1 Introduction

Leonurus japonicus var. tongzi is a variant of the Leonurus genus in the Lamiaceae family, primarily distributed in Guizhou, Sichuan, and other regions of China. It exhibits notable therapeutic efficacy and strong environmental adaptability, making it an important component of local traditional medicine systems (Ou et al., 2025). As a commonly used gynecological herb, its medicinal applications can be traced back to ancient texts such as the Shennong Ben Cao Jing and the Compendium of Materia Medica, where it was traditionally prescribed for irregular menstruation, postpartum abdominal pain, and threatened miscarriage. Modern studies have further confirmed its efficacy in promoting uterine contraction, improving blood circulation, and exerting anti-inflammatory and analgesic effects (Miao et al., 2019). In addition, L. japonicus var. tongzi possesses heat-clearing, detoxifying, anti-swelling, and diuretic properties. In recent years, its potential in treating cardiovascular and cerebrovascular diseases and modulating immune function has gained increasing attention. Compared with common Leonurus japonicus, this variety shows unique characteristics and application value in terms of bioactive compound accumulation, ecological adaptability, and localized medicinal use experience.

The herb contains a range of bioactive molecules, including alkaloids, flavonoids, and polysaccharides, that all contribute to confering to it therapeutic activity. These types of compounds possess anti-inflammatory, antioxidant, immunomodulatory, and vasoprotective activities that are behind its typical medicinal use. Current genomics provides robust capabilities to explore biosynthesis and regulation of active constituents of medicinal plants. Genomic approaches, combined with transcriptomics, proteomics, and metabolomics, enable systematical identification of functional genes, regulatory networks, and enzyme pathways and supply mechanistic data on biosynthesis of bioactive metabolites (Miao et al., 2019; Shi et al., 2022).

This study extensively summarizes the recent developments in genomic studies of L. japonicus var. tongzi focusing on identification of biosynthetic pathways and regulation mechanism of its major bioactive metabolites. Integrating genomics with multi-omics data, it aims to yield a complete view of metabolite biosynthesis towards resource development, metabolic engineering, and rationalization of traditional Chinese medicine.

2 Genomic Research Progress of Leonurus japonicus var. tongzi

2.1 Genome sequencing and assembly status

A chromosome-level genome assembly at high resolution of L. japonicus was achieved with ONT long read and Hi-C combined. The assembly length is 489.34 Mb, has ten anchored chromosomes, a scaffold N50 of 50.86 Mb, and a contig N50 of 7.27 Mb. Assembly quality is guaranteed by having a BUSCO score of 99.2%, and 22,531 protein-coding genes are annotated, which offers a solid foundation for functional and comparative genomics (Figure 1) (Yang et al., 2022; Li et al., 2023; Wang et al., 2024).

Figure 1 Genomic analysis of L. japonicus and L. sibiricus. (A) Overview of the genome assemblies and annotations of L. japonicus and L. sibiricus; (B) Collinearity analysis between L. japonicus and L. sibiricus chromosomes (Adopted from Li et al., 2023)

2.2 Transcriptome analysis and functional gene identification

Transcriptomic information from various tissues has allowed protein-coding gene annotation and description of significant enzymes involved in special metabolism, such as diterpenoid and alkaloid biosynthesis. Multi-omics integration revealed the roles of arginine decarboxylase (ADC), uridine diphosphate glucosyltransferase (UGT), and serine carboxypeptidase-like (SCPL) acyltransferase in leonurine biosynthesis, with geneset-specific clusters and L. japonicus regulatory networks (Wang et al., 2022; Li et al., 2023; Chen et al., 2024).

2.3 Gene family expansion and evolutionary characteristics

Comparative phylogenomic analysis revealed 58 expanded gene families in L. japonicus, particularly those related to specialized metabolism, e.g., diterpenoid biosynthesis. Gene duplication and neofunctionalization events, particularly within the UGT-SCPL gene cluster, have been involved in the special accumulation of leonurine in L. japonicus compared to related taxa (Wang et al., 2024).

