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A special issue of Current Issues in Molecular Biology (ISSN 1467-3045). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: closed (31 May 2023) | Viewed by 34178

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Dr. Chiara Roberta Girelli

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Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
Interests: nuclear magnetic resonance (NMR) spectroscopy; chemometrics; foodomics; metabolomics; foodstuff geographical origin and quality assessment
Special Issues, Collections and Topics in MDPI journals

Dr. Laura Del Coco

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Department of Biological and Environmental Sciences and Technologies, University of Salento, Via Province of Lecce-Monteroni, 73100 Lecce, Italy
Interests: metabolomic analysis of biofluids (blood, urine, synovial fluid, cell lysates) and plant extracts using NMR spectroscopy and multivariate statistical methods; biomarker detection and molecular characterization in agrifood (EVOOs) and pharmaceuticals and medical use (human diseases); metabolomic analysis for sustainable farming, fisheries, and aquaculture
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Plant metabolomics has already been successfully employed in plant functional genomics, food science, and human nutrition. High-throughput analytical techniques (mass (MS) or nuclear magnetic resonance (NMR) spectroscopy) in combination with statistical methods aim at the characterization of the plant metabolome and the role of primary and secondary metabolites as end products of the cell pathways. Moreover, metabolomics has emerged as an effective tool in food and nutrition sciences, providing chemical characterization of bioactive compounds present and their possible nutraceutical value for human health. This Special Issue will focus on the study of plants metabolic profiles and interaction with external agents as environmental variations or pathogen attack, with the detection of relevant biomarkers. In particular, we invite the submission of manuscripts on plant metabolomes as well as on their application for biomarker detection, quality control, and/or origin discrimination. All studies, including research papers and reviews related to these items, will be considered for publication.

Dr. Chiara Roberta Girelli
Dr. Laura Del Coco
Guest Editors

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Keywords

plant fingerprinting
plant pathogens interactions
secondary metabolites
plant physiology
metabolomics
NMR spectroscopy
MS spectroscopy
antioxidants
phytochemistry
food chemistry

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Published Papers (12 papers)

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Editorial

Jump to: Research, Review

3 pages, 184 KiB

Open AccessEditorial

Editorial for the Special Issue “Advanced Research in Plant Metabolomics”

by Chiara Roberta Girelli

Curr. Issues Mol. Biol. 2023, 45(8), 6701-6703; https://doi.org/10.3390/cimb45080423 - 14 Aug 2023

Viewed by 1193

Abstract

The study of plant metabolome and the role of cellular pathway end products has gained increased attention [...] Full article

(This article belongs to the Special Issue Advanced Research in Plant Metabolomics)

Research

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14 pages, 2554 KiB

Open AccessArticle

Metabolites and Plant Hormones Related to the Resistance Response to Feeding Stimulation and Leaf Clipping Control in Chinese Pine (Pinus tabuliformis Carr.)

by Yanan Zhao, Guona Zhou, Tianhua Sun, Lifeng Wang, Qiang Xu, Junxia Liu and Baojia Gao

Curr. Issues Mol. Biol. 2023, 45(2), 1086-1099; https://doi.org/10.3390/cimb45020072 - 30 Jan 2023

Cited by 5 | Viewed by 1896

Abstract

This experiment was conducted to define changes in metabolic pathways in response to mandibulate insect feeding and to provide a reference for further investigation of the molecular mechanisms underlying the development of conifer resistance. Chinese pine (Pinus tabuliformis Carr.) in good growth status in natural condition was chosen for stimulation by 10 pine caterpillars (Dendrolimus tabulaefomis Tsai et Liu) as feeding stimulation (FS), leaf clipping control (LCC) as mechanical damage, and CK group (with no treatment) (recorded as 0 h). The metabolome and total flavonoid content were measured in the needles at 0, 2, and 8 h after treatment. Plant hormones were measured with needles at 0, 0.5, 1, 1.5, 2, 4, 6, and 8 h after different treatments. The results show that a total of 30.8% flavonoids are identified by metabolomics analysis. Compared with leaf clipping control, feeding stimulation of Chinese pine caterpillars significantly induced the upregulation of metabolites in the flavonoid pathway in Chinese pine, and the plant hormones JA and IAA showed expression trends consistent with those of the metabolome. According to the biological processes of the four plant hormones involved, JA and SA are mostly involved in resistance formation, and in this study, both of them also have fluctuating expressions influenced by feeding stimulation, while the expressions of the growth-related hormones IAA and ABA have no significant changes at other time points except for 1 h after treatment. Thus, the flavonoid pathway is one of the main pathways involved in resistance formation in conifers, and JA and IAA are involved in the formation of resistance. Full article

