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Biosynthesis and Regulatory Mechanism of Secondary Metabolites in Medicinal Plants: 2nd Edition

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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: 20 July 2025 | Viewed by 9950

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Prof. Dr. Shanfa Lu

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Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
Interests: medicinal plant; bioactive compound; biosynthetic pathway; noncoding RNA; transcription factor; genome; transcriptome; metabolome
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Dear Colleagues,

Medicinal plants are an important resource for humans. However, compared with model systems and crops, the number of studies on medicinal plants has fallen far behind the amount of research conducted on other topics. Recently, with the increase in demand for medicinal plants and the development and application of high-throughput technologies, the research field of medicinal plants has rapidly expanded. Significant progress has been made in the genomics, epigenomics, transcriptomics and metabolomics of medicinal plants. Numerous studies have contributed to the biosynthetic pathway of secondary metabolites, genes encoding key enzymes of the pathway, and the regulatory mechanisms of secondary metabolism. This enables the production of secondary metabolites through metabolic engineering and synthetic biology. Moreover, novel technologies and strategies are being developed and applied to this research field. This open access Special Issue of IJMS is devoted to publishing original research and review articles on medicinal plant studies, highlighting the recent advances in the biosynthesis and regulatory mechanisms of secondary metabolites, particularly the significant discoveries from intensive studies, and the development and application of novel technologies. This Special Issue aims to provide an accessible collection of research that shares the latest innovative results from the research field of medicinal plants to aid further studies on secondary metabolism, medicinal plant improvement, and the production of functionally important secondary metabolites.

Topics of this Special Issue include, but are not limited to, the following:

The genomics, epigenomics, transcriptomics and metabolomics of medicinal plants;
The biosynthetic pathway of secondary metabolites;
Key enzyme genes involved in the biosynthesis of secondary metabolites;
The epigenetic regulation of secondary metabolism: microRNA, long noncoding RNA, DNA methylation, RNA methylation, etc.;
Transcription factor and regulatory network in medicinal plants;
The metabolic engineering and synthetic biology of secondary metabolites;
The application of high-throughput sequencing technologies;
Databases associated with the biosynthesis and regulation of secondary metabolites;
Novel technologies and strategies for secondary metabolism studies.

Prof. Dr. Shanfa Lu
Guest Editor

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Keywords

biosynthetic pathway
epigenetic regulation
high-throughput sequencing
medicinal plant
metabolic engineering
omics
regulatory mechanism
secondary metabolite
synthetic biology
transcription factor

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Biosynthesis and Regulatory Mechanism of Secondary Metabolites in Medicinal Plants in International Journal of Molecular Sciences (13 articles)

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19 pages, 4606 KiB

Open AccessArticle

Genome-Wide Identification and Functional Analysis of the Norcoclaurine Synthase Gene Family in Aristolochia contorta

by Yayun Xu, Sixuan Zhang, Fanqi Meng, Wenjing Liang, Yunliang Peng, Butuo Zhu, Lili Niu, Chunling Wang, Caili Li and Shanfa Lu

Int. J. Mol. Sci. 2025, 26(9), 4314; https://doi.org/10.3390/ijms26094314 - 1 May 2025

Viewed by 124

Abstract

Aristolochia contorta Bunge has been widely used as traditional Chinese medicine materials. However, its utility faces a great challenge due to the presence of aristolochic acids (AAs), a class of benzylisoquinoline alkaloid (BIA) derivatives. The first step in BIA skeleton formation is catalysis by norcoclaurine synthase (NCS). To gain knowledge of BIA and AA biosynthesis in A. contorta, genome-wide characterizations of NCS genes were carried out. This resulted in the identification of 15 A. contorta NCSs, namely, AcNCS1–AcNCS15. The AcNCS1–AcNCS8 proteins contained one catalytic domain, whereas the AcNCS9–AcNCS15 proteins had two. Phylogenetic analysis shows that AcNCS proteins can be classified into two clades. Gene expression analysis shows that five AcNCSs, including AcNCS2, AcNCS4, AcNCS5, AcNCS14, and AcNCS15, exhibited relatively high expression in roots and flowers, where norcoclaurine accumulated. An enzyme catalytic activity assay shows that all five of the AcNCSs can catalyze norcoclaurine formation with AcNCS14 and AcNCS15, exhibiting higher catalytic efficiency. Precolumn derivatization analysis shows that the formed norcoclaurine included (S)- and (R)-norcoclaurine, with more (S)-configuration. The results provide useful information for further understanding BIA and AA biosynthesis in A. contorta and for AA elimination and bioactive compound improvement in AA-containing medicinal materials. Full article

