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Advances in Plant Metabolite Research

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 November 2025 | Viewed by 8533

Special Issue Editor

Prof. Dr. Lingqiang Wang

E-Mail Website
Guest Editor
State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China
Interests: plant metabolites; regulatory networks; plant biochemistry

Special Issue Information

Dear Colleagues,

Plant metabolites comprise a diverse array of small molecules synthesized by plants, and play crucial roles in plant growth, development, defense and interactions with the environment. This Special Issue offers a comprehensive overview of the latest advancements in plant metabolism research at the molecular level, showcasing the intricate interplay of biosynthetic pathways, regulatory mechanisms and biological functions of plant metabolites. By harnessing the power of metabolomics, genomics, proteomics and metabolic engineering, researchers are unraveling the mysteries of nature’s biochemical arsenal, paving the way for innovative applications in agriculture, medicine and biotechnology. This collection of research articles showcases cutting-edge studies that unravel the complexities of plant metabolism, shedding light on the biosynthetic pathways, regulatory mechanisms and biological roles of plant metabolites. The findings presented in this collection of articles provide valuable insights into the molecular underpinnings of plant metabolism and open new avenues for harnessing the potential of plant metabolites in various fields, from agriculture to medicine and beyond. The topics of interest include, but are not limited to, the following:

  1. Biosynthetic pathways of plant metabolites;
  2. Regulatory mechanisms of plant metabolites;
  3. Biological functions of plant metabolites;
  4. Emerging metabolomics technologies and methodologies;
  5. Functional role of plant metabolites during abiotic and biotic stresses.

Prof. Dr. Lingqiang Wang
Guest Editor

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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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

  • metabolomics
  • regulatory networks
  • metabolic engineering
  • plant secondary metabolic defense
  • phytochemicals
  • antioxidant properties
  • mass spectrometry imaging
  • biotechnological applications
  • plant biochemistry

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Published Papers (6 papers)