(This article belongs to the Special Issue Advanced Research in Plant Metabolomics)

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12 pages, 2033 KiB

Open AccessArticle

The Key Metabolites in Rice Quality Formation of Conventional japonica Varieties

by Qiangqiang Xiong, Changhui Sun, Runnan Wang, Ruizhi Wang, Xiaoyu Wang, Yu Zhang and Jinyan Zhu

Curr. Issues Mol. Biol. 2023, 45(2), 990-1001; https://doi.org/10.3390/cimb45020064 - 20 Jan 2023

Cited by 9 | Viewed by 1788

Abstract

To understand differences in the quality of different conventional japonica rice varieties and variations in metabolites related to rice quality, the quality of three conventional japonica varieties was determined, and the metabolites of the milled rice were investigated using nontargeted metabolomics technology. The results showed that the taste value (TV) of Yangda 4Hao (YD4) was significantly higher than that of Yangda 3Hao (YD3) and Huaidao 5Hao (HD5). The protein content (PC) of HD5 was significantly higher than that of YD3 and YD4. PC was significantly negatively correlated with TV. Ninety-one differential metabolites (59 increased and 32 decreased) were identified between YD3 and HD5. A total of 144 differential metabolites (96 upregulated and 48 downregulated) were identified between YD4 and HD5. A total of 114 differential metabolites (40 increased and 74 decreased) were identified between YD3 and YD4. The metabolites with a high correlation to rice quality were mostly involved in the amino acid metabolism pathway. Amino acid metabolites play an important role in the formation of rice quality. The key metabolites in the synthesis and regulation of metabolic pathways are sucrose, levan, and amylose, which are carbohydrates, and L-glutamine, L-aspartic acid, and L-asparagine, which are amino acid metabolites. It can be seen from this study that the metabolites of sucrose, levan, amylose, L-glutamine, L-aspartic acid, and L-asparagine may be the key metabolites in the quality formation of high-quality rice varieties. Full article

(This article belongs to the Special Issue Advanced Research in Plant Metabolomics)

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13 pages, 3015 KiB

Open AccessArticle

Targeted Metabolic and Transcriptomic Analysis of Pinus yunnanensis var. pygmaea with Loss of Apical Dominance

by Feng Xiao, Yang Zhao, Xiurong Wang and Yao Yang

Curr. Issues Mol. Biol. 2022, 44(11), 5485-5497; https://doi.org/10.3390/cimb44110371 - 3 Nov 2022

Cited by 6 | Viewed by 2020

Abstract

Pinus yunnanensis var. pygmaea demonstrates obvious loss of apical dominance, inconspicuous main trunk, which can be used as an ideal material for dwarfing rootstocks. In order to find out the reasons for the lack of apical dominance of P. pygmaea, endogenous phytohormone content determination by liquid chromatography–tandem mass spectrometry (LC–MS/MS) and comparative transcriptomes were performed on the shoot apical meristem and root apical meristem of three pine species (P. massoniana, P. pygmaea, and P. elliottii). The results showed that the lack of CK and the massive accumulation of ABA and GA-related hormones may be the reasons for the loss of shoot apical dominance and the formation of multi-branching, the abnormal synthesis of diterpenoid biosynthesis may lead to the influence of GA-related synthesis, and the high expression of GA 2-oxidase (GA2ox) gene may be the cause of dwarfing. Weighted correlation network analysis (WGCNA) screened some modules that were highly expressed in the shoot apical meristem of P. pygmaea. These findings provided valuable information for identifying the network regulation of shoot apical dominance loss in P. pygmaea and enhanced the understanding of the molecular mechanism of shoot apical dominance growth differences among Pinus species. Full article

