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

Deadline for manuscript submissions: closed (31 July 2023) | Viewed by 15723

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Dr. Yanjie Zhang

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Guest Editor

School of Agricultural Sciences, Zhengzhou University, Kexue Avenue 100, Zhengzhou 450001, China
Interests: metabolism; flavonoid; genetic engineering; gene editing; fruit quality

Dr. Yan Li

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Guest Editor

The Center of Advanced Analysis and Gene Sequencing, Zhengzhou University, Kexue Avenue 100, Zhengzhou 450001, China
Interests: metabolume; transcriptome; synthetic biology; mass spectrometry imaging

Special Issue Information

Dear Colleagues,

Innumerable chemicals that fulfill the needs of human beings are produced through complex biosynthetic pathways in the plant kingdom. Because of the acceleration of global problems such as species extinction, disease, plague, starvation, and population growth, we now have to rethink the availability of these natural compounds. Plant metabolic engineering is an effective and beneficial strategy in producing desired chemicals or other products, such as edible vaccines, in a short amount of time and requiring little space. By applying plant metabolic engineering, natural compounds can be produced in higher quantities, and newer metabolites can even be envisaged in genetically modified plants, which can also effectively avoid the side effects of chemical engineering. To boost the development of genetically modified plants, there is an urgent need to invent new technologies for the rapid identification of metabolites and isolate the key genes involved in the biosynthesis or regulation of these metabolites.

In this Special Issue, we ask for contributions relating to plant metabolic engineering and synthetic biology. We would like to focus on metabolite identification, the isolation of key structural and/or regulatory genes, and precise genome engineering. We believe that quantitative approaches in metabolite analysis will help to reduce the time required to establish an efficient whole-cell biocatalyst, and the systems biology approach is helpful in reducing these unnecessary experiments at the wet-lab level and refining our targets (genes/enzymes) in the application of metabolic engineering. Therefore, successful examples of plant metabolic engineering using synthetic biology tools are also welcomed. We believe that slow but steady progress in plant metabolic engineering will soon result in a miracle growth in this field of research, and provide solutions for global challenges.

Dr. Yanjie Zhang
Dr. Yan Li
Guest Editors

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Keywords

metabolic engineering
metabolites
metabolomics
synthetic biology
genetic reconstitution
systems biology
biosynthetic modules
isolation of enzyme complexes
photosynthesis
fortification
plastids
bioenergy

Published Papers (9 papers)

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Research

13 pages, 6829 KiB

Open AccessArticle

SlbHLH22-Induced Hypertrophy Development Is Related to the Salt Stress Response of the GTgamma Gene in Tomatoes

by Baolu Cui, Min Yu, Jiaojiao Bai and Zhiguo Zhu

Metabolites 2023, 13(12), 1195; https://doi.org/10.3390/metabo13121195 - 11 Dec 2023

Viewed by 1038

Abstract

Hypertrophy development induced by the overexpression of SlbHLH22 (also called SlUPA-like) was susceptible to Xanthomonas in tomatoes. Transcriptome and metabolome analyses were performed on the hypertrophy leaves of a SlbHLH22-overexpressed line (OE) and wild type (WT) to investigate the molecular mechanism. Metabolome analysis revealed that six key metabolites were over-accumulated in the OE, including Acetylserine/O-Acetyl-L-serine, Glucono-1,5-lactone, Gluconate, 2-Oxoglutarate, and Loganate, implying that the OE plants increased salt or oxidant resistance under normal growth conditions. The RNA-seq analysis showed the changed expressions of downstream genes involved in high-energy consumption, photosynthesis, and transcription regulation in OE lines, and we hypothesized that these biological processes were related to the GTgamma subfamily of trihelix factors. The RT-PCR results showed that the expressions of the GTgamma genes in tomatoes, i.e., SlGT-7 and SlGT-36, were suppressed in the hypertrophy development. The expression of the GTgamma gene was downregulated by salinity, indicating a coordinated role of GTgamma in hypertrophy development and salt stress. Further research showed that both SlGT-7 and SlGT-36 were highly expressed in leaves and could be significantly induced by abscisic acid (ABA). The GTgamma protein had a putative phosphorylation site at S⁹⁶. These results suggested GTgamma’s role in hypertrophy development by increasing the salt resistance. Full article

(This article belongs to the Special Issue Plant Metabolic Genetic Engineering)

