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Advances in Plant Physiology, Biochemistry, and Biotechnology for Natural Product Synthesis

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: 30 July 2025 | Viewed by 6303

Special Issue Editor

Dr. Farzana Sabir

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Guest Editor
1. LEAF, Linking Landscape, Environment, Agriculture and Food (LEAF), Departmento de Recursos Biológicos, Ambiente e Território (DRAT), Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisboa, Portugal
2. Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisbon, Portugal
Interests: plant physiology; plant molecular biology; plant biochemistry; medicinal plants; natural products; plant membrane transporters; abiotic stress
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The plant kingdom represents an immense reservoir of pharmacologically active compounds. Plants produce a broad array of secondary metabolites, and plant-derived compounds have been of human interest for centuries as flavours, fragrances, dyes, pesticides, and pharmaceuticals. They can be utilized—either in their original or semi-synthetic states. Presently, these natural products are mainly extracted from wild or cultivated plants in order to supply phytomolecules on demand. However, due to climate change, numerous environmental factors like drought, salinity, temperature, and heavy metals now affect the physiology and biochemistry of plants, eventually impeding the biosynthesis of their secondary metabolites. The biotechnological approach, centred upon utilizing plant cell cultures as green factories, is an attractive alternative. However, the lack of understanding of the biosynthetic pathways of many secondary metabolites limits the upscaling of their production at the cellular level. Recent advances in plant genomics and metabolite profiling offer tremendous prospects for exploring the complex biosynthesis of natural products to enhance their production and also produce value-added compounds. Additionally, utilizing combinatorial tools can also open the possibility of synthesizing rare and expensive natural products and generating entirely new compounds.

Leading by Dr. Farzana Sabir and assisting by our Topical Advisory Panel Member Dr. Małgorzata Adamiec (Department of Plant Physiology, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University, Poland), this Special Issue intends to emphasize recent research advances related to the production of secondary metabolites from medicinal plants. Specifically, this Issue will present studies dealing with physiological and biochemical changes of the medicinal plants under conditions of abiotic stress, various biotechnological approaches to enhancing the production of natural products. We welcome authors to submit original research articles, reviews, and short communications.

Dr. Farzana Sabir
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

  • medicinal plants
  • natural products
  • phytomedicine

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Published Papers (5 papers)

