Submit to Special Issue Submit Abstract to Special Issue Review for IJMS Propose a Special Issue

Journal Menu

Journal Browser

Plant Metabolomics: Uncovering the Hidden World of Plant Secondary Metabolites

Special Issue Editors
Special Issue Information
Keywords
Benefits of Publishing in a Special Issue
Published Papers

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 January 2025 | Viewed by 10500

Share This Special Issue

Special Issue Editor

Prof. Dr. Jen-Tsung Chen

E-Mail Website
Guest Editor

Department of Life Sciences, National University of Kaohsiung, Kaohsiung 811, Taiwan
Interests: bioactive compounds; chromatography techniques; medicinal plants; phytochemicals; plant biotechnology; plant growth regulators; plant secondary metabolites
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Plant secondary metabolites are involved in certain major activities of plants including reproduction, defense, and competition in their own environment, and have been well-recognized to possess health benefits and therapeutics for a wide range of diseases. Of great interest to scientists are the function and production of plant secondary metabolites derived from foods and medicinal plants. This Special Issue aims to explore the knowledge on this topic by researching the recent achievements in the research field of plant secondary metabolites based on the metabolomics strategy, which is an essential component of plant functional genomics using powerful technology to profile metabolites in a high-throughput manner. The Special Issue covers, but is not limited to, the following subtopics:

Metabolomics for discovering plant secondary metabolites;
Metabolomics for advancing the production of plant secondary metabolites;
Emerging technologies for plant metabolomics;
Plant metabolomics for plant secondary metabolism;
Plant metabolomics for plant stress responses and tolerance;
Plant metabolomics for traditional and herbal medicines;
Plant metabolomics for plant–microbial interaction.

Prof. Dr. Jen-Tsung Chen
Guest Editor

Manuscript Submission Information

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

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

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

metabolomics
secondary metabolites
plant biochemistry
mass spectrometry
NMR spectroscopy
plant signaling pathways
natural products
chemical ecology
metabolic profiling
phytochemicals
medicinal plants
herbal medicines

Benefits of Publishing in a Special Issue

Ease of navigation: Grouping papers by topic helps scholars navigate broad scope journals more efficiently.
Greater discoverability: Special Issues support the reach and impact of scientific research. Articles in Special Issues are more discoverable and cited more frequently.
Expansion of research network: Special Issues facilitate connections among authors, fostering scientific collaborations.
External promotion: Articles in Special Issues are often promoted through the journal's social media, increasing their visibility.
e-Book format: Special Issues with more than 10 articles can be published as dedicated e-books, ensuring wide and rapid dissemination.

Further information on MDPI's Special Issue polices can be found here.

Published Papers (8 papers)

Download All Papers

Order results

Result details

Show export options Show export options

Select all

Export citation of selected articles as:

Research

16 pages, 7240 KiB

Open AccessArticle

Comparative Metabolomics to Unravel the Biochemical Mechanism Associated with Rancidity in Pearl Millet (Pennisetum glaucum L.)

by Kalenahalli Yogendra, Hemalatha Sanivarapu, Tejaswi Avuthu, Shashi Kumar Gupta, Priyanka Durgalla, Roopa Banerjee, Anitha Raman and Wricha Tyagi

Int. J. Mol. Sci. 2024, 25(21), 11583; https://doi.org/10.3390/ijms252111583 - 29 Oct 2024

Viewed by 671

Abstract

Despite being a highly nutritious and resilient cereal, pearl millet is not popular among consumers and food industries due to the short shelf-life of flour attributed to rapid rancidity development. The biochemical mechanism underlying rancidity, a complex and quantitative trait, needs to be better understood. The present study aims to elucidate the differential accumulation of metabolites in pearl millet that impact the rancidity process. Metabolite profiling was conducted on ten pearl millet genotypes with varying levels of rancidity—comprising high, low, and medium rancid genotypes—utilizing liquid chromatography and high-resolution mass spectrometry (LC-HRMS) at different accelerated ageing conditions. Through non-targeted metabolomic analysis, crucial metabolites associated with rancidity were identified across various biochemical pathways, including fatty acids, glycerophospholipids, sphingolipids, glycerol lipids, flavonoids, alkaloids, and terpenoids. Notably, metabolites such as fatty aldehydes, fatty alcohols, fatty esters, fatty acyls, fatty esters, and fatty amides were significantly elevated in high rancid genotypes, indicating their involvement in the rancidity process. These fatty acids-related metabolites further break down into saturated and unsaturated fatty acids. Four key fatty acids—stearic, palmitic, linoleic and linolenic acid—were quantified in the ten pearl millet genotypes, confirming their role in rancidity development. This investigation promises novel insights into utilizing metabolomics to understand the biochemical processes and facilitate precision breeding for developing low-rancidity pearl millet lines. Full article

