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Biosynthetic Pathways and Molecular Regulatory Mechanisms of Active Ingredients in...
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Biosynthetic Pathways and Molecular Regulatory Mechanisms of Active Ingredients in Medicinal Plants

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Phytochemistry".

Deadline for manuscript submissions: 31 May 2025 | Viewed by 6489

Special Issue Editors

Dr. Qi Tang

E-Mail Website
Guest Editor
College of Horticulture, Hunan Agricultural University, Changsha 410128, China
Interests: molecular biology in medicinal plants; biosynthetic pathway; genome, transcriptome and proteome; synthetic biology
Special Issues, Collections and Topics in MDPI journals
Dr. Zhixing Qing

E-Mail Website
Guest Editor
College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, China
Interests: natural products research; LC-MS; structural identification; biological activity; biosynthetic pathway

Special Issue Information

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 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 genomics, epigenomics, transcriptomics, proteomics and metabolomics of medicinal plants. Numerous studies have contributed to the biosynthetic pathway of active Ingredients, genes encoding key enzymes of the pathway, and regulatory mechanisms of active ingredients. 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 Plants is devoted to publishing original research and review articles on medicinal plant studies, highlighting recent advances in the biosynthesis and regulatory mechanisms of active ingredients, particularly 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:

  • Genomics, epigenomics, transcriptomics, protomics and metabolomics of medicinal plants;
  • Biosynthetic pathway of secondary metabolites;
  • Key enzyme genes involved in the biosynthesis of secondary metabolites;
  • Transcription factors and regulatory networks in medicinal plants;
  • Metabolic engineering and synthetic biology of active ingredients;
  • Application of high-throughput sequencing technologies;
  • Databases associated with the biosynthesis and regulation of active ingredients;
  • Novel technologies and strategies for secondary metabolism studies.

Dr. Qi Tang
Dr. Zhixing Qing
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Plants is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • medicinal plants
  • biosynthetic pathway
  • molecular regulatory mechanisms
  • gene annotation
  • transcription factor
  • high-throughput sequencing
  • metabolic engineering
  • secondary metabolites
  • gene editing
  • multi-omics
  • genome, transcriptome and proteome metabolomics
  • synthetic biology
  • metabolic analysis
  • metabolic outline

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Published Papers (5 papers)