2.4 Comparative genomics with other medicinal plants

Comparative genomic comparison of L. japonicus and L. sibiricus revealed differences in genome structure and gene content, such as biosynthetic biosynthetic pathways of leonurine. Syntenic and phylogenetic comparison with other medicinal plants and Lamiaceae family members revealed whole-genome duplication histories and evolutionary orientations of biosynthetic gene clusters underpinning the intriguing metabolic potential of L. japonicus (Yang et al., 2022; Chen et al., 2024).

3 Elucidation of Metabolic Pathways of Bioactive Components

3.1 Biosynthetic pathways and key functional enzymes of alkaloids

Leonurine and stachydrine are significant alkaloids in L. japonicus. The leonurine biosynthesis was disclosed by multi-omics approaches, and arginine decarboxylase (ADC), uridine diphosphate glucosyltransferase (UGT), and serine carboxypeptidase-like (SCPL) acyltransferase were confirmed to be crucial enzymes. The UGT-SCPL gene cluster, which is developed through gene duplication and neofunctionalization, participates in leonurine accumulation in L. japonicus. Whereas the metabolic pathway of stachydrine is thoroughly explained, its anabolic (biosynthetic) pathway is inadequately reported and a subject of continued study (Li et al., 2023; He et al., 2024; Ou et al., 2025).

3.2 Biosynthesis and regulatory mechanisms of flavonoids

Flavonols such as luteolin and luteolin-7-methylether are major pharmacological components of L. japonicus. They inhibit aromatase (CYP19) expression and estrogen biosynthesis by regulating the MAPK/CREB pathway. Transcriptomics analysis revealed that flavonoids regulate gene expression of estrogen biosynthesis and inflammation, which is the molecular basis of their therapeutic activities (Du et al., 2020; Shi et al., 2024).

3.3 Biosynthetic pathways of polysaccharides and their precursors

Even though the complete biosynthetic routes of the polysaccharides in L. japonicus are not yet as well described as in the case of alkaloids and flavonoids, genomic resources and transcriptomics now enable identification of candidate genes for the biosynthesis of the polysaccharides. These include glycosyltransferase-coding genes and precursor sugar-producing enzyme-coding genes that are overrepresented in specialized metabolic gene families (Wang et al., 2024).

3.4 Formation and characteristics of unique or enriched metabolites

L. japonicus var. tongzi is remarkable due to the accumulation of leonurine, as a consequence of neofunctionalization and gene cluster expansion of the UGT-SCPL genes. Furthermore, labdane diterpenoids and stachydrine analogues are abundant in this taxon, whose localization within glandular trichomes and quantitation in diverse plant sources were recently characterized. These new metabolites explain the plant's pharmacological profile and ecological acclimation (Figure 2) (Xiao et al., 2017; Lee et al., 2020; Zhang et al., 2025) .

Figure 2 Metabolic Pathways of Active Compounds and Pharmacological Properties of Leonurus japonicus var. Tongzi (Adopted from Lee et al., 2020)

4 Research Strategies Integrating Genomics and Multi-omics

4.1 Transcriptomic approaches revealing expression patterns

Transcriptome profiling by RNA sequencing of various tissues has enabled the identification and annotation of more than 22 000 protein-coding genes in L. japonicus. The research has provided expression profiles of significant genes, including biosynthetic genes for the specialized metabolites diterpenoids and alkaloids. For example, transcriptomics found arginine decarboxylase (ADC), uridine diphosphate glucosyltransferase (UGT), and serine carboxypeptidase-like (SCPL) acyltransferase genes are vital for biosynthesis of leonurine, and also transcription factors playing roles in ecological utilization and medicinals (Li et al., 2023; Chen et al., 2024).

4.2 Applications of proteomics in functional enzyme identification

Proteomic methods, alongside enzyme assays, have authenticated the role of catalysts in diterpenoids' and leonurine's biosynthesis pathways. Functional analysis of diterpene synthases, for instance, has identified enzymatic reactions leading to the biosynthesis of characteristic spiro-labdane diterpenoids in L. japonicus (Li et al., 2023).

4.3 Contributions of metabolomics to studying metabolite accumulation

Metabolomics, in recent years due to the potency of mass spectrometry, has made large-scale profiling of isomers and signature markers between hundreds of metabolites possible. Studies have identified unique differences in the accumulation of metabolites between plant organs, areas, and states, thus making quality control as well as resource utilization feasible (Garran et al., 2019; Zhang et al., 2025).