(This article belongs to the Special Issue Plant Metabolomics: Uncovering the Hidden World of Plant Secondary Metabolites)

► Show Figures

Figure 1

13 pages, 2689 KiB

Open AccessArticle

NMR-Based Metabolomic Analysis of Biotic Stress Responses in the Traditional Korean Landrace Red Pepper (Capsicum annuum var. annuum, cv. Subicho)

by Gi-Un Seong, Dae-Yong Yun, Dong-Hyeok Shin, Jeong-Seok Cho, Seul-Ki Park, Jeong Hee Choi, Kee-Jai Park and Jeong-Ho Lim

Int. J. Mol. Sci. 2024, 25(18), 9903; https://doi.org/10.3390/ijms25189903 - 13 Sep 2024

Viewed by 584

Abstract

Korean landrace red peppers (Capsicum annuum var. Subicho), such as the traditional representative Subicho variety, are integral to Korean foods and are often consumed raw or used as a dried powder for cuisine. However, the known vulnerability of local varieties of landrace to biotic stresses can compromise their quality and yield. We employed nuclear magnetic resonance (NMR) spectroscopy coupled with a multivariate analysis to uncover and compare the metabolomic profiles of healthy and biotic-stressed Subicho peppers. We identified 42 metabolites, with significant differences between the groups. The biotic-stressed Subicho red peppers exhibited lower sucrose levels but heightened concentrations of amino acids, particularly branched-chain amino acids (valine, leucine, and isoleucine), suggesting a robust stress resistance mechanism. The biotic-stressed red peppers had increased levels of TCA cycle intermediates (acetic, citric, and succinic acids), nitrogen metabolism-related compounds (alanine, asparagine, and aspartic acid), aromatic amino acids (tyrosine, phenylalanine, and tryptophan), and γ-aminobutyric acid. These findings reveal the unique metabolic adaptations of the Subicho variety, underscoring its potential resilience to biotic stresses. This novel insight into the stress response of the traditional Subicho pepper can inform strategies for developing targeted breeding programs and enhancing the quality and economic returns in the pepper and food industries. Full article

(This article belongs to the Special Issue Plant Metabolomics: Uncovering the Hidden World of Plant Secondary Metabolites)

► Show Figures

Graphical abstract

13 pages, 5120 KiB

Open AccessArticle

The Metabolomic Profiling of the Flavonoid Compounds in Red Wine Grapes and the Impact of Training Systems in the Southern Subtropical Region of China

by Huan Yu, Hong-Yan Li, Si-Hong Zhou, Guo Cheng, Rong-Fu Wei, Yong-Mei Zhou, Ying Zhang, Tai-Li Xie and Lan Zhang

Int. J. Mol. Sci. 2024, 25(16), 8624; https://doi.org/10.3390/ijms25168624 - 7 Aug 2024