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35 pages, 4929 KiB

Open AccessArticle

Comparative Metabolomics Profiling Reveals Key Metabolites and Associated Pathways Regulating Tuber Dormancy in White Yam (Dioscorea rotundata Poir.)

by Jeremiah S. Nwogha, Abtew G. Wosene, Muthurajan Raveendran, Jude E. Obidiegwu, Happiness O. Oselebe, Rohit Kambale, Cynthia A. Chilaka and Veera Ranjani Rajagopalan

Metabolites 2023, 13(5), 610; https://doi.org/10.3390/metabo13050610 - 28 Apr 2023

Cited by 3 | Viewed by 1969

Abstract

Yams are economic and medicinal crops with a long growth cycle, spanning between 9–11 months due to their prolonged tuber dormancy. Tuber dormancy has constituted a major constraint in yam production and genetic improvement. In this study, we performed non-targeted comparative metabolomic profiling of tubers of two white yam genotypes, (Obiaoturugo and TDr1100873), to identify metabolites and associated pathways that regulate yam tuber dormancy using gas chromatography–mass spectrometry (GC–MS). Yam tubers were sampled between 42 days after physiological maturity (DAPM) till tuber sprouting. The sampling points include 42-DAPM, 56-DAPM, 87DAPM, 101-DAPM, 115-DAPM, and 143-DAPM. A total of 949 metabolites were annotated, 559 in TDr1100873 and 390 in Obiaoturugo. A total of 39 differentially accumulated metabolites (DAMs) were identified across the studied tuber dormancy stages in the two genotypes. A total of 27 DAMs were conserved between the two genotypes, whereas 5 DAMs were unique in the tubers of TDr1100873 and 7 DAMs were in the tubers of Obiaoturugo. The differentially accumulated metabolites (DAMs) spread across 14 major functional chemical groups. Amines and biogenic polyamines, amino acids and derivatives, alcohols, flavonoids, alkaloids, phenols, esters, coumarins, and phytohormone positively regulated yam tuber dormancy induction and maintenance, whereas fatty acids, lipids, nucleotides, carboxylic acids, sugars, terpenoids, benzoquinones, and benzene derivatives positively regulated dormancy breaking and sprouting in tubers of both yam genotypes. Metabolite set enrichment analysis (MSEA) revealed that 12 metabolisms were significantly enriched during yam tuber dormancy stages. Metabolic pathway topology analysis further revealed that six metabolic pathways (linoleic acid metabolic pathway, phenylalanine metabolic pathway, galactose metabolic pathway, starch and sucrose metabolic pathway, alanine-aspartate-glutamine metabolic pathways, and purine metabolic pathway) exerted significant impact on yam tuber dormancy regulation. This result provides vital insights into molecular mechanisms regulating yam tuber dormancy. Full article

(This article belongs to the Special Issue Plant Metabolic Genetic Engineering)

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17 pages, 3961 KiB

Open AccessArticle

Transcription and Metabolism Pathways of Anthocyanin in Purple Shamrock (Oxalis triangularis A.St.-Hil.)

by Baobing Luo, Liujun Chen, Guoping Chen, Yunshu Wang, Qiaoli Xie, Xuqing Chen and Zongli Hu

Metabolites 2022, 12(12), 1290; https://doi.org/10.3390/metabo12121290 - 19 Dec 2022

Cited by 4 | Viewed by 1618

Abstract

Anthocyanins are water-soluble pigments that can impart various colors to plants. Purple shamrock (Oxalis triangularis) possesses unique ornamental value due to its purple leaves. In this study, three anthocyanins, including malvidin 3-O-(4-O-(6-O-malonyl-glucopyranoside)-rhamnopyranosyl)-5-O-(6-O-malonyl-glucopyranoside), delphinidin-3-O-rutinoside and malvidin-3,5-di-O-glucoside, were characterized with ultra-performance liquid chromatography-electrospray ionization tandem mass spectrometry (UPLC-ESI-MS/MS) in purple shamrock. To investigate the molecular mechanism of anthocyanin biosynthesis in green shamrock (Oxalis corymbosa) and purple shamrock, RNA-seq and qRT-PCR were performed, and the results showed that most of the anthocyanin biosynthetic and regulatory genes were up-regulated in purple shamrock. Then, dark treatment and low temperature treatment experiments in purple shamrock showed that both light and low temperature can induce the biosynthesis of anthocyanins. Full article

