1 Introduction

Panax ginseng C.A. Meyer, a perennial herb of Araliaceae, has been used in traditional medicine in East Asia for thousands of years and is regarded as one of the most valuable plant resources. Its root, stem, and leaf contain large amounts of bioactive ingredients that are accountable for its curative effect. Apart from its medicinal purpose, ginseng has become an important economic crop with extensive application in the pharmaceutical, nutraceutical, functional foods, and cosmetic industries. The rising demand for natural health products globally has also augmented the industrial worth of ginseng, which is now a high-priority target for both research by scholars and commercial use (Ratan et al., 2020).

Among the numerous secondary metabolites in ginseng, ginsenosides (triterpenoid saponins) and polysaccharides are the two major classes of pharmacologically active molecules. Ginsenosides exhibit broad spectrum of biological activities from antioxidant, anti-inflammatory, anticancer, neuroprotective, to cardioprotective activity. Ginseng polysaccharides are responsible for immunomodulation, anti-fatigue activity, metabolic control, and gut microbiota modulation. The harmonizing and sometimes complementary effect of these molecules forms the foundation of the pharmacology of ginseng's wide ranging therapeutic use (Hyun et al., 2021).

Clarification of ginsenoside and polysaccharide biosynthetic pathways is central to the interpretation of the molecular and biochemical mechanism of their diversity and accumulation. Information regarding precursor supply, rate-limiting enzymes, glycosylation reactions, and transcriptional control provides a foundation for both fundamental biological research and applied biotechnology. In addition, pathway elucidation allows for the identification of targets for metabolic engineering, synthetic biology, and molecular breeding, offering a means to enhance yield, quality improvement, and designing new ginseng-derived products (Mancusoand Santangelo, 2017).

This study analyzed the research progress in the biosynthetic pathways of ginsenosides and polysaccharides in recent years, summarized the role of precursor metabolic pathways, key enzymes, regulatory factors, and multi-omics methods in revealing the biosynthetic network. Meanwhile, the latest progress in synthetic biology and metabolic engineering strategies for increasing the yield of metabolites was sorted out. By integrating basic research with potential applications, this study emphasizes the significant importance of biosynthesis research in the efficient utilization of ginseng resources, industrial development, and the modernization process of traditional medicines.

2 Biosynthetic Pathways of Ginsenosides in Ginseng

2.1 Precursors and primary metabolic pathways

Biosynthesis of ginsenosides is triggered by the formation of isoprenoid precursors, isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP), via two distinct pathways: the cytosolic mevalonate (MVA) pathway and the plastidic methylerythritol phosphate (MEP) pathway. Both these pathways participate in the biosynthesis of ginsenosides in ginseng roots, while the MEP pathway is more active in leaves. Specifically, the IspD enzyme was identified as a candidate rate-limiting step of the MEP pathway, and its expression level was correlated with ginsenoside accumulation in different tissues (Xue et al., 2019; Yang et al., 2020).

2.2 Key rate-limiting enzymes and their regulation

Key enzymes such as 3-hydroxy-3-methylglutaryl-CoA reductase (HMGR), squalene synthase (SS), squalene epoxidase (SE), and dammarenediol-II synthase (DS) are in charge of controlling the metabolic pathway toward ginsenoside biosynthesis. Environmental conditions, especially blue and red light, can strongly stimulate the expression of these genes, thereby the ginsenoside accumulation in leaves and roots (Di et al., 2023; Liu et al., 2023). Transcription factors (e.g., MYC2, GRAS) and microRNAs likewise control expression of these biosynthetic genes with developmental and environmental signals integrated (Eom and Hyun, 2025; Wang et al., 2025).

2.3 Cytochrome P450 enzymes and glycosyltransferases involved in triterpenoid saponin biosynthesis

Cytochrome P450 monooxygenases (specifically the CYP716A family) introduce hydroxyl moieties onto the triterpene framework, and UDP-glycosyltransferases (UGTs) introduce sugar moieties, creating the structural diversity of ginsenosides. Some UGTs were recently identified and characterized, including UGT94 and UGT73 families, which are responsible for specific glycosylation reactions in both protopanaxadiol (PPD) type and protopanaxatriol (PPT) type ginsenosides (Hou et al., 2022; Zhang et al., 2022; Yuan et al., 2024; Yu et al., 2024). Synthetic biology advances have also enabled these pathways to be recreated in yeast to produce ginsenosides in high yields (Jiang et al., 2022; Li et al., 2022).