4.4 Multi-omics integration and metabolic regulatory network models

The integration of genomics, transcriptomics, proteomics, and metabolomics made it possible to create metabolic regulatory networks. Such models indicate how enzyme activity, gene expression, and metabolite accumulation are regulated, permitting system-level understanding of biosynthesis and regulation of bioactive compounds in L. japonicus (Li et al., 2023; Wang et al., 2024).

5 Regulatory Mechanisms of Metabolism

5.1 Roles of transcription factors in metabolic pathway regulations

Transcription factors such as MYB, bHLH, and WRKY have been reported to be vital in plant secondary metabolism regulation, including alkaloid, flavonoid, and terpenoid biosynthesis. In L. japonicus, from transcriptomic and multi-omics, biosynthetic gene clusters and regulatory modules for the biosynthesis of some of the major metabolites such as leonurine and stachydrine have been identified. Although direct functional investigation on some of the MYB, bHLH, or WRKY factors in L. While functional studies in M. japonicus are in their infancy, the families play a part in the regulation of metabolic gene expression, as indicated by coordinated biosynthetic gene expression and amplification of gene clusters for specialized metabolism (Li et al., 2023; Wang et al., 2024). In addition, the MAPK signal pathway, being transcription factor-controllable, was discovered to regulate the expression of genes involved in estrogen biosynthesis and other metabolism (Du et al., 2020; Shi et al., 2024).

5.2 Signal regulation by plant hormones and environmental factors

Plant hormones and the environment influence L. japonicus metabolic pathways tremendously. For example, MAPK and PI3K/AKT/NF-κB signaling pathways are involved in the modulation of estrogen biosynthesis, anti-inflammation reactions, and even wound healing, generally under hormonal or environmental stimuli (Shi et al., 2022; Ou et al., 2025). Chemical entities like luteolin and analogs influence such pathways, regulating the expression of such major metabolic enzymes and mediators. In addition, environmental stresses such as pathogen infection or oxidative stress trigger signal cascades that alter the accumulation of secondary metabolites, the sources of plant adaptability and medicinal value (Park et al., 2022; He et al., 2024).

5.3 Influence of epigenetics

New findings show that epigenetic processes—DNA methylation, histone modification, and non-coding RNAs—are engaged in gene expression and metabolite accumulation regulation in medicinal plants. For L. japonicus, microRNA (miR-19a-3p) regulated apoptosis-related pathways, which influenced the anti-cancer activity of the plant through PTEN/PI3K/AKT pathway modulation (Park et al., 2022). Immediate research regarding DNA methylation and histone modification for L. is unavailable. When japonicus are not available, these mechanisms are likely to be involved in the dynamic regulation of biosynthetic gene clusters and tissue-specific bioactive compound accumulation, as observed in other medicinal crops.

6 Prospects of Synthetic Biology and Metabolic Engineering Applications

6.1 Construction and optimization of microbial heterologous expression platforms

Identification of biosynthetic key genes (e.g., ADC, UGT, and SCPL for leonurine) makes reconstruction of plant metabolic pathways in microbial hosts possible. Large-scale production and functional validation of plant metabolites are possible through heterologous expression in bacteria or yeast. The use of strong microbial chassis, platform vector modularity, and genetically encoded biosensors also enhances the efficiency and precision of these platforms to produce valuable compounds in extranatural plant environments (Calero and Nikel, 2018; Li et al., 2023; Yu et al., 2023).

6.2 Application of gene editing technologies in functional gene validation and metabolic improvement

CRISPR/Cas9 and other gene editing technologies are more and more being employed to validate gene function and modulate metabolic pathways. The technologies enable efficient management of biosynthetic genes, pathway regulators, and gene clusters in microbial platforms as well as even in L. japonicus itself. Multigene editing and synthetic gene circuits allow coordinated regulation of complex pathways, promoting yield and enabling the synthesis of new derivatives (Lee et al., 2018; Zhu et al., 2019; Lv et al., 2022; Kwan et al., 2023).