(This article belongs to the Special Issue Advanced Research in Plant Metabolomics)

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17 pages, 3733 KiB

Open AccessArticle

Phosphorus Regulates the Level of Signaling Molecules in Rice to Reduce Cadmium Toxicity

by Qiaoyu Chen, Yanyan Hu, Lijun Yang, Benguo Zhu and Feng Luo

Curr. Issues Mol. Biol. 2022, 44(9), 4070-4086; https://doi.org/10.3390/cimb44090279 - 7 Sep 2022

Cited by 6 | Viewed by 2254

Abstract

Phosphorus treatment can reduce Cd accumulation and Cd toxicity in rice, but alterations in the internal regulatory network of rice during this process have rarely been reported. We have removed the effect of cadmium phosphate precipitation from the hydroponic system, treated a pair of different Cd-response rice varieties with different levels of phosphorus and cadmium and examined the changes in physiological indicators and regulatory networks. The results demonstrated that phosphorus treatment significantly reduced Cd accumulation in both types of rice, although the antioxidant systems within the two types of rice produced opposite responses. Overall, 3 mM phosphorus treatment to Cd-N decreased the expression of OsIAA17 and OsACO1 by 32% and 37%, respectively, while increasing the expression of OsNR2 by 83%; these three genes regulate the synthesis of auxin, ethylene, and nitric oxide in rice. IAA and NO levels in rice shoots increased by 24% and 96%, respectively, and these changes contribute to Cd detoxification. The cadmium transporter genes OsHMA2, OsIRT1, and OsABCC1 were significantly down-regulated in Cd-N roots after triple phosphorus treatment. These data suggest that phosphorus treatment can reduce Cd accumulation and enhance Cd resistance in rice by affecting the expression of signaling molecules. Full article

(This article belongs to the Special Issue Advanced Research in Plant Metabolomics)

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12 pages, 2175 KiB

Open AccessArticle

Daphne odora Exerts Depigmenting Effects via Inhibiting CREB/MITF and Activating AKT/ERK-Signaling Pathways

by Young Sic Eom, Dongho Jeong, A-Reum Ryu, Keon-Hyoung Song, Dai Sig Im and Mi-Young Lee

Curr. Issues Mol. Biol. 2022, 44(8), 3312-3323; https://doi.org/10.3390/cimb44080228 - 22 Jul 2022

Cited by 5 | Viewed by 1998

Abstract

Daphne odora, a blooming shrub, has been traditionally used for various medicinal purposes. However, information on its anti-melanogenic activity and dermal application is limited. In this study, the Daphne odora extract (DOE), with constituents including daphnetin, was used to investigate depigmenting activity and the underlying mechanism of Daphne odora. DOE inhibited in vitro and cellular tyrosinase activity in a dose-dependent manner, and reduced the α-MSH-induced melanin biosynthesis to a control level. The protein expressions of melanin synthesis-related enzymes were also significantly reduced by DOE. Moreover, DOE decreased the phosphorylation of cAMP-response element binding proteins (CREBs) induced by α-MSH in B16F10 cells, while it activated phosphorylated extra-cellular signal-regulated kinases (ERKs) and protein kinase B (AKT) expression. These results suggest that DOE might inhibit the melanogenesis signaling pathways by activating ERK- and AKT-signaling pathways to regulate the expression of CREB and MITF and its downstream pathways. Therefore, DOE could potentially be developed as a depigmenting agent. Full article

(This article belongs to the Special Issue Advanced Research in Plant Metabolomics)

