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Metabolites
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Metabolic Alterations and Gene Regulation in Plants under Stress
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Metabolic Alterations and Gene Regulation in Plants under Stress

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

Deadline for manuscript submissions: closed (20 December 2023) | Viewed by 10198

Special Issue Editors

Dr. Changjun Ding

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Guest Editor
Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
Interests: forest genetic and tree breeding
Dr. Weixi Zhang

E-Mail
Guest Editor
Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
Interests: transgenic breeding; gene editing breeding; tree breeding; forest genetics; biotechnology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

As the final product of gene and protein expression, metabolites are the material basis of plant phenotypes; further, they can also affect gene expression and protein activity. Metabolism can distinguish the genotype effectively through its ability of reflect and amplify the small changes in the genome, transcriptome and proteome. With global climate change, the environment of plant growth has changed significantly, causing a series of changes in physiological and metabolic processes.

This Special Issue of Metabolites will publish reviews and original articles covering the latest developments in plant metabolic processes in different periods or organs under abiotic stresses, especially the quantitative analysis of the composition and content of metabolites under stress conditions, and also the molecular regulatory mechanisms of the metabolic process.

Dr. Changjun Ding
Dr. Weixi Zhang
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

  • metabolic alterations
  • metabolic process
  • abiotic stresses
  • molecular mechanisms
  • gene regulation

Published Papers (6 papers)