Viewed by 797

Abstract

Flavonoids play an important role in forming wine grapes and wine quality characteristics. The flavonoids of three winter red wine grapes, Yeniang No. 2 (YN2), Marselan (Mar), and Guipu No. 6 (GP6), were analyzed by ultra-high-performance liquid chromatography–triple quadrupole mass spectrometry (UPLC-QQQ-MS). Furthermore, the flavonoids in GP6 grapevines using two types of training systems, namely, trellis (T) and espaliers (E), were also compared in this study. Overall, 196 flavonoid metabolites, including 96 flavones, 38 flavonols, 19 flavanones, 18 polyphenols, 15 anthocyanins, 7 isoflavones, and 3 proanthocyanidins, were identified. The flavonoid profiles were remarkably different among these three grape varieties, while they did not change much in the GP6 managed on trellis and espaliers. Grape varieties with different genetic backgrounds have their own unique flavonoid profiles. Compared with Mar-T, isoflavones and flavonols presented higher contents in GP6-T and YN2-T, which mainly contain glycitein, genistin, calycosin, kaempferide, isotrifoliin, and ayanin. The anthocyanin content was significantly higher in YN2-T than in the other two varieties. YN2 and GP6-T present a more stable color, with significantly more acetylated diglucosides and methylated anthocyanins in YN2-T and GP6-T than in Mar-T. Notably, GP6 had more varied flavonoids and the better characteristics to its flavonoid profile out of these three varieties, due to it containing a higher number of anthocyanins, flavone, and flavonols and the greatest number of different flavonoid metabolites (DFMs), with higher contents than YN2 and Mar. Compared with the trellis training system, the espaliers training system increased the content of flavonoids detected in GP6 grape berries; however, the composition of flavonoids strictly depends on the grape variety. Full article

(This article belongs to the Special Issue Plant Metabolomics: Uncovering the Hidden World of Plant Secondary Metabolites)

► Show Figures

Figure 1

23 pages, 6015 KiB

Open AccessArticle

Metabolic and Transcriptomic Profile Revealing the Differential Accumulating Mechanism in Different Parts of Dendrobium nobile

by Ruoxi Zhao, Shou Yan, Yadong Hu, Dan Rao, Hongjie Li, Ze Chun and Shigang Zheng

Int. J. Mol. Sci. 2024, 25(10), 5356; https://doi.org/10.3390/ijms25105356 - 14 May 2024

Viewed by 1169

Abstract

Dendrobium nobile is an important orchid plant that has been used as a traditional herb for many years. For the further pharmaceutical development of this resource, a combined transcriptome and metabolome analysis was performed in different parts of D. nobile. First, saccharides, organic acids, amino acids and their derivatives, and alkaloids were the main substances identified in D. nobile. Amino acids and their derivatives and flavonoids accumulated strongly in flowers; saccharides and phenols accumulated strongly in flowers and fruits; alkaloids accumulated strongly in leaves and flowers; and a nucleotide and its derivatives and organic acids accumulated strongly in leaves, flowers, and fruits. Simultaneously, genes for lipid metabolism, terpenoid biosynthesis, and alkaloid biosynthesis were highly expressed in the flowers; genes for phenylpropanoids biosynthesis and flavonoid biosynthesis were highly expressed in the roots; and genes for other metabolisms were highly expressed in the leaves. Furthermore, different members of metabolic enzyme families like cytochrome P450 and 4-coumarate-coA ligase showed differential effects on tissue-specific metabolic accumulation. Members of transcription factor families like AP2-EREBP, bHLH, NAC, MADS, and MYB participated widely in differential accumulation. ATP-binding cassette transporters and some other transporters also showed positive effects on tissue-specific metabolic accumulation. These results systematically elucidated the molecular mechanism of differential accumulation in different parts of D. nobile and enriched the library of specialized metabolic products and promising candidate genes. Full article

(This article belongs to the Special Issue Plant Metabolomics: Uncovering the Hidden World of Plant Secondary Metabolites)

► Show Figures

Figure 1

15 pages, 3734 KiB

Open AccessArticle

Radiocarbon Flux Measurements Reveal Mechanistic Insight into Heat-Stress Induction of Nicotine Biosynthesis in Nicotiana attenuata

by Spenser Waller, Avery Powell, Randi Noel, Michael J. Schueller and Richard A. Ferrieri

Int. J. Mol. Sci. 2023, 24(21), 15509; https://doi.org/10.3390/ijms242115509 - 24 Oct 2023

