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Metabolites
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Identification of Secondary Metabolites by Multi-Omics Methods
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Identification of Secondary Metabolites by Multi-Omics Methods

A special issue of Metabolites (ISSN 2218-1989). This special issue belongs to the section "Plant Metabolism".

Deadline for manuscript submissions: closed (31 December 2023) | Viewed by 10270

Special Issue Editors

Prof. Dr. Xin Fang

E-Mail Website
Guest Editor
State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
Interests: plant specialized metabolites biosynthesis; plant natural products chemistry; plant genomics; terpenoids; enzymology
Prof. Dr. Zhonghua Tang

E-Mail Website
Guest Editor
College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin 150040, China
Interests: research based on multi-omics to investigate the mechanism of metabolic regulation of plant resources

Special Issue Information

Dear Colleagues，

Plant secondary metabolites (SMs) are widely used as drugs, food supplements, dyes and so on. Although the isolation of individual metabolites from plant material and the application of appropriate biological assays is still a common method to evaluate the function of SMs, the emergence of omics, such as transcriptome and metabolomics, can systematically scan changes in the metabolites in vivo, providing an unbiased view of the biological processes. Therefore, omics is widely used in the active ingredients of traditional herbs, nutrition for crops and functional factors in food. This Special Issue aims to explore applications of metabolomic tools in natural products from plants, herbs or food materials. The submission of manuscripts focusing on new structures (including isolation and structure determination), the functions of natural products, as well as changes in SMs of a crop or herb during growth or post-harvest using metabolomics or metabolomics-based omics is strongly encouraged.

Prof. Dr. Xin Fang
Prof. Dr. Zhonghua Tang
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Metabolites is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • crop
  • fermentation
  • metabolomics
  • phytochemistry
  • transcriptome

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Published Papers (6 papers)

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Editorial

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3 pages, 156 KiB  
Editorial
Identification of Secondary Metabolites by Multi-Omics Methods
by Xin Fang
Metabolites 2024, 14(11), 597; https://doi.org/10.3390/metabo14110597 - 6 Nov 2024
Viewed by 405
Abstract
Plant natural products, also known as plant specialized metabolites (SMs) due to their lineage-specific distribution, are small molecules synthesized by plants to adapt to changing environments [...] Full article
(This article belongs to the Special Issue Identification of Secondary Metabolites by Multi-Omics Methods)