(This article belongs to the Special Issue Biosynthesis and Regulatory Mechanism of Secondary Metabolites in Medicinal Plants: 2nd Edition)

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18 pages, 10646 KiB

Open AccessArticle

Overexpression of the Glycyrrhiza uralensis Phenylalanine Ammonia-Lyase Gene GuPAL1 Promotes Flavonoid Accumulation in Arabidopsis thaliana

by Xifeng Chen, Chao Jiang, Mengqian Long, Xiangxiang Hu, Shouhao Xu, Haotong Huo, Ruixin Shi, Qing Xu, Shuangquan Xie, Zihan Li, Haitao Shen, Fei Wang, Guanghui Xiao, Quanliang Xie, Shandang Shi and Hongbin Li

Int. J. Mol. Sci. 2025, 26(9), 4073; https://doi.org/10.3390/ijms26094073 - 25 Apr 2025

Viewed by 191

Abstract

Phenylalanine ammonia-lyase (PAL) serves as a pivotal regulatory enzyme at the initial branching point of the phenylpropanoid pathway, exerting a profound influence on downstream reactions essential for flavonoid biosynthesis. Glycyrrhiza species are important medicinal plants and provide plenty of roots as raw materials for further utilization, with the components of glycyrrhizic acid and flavonoids as two major active ingredients. However, functional studies of the PAL genes in the medicinal Glycyrrhiza species remain limited. In this study, we identified seven PAL family genes from each of the three medicinal Glycyrrhiza species, Glycyrrhiza uralensis Fisch., G. inflata Bat., and G. glabra L., and comprehensively analyzed their phylogenetic relationships, gene structures, motif distributions, and promoter cis-elements. Gene expression profiling revealed that PAL1 is highly expressed in roots and significantly induced by drought and salt stresses. We further selected G. uralensis GuPAL1 for functional investigation in Arabidopsis. GuPAL1-overexpression lines (GuPAL1-OE) demonstrated significant enhancements in plant growth, flavonoid accumulation, and hormone levels in Arabidopsis thaliana. Conversely, the Atpal1 mutant plants displayed marked reductions in these traits, while the transgenic lines of GuPAL1-OE in the Atpal1 mutant (Atpal1/GuPAL1) recovered to the normal phenotypes similar to wild type (WT). Transcriptomic analysis of the GuPAL1-OE plants compared to WT demonstrated that several key genes in the phenylpropanoid and flavonoid metabolic pathways (4CL, CCoAOMT, CAD, POD, F3H, FLS) were significantly enriched, suggesting that GuPAL1 may promote plant growth and flavonoid biosynthesis by regulating diverse cellular functions, metabolic pathways, and associated gene expressions. These findings highlight the functional importance of GuPAL1 in flavonoid biosynthesis, and provide valuable insights into the molecular mechanisms underlying the medicinal properties of Glycyrrhiza species. Full article

(This article belongs to the Special Issue Biosynthesis and Regulatory Mechanism of Secondary Metabolites in Medicinal Plants: 2nd Edition)

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20 pages, 4545 KiB

Open AccessArticle

A Comprehensive Analysis of Transcriptomics and Metabolomics Reveals Key Genes Involved in Terpenes Biosynthesis Pathway of Litsea cubeba Under Light and Darkness Treatments

by Jiahui Yang, Yunxiao Zhao, Yicun Chen, Yangdong Wang and Ming Gao

Int. J. Mol. Sci. 2025, 26(7), 2992; https://doi.org/10.3390/ijms26072992 - 25 Mar 2025

