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Mascellani Bergo A, Leiss K, Havlik J. Twenty Years of 1H NMR Plant Metabolomics: A Way Forward toward Assessment of Plant Metabolites for Constitutive and Inducible Defenses to Biotic Stress. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:8332-8346. [PMID: 38501393 DOI: 10.1021/acs.jafc.3c09362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
Metabolomics has become an important tool in elucidating the complex relationship between a plant genotype and phenotype. For over 20 years, nuclear magnetic resonance (NMR) spectroscopy has been known for its robustness, quantitative capabilities, simplicity, and cost-efficiency. 1H NMR is the method of choice for analyzing a broad range of relatively abundant metabolites, which can be used for both capturing the plant chemical profile at one point in time and understanding the pathways that underpin plant defense. This systematic Review explores how 1H NMR-based plant metabolomics has contributed to understanding the role of various compounds in plant responses to biotic stress, focusing on both primary and secondary metabolites. It clarifies the challenges and advantages of using 1H NMR in plant metabolomics, interprets common trends observed, and suggests guidelines for method development and establishing standard procedures.
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Affiliation(s)
- Anna Mascellani Bergo
- Department of Food Science, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, 16500 Prague, Czechia
| | - Kirsten Leiss
- Business Unit Greenhouse Horticulture, Wageningen University & Research, 2665MV Bleiswijk, Netherlands
| | - Jaroslav Havlik
- Department of Food Science, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, 16500 Prague, Czechia
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Wilson ID, Broeckling C, Gethings LA, Munjoma NC, Trengove R, Rainville PD, Lai SK, Isaac G, Plumb RS. Development of a single mobile phase for LC-IM-MS-based discovery lipidomics and metabolic phenotyping: Application to methapyrilene hepatotoxicity in the rat. J Chromatogr A 2024; 1714:464552. [PMID: 38113579 DOI: 10.1016/j.chroma.2023.464552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 11/18/2023] [Accepted: 11/30/2023] [Indexed: 12/21/2023]
Abstract
The untargeted global profiling of endogenous metabolites and lipids has the potential to increase knowledge and understanding in many areas of biology. LC-MS/MS is a key technology for such analyses however, several different LC methodologies, using different mobile phase compositions, are required to cover the diversity in polarity and analyte structure encountered in biological samples. Most notably many lipid screening methods make use of isopropanol (IPA) as a major component of mobile phases employed for comprehensive lipidomic profiling. In order to increase laboratory efficiency, and minimize opportunities for errors, a suite of methods, based on a single acetonitrile (ACN)-aqueous buffer mobile phase combination, has been developed. This mobile phase can be used for hydrophobic interaction liquid chromatography on an amide stationary phase (for polar analytes), reversed-phase (RP) LC analysis on a C8 stationary phase (for moderately polar-non-polar compounds) and RPLC using a CSH phenyl-hexyl bonded column (for lipids). All of these sub 10 minute separations had good throughput and reproducibility with CV's of analyte response <25 % whilst eliminating the need for complex mobile phase preparation and the use of IPA as an organic modifier for lipidomics. Advantages of removing IPA and replacing it with the ACN-based method were a 58 % increase in peak capacity for lipids, with improved resolution for the di- and triglycerides and cholesterol esters compared to current methods. Compared to the IPA-containing solvent system the ACN-based mobile phase also resulted in a 61 % increase in lipid feature detection. The utility of this "universal" mobile phase approach was demonstrated by its application to a rat toxicology study investigating the consequences of methapyrilene administration through on the endogenous metabolite profiles of plasma and urine. Methapyrilene and its metabolites were also profiled in these samples.
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Affiliation(s)
- Ian D Wilson
- Computational & Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College, Burlington Danes Building, Du Cane Road, London, W12 0NN, UK
| | - Corey Broeckling
- Bioanalysis and Omics, Colorado State University, Fort Collins, CO 8052, USA
| | | | | | - Robert Trengove
- Curtin Health Innovation Research Institute, Curtin University, Kent St, Bentley WA 6102, Australia.
| | | | | | - Giorgis Isaac
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
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Wang Y, Guan X, Liu Z, Li Y, Yu F, Liu K. Photosynthesis-related physiology and metabolomics responses of Polygonum lapathifolium in contrasting manganese environments. FUNCTIONAL PLANT BIOLOGY : FPB 2023; 50:242-255. [PMID: 36536492 DOI: 10.1071/fp22208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 11/16/2022] [Indexed: 06/17/2023]
Abstract
Manganese (Mn) plays an essential role in plant growth; however, excessive Mn is toxic to plants. Polygonum lapathifolium Linn. was tested as a novel Mn-hyperaccumulating species in our previous study, but the underlying mechanisms of this hyperaccumulation are poorly understood. A hydroponic experiment with (8mmolL-1 ) and without additional Mn (CK) was established to explore the possible mechanisms through the effects on photosynthesis-related physiological characteristics and metabolomics. The results showed that additional Mn increased plant biomass, photosynthesis, and stomatal conductance related to increases in the effective photochemical quantum yield of photosystem II and relative electron transport rate (P <0.05). The results from liquid chromatography-mass spectrometry revealed 56 metabolites differentially accumulated between the plants composing these two groups. Metabolites were enriched in 20 metabolic pathways at three levels (environmental information processing, genetic information processing, and metabolism), of which five metabolic pathways were associated with significant or extremely significant changes (P <0.05). These five enriched pathways were ABC transporters (environmental information processing), aminoacyl-tRNA biosynthesis (genetic information processing), biosynthesis of amino acids , d -arginine and d -ornithine metabolism , and arginine biosynthesis (metabolism). Flavonoids may play a key role in Mn tolerance, as they accumulated more than 490-fold, and the relationship between flavonoids and Mn tolerance needs to be studied in the future.
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Affiliation(s)
- Yongsen Wang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Guangxi Normal University, Ministry of Education, 541004 Guilin, China; and Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in the Lijiang River Basin, Guangxi Normal University, 541004 Guilin, China
| | - Xiaojin Guan
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Guangxi Normal University, Ministry of Education, 541004 Guilin, China; and Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in the Lijiang River Basin, Guangxi Normal University, 541004 Guilin, China
| | - Zongbao Liu
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Guangxi Normal University, Ministry of Education, 541004 Guilin, China; and Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in the Lijiang River Basin, Guangxi Normal University, 541004 Guilin, China
| | - Yi Li
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Guangxi Normal University, Ministry of Education, 541004 Guilin, China; and College of Environment and Resource, Guangxi Normal University, Guilin, China
| | - Fangming Yu
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Guangxi Normal University, Ministry of Education, 541004 Guilin, China; and College of Environment and Resource, Guangxi Normal University, Guilin, China
| | - Kehui Liu
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Guangxi Normal University, Ministry of Education, 541004 Guilin, China; and Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in the Lijiang River Basin, Guangxi Normal University, 541004 Guilin, China
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Advances in Plant Metabolomics and Its Applications in Stress and Single-Cell Biology. Int J Mol Sci 2022; 23:ijms23136985. [PMID: 35805979 PMCID: PMC9266571 DOI: 10.3390/ijms23136985] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 06/19/2022] [Accepted: 06/19/2022] [Indexed: 02/04/2023] Open
Abstract
In the past two decades, the post-genomic era envisaged high-throughput technologies, resulting in more species with available genome sequences. In-depth multi-omics approaches have evolved to integrate cellular processes at various levels into a systems biology knowledge base. Metabolomics plays a crucial role in molecular networking to bridge the gaps between genotypes and phenotypes. However, the greater complexity of metabolites with diverse chemical and physical properties has limited the advances in plant metabolomics. For several years, applications of liquid/gas chromatography (LC/GC)-mass spectrometry (MS) and nuclear magnetic resonance (NMR) have been constantly developed. Recently, ion mobility spectrometry (IMS)-MS has shown utility in resolving isomeric and isobaric metabolites. Both MS and NMR combined metabolomics significantly increased the identification and quantification of metabolites in an untargeted and targeted manner. Thus, hyphenated metabolomics tools will narrow the gap between the number of metabolite features and the identified metabolites. Metabolites change in response to environmental conditions, including biotic and abiotic stress factors. The spatial distribution of metabolites across different organs, tissues, cells and cellular compartments is a trending research area in metabolomics. Herein, we review recent technological advancements in metabolomics and their applications in understanding plant stress biology and different levels of spatial organization. In addition, we discuss the opportunities and challenges in multiple stress interactions, multi-omics, and single-cell metabolomics.
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Zhou J, Wang J, Tao Y, Wang Y, Liu L, Wang S, Li Y, Zheng Q, Chen H. Metabolic response of bok choy leaves under chromium pollution stress. ECOTOXICOLOGY (LONDON, ENGLAND) 2021; 30:231-239. [PMID: 33483874 DOI: 10.1007/s10646-020-02344-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 12/30/2020] [Indexed: 06/12/2023]
Abstract
Chromium (Cr) pollution in farmlands is a common environmental issue, that can seriously inhibit plant growth, damage plant cells, and even cause plant death. In this study, bok choy (Brassica campestris L. ssp. chinensis Makino (var. communis Tsen et Lee)) was selected as a model plant to investigate the metabolic response to Cr stress at concentrations of 2.0 mg/L and 8.0 mg/L. Metabolites were identified using gas chromatography-mass spectrometry. Principal component analysis and orthogonal projections to latent structure discriminant analysis revealed the notable effect of Cr stress on the metabolites of bok choy. Under Cr stress, 145 metabolites were identified in the bok choy leaves. At 2.0 mg/L Cr stress, 10 and 26 metabolites changed compared to the control after 7 d and 14 d, respectively. At 8.0 mg/L Cr stress, 24 and 24 metabolites changed significantly after 7 and 14 d, respectively. The data showed that metabolism was affected by the Cr stress concentration and exposure time. Specifically, under the Cr stress, the tricarboxylic acid cycle, glutamine synthetase/glutamate synthase cycle, and partial amino acid metabolic pathways were blocked, inhibiting the normal growth and development of bok choy. The change of citric acid content was the most significant, and the accumulation of citric acid indicated the degree of plant Cr toxicity and resistance. These results would facilitate further dissection of the mechanisms of heavy metal accumulation/tolerance in plants and the effective management of such contamination in vegetable crops by genetic manipulation.
