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Molecular and Metabolic Regulation of Plant Secondary Metabolism
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Molecular and Metabolic Regulation of Plant Secondary Metabolism

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: closed (20 February 2025) | Viewed by 34836

Special Issue Editors

Dr. Alexandra S. Dubrovina

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Guest Editor
Laboratory of Biotechnology, Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, 690022 Vladivostok, Russia
Interests: plant secondary metabolism; RNA interference; plant gene regulation; abiotic stress; transgenic plants; calcium sensor proteins
Special Issues, Collections and Topics in MDPI journals
Dr. Konstantin V. Kiselev

E-Mail Website
Guest Editor
Laboratory of Biotechnology, Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, 690022 Vladivostok, Russia
Interests: plant secondary metabolism; stilbenes; plant gene expression; plant cell cultures; calcium signaling
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Plant secondary metabolites have been the subject of intensive research due to their valuable pharmaceutical effects and contribution to plant disease resistance. This Special Issue is aimed to present new advances in understanding the natural mechanisms regulating plant secondary metabolism and new biotechnological approaches for plant secondary metabolite production. We invite original research papers, reviews, communications, and opinion papers devoted to molecular and metabolic regulation of plant secondary metabolism. Understanding secondary metabolite biosynthesis in plants could be useful for both the development of new plant protection strategies and for commercial biologically active compound production.

We welcome papers related but not limited to the following specific topics:

  • Environmental factors and cell signaling pathway regulating plant secondary metabolism.
  • Advancements in understanding biosyntesis of plant secondary metabolites.
  • Transcriptional regulation of plant secondary metabolism.
  • Biotechnological approaches for plant secondary metabolism regulation.
  • Production of plant secondary metabolites by biotechnological methods (plant cell cultures, microbial biotransformation etc.).

Dr. Alexandra S. Dubrovina
Dr. Konstantin V. Kiselev
Guest Editors

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Keywords

  • plant secondary metabolism
  • bioactive natural products
  • phytochemistry
  • plant cell cultures
  • secondary metabolite biosynthesis
  • plant biotechnology

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Published Papers (20 papers)

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15 pages, 4322 KiB  
Article
Application of Synephrine to Grape Increases Anthocyanin via Production of Hydrogen Peroxide, Not Phytohormones
by Masaya Suzuki, Aoi Kimura, Shunji Suzuki and Shinichi Enoki
Int. J. Mol. Sci. 2024, 25(11), 5912; https://doi.org/10.3390/ijms25115912 - 29 May 2024
Viewed by 1166
Abstract
Global warming has caused such problems as the poor coloration of grape skin and the decreased production of high-quality berries. We investigated the effect of synephrine (Syn) on anthocyanin accumulation. Anthocyanin accumulation in cultured grape cells treated with Syn at concentrations of 1 [...] Read more.
Global warming has caused such problems as the poor coloration of grape skin and the decreased production of high-quality berries. We investigated the effect of synephrine (Syn) on anthocyanin accumulation. Anthocyanin accumulation in cultured grape cells treated with Syn at concentrations of 1 mM or higher showed no significant difference, indicating that the accumulation was concentration-independent. On the other hand, anthocyanin accumulation was dependent on the compound used for treatment. The sugar/acid ratio of the juice from berries treated with Syn did not differ from the control. The expression of anthocyanin-biosynthesis-related genes, but not phytohormones, was increased by the treatment with Syn at 24 h or later. The Syn treatment of cultured cells increased SOD3 expression and hydrogen peroxide (H2O2) production from 3 to 24 h after treatment. Subsequently, the expression of CAT and APX6 encoding H2O2-scavenging enzymes was also increased. Treatment of cultured cells with Syn and H2O2 increased the expression of the H2O2-responsive gene Chit4 and the anthocyanin-biosynthesis-related genes mybA1 and UFGT 4 days after the treatment and increased anthocyanin accumulation 7 days after the treatment. On the other hand, the treatment of berries with Syn and H2O2 increased anthocyanin accumulation after 9 days. These results suggest that Syn increases anthocyanin accumulation through H2O2 production without changing phytohormone biosynthesis. Syn is expected to improve grape skin coloration and contribute to high-quality berry production. Full article
(This article belongs to the Special Issue Molecular and Metabolic Regulation of Plant Secondary Metabolism)
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24 pages, 4486 KiB  
Article
Adventitious and Hairy Root Cultures of Salvia apiana as a Source of Rosmarinic Acid
by Agata Krol, Adam Kokotkiewicz, Aleksandra Krolicka, Krzysztof Hinc, Anna Badura, Andzelika Lorenc, Urszula Marzec-Wroblewska, Adam Bucinski, Lukasz Kuzma and Maria Luczkiewicz
Int. J. Mol. Sci. 2025, 26(7), 3138; https://doi.org/10.3390/ijms26073138 - 28 Mar 2025
Viewed by 464
Abstract
For the first time, adventitious and hairy root cultures of Salvia apiana (white sage) have been established and analyzed for the content of secondary metabolites. Non-transformed roots derived from sterile seedlings were maintained on a full-strength IBA-supplemented SH medium. Adventitious roots yielded up [...] Read more.
For the first time, adventitious and hairy root cultures of Salvia apiana (white sage) have been established and analyzed for the content of secondary metabolites. Non-transformed roots derived from sterile seedlings were maintained on a full-strength IBA-supplemented SH medium. Adventitious roots yielded up to 44.5 mg/g and 18.7 mg/g DW rosmarinic acid when grown in shake flasks and immersion-column bioreactors, respectively. Transformed root cultures were established from S. apiana microshoots, infected with A4 and LBA9402 strains of Rhizobium rhizogenes. The obtained hairy root cultures (three and two clonal lines established using A4 and LBA9402 strains, respectively) were maintained in the PGR-free, full-strength SH medium. The most productive root line, established using A4 strain, accumulated rosmarinic acid at 38.1 and 39.6 mg/g DW when grown in shake flasks and spray bioreactors, respectively. Neither adventitious nor transformed roots of S. apiana produced diterpenoids, identified in roots of the field-grown plants, and instead proved to be a selective source of rosmarinic acid. Full article
(This article belongs to the Special Issue Molecular and Metabolic Regulation of Plant Secondary Metabolism)
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21 pages, 9752 KiB  
Article
Enhancing the Quality of Indoor-Grown Basil Microgreens with Low-Dose UV-B or UV-C Light Supplementation
by Ernest Skowron, Magdalena Trojak, Ilona Pacak, Paulina Węzigowska and Julia Szymkiewicz
Int. J. Mol. Sci. 2025, 26(5), 2352; https://doi.org/10.3390/ijms26052352 - 6 Mar 2025
Viewed by 491
Abstract
Controlled-environment crop production often weakens plants’ defense mechanisms, reducing the accumulation of protective phytochemicals essential to human health. Our previous studies demonstrated that short-term supplementation of low-dose ultraviolet (UV) light to the red–green–blue (RGB) spectrum effectively boosts secondary metabolite (SM) synthesis and antioxidant [...] Read more.
