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Advances in Plant Natural Products Biosynthesis and Metabolic Engineering
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Advances in Plant Natural Products Biosynthesis and Metabolic Engineering

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

Deadline for manuscript submissions: 30 June 2025 | Viewed by 5437

Special Issue Editors

Dr. Xiang Pu

E-Mail Website
Guest Editor
College of Science, Sichuan Agricultural University, Ya’an 625014, China
Interests: plant secondary metabolism; biosynthetic chemistry; multi-omics; enzyme element characterization
Dr. Wei Wu

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 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 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

  • plant
  • natural product
  • biosynthesis
  • metabolic engineering

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Published Papers (6 papers)

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Research

16 pages, 2745 KiB  
Article
Untargeted Metabolomics Analysis Reveals Differential Accumulation of Flavonoids Between Yellow-Seeded and Black-Seeded Rapeseed Varieties
by Shulin Shen, Yunshan Tang, Daiqin Liu, Lulu Chen, Yi Zhang, Kaijie Ye, Fujun Sun, Xingzhi Wei, Hai Du, Huiyan Zhao, Jiana Li, Cunmin Qu and Nengwen Yin
Plants 2025, 14(5), 753; https://doi.org/10.3390/plants14050753 - 1 Mar 2025
Viewed by 486
Abstract
Rapeseed (Brassica napus) is an important oilseed crop and yellow-seeded and black-seeded varieties have different metabolite profiles, which determines the quality and edibility of their oil. In this study, we performed a non-targeted metabolomics analysis of seeds from four rapeseed varieties [...] Read more.
Rapeseed (Brassica napus) is an important oilseed crop and yellow-seeded and black-seeded varieties have different metabolite profiles, which determines the quality and edibility of their oil. In this study, we performed a non-targeted metabolomics analysis of seeds from four rapeseed varieties at eight developmental stages. This analysis identified 4540 features, of which 366 were annotated as known metabolites. The content of these metabolites was closely related to seed developmental stage, with the critical period for seed metabolite accumulation being between 10 and 20 days after pollination. Through a comparative analysis, we identified 18 differentially abundant flavonoid features between yellow-seeded and black-seeded rapeseed varieties. By combining the flavonoid data with transcriptome data, we constructed a gene regulatory network that may reflect the accumulation of differentially abundant flavonoid features. Finally, we predicted 38 unknown features as being flavonoid features through molecular networking. These results provide valuable metabolomics information for the breeding of yellow-seeded rapeseed varieties. Full article
(This article belongs to the Special Issue Advances in Plant Natural Products Biosynthesis and Metabolic Engineering)
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17 pages, 6123 KiB  
Article
Transcriptomic and Metabolomic Insights into Key Genes Involved in Kinsenoside Biosynthesis in Anoectochilus roxburghii
by Peiyu Wang, Peipei Yan, Zunwen Li, Jinlan Jiang, Yuling Lin and Wei Ye
Plants 2025, 14(5), 688; https://doi.org/10.3390/plants14050688 - 24 Feb 2025
Viewed by 443
Abstract
As the main active ingredient in Anoectochilus roxburghii, kinsenoside has important health and medical effects including hepatoprotective, anti-oxidant, and bacteriostasis, among others. In recent years, with the limited application of high-throughput technology to A. roxburghii, there has been no research on the [...] Read more.
As the main active ingredient in Anoectochilus roxburghii, kinsenoside has important health and medical effects including hepatoprotective, anti-oxidant, and bacteriostasis, among others. In recent years, with the limited application of high-throughput technology to A. roxburghii, there has been no research on the key regulatory genes involved in the synthesis of kinsenoside. Therefore, we examined three species of A. roxburghii that are widely planted in mainland China and Taiwan Province, A. roxburghii cultivar ‘Jian ye’, Anoectochilus formosanus, and Anoectochilus burmannicus, determining the content of kinsenoside, performing transcriptomic and metabolomic sequencing, identifying UDP glycosyltransferases, and screening for UDP glycosyltransferases that may be involved in kinsenoside synthesis. The results showed that among the three species of A. roxburghii, the content of kinsenoside in A. roxburghii cv. ‘Jian ye’ was the highest. Transcriptome and metabolome data showed that A. roxburghii cv. ‘Jian ye’ and the two other species of A. roxburghii have 3702 and 5369 differentially expressed genes and 69 and 120 differentially accumulated metabolites, respectively. Meanwhile, differentially expressed genes and differentially accumulated metabolites are enriched in the glucose metabolism and hormone pathways. We also treated the A. roxburghii samples with exogenous auxin and characterized the related genes. In A. roxburghii, we identified 73 members of the UDP glycosyltransferase family. Through phylogenetic tree, transcriptome data expression profile, and qPCR analyses, we screened for members that may be involved in the synthesis of kinsenoside. In summary, the results of this study provide insights for breeding high-kinsenoside-content and high-intron varieties of A. roxburghii. Full article