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Affiliation(s)
- Jiangmin Zhou
- College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, China
| | - Jingjing Wang
- College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, China
| | - Yueliang Tao
- College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, China
| | - Yufeng Wang
- Zhejiang Zone-King Environmental Science & Technolgy Co., Ltd, Hangzhou, 310014, China
| | - Lei Liu
- Zhejiang Zone-King Environmental Science & Technolgy Co., Ltd, Hangzhou, 310014, China
| | - Shuijuan Wang
- College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, China
| | - Yuechang Li
- College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, China
| | - Qiansong Zheng
- Zhejiang Zone-King Environmental Science & Technolgy Co., Ltd, Hangzhou, 310014, China
| | - Hualin Chen
- College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, China.
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Sulaiman F, Ahmad Azam A, Ahamad Bustamam MS, Fakurazi S, Abas F, Lee YX, Ismail AA, Mohd Faudzi SM, Ismail IS. Metabolite Profiles of Red and Yellow Watermelon ( Citrullus lanatus) Cultivars Using a 1H-NMR Metabolomics Approach. Molecules 2020; 25:E3235. [PMID: 32679913 PMCID: PMC7397335 DOI: 10.3390/molecules25143235] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 05/31/2020] [Accepted: 06/05/2020] [Indexed: 12/12/2022] Open
Abstract
Watermelon, a widely commercialized fruit, is famous for its thirst-quenching property. The broad range of cultivars, which give rise to distinct color and taste, can be attributed to the differences in their chemical profile, especially that of the carotenoids and volatile compounds. In order to understand this distribution properly, water extracts of red and yellow watermelon pulps with predominantly polar metabolites were subjected to proton nuclear magnetic resonance (1H-NMR) analysis. Deuterium oxide (D2O) and deuterated chloroform (CDCl3) solvents were used to capture both polar and non-polar metabolites from the same sample. Thirty-six metabolites, of which six are carotenoids, were identified from the extracts. The clustering of the compounds was determined using unsupervised principal component analysis (PCA) and further grouping was achieved using supervised orthogonal partial least squares discriminant analysis (OPLS-DA). The presence of lycopene, β-carotene, lutein, and prolycopene in the red watermelon plays an important role in its differentiation from the yellow cultivar. A marked difference in metabolite distribution was observed between the NMR solvents used as evidenced from the PCA model. OPLS-DA and relative quantification of the metabolites, on the other hand, helped in uncovering the discriminating metabolites of the red and yellow watermelon cultivars from the same solvent system.
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Affiliation(s)
- Fadzil Sulaiman
- Laboratory of Natural Products, Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Malaysia; (F.S.); (A.A.A.); (M.S.A.B.); (F.A.); (Y.X.L.); (A.A.I.); (S.M.M.F.)
| | - Amalina Ahmad Azam
- Laboratory of Natural Products, Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Malaysia; (F.S.); (A.A.A.); (M.S.A.B.); (F.A.); (Y.X.L.); (A.A.I.); (S.M.M.F.)
| | - Muhammad Safwan Ahamad Bustamam
- Laboratory of Natural Products, Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Malaysia; (F.S.); (A.A.A.); (M.S.A.B.); (F.A.); (Y.X.L.); (A.A.I.); (S.M.M.F.)
| | - Sharida Fakurazi
- Laboratory of Vaccines and Immunotherapeutics, Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Malaysia;
| | - Faridah Abas
- Laboratory of Natural Products, Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Malaysia; (F.S.); (A.A.A.); (M.S.A.B.); (F.A.); (Y.X.L.); (A.A.I.); (S.M.M.F.)
| | - Yee Xuan Lee
- Laboratory of Natural Products, Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Malaysia; (F.S.); (A.A.A.); (M.S.A.B.); (F.A.); (Y.X.L.); (A.A.I.); (S.M.M.F.)
| | - Atira Adriana Ismail
- Laboratory of Natural Products, Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Malaysia; (F.S.); (A.A.A.); (M.S.A.B.); (F.A.); (Y.X.L.); (A.A.I.); (S.M.M.F.)
| | - Siti Munirah Mohd Faudzi
- Laboratory of Natural Products, Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Malaysia; (F.S.); (A.A.A.); (M.S.A.B.); (F.A.); (Y.X.L.); (A.A.I.); (S.M.M.F.)
| | - Intan Safinar Ismail
- Laboratory of Natural Products, Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Malaysia; (F.S.); (A.A.A.); (M.S.A.B.); (F.A.); (Y.X.L.); (A.A.I.); (S.M.M.F.)
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Cosio C, Renault D. Effects of cadmium, inorganic mercury and methyl-mercury on the physiology and metabolomic profiles of shoots of the macrophyte Elodea nuttallii. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 257:113557. [PMID: 31733966 DOI: 10.1016/j.envpol.2019.113557] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 10/31/2019] [Accepted: 10/31/2019] [Indexed: 05/28/2023]
Abstract
Macrophytes are known to bioaccumulate metals, but a thorough understanding of tolerance strategies and molecular impact of metals in aquatic plants is still lacking. The present study aimed to compare Hg and Cd effects in a representative macrophyte, Elodea nuttallii using physiological endpoints and metabolite profiles in shoots and cytosol. Exposure 24 h to methyl-Hg (30 ng L-1), inorganic Hg (70 ng L-1) and Cd (280 μg L-1) did not affect photosynthesis, or antioxidant enzymes despite the significant accumulation of metals, confirming a sublethal stress level. In shoots, Cd resulted in a higher level of regulation of metabolites than MeHg, while MeHg resulted in the largest number of regulated metabolites and IHg treatment regulated no metabolites significantly. In cytosol, Cd regulated more metabolites than IHg and only arginine, histidine and mannose were reduced by MeHg exposure. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of data suggested that exposure to MeHg resulted in biochemical changes including aminoacyl-tRNA biosynthesis, glycine, serine and threonine metabolism, nitrogen metabolism, arginine and proline metabolism, cyanoamino acid metabolism, while the treatment of Cd stress caused significant variations in aminoacyl-tRNA biosynthesis and branched-chain amino acids pathways. Data supports an impact of MeHg on N homeostasis, while Cd resulted in an osmotic stress-like pattern and IHg had a low impact. Marked differences in the responses to MeHg and IHg exposure were evidenced, supporting different molecular toxicity pathways and main impact of MeHg on non-soluble compartment, while main impact of IHg was on soluble compartment. Metabolomics was used for the first time in this species and proved to be very useful to confirm and complement recent knowledge gained by transcriptomics and proteomics, highlighting the high interest of multi-omics approaches to identify early impact of environmental pollution.
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Affiliation(s)
- Claudia Cosio
- Université de Reims Champagne-Ardenne, UMR-I 02 INERIS-URCA-ULH SEBIO, F-51687 Reims, France.
| | - David Renault
- Université de Rennes 1, UMR 6553 EcoBio CNRS, F-35042 Rennes, France; Institut Universitaire de France, 1 rue Descartes, 75231 Paris CEDEX 05, France
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Kharbach M, Marmouzi I, El Jemli M, Bouklouze A, Vander Heyden Y. Recent advances in untargeted and targeted approaches applied in herbal-extracts and essential-oils fingerprinting - A review. J Pharm Biomed Anal 2020; 177:112849. [DOI: 10.1016/j.jpba.2019.112849] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Revised: 08/27/2019] [Accepted: 08/29/2019] [Indexed: 12/12/2022]
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Chen Y, Lin D, Chen Z, Feng J, Liao N. Revealing Different Lung Metastatic Potentials Induced Metabolic Alterations of Hepatocellular Carcinoma Cells via Proton Nuclear Magnetic Resonance Spectroscopy. J Cancer 2018; 9:4696-4705. [PMID: 30588254 PMCID: PMC6299397 DOI: 10.7150/jca.27329] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 09/09/2018] [Indexed: 11/05/2022] Open
Abstract
Background: Hepatocellular carcinoma (HCC) causes death mainly by disseminated metastasis progression and major challenge of clinical management is to distinguish lethal metastatic stage from indolent stage. It is shown that metastatic progression is closely related to cellular metabolism. But detailed metabolic alterations and molecular mechanisms still kept unclear between subtypes of different lung metastatic potentials. Methods: The current work used NMR-based metabolomics in the study of HCC cells with high malignancy but differed in lung metastatic potentials. Cell extracts and cultured media from MHCC97L and MHCC97H were utilized to reveal metabolic alterations related to metastatic potentials. Multivariate analyses were performed to identify characteristic metabolites which were used subsequently to draw the map of relative biochemical pathways by combining KEGG database. Results: The NMR spectra of both MHCC97L and MHCC97H include various signals from necessary nutritional components and metabolic intermediates. A series of characteristic metabolites were determined from both cell extracts and media. The ability on nutrient uptake varied from cell lines. Most of amino acids decreased in high metastatic cell line, so altered amino acid metabolisms and energy metabolism were revealed in high metastatic MHCC97H cell line. The majority pathways involved six essential amino acids in which the observed branched-chain amino acids together with lysine contributed to biosynthesis or degradation. Basically MHCC97H cell line could induce more active events than that of MHCC97L to progress to high metastasis with certain molecular events. Characteristic metabolites-derived classifiers performed robustly during prediction and confirmed their critical role in supporting metastasis progression. Conclusions: Our results provide evidence that NMR-metabolomics analyses of cells are able to understand metastatic characteristics accountable for biological properties. The proposed characteristic metabolites will help to understand HCC metastatic characterizations and may be filtered as potential biomarkers.
