Advances in Plant Natural Products Biosynthesis and Metabolic Engineering—2nd Edition

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

Deadline for manuscript submissions: 30 June 2026 | Viewed by 4289

Special Issue Editors


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Guest Editor
College of Science, Sichuan Agricultural University, Ya’an 625014, China
Interests: plant secondary metabolism; biosynthetic chemistry; multi-omics; enzyme element characterization
Special Issues, Collections and Topics in MDPI journals

E-Mail Website
Guest Editor
Agronomy College, Sichuan Agricultural University, Chengdu 611130, China
Interests: plant secondary metabolism; biosynthetic regulation; evaluation and utilization of medicinal plant resources
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Plant natural products contribute to many biological and ecological functions. They are synthesized by plants to interact with the biotic and abiotic environments, playing roles in plant defense, growth, and development. Additionally, plant natural products have widespread applications in human industries, including food additives, cosmetics, dyes, insecticides, and drugs. The biosynthesis of these natural products is complex and dynamic, with more than one million natural products identified from terrestrial and aquatic plants. Despite their structural diversity, plants produce limited quantities of these valuable products in a metabolic cost-saving way. This has greatly limited their commercial application, and the overexploitation of source plants has raised concerns about their sustainability and highlighted the need for advanced research.

Recent advances in genomics, transcriptomics, proteomics, and metabolomics technologies have revolutionized our understanding of plant biology, enabling the discovery of new plant natural products and their biosynthetic pathways. Functional plant genomics approaches, such as targeted genome mining, genome-wide association studies, co-expression analysis, and virus-induced gene silence approach, have facilitated the identification and characterization of genes and enzymes involved in the biosynthesis of specific natural products. Metabolic engineering approaches have enabled the manipulation of plant metabolism to improve the yield and quality of specific natural products of interest or to produce them in heterologous cultures. These advances have created new opportunities for the sustainable production and utilization of plant natural products.

Topics of interest include the following:

  • Elucidating the biosynthetic pathways of plant natural products, such as alkaloids, terpenes, phenolics, etc.
  • Identifying and characterizing genes and enzymes involved in the biosynthesis of plant natural products.
  • Discovering and characterizing transcription factors responsible for the positive or negative regulation of plant natural product biosynthesis.
  • Developing and employing metabolic engineering techniques to improve the yield of specific natural products of interest, or biomanufacturing plant natural products in engineered plants or yeast.

Original research papers and reviews related to these topics will be considered for publication.

Dr. Xiang Pu
Dr. Wei Wu
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 250 words) can be sent to the Editorial Office for assessment.

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

  • plant
  • natural product
  • biosynthesis
  • metabolic engineering

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Published Papers (4 papers)