Research

Jump to: Editorial

15 pages, 1920 KiB  
Article
Combined Activity of Saponin B Isolated from Dodonaea viscosa Seeds with Pesticide Azadirachtin against the Pest Spodoptera litura
by Hang Yu, Boyu Liu, Yuhan Zhao, Jinliang Li, Guoxing Wu, Junhong Ma, Furong Gui, Feng Tao, Xiaojiang Hao, Xiao Ding and Xiaoping Qin
Metabolites 2024, 14(1), 15; https://doi.org/10.3390/metabo14010015 - 25 Dec 2023
Viewed by 1595
Abstract
Azadirachtin is regarded as one of the best botanical pesticides due to its broad spectrum of insecticides and low interference with natural enemies. To enhance the effect of azadirachtin and slow down the generation of resistance, the combined activity was studied. Here, we [...] Read more.
Azadirachtin is regarded as one of the best botanical pesticides due to its broad spectrum of insecticides and low interference with natural enemies. To enhance the effect of azadirachtin and slow down the generation of resistance, the combined activity was studied. Here, we found that Dodonaea viscosa saponin B (DVSB) isolated from the seeds of Dodonaea viscosa has good combined activity with the azadirachtin. The mixture of DVSB and azadirachtin in a volume ratio of 1:4 had the strongest combined effect against Spodoptera litura, with a co-toxicity coefficient (CTC) of 212.87. DVSB exerted its combined activity by affecting the contact angle, surface tension, maximum retention and cell membrane permeability. When mixed with DVSB, the contact angle and surface tension decreased by 30.38% and 23.68%, and the maximum retention increased by 77.15%. DVSB was screened as an effective combined activity botanical compound of azadirachtin upon the control of S. litura and highlights the potential application of botanical compounds as pesticide adjuvants in the pest management. Full article
(This article belongs to the Special Issue Identification of Secondary Metabolites by Multi-Omics Methods)
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16 pages, 3038 KiB  
Article
Altitudinal Variation on Metabolites, Elements, and Antioxidant Activities of Medicinal Plant Asarum
by Liben Pan, Nan Yang, Yushu Sui, Yi Li, Wen Zhao, Liqiu Zhang, Liqiang Mu and Zhonghua Tang
Metabolites 2023, 13(12), 1193; https://doi.org/10.3390/metabo13121193 - 9 Dec 2023
Cited by 5 | Viewed by 1794
Abstract
Asarum (Asarum sieboldii Miq. f. seoulense (Nakai) C. Y. Cheng et C. S. Yang) is a medicinal plant that contains asarinin and sesamin, which possess extensive medicinal value. The adaptation and distribution of Asarum’s plant growth are significantly affected by altitude. [...] Read more.
Asarum (Asarum sieboldii Miq. f. seoulense (Nakai) C. Y. Cheng et C. S. Yang) is a medicinal plant that contains asarinin and sesamin, which possess extensive medicinal value. The adaptation and distribution of Asarum’s plant growth are significantly affected by altitude. Although most studies on Asarum have concentrated on its pharmacological activities, little is known about its growth and metabolites with respect to altitude. In this study, the physiology, ionomics, and metabolomics were investigated and conducted on the leaves and roots of Asarum along an altitude gradient, and the content of its medicinal components was determined. The results showed that soil pH and temperature both decreased along the altitude, which restricts the growth of Asarum. The accumulation of TOC, Cu, Mg, and other mineral elements enhanced the photosynthetic capacity and leaf plasticity of Asarum in high-altitude areas. A metabolomics analysis revealed that, at high altitude, nitrogen metabolism in leaves was enhanced, while carbon metabolism in roots was enhanced. Furthermore, the metabolic pathways of some phenolic substances, including syringic acid, vanillic acid, and ferulic acid, were altered to enhance the metabolism of organic acids. The study uncovered the growth and metabolic responses of Asarum to varying altitudes, providing a theoretical foundation for the utilization and cultivation of Asarum. Full article
(This article belongs to the Special Issue Identification of Secondary Metabolites by Multi-Omics Methods)
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14 pages, 2262 KiB  
Article
Miltiradiene Production by Cytoplasmic Metabolic Engineering in Nicotiana benthamiana
by Xiangxiang Ren, Chuhang Lin, Yanbo Huang, Tao Su, Juan Guo and Lei Yang
Metabolites 2023, 13(12), 1188; https://doi.org/10.3390/metabo13121188 - 6 Dec 2023
Cited by 1 | Viewed by 1850
Abstract
Plant natural products are important sources of innovative drugs, but the extraction and isolation of medicinal natural products from plants is challenging as these compounds have complex structures that are difficult to synthesize chemically. Therefore, utilizing heterologous expression systems to produce medicinal natural [...] Read more.