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Affiliation(s)
- Yang Chen
- Department of Laboratory Medicine, Fujian Medical University, Fuzhou, China.,Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Xiamen University, Xiamen, China
| | - Donghong Lin
- Department of Laboratory Medicine, Fujian Medical University, Fuzhou, China
| | - Zhong Chen
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Xiamen University, Xiamen, China
| | - Jianghua Feng
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Xiamen University, Xiamen, China
| | - Naishun Liao
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, China
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Effects of glaucocalyxin A on human liver cancer cells as revealed by GC/MS- and LC/MS-based metabolic profiling. Anal Bioanal Chem 2018; 410:3325-3335. [DOI: 10.1007/s00216-018-0996-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 02/17/2018] [Accepted: 03/05/2018] [Indexed: 11/26/2022]
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Guo R, Shi L, Jiao Y, Li M, Zhong X, Gu F, Liu Q, Xia X, Li H. Metabolic responses to drought stress in the tissues of drought-tolerant and drought-sensitive wheat genotype seedlings. AOB PLANTS 2018; 10:ply016. [PMID: 29623182 PMCID: PMC5881611 DOI: 10.1093/aobpla/ply016] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
An in-depth understanding of the effects of drought stress on plant metabolism is necessary to improve the drought tolerance of wheat and to utilize genetic resources for the development of drought stress-tolerant wheat varieties. In this study, the profiles of 58 key metabolites produced by wheat seedlings in response to drought stress were investigated to determine various physiological processes related to drought tolerance between drought-tolerant and drought-sensitive wheat genotypes. Results showed that the wheat metabolome was dominated by sugars, organic acids and amino acids; the wheat metabolome played important roles to enhance the drought tolerance of shoots. Under drought stress, JD17 exhibited higher growth indices and higher photosynthesis ability than JD8. A high level of compatible solutes and energy in shoots were essential for wheat to develop drought tolerance. Drought also caused system alterations in widespread metabolic networks involving transamination, tricarboxylic acid cycle, glycolysis, glutamate-mediated proline biosynthesis, shikimate-mediated secondary metabolisms and γ-aminobutyric acid metabolisms. Long-term drought stress resulted in the drought-tolerant wheat genotype JD17, which induced metabolic shifts in the tricarboxylic acid cycle and glycolysis with the depletion of the γ-aminobutyric acid shut process. In JD17, the prolonged drought stress induced a progressive accumulation of osmolytes, including proline, sucrose, fructose, mannose and malic acid. This research extended our understanding of the mechanisms involved in wheat seedling drought tolerance; this study also demonstrated that gas chromatography-mass spectrometry metabolomics could be an effective approach to understand the drought effects on plant biochemistry.
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Affiliation(s)
- Rui Guo
- Institute of Environment and Sustainable Development in Agriculture (IEDA), Chinese Academy of Agricultural Sciences (CAAS)/Key Laboratory of Dryland Agriculture, Ministry of Agriculture, Beijing, P.R. China
- Corresponding author’s e-mail address: ;
| | - LianXuan Shi
- School of Life Sciences, Northeast Normal University, Changchun, China
- Corresponding author’s e-mail address: ;
| | - Yang Jiao
- School of Life Sciences, Northeast Normal University, Changchun, China
| | - MingXia Li
- School of Life Sciences, Northeast Normal University, Changchun, China
| | - XiuLi Zhong
- Institute of Environment and Sustainable Development in Agriculture (IEDA), Chinese Academy of Agricultural Sciences (CAAS)/Key Laboratory of Dryland Agriculture, Ministry of Agriculture, Beijing, P.R. China
| | - FengXue Gu
- Institute of Environment and Sustainable Development in Agriculture (IEDA), Chinese Academy of Agricultural Sciences (CAAS)/Key Laboratory of Dryland Agriculture, Ministry of Agriculture, Beijing, P.R. China
| | - Qi Liu
- Institute of Environment and Sustainable Development in Agriculture (IEDA), Chinese Academy of Agricultural Sciences (CAAS)/Key Laboratory of Dryland Agriculture, Ministry of Agriculture, Beijing, P.R. China
| | - Xu Xia
- Institute of Environment and Sustainable Development in Agriculture (IEDA), Chinese Academy of Agricultural Sciences (CAAS)/Key Laboratory of Dryland Agriculture, Ministry of Agriculture, Beijing, P.R. China
| | - HaoRu Li
- Institute of Environment and Sustainable Development in Agriculture (IEDA), Chinese Academy of Agricultural Sciences (CAAS)/Key Laboratory of Dryland Agriculture, Ministry of Agriculture, Beijing, P.R. China
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Chen Y, Chen Z, Feng JH, Chen YB, Liao NS, Su Y, Zou CY. Metabolic profiling of normal hepatocyte and hepatocellular carcinoma cells via 1
H nuclear magnetic resonance spectroscopy. Cell Biol Int 2017; 42:425-434. [PMID: 29144590 DOI: 10.1002/cbin.10911] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 11/12/2017] [Indexed: 12/12/2022]
Affiliation(s)
- Yang Chen
- Department of Electronic Science; Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Xiamen University; Xiamen 361005 China
- Department of Laboratory Medicine; Fujian Medical University; Fuzhou 350004 China
| | - Zhong Chen
- Department of Electronic Science; Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Xiamen University; Xiamen 361005 China
| | - Jiang-Hua Feng
- Department of Electronic Science; Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Xiamen University; Xiamen 361005 China
| | - Yun-Bin Chen
- Department of Radiology; Fujian Provincial Cancer Hospital; Fuzhou 350014 China
| | - Nai-Shun Liao
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province; Mengchao Hepatobiliary Hospital of Fujian Medical University; Fuzhou 350025 China
| | - Ying Su
- Department of Radiology; Fujian Provincial Cancer Hospital; Fuzhou 350014 China
| | - Chang-Yan Zou
- Department of Radiology; Fujian Provincial Cancer Hospital; Fuzhou 350014 China
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Sexual Dimorphism in the Response of Mercurialis annua to Stress. Metabolites 2016; 6:metabo6020013. [PMID: 27128954 PMCID: PMC4931544 DOI: 10.3390/metabo6020013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 04/18/2016] [Accepted: 04/21/2016] [Indexed: 11/17/2022] Open
Abstract
The research presented stemmed from the observations that female plants of the annual dioecious Mercurialis annua outlive male plants. This led to the hypothesis that female plants of M. annua would be more tolerant to stress than male plants. This hypothesis was addressed in a comprehensive way, by comparing morphological, biochemical and metabolomics changes in female and male plants during their development and under salinity. There were practically no differences between the genders in vegetative development and physiological parameters. However, under salinity conditions, female plants produced significantly more new reproductive nodes. Gender-linked differences in peroxidase (POD) and glutathione transferases (GSTs) were involved in anti-oxidation, detoxification and developmental processes in M. annua. 1H NMR metabolite profiling of female and male M. annua plants showed that under salinity the activity of the TCA cycle increased. There was also an increase in betaine in both genders, which may be explainable by its osmo-compatible function under salinity. The concentration of ten metabolites changed in both genders, while ‘Female-only-response’ to salinity was detected for five metabolites. In conclusion, dimorphic responses of M. annua plant genders to stress may be attributed to female plants’ capacity to survive and complete the reproductive life cycle.
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Liu X, Lai Y, Sun H, Wang Y, Zou N. The interactive effects of mercury and selenium on metabolic profiles, gene expression and antioxidant enzymes in halophyte Suaeda salsa. ENVIRONMENTAL TOXICOLOGY 2016; 31:440-451. [PMID: 25346288 DOI: 10.1002/tox.22057] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Revised: 09/25/2014] [Accepted: 10/01/2014] [Indexed: 06/04/2023]
Abstract
Suaeda salsa is the pioneer halophyte in the Yellow River Delta and was consumed as a popular vegetable. Mercury has become a highly risky contaminant in the sediment of intertidal zones of the Yellow River Delta. In this work, we investigated the interactive effects of mercury and selenium in S. salsa on the basis of metabolic profiling, antioxidant enzyme activities and gene expression quantification. Our results showed that mercury exposure (20 μg L(-1)) inhibited plant growth of S. salsa and induced significant metabolic responses and altered expression levels of INPS, CMO, and MDH in S. salsa samples, together with the increased activities of antioxidant enzymes including SOD and POD. Overall, these results indicated osmotic and oxidative stresses, disturbed protein degradation and energy metabolism change in S. salsa after mercury exposures. Additionally, the addition of selenium could induce both antagonistic and synergistic effects including alleviating protein degradation and aggravating osmotic stress caused by mercury.
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Affiliation(s)
- Xiaoli Liu
- School of Life Sciences, Ludong University, Yantai 264025, People's Republic of China
| | - Yongkai Lai
- School of Life Sciences, Ludong University, Yantai 264025, People's Republic of China
| | - Hushan Sun
- School of Life Sciences, Ludong University, Yantai 264025, People's Republic of China
| | - Yiyan Wang
- School of Life Sciences, Ludong University, Yantai 264025, People's Republic of China
| | - Ning Zou
- School of Life Sciences, Ludong University, Yantai 264025, People's Republic of China
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Pidatala VR, Li K, Sarkar D, Ramakrishna W, Datta R. Identification of Biochemical Pathways Associated with Lead Tolerance and Detoxification in Chrysopogon zizanioides L. Nash (Vetiver) by Metabolic Profiling. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:2530-7. [PMID: 26843403 DOI: 10.1021/acs.est.5b04725] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Lead (Pb) is a major urban pollutant, due to deteriorating lead-based paint in houses built before 1978. Phytoremediation is an inexpensive and effective technique for remediation of Pb-contaminated homes. Vetiver (Chrysopogon zizanioides), a noninvasive, fast-growing grass with high biomass, can tolerate and accumulate large quantities of Pb in its tissues. Lead is known to induce phytochelatins and antioxidative enzymes in vetiver; however, the overall impact of Pb stress on metabolic pathways of vetiver is unknown. In the current study, vetiver plants were treated with different concentrations of Pb in a hydroponic setup. Metabolites were extracted and analyzed using LC/MS/MS. Multivariate analysis of metabolites in both root and shoot tissue showed tremendous induction in key metabolic pathways including sugar metabolism, amino acid metabolism, and an increase in production of osmoprotectants, such as betaine and polyols, and metal-chelating organic acids. The data obtained provide a comprehensive insight into the overall stress response mechanisms in vetiver.