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Research

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24 pages, 8644 KB  
Article
Integrated Volatile Metabolome and Transcriptome Analysis Provides Insights into Floral Aroma Biosynthesis in Waterlilies (Nymphaea L.)
by Qun Su, Fengshun Wang, Jiahui Zhao, Jianxun Lu, Hongyan Wang, Yanfei La, Zhenglin Wan, Yuling Lin, Min Tian, Lingyun Wang and Zhongxiong Lai
Plants 2026, 15(3), 384; https://doi.org/10.3390/plants15030384 - 27 Jan 2026
Viewed by 678
Abstract
Waterlily (Nymphaea L.), a globally renowned aquatic ornamental plant, is prized for its aesthetic flowers and intense floral fragrance. However, the molecular mechanisms underlying floral scent biosynthesis in waterlily remain poorly characterized, and integrated analyses of dynamic volatile emission patterns and their [...] Read more.
Waterlily (Nymphaea L.), a globally renowned aquatic ornamental plant, is prized for its aesthetic flowers and intense floral fragrance. However, the molecular mechanisms underlying floral scent biosynthesis in waterlily remain poorly characterized, and integrated analyses of dynamic volatile emission patterns and their associated biosynthetic pathways are lacking. In this study, we combined headspace solid-phase microextraction/gas chromatography–mass spectrometry (HS-SPME/GC-MS) with transcriptome sequencing (RNA-seq) to investigate the composition, emission dynamics, and biosynthesis of volatile organic compounds (VOCs) in the stamens of Nymphaea ‘Paul Stetson’ across three developmental stages. A total of 671 VOCs, classified into 14 categories, were identified. Transcriptome analysis revealed 47,951 differentially expressed genes (DEGs). Integrative omics analysis demonstrated correlated DEGs and differentially accumulated volatiles were significantly enriched in pathways related to phenylpropanoid biosynthesis, terpenoid backbone biosynthesis, diterpenoid biosynthesis, and ubiquinone/other terpenoid-quinone biosynthesis. Five candidate functional genes exhibiting strong positive correlations with VOC accumulation levels were identified, three of which are implicated in terpenoid biosynthesis. These findings provide a theoretical foundation for elucidating aroma composition and biosynthesis in waterlily and offer novel avenues for the genetic improvement of fragrance traits for ornamental, beverage, and cosmetic applications. Full article
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19 pages, 3192 KB  
Article
Genomic Identification and Biochemical Characterization of Methyl Jasmonate (MJ)-Inducible Terpene Synthase Genes in Lettuce (Lactuca sativa L. cv. Salinas)
by Akhileshwar Singh, Moon-Soo Chung, Seung Sik Lee, Byung Yeoup Chung and Sungbeom Lee
Plants 2026, 15(1), 55; https://doi.org/10.3390/plants15010055 - 24 Dec 2025
Viewed by 834
Abstract
Terpenes are diverse plant metabolites with essential ecological and physiological functions, yet their biosynthetic regulation in lettuce (Lactuca sativa L.) remains poorly understood. By integrating volatile profiling, genome-wide identification, and biochemical characterization of terpene synthase (TPS) genes, we elucidated how methyl jasmonate [...] Read more.
Terpenes are diverse plant metabolites with essential ecological and physiological functions, yet their biosynthetic regulation in lettuce (Lactuca sativa L.) remains poorly understood. By integrating volatile profiling, genome-wide identification, and biochemical characterization of terpene synthase (TPS) genes, we elucidated how methyl jasmonate (MJ) induces terpene formation in lettuce seedlings. Headspace analysis of 10-day-old seedlings revealed that while mock-treated tissues emitted no detectable volatiles, MJ elicitation triggered the de novo production of a terpene blend dominated by (E)-β-ocimene (9.3–14.6%), (E)-β-caryophyllene (37.2–46.9%), and caryophyllene oxide (26.2–41.4%). A genome-wide search identified 54 putative LsTPS genes, often clustered with prenyl transferases or cytochrome P450 genes. Gene expression assays revealed 17 MJ-responsive LsTPS genes; among them, LsTPS21, LsTPS23, LsTPS28, LsTPS51, and LsTPS52 showed strong (>200-fold) induction, with LsTPS52 exceeding a 20,000-fold increase. Functional characterization of six recombinant enzymes demonstrated diverse substrate specificities: LsTPS8 as an α-copaene synthase, LsTPS16 as a linalool synthase, LsTPS24 as an (E)-nerolidol synthase, LsTPS21 and LsTPS23 as (E)-β-ocimene synthases, and LsTPS10 as an (E)-β-caryophyllene synthase. Phylogenetic analyses confirmed conserved domains characteristic of the TPS-a and TPS-b subfamilies. This study presents the first comprehensive framework for MJ-induced terpene biosynthesis in lettuce, offering new insights into Asteraceae terpenoid metabolism. Full article
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19 pages, 3849 KB  
Article
A Multidrug and Toxic Compound Extrusion Transporter, RgMATE6, Facilitates Vacuolar Transport of Acteoside in Rehmannia glutinosa
by Yanhui Yang, Yuying Li, Yuxuan Wang, Mingjie Li, Zhongyi Zhang, Ruifang Li, Weiwei Wang, Fuxi Shen and Mengman Yan
Plants 2025, 14(23), 3608; https://doi.org/10.3390/plants14233608 - 26 Nov 2025
Viewed by 720
Abstract
Acteoside (ACT), a prominent compound of the hydroxytyrosol-type phenylethanol glycoside (HPG) class, is present in plants and holds significant potential for food and pharmaceutical applications. However, the limited production of ACT in plants restricts its broader utilization. Although the biosynthetic pathways of ACT [...] Read more.
Acteoside (ACT), a prominent compound of the hydroxytyrosol-type phenylethanol glycoside (HPG) class, is present in plants and holds significant potential for food and pharmaceutical applications. However, the limited production of ACT in plants restricts its broader utilization. Although the biosynthetic pathways of ACT are increasingly understood, its transport mechanisms within plants remain unclear. RgMATE6, a vacuolar-type Multidrug and Toxic Compound Extrusion (MATE) transporter identified in Rehmannia glutinosa (a plant known for ACT p roduction), was selected for investigation. This study aims to elucidate the role of RgMATE6 in ACT transport and its impact on ACT biosynthesis. Our study utilized a multidisciplinary approach, including in silico analysis to predict substrate specificity, quantitative real-time PCR (qRT-PCR) to quantify gene expression, HPLC to measure HPG levels, vacuolar membrane vesicle uptake assays to validate RgMATE6 transport activity in vitro, and genetic transformation in R. glutinosa to assess its functional roles in vivo. In silico analysis identified RgMATE6 as a phenolic compound transporter, and correlation analysis revealed a strong positive association between the HPG accumulation and RgMATE6 expression in R. glutinosa. Functional validation through vacuolar membrane vesicle uptake assays in Nicotiana benthamiana confirmed RgMATE6’s role as an HPG transporter, demonstrating a significant preference for ACT. Overexpression and repression experiments in R. glutinosa further demonstrated that RgMATE6 facilitates ACT import into vacuoles and enhances its production. Additionally, tissue-specific expression analysis revealed the coordinated expression patterns between RgMATE6 and six ACT biosynthetic genes in the transgenic plants. RgMATE6 facilitates the transport and accumulation of ACT within vacuoles, and its expression might synergize with ACT biosynthesis. These findings establish a framework for improving ACT and other HPG production through targeted manipulation of plant MATE transporters. Full article
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Review

