Plants Metabolome Study: Emerging Tools and Techniques
Abstract
:1. Metabolomics: Plant Biology Perspective
1.1. Primary Metabolites
Plant Species | Class | Analytical Tools | Key Metabolites | Reference |
---|---|---|---|---|
Primary metabolites | ||||
Plantago ovata | Fatty acids | GC-MS | α-linolenic acid, linoleic acid and palmitic acid | [10] |
P. ovata | Fatty acids | GC-MS | Pentadecanoic acid, palmitic acid, heptadecanoic acid, stearic acid, oleic acid, linoleic acid, γ-linolenic acid and arachidic acid | [9] |
Jatropha curcas | Fatty acids | GC | Oleic acid, palmitic acid and linolenic acid | [29] |
Paeonia rockii, P. potaninii, and P. lutea | Fatty acids | GC-MS | α-linolenic acid, oleic acid and linoleic acid | [27] |
Cicer arietinum | Fatty acids | GC-MS | Pentadecanoic acid, palmitic acid, palmitoleic acid, stearic acid, oleic acid, linoleic acid, α-linolenic acid and arachidic acid | [33] |
P. ovata | Amino acids | HPLC | Isoleucine, threonine, leucine, histidine and lysine | [10] |
P. ovata | Amino acids | HPLC | Aspartate, glutamine, glycine, alanine, arginine, serine, proline, isoleucine and methionine | [9] |
Fritillaria thunbergii | Amino acids | GC-MS | Tryptophan, phenylalanine and histidine | [31] |
C. arietinum | Amino acids | GC-MS | L-glutamic acid, L-tryptophan, phenylalanine, glycine, serine, L-threonine, L-valine, L-ornithine and L-proline | [33] |
C. arietinum | Sugars and Sugar alcohols | GC-MS | Sucrose, cellobiose, galactose, methylgalactoside, myo-inositol | [33] |
C. arietinum | Sugar alcohols | GC-QqQ-MS | Galactitol, erythritol, arabitol, xylitol, mannitol and inositol | [32] |
Secondary metabolites | ||||
Beta vulgaris | Terpenes | HPLC-MS | Oleanolic acid, hederagenin, akebonoic acid and gypsogenin | [34] |
Ocimum gratissimum | Terpenes | GC-MS | m-chavicol, t-anethole, germacrene-D, naphthalene, ledene, eucalyptol, azulene and comphore | [35] |
Mentha piperita | Terpenes | GC-MS | Menthone, menthol, pulegone and menthofuran | [36] |
M. arvensis | Terpenes | GLC | Menthol, isomenthone, L-methone and menthyl acetate | [37] |
Achyranthes bidentata | Terpenes | HPLC | Oleanolic acid and ecdysterone | [38] |
Arabidopsis thaliana | Phenolics | UHPLC-MS | Scopoletin, umbelliferone and esculetin, scopolin, skimmin and esculin | [39] |
P. ovata | Phenolics | LC-MS | Luteolin, quercetagetin, syringetin, kaempferol, limocitrin, helilupolone and catechin | [10] |
P. ovata | Phenolics | LC-MS | Kaempferol 3-(2″,3″-diacetylrhamnoside)-7-rhamnoside and apigenin 7-rhamnoside | [9] |
P. ovata | Alkaloids | LC-MS | Lunamarine, hordatine B and pinidine | [10] |
Dendrobium Snowflake ‘Red Star’ | Alkaloids | 1H and 2D NMR | Dendrobine and nobilonine | [40] |
1.2. Secondary Metabolites
2. Involvement of Metabolomics in Genetically Modified (GM) Crops
3. Significance of Sample Preparation in Plant Metabolites
3.1. Sample Harvesting and Storage
3.2. Sample Preparation
4. Analytical Techniques Used for Plant Metabolome
4.1. Gas Chromatography-Mass Spectrometry (GC-MS)
4.2. Liquid Chromatography-Mass Spectrometry (LC-MS)
4.3. Capillary Electrophoresis-Mass Spectrometry (CE-MS)
4.4. Fourier Transform ion Cyclotron Resonance-Mass Spectrometry (FTICR-MS)
4.5. Matrix-Assisted Laser Desorption/Ionization (MALDI)
4.6. Ion Mobility Spectrometry (IMS)
4.7. Nuclear Magnetic Resonance (NMR)
5. Metabolomic Data Processing, Annotation, Database and Bioinformatics Tools for Plants METABOLOME Analysis
5.1. Data Processing and Annotation
5.2. Network Analysis
6. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Transgenic Plants | Analytical Techniques | Key Metabolites | References |
---|---|---|---|
Artemisia annua | GC-TOF-MS | Borneol, phytol, β-farnesene, germacrene D, artemisinic acid, dihydroartemisinic acid, and artemisinin | [46] |
Lactuca sativa | NMR | Asparagine, glutamine, valine, isoleucine, α-chetoglutarate, succinate, fumarate, malate, sucrose, and fructose | [47] |