2.4 Tissue specificity and secondary metabolic regulation of ginsenoside biosynthesis

Ginsenoside biosynthesis is strongly tissue-specific and developmentally regulated. Gene expression and ginsenoside accumulation vary among roots, leaves, and flowers, of which the most significant ginsenoside storage tissue are the roots (Xue et al., 2019; Di et al., 2023; Liu et al., 2023). Environmental factors (e.g., light quality) and hormone also control gene expression and metabolite accumulation. Transcription factors and microRNAs are also major regulators of the ginsenoside biosynthetic fine-tuning against developmental and environmental cues (Eom and Hyun, 2025; Wang et al., 2025) (Figure 1).

Figure 1 Correlation between physiological indicators and ginsenosides. * Significant at p≤0.05, ** significant at p≤0.01 (Adopted from Di et al., 2023)

3 Biosynthetic Pathways of Ginseng Polysaccharides

3.1 Classification and structural characteristics of ginseng polysaccharides

Ginseng polysaccharides are complex biological macromolecules composed of various monosaccharide units connected by glycosidic linkages. They are mainly classified into neutral and acidic polysaccharides, and their composition differs depending on the plant part (roots, leaves, flowers, berries) and cultivation conditions. Glucose is the predominant monosaccharide, with other sugars such as rhamnose, arabinose, galactose, galacturonic acid, and mannose present in varying proportions. Their structure, including branching patterns and uronic acid content, is directly linked to their biological activities like immunomodulation and antioxidant activities (Guo et al., 2020; Ji et al., 2020; Fang et al., 2022).

3.2 Precursor pathways of monosaccharide activation and polysaccharide synthesis

Biosynthesis of ginseng polysaccharides proceeds with the activation of monosaccharides through metabolic pathways that yield nucleotide sugars (e.g., UDP-glucose, GDP-mannose). Key enzymes such as phosphoglucomutase (PGM), glucose-6-phosphate isomerase (GPI), UTP-glucose-1-phosphate uridylyltransferase (UGP2), fructokinase (scrK), mannose-1-phosphate guanylyltransferase (GMPP), phosphomannomutase (PMM), and UDP-glucose 4-epimerase (GALE) are integral to these processes. These enzymes catalyze the conversion of primary metabolites to activated sugar donors required to synthesize polysaccharides (Fang et al., 2022).

3.3 Roles of polysaccharide synthases and glycosyltransferases in biosynthesis

Polysaccharide synthases and glycosyltransferases catalyze the modification and polymerization of the sugar residues, determining the final structure and function of ginseng polysaccharides. Transcriptome analysis identified 19 candidate enzymes in the synthesis of polysaccharides among which 17 were highly correlated with polysaccharide content. The genes encoding these enzymes are regulated by transcription factors such as MYB, AP2/ERF, bZIP, and NAC that combine the biosynthetic machinery in response to developmental and environmental cues (Fang et al., 2022).

3.4 Relationship between polysaccharide biosynthesis, cell wall metabolism, and storage substances

Ginseng polysaccharide biosynthesis is closely associated with cell wall metabolism since the majority of polysaccharides are structural materials or reserve substances. Roots have the highest proportion of polysaccharides and their monosaccharide compositions, which reflects storage and structural roles. Polysaccharide biosynthesis is regulated dynamically to facilitate cell wall building and reserve carbohydrate deposition, thus enhancing plant growth, stress tolerance, and medicinal property (Guo et al., 2020).

4 Regulatory Mechanisms of Ginsenoside and Polysaccharide Biosynthesis

4.1 Roles of transcription factors in ginsenoside and polysaccharide biosynthesis

Transcription factors (TFs) such as bHLH, WRKY, MYB, NAC, and GRAS are central regulators of ginsenoside and polysaccharide biosynthesis in Panax ginseng. For ginsenosides, bHLH, WRKY, MYB, and ERF TFs have been shown to directly regulate the expression of important biosynthetic genes such as those encoding cytochrome P450s and glycosyltransferases (Wei et al., 2024). For example, PgWRKY4X activates the transcription of squalene epoxidase to promote ginsenoside accumulation (Yao et al., 2020), and PgNAC72 responds to methyl jasmonate (MeJA) and regulates saponin biosynthesis by upregulating dammarenediol synthase (Jiang et al., 2024). GRAS TFs, for example, PgGRAS68-01, also modulate ginsenoside biosynthesis through spatiotemporal gene expression (Liu et al., 2023). In polysaccharide biosynthesis, MYB, AP2/ERF, bZIP, and NAC TFs are linked to the expression of key enzymes involved in sugar metabolism and polymerization, indicating their regulation on polysaccharide structure and content (Fang et al., 2022; Hou et al., 2022) (Figure 2).