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Research

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17 pages, 4808 KiB  
Article
Eco-Physiological Responses of Avicennia marina (Forssk.) Vierh. to Trace Metals Pollution via Intensifying Antioxidant and Secondary Metabolite Contents
by Basmah M. Alharbi, Awatif M. Abdulmajeed, Alae A. Jabbour and Ahmed M. Hashim
Metabolites 2023, 13(7), 808; https://doi.org/10.3390/metabo13070808 - 29 Jun 2023
Viewed by 1013
Abstract
Mangrove is one of the most precious ecosystems with the greatest losses due to climate change, human activities, and pollution. The objective of this study is to assess the accumulation and distribution of some trace metals (Cu, Cd, Ni, Pb, and Zn) in [...] Read more.
Mangrove is one of the most precious ecosystems with the greatest losses due to climate change, human activities, and pollution. The objective of this study is to assess the accumulation and distribution of some trace metals (Cu, Cd, Ni, Pb, and Zn) in sediments and Avicennia marina roots and leaves and to discuss the antioxidant potential of A. marina under metallic pollution stress. Sediments, leaf, and root samples of A. marina were collected from five sites along the Red Sea Coast of Egypt. Several ecological pollution indices, including the geo accumulation index (Igeo), contamination factor (CF), pollution load index (PLI), bioconcentration factor (BCF), and translocation factor (TF), were used to assess the pollution load. Cu, Cd, Ni, Pb, and Zn average concentrations in sediments were 167.4, 0.75, 110.65, 39.79, and 220 μg g−1, respectively, and the average values of these metals in A. marina roots were 44.9, 0.5, 87.96, 39.02, and 54.68 μg g−1, respectively, while in leaves their concentration were 50.46, 0.5572, 88.24, 40.08, and 56.08 μg g−1, respectively. The values of the Igeo, CF, and PLI index indicated that location 1 and 5 are moderate-to-heavily contaminated sites. On the other hand, leaves and roots of A. marina grown in polluted locations 1 and 5 showed high accumulation of malondialdehyde (MDA), low chlorophyll a and chlorophyll b contents concomitant with a decrease in total soluble sugars. High total antioxidant capacity was associated with a significant increase in activity levels of antioxidant enzymes (Catalase, Polyphenol oxidase, Polyphenol peroxidase, and Ascorbic acid oxidase), accumulation of secondary metabolites (total phenols, flavonoids, and tannins), and proline and carotenoids content increase. Overall, the present study suggests that the mangrove habitat of the Egyptian Red Sea coast is under the stress of anthropogenic activities, which necessitates a conservation plan to avoid further contamination and protect the unique biota of this distinctive habitat. Full article
(This article belongs to the Special Issue Metabolic Alterations and Gene Regulation in Plants under Stress)
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15 pages, 1773 KiB  
Article
Changes in Metabolite Profiling and Expression Levels of Key Genes Involved in the Terpenoid Biosynthesis Pathway in Garden Sage (Salvia officinalis) under the Effect of Hydrazine Hydrate
by Mohammed Ali, Aisha M. Abdelkawy, Doaa Bahaa Eldin Darwish, Hanan Ali Alatawi, Dikhnah Alshehri, Hadba Al-Amrah and Fathia A. Soudy
Metabolites 2023, 13(7), 807; https://doi.org/10.3390/metabo13070807 - 29 Jun 2023
Viewed by 964
Abstract
Mutagenesis is a highly efficient tool for establishing genetic variation and is widely used for genetic enhancement in various plants. The key benefit of mutation breeding is the prospect of enhancing one or several characteristics of a variety without altering the genetic background. [...] Read more.
Mutagenesis is a highly efficient tool for establishing genetic variation and is widely used for genetic enhancement in various plants. The key benefit of mutation breeding is the prospect of enhancing one or several characteristics of a variety without altering the genetic background. In this study, we exposed the seeds of Salvia officinalis to four concentrations of hydrazine hydrate (HZ), i.e., (0%, 0.1%, 0.2%, and 0.3%) for 6 h. The contents of terpenoid compounds in the S. officinalis plantlets driven from the HZ-treated seeds were determined by GC-MS, which resulted in the identification of a total of 340 phytochemical compounds; 163 (87.48%), 145 (84.49%), 65 (97.45%), and 62 (98.32%), from the four concentrations of HZ (0%, 0.1%, 0.2%, and 0.3%), respectively. Furthermore, we used the qRT-PCR system to disclose the “transcriptional control” for twelve TPS genes related to terpenoid and terpene biosynthesis, namely, SoGPS, SoMYRS, SoNEOD, SoCINS, SoSABS, SoLINS, SoFPPS, SoHUMS, SoTPS6, SoSQUS, SoGGPS, and SoGA2. Altogether, results are likely to ensure some positive relationship between the concentrations of the chemical mutagen HZ used for treating the seeds, the type and amount of the produced terpenes, and the expression of their corresponding genes. Full article
(This article belongs to the Special Issue Metabolic Alterations and Gene Regulation in Plants under Stress)
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24 pages, 3358 KiB  
Article
Exploring the Biologically Active Metabolites Produced by Bacillus cereus for Plant Growth Promotion, Heat Stress Tolerance, and Resistance to Bacterial Soft Rot in Arabidopsis
by Sih-Huei Tsai, Yi-Chun Hsiao, Peter E. Chang, Chen-En Kuo, Mei-Chun Lai and Huey-wen Chuang
Metabolites 2023, 13(5), 676; https://doi.org/10.3390/metabo13050676 - 22 May 2023
Cited by 4 | Viewed by 1692
Abstract
Eight gene clusters responsible for synthesizing bioactive metabolites associated with plant growth promotion were identified in the Bacillus cereus strain D1 (BcD1) genome using the de novo whole-genome assembly method. The two largest gene clusters were responsible for synthesizing volatile organic compounds (VOCs) [...] Read more.
Eight gene clusters responsible for synthesizing bioactive metabolites associated with plant growth promotion were identified in the Bacillus cereus strain D1 (BcD1) genome using the de novo whole-genome assembly method. The two largest gene clusters were responsible for synthesizing volatile organic compounds (VOCs) and encoding extracellular serine proteases. The treatment with BcD1 resulted in an increase in leaf chlorophyll content, plant size, and fresh weight in Arabidopsis seedlings. The BcD1-treated seedlings also accumulated higher levels of lignin and secondary metabolites including glucosinolates, triterpenoids, flavonoids, and phenolic compounds. Antioxidant enzyme activity and DPPH radical scavenging activity were also found to be higher in the treated seedlings as compared with the control. Seedlings pretreated with BcD1 exhibited increased tolerance to heat stress and reduced disease incidence of bacterial soft rot. RNA-seq analysis showed that BcD1 treatment activated Arabidopsis genes for diverse metabolite synthesis, including lignin and glucosinolates, and pathogenesis-related proteins such as serine protease inhibitors and defensin/PDF family proteins. The genes responsible for synthesizing indole acetic acid (IAA), abscisic acid (ABA), and jasmonic acid (JA) were expressed at higher levels, along with WRKY transcription factors involved in stress regulation and MYB54 for secondary cell wall synthesis. This study found that BcD1, a rhizobacterium producing VOCs and serine proteases, is capable of triggering the synthesis of diverse secondary metabolites and antioxidant enzymes in plants as a defense strategy against heat stress and pathogen attack. Full article
(This article belongs to the Special Issue Metabolic Alterations and Gene Regulation in Plants under Stress)
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15 pages, 1460 KiB  
Article
Changes in the Carbohydrate Profile in Common Buckwheat (Fagopyrum esculentum Moench) Seedlings Induced by Cold Stress and Dehydration
by Lesław B. Lahuta, Ryszard J. Górecki, Joanna Szablińska-Piernik and Marcin Horbowicz
Metabolites 2023, 13(5), 672; https://doi.org/10.3390/metabo13050672 - 19 May 2023
Viewed by 1251
Abstract
Plant species are sensitive to stresses, especially at the seedling stage, and they respond to these conditions by making metabolic changes to counteract the negative effects of this. The objectives of this study were to determine carbohydrate profile in particular organs (roots, hypocotyl, [...] Read more.
Plant species are sensitive to stresses, especially at the seedling stage, and they respond to these conditions by making metabolic changes to counteract the negative effects of this. The objectives of this study were to determine carbohydrate profile in particular organs (roots, hypocotyl, and cotyledons) of common buckwheat seedlings and to verify whether carbohydrate accumulation is similar or not in the organs in response to cold stress and dehydration. Roots, hypocotyl, and cotyledons of common buckwheat seedlings have various saccharide compositions. The highest concentrations of cyclitols, raffinose, and stachyose were found in the hypocotyl, indicating that they may be transported from cotyledons, although this needs further studies. Accumulation of raffinose and stachyose is a strong indicator of the response of all buckwheat organs to introduced cold stress. Besides, cold conditions reduced d-chiro-inositol content, but did not affect d-pinitol level. Enhanced accumulation of raffinose and stachyose were also a distinct response of all organs against dehydration at ambient temperature. The process causes also a large decrease in the content of d-pinitol in buckwheat hypocotyl, which may indicate its transformation to d-chiro-inositol whose content increased at that time. In general, the sucrose and its galactosides in hypocotyl tissues were subject to the highest changes to the applied cold and dehydration conditions compared to the cotyledons and roots. This may indicate tissue differences in the functioning of the protective system(s) against such threats. Full article
(This article belongs to the Special Issue Metabolic Alterations and Gene Regulation in Plants under Stress)
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Review