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Affiliation(s)
- Venkataramana R Pidatala
- Department of Biological Sciences, Michigan Technological University , 1400 Townsend Drive, Houghton, Michigan 49931, United States
| | - Kefeng Li
- School of Medicine, University of California, San Diego , San Diego, California 92103, United States
| | - Dibyendu Sarkar
- Department of Civil, Environmental and Ocean Engineering, Stevens Institute of Technology , Hoboken, New Jersey 07030, United States
| | - Wusirika Ramakrishna
- Department of Biological Sciences, Michigan Technological University , 1400 Townsend Drive, Houghton, Michigan 49931, United States
| | - Rupali Datta
- Department of Biological Sciences, Michigan Technological University , 1400 Townsend Drive, Houghton, Michigan 49931, United States
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Wang Y, Xu L, Shen H, Wang J, Liu W, Zhu X, Wang R, Sun X, Liu L. Metabolomic analysis with GC-MS to reveal potential metabolites and biological pathways involved in Pb &Cd stress response of radish roots. Sci Rep 2015; 5:18296. [PMID: 26673153 PMCID: PMC4682141 DOI: 10.1038/srep18296] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 11/16/2015] [Indexed: 12/24/2022] Open
Abstract
The radish (Raphanus sativus L.) is an important root vegetable crop. In this study, the metabolite profiling analysis of radish roots exposed to lead (Pb) and cadmium (Cd) stresses has been performed using gas chromatography-mass spectrometry (GC-MS). The score plots of principal component analysis (PCA) and partial least squares-discriminate analysis (PLS-DA) showed clear discrimination between control and Pb- or Cd-treated samples. The metabolic profiling indicated Pb or Cd stress could cause large metabolite alteration mainly on sugars, amino acids and organic acids. Furthermore, an integrated analysis of the effects of Pb or Cd stress was performed on the levels of metabolites and gene transcripts from our previous transcriptome work in radish roots. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of integration data demonstrated that exposure of radish to Pb stress resulted in profound biochemical changes including carbohydrate metabolism, energy metabolism and glutathione metabolism, while the treatment of Cd stress caused significant variations in energy production, amino acid metabolism and oxidative phosphorylation-related pathways. These results would facilitate further dissection of the mechanisms of heavy metal (HM) accumulation/tolerance in plants and the effective management of HM contamination in vegetable crops by genetic manipulation.
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Affiliation(s)
- Yan Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement; Engineering Research Center of Horticultural Crop Germplasm Enhancement and Utilization, Ministry of Education of P.R. China; College of Horticulture, Nanjing Agricultural University, Nanjing 210095, P.R. China
| | - Liang Xu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement; Engineering Research Center of Horticultural Crop Germplasm Enhancement and Utilization, Ministry of Education of P.R. China; College of Horticulture, Nanjing Agricultural University, Nanjing 210095, P.R. China
| | - Hong Shen
- National Key Laboratory of Crop Genetics and Germplasm Enhancement; Engineering Research Center of Horticultural Crop Germplasm Enhancement and Utilization, Ministry of Education of P.R. China; College of Horticulture, Nanjing Agricultural University, Nanjing 210095, P.R. China
| | - Juanjuan Wang
- The National Agro-Tech Extension and Service Center, Beijing 100125, P.R. China
| | - Wei Liu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement; Engineering Research Center of Horticultural Crop Germplasm Enhancement and Utilization, Ministry of Education of P.R. China; College of Horticulture, Nanjing Agricultural University, Nanjing 210095, P.R. China
| | - Xianwen Zhu
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58108, USA
| | - Ronghua Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement; Engineering Research Center of Horticultural Crop Germplasm Enhancement and Utilization, Ministry of Education of P.R. China; College of Horticulture, Nanjing Agricultural University, Nanjing 210095, P.R. China
| | - Xiaochuan Sun
- National Key Laboratory of Crop Genetics and Germplasm Enhancement; Engineering Research Center of Horticultural Crop Germplasm Enhancement and Utilization, Ministry of Education of P.R. China; College of Horticulture, Nanjing Agricultural University, Nanjing 210095, P.R. China
| | - Liwang Liu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement; Engineering Research Center of Horticultural Crop Germplasm Enhancement and Utilization, Ministry of Education of P.R. China; College of Horticulture, Nanjing Agricultural University, Nanjing 210095, P.R. China
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Jung Y, Ha M, Lee J, Ahn YG, Kwak JH, Ryu DH, Hwang GS. Metabolite Profiling of the Response of Burdock Roots to Copper Stress. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2015; 63:1309-1317. [PMID: 25578619 DOI: 10.1021/jf503193c] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Arctium lappa L. (Asteraceae), also known as burdock, has a long history of cultivation as a dietary vegetable worldwide. Stress in plants disrupts metabolic homeostasis and requires adjustment of metabolic pathways. Exposure to heavy metals is one of the most prevalent environmental stresses encountered by plants. In this study, metabolite profiling based on 1H NMR and GC-MS was used to obtain a holistic view of the response of burdock roots to copper stress. The principal component analysis model generated from the NMR data showed significant separation between groups. Copper-treated burdock roots were characterized by increased levels of phenols and decreased levels of primary metabolites. These results suggest that copper stress leads to activation of the phenylpropanoid pathway and growth inhibition. GC-MS analyses revealed increased levels of unsaturated fatty acids and decreased levels of sterols in the copper-treated group. Changes in metabolite concentrations were analyzed by UPLC/QTRAP-MS, and the significances were confirmed by two-way analysis of variance and Bonferroni's test. Interestingly, linoleic acid was increased about 2.7-fold, from 316 ± 64.5 to 855 ± 111 ppm, in the group treated with copper for 6 days. This study demonstrates that metabolomic profiling is an effective analytical approach to understanding the metabolic pathway(s) associated with copper stress in burdock roots.
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Affiliation(s)
- Youngae Jung
- Integrated Metabolomics Research Group, Western Seoul Center, Korea Basic Science Institute , Seoul 120-140, Republic of Korea
| | - Miyoung Ha
- Integrated Metabolomics Research Group, Western Seoul Center, Korea Basic Science Institute , Seoul 120-140, Republic of Korea
- Nonghyup Food Safety Research Institute , Seoul 137-130, Republic of Korea
| | - Jueun Lee
- Integrated Metabolomics Research Group, Western Seoul Center, Korea Basic Science Institute , Seoul 120-140, Republic of Korea
| | - Yun Gyong Ahn
- Integrated Metabolomics Research Group, Western Seoul Center, Korea Basic Science Institute , Seoul 120-140, Republic of Korea
| | | | | | - Geum-Sook Hwang
- Integrated Metabolomics Research Group, Western Seoul Center, Korea Basic Science Institute , Seoul 120-140, Republic of Korea
- Graduate School of Analytical Science and Technology, Chungnam National University , Daejeon 305-764, Republic of Korea
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Xie Y, Hu L, Du Z, Sun X, Amombo E, Fan J, Fu J. Effects of cadmium exposure on growth and metabolic profile of bermudagrass [Cynodon dactylon (L.) Pers]. PLoS One 2014; 9:e115279. [PMID: 25545719 PMCID: PMC4278907 DOI: 10.1371/journal.pone.0115279] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Accepted: 11/23/2014] [Indexed: 11/21/2022] Open
Abstract
Metabolic responses to cadmium (Cd) may be associated with variations in Cd tolerance in plants. The objectives of this study were to examine changes in metabolic profiles in bermudagrass in response to Cd stress and to identify predominant metabolites associated with differential Cd tolerance using gas chromatography-mass spectrometry. Two genotypes of bermudagrass with contrasting Cd tolerance were exposed to 0 and 1.5 mM CdSO4 for 14 days in hydroponics. Physiological responses to Cd were evaluated by determining turf quality, growth rate, chlorophyll content and normalized relative transpiration. All these parameters exhibited higher tolerance in WB242 than in WB144. Cd treated WB144 transported more Cd to the shoot than in WB242. The metabolite analysis of leaf polar extracts revealed 39 Cd responsive metabolites in both genotypes, mainly consisting of amino acids, organic acids, sugars, fatty acids and others. A difference in the metabolic profiles was observed between the two bermudagrass genotypes exposed to Cd stress. Seven amino acids (norvaline, glycine, proline, serine, threonine, glutamic acid and gulonic acid), four organic acids (glyceric acid, oxoglutaric acid, citric acid and malic acid,) and three sugars (xylulose, galactose and talose) accumulated more in WB242 than WB144. However, compared to the control, WB144 accumulated higher quantities of sugars than WB242 in the Cd regime. The differential accumulation of these metabolites could be associated with the differential Cd tolerance in bermudagrass.
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Affiliation(s)
- Yan Xie
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan City, Hubei, People's Republic of China
- Graduate University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Longxing Hu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan City, Hubei, People's Republic of China
| | - Zhimin Du
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan City, Hubei, People's Republic of China
- Graduate University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Xiaoyan Sun
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan City, Hubei, People's Republic of China
- Graduate University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Erick Amombo
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan City, Hubei, People's Republic of China
| | - Jibiao Fan
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan City, Hubei, People's Republic of China
- Graduate University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Jinmin Fu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan City, Hubei, People's Republic of China
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19
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Go YM, Roede JR, Orr M, Liang Y, Jones DP. Integrated redox proteomics and metabolomics of mitochondria to identify mechanisms of cd toxicity. Toxicol Sci 2014; 139:59-73. [PMID: 24496640 DOI: 10.1093/toxsci/kfu018] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Cadmium (Cd) exposure contributes to human diseases affecting liver, kidney, lung, and other organ systems, but mechanisms underlying the pleotropic nature of these toxicities are poorly understood. Cd accumulates in humans from dietary, environmental (including cigarette smoke), and occupational sources, and has a twenty-year biologic half-life. Our previous mouse and cell studies showed that environmental low-dose Cd exposure altered protein redox states resulting in stimulation of inflammatory signaling and disruption of the actin cytoskeleton system, suggesting that Cd could impact multiple mechanisms of disease. In the current study, we investigated the effects of acute Cd exposure on the redox proteome and metabolome of mouse liver mitochondria to gain insight into associated toxicological mechanisms and functions. We analyzed redox states of liver mitochondrial proteins by redox proteomics using isotope coded affinity tag (ICAT) combined mass spectrometry. Redox ICAT identified 2687 cysteine-containing peptides (peptidyl Cys) of which 1667 peptidyl Cys (657 proteins) were detected in both control and Cd-exposed samples. Of these, 46% (1247 peptidyl Cys, 547 proteins) were oxidized by Cd more than 1.5-fold relative to controls. Bioinformatics analysis using MetaCore software showed that Cd affected 86 pathways, including 24 Cys in proteins functioning in branched chain amino acid (BCAA) and 14 Cys in proteins functioning in fatty acid (acylcarnitine/carnitine) metabolism. Consistently, high-resolution metabolomics data showed that Cd treatment altered levels of BCAA and carnitine metabolites. Together, these results show that mitochondrial protein redox and metabolites are targets in Cd-induced hepatotoxicity. The results further indicate that redox proteomics and metabolomics can be used in an integrated systems approach to investigate complex disease mechanisms.