(This article belongs to the Special Issue Advances in Plant Natural Products Biosynthesis and Metabolic Engineering)
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21 pages, 11636 KiB  
Article
Metabolome and Transcriptome Analysis Reveals the Regulatory Effect of Magnesium Treatment on EGCG Biosynthesis in Tea Shoots (Camellia sinensis)
by Zixuan Feng, Zhuan Li, Rui Yan, Nan Yang, Meichen Liu, Yueting Bai, Yuyuan Mao, Chengzhe Zhou, Yuqiong Guo, Yulin Zeng, Yuhang Ji, Yangshun Lin, Jiayong Chen and Shuilian Gao
Plants 2025, 14(5), 684; https://doi.org/10.3390/plants14050684 - 23 Feb 2025
Viewed by 607
Abstract
Epigallocatechin-3-O-gallate (EGCG) is an important ingredient that indicates tea quality and has healthcare functions. Magnesium nutrition can improve the quality and yield of tea plants, but its regulatory role in the biosynthesis of EGCG in tea plants has not been clarified. Herein, we [...] Read more.
Epigallocatechin-3-O-gallate (EGCG) is an important ingredient that indicates tea quality and has healthcare functions. Magnesium nutrition can improve the quality and yield of tea plants, but its regulatory role in the biosynthesis of EGCG in tea plants has not been clarified. Herein, we performed a comprehensive analysis of the metabolomics and transcriptomics of the shoots of ‘Huangdan’ at five magnesium concentrations: L1-L5 (0, 0.15, 0.45, 0.6, and 0.9 mmol/L mg2+, respectively). The results showed that the EGCG content of tea shoots treated with low magnesium concentrations was higher compared to those treated with high magnesium concentrations. The contents of related metabolites such as p-coumaric acid and cyanide in the EGCG synthesis pathway increased in the L4 and L5 treatment groups, while those of dihydroquercetin, dinnamic acid, and epicatechin increased significantly in the L2 and L3 treatment groups. Under the influence of magnesium treatment, the biosynthesis of EGCG was affected by a series of structural genes: CsPAL (HD.01G0005520), HD.02G0024350), Cs4CL (HD.15G0008250, HD.13G0010220), CsDFR (HD.04G0026220), CsANS(HD.12G0016700) with CsaroDE (HD.03G0002480)-positive regulation, and CsPAL (HD.13G0009900, HD.06G0008610), CsC4H (HD.06G0017130), Cs4CL (HD.02G0027390, HD.04G0003270), CsCHS (HD.10G0022640), CsCHI (HD.01G0011100), CsF3′H (HD.15G0015490), CsF3′5′H (HD.13G0004300), CsANS (HD.07G0023630), and Csaro B (HD.01G0028400) with CsSCPL (HD.01G0041070)-negative regulation. Transcription factors MYB 44 and WRKY 17 may play a key role in EGCG biosynthesis, which is significantly induced by magnesium nutrition in tea tree shoots. This study elucidates the effect of magnesium nutrition on EGCG biosynthesis in tea plants and provides key candidate transcription factors to provide a reference for further research on high-EGCG tea varieties to improve tea quality. Full article
(This article belongs to the Special Issue Advances in Plant Natural Products Biosynthesis and Metabolic Engineering)
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24 pages, 15009 KiB  
Article
Differential Expression of Amaranth AtrDODA Gene Family Members in Betalain Synthesis and Functional Analysis of AtrDODA1-1 Promoter
by Huiying Xie, Jiajing Zeng, Wenli Feng, Wei Gao, Zhongxiong Lai and Shengcai Liu
Plants 2025, 14(3), 454; https://doi.org/10.3390/plants14030454 - 4 Feb 2025
Viewed by 724
Abstract
Betalains differ from anthocyanins, and they cannot coexist in the same plant under natural conditions. The L-DOPA 4,5-dioxygenase encoded by the DODA gene is a key step in the pathway of betalain biosynthesis in Caryophyllales plants. Amaranth is an important resource for the [...] Read more.
Betalains differ from anthocyanins, and they cannot coexist in the same plant under natural conditions. The L-DOPA 4,5-dioxygenase encoded by the DODA gene is a key step in the pathway of betalain biosynthesis in Caryophyllales plants. Amaranth is an important resource for the study and extraction of betalains. In order to clarify the function of AtrDODA family genes in betalain biosynthesis, we screened out three AtrDODA family gene members associated with betalains based on a genome database and RNA-seq databases of Amaranthus tricolor. Their characterization and expression pattern were further analyzed. The result of subcellular localization showed that all three AtrDODA members were located in the nucleus. Betacyanin and betaxanthin were promoted by paclobutrazol treatment in the leaves and stems of ‘Suxian No.1’ (red), while they were inhibited by gibberellin and darkness, which were consistent with the gene expression pattern of AtrDODAs. After heterologous transformation of the AtrDODA1-1 promoter into tobacco with GUS staining analysis, the promoter activity of AtrDODA1-1 of ‘Suxian No.1’ (red) amaranth was significantly higher than that of ‘Suxian No.2’ (green) amaranth. Furthermore, we analyzed the promoter activity of AtrDODA1-1 by GUS staining and qRT-PCR after sprayed exogenous MeJA and GA3 on the AtrDODA1-1 promoter transformed tobacco plants. The results showed that AtrDODA1-1 responded to plant hormones. This study could lay a foundation for revealing the biological functions of the amaranth DODA gene family, and provide new clues for the molecular mechanism of betalain synthesis. Full article