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30 pages, 8269 KiB  
Review
Decoding Metabolic Reprogramming in Plants under Pathogen Attacks, a Comprehensive Review of Emerging Metabolomics Technologies to Maximize Their Applications
by Ahmed Serag, Mohamed A. Salem, Shilin Gong, Jian-Lin Wu and Mohamed A. Farag
Metabolites 2023, 13(3), 424; https://doi.org/10.3390/metabo13030424 - 13 Mar 2023
Cited by 7 | Viewed by 2648
Abstract
In their environment, plants interact with a multitude of living organisms and have to cope with a large variety of aggressions of biotic or abiotic origin. What has been known for several decades is that the extraordinary variety of chemical compounds the plants [...] Read more.
In their environment, plants interact with a multitude of living organisms and have to cope with a large variety of aggressions of biotic or abiotic origin. What has been known for several decades is that the extraordinary variety of chemical compounds the plants are capable of synthesizing may be estimated in the range of hundreds of thousands, but only a fraction has been fully characterized to be implicated in defense responses. Despite the vast importance of these metabolites for plants and also for human health, our knowledge about their biosynthetic pathways and functions is still fragmentary. Recent progress has been made particularly for the phenylpropanoids and oxylipids metabolism, which is more emphasized in this review. With an increasing interest in monitoring plant metabolic reprogramming, the development of advanced analysis methods should now follow. This review capitalizes on the advanced technologies used in metabolome mapping in planta, including different metabolomics approaches, imaging, flux analysis, and interpretation using bioinformatics tools. Advantages and limitations with regards to the application of each technique towards monitoring which metabolite class or type are highlighted, with special emphasis on the necessary future developments to better mirror such intricate metabolic interactions in planta. Full article
(This article belongs to the Special Issue Metabolic Alterations and Gene Regulation in Plants under Stress)
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Other

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5 pages, 535 KiB  
Opinion
Real-Time Quantitative PCR: Primer Design, Reference Gene Selection, Calculations and Statistics
by Zhiwei Chen, Nigel G. Halford and Chenghong Liu
Metabolites 2023, 13(7), 806; https://doi.org/10.3390/metabo13070806 - 28 Jun 2023
Cited by 4 | Viewed by 2033
Abstract
Real-time quantitative PCR is a technique that can measure the content of the target nucleic acid sequence of interest in a given sample. It is mainly divided into absolute and relative quantitative methods. The relative quantification is mainly used in gene expressions for [...] Read more.
Real-time quantitative PCR is a technique that can measure the content of the target nucleic acid sequence of interest in a given sample. It is mainly divided into absolute and relative quantitative methods. The relative quantification is mainly used in gene expressions for functional genomic and transcriptome studies. However, to use this technology accurately, there are some key points to master. First, specific primers need to be designed to ensure amplification of the gene of interest (GOI). Second, the appropriate reference gene or reference gene combination has to be selected. Finally, scientific gene expression level calculations and statistics are required to obtain accurate results. Therefore, this work proposes a workflow for relative quantitative PCR and introduces the relevant points so that beginners can better understand and use this technology. Full article
(This article belongs to the Special Issue Metabolic Alterations and Gene Regulation in Plants under Stress)
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