Controlled-environment crop production often weakens plants’ defense mechanisms, reducing the accumulation of protective phytochemicals essential to human health. Our previous studies demonstrated that short-term supplementation of low-dose ultraviolet (UV) light to the red–green–blue (RGB) spectrum effectively boosts secondary metabolite (SM) synthesis and antioxidant capacity in lettuce. This study explored whether similar effects occur in basil cultivars by supplementing the RGB spectrum with ultraviolet B (UV-B, 311 nm) or ultraviolet C (UV-C, 254 nm) light shortly before harvest. Molecular analyses focused on UV-induced polyphenol synthesis, particularly chalcone synthase (CHS) level, and UV light perception via the UVR8 receptor. The impact of high-energy UV radiation on the photosynthetic apparatus (PA) was also monitored. The results showed that UV-B supplementation did not harm the PA, while UV-C significantly impaired photosynthesis and restricted plant growth and biomass accumulation. In green-leaf (Sweet Large, SL) basil, UV-B enhanced total antioxidant capacity (TAC), increasing polyphenolic secondary metabolites and ascorbic acid (AsA) levels. UV-C also stimulated phenolic compound accumulation in SL basil but had no positive effects in the purple-leaf (Dark Opal, DO) cultivar. Interestingly, while the UV-B treatment promoted UVR8 monomerization in both cultivars, the enhanced CHS level and concomitant SM synthesis were noted only for SL basil. In addition, UV-C also induced CHS activity and SM synthesis in SL basil but clearly in a UVR8-independeted manner. These findings underscore the potential of UV light supplementation for enhancing plant functional properties, highlighting species- and cultivar-specific effects without compromising photosynthetic performance. Full article
(This article belongs to the Special Issue Molecular and Metabolic Regulation of Plant Secondary Metabolism)
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50 pages, 5112 KiB  
Review
Regulation of Flavonoid Biosynthesis by the MYB-bHLH-WDR (MBW) Complex in Plants and Its Specific Features in Cereals
by Andrey N. Bulanov, Elena A. Andreeva, Natalia V. Tsvetkova and Pavel A. Zykin
Int. J. Mol. Sci. 2025, 26(2), 734; https://doi.org/10.3390/ijms26020734 - 16 Jan 2025
Cited by 4 | Viewed by 1659
Abstract
Flavonoids are a large group of secondary metabolites, which are responsible for pigmentation, signaling, protection from unfavorable environmental conditions, and other important functions, as well as providing numerous benefits for human health. Various stages of flavonoid biosynthesis are subject to complex regulation by [...] Read more.
Flavonoids are a large group of secondary metabolites, which are responsible for pigmentation, signaling, protection from unfavorable environmental conditions, and other important functions, as well as providing numerous benefits for human health. Various stages of flavonoid biosynthesis are subject to complex regulation by three groups of transcription regulators—MYC-like bHLH, R2R3-MYB and WDR which form the MBW regulatory complex. We attempt to cover the main aspects of this intriguing regulatory system in plants, as well as to summarize information on their distinctive features in cereals. Published data revealed the following perspectives for further research: (1) In cereals, a large number of paralogs of MYC and MYB transcription factors are present, and their diversification has led to spatial and biochemical specialization, providing an opportunity to fine-tune the distribution and composition of flavonoid compounds; (2) Regulatory systems formed by MBW proteins in cereals possess distinctive features that are not yet fully understood and require further investigation; (3) Non-classical MB-EMSY-like complexes, WDR-independent MB complexes, and solely acting R2R3-MYB transcription factors are of particular interest for studying unique regulatory mechanisms in plants. More comprehensive understanding of flavonoid biosynthesis regulation will allow us to develop cereal varieties with the required flavonoid content and spatial distribution. Full article
(This article belongs to the Special Issue Molecular and Metabolic Regulation of Plant Secondary Metabolism)
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15 pages, 1784 KiB  
Review
The Scent of Lily Flowers: Advances in the Identification, Biosynthesis, and Regulation of Fragrance Components
by Yiwei Chen, Xiaoxuan Lu, Ting Gao and Yiwei Zhou
Int. J. Mol. Sci. 2025, 26(2), 468; https://doi.org/10.3390/ijms26020468 - 8 Jan 2025
Viewed by 1153
Abstract
Lilies (Lilium spp.) are renowned for their diverse and captivating floral scents, which are highly valued both commercially and ornamentally. This review provides a comprehensive overview of recent advancements in the identification, biosynthesis, and regulation of fragrance components in lily flowers. Various [...] Read more.