Figure 2 Ginsenoside biosynthesis pathway (A) and saponin skeleton biosynthesis gene expression pattern (B) (Adopted from Hou et al., 2022)

4.2 Influence of signal transduction pathways

Environmental stresses, exogenous elicitors, and hormone signals are highly important for ginsenoside and polysaccharide biosynthesis. Methyl jasmonate (MeJA) is a potent elicitor, inducing TFs like NAC and MYB and initiating gene activation in the ginsenoside pathway (Zhang et al., 2021; Jiang et al., 2024). Sucrose is a metabolic signal, inducing ginsenoside biosynthesis by promoting glycolysis and the mevalonate pathway, particularly by activating HMGR (Rui et al., 2022). Environmental elicitors such as fungal elicitors (e.g., Chaetomium globosum) and cerium ions also enhance ginsenoside accumulation by initiating ROS signaling and endogenous MeJA biosynthesis (Yao et al., 2020; Zhang et al., 2021). WRKY TFs also respond to various abiotic stresses (heat, cold, drought), associating stress adaptation with the generation of secondary metabolites (Di et al., 2021). In polysaccharides, similar regulatory networks with hormone- and stress-inducible TFs direct biosynthetic gene expression (Fang et al., 2022).

4.3 Epigenetic regulation

Epigenetic pathways, particularly non-coding RNAs such as microRNAs (miRNAs), are also emerging as important regulators of ginsenoside biosynthesis. miRNAs can target and silence key biosynthetic genes, such as dammarenediol synthase and protopanaxatriol synthase, by regulating triterpenoid biosynthesis (Wei et al., 2024; Eom and Hyun, 2025). Although DNA methylation and histone modification research in ginseng is still limited, these epigenetic changes will definitely influence the chromatin state and transcriptional activity of biosynthetic genes. The integration of multi-omics approaches and genome editing technologies will keep revealing the active epigenetic regulation of ginsenoside and polysaccharide biosynthesis.

5 Application of Multi-Omics in Biosynthetic Pathway Studies

5.1 Transcriptomics revealing key gene expression patterns

Transcriptome analyses, including bulk and single-cell RNA sequencing, have made possible the discovery of genes and gene clusters involved in ginsenoside and polysaccharide biosynthesis. Coexpression network analysis associates gene expression profiles with specific biosynthetic steps, showing tissue-specific and developmental regulation of pathway genes. Time-series transcriptomics also enables determination of regulatory genes and dynamic variation upon environmental or developmental cues (Singh et al., 2022; Wang et al., 2024).

5.2 Proteomics in metabolic pathway elucidation

Proteomics complements transcriptomics by confirming the presence, abundance, and post-translational modifications of enzymes in biosynthetic pathways. Quantitative proteomic profiling is used for the validation of candidate genes, the discovery of enzyme complexes, and the determination of the functional organization of metabolic networks. Integration with transcriptomic data enhances the accuracy of pathway reconstruction and functional annotation (Yang et al., 2021).

5.3 Metabolomics for tracing accumulation patterns of secondary metabolites in ginseng

Metabolomics quantifies ginsenosides, polysaccharides, and intermediates directly, enabling the monitoring of metabolite accumulation in various tissues, developmental stages, and environmental conditions. The alignment of metabolite profiles with gene and protein expression datasets enables the identification of regulatory bottlenecks and key nodes in biosynthetic pathways (Singh et al., 2022).

5.4 Multi-omics integration and construction of regulatory network models

Integrative multi-omics strategies combine transcriptomic, proteomic, and metabolomic data to construct large-scale models of gene-protein-metabolite interactions and regulatory modules. These models give insight into pathway behavior under varying conditions, identify regulatory modules, and enable predictions regarding gene-protein-metabolite interaction networks (GPMN). Advanced computational capabilities and unsupervised integration techniques such as correlation-based network analysis and machine learning facilitate the discovery of novel pathway components and regulatory interactions, giving a global view of specialized metabolism in ginseng (Singh et al., 2022; Wieder et al., 2024).

6 Advances in Synthetic Biology and Metabolic Engineering

6.1 Establishment of microbial heterologous expression systems

Microbial hosts such as Saccharomyces cerevisiae (yeast) and Escherichia coli have also been genetically modified to express plant biosynthetic pathways, whereby complex isoprenoids and ginsenosides are synthesized. These systems are blessed with well-characterized genetics, ease of manipulation, and scalable fermentations and therefore most appropriate for industrial application. Non-conventional yeasts and bacteria are also being explored because they are metabolically flexible and capable of utilizing various substrates (Navale et al., 2021; Patra et al., 2021).

6.2 Optimization of metabolic pathways and strategies for high-yield synthesis

Optimization techniques are modular pathway design, metabolic flux balance, and dynamic control systems. SynBio tools support the reconstruction of multi-gene pathways across various species, and computational modeling and machine learning guide pathway design and predict bottlenecks. Techniques such as chromosomal integration, enzyme engineering, and compartmentalization further optimize yield and stability (Lee et al., 2018; Choi et al., 2019; García-Granados et al., 2019).

