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Ren Z, Qin L, Chen L, Xu H, Liu H, Guo H, Li J, Yang C, Hu H, Wu R, Zhou Y, Xue K, Liu B, Wang X. Spatial Lipidomics of EPSPS and PAT Transgenic and Non-Transgenic Soybean Seeds Using Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023. [PMID: 37318082 DOI: 10.1021/acs.jafc.3c01377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Herbicide-resistant soybeans are among the most widely planted transgenic crops. The in situ evaluation of spatial lipidomics in transgenic and non-transgenic soybeans is important for directly assessing the unintended effects of exogenous gene introduction. In this study, matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI)-based non-targeted analytical strategies were used for the first time for in situ detection and imaging of endogenous lipid distributions in transgenic (EPSPS and PAT genes) herbicide-resistant soybean (Glycine max Merrill) (S4003.14) and non-transgenic soybean (JACK) seeds. Statistical analysis revealed significant differences in lipids between S4003.14 and JACK seeds. The variable importance of projection analysis further revealed that 18 identified lipids, including six phosphatidylcholines (PCs), four phosphatidylethanolamines (PEs), five triacylglycerols (TAGs), and three cytidine diphosphate-diacylglycerols (CDP-DAGs), had the strongest differential expression between S4003.14 and JACK seeds. Among those, the upregulated expressions of PC(P-36:1), PC(36:2), PC(P-36:0), PC(37:5), PE(40:2), TAG(52:1), TAG(55:5), and CDP-DAG(37:2) and the downregulated expressions of PC (36:1), TAG(43:0), and three PEs (i.e., PE(P-38:1), PE(P-38:0), and PE(P-40:3)) were successfully found in the S4003.14 seeds, compared to these lipids detected in the JACK seeds. Meanwhile, the lipids of PC (44:8), CDP-DAG(38:0), and CDP-DAG(42:0) were uniquely detected in the S4003.14 soybean seeds, and TAG(45:2) and TAG(57:10) were detected as the unique lipids in the JACK seeds. The heterogeneous distribution of these lipids in the soybean seeds was also clearly visualized using MALDI-MSI. MSI results showed that lipid expression was significantly up/downregulated in S4003.14 seeds, compared to that in JACK seeds. This study improves our understanding of the unintended effects of herbicide-resistant EPSPS and PAT gene transfers on spatial lipidomes in soybean seeds and enables the continued progression of MALDI-MSI as an emerging, reliable, and rapid molecular imaging tool for evaluating unintended effects in transgenic plants.
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Affiliation(s)
- Zhentao Ren
- College of Life and Environmental Sciences, Centre for Imaging & Systems Biology, Minzu University of China, Beijing 100081, China
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, China
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics (Minzu University of China), State Ethnic Affairs Commission, Beijing 100081, China
| | - Liang Qin
- College of Life and Environmental Sciences, Centre for Imaging & Systems Biology, Minzu University of China, Beijing 100081, China
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics (Minzu University of China), State Ethnic Affairs Commission, Beijing 100081, China
| | - Lulu Chen
- College of Life and Environmental Sciences, Centre for Imaging & Systems Biology, Minzu University of China, Beijing 100081, China
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics (Minzu University of China), State Ethnic Affairs Commission, Beijing 100081, China
| | - Hualei Xu
- College of Life and Environmental Sciences, Centre for Imaging & Systems Biology, Minzu University of China, Beijing 100081, China
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics (Minzu University of China), State Ethnic Affairs Commission, Beijing 100081, China
| | - Haiqiang Liu
- College of Life and Environmental Sciences, Centre for Imaging & Systems Biology, Minzu University of China, Beijing 100081, China
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics (Minzu University of China), State Ethnic Affairs Commission, Beijing 100081, China
| | - Hua Guo
- College of Life and Environmental Sciences, Centre for Imaging & Systems Biology, Minzu University of China, Beijing 100081, China
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics (Minzu University of China), State Ethnic Affairs Commission, Beijing 100081, China
| | - Jinrong Li
- College of Life and Environmental Sciences, Centre for Imaging & Systems Biology, Minzu University of China, Beijing 100081, China
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics (Minzu University of China), State Ethnic Affairs Commission, Beijing 100081, China
| | - Chenyu Yang
- College of Life and Environmental Sciences, Centre for Imaging & Systems Biology, Minzu University of China, Beijing 100081, China
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics (Minzu University of China), State Ethnic Affairs Commission, Beijing 100081, China
| | - Hao Hu
- College of Life and Environmental Sciences, Centre for Imaging & Systems Biology, Minzu University of China, Beijing 100081, China
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics (Minzu University of China), State Ethnic Affairs Commission, Beijing 100081, China
| | - Ran Wu
- College of Life and Environmental Sciences, Centre for Imaging & Systems Biology, Minzu University of China, Beijing 100081, China
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics (Minzu University of China), State Ethnic Affairs Commission, Beijing 100081, China
| | - Yijun Zhou
- College of Life and Environmental Sciences, Centre for Imaging & Systems Biology, Minzu University of China, Beijing 100081, China
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics (Minzu University of China), State Ethnic Affairs Commission, Beijing 100081, China
| | - Kun Xue