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34 pages, 2380 KB  
Review
A Comprehensive Review on Steviol Glycosides: Sources, Properties, Bioactivities, Sensory-Functional Enhancement and Bioproduction Strategies
by Liangzhen Jiang, Xun Zhao, Wei Li, Guiru Tang, Yiming Yuan, Jie Cheng, Jun Hua and Liang Zou
Plants 2026, 15(2), 324; https://doi.org/10.3390/plants15020324 - 21 Jan 2026
Cited by 1 | Viewed by 1719
Abstract
Steviol glycosides (SGs) are high-intensity, zero-calorie natural sweeteners with demonstrated safety and potential health benefits, positioning them as ideal sucrose substitutes for metabolic disorder management. However, their broad application is limited by inherent drawbacks such as bitterness, low solubility, and inefficient production systems. [...] Read more.
Steviol glycosides (SGs) are high-intensity, zero-calorie natural sweeteners with demonstrated safety and potential health benefits, positioning them as ideal sucrose substitutes for metabolic disorder management. However, their broad application is limited by inherent drawbacks such as bitterness, low solubility, and inefficient production systems. This review provides a comprehensive summary of recent advances in SG research, covering their sources, properties, and bioactivities. A particular focus is placed on innovative bioproduction strategies—including enzyme engineering, metabolic pathway optimization, and sustainable extraction techniques. Strategies to overcome these challenges through sensory-function enhancement—including formulation and structural modification—are discussed. Furthermore, it highlights emerging trends like microbial chassis-based production and next-generation sweetener design, providing actionable insights for overcoming industrial bottlenecks. By integrating multidisciplinary advances in bioengineering, sensory science, and sustainable processing, this review offers a forward-looking perspective on the development and application of SGs as functional sweeteners in the global food industry. Full article
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