Lilies (Lilium spp.) are renowned for their diverse and captivating floral scents, which are highly valued both commercially and ornamentally. This review provides a comprehensive overview of recent advancements in the identification, biosynthesis, and regulation of fragrance components in lily flowers. Various volatile organic compounds (VOCs) that contribute to the unique scents of different lily species and cultivars, including terpenoids, benzenoids/phenylpropanoids, and fatty acid derivatives, are discussed. The release patterns of these compounds from different floral tissues and at different developmental stages are examined, highlighting the significant role of tepals. Detection methods such as gas chromatography–mass spectrometry (GC-MS) and sensory analysis are evaluated for their effectiveness in fragrance research. Additionally, the biosynthetic pathways of key fragrance compounds are explored, focusing on the terpenoid and benzenoid/phenylpropanoid pathways and the regulatory mechanisms involving transcription factors and environmental factors. This review also addresses the influence of genetic and environmental factors on fragrance production and proposes future research directions to enhance the aromatic qualities of lilies through selective genetic and breeding approaches. Emphasis is placed on the potential applications of these findings in the floral industry to improve the commercial value and consumer appeal of lily flowers. Full article
(This article belongs to the Special Issue Molecular and Metabolic Regulation of Plant Secondary Metabolism)
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19 pages, 5407 KiB  
Article
OsbHLH5 Synergically Regulates Phenolamide and Diterpenoid Phytoalexins Involved in the Defense of Rice Against Pathogens
by Shen Zhou, Ran Zhang, Qiming Wang, Jinjin Zhu, Junjie Zhou, Yangyang Sun, Shuangqian Shen and Jie Luo
Int. J. Mol. Sci. 2024, 25(22), 12152; https://doi.org/10.3390/ijms252212152 - 12 Nov 2024
Cited by 1 | Viewed by 1121
Abstract
Rice (Oryza sativa) produces phenolamides and diterpenoids as major phytoalexins. Although the biosynthetic pathways of phenolamides and diterpenoids in plants have been revealed, knowledge of their accumulation regulatory mechanisms remains limited, and, in particular, no co-regulatory factor has been identified to [...] Read more.
Rice (Oryza sativa) produces phenolamides and diterpenoids as major phytoalexins. Although the biosynthetic pathways of phenolamides and diterpenoids in plants have been revealed, knowledge of their accumulation regulatory mechanisms remains limited, and, in particular, no co-regulatory factor has been identified to date. Here, using a combined co-expression and evolutionary analysis, we identified the basic helix–loop–helix (bHLH) transcription factor OsbHLH5 as a positive bifunctional regulator of phenolamide and diterpenoid biosynthesis in rice. Metabolomic analysis revealed that OsbHLH5 significantly increased the content of phenolamides (such as feruloyl tryptamine (Fer-Trm) and p-coumaroyl tyramine (Cou-Tyr)) and diterpenoid phytoalexins (such as momilactones A, momilactones B) in the overexpression lines, while their content was reduced in the OsbHLH5 knockout lines. Gene expression and dual-luciferase assays revealed that OsbHLH5 activates phenolamide biosynthetic genes (including putrescine hydroxycinnamoyltransferase 3 (OsPHT3), tyramine hydroxycinnamoyltransferases 1/2 (OsTHT1/2), and tryptamine benzoyltransferase 2 (OsTBT2)) as well as diterpenoid biosynthetic genes (including copalyl diphosphate synthase 4 (OsCPS4) and kaurene synthase-like 4/7/10/11 (OsKSL4/7/10/11)). Furthermore, we have demonstrated that OsbHLH5 is induced by jasmonic acid (JA), while pathogen inoculation assays indicated that the overexpression of OsbHLH5 in transgenic rice plants leads to enhanced resistance to Xanthomonas oryzae pv. oryzae (Xoo). Overall, we have identified a positive regulator of phenolamide and diterpenoid biosynthesis and have demonstrated that biotic stress induces phytoalexin accumulation partly in an OsbHLH5-dependent manner, providing new insights into the metabolic interactions involved in pathogen response and offering valuable gene resources for the development, through genetic improvement, of new rice varieties that are resistant to diseases. Full article
(This article belongs to the Special Issue Molecular and Metabolic Regulation of Plant Secondary Metabolism)
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21 pages, 6858 KiB  
Article
Genome-Wide Identification of the bHLH Gene Family in Callerya speciosa Reveals Its Potential Role in the Regulation of Isoflavonoid Biosynthesis
by Liuping Chen, Xiaoming Tan, Ruhong Ming, Ding Huang, Yong Tan, Liangbo Li, Rongshao Huang and Shaochang Yao
Int. J. Mol. Sci. 2024, 25(22), 11900; https://doi.org/10.3390/ijms252211900 - 6 Nov 2024
Cited by 1 | Viewed by 1073
Abstract
Callerya speciosa (Champ. ex Benth.) Schot is a significant leguminous plant valued for its edible tuberous roots, which are a plentiful source of isoflavonoids. Basic helix–loop–helix (bHLH) transcription factors (TFs) have been reported to regulate secondary metabolism in plants, especially flavonoid biosynthesis. However, [...] Read more.
Callerya speciosa (Champ. ex Benth.) Schot is a significant leguminous plant valued for its edible tuberous roots, which are a plentiful source of isoflavonoids. Basic helix–loop–helix (bHLH) transcription factors (TFs) have been reported to regulate secondary metabolism in plants, especially flavonoid biosynthesis. However, the bHLH genes in C. speciosa have not yet been reported, and their regulatory role in isoflavonoid biosynthesis remains unexplored. Here, 146 CsbHLH genes were identified in the C. speciosa genome, classifying them into 23 subfamilies based on the gene structures and phylogenetic relationships. All the CsbHLH proteins contained both motifs 1 and 2, whereas motif 8 was only distributed in subgroup III (d + e). Collinearity analysis demonstrated that fragmental replications are the primary driver of CsbHLH evolution, with the majority of duplicated CsbHLH gene pairs experiencing selective pressure. Nine candidate CsbHLH genes were found to play a potential role in regulating isoflavonoid biosynthesis through a combination of gene-to-metabolite correlation analysis and weighted gene co-expression network analysis (WGCNA). Additionally, the cis-regulatory elements and response to MeJA of these nine genes were characterized and confirmed through quantitative real-time PCR (qRT-PCR) analysis. Among them, three CsbHLHs (CsbHLH9, CsbHLH89, and CsbHLH95) were selected for further investigation. Yeast two-hybrid (Y2H), dual-luciferase (LUC) assays, bimolecular fluorescence complementation (BiFC) assays, and transient transformation demonstrated that CsbHLH9 acted as a transcriptional activator through its interaction with CsMYB36 and binding to the promoters of isoflavonoid biosynthesis genes in a MeJA-induced manner, such as CsIFR2, CsI3′H2, and CsCHS4, to promote isoflavonoid (calycosin, calycosin-7-o-glucoside, and formononetin) accumulation. Our results establish a basis for the functional analysis of bHLH genes and investigations into the molecular mechanisms underlying isoflavonoid biosynthesis in C. speciosa. Full article
(This article belongs to the Special Issue Molecular and Metabolic Regulation of Plant Secondary Metabolism)
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14 pages, 2272 KiB  
Article
Functional and Physiological Characterization of Tyrosine Decarboxylases from Olea europaea L. Involved in the Synthesis of the Main Phenolics in Olive Fruit and Virgin Olive Oil
by Pilar Luaces, Rosario Sánchez, Jesús Expósito, Antonio J. Pérez-Pulido, Ana G. Pérez and Carlos Sanz
Int. J. Mol. Sci. 2024, 25(20), 10892; https://doi.org/10.3390/ijms252010892 - 10 Oct 2024
Viewed by 1029
Abstract
The phenolic composition of virgin olive oil (VOO) primarily depends on the phenolic content of the olive fruit. The purpose of this work was to characterize the first metabolic step in the synthesis of tyrosol (Ty) and hydroxytyrosol (HTy), whose derivatives are by [...] Read more.