Viewed by 370

Abstract

Light is an important environmental regulator of plant secondary metabolism. Terpenoids, the most abundant secondary metabolites in plants, demonstrate a wide spectrum of biologically significant properties, encompassing antimicrobial, antioxidative, and analgesic activities. Litsea cubeba (Lour.) Pers., a core species within the Lauraceae family, exhibits notable pharmacological potential, including antimicrobial and antitumor effects. Here, we found that darkness treatment significantly suppressed terpenoid accumulation in L. cubeba fruits. To clarify the molecular mechanisms underlying the regulatory effect of light and darkness treatments on terpenoid biosynthesis, we conducted a comparative transcriptome profiling of L. cubeba fruits under light and darkness treatments. A total of 13,074 differentially expressed genes (DEGs) were identified among four sampling time points (L1-L2-L3-L4 vs. D1-D2-D3-D4). These genes were enriched in various pathways, with significant enrichment being observed in the terpenoid and other secondary metabolism pathways. Additionally, the enrichment of DEGs in L2 and D2 stages was further studied, and it was found that nine DEGs were significantly enriched in the monoterpene synthesis pathway. The weighted gene co-expression network analysis (WGCNA) showed that alcohol dehydrogenase (ADH), a key enzyme in terpenoid synthesis, had the same expression pattern as WRKY and NAC transcription factors, suggesting their involvement in the biosynthesis of terpenoids in L. cubeba. Expression profiling demonstrated that plastid-localized terpenoid pathway genes were markedly downregulated under darkness treatment. qRT-PCR validation of key genes (LcDXS3, LcHMGS1, LcMDS, and LcTPS19) confirmed the reliability of the transcriptome data, with LcDXS3 exhibiting pronounced declines in expression after 6 h (2.76-fold decrease) and 12 h (2.63-fold decrease) of darkness treatment. These findings provide novel insights into the photoregulatory mechanisms governing terpenoid metabolism in L. cubeba. Full article

(This article belongs to the Special Issue Biosynthesis and Regulatory Mechanism of Secondary Metabolites in Medicinal Plants: 2nd Edition)

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15 pages, 10104 KiB

Open AccessArticle

Enhancement of Dendrobine Production by CRISPR/Act3.0-Mediated Transcriptional Activation of Multiple Endogenous Genes in Dendrobium Plants

by Meili Zhao, Zhenyu Yang, Jian Li, Feng Ming, Demin Kong, Haifeng Xu, Yu Wang, Peng Chen, Xiaojuan Duan, Meina Wang and Zhicai Wang

Int. J. Mol. Sci. 2025, 26(4), 1487; https://doi.org/10.3390/ijms26041487 - 11 Feb 2025

Viewed by 660

Abstract

Dendrobine, a significant medicinal compound, typically accumulates at low concentrations within several Dendrobium species, including Dendrobium nobile, Dendrobium catenatum, and Dendrobium moniliforme. As D. nobile and D. catenatum are established ingredients in traditional Chinese medicine and have been cultivated extensively, they present ideal plant chassis for upscaling dendrobine production for industrial and research applications. This study employed two approaches: the ectopic overexpression of seven genes through multigene stacking and the activation of multiple key endogenous genes in the dendrobine synthesis pathway using CRISPR/Act3.0 in either D. nobile or D. catenatum. These methods enhanced dendrobine production in transiently infiltrated leaves by 30.1% and transgenic plants by 35.6%. The study is the first to apply CRISPR/Act3.0 to Dendrobium orchids, enhancing dendrobine production, and thus laying a solid foundation for further improvements. CRISPR/Act3.0 is a recently developed technique that demonstrates high efficiency in model plant species, including rice, maize, and Arabidopsis. By combining CRISPR with transcriptional regulatory modules, activation of multiple endogenous genes in the metabolic pathway can be achieved. The successful application in orchid molecular breeding reveals promising potential for further exploration. Full article