Viewed by 1222

Abstract

The effect of high-temperature (HT) stress on nicotine biosynthesis in Nicotiana attenuata was examined. Nicotine content was measured in mature leaves, young sink leaves, and in roots from well-watered plants grown at 25 °C as controls and from plants exposed to 38 °C and 43 °C temperatures applied for 24, 48, 72, and 96 h duration. At 38 °C, all leaf nicotine levels were significantly less than control plants for up to 72 h exposure but rose sharply thereafter to levels significantly greater than controls with 96 h exposure. In contrast, plants exposed to 43 °C never exhibited a reduction in leaf nicotine content and showed an increase in content with just 48 h exposure. Using radioactive ¹¹CO₂ and ¹³NO₃⁻, we found that HT stress reduced both CO₂ fixation and nitrate uptake. Furthermore, radiocarbon flux analysis revealed that ‘new’ carbon partitioning (as ¹¹C) into the ¹¹C-radiolabeled amino acid (AA) pool was significantly reduced with HT stress as were yields of [¹¹C]-aspartic acid, an important AA in nicotine biosynthesis, and its beta-amido counterpart [¹¹C]-asparagine. In contrast, [¹²C]-aspartic acid levels appeared unaffected at 38 °C but were elevated at 43 °C relative to controls. [¹²C]-Asparagine levels were noted to be elevated at both stress temperatures. Since HT reductions in carbon input and nitrogen uptake were noted to impede de novo AA biosynthesis, protein degradation at HT was examined as a source of AAs. Here, leaf total soluble protein (TSP) content was reduced 39% with long exposures to both stress temperatures. However, Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) which was 41% TSP appeared unaffected. Altogether, these results support the theory that plant proteins other than Rubisco degrade at elevated temperatures freeing up essential AAs in support of nicotine biosynthesis. Full article

(This article belongs to the Special Issue Plant Metabolomics: Uncovering the Hidden World of Plant Secondary Metabolites)

► Show Figures

Figure 1

14 pages, 2055 KiB

Open AccessArticle

Comparative Analysis of Volatile Compounds from Four Radish Microgreen Cultivars Based on Ultrasonic Cell Disruption and HS-SPME/GC–MS

by Yuan Zhong, Zhilong Jia, Hailong Zhou, Dan Zhang, Guichen Li and Jihua Yu

Int. J. Mol. Sci. 2023, 24(19), 14988; https://doi.org/10.3390/ijms241914988 - 8 Oct 2023

Cited by 4 | Viewed by 2153

Abstract

The ultrasonic cell disruption method was used to efficiently extract isothiocyanates and other volatile compounds from radish microgreens. A total of 51 volatiles were identified and quantified by headspace solid-phase micro-extraction and gas chromatography–mass spectrometry (HS-SPME/GC–MS) in four radish microgreen cultivars, mainly including alcohols, aldehydes, isothiocyanates, sulfides, ketones, esters, terpenes, and hydrocarbons. The correlation between cultivars and volatile compounds was determined by chemometrics analysis, including principal component analysis (PCA) and hierarchical clustering heat maps. The aroma profiles were distinguished based on the odor activity value (OAV), odor contribution rate (OCR), and radar fingerprint chart (RFC) of volatile compounds. This study not only revealed the different flavor characteristics in four cultivars but also established a theoretical basis for the genetic improvement of radish microgreen flavors. Full article

(This article belongs to the Special Issue Plant Metabolomics: Uncovering the Hidden World of Plant Secondary Metabolites)

► Show Figures

Figure 1

16 pages, 8373 KiB

Open AccessArticle

γ-Aminobutyric Acid Priming Alleviates Acid-Aluminum Toxicity to Creeping Bentgrass by Regulating Metabolic Homeostasis

by Min Zhou, Yan Yuan, Junnan Lin, Long Lin, Jianzhen Zhou and Zhou Li

Int. J. Mol. Sci. 2023, 24(18), 14309; https://doi.org/10.3390/ijms241814309 - 20 Sep 2023