The phenolic composition of virgin olive oil (VOO) primarily depends on the phenolic content of the olive fruit. The purpose of this work was to characterize the first metabolic step in the synthesis of tyrosol (Ty) and hydroxytyrosol (HTy), whose derivatives are by far the predominant phenolics in both olive fruit and VOO. To this end, two genes encoding tyrosine/DOPA decarboxylase enzymes, OeTDC1 and OeTDC2, have been identified and functionally and physiologically characterized. Both olive TDC proteins exclusively accept aromatic amino acids with phenolic side chains, such as tyrosine and 3,4-dihydroxyphenylalanine (DOPA), as substrates to produce tyramine and dopamine, respectively. These proteins exhibited a higher affinity for DOPA than for tyrosine, and the catalytic efficiency of both proteins was greater when DOPA was used as a substrate. Both olive TDC genes showed a fairly similar expression profile during olive fruit ontogeny, with OeTDC1 consistently expressed at higher levels than OeTDC2. Expression was particularly intense during the first few weeks after fruit set, coinciding with the active accumulation of Ty and HTy derivatives. The data suggest that both olive TDCs are responsible for the initial step in the synthesis of the most important phenolics, both quantitatively and functionally, in VOO. Full article
(This article belongs to the Special Issue Molecular and Metabolic Regulation of Plant Secondary Metabolism)
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23 pages, 18701 KiB  
Article
Physiological, Metabolome and Gene Expression Analyses Reveal the Accumulation and Biosynthesis Pathways of Soluble Sugars and Amino Acids in Sweet Sorghum under Osmotic Stresses
by Yan-Nong Cui, Shi-Jie Yan, Yi-Nuo Zhang, Rong Wang, Le-Ling Song, Yue Ma, Huan Guo and Pei-Zhi Yang
Int. J. Mol. Sci. 2024, 25(16), 8942; https://doi.org/10.3390/ijms25168942 - 16 Aug 2024
Cited by 1 | Viewed by 1048
Abstract
Water scarcity is a major environmental constraint on plant growth in arid regions. Soluble sugars and amino acids are essential osmolytes for plants to cope with osmotic stresses. Sweet sorghum is an important bioenergy crop and forage with strong adaptabilities to adverse environments; [...] Read more.
Water scarcity is a major environmental constraint on plant growth in arid regions. Soluble sugars and amino acids are essential osmolytes for plants to cope with osmotic stresses. Sweet sorghum is an important bioenergy crop and forage with strong adaptabilities to adverse environments; however, the accumulation pattern and biosynthesis basis of soluble sugars and amino acids in this species under osmotic stresses remain elusive. Here, we investigated the physiological responses of a sweet sorghum cultivar to PEG-induced osmotic stresses, analyzed differentially accumulated soluble sugars and amino acids after 20% PEG treatment using metabolome profiling, and identified key genes involved in the biosynthesis pathways of soluble sugars and amino acids using transcriptome sequencing. The results showed that the growth and photosynthesis of sweet sorghum seedlings were significantly inhibited by more than 20% PEG. After PEG treatments, the leaf osmotic adjustment ability was strengthened, while the contents of major inorganic osmolytes, including K+ and NO3−, remained stable. After 20% PEG treatment, a total of 119 and 188 differentially accumulated metabolites were identified in the stems and leaves, respectively, and the accumulations of soluble sugars such as raffinose, trehalose, glucose, sucrose, and melibiose, as well as amino acids such as proline, leucine, valine, serine, and arginine were significantly increased, suggesting that these metabolites should play key roles in osmotic adjustment of sweet sorghum. The transcriptome sequencing identified 1711 and 4978 DEGs in the stems, as well as 2061 and 6596 DEGs in the leaves after 20% PEG treatment for 6 and 48 h, respectively, among which the expressions of genes involved in biosynthesis pathways of sucrose (such as SUS1, SUS2, etc.), trehalose (including TPS6), raffinose (such as RAFS2 and GOLS2, etc.), proline (such as P5CS2 and P5CR), leucine and valine (including BCAT2), and arginine (such as ASS and ASL) were significantly upregulated. These genes should be responsible for the large accumulation of soluble sugars and amino acids under osmotic stresses. This study deepens our understanding of the important roles of individual soluble sugars and amino acids in the adaptation of sweet sorghum to water scarcity. Full article
(This article belongs to the Special Issue Molecular and Metabolic Regulation of Plant Secondary Metabolism)
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13 pages, 4389 KiB  
Article
Gas Chromatography–Mass Spectrometry Metabolite Analysis Combined with Transcriptomics Reveals Genes Involved in Wax Biosynthesis in Allium fistulosum L.
by Jiayi Xing, Huanhuan Xu, Mingzhao Zhu, Yuchen Zhang, Mifeng Bai, Xuyang Zhou, Huiying Liu and Yongqin Wang
Int. J. Mol. Sci. 2024, 25(11), 6106; https://doi.org/10.3390/ijms25116106 - 1 Jun 2024
Viewed by 1520
Abstract
Cuticular waxes are essential for protecting plants from various environmental stresses. Allium fistulosum serves as an excellent model for investigating the regulatory mechanisms underlying cuticular wax synthesis with notable epidermal wax characteristics. A combination of gas chromatography–mass spectrometry (GC–MS) metabolite analysis and transcriptomics [...] Read more.