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Research

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19 pages, 2718 KiB  
Article
Integrated Analysis of Terpenoid Profiles and Full-Length Transcriptome Reveals the Central Pathways of Sesquiterpene Biosynthesis in Atractylodes chinensis (DC.) Koidz
by Zheng Zhang, Yelin Tian, Xu Qiao, Hanqiu Li, Lizhi Ouyang, Xinyu Li, Xin Geng, Li Xiao, Yimian Ma and Yuan Li
Int. J. Mol. Sci. 2025, 26(3), 1074; https://doi.org/10.3390/ijms26031074 - 26 Jan 2025
Viewed by 805
Abstract
Atractylodes chinensis (DC.) Koidz. is an aromatic and medicinal plant in East Asia. The primary bioactive compounds in this species are sesquiterpenes, particularly β-eudesmol, hinesol, and atractylon. Cultivation techniques require improvement to meet the medicinal demands of this species. In this study, gas [...] Read more.
Atractylodes chinensis (DC.) Koidz. is an aromatic and medicinal plant in East Asia. The primary bioactive compounds in this species are sesquiterpenes, particularly β-eudesmol, hinesol, and atractylon. Cultivation techniques require improvement to meet the medicinal demands of this species. In this study, gas chromatography–mass spectrometry analysis of an A. chinensis germplasm showed its essential oil contained various sesquiterpenes, including a high relative ratio of β-eudesmol. Full-length transcriptome profiling of A. chinensis revealed 26 genes related to terpenoid biosynthesis. These genes belonged to 13 gene families, including five in the isopentenyl pyrophosphate synthase gene family and four in the terpene synthase gene family. The functions of the four terpene synthase genes were proposed based on gene expression patterns and phylogenetic relationships: one was thought to encode monoterpene synthase and three to encode sesquiterpene synthase. Based on the results, the central biosynthesis pathways of the major sesquiterpenes in the A. chinensis rhizome were proposed, and three sesquiterpene synthase genes were identified as expressed in the rhizome for the first time. AcHMGR, AcFPPS, and the three sesquiterpene synthase genes were proposed as potential targets for molecular breeding in A. chinensis to enhance its sesquiterpene content. Full article
(This article belongs to the Special Issue Advances in Plant Metabolite Research)
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23 pages, 8364 KiB  
Article
Orf116b Induces Pollen Abortion in a Novel Cotton (Gossypium hirsutum L.) Cytoplasmic Male Sterile Line J4A
by Min Li, Aziz Khan, Jie Zheng, Jingyi You, Li Chen, Najeeb Ullah, Songguo Wu, Xiaoshuang Wei, Munsif Ali Shad, Ruiyang Zhou and Lingqiang Wang
Int. J. Mol. Sci. 2024, 25(22), 12257; https://doi.org/10.3390/ijms252212257 - 14 Nov 2024
Viewed by 1057
Abstract
Cytoplasmic male sterile (CMS) systems have great potential in hybrid seed production in many plants. However, the incompatibility between the cytoplasmic and nuclear genes and the availability of fewer CMS lines limit the system’s application in cotton heterosis. Therefore, the present study sequenced [...] Read more.
Cytoplasmic male sterile (CMS) systems have great potential in hybrid seed production in many plants. However, the incompatibility between the cytoplasmic and nuclear genes and the availability of fewer CMS lines limit the system’s application in cotton heterosis. Therefore, the present study sequenced the mitochondrial (mt) genomes of a novel cotton (Gossypium hirsutum L.) CMS line J4A and its cytoplasmic nuclear homologous maintainer line J4B to investigate the mechanism underlying CMS and improve its application. A novel CMS gene, orf116b, was identified in the CMS line. Ectopic expression of orf116b in Escherichia coli suppressed growth, while its overexpression in Arabidopsis, rice, tobacco, and cotton led to complete or partial male sterility. Further analysis of anthers revealed mt disruption in J4A with higher levels of hydrogen peroxide (H2O2) and malondialdehyde (MDA), but lower levels of ATP and ribosomal protein (RP) than in J4B. Finally, a membrane-based yeast two-hybrid (MYTH) assay and bimolecular fluorescence complementation (BiFC) assays demonstrated that orf116b probably interacts with an anther-specific protein, LAT52. These observations collectively proved that orf116b is associated with early and stable pollen abortion in cotton, providing a foundation for further research on cotton fertility restoration and heterosis breeding. Full article
(This article belongs to the Special Issue Advances in Plant Metabolite Research)
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23 pages, 15226 KiB  
Article