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Affiliation(s)
- Young-Mi Go
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Emory University, Atlanta, Georgia 30322
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20
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Wu H, Liu X, Zhao J, Yu J, Pang Q, Feng J. Toxicological effects of environmentally relevant lead and zinc in halophyte Suaeda salsa by NMR-based metabolomics. ECOTOXICOLOGY (LONDON, ENGLAND) 2012; 21:2363-2371. [PMID: 22926641 DOI: 10.1007/s10646-012-0992-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 08/18/2012] [Indexed: 06/01/2023]
Abstract
Lead (Pb) and zinc (Zn) are two typical metal contaminants with high levels in both seawater and sediment in the intertidal zones of the Bohai Sea. Suaeda salsa is the pioneer halophyte plant in the intertidal zones of the Bohai Sea. In the present work, the short (1 week) and long term (1 month) toxicological effects of environmentally relevant concentrations of Pb and Zn were characterized in S. salsa using NMR-based metabolomics combined with antioxidant enzyme activities. After metal exposure for 1 week, no significant metabolic responses were detected in root tissues of S. salsa. The significant metabolic responses included the increase of isocaproate, glucose and fructose, and decrease of malate, citrate and sucrose in root tissues of S. salsa exposed to Pb for 1 month. The increased phosphocholine and betaine, and decreased choline were uniquely found in Zn-exposed samples. The metabolic changes including decreased malate, citrate and sucrose were detected in both Pb and Zn-exposed groups. These metabolic biomarkers revealed that both Pb and Zn exposures could induce osmotic stress and disturbances in energy metabolism in S. salsa after exposures for 1 month. Overall, this work demonstrates that metabolomics can be used to elucidate toxicological effects of environmentally relevant metal contaminants using halophyte S. salsa as the bioindicator.
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Affiliation(s)
- Huifeng Wu
- Key Laboratory of Coastal Zone Environmental Processes, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS), Yantai, 264003, Shandong, People's Republic of China.
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21
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Petersen IL, Tomasi G, Sørensen H, Boll ES, Hansen HCB, Christensen JH. The use of environmental metabolomics to determine glyphosate level of exposure in rapeseed (Brassica napus L.) seedlings. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2011; 159:3071-7. [PMID: 21555174 DOI: 10.1016/j.envpol.2011.04.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2010] [Revised: 03/29/2011] [Accepted: 04/07/2011] [Indexed: 05/30/2023]
Abstract
Metabolic profiling in plants can be used to differentiate between treatments and to search for biomarkers for exposure. A methodology for processing Ultra-High-Performance Liquid Chromatography-Diode-Array-Detection data is devised. This methodology includes a scheme for selecting informative wavelengths, baseline removal, retention time alignment, selection of relevant retention times, and principal component analysis (PCA). Plant crude extracts from rapeseed seedling exposed to sublethal concentrations of glyphosate are used as a study case. Through this approach, plants exposed to concentrations down to 5 μM could be distinguished from the controls. The compounds responsible for this differentiation were partially identified and were different from those specific for high exposure samples, which suggests that two different responses to glyphosate are elicited in rapeseed depending on the level of exposure. The PCA loadings indicate that a combination of other metabolites could be more sensitive than the response of shikimate to detect glyphosate exposure.
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Affiliation(s)
- Iben Lykke Petersen
- Department of Basic Sciences and Environment, Faculty of Life Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
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Michl J, Modarai M, Edwards S, Heinrich M. Metabolomic analysis of Ranunculus spp. as potential agents involved in the etiology of equine grass sickness. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2011; 59:10388-10393. [PMID: 21842884 DOI: 10.1021/jf201430k] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Identification of toxic or harmful agents continues to be a key goal in agricultural chemistry. This paper reports a metabolomic analysis of Ranunculus repens and related species, which were recently postulated to be cocausative agents in the etiology of equine grass sickness (EGS). Specifically, samples collected at EGS sites were compared with those from non-EGS sites. Furthermore, interspecific and seasonal variations and the species' response to edaphic and climatic factors were investigated. (1)H NMR spectroscopy in combination with multivariate data analysis was applied to the crude methanol extracts of the Ranunculus samples, as well as their chloroform fractions. Samples from EGS sites were significantly different from control samples. The metabolite composition varied greatly between different Ranunculus species. No significant changes could be observed between samples collected in different seasons. This work provides strong evidence that Ranunculus is involved in the etiology of EGS and has implications for agricultural management of pastures.
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Affiliation(s)
- Johanna Michl
- Centre for Pharmacognosy and Phytotherapy, The School of Pharmacy, University of London, 29-39 Brunswick Square, London WC1N 1AX, United Kingdom
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Booth SC, Workentine ML, Weljie AM, Turner RJ. Metabolomics and its application to studying metal toxicity. Metallomics 2011; 3:1142-52. [PMID: 21922109 DOI: 10.1039/c1mt00070e] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Here we explain the omics approach of metabolomics and how it can be applied to study a physiological response to toxic metal exposure. This review aims to educate the metallomics field to the tool of metabolomics. Metabolomics is becoming an increasingly used tool to compare natural and challenged states of various organisms, from disease states in humans to toxin exposure to environmental systems. This approach is key to understanding and identifying the cellular or biochemical targets of metals and the underlying physiological response. Metabolomics steps are described and overviews of its application to metal toxicity to organisms are given. As this approach is very new there are yet only a small number of total studies and therefore only a brief overview of some metal metabolomics studies is described. A frank critical evaluation of the approach is given to provide newcomers to the method a clear idea of the challenges and the rewards of applying metabolomics to their research.
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Affiliation(s)
- Sean C Booth
- Department of Biological Sciences, Faculty of Science, University of Calgary, Calgary, Alberta, Canada
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Liu X, Yang C, Zhang L, Li L, Liu S, Yu J, You L, Zhou D, Xia C, Zhao J, Wu H. Metabolic profiling of cadmium-induced effects in one pioneer intertidal halophyte Suaeda salsa by NMR-based metabolomics. ECOTOXICOLOGY (LONDON, ENGLAND) 2011; 20:1422-1431. [PMID: 21573875 DOI: 10.1007/s10646-011-0699-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 05/02/2011] [Indexed: 05/30/2023]
Abstract
Cadmium is a non-essential element to living organisms and has become the severe contaminant in both seawater and sediment in the intertidal zones of the Bohai Sea. The halophyte, Suaeda salsa is the pioneer plant in the intertidal zones of Bohai Sea and has been widely applied in environmental sciences. In this study, the dose- and time-dependent effects induced by environmentally relevant concentrations (2, 10 and 50 μg l(-1)) of cadmium were characterized in S. salsa using NMR-based metabolomics. The levels of amino acids (valine, leucine, glutamate, tyrosine, etc.), carbohydrates (glucose, sucrose and fructose), intermediates of tricarboxylic acid cycle (succinate, citrate, etc.) and osmolyte (betaine) were altered in the S. salsa samples after cadmium exposures. These metabolic biomarkers indicated the elevated protein degradation and disturbances in the osmotic regulation and energy metabolism caused by cadmium in S. salsa. Overall, our results demonstrated the applicability of NMR-based metabolomics for the detection of metabolic biomarkers that could be used for the interpretation of toxicological effects induced by contaminants in the pioneer plant S. salsa in the intertidal zones. In addition, the metabolic biomarkers could be potentially useful for the bio-monitoring of contaminants in the intertidal zones.
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Affiliation(s)
- Xiaoli Liu
- Key Laboratory of Coastal Zone Environment Processes, Chinese Academy of Sciences, Yantai, People's Republic of China
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26
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Leiss KA, Choi YH, Verpoorte R, Klinkhamer PGL. An overview of NMR-based metabolomics to identify secondary plant compounds involved in host plant resistance. PHYTOCHEMISTRY REVIEWS : PROCEEDINGS OF THE PHYTOCHEMICAL SOCIETY OF EUROPE 2011; 10:205-216. [PMID: 21765818 PMCID: PMC3105236 DOI: 10.1007/s11101-010-9175-z] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2009] [Accepted: 01/22/2010] [Indexed: 05/08/2023]
Abstract
Secondary metabolites provide a potential source for the generation of host plant resistance and development of biopesticides. This is especially important in view of the rapid and vast spread of agricultural and horticultural pests worldwide. Multiple pests control tactics in the framework of an integrated pest management (IPM) programme are necessary. One important strategy of IPM is the use of chemical host plant resistance. Up to now the study of chemical host plant resistance has, for technical reasons, been restricted to the identification of single compounds applying specific chemical analyses adapted to the compound in question. In biological processes however, usually more than one compound is involved. Metabolomics allows the simultaneous detection of a wide range of compounds, providing an immediate image of the metabolome of a plant. One of the most universally used metabolomic approaches comprises nuclear magnetic resonance spectroscopy (NMR). It has been NMR which has been applied as a proof of principle to show that metabolomics can constitute a major advancement in the study of host plant resistance. Here we give an overview on the application of NMR to identify candidate compounds for host plant resistance. We focus on host plant resistance to western flower thrips (Frankliniella occidentalis) which has been used as a model for different plant species.
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Affiliation(s)
- Kirsten A. Leiss
- Section Plant Ecology and Metabolomics, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Young H. Choi
- Section Plant Ecology and Metabolomics, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Robert Verpoorte
- Section Plant Ecology and Metabolomics, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Peter G. L. Klinkhamer
- Section Plant Ecology and Metabolomics, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
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Villiers F, Ducruix C, Hugouvieux V, Jarno N, Ezan E, Garin J, Junot C, Bourguignon J. Investigating the plant response to cadmium exposure by proteomic and metabolomic approaches. Proteomics 2011; 11:1650-63. [PMID: 21462346 DOI: 10.1002/pmic.201000645] [Citation(s) in RCA: 144] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2010] [Revised: 01/25/2011] [Accepted: 02/01/2011] [Indexed: 11/10/2022]
Abstract
Monitoring molecular dynamics of an organism upon stress is probably the best approach to decipher physiological mechanisms involved in the stress response. Quantitative analysis of proteins and metabolites is able to provide accurate information about molecular changes allowing the establishment of a range of more or less specific mechanisms, leading to the identification of major players in the considered pathways. Such tools have been successfully used to analyze the plant response to cadmium (Cd), a major pollutant capable of causing severe health issues as it accumulates in the food chain. We present a summary of proteomics and metabolomics works that contributed to a better understanding of the molecular aspects involved in the plant response to Cd. This work allowed us to provide a finer picture of general signaling, regulatory and metabolic pathways that appeared to be affected upon Cd stress. In particular, we conclude on the advantage of employing different approaches of global proteome- and metabolome-wide techniques, combined with more targeted analysis to answer molecular questions and unravel biological networks. Finally, we propose possible directions and methodologies for future prospectives in this field, as many aspects of the plant-Cd interaction remain to be discovered.