Cuticular waxes are essential for protecting plants from various environmental stresses. Allium fistulosum serves as an excellent model for investigating the regulatory mechanisms underlying cuticular wax synthesis with notable epidermal wax characteristics. A combination of gas chromatography–mass spectrometry (GC–MS) metabolite analysis and transcriptomics was used to investigate variations in metabolites and gene expression patterns between the wild type (WT) and glossy mutant type (gl2) of A. fistulosum. The WT surface had a large number of acicular and lamellar waxy crystals, whereas the leaf surface of gl2 was essentially devoid of waxy crystals. And the results revealed a significant decrease in the content of 16-hentriacontanone, the principal component of cuticular wax, in the gl2 mutant. Transcriptomic analysis revealed 3084 differentially expressed genes (DEGs) between WT and gl2. Moreover, we identified 12 genes related to fatty acid or wax synthesis. Among these, 10 DEGs were associated with positive regulation of wax synthesis, whereas 2 genes exhibited negative regulatory functions. Furthermore, two of these genes were identified as key regulators through weighted gene co-expression network analysis. Notably, the promoter region of AfisC5G01838 (AfCER1-LIKE1) exhibited a 258-bp insertion upstream of the coding region in gl2 and decreased the transcription of the AfCER1-LIKE1 gene. This study provided insights into the molecular mechanisms governing cuticular wax synthesis in A. fistulosum, laying the foundation for future breeding strategies. Full article
(This article belongs to the Special Issue Molecular and Metabolic Regulation of Plant Secondary Metabolism)
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18 pages, 4860 KiB  
Article
The Chemical Composition and Transcriptome Analysis Reveal the Mechanism of Color Formation in Tea (Camellia sinensis) Pericarp
by Yueyang Du, Yongen Lin, Kaikai Zhang, Dylan O’Neill Rothenberg, Huan Zhang, Hui Zhou, Hongfeng Su and Lingyun Zhang
Int. J. Mol. Sci. 2023, 24(17), 13198; https://doi.org/10.3390/ijms241713198 - 25 Aug 2023
Cited by 2 | Viewed by 2252
Abstract
To elucidate the molecular mechanisms underlying the differential metabolism of albino (white), green, and purple pericarp coloration, biochemical profiling and transcriptome sequencing analyses were performed on three different tea pericarps, Zhongbaiyihao (Camellia sinensis L. var. Zhongbai), Jinxuan (Camellia sinensis L. var. [...] Read more.
To elucidate the molecular mechanisms underlying the differential metabolism of albino (white), green, and purple pericarp coloration, biochemical profiling and transcriptome sequencing analyses were performed on three different tea pericarps, Zhongbaiyihao (Camellia sinensis L. var. Zhongbai), Jinxuan (Camellia sinensis L. var. Jinxuan), and Baitangziya (Camellia sinensis L. var. Baitang). Results of biochemical analysis revealed that low chlorophyll content and low chlorophyll/carotene ratio may be the biochemical basis for albino characteristics in the ‘Zhongbaiyihao’ pericarp. The differentially expressed genes (DEGs) involved in anthocyanin biosynthesis, including DFR, F3′5′H, CCoAOMT, and 4-coumaroyl-CoA, were highly expressed in the purple ‘Baitangziya’ pericarp. In the chlorophyll synthesis of white pericarp, GUN5 (Genome Uncoupled 5) and 8-vinyl-reductase both showed high expression levels compared to the green one, which indicated that albino ‘Zhongbaiyihao’ pericarp had a higher chlorophyll synthesis capacity than ‘Jinxuan’. Meanwhile, chlorophyllase (CLH, CSS0004684) was lower in ‘Baitang’ than in ‘Jinxuan’ and ‘Zhongbaiyihao’ pericarp. Among the differentially expressed transcription factors, MYB59, WRKY41-like2 (CS ng17509), bHLH62 like1 (CS ng6804), and bHLH62-like3 (CSS0039948) were downregulated in Jinxuan pericarp, suggesting that transcription factors played a role in regulating tea pericarp coloration. These findings provide a better understanding of the molecular mechanisms and theoretical basis for utilizing functional components of tea pericarp. Full article
(This article belongs to the Special Issue Molecular and Metabolic Regulation of Plant Secondary Metabolism)
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23 pages, 700 KiB  
Review
Influence of Abiotic and Biotic Elicitors on Organogenesis, Biomass Accumulation, and Production of Key Secondary Metabolites in Asteraceae Plants
by Maria Petrova, Kamelia Miladinova-Georgieva and Maria Geneva
Int. J. Mol. Sci. 2024, 25(8), 4197; https://doi.org/10.3390/ijms25084197 - 10 Apr 2024
Cited by 15 | Viewed by 3070
Abstract
The medicinal plants of the Asteraceae family are a valuable source of bioactive secondary metabolites, including polyphenols, phenolic acids, flavonoids, acetylenes, sesquiterpene lactones, triterpenes, etc. Under stressful conditions, the plants develop these secondary substances to carry out physiological tasks in plant cells. Secondary [...] Read more.
The medicinal plants of the Asteraceae family are a valuable source of bioactive secondary metabolites, including polyphenols, phenolic acids, flavonoids, acetylenes, sesquiterpene lactones, triterpenes, etc. Under stressful conditions, the plants develop these secondary substances to carry out physiological tasks in plant cells. Secondary Asteraceae metabolites that are of the greatest interest to consumers are artemisinin (an anti-malarial drug from Artemisia annua L.—sweet wormwood), steviol glycosides (an intense sweetener from Stevia rebaudiana Bert.—stevia), caffeic acid derivatives (with a broad spectrum of biological activities synthesized from Echinacea purpurea (L.) Moench—echinacea and Cichorium intybus L.—chicory), helenalin and dihydrohelenalin (anti-inflammatory drug from Arnica montana L.—mountain arnica), parthenolide (“medieval aspirin” from Tanacetum parthenium (L.) Sch.Bip.—feverfew), and silymarin (liver-protective medicine from Silybum marianum (L.) Gaertn.—milk thistle). The necessity to enhance secondary metabolite synthesis has arisen due to the widespread use of these metabolites in numerous industrial sectors. Elicitation is an effective strategy to enhance the production of secondary metabolites in in vitro cultures. Suitable technological platforms for the production of phytochemicals are cell suspension, shoots, and hairy root cultures. Numerous reports describe an enhanced accumulation of desired metabolites after the application of various abiotic and biotic elicitors. Elicitors induce transcriptional changes in biosynthetic genes, leading to the metabolic reprogramming of secondary metabolism and clarifying the mechanism of the synthesis of bioactive compounds. This review summarizes biotechnological investigations concerning the biosynthesis of medicinally essential metabolites in plants of the Asteraceae family after various elicitor treatments. Full article
(This article belongs to the Special Issue Molecular and Metabolic Regulation of Plant Secondary Metabolism)
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17 pages, 8370 KiB  
Article
Tartary Buckwheat (Fagopyrum tataricum) FtTT8 Inhibits Anthocyanin Biosynthesis and Promotes Proanthocyanidin Biosynthesis
by Jiao Deng, Lijuan Wang, Lan Zhang, Chaojie Yang, Juan Huang, Liwei Zhu, Qingfu Chen, Ziye Meng, Fang Cai and Taoxiong Shi
Int. J. Mol. Sci. 2023, 24(24), 17368; https://doi.org/10.3390/ijms242417368 - 11 Dec 2023
Cited by 3 | Viewed by 1575
Abstract
Tartary buckwheat (Fagopyrum tataricum) is an important plant, utilized for both medicine and food. It has become a current research hotspot due to its rich content of flavonoids, which are beneficial for human health. Anthocyanins (ATs) and proanthocyanidins (PAs) are the [...] Read more.