(This article belongs to the Special Issue Biosynthesis and Regulatory Mechanism of Secondary Metabolites in Medicinal Plants: 2nd Edition)

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21 pages, 6015 KiB

Open AccessArticle

AdNAC20 Regulates Lignin and Coumarin Biosynthesis in the Roots of Angelica dahurica var. formosana

by Wenjie Qu, Wenjuan Huang, Chen Chen, Jinsong Chen, Lin Zhao, Yijie Jiang, Xuan Du, Renlang Liu, Yinyin Chen, Kai Hou, Dongbei Xu and Wei Wu

Int. J. Mol. Sci. 2024, 25(14), 7998; https://doi.org/10.3390/ijms25147998 - 22 Jul 2024

Cited by 1 | Viewed by 1223

Abstract

Angelica dahurica var. formosana (ADF), which belongs to the Umbelliferae family, is one of the original plants of herbal raw material Angelicae Dahuricae Radix. ADF roots represent an enormous biomass resource convertible for disease treatment and bioproducts. But, early bolting of ADF resulted in lignification and a decrease in the coumarin content in the root, and roots lignification restricts its coumarin for commercial utility. Although there have been attempts to regulate the synthesis ratio of lignin and coumarin through biotechnology to increase the coumarin content in ADF and further enhance its commercial value, optimizing the biosynthesis of lignin and coumarin remains challenging. Based on gene expression analysis and phylogenetic tree profiling, AdNAC20 as the target for genetic engineering of lignin and coumarin biosynthesis in ADF was selected in this study. Early-bolting ADF had significantly greater degrees of root lignification and lower coumarin contents than that of the normal plants. In this study, overexpression of AdNAC20 gene plants were created using transgenic technology, while independent homozygous transgenic lines with precise site mutation of AdNAC20 were created using CRISPR/Cas9 technology. The overexpressing transgenic ADF plants showed a 9.28% decrease in total coumarin content and a significant 12.28% increase in lignin content, while knockout mutant plants showed a 16.3% increase in total coumarin content and a 33.48% decrease in lignin content. Furthermore, 29,671 differentially expressed genes (DEGs) were obtained by comparative transcriptomics of OE-NAC20, KO-NAC20, and WT of ADF. A schematic diagram of the gene network interacting with AdNAC20 during the early-bolting process of ADF was constructed by DEG analysis. AdNAC20 was predicted to directly regulate the transcription of several genes with SNBE-like motifs in their promoter, such as MYB46, C3H, and CCoAOMT. In this study, AdNAC20 was shown to play a dual pathway function that positively enhanced lignin formation but negatively controlled coumarin formation. And the heterologous expression of the AdNAC20 gene at Arabidopsis thaliana proved that the AdNAC20 gene also plays an important role in the process of bolting and flowering. Full article

(This article belongs to the Special Issue Biosynthesis and Regulatory Mechanism of Secondary Metabolites in Medicinal Plants: 2nd Edition)

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19 pages, 10776 KiB

Open AccessArticle

Genome-Wide Identification of Seven in Absentia E3 Ubiquitin Ligase Gene Family and Expression Profiles in Response to Different Hormones in Uncaria rhynchophylla

by Jinxu Lan, Conglong Lian, Yingying Shao, Suiqing Chen, Ying Lu, Lina Zhu, Detian Mu and Qi Tang

Int. J. Mol. Sci. 2024, 25(14), 7636; https://doi.org/10.3390/ijms25147636 - 11 Jul 2024