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Affiliation(s)
- Florent Villiers
- Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Recherches en Technologies et Sciences pour le Vivant, Laboratoire de Physiologie Cellulaire Végétale, Grenoble, France
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Gibon Y, Rolin D. Aspects of experimental design for plant metabolomics experiments and guidelines for growth of plant material. Methods Mol Biol 2011; 860:13-30. [PMID: 22351168 DOI: 10.1007/978-1-61779-594-7_2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Experiments involve the deliberate variation of one or more factors in order to provoke responses, the identification of which then provides the first step towards functional knowledge. Because environmental, biological, and/or technical noise is unavoidable, biological experiments usually need to be designed. Thus, once the major sources of experimental noise have been identified, individual samples can be grouped, randomised, and/or pooled. Like other 'omics approaches, metabolomics is characterised by the numbers of analytes largely exceeding sample number. While this unprecedented singularity in biology dramatically increases false discovery, experimental error can nevertheless be decreased in plant metabolomics experiments. For this, each step from plant cultivation to data acquisition needs to be evaluated in order to identify the major sources of error and then an appropriate design can be produced, as with any other experimental approach. The choice of technology, the time at which tissues are harvested, and the way metabolism is quenched also need to be taken into consideration, as they decide which metabolites can be studied. A further recommendation is to document data and metadata in a machine readable way. The latter should also describe every aspect of the experiment. This should provide valuable hints for future experimental design and ultimately give metabolomic data a second life. To facilitate the identification of critical steps, a list of items to be considered before embarking on time-consuming and costly metabolomic experiments is proposed.
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Affiliation(s)
- Yves Gibon
- INRA, Centre INRA de Bordeaux, Villenave d'Ornon, France.
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Kováčik J, Klejdus B, Hedbavny J, Bačkor M. Tolerance of Silene vulgaris to copper: population-related comparison of selected physiological parameters. ENVIRONMENTAL TOXICOLOGY 2010; 25:581-592. [PMID: 19565632 DOI: 10.1002/tox.20519] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Tolerance of three Slovak populations of Silene vulgaris [from the localities "Harmanec" (total soil Cu 34.1 mg kg⁻¹), "Lubietová"; (total soil Cu 831.6 mg kg⁻¹) and "Špania dolina" (total soil Cu 1368.7 mg kg⁻¹) referred as SV1, SV2, and SV3, respectively] and Silene dioica (SD; from the locality "Špania dolina") exposed to 60 μM Cu for 7 days has been studied. Respective controls with 0.21 μM Cu were also cultured. SV3 and SD contained higher total shoot Cu than SV1. Methanol-soluble shoot Cu represented 60, 59, 59, and 55% from total shoot Cu and roots contained 16.7-, 20.4-, 9.9- and 28.9-fold more Cu than shoots in SV1, SV2, SV3, and SD, respectively. Soluble proteins were the least affected in SV3 and SD when Cu-exposed and control plants were compared. Root hydrogen peroxide and superoxide showed similar trend and were correlated with enhancement of ascorbate- and guaiacol-peroxidase activities. Malondialdehyde accumulation increased in SV1 and SV2. Phenylalanine ammonia-lyase activity and total soluble phenols were higher in SV3 Cu-exposed plants compared to SV1 and SV2. Shikimate dehydrogenase activity was enhanced in all Cu-exposed populations. Cinnamyl alcohol dehydrogenase activity and root lignin content were not affected and polyphenol oxidase activity was not detected. Within 14 detected free amino acids, majority of them decreased preferentially in the roots. Only serine increased in shoots and decreased in roots of all populations. Potassium content was not affected in SV3. Na, Ca, and Fe increased in roots of Cu-exposed plants of all populations, while Mg was the least affected and Zn increased in SV2 and SV3 shoots and roots. This study revealed the highest tolerance in population from the locality with the highest soil Cu content. Present findings as complex metabolic responses to Cu stress with special emphasis on phenolic metabolism are discussed.
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Affiliation(s)
- Jozef Kováčik
- Department of Botany, Institute of Biology and Ecology, Faculty of Science, P. J. Šafárik University, Mánesova 23, 04167 Košice, Slovak Republic.
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Distinguishing transgenic from non-transgenic Arabidopsis plants by (1)H NMR-based metabolic fingerprinting. J Genet Genomics 2010; 36:621-8. [PMID: 19840760 DOI: 10.1016/s1673-8527(08)60154-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2009] [Revised: 09/08/2009] [Accepted: 09/16/2009] [Indexed: 11/21/2022]
Abstract
We have recently reported the construction of an nuclear magnetic resonance (NMR)-based metabonomics study platform, Automics. To examine the application of Automics in transgenic plants, we performed metabolic fingerprinting analysis, i.e., (1)H NMR spectroscopy and multivariate analysis, on wild-type and transgenic Arabidopsis. We found that it was possible to distinguish wild-type from four transgenic plants by PLS-DA following application of orthogonal signal correction (OSC). Scores plot following OSC clearly demonstrates significant variation between the transgenic and non-transgenic groups, suggesting that the metabolic changes among wild-type and transgenic lines are possibly associated with transgenic event. We also found that the major contributing metabolites were some specific amino acids (i.e., threonine and alanine), which could correspond to the insertion of the selective marker BAR gene in the transgenic plants. Our data suggests that NMR-based metabonomics is an efficient method to distinguish fingerprinting difference between wild-type and transgenic plants, and can potentially be applied in the bio-safety assessment of transgenic plants.
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Ovenden SPB, Gordon BR, Bagas CK, Muir B, Rochfort S, Bourne DJ. A Study of the Metabolome of Ricinus communis for Forensic Applications. Aust J Chem 2010. [DOI: 10.1071/ch09293] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Investigations were undertaken to ascertain the appropriateness of studying the metabolome of Ricinus communis for cultivar and provenance determination. Seeds from 14 R. communis specimens (a total of 56 seeds) collected from the east coast of Australia were analyzed by high pressure liquid chromatography with UV detection (HPLC-UV), liquid chromatography–mass spectrometry (LC-MS), and 1H NMR spectroscopy. The collected data were then analyzed using principle component analysis (PCA). For HPLC-UV analysis, six R. communis specimens were unambiguously identified by PCA as belonging to separate classes relating to specimen. LC-MS data allowed unique ions to be identified for four specimens. Conversely 10 specimens were unambiguously segregated in the PCA of the 1H NMR data. The ratio of ricinine 1 to demethylricinine analogues 2 and 3 was found to be important for specimen determination. These combined analyses suggested that a combination of HPLC-UV and 1H NMR in conjunction with PCA could allow for specimen differentiation.
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Hughes SL, Bundy JG, Want EJ, Kille P, Stürzenbaum SR. The Metabolomic Responses of Caenorhabditis elegans to Cadmium Are Largely Independent of Metallothionein Status, but Dominated by Changes in Cystathionine and Phytochelatins. J Proteome Res 2009; 8:3512-9. [DOI: 10.1021/pr9001806] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Samantha L. Hughes
- School of Biomedical and Health Sciences, Pharmaceutical Science Division, King’s College London, Franklin Wilkins Building, Stamford Street, London SE1 9NH, United Kingdom, School of Biosciences, University of Cardiff, Main Building, Park Place, Cardiff CF10 3TL, United Kingdom, and Department of Biomolecular Medicine, Division of Surgery, Oncology, Reproductive Biology, and Anaesthetics, Faculty of Medicine, Imperial College London, Sir Alexander Fleming Building, London SW7 2AZ, United Kingdom
| | - Jacob G. Bundy
- School of Biomedical and Health Sciences, Pharmaceutical Science Division, King’s College London, Franklin Wilkins Building, Stamford Street, London SE1 9NH, United Kingdom, School of Biosciences, University of Cardiff, Main Building, Park Place, Cardiff CF10 3TL, United Kingdom, and Department of Biomolecular Medicine, Division of Surgery, Oncology, Reproductive Biology, and Anaesthetics, Faculty of Medicine, Imperial College London, Sir Alexander Fleming Building, London SW7 2AZ, United Kingdom
| | - Elizabeth J. Want
- School of Biomedical and Health Sciences, Pharmaceutical Science Division, King’s College London, Franklin Wilkins Building, Stamford Street, London SE1 9NH, United Kingdom, School of Biosciences, University of Cardiff, Main Building, Park Place, Cardiff CF10 3TL, United Kingdom, and Department of Biomolecular Medicine, Division of Surgery, Oncology, Reproductive Biology, and Anaesthetics, Faculty of Medicine, Imperial College London, Sir Alexander Fleming Building, London SW7 2AZ, United Kingdom
| | - Peter Kille
- School of Biomedical and Health Sciences, Pharmaceutical Science Division, King’s College London, Franklin Wilkins Building, Stamford Street, London SE1 9NH, United Kingdom, School of Biosciences, University of Cardiff, Main Building, Park Place, Cardiff CF10 3TL, United Kingdom, and Department of Biomolecular Medicine, Division of Surgery, Oncology, Reproductive Biology, and Anaesthetics, Faculty of Medicine, Imperial College London, Sir Alexander Fleming Building, London SW7 2AZ, United Kingdom
| | - Stephen R. Stürzenbaum
- School of Biomedical and Health Sciences, Pharmaceutical Science Division, King’s College London, Franklin Wilkins Building, Stamford Street, London SE1 9NH, United Kingdom, School of Biosciences, University of Cardiff, Main Building, Park Place, Cardiff CF10 3TL, United Kingdom, and Department of Biomolecular Medicine, Division of Surgery, Oncology, Reproductive Biology, and Anaesthetics, Faculty of Medicine, Imperial College London, Sir Alexander Fleming Building, London SW7 2AZ, United Kingdom
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Yang MS, Yu LC, Gupta RC. Analysis of Multiple Metabolomic Subsets In Vitro: Methodological Considerations. Toxicol Mech Methods 2008; 15:29-32. [DOI: 10.1080/15376520490446383] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Abstract
Stress in plants could be defined as any change in growth condition(s) that disrupts metabolic homeostasis and requires an adjustment of metabolic pathways in a process that is usually referred to as acclimation. Metabolomics could contribute significantly to the study of stress biology in plants and other organisms by identifying different compounds, such as by-products of stress metabolism, stress signal transduction molecules or molecules that are part of the acclimation response of plants. These could be further tested by direct measurements, correlated with changes in transcriptome and proteome expression and confirmed by mutant analysis. In this review, we will discuss recent application of metabolomics and system biology to the area of plant stress response. We will describe approaches such as metabolic profiling and metabolic fingerprinting as well as combination of different 'omics' platforms to achieve a holistic view of the plant response stress and conduct detailed pathway analysis.