Tartary buckwheat (Fagopyrum tataricum) is an important plant, utilized for both medicine and food. It has become a current research hotspot due to its rich content of flavonoids, which are beneficial for human health. Anthocyanins (ATs) and proanthocyanidins (PAs) are the two main kinds of flavonoid compounds in Tartary buckwheat, which participate in the pigmentation of some tissue as well as rendering resistance to many biotic and abiotic stresses. Additionally, Tartary buckwheat anthocyanins and PAs have many health benefits for humans and the plant itself. However, little is known about the regulation mechanism of the biosynthesis of anthocyanin and PA in Tartary buckwheat. In the present study, a bHLH transcription factor (TF) FtTT8 was characterized to be homologous with AtTT8 and phylogenetically close to bHLH proteins from other plant species. Subcellular location and yeast two-hybrid assays suggested that FtTT8 locates in the nucleus and plays a role as a transcription factor. Complementation analysis in Arabidopsis tt8 mutant showed that FtTT8 could not recover anthocyanin deficiency but could promote PAs accumulation. Overexpression of FtTT8 in red-flowering tobacco showed that FtTT8 inhibits anthocyanin biosynthesis and accelerates proanthocyanidin biosynthesis. QRT-PCR and yeast one-hybrid assay revealed that FtTT8 might bind to the promoter of NtUFGT and suppress its expression, while binding to the promoter of NtLAR and upregulating its expression in K326 tobacco. This displayed the bidirectional regulating function of FtTT8 that negatively regulates anthocyanin biosynthesis and positively regulates proanthocyanidin biosynthesis. The results provide new insights on TT8 in Tartary buckwheat, which is inconsistent with TT8 from other plant species, and FtTT8 might be a high-quality gene resource for Tartary buckwheat breeding. Full article
(This article belongs to the Special Issue Molecular and Metabolic Regulation of Plant Secondary Metabolism)
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15 pages, 3911 KiB  
Article
Integrated Metabolomics, Transcriptome and Functional Analysis Reveal Key Genes Are Involved in Tree Age-Induced Amino Acid Accumulation in Torreya grandis Nuts
by Weijie Chen, Jingwei Yan, Shan Zheng, Jinwei Suo, Heqiang Lou, Lili Song and Jiasheng Wu
Int. J. Mol. Sci. 2023, 24(23), 17025; https://doi.org/10.3390/ijms242317025 - 1 Dec 2023
Cited by 2 | Viewed by 1492
Abstract
Torreya grandis is native Chinese tree species of economic significance, renowned for its long lifespan and the rich nutritional value of its nuts. In this study, we analyzed the morphological characteristics, metabolites, associated gene expressions, and regulatory mechanism in nuts from young (10 [...] Read more.
Torreya grandis is native Chinese tree species of economic significance, renowned for its long lifespan and the rich nutritional value of its nuts. In this study, we analyzed the morphological characteristics, metabolites, associated gene expressions, and regulatory mechanism in nuts from young (10 years old) and old (1000 years old) T. grandis trees. We observed that the length, width, and weight of nuts from older trees were considerably greater than those from younger trees. Metabolomic analysis revealed that the concentrations of 18 amino acids and derivatives (including histidine and serine) in nuts from older trees were markedly higher than those in nuts from younger trees. Transcriptome and metabolomic correlation analysis identified 16 genes, including TgPK (pyruvate kinase), TgGAPDH (glyceraldehyde 3-phosphate dehydrogenase), and others, which exhibit higher expression levels in older trees compared to younger trees, as confirmed by qRT-PCR. These genes are associated with the biosynthesis of histidine, glutamic acid, tryptophan, and serine. Transient expression of TgPK in tobacco led to increased pyruvate kinase activity and amino acid content (histidine, tryptophan, and serine). Additionally, dual-luciferase assays and yeast one-hybrid results demonstrated that TgWRKY21 positively regulates TgPK expression by directly binding to the TgPK promoter. These findings not only demonstrate the nutritional differences between nuts from young and old trees but also offer fresh insights into the development of nutritional sources and functional components based on nuts from old trees, enriching our understanding of the potential benefits of utilizing nuts from older trees. Full article
(This article belongs to the Special Issue Molecular and Metabolic Regulation of Plant Secondary Metabolism)
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18 pages, 3557 KiB  
Article
Enhancement of Growth and Secondary Metabolites by the Combined Treatment of Trace Elements and Hydrogen Water in Wheat Sprouts
by Muniba Kousar, Yu Rim Kim, Ji Yeon Kim and Joonho Park
Int. J. Mol. Sci. 2023, 24(23), 16742; https://doi.org/10.3390/ijms242316742 - 25 Nov 2023
Cited by 3 | Viewed by 1765
Abstract
This study aimed to evaluate the response of Triticum aestivum to hydrogen water (HW) and trace elements treated with HW. A pot experiment was conducted to assess the growth indices, secondary metabolites, and antioxidant levels. The response surface methodology (RSM) approach was used [...] Read more.