(This article belongs to the Special Issue Advances in Plant Natural Products Biosynthesis and Metabolic Engineering)
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21 pages, 18027 KiB  
Article
Genome-Wide Analysis of the Cis-Prenyltransferase (CPT) Gene Family in Taraxacum kok-saghyz Provides Insights into Its Expression Patterns in Response to Hormonal Treatments
by Liyu Zhang, Huan He, Jiayin Wang, Pingping Du, Lili Wang, Guangzhi Jiang, Lele Liu, Lu Yang, Xiang Jin, Hongbin Li and Quanliang Xie
Plants 2025, 14(3), 386; https://doi.org/10.3390/plants14030386 - 27 Jan 2025
Viewed by 1006
Abstract
Taraxacum kok-saghyz (TKS) is a natural rubber (NR)-producing plant with great development prospects. Accurately understanding the molecular mechanism of natural rubber biosynthesis is of great significance. Cis-prenyltransferase (CPT) and cis-prenyltransferase-like (CPTL) proteins catalyze the elongation of natural rubber molecular chains and play an [...] Read more.
Taraxacum kok-saghyz (TKS) is a natural rubber (NR)-producing plant with great development prospects. Accurately understanding the molecular mechanism of natural rubber biosynthesis is of great significance. Cis-prenyltransferase (CPT) and cis-prenyltransferase-like (CPTL) proteins catalyze the elongation of natural rubber molecular chains and play an essential role in rubber biosynthesis. In this study, we performed a genome-wide identification of the TkCPT/CPTL family, with eight CPT and two CPTL members. We analyzed the gene structures, evolutionary relationships and expression patterns, revealing five highly conserved structural domains. Based on systematic evolutionary analysis, CPT/CPTL can be divided into six subclades, among which the family members are most closely related to the orthologous species Taraxacum mongolicum. Collinearity analyses showed that fragment duplications were the primary factor of amplification in the TkCPT/CPTL gene family. Induced by ethylene and methyl jasmonate hormones, the expression levels of most genes increased, with significant increases in the expression levels of TkCPT5 and TkCPT6. Our results provide a theoretical basis for elucidating the role of the TkCPT/CPTL gene family in the mechanism of natural rubber synthesis and lay a foundation for molecular breeding of T. kok-saghyz and candidate genes for regulating natural rubber biosynthesis in the future. Full article
(This article belongs to the Special Issue Advances in Plant Natural Products Biosynthesis and Metabolic Engineering)
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21 pages, 8299 KiB  
Article
Genome-Wide Identification of the Geranylgeranyl Pyrophosphate Synthase (GGPS) Gene Family Associated with Natural Rubber Synthesis in Taraxacum kok-saghyz L. Rodin
by Lili Wang, Huan He, Jiayin Wang, Zhuang Meng, Lei Wang, Xiang Jin, Jianhang Zhang, Pingping Du, Liyu Zhang, Fei Wang, Hongbin Li and Quanliang Xie
Plants 2024, 13(19), 2788; https://doi.org/10.3390/plants13192788 - 4 Oct 2024
Viewed by 1485
Abstract
Taraxacum kok-saghyz Rodin (TKS) is a recognized alternative source of natural rubber comparable to the rubber tree. The geranylgeranyl pyrophosphate synthase (GGPS) catalyzed the synthesis of geranylgeranyl pyrophosphate (GGPP), which is an important enzyme in the secondary metabolism pathway. In this study, we [...] Read more.
Taraxacum kok-saghyz Rodin (TKS) is a recognized alternative source of natural rubber comparable to the rubber tree. The geranylgeranyl pyrophosphate synthase (GGPS) catalyzed the synthesis of geranylgeranyl pyrophosphate (GGPP), which is an important enzyme in the secondary metabolism pathway. In this study, we present the first analysis of the GGPS gene family in TKS, where a total of seven TkGGPS family members were identified. Their core motifs, conserved structural domains, gene structures, and cis-acting elements were described. In addition, two phylogenetic trees were constructed based on the Neighbor-Joining and Maximum-Likelihood methods, and the TkGGPSs were highly conserved and exhibited good collinearity with the other species. Transcriptome data showed that seven TkGGPS gene members were expressed in all the 12 tissues measured, and TkGGPS1, TkGGPS3, and TkGGPS6 were highly expressed in latex, suggesting that they may be associated with natural rubber synthesis. Meanwhile, quantitative real-time PCR (qRT-PCR) showed that the expression levels of the TkGGPS genes were regulated by the ethylene and methyl jasmonate (MeJA) pathways. Subcellular localization results indicated that all the TkGGPS proteins were also located in chloroplasts involved in photosynthesis in plants. This study will provide valuable insights into the selection of candidate genes for molecular breeding and natural rubber biosynthesis in TKS. Full article
(This article belongs to the Special Issue Advances in Plant Natural Products Biosynthesis and Metabolic Engineering)
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