(This article belongs to the Special Issue Plant Metabolic Genetic Engineering)

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14 pages, 1845 KiB

Open AccessArticle

Identification and Dissipation of Chlorpyrifos and Its Main Metabolite 3,5,6-TCP during Wheat Growth with UPLC-QTOF/MS

by Lili Yu, Jia Li, Meiqin Feng, Qian Tang, Zejun Jiang, Hui Chen, Tingting Shan and Junhui Li

Metabolites 2022, 12(12), 1162; https://doi.org/10.3390/metabo12121162 - 23 Nov 2022

Cited by 1 | Viewed by 1554

Abstract

Ultrahigh-performance liquid chromatography system coupled to a hybrid quadrupole time-of-flight mass spectrometer (UPLC-QTOF/MS) technology was used to investigate the degradation and metabolism of chlorpyrifos during wheat growth by spraying plants with different doses of chlorpyrifos 7 days after the flowering and filling stage. We analyzed and identified chlorpyrifos metabolites in different parts of wheat in full-scan MS^E mode, and established a chlorpyrifos metabolite screening library using UNIFI software. The results show that the residues of chlorpyrifos in wheat ears, leaves, and stems exhibited a decreasing trend with the prolongation of application time, and the degradation kinetics could be fitted with the first-order kinetic equation C_t = C₀ e^−k^t. The initial residues of chlorpyrifos in different parts of the wheat were different, in the order of leaves > wheat ears > stems. The degradation rate of chlorpyrifos under field conditions is relatively fast, and the half-life value is 2.33–5.05 days. Chlorpyrifos can undergo a nucleophilic addition substitution reaction under the action of hydrolase to generate secondary metabolite 3,5,6-trichloro-2-pyridinol (3,5,6-TCP). The residual amount of 3,5,6-TCP in each part of wheat first showed an increasing trend and then decreased over time. It reached the maximum on the 3rd, 7th, or 11th day after application, and then gradually degraded. Considering that 3,5,6-TCP is a biomarker with potential threats to humans and animals, it is recommended that 3,5,6-TCP be included in the relevant regulations for dietary exposure risk assessment. Full article

(This article belongs to the Special Issue Plant Metabolic Genetic Engineering)

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13 pages, 3765 KiB

Open AccessArticle

Integrated Analysis of Metabolome and Transcriptome Reveals the Difference in Flavonoid Biosynthesis between the Red- and White-Sarcocarp Pomelo Fruits

by Chenxu Zhao, Jiajia Wang, Yuxia Li, Lei Zhang, Ghazala Nawaz, Shaoyuan Wu and Tao Xu

Metabolites 2022, 12(12), 1161; https://doi.org/10.3390/metabo12121161 - 23 Nov 2022

Cited by 1 | Viewed by 1507

Abstract

Flavonoids are bioactive secondary metabolites that play multiple roles in plants. However, studies on the flavonoid accumulation of the pomelo fruit are rare. In this study, we conducted a widely targeted metabolome analysis by using ultra-performance liquid chromatography and tandem mass spectrometry and identified 550 metabolites in the sarcocarp from red (C. maxima Merr. var. Tubtim Siam) and white pomelos (C. maxima (Burm.) Osbeck). A total of 263 significantly changed metabolites were detected from the 550 metabolites. Content analysis of the significantly changed metabolites (SCMs) showed that 138 SCMs were highly accumulated, whereas 125 SCMs were observed with lower content in red-sarcocarp pomelo. Importantly, 103 of the 263 SCMs were flavonoids, including 34 flavonoids, 29 flavonols, 18 flavonoid carbonosides, 9 dihydroflavones, 6 isoflavones, 5 anthocyanins, 1 dihydroflavonol, and 1 chalcone. Gene ontology analysis indicated that upregulated genes in red-sarcocarp pomelo were significantly enriched in GO terms related to flavonoids including flavonoid biosynthetic processes. Several important differentially expressed genes were detected in the correlation network, especially Cg2g009540 which is an orthologous gene of AtCHS, also detected in flavonoid biosynthesis networks, and which could be related to the high level of total flavonoids in the red-sarcocarp pomelo. Our study demonstrated the fluctuation of flavonoid biosynthesis in the two pomelo cultivars and laid a theoretical foundation for pomelo breeding to generate fruits with a high flavonoid content. Full article