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21 pages, 5751 KiB

Open AccessArticle

The Effects of NAA on the Tuberous Root Yield and Quality of Rehmannia glutinosa and Its Regulatory Mechanism by Transcriptome and Metabolome Profiling

by Jianjun Li, Jialin Zhu, Huimin Li, Jingxiao Ma, Peilei Chen and Yanqing Zhou

Curr. Issues Mol. Biol. 2022, 44(8), 3291-3311; https://doi.org/10.3390/cimb44080227 - 22 Jul 2022

Cited by 2 | Viewed by 2299

Abstract

Naphthylacetic acid (NAA) was used to increase the tuberous root yield of Rehmannia glutinosa, but the differences between its NAA-treated and control tuberous roots (NT and CG) and the regulatory mechanism of NAA effect remain unclear. In order to investigate them, NTs and CGs were used as materials, and both yield-related indices were measured; the metabolomics and transcriptomics were used to capture differentially accumulated metabolites (DAM) and to validate them via mining differentially expressed genes (DEGs), respectively. The effects of NAA treatment: increased NT mass per plant by 21.14%, through increasing the number of roots and increasing the mean root diameter; increased catalpol content by 1.2234% (p < 0.05); up-regulated 11DAMs and 596DEGs; and down-regulated 18 DAMs and 517DEGs. In particular, we discovered that NAA regulated its DAMs and biomass via 10 common metabolic pathways, and that the number of NAA-down-regulated DAMs was more than that of NAA-up-regulated DAMs in its tuberous root. Furthermore, HPLC validated the changes of several DAMs and 15 DEGs (4CL, ARF, CCoAOMT, ARGOS, etc.) associated with the yield increase and DAMs were verified by RT-qPCR. This study provided some valuable resources, such as tuberous root indices, key genes, and DAMs of Rehmannia glutinosa in response to NAA for distinguishing the CGs from NTs, and novel insights into the regulatory mechanism of NAA effects on both at the transcriptomic and metabolomic levels, so it will lay a theoretical foundation for NAA-regulated plant yield and quality, and provide references for prohibiting the uses of NAA as a swelling agent in medicinal tuber plants in China. Full article

(This article belongs to the Special Issue Advanced Research in Plant Metabolomics)

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14 pages, 2379 KiB

Open AccessArticle

Juglone from Walnut Produces Cardioprotective Effects against Isoproterenol-Induced Myocardial Injury in SD Rats

by Taseer Ahmad, Taous Khan, Tahira Tabassum, Yahya S. Alqahtani, Mater H. Mahnashi, Bandar A. Alyami, Ali O. Alqarni, Mohammed Y. Alasmary, Sultan A. Almedhesh and Abdul Jabbar Shah

Curr. Issues Mol. Biol. 2022, 44(7), 3180-3193; https://doi.org/10.3390/cimb44070220 - 16 Jul 2022

Cited by 6 | Viewed by 2910

Abstract

Therapeutic and/or preventive interventions using phytochemical constituents for ischemic heart disease have gained considerable attention worldwide, mainly due to their antioxidant activity. This study investigated the cardioprotective effect and possible mechanism of juglone, a major constituent of the walnut tree, using an isoproterenol (ISO)-induced myocardial infarction (MI) model in rats. Rats were pretreated for five (5) days with juglone (1, 3 mg/kg, i.p) and atenolol (1 mg/kg, i.p) in separate experiments before inducing myocardial injury by administration of ISO (80 mg/kg, s.c) at an interval of 24 h for 2 consecutive days (4th and 5th day). The cardioprotective effect of juglone was confirmed through a lead II electrocardiograph (ECG), cardiac biomarkers (cTnI, CPK, CK-MB, LDH, ALT and AST) and histopathological study. The results of our present study suggest that prior administration of juglone (1 and 3 mg/kg) proved to be effective as a cardioprotective therapeutic agent in reducing the extent of myocardial damage (induced by ISO) by fortifying the myocardial cell membrane, preventing elevated T-waves, deep Q-waves in the ECG, heart to body weight ratio, infarction and also by normalizing cardiac marker enzymes (cTnI, CPK, CK-MB, LDH, ALT and AST) and histopathological changes, such as inflammation, edema and necrosis. In conclusion, this study has identified phytochemical constituents, in particular juglone, as a potential cardioprotective agent. Full article

