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Molecular and Metabolic Regulation of Plant Secondary Metabolism

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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 September 2024 | Viewed by 10306

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Dr. Alexandra S. Dubrovina

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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
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Dr. Konstantin V. Kiselev

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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

Published Papers (10 papers)

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17 pages, 2990 KiB

Open AccessArticle

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 771

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 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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15 pages, 4227 KiB

Open AccessArticle

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

Viewed by 1032

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 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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18 pages, 3557 KiB

Open AccessArticle

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

Viewed by 929

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 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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23 pages, 700 KiB

Open AccessReview

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

Viewed by 487

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 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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15 pages, 2296 KiB

Open AccessReview

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

Viewed by 1671

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 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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18 pages, 14434 KiB

Open AccessArticle

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 1 | Viewed by 1039

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 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, 3911 KiB

Open AccessArticle

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 - 01 Dec 2023

Viewed by 764

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 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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14 pages, 1420 KiB

Open AccessArticle

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

Viewed by 696

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 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, 8370 KiB

Open AccessArticle

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

Viewed by 758

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 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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18 pages, 4860 KiB

Open AccessArticle

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 1 | Viewed by 1190

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. 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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