This study aimed to evaluate the response of Triticum aestivum to hydrogen water (HW) and trace elements treated with HW. A pot experiment was conducted to assess the growth indices, secondary metabolites, and antioxidant levels. The response surface methodology (RSM) approach was used to ascertain the concentrations and significant interaction between treatments. The outcomes demonstrated that the combined treatment of Se acid and Mo oxide exhibited a notable positive effect on the growth and secondary metabolites, when treated with HW as compared to distilled water (DW). Notably, the interaction between these two treatments is significant, and the higher response was observed at the optimal concentration of 0.000005% for Se acid and 0.06% for Mo oxide. Additionally, an in vitro experiment revealed that the mixture treatment inhibits the accumulation of lipids in HepG2 hepatocytes cells. Moreover, metabolic analysis revealed that upregulated metabolites are linked to the inhibition of lipid accumulation. In addition, the analysis emphasizes that the continued benefits of higher plants as a renewable supply for chemicals compounds, especially therapeutic agents, are being expanded and amplified by these state-of-the-art technologies. Full article
(This article belongs to the Special Issue Molecular and Metabolic Regulation of Plant Secondary Metabolism)
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15 pages, 4227 KiB  
Article
Transcriptomic Analysis of the Reduction in Seed Oil Content through Increased Nitrogen Application Rate in Rapeseed (Brassica napus L.)
by Pengfei Hao, Yun Ren, Baogang Lin, Kaige Yi, Lan Huang, Xi Li, Lixi Jiang and Shuijin Hua
Int. J. Mol. Sci. 2023, 24(22), 16220; https://doi.org/10.3390/ijms242216220 - 12 Nov 2023
Cited by 1 | Viewed by 1926
Abstract
Nitrogen is essential for improving the seed oil yield of rapeseed (Brassica napus L.). However, the molecular mechanism by which increased nitrogen rates impact seed oil content is largely unknown. Therefore, a field experiment was conducted to determine how three nitrogen application [...] Read more.
Nitrogen is essential for improving the seed oil yield of rapeseed (Brassica napus L.). However, the molecular mechanism by which increased nitrogen rates impact seed oil content is largely unknown. Therefore, a field experiment was conducted to determine how three nitrogen application rates (120, 240, and 360 kg ha−1) regulated seed oil content via transcriptomic analysis. The results showed that the seed yield and the protein and total N contents increased from N1 to N3, with average increases of 57.2%, 16.9%, and 79.5%, respectively. However, the seed oil content significantly decreased from N1 to N3, with an average decrease of 8.6%. These results were repeated over a number of years. The quantity of oil protein bodies observed under a transmission electron microscope was in accordance with the ultimate seed oil and protein contents. As the nitrogen application rate increased, a substantial number of genes involved in the photosynthesis, glycolysis, and phenylpropanoid biosynthesis pathways were up-regulated, as were TF families, such as AP2/ERF, MYB, and NAC. The newly identified genes were mainly involved in carbohydrate, lipid, and amino acid metabolism. Metabolic flux analysis showed that most of the genes involved in glycolysis and fatty acid biosynthesis had higher transcript levels in the early development stages. Our results provide new insights into the molecular regulation of rapeseed seed oil content through increased nitrogen application rates. Full article
(This article belongs to the Special Issue Molecular and Metabolic Regulation of Plant Secondary Metabolism)
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14 pages, 1420 KiB  
Article
Involvement of the Calmodulin-like Protein Gene VaCML92 in Grapevine Abiotic Stress Response and Stilbene Production
by Olga A. Aleynova, Konstantin V. Kiselev, Andrey R. Suprun, Alexey A. Ananev and Alexandra S. Dubrovina
Int. J. Mol. Sci. 2023, 24(21), 15827; https://doi.org/10.3390/ijms242115827 - 31 Oct 2023
Cited by 9 | Viewed by 1361
Abstract
Calmodulin-like proteins (CMLs) are an important family of plant calcium sensor proteins that sense and decode changes in the intracellular calcium concentration in response to environmental and developmental stimuli. Nonetheless, the specific functions of individual CML family members remain largely unknown. This study [...] Read more.
Calmodulin-like proteins (CMLs) are an important family of plant calcium sensor proteins that sense and decode changes in the intracellular calcium concentration in response to environmental and developmental stimuli. Nonetheless, the specific functions of individual CML family members remain largely unknown. This study aims to explore the role of the Vitis amurensis VaCML92 gene in the development of its high stress resistance and the production of stilbenes. The expression of VaCML92 was sharply induced in V. amurensis cuttings after cold stress. The VaCML92 gene was cloned and its role in the abiotic stress responses and stilbene production in grapevine was further investigated. The VaCML92-overexpressing callus cell cultures of V. amurensis and soil-grown plants of Arabidopsis thaliana exhibited enhanced tolerance to cold stress and, to a lesser extent, to the drought, while their tolerance to heat stress and high salinity was not affected. In addition, the overexpression of VaCML92 increased stilbene production in the V. amurensis cell cultures by 7.8–8.7-fold. Taken together, the data indicate that the VaCML92 gene is involved as a strong positive regulator in the rapid response to cold stress, the induction of cold stress resistance and in stilbene production in wild grapevine. Full article
(This article belongs to the Special Issue Molecular and Metabolic Regulation of Plant Secondary Metabolism)
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18 pages, 14434 KiB  
Article
Genome-Wide Identification, Evolution, and Expression Analysis of the WD40 Subfamily in Oryza Genus
by Simin Ke, Yifei Jiang, Mingao Zhou and Yangsheng Li
Int. J. Mol. Sci. 2023, 24(21), 15776; https://doi.org/10.3390/ijms242115776 - 30 Oct 2023
Cited by 9 | Viewed by 2296
Abstract
The WD40 superfamily is widely found in eukaryotes and has essential subunits that serve as scaffolds for protein complexes. WD40 proteins play important regulatory roles in plant development and physiological processes, such as transcription regulation and signal transduction; it is also involved in [...] Read more.