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Affiliation(s)
- Vladimir Shulaev
- Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA.
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Nocito FF, Espen L, Crema B, Cocucci M, Sacchi GA. Cadmium induces acidosis in maize root cells. THE NEW PHYTOLOGIST 2008; 179:700-711. [PMID: 18537888 DOI: 10.1111/j.1469-8137.2008.02509.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
* Cadmium (Cd) stress increases cell metabolic demand for sulfur, reducing equivalents, and carbon skeletons, to sustain phytochelatin biosynthesis for Cd detoxification. In this condition the induction of potentially acidifying anaplerotic metabolism in root tissues may be expected. For these reasons the effects of Cd accumulation on anaplerotic metabolism, glycolysis, and cell pH control mechanisms were investigated in maize (Zea mays) roots. * The study compared root apical segments, excised from plants grown for 24 h in a nutrient solution supplemented, or not, with 10 microM CdCl(2), using physiological, biochemical and (31)P-nuclear magnetic resonance (NMR) approaches. * Cadmium exposure resulted in a significant decrease in both cytosolic and vacuolar pH of root cells and in a concomitant increase in the carbon fluxes through anaplerotic metabolism leading to malate biosynthesis, as suggested by changes in dark CO2 fixation, metabolite levels and enzyme activities along glycolysis, and mitochondrial alternative respiration capacity. This scenario was accompanied by a decrease in the net H(+) efflux from the roots, probably related to changes in plasma membrane permeability. * It is concluded that anaplerotic metabolism triggered by Cd detoxification processes might lead to an imbalance in H(+) production and consumption, and then to cell acidosis.
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Affiliation(s)
- Fabio Francesco Nocito
- Dipartimento di Produzione Vegetale, Università degli Studi di Milano, I-20133 Milan, Italy
| | - Luca Espen
- Dipartimento di Produzione Vegetale, Università degli Studi di Milano, I-20133 Milan, Italy
| | - Barbara Crema
- Dipartimento di Produzione Vegetale, Università degli Studi di Milano, I-20133 Milan, Italy
| | - Maurizio Cocucci
- Dipartimento di Produzione Vegetale, Università degli Studi di Milano, I-20133 Milan, Italy
| | - Gian Attilio Sacchi
- Dipartimento di Produzione Vegetale, Università degli Studi di Milano, I-20133 Milan, Italy
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Soares PK, Scarminio IS. Multivariate chromatographic fingerprint preparation and authentication of plant material from the genus Bauhinia. PHYTOCHEMICAL ANALYSIS : PCA 2008; 19:78-85. [PMID: 17685491 DOI: 10.1002/pca.1020] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Multivariate analysis and statistical mixture designs were used for chromatographic fingerprint preparation and authentication of the plant material of three species of the genus Bauhinia. The extracts were analysed by reversed-phase high-performance liquid chromatography. Mixture design gave an optimum solvent composition for extracting components from the plants of 36% dichloromethane, 17% ethanol and 47% ethyl acetate (by volume), while an optimum mobile phase for chromatographic analyses was found to be 27% methanol, 27% acetonitrile and 46% of water (by volume). Results from principal component analysis, hierarchical analysis and soft independent modelling by class analogy showed that Bauhinia candicans cannot be synonymous with B. forficata Link. It was also possible to trace the metabolic profile without identifying its chemical constituents and to determine a chromatographic discriminating region. The characteristics responsible for discrimination between B. candicans and B. forficata were more polar substances that presented peaks with retention times around 1.65 and 1.81 min.
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Affiliation(s)
- Patricia Kaori Soares
- Departamento de Química, Universidade Estadual de Londrina, Londrina, 86051-990 Paraná, Brazil
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Griffin JL, Nicholls AW. Metabolomics as a functional genomic tool for understanding lipid dysfunction in diabetes, obesity and related disorders. Pharmacogenomics 2006; 7:1095-107. [PMID: 17054419 DOI: 10.2217/14622416.7.7.1095] [Citation(s) in RCA: 107] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
With the rise of systems biology, a number of approaches have been developed to globally profile a tier of organization in a cell, tissue or organism. Metabolomics is an approach that attempts to profile all the metabolites in a biological matrix. One of the major challenges of this approach, as with other 'omic' technologies, is that the metabolome is context-dependent and will vary with pathology, developmental stage and environmental factors. Thus, the possibility of globally profiling the metabolome of an organism is a genuine analytical challenge, as by definition this must also take into consideration all relevant factors that influence metabolism. Despite these challenges, the approach has already been applied to understand the metabolism in a range of animal models, and has more recently started to be projected into the clinical situation. In this review, the technologies currently being used in metabolomics will be assessed prior to examining their use to study diseases related to the metabolic syndrome, including Type II diabetes, obesity, cardiovascular disease and fatty liver disease.
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Affiliation(s)
- Julian L Griffin
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK.
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Harada K, Fukusaki E, Kobayashi A. Pressure-assisted capillary electrophoresis mass spectrometry using combination of polarity reversion and electroosmotic flow for metabolomics anion analysis. J Biosci Bioeng 2006; 101:403-9. [PMID: 16781469 DOI: 10.1263/jbb.101.403] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2005] [Accepted: 02/07/2006] [Indexed: 11/17/2022]
Abstract
We have developed a method based on capillary electrophoresis (CE) coupled to mass spectrometry (MS) that is a powerful tool for metabolome analysis. In this paper, a simple method for the simultaneous analysis of anionic metabolites such as sugar phosphates, organic acids, nucleotides and CoA compounds based on pressure-assisted capillary electrophoresis coupled to electrospray ionization mass spectrometry (PACE/ESI-MS) is described. The feature of this method is that CE polarity, where the inlet of the capillary is at the anode and the outlet at the cathode, is inverted from conventional CE analysis for anions. Moreover, an ordinary fused silica capillary was chosen instead of a specific cationic polymer-coated capillary (SMILE (+) capillary). A robust and inexpensive analytical method was established from the above-mentioned CE polarity and noncoated fused silica capillary. A trimethylamine acetate electrolyte, pH 10.0, provides a high resolution between isomers. Electrolyte flow using an air pump after electrophoresis enables the comprehensive and simultaneous analyses of sugar phosphates, organic acids, nucleotides and a CoA compound that to date have been impossible to analyze. Our method can be used as a de facto standard for metabolome analysis.
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Affiliation(s)
- Kazuo Harada
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Japan
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Griffin JL. Understanding mouse models of disease through metabolomics. Curr Opin Chem Biol 2006; 10:309-15. [PMID: 16815732 DOI: 10.1016/j.cbpa.2006.06.027] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2006] [Accepted: 06/22/2006] [Indexed: 02/01/2023]
Abstract
Metabolomics is widely applicable to a number of fields including toxicology, plant metabolism and functional genomics. In the area of functional genomics, a number of studies have demonstrated the potential of this approach, which combines high-throughput metabolite profiling with computer-assisted pattern recognition approaches. In this review, recent applications of metabolomics to understanding mouse models of disease are considered. This includes studies on the impact of mouse strain on disease models, as well as metabolic profiling of cardiovascular, metabolic and neurodegenerative diseases. This versatile tool is set to increase in popularity as functional genomic approaches produce more mouse models for phenotyping.
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Affiliation(s)
- Julian L Griffin
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK.
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Griffin JL. The Cinderella story of metabolic profiling: does metabolomics get to go to the functional genomics ball? Philos Trans R Soc Lond B Biol Sci 2006; 361:147-61. [PMID: 16553314 PMCID: PMC1626538 DOI: 10.1098/rstb.2005.1734] [Citation(s) in RCA: 113] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
To date most global approaches to functional genomics have centred on genomics, transcriptomics and proteomics. However, since a number of high-profile publications, interest in metabolomics, the global profiling of metabolites in a cell, tissue or organism, has been rapidly increasing. A range of analytical techniques, including 1H NMR spectroscopy, gas chromatography-mass spectrometry (GC-MS), liquid chromatography-mass spectrometry (LC-MS), Fourier Transform mass spectrometry (FT-MS), high performance liquid chromatography (HPLC) and electrochemical array (EC-array), are required in order to maximize the number of metabolites that can be identified in a matrix. Applications have included phenotyping of yeast, mice and plants, understanding drug toxicity in pharmaceutical drug safety assessment, monitoring tumour treatment regimes and disease diagnosis in human populations. These successes are likely to be built on as other analytical and bioinformatic approaches are developed to fully exploit the information obtained in metabolic profiles. To assist in this process, databases of metabolomic data will be necessary to allow the passage of information between laboratories. In this prospective review, the capabilities of metabolomics in the field of medicine will be assessed in an attempt to predict the impact this 'Cinderella approach' will have at the 'functional genomic ball'.
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Affiliation(s)
- Julian L Griffin
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK.
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Pereira GE, Gaudillere JP, Leeuwen CV, Hilbert G, Maucourt M, Deborde C, Moing A, Rolin D. 1H NMR metabolite fingerprints of grape berry: Comparison of vintage and soil effects in Bordeaux grapevine growing areas. Anal Chim Acta 2006. [DOI: 10.1016/j.aca.2005.11.007] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Fukusaki E, Kobayashi A. Plant metabolomics: potential for practical operation. J Biosci Bioeng 2005; 100:347-54. [PMID: 16310723 DOI: 10.1263/jbb.100.347] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2005] [Accepted: 06/11/2005] [Indexed: 11/17/2022]
Abstract
In the postgenomic era, metabolomics is expected to be the newest useful omics science for functional genomics. However, in plant science, the present metabolomics technology cannot be considered a universal tool to perfectly elucidate perturbations imposed on sample plants although this is desired by plant physiologists. Despite it being an immature technology, metabolomics has already been used as a powerful tool for precise phenotyping, particularly for industrial application. Metabolomics is the best technology for the analysis of large mutant or transgenic libraries of model experimental plants, such as Arabidopsis, rice, etc. Here, we review the applications and technical problems of metabolomics. We also suggest the potential of metabolomics for plant post-genomic science.