(This article belongs to the Special Issue Advanced Research in Plant Metabolomics)

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19 pages, 38466 KiB

Open AccessArticle

Exogenous Zeaxanthin Alleviates Low Temperature Combined with Low Light Induced Photosynthesis Inhibition and Oxidative Stress in Pepper (Capsicum annuum L.) Plants

by Dongxia Ding, Jing Li, Jianming Xie, Nenghui Li, Emily Patience Bakpa, Kangning Han, Yan Yang and Cheng Wang

Curr. Issues Mol. Biol. 2022, 44(6), 2453-2471; https://doi.org/10.3390/cimb44060168 - 25 May 2022

Cited by 12 | Viewed by 2437

Abstract

Low temperature combined with low light (LL) affects crop production, especially the yield and quality of peppers, in northwest China during the winter and spring seasons. Zeaxanthin (Z) is a known lipid protectant and active oxygen scavenger. However, whether exogenous Z can mitigate LL-induced inhibition of photosynthesis and oxidative stress in peppers remains unclear. In this study, we investigated the effects of exogenous Z on photosynthesis and the antioxidant machinery of pepper seedlings subject to LL stress. The results showed that the growth and photosynthesis of pepper seedlings were significantly inhibited by LL stress. In addition, the antioxidant machinery was disturbed by the uneven production and elimination of reactive oxygen species (ROS), which resulted in damage to the pepper. For example, membrane lipid peroxidation increased ROS content, and so on. However, exogenous application of Z before LL stress significantly increased the plant height, stem diameter, net photosynthetic rate (Pn), and stomata, which were obviously closed at LL. The activities of antioxidant enzymes superoxide dismutase (SOD), catalase (CAT), mono de-hydroascorbate reductase (MDHAR), de-hydroascorbate reductase (DHAR), ascorbate peroxidase (APX), and ascorbate oxidase (AAO) improved significantly due to the increased expression of CaSOD, CaCAT, CaAPX, CaMDHAR, and CaDHAR. The ascorbic (AsA) and glutathione (GSH) contents and ascorbic/dehydroascorbate (AsA/DHA) and glutathione/oxidized glutathione (GSH/GSSG) ratios also increased significantly, resulting in the effective removal of hydrogen peroxide (H₂O₂) and superoxide anions (O₂^•−) caused by LL stress. Thus, pre-treatment with Z significantly reduced ROS accumulation in pepper seedlings under LL stress by enhancing the activity of antioxidant enzymes and accumulation of components of the ascorbate–glutathione (AsA–GSH) cycle and upregulated key genes in the AsA–GSH cycle. Full article

(This article belongs to the Special Issue Advanced Research in Plant Metabolomics)

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Review

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16 pages, 1020 KiB

Open AccessReview

Metabolomics as a Prospective Tool for Soybean (Glycine max) Crop Improvement

by Efficient Ncube, Keletso Mohale and Noluyolo Nogemane

Curr. Issues Mol. Biol. 2022, 44(9), 4181-4196; https://doi.org/10.3390/cimb44090287 - 12 Sep 2022