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Research

16 pages, 7315 KiB  
Article
Effects of CSN1/CSN2 Mutants in Flavonoid Metabolism on Rice (Oryza sativa L.)
by Xinhai Yu, Weijie Yue, Xinyue Jia, Hua Zeng, Yanxi Liu, Miao Xu, Ming Wu and Liquan Guo
Int. J. Mol. Sci. 2025, 26(6), 2677; https://doi.org/10.3390/ijms26062677 - 17 Mar 2025
Viewed by 211
Abstract
The key flavonoid biosynthesis-related genes and their molecular features in rice have not been comprehensively and systematically characterized. In this study, we investigated the glumes of OsCSN1 mutants and OsCSN2 mutants and found the changes in the total flavonoid contents of the OsCSN2 [...] Read more.
The key flavonoid biosynthesis-related genes and their molecular features in rice have not been comprehensively and systematically characterized. In this study, we investigated the glumes of OsCSN1 mutants and OsCSN2 mutants and found the changes in the total flavonoid contents of the OsCSN2 mutants to be more pronounced than those of the OsCSN1 mutants and the changes in the anthocyanin contents of the OsCSN1 mutants to be more pronounced than those of the OsCSN2 mutants. In addition, key genes related to flavonoid synthesis, OsCHI, showed a more pronounced up-regulation trend, and the OsDFR gene, which encodes a precursor enzyme for anthocyanin synthesis, showed a clear down-regulation trend. And yeast two-hybrid experiments showed that OsCSN1 and OsCSN2 had the ability to interact with OsCUL4. In summary, OsCSN1 and OsCSN2 may regulate the metabolism of flavonoids in rice through CUL4-based E3 ligase, and the two subunits play different roles, laying a foundation for the study of the mechanism of flavonoid metabolism in monocotyledonous plants. Full article
(This article belongs to the Special Issue Advances in Plant Physiology, Biochemistry, and Biotechnology for Natural Product Synthesis)
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21 pages, 13386 KiB  
Article
Unveiling the Role of β-Glucosidase Genes in Bletilla striata’s Secondary Metabolism: A Genome-Wide Analysis
by Mengwei Xu, Hongwei Li, Hongyuan Luo, Jingyi Liu, Kunqian Li, Qingqing Li, Ning Yang and Delin Xu
Int. J. Mol. Sci. 2024, 25(23), 13191; https://doi.org/10.3390/ijms252313191 - 8 Dec 2024
Cited by 1 | Viewed by 1126
Abstract
β-glucosidases (BGLUs) are abundant enzymes in plants that play pivotal roles in cell wall modification, hormone signal transduction, secondary metabolism, defense against herbivores, and volatile compound release. Bletilla striata, a perennial herb revered for its therapeutic properties, lacks a comprehensive analysis of [...] Read more.
β-glucosidases (BGLUs) are abundant enzymes in plants that play pivotal roles in cell wall modification, hormone signal transduction, secondary metabolism, defense against herbivores, and volatile compound release. Bletilla striata, a perennial herb revered for its therapeutic properties, lacks a comprehensive analysis of its BGLU gene family despite the critical role these genes play in plant secondary metabolism. This study aims to perform a genome-wide analysis of the BGLU gene family in B. striata (BsBGLU) to elucidate their functions and regulatory mechanisms in secondary metabolite biosynthesis. We conducted a genome-wide screening to identify BsBGLU, followed by phylogenetic analysis to classify these genes into groups. Sequence characteristics were analyzed to predict functional roles. Simple sequence repeat (SSR) markers were examined to assess conservation and polymorphism among different landraces. Expression profiles of BsBGLUs were evaluated under sodium acetate and salicylic acid elicitor treatments and across different tissues. The accumulation of phylogenetic metabolites in different treatments and tissues was also analyzed by HPLC and LCMS detection to explore the correlation between gene expression and metabolite accumulation. A total of 23 BsBGLU genes were identified and classified into eight distinct groups. Sequence analysis suggested diverse functions related to hormone responses, secondary metabolism, and stress resistance. BsBGLUs with SSR sequences were conserved yet showed polymorphism among different B. striata landraces. Under elicitor treatments, expression profiling revealed that BsBGLUs significantly modulate the synthesis of secondary metabolites such as dactylorhin A and militarine. Tissue-specific expression analysis indicated that BsBGLU15 and BsBGLU28 were highly expressed in tubers compared to other tissues, suggesting their central role and a potential negative regulatory effect in metabolite accumulation. The elicitor NaAc can regulate metabolite synthesis by modulating the expression of BsBGLUs. The BsBGLU gene family in B. striata is integral to the modulation of secondary metabolite biosynthesis and accumulation and can respond to elicitors to promote the synthesis of militarine. These findings provide a theoretical foundation for the further exploration of BsBGLU gene functions and their regulatory mechanisms, advancing the production of medicinally active compounds in B. striata. Full article
(This article belongs to the Special Issue Advances in Plant Physiology, Biochemistry, and Biotechnology for Natural Product Synthesis)
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9 pages, 1451 KiB  
Article
Heterologous Expression of MYB Gene (Rosea1) or bHLH Gene (Delila) from Antirrhinum Increases the Phenolics Pools in Salvia miltiorrhiza
by Qian Tian, Wei Han, Donghao Wang and Zhezhi Wang
Int. J. Mol. Sci. 2024, 25(22), 11917; https://doi.org/10.3390/ijms252211917 - 6 Nov 2024
Viewed by 774
Abstract
Phenolic acids have health-promoting properties, however, but their low concentrations in Salvia miltiorrhiza limit broader medicinal applications. MYB and bHLH transcription factors activate multiple target genes involved in phenylpropanoid metabolism, thereby enhancing the production of various secondary metabolites. We introduced the MYB transcription [...] Read more.