Cited by 1 | Viewed by 1100

Abstract

SINA (Seven in absentia) E3 ubiquitin ligases are a family of RING (really interesting new gene) E3 ubiquitin ligases, and they play a crucial role in regulating plant growth and development, hormone response, and abiotic and biotic stress. However, there is little research on the SINA gene family in U. rhynchophylla. In this study, a total of 10 UrSINA genes were identified from the U. rhynchophylla genome. The results of multiple sequence alignments and chromosomal locations show that 10 UrSINA genes were unevenly located on 22 chromosomes, and each UrSINA protein contained a SINA domain at the N-terminal and RING domains at the C-terminal. Synteny analysis showed that there are no tandem duplication gene pairs and there are four segmental gene pairs in U. rhynchophylla, contributing to the expansion of the gene family. Furthermore, almost all UrSINA genes contained the same gene structure, with three exons and two introns, and there were many cis-acting elements relating to plant hormones, light responses, and biotic and abiotic stress. The results of qRT-PCR show that most UrSINA genes were expressed in stems, with the least expression in roots; meanwhile, most UrSINA genes and key enzyme genes were responsive to ABA and MeJA hormones with overlapping but different expression patterns. Co-expression analysis showed that UrSINA1 might participate in the TIA pathway under ABA treatment, and UrSINA5 and UrSINA6 might participate in the TIA pathway under MeJA treatment. The mining of UrSINA genes in the U. rhynchophylla provided novel information for understanding the SINA gene and its function in plant secondary metabolites, growth, and development. Full article

(This article belongs to the Special Issue Biosynthesis and Regulatory Mechanism of Secondary Metabolites in Medicinal Plants: 2nd Edition)

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25 pages, 6586 KiB

Open AccessArticle

Heat Stress and Microbial Stress Induced Defensive Phenol Accumulation in Medicinal Plant Sparganium stoloniferum

by Mengru Sang, Qinan Liu, Dishuai Li, Jingjie Dang, Chenyan Lu, Chanchan Liu and Qinan Wu

Int. J. Mol. Sci. 2024, 25(12), 6379; https://doi.org/10.3390/ijms25126379 - 9 Jun 2024

Cited by 2 | Viewed by 1392

Abstract

An approach based on the heat stress and microbial stress model of the medicinal plant Sparganium stoloniferum was proposed to elucidate the regulation and mechanism of bioactive phenol accumulation. This method integrates LC–MS/MS analysis, 16S rRNA sequencing, RT–qPCR, and molecular assays to investigate the regulation of phenolic metabolite biosynthesis in S. stoloniferum rhizome (SL) under stress. Previous research has shown that the metabolites and genes involved in phenol biosynthesis correlate to the upregulation of genes involved in plant–pathogen interactions. High-temperature and the presence of Pseudomonas bacteria were observed alongside SL growth. Under conditions of heat stress or Pseudomonas bacteria stress, both the metabolites and genes involved in phenol biosynthesis were upregulated. The regulation of phenol content and phenol biosynthesis gene expression suggests that phenol-based chemical defense of SL is stimulated under stress. Furthermore, the rapid accumulation of phenolic substances relied on the consumption of amino acids. Three defensive proteins, namely Ss4CL, SsC4H, and SsF3′5′H, were identified and verified to elucidate phenol biosynthesis in SL. Overall, this study enhances our understanding of the phenol-based chemical defense of SL, indicating that bioactive phenol substances result from SL’s responses to the environment and providing new insights for growing the high-phenol-content medicinal herb SL. Full article

(This article belongs to the Special Issue Biosynthesis and Regulatory Mechanism of Secondary Metabolites in Medicinal Plants: 2nd Edition)

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17 pages, 3653 KiB

Open AccessArticle

Genome-Wide Identification and Functional Analysis of Salvia miltiorrhiza MicroRNAs Reveal the Negative Regulatory Role of Smi-miR159a in Phenolic Acid Biosynthesis

by Hong Zhou, Maochang Jiang, Jiang Li, Yayun Xu, Caili Li and Shanfa Lu

Int. J. Mol. Sci. 2024, 25(10), 5148; https://doi.org/10.3390/ijms25105148 - 9 May 2024