The WD40 superfamily is widely found in eukaryotes and has essential subunits that serve as scaffolds for protein complexes. WD40 proteins play important regulatory roles in plant development and physiological processes, such as transcription regulation and signal transduction; it is also involved in anthocyanin biosynthesis. In rice, only OsTTG1 was found to be associated with anthocyanin biosynthesis, and evolutionary analysis of the WD40 gene family in multiple species is less studied. Here, a genome-wide analysis of the subfamily belonging to WD40-TTG1 was performed in nine AA genome species: Oryza sativa ssp. japonica, Oryza sativa ssp. indica, Oryza rufipogon, Oryza glaberrima, Oryza meridionalis, Oryza barthii, Oryza glumaepatula, Oryza nivara, and Oryza longistaminata. In this study, 383 WD40 genes in the Oryza genus were identified, and they were classified into four groups by phylogenetic analysis, with most members in group C and group D. They were found to be unevenly distributed across 12 chromosomes. A total of 39 collinear gene pairs were identified in the Oryza genus, and all were segmental duplications. WD40s had similar expansion patterns in the Oryza genus. Ka/Ks analyses indicated that they had undergone mainly purifying selection during evolution. Furthermore, WD40s in the Oryza genus have similar evolutionary patterns, so Oryza sativa ssp. indica was used as a model species for further analysis. The cis-acting elements analysis showed that many genes were related to jasmonic acid and light response. Among them, OsiWD40-26/37/42 contained elements of flavonoid synthesis, and OsiWD40-15 had MYB binding sites, indicating that they might be related to anthocyanin synthesis. The expression profile analysis at different stages revealed that most OsiWD40s were expressed in leaves, roots, and panicles. The expression of OsiWD40s was further analyzed by qRT-PCR in 9311 (indica) under various hormone treatments and abiotic stresses. OsiWD40-24 was found to be responsive to both phytohormones and abiotic stresses, suggesting that it might play an important role in plant stress resistance. And many OsiWD40s might be more involved in cold stress tolerance. These findings contribute to a better understanding of the evolution of the WD40 subfamily. The analyzed candidate genes can be used for the exploration of practical applications in rice, such as cultivar culture for colored rice, stress tolerance varieties, and morphological marker development. Full article
(This article belongs to the Special Issue Molecular and Metabolic Regulation of Plant Secondary Metabolism)
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15 pages, 2296 KiB  
Review
Overview and Recent Progress on the Biosynthesis and Regulation of Flavonoids in Ginkgo biloba L.
by Jing Guo, Yeqiao Wang, Jiaqi Li, Jingjing Zhang, Yaqiong Wu and Guibin Wang
Int. J. Mol. Sci. 2023, 24(19), 14604; https://doi.org/10.3390/ijms241914604 - 27 Sep 2023
Cited by 10 | Viewed by 4934
Abstract
Flavonoids and their derivatives play important roles in plants, such as exerting protective activity against biotic and abiotic stresses, functioning in visual signaling to attract pollinators, and regulating phytohormone activity. They are also important secondary metabolites that are beneficial to humans. Ginkgo biloba [...] Read more.
Flavonoids and their derivatives play important roles in plants, such as exerting protective activity against biotic and abiotic stresses, functioning in visual signaling to attract pollinators, and regulating phytohormone activity. They are also important secondary metabolites that are beneficial to humans. Ginkgo biloba L. is a well-known relict plant considered to be a “living fossil”. Flavonoids present in ginkgo leaves have antioxidant and anti-aging capacities and show good therapeutic effects on a variety of neurological diseases. To date, studies on flavonoids have mainly focused on their extraction, pharmacological effects, and component analysis and on the expression levels of the key genes involved. However, a systematic review summarizing the biosynthesis and regulatory mechanisms of ginkgo flavonoids is still lacking. Thus, this review was conducted to comprehensively introduce the biological characteristics, value, and utilization status of ginkgo; summarize the effects, biosynthetic pathways, and transcriptional regulation of flavonoids; and finally, discuss the factors (ecological factors, hormones, etc.) that regulate the biosynthesis of flavonoids in ginkgo. This review will provide a reference basis for future research on the biosynthesis and efficient utilization of flavonoids in ginkgo. Full article
(This article belongs to the Special Issue Molecular and Metabolic Regulation of Plant Secondary Metabolism)
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17 pages, 2990 KiB  
Article
Isoenzymes of the Flavonoid and Phenylpropanoid Pathways Show Organ-Specific Regulation during Apple Fruit Development
by Paolo Baldi, Elisa Asquini, Giovanni Nicolussi Golo, Francesca Populin and Mirko Moser
Int. J. Mol. Sci. 2023, 24(18), 14353; https://doi.org/10.3390/ijms241814353 - 20 Sep 2023
Viewed by 1406
Abstract
Elucidating the molecular mechanisms controlling fruit development is a primary target for the improvement of new apple (Malus × domestica Borkh.) cultivars. The first two weeks of development following pollination are crucial to determine fruit characteristics. During this period, a lot of [...] Read more.
Elucidating the molecular mechanisms controlling fruit development is a primary target for the improvement of new apple (Malus × domestica Borkh.) cultivars. The first two weeks of development following pollination are crucial to determine fruit characteristics. During this period, a lot of changes take place in apple fruit, going from rapid cell division to the production of important metabolites. In this work, attention was focused on the phenylpropanoid and flavonoid pathways responsible for the production of numerous compounds contributing to fruit quality, such as flavonols, catechins, dihydrochalcones and anthocyanins. A total of 17 isoenzymes were identified, belonging to seven classes of the phenylpropanoid and flavonoid pathways that, despite showing more than 80% sequence identity, showed differential expression regulation during the first two weeks of apple fruit development. This feature seems to be quite common for most of the enzymes of both pathways. Differential regulation of isoenzymes was shown to be present in both ‘Golden Delicious’ and a wild relative (Malus mandshurica), even though differences were also present. Each isoenzyme showed a specific pattern of expression in the flower and fruit organs, suggesting that genes coding for enzymes with the same function may control different aspects of plant biology. Finally, promoter analysis was performed in order to highlight differences in the number and type of regulatory motifs. Overall, our results indicate that the control of the expression of genes involved in the phenylpropanoid and flavonoid pathways may be very complex as not only enzymes belonging to the same class, but even putative isoenzymes, can have different roles for the plant. Such genes may represent an important regulatory mechanism, as they would allow the plant to fine-tune the processing of metabolic intermediates towards different branches of the pathway, for example, in an organ-specific way. Full article
(This article belongs to the Special Issue Molecular and Metabolic Regulation of Plant Secondary Metabolism)
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