Exploring Lignin Biosynthesis Genes in Rice: Evolution, Function, and Expression
by Munsif Ali Shad, Xukai Li, Muhammad Junaid Rao, Zixuan Luo, Xianlong Li, Aamir Ali and Lingqiang Wang
Int. J. Mol. Sci. 2024, 25(18), 10001; https://doi.org/10.3390/ijms251810001 - 17 Sep 2024
Cited by 1 | Viewed by 2387
Abstract
Lignin is nature’s second most abundant vascular plant biopolymer, playing significant roles in mechanical support, water transport, and stress responses. This study identified 90 lignin biosynthesis genes in rice based on phylogeny and motif constitution, and they belong to PAL, C4H, [...] Read more.
Lignin is nature’s second most abundant vascular plant biopolymer, playing significant roles in mechanical support, water transport, and stress responses. This study identified 90 lignin biosynthesis genes in rice based on phylogeny and motif constitution, and they belong to PAL, C4H, 4CL, HCT, C3H, CCoAOMT, CCR, F5H, COMT, and CAD families. Duplication events contributed largely to the expansion of these gene families, such as PAL, CCoAOMT, CCR, and CAD families, mainly attributed to tandem and segmental duplication. Microarray data of 33 tissue samples covering the entire life cycle of rice suggested fairly high PAL, HCT, C3H, CCoAOMT, CCR, COMT, and CAD gene expressions and rather variable C4H, 4CL, and F5H expressions. Some members of lignin-related genes (OsCCRL11, OsHCT1/2/5, OsCCoAOMT1/3/5, OsCOMT, OsC3H, OsCAD2, and OsPAL1/6) were expressed in all tissues examined. The expression patterns of lignin-related genes can be divided into two major groups with eight subgroups, each showing a distinct co-expression in tissues representing typically primary and secondary cell wall constitutions. Some lignin-related genes were strongly co-expressed in tissues typical of secondary cell walls. Combined HPLC analysis showed increased lignin monomer (H, G, and S) contents from young to old growth stages in five genotypes. Based on 90 genes’ microarray data, 27 genes were selected for qRT-PCR gene expression analysis. Four genes (OsPAL9, OsCAD8C, OsCCR8, and OsCOMTL4) were significantly negatively correlated with lignin monomers. Furthermore, eleven genes were co-expressed in certain genotypes during secondary growth stages. Among them, six genes (OsC3H, OsCAD2, OsCCR2, OsCOMT, OsPAL2, and OsPAL8) were overlapped with microarray gene expressions, highlighting their importance in lignin biosynthesis. Full article
(This article belongs to the Special Issue Advances in Plant Metabolite Research)
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14 pages, 36755 KiB  
Article
Identification of the Key Gene DfCCoAOMT1 through Comparative Analysis of Lignification in Dendrocalamus farinosus XK4 and ZPX Bamboo Shoots during Cold Storage
by Xin Zhao, Wenjuan Song, Sen Chen, Gang Xu, Zhijian Long, Heyi Yang, Ying Cao and Shanglian Hu
Int. J. Mol. Sci. 2024, 25(15), 8065; https://doi.org/10.3390/ijms25158065 - 24 Jul 2024
Cited by 2 | Viewed by 1048
Abstract
Dendrocalamus farinosus bamboo shoots, a species with rich nutritional value, are important in Southwest China. Lignin is an important factor affecting the postharvest flavor quality of bamboo shoots; however, the underlying mechanism of lignin deposition in D. farinosus bamboo shoots during cold storage is [...] Read more.
Dendrocalamus farinosus bamboo shoots, a species with rich nutritional value, are important in Southwest China. Lignin is an important factor affecting the postharvest flavor quality of bamboo shoots; however, the underlying mechanism of lignin deposition in D. farinosus bamboo shoots during cold storage is still not fully understood. In this study, the mutant D. farinosus XK4 with low lignin content at 3.11% and the cultivated variety ZPX at 4.47% were used as experimental materials. The lignin content of D. farinosus XK4 and ZPX, as well as the gene expression differences between them, were compared and analyzed during cold storage using transcriptomic and physiological methods. Our analysis revealed several key genes and found that D. farinosus CCoAOMT1 plays a key role in the regulatory network of bamboo shoots during cold storage. Tobacco heterologous transformation experiments demonstrated that overexpression of DfCCoAOMT1 significantly increases lignin content. This study provides a novel foundation for future research aimed at improving the postharvest quality and flavor of D. farinosus bamboo shoots through targeted genetic manipulation during cold storage. Full article
(This article belongs to the Special Issue Advances in Plant Metabolite Research)
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Review