Cited by 6 | Viewed by 1502

Abstract

MicroRNAs (miRNAs) are a group of endogenous small non-coding RNAs in plants. They play critical functions in various biological processes during plant growth and development. Salvia miltiorrhiza is a well-known traditional Chinese medicinal plant with significant medicinal, economic, and academic values. In order to elucidate the role of miRNAs in S. miltiorrhiza, six small RNA libraries from mature roots, young roots, stems, mature leaves, young leaves and flowers of S. miltiorrhiza and one degradome library from mixed tissues were constructed. A total of 184 miRNA precursors, generating 137 known and 49 novel miRNAs, were genome-widely identified. The identified miRNAs were predicted to play diversified regulatory roles in plants through regulating 891 genes. qRT-PCR and 5′ RLM-RACE assays validated the negative regulatory role of smi-miR159a in SmMYB62, SmMYB78, and SmMYB80. To elucidate the function of smi-miR159a in bioactive compound biosynthesis, smi-miR159a transgenic hairy roots were generated and analyzed. The results showed that overexpression of smi-miR159a caused a significant decrease in rosmarinic acid and salvianolic acid B contents. qRT-PCR analysis showed that the targets of smi-miR159a, including SmMYB62, SmMYB78, and SmMYB80, were significantly down-regulated, accompanied by the down-regulation of SmPAL1, SmC4H1, Sm4CL1, SmTAT1, SmTAT3, SmHPPR1, SmRAS, and SmCYP98A14 genes involved in phenolic acid biosynthesis. It suggests that smi-miR159a is a significant negative regulator of phenolic acid biosynthesis in S. miltiorrhiza. Full article

(This article belongs to the Special Issue Biosynthesis and Regulatory Mechanism of Secondary Metabolites in Medicinal Plants: 2nd Edition)

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13 pages, 5791 KiB

Open AccessArticle

Functional Identification of HhUGT74AG11—A Key Glycosyltransferase Involved in Biosynthesis of Oleanane-Type Saponins in Hedera helix

by Han Yu, Jun Zhou, Jing Zhang, Xinyi He, Siqing Peng, Hao Ling, Zhuang Dong, Xiangyang Lu, Yun Tian, Guiping Guan, Qi Tang, Xiaohong Zhong and Yuedong He

Int. J. Mol. Sci. 2024, 25(7), 4067; https://doi.org/10.3390/ijms25074067 - 5 Apr 2024

Cited by 2 | Viewed by 2240

Abstract

Hedera helix is a traditional medicinal plant. Its primary active ingredients are oleanane-type saponins, which have extensive pharmacological effects such as gastric mucosal protection, autophagy regulation actions, and antiviral properties. However, the glycosylation-modifying enzymes responsible for catalyzing oleanane-type saponin biosynthesis remain unidentified. Through transcriptome, cluster analysis, and PSPG structural domain, this study preliminarily screened four candidate UDP-glycosyltransferases (UGTs), including Unigene26859, Unigene31717, CL11391.Contig2, and CL144.Contig9. In in vitro enzymatic reactions, it has been observed that Unigene26859 (HhUGT74AG11) has the ability to facilitate the conversion of oleanolic acid, resulting in the production of oleanolic acid 28-O-glucopyranosyl ester. Moreover, HhUGT74AG11 exhibits extensive substrate hybridity and specific stereoselectivity and can transfer glycosyl donors to the C-28 site of various oleanane-type triterpenoids (hederagenin and calenduloside E) and the C-7 site of flavonoids (tectorigenin). Cluster analysis found that HhUGT74AG11 is clustered together with functionally identified genes AeUGT74AG6, CaUGT74AG2, and PgUGT74AE2, further verifying the possible reason for HhUGT74AG11 catalyzing substrate generalization. In this study, a novel glycosyltransferase, HhUGT74AG11, was characterized that plays a role in oleanane-type saponins biosynthesis in H. helix, providing a theoretical basis for the production of rare and valuable triterpenoid saponins. Full article

(This article belongs to the Special Issue Biosynthesis and Regulatory Mechanism of Secondary Metabolites in Medicinal Plants: 2nd Edition)

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