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Research

18 pages, 1233 KiB  
Article
The Mining of Candidate Genes Involved in the Camphor Biosynthesis Pathway of Cinnamomum camphora
by Yan Yang, Shengcai Zhou, Mingyang Ni, Yuting Zhang, Shixiong Lin, Junhong Zhang and Zaikang Tong
Plants 2025, 14(7), 991; https://doi.org/10.3390/plants14070991 - 21 Mar 2025
Viewed by 59
Abstract
Cinnamomum camphora is widely cultivated for its camphor in essential oil (EO), which is used in pharmaceutical industries. However, the candidate genes for the camphor biosynthesis pathway are unknown. Gas chromatography–mass spectrometry (GC-MS) was used to identify differences in the composition of camphor- [...] Read more.
Cinnamomum camphora is widely cultivated for its camphor in essential oil (EO), which is used in pharmaceutical industries. However, the candidate genes for the camphor biosynthesis pathway are unknown. Gas chromatography–mass spectrometry (GC-MS) was used to identify differences in the composition of camphor- and linalool-type camphor EOs and in conjunction with transcriptional analysis to identify terpene biosynthesis-related genes. The GC-MS analysis of C. camphora revealed 67 chemical components, including 32 monoterpenes and 35 sesquiterpenes, with camphor-type leaves dominated by camphor and linalool-type leaves by linalool. Transcriptome analysis revealed 6499 differentially expressed genes (DEGs) between camphor- and linalool-type C. camphora, with 4244 upregulated and 2255 downregulated in the camphor-type. GO enrichment highlighted DEGs involved in monoterpene biosynthesis, cell wall organization, and membrane-related processes. KEGG analysis identified pathways such as monoterpenoid, diterpenoid, and phenylpropanoid biosynthesis as significantly enriched. Furthermore, DEGs encoding TPS, dehydrogenases, and transcription factors, which might contribute to the terpenoid diversity in C. camphora, were identified. Twenty-one candidate genes involved in the camphor biosynthesis pathway were identified, providing a foundation for further elucidating the genetic mechanisms underlying camphor production in C. camphora. Full article
(This article belongs to the Special Issue Biosynthetic Pathways and Molecular Regulatory Mechanisms of Active Ingredients in Medicinal Plants)
18 pages, 4337 KiB  
Article
Widely Targeted Metabolomics Analyses Provide Insights into the Transformation of Active Ingredients During Drying and the Mechanisms of Color Change for Forest Ginseng (Panax ginseng C. A. Mey. cv. Sativi-nemoralis)
by Junjia Xing, Limin Yang, Lianxue Zhang, Jiahong Han and Enbo Cai
Plants 2025, 14(3), 494; https://doi.org/10.3390/plants14030494 - 6 Feb 2025
Viewed by 597
Abstract
In this study, we investigated the mechanism of conversion of active components as well as the color change of forest ginseng (FG) during the drying process with the self-developed negative-pressure circulating airflow-assisted desiccator (PCAD) drying method, using a widely targeted metabolomics analytical method [...] Read more.
In this study, we investigated the mechanism of conversion of active components as well as the color change of forest ginseng (FG) during the drying process with the self-developed negative-pressure circulating airflow-assisted desiccator (PCAD) drying method, using a widely targeted metabolomics analytical method based on ultraperformance liquid chromatography–tandem mass spectrometry (UPLC-MS/MS). During the drying process, a total of 1862 metabolites were identified in FG, along with 748 differential abundant metabolites (DAMs). Further analysis of the types and metabolic pathways of the DAMs revealed that both primary and secondary metabolites changed by 50–70% moisture content (MC); secondary metabolites dominated with a 30–50% MC, and primary metabolites dominated with a 10–30% MC, which revealed the differences in the transformation of the active ingredients in the drying process. In addition, the results showed the browning characteristics during the drying process. MC-50 and MC-10 showed the smallest and largest color changes, as well as enzyme activities, compared to the other MCs, respectively. As drying proceeded, browning reactions were mainly related to lipid and nucleotide metabolism and phenylpropane and flavonoid biosynthesis. In conclusion, the present study provides theoretical support for the mechanisms of active ingredient transformation as well as the color change of FG during PCAD drying. Full article
(This article belongs to the Special Issue Biosynthetic Pathways and Molecular Regulatory Mechanisms of Active Ingredients in Medicinal Plants)
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20 pages, 6990 KiB  
Article
Multi-Omics Analyses Uncover the Mechanism Underlying Polyploidization-Enhanced Steviol Glycosides Biosynthesis in Stevia rebaudiana
by Juan Liu, Jiaxue Wang, Mingjia Chen, Wenna Meng, Anping Ding, Miao Chen, Rongping Ding, Mingpu Tan and Zengxu Xiang
Plants 2024, 13(18), 2542; https://doi.org/10.3390/plants13182542 - 10 Sep 2024
Viewed by 1624
Abstract
Stevia rebaudiana (Bertoni) is a valuable sweetener plant whose sweetness primarily derives from steviol glycosides (SGs), especially rebaudioside A (RA). Polyploidization has the potential to enhance the content of active ingredients in medicinal plants, making this strategy a promising avenue for genetic improvement. [...] Read more.
Stevia rebaudiana (Bertoni) is a valuable sweetener plant whose sweetness primarily derives from steviol glycosides (SGs), especially rebaudioside A (RA). Polyploidization has the potential to enhance the content of active ingredients in medicinal plants, making this strategy a promising avenue for genetic improvement. However, the underlying regulatory mechanisms that contribute to the fluctuating SGs content between autotetraploid and diploid stevia remain unclear. In this study, we employed metabolic analysis to identify 916 differentially accumulated metabolites (DAMs), with the majority, specifically terpenoids, flavonoids, and lipids, exhibiting upregulation due to polyploidization. Notably, the content of stevia’s signature metabolite SGs (including RA, steviolbioside, and rebaudioside C), along with their precursor steviol, increased significantly after polyploidization. Furthermore, a comprehensive analysis of the transcriptome and metabolome revealed that the majority of differentially expressed genes (DEGs) involved in the