6.3 Application of CRISPR/Cas gene editing in pathway regulation

CRISPR/Cas systems have revolutionized metabolic engineering with the potential to introduce precise, multiplexed genome modifications. CRISPR/Cas9 is used in bacteria and yeast for specific gene knockouts, pathway streamlining, and insertion of large biosynthetic gene clusters (Patra et al., 2021; Lv et al., 2022). This not only accelerates strain development but also allows gene expression fine-tuning for improved metabolite yields.

6.4 Industrial synthesis: prospects and challenges

Industrial production of ginsenosides is constrained by metabolic load, pathway bottlenecks, and demand for robust, high-yielding strains. These limitations are being overcome by recent advances in systems metabolic engineering, genome-scale modeling, and high cell-density fermentation. Better genetic stability, scalability of process, and cost-effectiveness are yet required for industrial applications on a large scale (Navale et al., 2021; Han et al., 2023).

7 Current Research Status and Limitations

7.1 Unresolved aspects in pathway elucidation

While significant progress has been achieved in the identification of key enzymes and intermediates of ginsenoside and polysaccharide biosynthesis, several important points remain unresolved. For ginsenosides, for example, the complete set of cytochrome P450s responsible for specific hydroxylation and oxidation reactions is yet to be completely delineated, and tissue- and development stage-specific accumulation patterns are not clearly understood. Similarly, for ginseng polysaccharides, the precise mechanisms of polymerization, modes of branching, and their regulation by upstream sugar nucleotide pools must be clarified. Limited data on subcellular localization and metabolite transport also hinders a thorough understanding of biosynthetic fluxes (Velte and Stawinoga, 2016).

7.2 Insufficient systematic identification of functional genes and enzymes

Although transcriptomic and proteomic studies provided numerous candidate genes, there is no comprehensive functionally validated set of enzymes and regulator proteins. Many predicted genes are uncharacterized due to heterologous expression difficulties, redundancy among enzyme family members, or very low in planta expression. Moreover, only on the rarest of occasions have been transcription factors and post-translational modifiers that regulate pathway activity identified, precluding systematic reconstruction of the regulatory network (Yousef, 2023).

7.3 Bottlenecks in translating basic research into applied outcomes

Translational applications, for instance, metabolic engineering, synthetic biology, large-scale production of high-value ginsenosides or polysaccharides, are presently still limited by incomplete pathway information. Low efficiency of heterologous expression systems, low pathway flux, uncontrolled stereochemistry, and the inability to reproduce tissue-specific or developmental regulation ex vivo are present bottlenecks. In addition, integration of multi-omics information into predictive models to optimize cultivation or bioengineer is in its infancy. Filling these gaps is required in order to move towards precision-guided manufacturing and industrial utilization (Shin, 2023).

8 Concluding Remarks

There have been significant developments in recent years toward elucidating the Panax ginseng biosynthetic pathways of ginsenosides and polysaccharides. These include the identification and functional characterization of ginsenoside formation rate-limiting enzymes, cytochrome P450s, and glycosyltransferases, and polysaccharide synthases and the precursor activation pathways for polysaccharide synthesis. Multidisciplinary omics approaches, including transcriptomics, proteomics, and metabolomics, provided new insights into tissue-specific profiles of accumulation, regulatory networks, and environmental or developmental control of metabolite biosynthesis. The combined results have complemented our understanding of the molecular process underlying the generation and complexity of ginseng bioactive compounds.

Understanding of ginsenoside and polysaccharide biosynthetic pathways has direct applications in the development and sustainable utilization of ginseng resources. Discovery of key genes, enzymes, and regulatory systems allows for specific metabolic engineering, uses of synthetic biology, and molecular breeding programs to enhance the yield and quality of metabolites. Furthermore, knowledge from pathway studies guides the standardization of ginseng products to give reproducible quality, efficacy, and safety for both traditional medicine and commercial purposes.

Future research will likely focus on integrating multi-omics information to develop precise regulatory networks for ginsenoside and polysaccharide biosynthesis. Genome editing, CRISPR/Cas-directed pathway remodeling, and synthetic biology promise much for the targeted overexpression of active metabolites. Sustainable industrialization strategies like bioreactor-based production and optimized cultivation practices will also be crucial to meet global demand while preserving natural ginseng resources. In total, long-term interdisciplinary research will drive both fundamental knowledge and practical applications, bridging the divide between ginseng biosynthetic research and industrial and therapeutic uses.

Acknowledgments

The authors sincerely thank the research team for their full assistance during the course of the study and their strong support in the compilation of relevant materials. They also extend heartfelt gratitude to the two anonymous reviewers, whose constructive suggestions provided valuable guidance for further improving this manuscript.

Conflict of Interest Disclosure

The authors affirm that this research was conducted without any commercial or financial relationships that could be construed as a potential conflict of interest.

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