6.3 Pathway optimization and strategies for efficient biosynthesis

Pathway optimization is to equilibrate gene expression, enzyme activity, and metabolic flux. Strategies include promoter engineering, enzyme engineering, dynamic regulation, and computational modeling for pathway performance prediction and optimization. Multigene stacking and assembly module systems can allow flexible reconstruction and fine-tuning of entire biosynthetic networks to optimize the yields of target metabolites (Zhu et al., 2019; Li et al., 2022; Lv et al., 2022; Kwan et al., 2023).

6.4 Challenges and opportunities in industrial development

The main challenges include pathway elucidation incompleteness, host cell metabolic burden, and scalable, efficient production systems needed. The opportunities are the exploration of systems metabolic engineering, integration of omics data, and development of new microbial chassis for industrial bioproduction. Future advances in synthetic biology tools, gene cluster discovery, and regulatory network modeling will propel translation of L. japonicus metabolic engineering from laboratory to industry (Choi et al., 2019; García-Granados et al., 2019; Ng et al., 2020; Bharadwaj et al., 2021).

7 Research Challenges and Limitations

7.1 Unresolved key steps in metabolic pathway elucidation

Despite significant progress in the elucidation of alkaloid, flavonoid, polysaccharide, and other specialized metabolite biosynthesis pathways, many of the crucial enzymatic steps remain poorly characterized. The comprehensive catalytic mechanisms, substrate specificity, and tissue- or developmental-stage-selective expression of such critical enzymes remain largely unknown, preventing full understanding of metabolite formation (Wei et al., 2023).

7.2 Insufficient systematic identification of functional genes and regulatory factors

Although transcriptomic and genomic studies have discovered large numbers of candidate genes, systematic verification of functional genes and regulatory factors such as transcriptional factors and signaling components is not yet sufficient. It limits the possibilities to build full regulatory networks for the biosynthesis of active compounds in L. japonicus (Lee et al., 2020).

7.3 Technical limitations and constraints in experimental systems

Technical issues, such as low-quality or availability of high-quality reference genomes, inefficient transformation, and variable in vivo or in vitro systems, make functional analyses difficult. Furthermore, the nature of metabolite profiling and multi-omics integration challenges pathway resolution and reproducibility (Birchfield and McIntosh, 2020; Zhang et al., 2023).

7.4 Gap between basic research and applied translation

Though basic research has enhanced understanding of biosynthesis of active metabolites, implementation of such insights into practical practices-e.g., metabolic engineering, high-yield large-scale cultivation, or mass production—remains to be fully achieved. Needed to promote laboratory-to-industry translation are enhanced gene function validation, pathway optimization, and scalable manufacturing technologies.

8 Concluding Remarks

Over the past few years, notable progress has been made in elucidating the biosynthetic pathways of the valuable bioactive metabolites of L. japonicus var. tongzi, including alkaloids, flavonoids, polysaccharides, and other special metabolites. Genomics sequencing, transcriptomics, proteomics, and metabolomics jointly disclosed a huge number of functional genes, biosynthetic enzymes, and regulatory factors, and it is easier nowadays to imagine the complex networks of active compound biosynthesis. These studies have enhanced tissue-specific expression, pathway regulation, and metabolite accumulation profile knowledge and offer a foundation for basic and applied research.

Genomic data has been identified to be central for the facilitation of sustainable exploitation of L. japonicus var. tongzi resources. They enable the identification of useful functional genes, contribute to targeted breeding or metabolic engineering projects, and facilitate precision agriculture for improved active compound production. Integration of genomic data with multi-omics tools maximizes the molecular mechanism-to-application link and offers new opportunities for resource maximization and medicinal product development.

The combination of synthetic biology and multi-omics approaches will likely encompass more understanding and rational regulation of metabolite biosynthesis. Network-scale investigation, pathway reconstruction, and heterologous expression systems might possibly ensure high-efficiency production of valuable compounds, including research using laboratory setting and application to industry. These approaches will not merely enhance present knowledge on L. japonicus var. tongzi metabolism but also accelerate its modernization, sustainable utilization, and its application in evidence-based medicine.

Acknowledgments

The authors express gratitude to the research team for their assistance and cooperation during the research process, as well as their support in data organization. At the same time, we would also like to express our gratitude to the two anonymous review experts for their constructive opinions and suggestions, which have provided useful references for the revision and improvement of the 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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