SG-synthesis pathway (ent-KAH, ent-KS1, UGT73E1, UGT74G1, UGT76G1, UGT85C2, and UGT91D2) were upregulated in autotetraploid stevia, and these DEGs exhibited a positive correlation with the polyploidization-enhanced SGs. Additionally, multi-omics network analysis indicated that several transcription factor families (such as five NACs, four WRKYs, three MYBs, eight bHLHs, and three AP2/ERFs), various transporter genes (four ABC transporters, three triose-phosphate transporters, and two sugar efflux transporters for intercellular exchange), as well as microorganisms (including Ceratobasidium and Flavobacterium) were positively correlated with the accumulation of RA and steviol. Overall, our results indicate the presence of a regulatory circuit orchestrated by polyploidization, which recruits beneficial rhizosphere microbes and modulates the expression of genes associated with SG biosynthesis, ultimately enhancing the SG content in stevia. This finding will provide new insights for promoting the propagation and industrial development of stevia. Full article
(This article belongs to the Special Issue Biosynthetic Pathways and Molecular Regulatory Mechanisms of Active Ingredients in Medicinal Plants)
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18 pages, 3168 KiB  
Article
Exploring the Effects of Different Drying Methods on Related Differential Metabolites of Pleurotus citrinopileatus Singer Based on Untargeted Metabolomics
by Huan Lu, Simin Peng, Ning Xu, Xiaodong Shang, Jianyu Liu, Zhen Xu, Ning Jiang, Haoran Dong, Ruijuan Wang and Hui Dong
Plants 2024, 13(12), 1594; https://doi.org/10.3390/plants13121594 - 7 Jun 2024
Cited by 3 | Viewed by 1542
Abstract
Pleurotus citrinopileatus Singer (PCS) has attracted increasing attention as a raw material for medicine and food. Its quality is greatly affected by the accumulation of metabolites, which varies with the applied drying methods. In this study, we utilize an approach based on ultra-high-performance [...] Read more.
Pleurotus citrinopileatus Singer (PCS) has attracted increasing attention as a raw material for medicine and food. Its quality is greatly affected by the accumulation of metabolites, which varies with the applied drying methods. In this study, we utilize an approach based on ultra-high-performance liquid chromatography/Q Exactive mass spectrometry (UHPLC-QE-MS) to reveal the metabolic profiles of PCS from three different drying methods (natural air-drying, NAD; hot-air-drying, HAD; vacuum freeze-drying, VFD). The results showed that lipids, amino acids and their derivatives were all important secondary metabolites produced during NAD, HAD and VFD treatments, with the key differential metabolites of PCS during drying including fifteen lipids and seven amino acids. Meanwhile, VFD was the best way for long-term preservation of dried PCS. Hot-drying methods, especially HAD, can improve the medicinal component of PCS. Furthermore, KEGG enrichment analysis highlighted 16 pathways and indicated that amino acid metabolism might be the key metabolite pathway for the PCS drying process. Our study elucidates the relationship between drying methods and metabolites or metabolic pathways of PCS to determine the mechanisms affecting the quality of PCS, and finally provides reference values for further development and application in functional food and medications. Full article
(This article belongs to the Special Issue Biosynthetic Pathways and Molecular Regulatory Mechanisms of Active Ingredients in Medicinal Plants)
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17 pages, 6748 KiB  
Article
Genome-Wide Mining of CULLIN E3 Ubiquitin Ligase Genes from Uncaria rhynchophylla
by Yingying Shao, Detian Mu, Yu Zhou, Xinghui Liu, Xueshuang Huang, Iain W. Wilson, Yuxin Qi, Ying Lu, Lina Zhu, Yao Zhang, Deyou Qiu and Qi Tang
Plants 2024, 13(4), 532; https://doi.org/10.3390/plants13040532 - 15 Feb 2024
Cited by 2 | Viewed by 1747
Abstract
CULLIN (CUL) protein is a subtype of E3 ubiquitin ligase that is involved in a variety of biological processes and responses to stress in plants. In Uncaria rhynchophylla, the CUL gene family has not been identified and its role in plant development, [...] Read more.
CULLIN (CUL) protein is a subtype of E3 ubiquitin ligase that is involved in a variety of biological processes and responses to stress in plants. In Uncaria rhynchophylla, the CUL gene family has not been identified and its role in plant development, stress response and secondary metabolite synthesis has not been studied. In this study, 12 UrCUL gene members all contained the typical N-terminal domain and C-terminal domain identified from the U. rhynchophylla genome and were classified into four subfamilies based on the phylogenetic relationship with CULs in Arabidopsis thaliana. They were unevenly distributed on eight chromosomes but had a similar structural composition in the same subfamily, indicating that they were relatively conserved and potentially had similar gene functions. An interspecific and intraspecific collinearity analysis showed that fragment duplication played an important role in the evolution of the CUL gene family. The analysis of the cis-acting elements suggests that the UrCULs may play an important role in various biological processes, including the abscisic acid (ABA) response. To investigate this hypothesis, we treated the roots of U. rhynchophylla tissue-cultured seedlings with ABA. The expression pattern analysis showed that all the UrCUL genes were widely expressed in roots with various expression patterns. The co-expression association analysis of the UrCULs and key enzyme genes in the terpenoid indole alkaloid (TIA) synthesis pathway revealed the complex expression patterns of 12 UrCUL genes and some key TIA enzyme genes, especially UrCUL1, UrCUL1-likeA, UrCUL2-likeA and UrCUL2-likeB, which might be involved in the biosynthesis of TIAs. The results showed that the UrCULs were involved in the response to ABA hormones, providing important information for elucidating the function of UrCULs in U. rhynchophylla. The mining of UrCULs in the whole genome of U. rhynchophylla provided new information for understanding the CUL gene and its function in plant secondary metabolites, growth and development. Full article
(This article belongs to the Special Issue Biosynthetic Pathways and Molecular Regulatory Mechanisms of Active Ingredients in Medicinal Plants)
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