Plant natural products are important sources of innovative drugs, but the extraction and isolation of medicinal natural products from plants is challenging as these compounds have complex structures that are difficult to synthesize chemically. Therefore, utilizing heterologous expression systems to produce medicinal natural products in plants is a novel, environmentally friendly, and sustainable method. In this study, Nicotiana benthamiana was used as the plant platform to successfully produce miltiradiene, the key intermediate of tanshinones, which are the bioactive constituents of the Chinese medicinal plant Salvia miltiorrhiza. The yield of miltiradiene was increased through cytoplasmic engineering strategies combined with the enhancement of isoprenoid precursors. Additionally, we discovered that overexpressing SmHMGR alone accelerated apoptosis in tobacco leaves. Due to the richer membrane systems and cofactors in tobacco compared to yeast, tobacco is more conducive to the expression of plant enzymes. Therefore, this study lays the foundation for dissecting the tanshinone biosynthetic pathway in tobacco, which is essential for subsequent research. Additionally, it highlights the potential of N. benthamiana as an alternative platform for the production of natural products in plants. Full article
(This article belongs to the Special Issue Identification of Secondary Metabolites by Multi-Omics Methods)
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35 pages, 10691 KiB  
Article
Non-Targeted Metabolomic Analysis of Arabidopsis thaliana (L.) Heynh: Metabolic Adaptive Responses to Stress Caused by N Starvation
by Jorge David Cadena-Zamudio, Juan Luis Monribot-Villanueva, Claudia-Anahí Pérez-Torres, Fulgencio Alatorre-Cobos, José Antonio Guerrero-Analco and Enrique Ibarra-Laclette
Metabolites 2023, 13(9), 1021; https://doi.org/10.3390/metabo13091021 - 18 Sep 2023
Viewed by 1693
Abstract
As sessile organisms, plants develop the ability to respond and survive in changing environments. Such adaptive responses maximize phenotypic and metabolic fitness, allowing plants to adjust their growth and development. In this study, we analyzed the metabolic plasticity of Arabidopsis thaliana in response [...] Read more.
As sessile organisms, plants develop the ability to respond and survive in changing environments. Such adaptive responses maximize phenotypic and metabolic fitness, allowing plants to adjust their growth and development. In this study, we analyzed the metabolic plasticity of Arabidopsis thaliana in response to nitrate deprivation by untargeted metabolomic analysis and using wild-type (WT) genotypes and the loss-of-function nia1/nia2 double mutant. Secondary metabolites were identified using seedlings grown on a hydroponic system supplemented with optimal or limiting concentrations of N (4 or 0.2 mM, respectively) and harvested at 15 and 30 days of age. Then, spectral libraries generated from shoots and roots in both ionization modes (ESI +/−) were compared. Totals of 3407 and 4521 spectral signals (m/z_rt) were obtained in the ESI+ and ESI− modes, respectively. Of these, approximately 50 and 65% were identified as differentially synthetized/accumulated. This led to the presumptive identification of 735 KEGG codes (metabolites) belonging to 79 metabolic pathways. The metabolic responses in the shoots and roots of WT genotypes at 4 mM of N favor the synthesis/accumulation of metabolites strongly related to growth. In contrast, for the nia1/nia2 double mutant (similar as the WT genotype at 0.2 mM N), metabolites identified as differentially synthetized/accumulated help cope with stress, regulating oxidative stress and preventing programmed cell death, meaning that metabolic responses under N starvation compromise growth to prioritize a defensive response. Full article
(This article belongs to the Special Issue Identification of Secondary Metabolites by Multi-Omics Methods)
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10 pages, 799 KiB  
Article
Chemical Constituents of Euphorbia stracheyi Boiss (Euphorbiaceae)
by Hui Zhu, Xiangxiang Ren, Yanbo Huang, Tao Su and Lei Yang
Metabolites 2023, 13(7), 852; https://doi.org/10.3390/metabo13070852 - 15 Jul 2023
Cited by 4 | Viewed by 1808
Abstract
Euphorbia stracheyi Boiss was used for hemostasis, analgesia, and muscular regeneration in traditional Chinese medicine. To study the chemical constituents of E. stracheyi, the ethyl acetate part of the methanol extract of the whole plant was separated by silica gel, sephadex LH-20 [...] Read more.
Euphorbia stracheyi Boiss was used for hemostasis, analgesia, and muscular regeneration in traditional Chinese medicine. To study the chemical constituents of E. stracheyi, the ethyl acetate part of the methanol extract of the whole plant was separated by silica gel, sephadex LH-20 column chromatography, and semi-preparative HPLC. The isolation led to the characterization of a new lathyrane type diterpenoid, euphostrachenol A (1), as well as eleven known compounds (2–11), including a lathyrane, three ingenane-type and two abietane-type diterpenoids, two ionones, and two flavonoids. The structures of these compounds were established using 1D- and 2D-NMR experiments, mass spectrometry, and X-ray crystallographic experiments. The MTT method was used to determine the cytotoxic activity of five cancer cell lines (Leukemia HL-60, lung cancer A-549, liver cancer SMMC-7721, breast cancer MCF-7, and colon cancer SW480) on the isolated compounds. However, only compound 4 showed moderate cytotoxicity against these cell lines, with IC50 values ranging from 10.28 to 29.70 μM, while the others were inactive. Our chemical investigation also confirmed the absence of jatrophane-type diterpenoids in the species, which may be related to its special habitat. Full article
(This article belongs to the Special Issue Identification of Secondary Metabolites by Multi-Omics Methods)
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