Cited by 3 | Viewed by 1415

Abstract

Aluminum (Al) toxicity is a major limiting factor for plant growth and crop production in acidic soils. This study aims to investigate the effects of γ-aminobutyric acid (GABA) priming on mitigating acid-Al toxicity to creeping bentgrass (Agrostis stolonifera) associated with changes in plant growth, photosynthetic parameters, antioxidant defense, key metabolites, and genes related to organic acids metabolism. Thirty-seven-old plants were primed with or without 0.5 mM GABA for three days and then subjected to acid-Al stress (5 mmol/L AlCl₃·6H₂O, pH 4.35) for fifteen days. The results showed that acid-Al stress significantly increased the accumulation of Al and also restricted aboveground and underground growths, photosynthesis, photochemical efficiency, and osmotic balance, which could be effectively alleviated by GABA priming. The application of GABA significantly activated antioxidant enzymes, including superoxide dismutase, peroxidase, catalase, and ascorbate peroxidase, to reduce oxidative damage to cells under acid-Al stress. Metabolomics analysis demonstrated that the GABA pretreatment significantly induced the accumulation of many metabolites such as quinic acid, pyruvic acid, shikimic acid, glycine, threonine, erythrose, glucose-6-phosphate, galactose, kestose, threitol, ribitol, glycerol, putrescine, galactinol, and myo-inositol associated with osmotic, antioxidant, and metabolic homeostases under acid-Al stress. In addition, the GABA priming significantly up-regulated genes related to the transportation of malic acid and citric acid in leaves in response to acid-Al stress. Current findings indicated GABA-induced tolerance to acid-Al stress in relation to scavenging of reactive oxygen species, osmotic adjustment, and accumulation and transport of organic metabolites in leaves. Exogenous GABA priming could improve the phytoremediation potential of perennial creeping bentgrass for the restoration of Al-contaminated soils. Full article

(This article belongs to the Special Issue Plant Metabolomics: Uncovering the Hidden World of Plant Secondary Metabolites)

► Show Figures

Figure 1

15 pages, 1698 KiB

Open AccessArticle

Non-Targeted Screening of Metabolites in Aqueous-Ethanol Extract from Spiraea hypericifolia (Rosaceae) Using LC-HRMS

by Vera A. Kostikova, Natalia V. Petrova, Tatiana M. Shaldaeva, Vladimir V. Koval and Alexander A. Chernonosov

Int. J. Mol. Sci. 2023, 24(18), 13872; https://doi.org/10.3390/ijms241813872 - 8 Sep 2023

Cited by 3 | Viewed by 1536

Abstract

By means of liquid chromatography combined with high-resolution mass spectrometry, metabolite profiling was performed on an aqueous-ethanol extract from Spiraea hypericifolia (Rosaceae) collected in Siberia (Russia). Up to 140 compounds were found in the extract, of which 47 were tentatively identified. The identified compounds were amino acids, sugars, phenylpropanoids, fatty acids and their derivatives, triterpenoids, flavonoids, and others. A quantitative analysis showed the predominance of phenolcarboxylic acids and flavonoids in the studied extract, but a qualitative analysis revealed the higher structural diversity of flavonoids. Of the 23 identified flavonoids, 13 were flavonols: quercetin, hyperoside, isoquercitrin, reynoutrin, avicularin, rutin, quercetin-3-O-(6″-O-malonyl)-β-D-glucoside, 3-O-methylquercetin-3′-O-β-D-glucopyranoside, isorhamnetin, rhamnetin-3-O-β-D-xylopyranosyl-β-D-glucopyranoside, kaempferol, tiliroside, and trifolin; six were catechins: catechin, (−)-epicatechin, (+)-epicatechin, (+)-catechin-7-O-β-D-xyloside, (2S,3R)-3,5-dihydroxy-2-(4-hydroxyphenyl)-3,4-dihydro-2H-chromen-7-yl-β-D-glucopyranoside, and catechin 7-O-apiofuranoside; two are isoflavones: genistin and genistein; and one was a flavone (luteolin-4′-O-β-D-glucopyranoside) and another was an anthocyanidin (pelargonidin). The aqueous-ethanol extract from S. hypericifolia showed antioxidant activity (half-maximal inhibitory concentration 102.95 μg/mL), which was likely related to the high concentrations of phenolcarboxylic acids (229.6 mg/g), flavonoids (118.3 mg/g), and tannins (62.9 mg/g). Full article

(This article belongs to the Special Issue Plant Metabolomics: Uncovering the Hidden World of Plant Secondary Metabolites)

► Show Figures

Journal Menu

Journal Browser

Plant Metabolomics: Uncovering the Hidden World of Plant Secondary Metabolites

Share This Special Issue

Special Issue Editor

Special Issue Information

Keywords

Benefits of Publishing in a Special Issue

Published Papers (8 papers)

Research

Further Information

Guidelines

MDPI Initiatives

Follow MDPI