Phenolic acids have health-promoting properties, however, but their low concentrations in Salvia miltiorrhiza limit broader medicinal applications. MYB and bHLH transcription factors activate multiple target genes involved in phenylpropanoid metabolism, thereby enhancing the production of various secondary metabolites. We introduced the MYB transcription factor Antirrhinum Rosea1 (AmROS1) or Delila (AmDEL) into S. miltiorrhiza and observed that antioxidant activity in transgenic plants increased by 1.40 to 1.80-fold. The total content was significantly higher in transformants compared to the controls. Furthermore, heterologous expression of AmROS1 or AmDEL triggered moderate accumulations of rosmarinic acid and salvianolic acid at various growth stages. Levels of total phenolics, total flavonoids, and anthocyanins were significantly elevated. These biological and phytochemical alterations were correlated with the upregulated expression of genes involved in phenolic acid biosynthesis. Our findings demonstrate that AmROS1 and AmDEL function as a transcriptional activator in phenolic acids biosynthesis. This study offers further insights into the heterologous or homologous regulation of phenolics production, potentially enabling its engineering in S. miltiorrhiza. Full article
(This article belongs to the Special Issue Advances in Plant Physiology, Biochemistry, and Biotechnology for Natural Product Synthesis)
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19 pages, 6321 KiB  
Article
Physiological, Biochemical, and Molecular Analyses Reveal Dark Heartwood Formation Mechanism in Acacia melanoxylon
by Ruping Zhang, Xiaogang Bai, Zhaoli Chen, Mengjiao Chen, Xiangyang Li, Bingshan Zeng and Bing Hu
Int. J. Mol. Sci. 2024, 25(9), 4974; https://doi.org/10.3390/ijms25094974 - 2 May 2024
Cited by 1 | Viewed by 1365
Abstract
Acacia melanoxylon is highly valued for its commercial applications, with the heartwood exhibiting a range of colors from dark to light among its various clones. The underlying mechanisms contributing to this color variation, however, have not been fully elucidated. In an effort to [...] Read more.
Acacia melanoxylon is highly valued for its commercial applications, with the heartwood exhibiting a range of colors from dark to light among its various clones. The underlying mechanisms contributing to this color variation, however, have not been fully elucidated. In an effort to understand the factors that influence the development of dark heartwood, a comparative analysis was conducted on the microstructure, substance composition, differential gene expression, and metabolite profiles in the sapwood (SW), transition zone (TZ), and heartwood (HW) of two distinct clones, SR14 and SR25. A microscopic examination revealed that heartwood color variations are associated with an increased substance content within the ray parenchyma cells. A substance analysis indicated that the levels of starches, sugars, and lignin were more abundant in SP compared to HW, while the concentrations of phenols, flavonoids, and terpenoids were found to be higher in HW than in SP. Notably, the dark heartwood of the SR25 clone exhibited greater quantities of phenols and flavonoids compared to the SR14 clone, suggesting that these compounds are pivotal to the color distinction of the heartwood. An integrated analysis of transcriptome and metabolomics data uncovered a significant accumulation of sinapyl alcohol, sinapoyl aldehyde, hesperetin, 2′, 3, 4, 4′, 6′-peptahydroxychalcone 4′-O-glucoside, homoeriodictyol, and (2S)-liquiritigenin in the heartwood of SR25, which correlates with the up-regulated expression of CCRs (evm.TU.Chr3.1751, evm.TU.Chr4.654_667, evm.TU.Chr4.675, evm.TU.Chr4.699, and evm.TU.Chr4.704), COMTs (evm.TU.Chr13.3082, evm.TU.Chr13.3086, and evm.TU.Chr7.1411), CADs (evm.TU.Chr10.2175, evm.TU.Chr1.3453, and evm.TU.Chr8.1600), and HCTs (evm.TU.Chr4.1122, evm.TU.Chr4.1123, evm.TU.Chr8.1758, and evm.TU.Chr9.2960) in the TZ of A. melanoxylon. Furthermore, a marked differential expression of transcription factors (TFs), including MYBs, AP2/ERFs, bHLHs, bZIPs, C2H2s, and WRKYs, were observed to be closely linked to the phenols and flavonoids metabolites, highlighting the potential role of multiple TFs in regulating the biosynthesis of these metabolites and, consequently, influencing the color variation in the heartwood. This study facilitates molecular breeding for the accumulation of metabolites influencing the heartwood color in A. melanoxylon, and offers new insights into the molecular mechanisms underlying heartwood formation in woody plants. Full article
(This article belongs to the Special Issue Advances in Plant Physiology, Biochemistry, and Biotechnology for Natural Product Synthesis)
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18 pages, 3379 KiB  
Article
Chemical Composition of Methanol Extracts from Leaves and Flowers of Anemonopsis macrophylla (Ranunculaceae)
by Vera A. Kostikova, Natalia V. Petrova, Alexander A. Chernonosov, Vladimir V. Koval, Evgeniia R. Kovaleva, Wei Wang and Andrey S. Erst
Int. J. Mol. Sci. 2024, 25(2), 989; https://doi.org/10.3390/ijms25020989 - 12 Jan 2024
Cited by 2 | Viewed by 1842
Abstract
Anemonopsis Siebold et Zucc. is an unstudied single-species genus belonging to the tribe Cimicifugeae (Ranunculaceae). The only species of this genus—Anemonopsis macrophylla Siebold and Zucc.—is endemic to Japan. There are no data on its chemical composition. This work is the first to [...] Read more.
Anemonopsis Siebold et Zucc. is an unstudied single-species genus belonging to the tribe Cimicifugeae (Ranunculaceae). The only species of this genus—Anemonopsis macrophylla Siebold and Zucc.—is endemic to Japan. There are no data on its chemical composition. This work is the first to determine (with liquid chromatography–high-resolution mass spectrometry, LC-HRMS) the chemical composition of methanol extracts of leaves and flowers of A. macrophylla. More than 100 compounds were identified. In this plant, the classes of substances are coumarins (13 compounds), furocoumarins (3), furochromones (2), phenolic acids (21), flavonoids (27), and fatty acids and their derivatives (15 compounds). Isoferulic acid (detected in extracts from this plant) brings this species closer to plants of the genus Cimicifuga, one of the few genera containing this acid and ferulic acid at the same time. Isoferulic acid is regarded as a reference component of a quality indicator of Cimicifuga raw materials. The determined profiles of substances are identical between the leaf and flower methanol extracts. Differences in levels of some identified substances were revealed between the leaf and flower extracts of A. macrophylla; these differences may have a substantial impact on the manifestation of the biological and pharmacological effects of the extracts in question. Full article
(This article belongs to the Special Issue Advances in Plant Physiology, Biochemistry, and Biotechnology for Natural Product Synthesis)
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