Cited by 8 | Viewed by 2997

Abstract

Global demand for soybean and its products has stimulated research into the production of novel genotypes with higher yields, greater drought and disease tolerance, and shorter growth times. Genetic research may be the most effective way to continue developing high-performing cultivars with desirable agronomic features and improved nutritional content and seed performance. Metabolomics, which predicts the metabolic marker for plant performance under stressful conditions, is rapidly gaining interest in plant breeding and has emerged as a powerful tool for driving crop improvement. The development of increasingly sensitive, automated, and high-throughput analytical technologies, paired with improved bioinformatics and other omics techniques, has paved the way for wide characterization of genetic characteristics for crop improvement. The combination of chromatography (liquid and gas-based) with mass spectrometry has also proven to be an indisputable efficient platform for metabolomic studies, notably plant metabolic fingerprinting investigations. Nevertheless, there has been significant progress in the use of nuclear magnetic resonance (NMR), capillary electrophoresis, and Fourier-transform infrared spectroscopy (FTIR), each with its own set of benefits and drawbacks. Furthermore, utilizing multivariate analysis, principal components analysis (PCA), discriminant analysis, and projection to latent structures (PLS), it is possible to identify and differentiate various groups. The researched soybean varieties may be correctly classified by using the PCA and PLS multivariate analyses. As metabolomics is an effective method for evaluating and selecting wild specimens with desirable features for the breeding of improved new cultivars, plant breeders can benefit from the identification of metabolite biomarkers and key metabolic pathways to develop new genotypes with value-added features. Full article

(This article belongs to the Special Issue Advanced Research in Plant Metabolomics)

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16 pages, 847 KiB

Open AccessReview

Molecular Aspects of MicroRNAs and Phytohormonal Signaling in Response to Drought Stress: A Review

by Hafiz Muhammad Ahmad, Xiukang Wang, Munazza Ijaz, Mahmood-Ur-Rahman, Sadaf Oranab, Muhammad Amjad Ali and Sajid Fiaz

Curr. Issues Mol. Biol. 2022, 44(8), 3695-3710; https://doi.org/10.3390/cimb44080253 - 16 Aug 2022

Cited by 19 | Viewed by 3341

Abstract

Phytohormones play an essential role in plant growth and development in response to environmental stresses. However, plant hormones require a complex signaling network combined with other signaling pathways to perform their proper functions. Thus, multiple phytohormonal signaling pathways are a prerequisite for understanding plant defense mechanism against stressful conditions. MicroRNAs (miRNAs) are master regulators of eukaryotic gene expression and are also influenced by a wide range of plant development events by suppressing their target genes. In recent decades, the mechanisms of phytohormone biosynthesis, signaling, pathways of miRNA biosynthesis and regulation were profoundly characterized. Recent findings have shown that miRNAs and plant hormones are integrated with the regulation of environmental stress. miRNAs target several components of phytohormone pathways, and plant hormones also regulate the expression of miRNAs or their target genes inversely. In this article, recent developments related to molecular linkages between miRNAs and phytohormones were reviewed, focusing on drought stress. Full article

(This article belongs to the Special Issue Advanced Research in Plant Metabolomics)

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19 pages, 669 KiB

Open AccessReview

CRISPR/Cas9 Technique for Temperature, Drought, and Salinity Stress Responses

by Xiaohan Li, Siyan Xu, Martina Bianca Fuhrmann-Aoyagi, Shaoze Yuan, Takeru Iwama, Misaki Kobayashi and Kenji Miura

Curr. Issues Mol. Biol. 2022, 44(6), 2664-2682; https://doi.org/10.3390/cimb44060182 - 8 Jun 2022

Cited by 32 | Viewed by 7568

Abstract

Global warming and climate change have severely affected plant growth and food production. Therefore, minimizing these effects is required for sustainable crop yields. Understanding the molecular mechanisms in response to abiotic stresses and improving agricultural traits to make crops tolerant to abiotic stresses have been going on unceasingly. To generate desirable varieties of crops, traditional and molecular breeding techniques have been tried, but both approaches are time-consuming. Clustered regularly interspaced short palindromic repeat/Cas9 (CRISPR/Cas9) and transcription activator-like effector nucleases (TALENs) are genome-editing technologies that have recently attracted the attention of plant breeders for genetic modification. These technologies are powerful tools in the basic and applied sciences for understanding gene function, as well as in the field of crop breeding. In this review, we focus on the application of genome-editing systems in plants to understand gene function in response to abiotic stresses and to improve tolerance to abiotic stresses, such as temperature, drought, and salinity stresses. Full article

(This article belongs to the Special Issue Advanced Research in Plant Metabolomics)

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