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Affiliation(s)
- Eiichiro Fukusaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.
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El-Zohri MHA, Cabala R, Frank H. Quantification of phytochelatins in plants by reversed-phase HPLC–ESI–MS–MS. Anal Bioanal Chem 2005; 382:1871-6. [PMID: 16001238 DOI: 10.1007/s00216-005-3331-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2005] [Revised: 05/13/2005] [Accepted: 05/19/2005] [Indexed: 10/25/2022]
Abstract
An on-line HPLC-ESI-MS-MS method has been developed for determination of glutathione and phytochelatins (PC) in plant tissues. For sample pretreatment, dithiothreitol (DTT) must be added at the very beginning, as an anti-oxidant. Optimization of instrumental conditions i.e. composition of HPLC mobile phase, ionization efficiency of the electrospray interface, and MS-MS detection in the multiple ion-monitoring mode, are the central aspects of this work. A polystyrene-packed column was found to be superior to a standard silica-packed reversed-phase column. A concave quadratic gradient of ammonium formate buffer and acetonitrile was found to be optimum. The limits of quantitation were 0.2 micromol kg(-1) plant tissue for glutathione and PC. The method has been applied to analysis of tissue samples from Vicia faba grown in Cd-containing nutrient solutions.
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Affiliation(s)
- M H A El-Zohri
- Environmental Chemistry and Ecotoxicology, University of Bayreuth, 95440 Bayreuth, Germany
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Tarpley L, Duran AL, Kebrom TH, Sumner LW. Biomarker metabolites capturing the metabolite variance present in a rice plant developmental period. BMC PLANT BIOLOGY 2005; 5:8. [PMID: 15927065 PMCID: PMC1175851 DOI: 10.1186/1471-2229-5-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2004] [Accepted: 05/31/2005] [Indexed: 05/02/2023]
Abstract
BACKGROUND This study analyzes metabolomic data from a rice tillering (branching) developmental profile to define a set of biomarker metabolites that reliably captures the metabolite variance of this plant developmental event, and which has potential as a basis for rapid comparative screening of metabolite profiles in relation to change in development, environment, or genotype. Changes in metabolism, and in metabolite profile, occur as a part of, and in response to, developmental events. These changes are influenced by the developmental program, as well as external factors impinging on it. Many samples are needed, however, to characterize quantitative aspects of developmental variation. A biomarker metabolite set could benefit screening of quantitative plant developmental variation by providing some of the advantages of both comprehensive metabolomic studies and focused studies of particular metabolites or pathways. RESULTS An appropriate set of biomarker metabolites to represent the plant developmental period including the initiation and early growth of rice tillering (branching) was obtained by: (1) determining principal components of the comprehensive metabolomic profile, then (2) identifying clusters of metabolites representing variation in loading on the first three principal components, and finally (3) selecting individual metabolites from these clusters that were known to be common among diverse organisms. The resultant set of 21 biomarker metabolites was reliable (P = 0.001) in capturing 83% of the metabolite variation in development. Furthermore, a subset of the biomarker metabolites was successful (P = 0.05) in correctly predicting metabolite change in response to environment as determined in another rice metabolomics study. CONCLUSION The ability to define a set of biomarker metabolites that reliably captures the metabolite variance of a plant developmental event was established. The biomarker metabolites are all commonly present in diverse organisms, so studies of their quantitative relationships can provide comparative information concerning metabolite profiles in relation to change in plant development, environment, or genotype.
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Affiliation(s)
- Lee Tarpley
- Texas A&M Agricultural Research and Extension Center, 1509 Aggie Dr, Beaumont, Texas, 77713, USA
- Soil and Crop Sciences Department, Texas A&M University, College Station, Texas, USA
| | - Anthony L Duran
- Analytical Research Laboratories, Oklahoma City, Oklahoma, USA
- Samuel Roberts Noble Foundation, Ardmore, Oklahoma, USA
| | - Tesfamichael H Kebrom
- Soil and Crop Sciences Department, Texas A&M University, College Station, Texas, USA
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Abstract
The post-genomics era has brought with it ever increasing demands to observe and characterise variation within biological systems. This variation has been studied at the genomic (gene function), proteomic (protein regulation) and the metabolomic (small molecular weight metabolite) levels. Whilst genomics and proteomics are generally studied using microarrays (genomics) and 2D-gels or mass spectrometry (proteomics), the technique of choice is less obvious in the area of metabolomics. Much work has been published employing mass spectrometry, NMR spectroscopy and vibrational spectroscopic techniques, amongst others, for the study of variations within the metabolome in many animal, plant and microbial systems. This review discusses the advantages and disadvantages of each technique, putting the current status of the field of metabolomics in context, and providing examples of applications for each technique employed.
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Affiliation(s)
- Warwick B Dunn
- Bioanalytical Sciences Group, School of Chemistry, University of Manchester, Faraday Building, Sackville Street, P. O. Box 88, Manchester, UKM60 1QD.
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Abstract
Metabonomics and its many pseudonyms (metabolomics, metabolic profiling, etc.) have exploded onto the scientific scene in the past 2 to 3 years. Nowhere has the impact been more profound than within the toxicology community. Within this community there exists a great deal of uncertainty about whether metabonomics is something to count on or just the most recent technological flash in the pan. Much of the uncertainty is due to unfamiliarity with analytical and chemometric facets of the technology and the attendant fear of any "black-box." With those fears in mind, metabonomics technology is reviewed with particular emphasis on toxicologic applications in preclinical drug development. The jargon, logistics, and applications of the technology are covered in some detail with emphasis on recent work in the field.
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Affiliation(s)
- Donald G Robertson
- Metabonomics Evaluation Group, Department of World-Wide Safety Sciences, Pfizer Global Research and Development, Ann Arbor, Michigan 48105, USA.
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Ratcliffe RG, Shachar-Hill Y. Revealing metabolic phenotypes in plants: inputs from NMR analysis. Biol Rev Camb Philos Soc 2005; 80:27-43. [PMID: 15727037 DOI: 10.1017/s1464793104006530] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Assessing the performance of the plant metabolic network, with its varied biosynthetic capacity and its characteristic subcellular compartmentation, remains a considerable challenge. The complexity of the network is such that it is not yet possible to build large-scale predictive models of the fluxes it supports, whether on the basis of genomic and gene expression analysis or on the basis of more traditional measurements of metabolites and their interconversions. This limits the agronomic and biotechnological exploitation of plant metabolism, and it undermines the important objective of establishing a rational metabolic engineering strategy. Metabolic analysis is central to removing this obstacle and currently there is particular interest in harnessing high-throughput and/or large-scale analyses to the task of defining metabolic phenotypes. Nuclear magnetic resonance (NMR) spectroscopy contributes to this objective by providing a versatile suite of analytical techniques for the detection of metabolites and the fluxes between them. The principles that underpin the analysis of plant metabolism by NMR are described, including a discussion of the measurement options for the detection of metabolites in vivo and in vitro, and a description of the stable isotope labelling experiments that provide the basis for metabolic flux analysis. Despite a relatively low sensitivity, NMR is suitable for high-throughput system-wide analyses of the metabolome, providing methods for both metabolite fingerprinting and metabolite profiling, and in these areas NMR can contribute to the definition of plant metabolic phenotypes that are based on metabolic composition. NMR can also be used to investigate the operation of plant metabolic networks. Labelling experiments provide information on the operation of specific pathways within the network, and the quantitative analysis of steady-state labelling experiments leads to the definition of large-scale flux maps for heterotrophic carbon metabolism. These maps define multiple unidirectional fluxes between branch-points in the metabolic network, highlighting the existence of substrate cycles and discriminating in favourable cases between fluxes in the cytosol and plastid. Flux maps can be used to define a functionally relevant metabolic phenotype and the extensive application of such maps in microbial systems suggests that they could have important applications in characterising the genotypes produced by plant genetic engineering.
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Affiliation(s)
- R G Ratcliffe
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, UK.
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Mesnard F, Ratcliffe RG. NMR analysis of plant nitrogen metabolism. PHOTOSYNTHESIS RESEARCH 2005; 83:163-80. [PMID: 16143850 DOI: 10.1007/s11120-004-2081-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2004] [Accepted: 07/17/2004] [Indexed: 05/04/2023]
Abstract
The analysis of primary and secondary nitrogen metabolism in plants by nuclear magnetic resonance (NMR) spectroscopy is comprehensively reviewed. NMR is a versatile analytical tool, and the combined use of (1)H, (2)H, (13)C, (14)N and (15)N NMR allows detailed investigation of the acquisition, assimilation and metabolism of nitrogen. The analysis of tissue extracts can be complemented by the in vivo NMR analysis of functioning tissues and cell suspensions, and by the application of solid state NMR techniques. Moreover stable isotope labelling with (2)H-, (13)C- and (15)N-labelled precursors provides direct insight into specific pathways, with the option of both time-course and steady state analysis increasing the potential value of the approach. The scope of the NMR method, and its contribution to studies of plant nitrogen metabolism, are illustrated with a wide range of examples. These include studies of the GS/GOGAT pathway of ammonium assimilation, investigations of the metabolism of glutamate, glycine and other amino acids, and applications to tropane alkaloid metabolism. The continuing development of the NMR technique, together with potential applications in the emerging fields of metabolomics and metabolic flux analysis, leads to the conclusion that NMR will play an increasingly valuable role in the analysis of plant nitrogen metabolism.
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Affiliation(s)
- F Mesnard
- EA 2084, Faculté de Pharmacie, Laboratoire de Phytotechnologie, 1 rue des Louvels, F-80037 Amiens Cedex 1, France
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50
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Griffin JL. The potential of metabonomics in drug safety and toxicology. DRUG DISCOVERY TODAY. TECHNOLOGIES 2004; 1:285-293. [PMID: 24981497 DOI: 10.1016/j.ddtec.2004.10.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Metabonomics (or metabolomics) defines a global profile of the metabolites in a cell, tissue or organism using either (1)H NMR spectroscopy or mass spectrometry in conjunction with statistical pattern recognition. Unlike other functional genomic tools, it is high-throughput and cheap on a per sample basis, providing a rapid screen for large scale drug toxicity testing and screening of large populations. However, for its widespread use in toxicology there is an urgent need for biomarker databases.:
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Affiliation(s)
- Julian L Griffin
- Department of Biochemistry, Tennis Court Road, University of Cambridge, Cambridge, UK CB2 1GA.
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