372, and N373 are critical residues for the activity and sugar donor recognition of HmF3RT, mutant V129A, and V129T greatly enhance the conversion rate of catalytic flavonol glucosides. HmRhs1 and HmRhs2 convert UDP-Glc to UDP-Rha, which could be further used by HmF3RT. The HmF3RT and HmRhs1 co-expressed strain RTS1 could produce quercetin 3-O-rhamnoside (quercitrin), kaempferol 3-O-rhamnoside (afzelin), and myricetin 3-O-rhamnoside (myricitrin) at yields of 85.1, 110.7, and 77.6 mg L^-1, respectively. It would provide a valuable reference for establishing a better and more efficient biocatalyst for preparing bioactive flavonol rhamnosides by identifying HmF3RT and HmRhs.