(This article belongs to the Special Issue Plant Metabolic Genetic Engineering)

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14 pages, 3048 KiB

Open AccessArticle

Comparative Transcriptome Analysis of MeJA Responsive Enzymes Involved in Phillyrin Biosynthesis of Forsythia suspensa

by Xiaoran Liu, Jiaqi Zhang, Hao Liu, Huixiang Shang, Xingli Zhao, Huawei Xu, Hongxiao Zhang and Dianyun Hou

Metabolites 2022, 12(11), 1143; https://doi.org/10.3390/metabo12111143 - 20 Nov 2022

Cited by 1 | Viewed by 1513

Abstract

Forsythia suspensa (Thunb.) has been widely used in traditional medicines in Asia. According to the 2020 edition of Chinese Pharmacopoeia, phillyrin is the main active ingredient in F. suspensa, which is effective in clearing heat, reducing swelling, and dispersing nodules. F. suspensa leaf is a non-toxic substance and it can be used to make a health tea. Here, we combine elicitors and transcriptomics to investigate the inducible biosynthesis of the phillyrin from the F. suspensa. After the fruits and leaves of F. suspensa were treated with different concentrations of methyl jasmonate (MeJA), the content of phillyrin in the fruits reached a peak at 200 µM MeJA for 12 h, but which was decreased in leaves. To analyze the differences in key enzyme genes involved in the phillyrin biosynthesis, we sequenced the transcriptome of F. suspensa leaves and fruits treated with 200 µM MeJA for 12 h. We hypothesized that nine genes related to coniferin synthesis including: F. suspensa UDP-glycosyltransferase (FsUGT); F. suspensa 4-coumarate coenzyme CoA ligase (Fs4CL); and F. suspensa Caffeoyl-CoA O-methyltransferase (FsCCoAOMT) etc. The qRT-PCR analysis of genes related to phillyrin biosynthesis was consistent with RNA-seq analysis. We also investigated the dynamic changes of genes in F. suspensa leaves and fruits at different time points after 200 µM MeJA treatment, which laid the foundation for further study of the molecular mechanisms regulating the biosynthesis of phillyrin. Full article

(This article belongs to the Special Issue Plant Metabolic Genetic Engineering)

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18 pages, 3523 KiB

Open AccessArticle

Integrated Metabolomic and Transcriptomic Analyses Reveal the Basis for Carotenoid Biosynthesis in Sweet Potato (Ipomoea batatas (L.) Lam.) Storage Roots

by Qingming Ren, Xiaoxi Zhen, Huiyu Gao, Yinpei Liang, Hongying Li, Juan Zhao, Meiqiang Yin, Yuanhuai Han and Bin Zhang

Metabolites 2022, 12(11), 1010; https://doi.org/10.3390/metabo12111010 - 23 Oct 2022

Cited by 3 | Viewed by 1493

Abstract

Carotenoids are important compounds of quality and coloration within sweet potato storage roots, but the mechanisms that govern the accumulation of these carotenoids remain poorly understood. In this study, metabolomic and transcriptomic analyses of carotenoids were performed using young storage roots (S2) and old storage roots (S4) from white-fleshed (variety S19) and yellow-fleshed (variety BS) sweet potato types. S19 storage roots exhibited significantly lower total carotenoid levels relative to BS storage roots, and different numbers of carotenoid types were detected in the BS-S2, BS-S4, S19-S2, and S19-S4 samples. β-cryptoxanthin was identified as a potential key driver of differences in root coloration between the S19 and BS types. Combined transcriptomic and metabolomic analyses revealed significant co-annotation of the carotenoid and abscisic acid (ABA) metabolic pathways, PSY (phytoene synthase), CHYB (β-carotene 3-hydroxylase), ZEP (zeaxanthin epoxidase), NCED3 (9-cis-epoxycarotenoid dioxygenase 3), ABA2 (xanthoxin dehydrogenase), and CYP707A (abscisic acid 8’-hydroxylase) genes were found to be closely associated with carotenoid and ABA content in these sweet potato storage roots. The expression patterns of the transcription factors OFP and FAR1 were associated with the ABA content in these two sweet potato types. Together, these results provide a valuable foundation for understanding the mechanisms governing carotenoid biosynthesis in storage roots, and offer a theoretical basis for sweet potato breeding and management. Full article