Lycopersicon esculentum | GC-MS | γ-aminobutyric acid, histidine, proline, pyrrol-2-carboxylate, galactitiol/sorbitol, glycerol, maltitol, 3-phosphoglyceric acid, allantoin, homo-cystine, caffeate, gluconate, ribonate, lysine, threonine, homo-serine, tyrosine, tryptophan, leucine, arginine and valine | [48] |
Nicotiana tabacum | NMR | Chlorogenic acid, 4-O-caffeoylquinic acid, malic acid, threonine, alanine, glycine, fructose, β-glucose, α-glucose, sucrose, fumaric acid and salicylic acid | [49] |
N. tabacum | GC-MS | 4-Aminobutanoic acid, asparagine, glutamine, glycine, leucine, phenylalanine, proline, serine, threonine, tryptophan, chlorogenic acid, quininic acid, threonic acid, citric acid, malic acid and ethanolamine | [50] |
Oryza sativa | GC-MS | Glycerol-3-phosphate, citric acid, linoleic acid, oleic acid, hexadecanoic acid, 2,3-dihydroxypropyl ester, sucrose, 9-octadecenoic acid, 2,3-dihydroxypropyl ester, sucrose, mannitol and glutamic acid | [44] |
O. sativa | LC-MS | Tryptophan, phytosphingosine, palmitic acid, 5-hydroxy-2-octadenoic acid 9,10,13-trihydroxyoctadec-11-enoic acid and ethanolamine | [51] |
Populus | GC-MS, HPLC | Caffeoyl and feruloyl conjugates, syringyl-to-guaiacyl ratio, asparagine, glutamine, aspartic acid, γ-amino-butyric acid, 5-oxo-proline, salicylic acid-2-O-glucoside, 2, 5-dihydroxybenzoic acid-5-O-glucoside, 2-methoxyhydroquinone-1-O-glucoside, 2-methoxyhydroquinone-4-O-glucoside, salicin, gallic acid, and dihydroxybenzoic acid | [52] |
Solanum tuberosum | LC-TOF-MS | Glutathione, γ-aminobutyric acid, β-cyanoalanine, 5-oxoproline, sucrose, glucose-1-phosphate, glucose-6-phosphate, fructose-6-phosphate, ethanolamine, adenosine, and guanosine | [45] |
Triticum aestivum | GC-MS | Guanine and 4-hydroxycinnamic acid | [53] |
T. aestivum | LC-MS | Aminoacyl-tRNA biosynthesis, phenylalanine, tyrosine, tryptophan glyoxylic, tartaric acid, oxalic acids, sucrose, galactose, mannitol, leucine, valine, glutamate, proline, pyridoxamine, glutathione, arginine, citrulline, adenosine, hypoxanthine, allantoin, and adenosine monophosphate | [54] |
Zea mays | 1H NMR | Lactic acid, citric acid, lysine, arginine, glycine-betaine, raffinose, trehalose, galactose, and adenine | [55] |
Analytical Method | Advantage | Disadvantage |
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GC-MS |
|
|
LC-MS |
|
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CE-MS |
|
|
FTICR-MS |
|
|
MALDI-MSI |
|
|
IMS |
|
|
NMR |
|
|
Database | Website (URL, Accessed on 29 June 2021) | References |
---|---|---|
AraCyc | https://www.plantcyc.org/typeofpublication/aracyc | [175] |
Cytoscape | http://www.cytoscape.org/ | [183] |
IMPaLA | http://impala.molgen.mpg.de | [184] |
iPath | http://pathways.embl.de/ | [185] |
KEGG | http://www.genome.jp/kegg/ | [173] |
MapMan | http://mapman.gabipd.org/web/guest/mapman | [186] |
MBRole | http://csbg.cnb.csic.es/mbrole/ | [187] |
Metabolonote | http://metabolonote.kazusa.or.jp/ | [188] |
MetaCrop | http://metacrop.ipk-gatersleben.de | [189] |
MetaCyc | http://www.metacyc.org | [174] |
MetPA | http://metpa.metabolomics.ca/MetPA/ | [190] |
MPEA | http://ekhidna.biocenter.helsinki.fi/poxo/mpea/ | [191] |
MSEA | http://www.msea.ca. or http://www.metaboanalyst.ca | [177] |
Pathcase | http://nashua.case.edu/PathwaysMAW/Web/ | [192] |
PathwayExplorer | http://genome.tugraz.at/pathwayexplorer/pathwayexplorer_description.shtml | [193] |
SMPDB | http://www.smpdb.ca | [176] |
VANTED | https://immersive-nalytics.infotech.monash.edu/vanted/ | [194] |
WikiPathways | http://wikipathways.org | [195] |
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Patel, M.K.; Pandey, S.; Kumar, M.; Haque, M.I.; Pal, S.; Yadav, N.S. Plants Metabolome Study: Emerging Tools and Techniques. Plants 2021, 10, 2409. https://doi.org/10.3390/plants10112409
Patel MK, Pandey S, Kumar M, Haque MI, Pal S, Yadav NS. Plants Metabolome Study: Emerging Tools and Techniques. Plants. 2021; 10(11):2409. https://doi.org/10.3390/plants10112409
Chicago/Turabian StylePatel, Manish Kumar, Sonika Pandey, Manoj Kumar, Md Intesaful Haque, Sikander Pal, and Narendra Singh Yadav. 2021. "Plants Metabolome Study: Emerging Tools and Techniques" Plants 10, no. 11: 2409. https://doi.org/10.3390/plants10112409