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38 pages, 943 KiB  
Review
Nutrients and Bioactive Compounds from Cannabis sativa Seeds: A Review Focused on Omics-Based Investigations
by Tiziana M. Sirangelo, Gianfranco Diretto, Alessia Fiore, Simona Felletti, Tatiana Chenet, Martina Catani and Natasha Damiana Spadafora
Int. J. Mol. Sci. 2025, 26(11), 5219; https://doi.org/10.3390/ijms26115219 - 29 May 2025
Viewed by 175
Abstract
Hemp (Cannabis sativa L.) is a versatile crop that can be processed to obtain different products with multiple applications. Its seeds are a well-documented ancient source of proteins, fibers and fats, all of which possess high nutritional value. Additionally, metabolites such as [...] Read more.
Hemp (Cannabis sativa L.) is a versatile crop that can be processed to obtain different products with multiple applications. Its seeds are a well-documented ancient source of proteins, fibers and fats, all of which possess high nutritional value. Additionally, metabolites such as flavones and phenols are present in the seeds, contributing to their antioxidant properties. Due to hemp seeds’ distinctive nutritional profile, the interest in exploring the potential use in food and nutraceuticals is growing, and they can be considered an interesting and promising alternative resource for human and animal feeding. Omics studies on hemp seeds and their by-products are also being developed, and they contribute to improving our knowledge about the genome, transcriptome, proteome, metabolome/lipidome, and ionome of these sustainable food resources. This review illustrates the main nutrients and bioactive compounds of hemp seeds and explores the most relevant omics techniques and investigations related to them. It also addresses the various products derived from processing the whole seed, such as oil, dehulled seeds, hulls, flour, cakes, meals, and proteins. Moreover, this work discusses research aimed at elucidating the molecular mechanisms underlying their protein, lipid, fiber, and metabolic profile. The advantages of using omics and multi-omics approaches to highlight the nutritional values of hemp seed by-products are also discussed. In our opinion, this work represents an excellent starting point for researchers interested in studying hemp seeds as source of nutrients and bioactive compounds from a multi-level molecular perspective. Full article
(This article belongs to the Special Issue Advances in Plant Metabolite Research)
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34 pages, 3100 KiB  
Review
Plant Secondary Metabolites as Modulators of Mitochondrial Health: An Overview of Their Anti-Oxidant, Anti-Apoptotic, and Mitophagic Mechanisms
by Julia Anchimowicz, Piotr Zielonka and Slawomir Jakiela
Int. J. Mol. Sci. 2025, 26(1), 380; https://doi.org/10.3390/ijms26010380 - 4 Jan 2025
Cited by 3 | Viewed by 2133
Abstract
Plant secondary metabolites (PSMs) are a diverse group of bioactive compounds, including flavonoids, polyphenols, saponins, and terpenoids, which have been recognised for their critical role in modulating cellular functions. This review provides a comprehensive analysis of the effects of PSMs on mitochondrial health, [...] Read more.
Plant secondary metabolites (PSMs) are a diverse group of bioactive compounds, including flavonoids, polyphenols, saponins, and terpenoids, which have been recognised for their critical role in modulating cellular functions. This review provides a comprehensive analysis of the effects of PSMs on mitochondrial health, with particular emphasis on their therapeutic potential. Emerging evidence shows that these metabolites improve mitochondrial function by reducing oxidative stress, promoting mitochondrial biogenesis, and regulating key processes such as apoptosis and mitophagy. Mitochondrial dysfunction, a hallmark of many pathologies, including neurodegenerative disorders, cardiovascular diseases, and metabolic syndrome, has been shown to benefit from the protective effects of PSMs. Recent studies show that PSMs can improve mitochondrial dynamics, stabilise mitochondrial membranes, and enhance bioenergetics, offering significant promise for the prevention and treatment of mitochondrial-related diseases. The molecular mechanisms underlying these effects, including modulation of key signalling pathways and direct interactions with mitochondrial proteins, are discussed. The integration of PSMs into therapeutic strategies is highlighted as a promising avenue for improving treatment efficacy while minimising the side effects commonly associated with synthetic drugs. This review also highlights the need for future research to elucidate the specific roles of individual PSMs and their synergistic interactions within complex plant matrices, which may further optimise their therapeutic utility. Overall, this work provides valuable insights into the complex role of PSMs in mitochondrial health and their potential as natural therapeutic agents targeting mitochondrial dysfunction. Full article
(This article belongs to the Special Issue Advances in Plant Metabolite Research)
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