(This article belongs to the Special Issue Plant Metabolic Genetic Engineering)

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15 pages, 2743 KiB

Open AccessFeature PaperArticle

GC-TOF-MS-Based Non-Targeted Metabolomic Analysis of Differential Metabolites in Chinese Ultra-Long-Term Industrially Fermented Kohlrabi and Their Associated Metabolic Pathways

by Xin Nie, Hongfan Chen, Lu Xiang, Yulin Zhang, Dayu Liu and Zhiping Zhao

Metabolites 2022, 12(10), 991; https://doi.org/10.3390/metabo12100991 - 19 Oct 2022

Cited by 8 | Viewed by 2065

Abstract

Fermented kohlrabi is a very popular side dish in China. Chinese kohlrabies industrially fermented for 0 years (0Y), 5 years (5Y), and 10 years (10Y) were employed and analyzed by non-targeted metabolomics based on GC-TOF-MS, and the differential metabolites were screened using multivariate statistical analysis techniques, including principal component analysis (PCA) and orthogonal partial least squares discrimination analysis (OPLS-DA). The results showed that 47, 38, and 33 differential metabolites were identified in the three treatment groups of 0Y and 5Y (A1), 0Y and 10Y (A2), and 5Y and 10Y (A3), respectively (VIP > 1, p < 0.05). The metabolites were mainly carbohydrates, amino acids, and organic acids. Furthermore, 13 differential metabolites were screened from the three groups, including L-glutamic acid, L-aspartic acid, γ-aminobutyric acid, and other compounds. Four metabolic pathways termed alanine, aspartate, and glutamate metabolism, arginine biosynthesis, arginine and proline metabolism, and glycolysis/gluconeogenesis were the most significant pathways correlated with the differential metabolites, as analyzed according to the Kyoto Encyclopedia of Genes and Genomes (KEGG). The odors for the three ultra-long-term industrially fermented kohlrabies were significantly different, as detected by E-nose. The present work describes the changes in metabolites between different ultra-long-term industrially fermented kohlrabies and the associated metabolic pathways, providing a theoretical basis for the targeted regulation of characteristic metabolite biosynthesis in Chinese fermented kohlrabi. Full article

(This article belongs to the Special Issue Plant Metabolic Genetic Engineering)

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15 pages, 5175 KiB

Open AccessArticle

SmMYB4 Is a R2R3-MYB Transcriptional Repressor Regulating the Biosynthesis of Phenolic Acids and Tanshinones in Salvia miltiorrhiza

by Qian Tian, Limin Han, Xiaoya Zhu, Caijuan Zhang, Yunyun Li, Xiaoshan Xue, Yueyue Wang, Donghao Wang, Junfeng Niu, Wenping Hua, Bin Li and Zhezhi Wang

Metabolites 2022, 12(10), 968; https://doi.org/10.3390/metabo12100968 - 12 Oct 2022

Cited by 6 | Viewed by 1577

Abstract

Salvia miltiorrhiza Bunge is one of the most famous traditional Chinese medicinal plants. The two most important classes of pharmaceutically relevant compounds in S. miltiorrhiza are phenolic acids and tanshinones. The MYB family of transcription factors may efficiently regulate the secondary metabolism in plants. In this study, a subgroup 4 R2R3MYB transcription factor gene, SmMYB4, was isolated from S. miltiorrhiza and functionally characterized using overexpression and a RNAi-mediated silencing. We achieved a total of six overexpressions and eight RNAi transgenic lines from the Agrobacterium leaf disc method. The content of the total phenolics, rosmarinic acid, and salvianolic acid B markedly decreased in the SmMYB4-overexpressing lines but increased in the SmMYB4-RNAi lines. The content of the total tanshinones, cryptotanshinone, and tanshinone IIA decreased in the SmMYB4-overexpressing transgenic lines but increased in the SmMYB4-RNAi lines. A gene expression analysis demonstrated that SmMYB4 negatively regulated the transcription of the critical enzyme genes involved in the phenolic acid and tanshinone biosynthesis. The genetic control of this transcriptional repressor may be used to improve the content of these bioactive compounds in the cultivated S. miltiorrhiza. Full article

(This article belongs to the Special Issue Plant Metabolic Genetic Engineering)

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