- College of Life and Environmental Sciences, Centre for Imaging & Systems Biology, Minzu University of China, Beijing 100081, China
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics (Minzu University of China), State Ethnic Affairs Commission, Beijing 100081, China
| | - Biao Liu
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, China
| | - Xiaodong Wang
- College of Life and Environmental Sciences, Centre for Imaging & Systems Biology, Minzu University of China, Beijing 100081, China
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics (Minzu University of China), State Ethnic Affairs Commission, Beijing 100081, China
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Villányi V, Gondor OK, Bánfalvi Z. Metabolite profiling of tubers of an early- and a late-maturing potato line and their grafts. Metabolomics 2022; 18:88. [PMID: 36334159 PMCID: PMC9637070 DOI: 10.1007/s11306-022-01950-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 10/29/2022] [Indexed: 11/06/2022]
Abstract
INTRODUCTION Earliness of tuberisation and the quality of potato tubers are important traits in potato breeding. The qualitative traits rely on the metabolite profile of tubers, which are storage organs and net importers of assimilates. Thus, the quality of tubers largely depends on the metabolites transported from leaves to developing tubers. OBJECTIVES To test the influence of canopy on the quality of tubers by metabolite profiling of tubers of an early- and a late-maturing potato line and their grafts. METHODS Potatoes were grown under greenhouse conditions, grafted and the tubers harvested at the end of the scions' vegetation period. Metabolite profiling of freshly harvested tubers was performed using gas chromatography coupled with mass spectrometry. Statistical analyses were applied to determine the significant differences between the different tubers. RESULTS 99 metabolites were identified and an additional 181 peaks detected in chromatograms, out of which 186 were polar and 94 non-polar compounds. The concentrations of 113 metabolites were significantly different in the tubers from the early-maturing CE3130 and the late-maturing CE3027 line. Hetero-grafting resulted in considerable changes in the metabolite content of tubers. Especially, the effect of CE3027 on the metabolite composition of tubers formed on CE3130 rootstocks was readily apparent. Nevertheless, many compounds were present at similar levels in the tubers of hetero-grafted plants as was found in the tubers of their scion counterparts. CONCLUSION Hetero-grafting resulted in many compounds at similar concentrations in rootstock tubers as in scion tubers suggesting that these are transported from the source leaves to tubers.
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Affiliation(s)
- Vanda Villányi
- Genetics and Biotechnology Institute, Hungarian University of Agriculture and Life Sciences, Szent-Györgyi A. u. 4, Gödöllő, 2100, Hungary
| | - Orsolya Kinga Gondor
- Centre for Agricultural Research, Eötvös Loránd Research Network, Brunszvik u. 2, Martonvásár, 2462, Hungary
| | - Zsófia Bánfalvi
- Genetics and Biotechnology Institute, Hungarian University of Agriculture and Life Sciences, Szent-Györgyi A. u. 4, Gödöllő, 2100, Hungary.
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Yan S, Bhawal R, Yin Z, Thannhauser TW, Zhang S. Recent advances in proteomics and metabolomics in plants. MOLECULAR HORTICULTURE 2022; 2:17. [PMID: 37789425 PMCID: PMC10514990 DOI: 10.1186/s43897-022-00038-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 06/20/2022] [Indexed: 10/05/2023]
Abstract
Over the past decade, systems biology and plant-omics have increasingly become the main stream in plant biology research. New developments in mass spectrometry and bioinformatics tools, and methodological schema to integrate multi-omics data have leveraged recent advances in proteomics and metabolomics. These progresses are driving a rapid evolution in the field of plant research, greatly facilitating our understanding of the mechanistic aspects of plant metabolisms and the interactions of plants with their external environment. Here, we review the recent progresses in MS-based proteomics and metabolomics tools and workflows with a special focus on their applications to plant biology research using several case studies related to mechanistic understanding of stress response, gene/protein function characterization, metabolic and signaling pathways exploration, and natural product discovery. We also present a projection concerning future perspectives in MS-based proteomics and metabolomics development including their applications to and challenges for system biology. This review is intended to provide readers with an overview of how advanced MS technology, and integrated application of proteomics and metabolomics can be used to advance plant system biology research.
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Affiliation(s)
- Shijuan Yan
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Ruchika Bhawal
- Proteomics and Metabolomics Facility, Institute of Biotechnology, Cornell University, 139 Biotechnology Building, 526 Campus Road, Ithaca, NY, 14853, USA
| | - Zhibin Yin
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | | | - Sheng Zhang
- Proteomics and Metabolomics Facility, Institute of Biotechnology, Cornell University, 139 Biotechnology Building, 526 Campus Road, Ithaca, NY, 14853, USA.
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Advances in Metabolomics-Driven Diagnostic Breeding and Crop Improvement. Metabolites 2022; 12:metabo12060511. [PMID: 35736444 PMCID: PMC9228725 DOI: 10.3390/metabo12060511] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 05/25/2022] [Accepted: 05/26/2022] [Indexed: 02/04/2023] Open
Abstract
Climate change continues to threaten global crop output by reducing annual productivity. As a result, global food security is now considered as one of the most important challenges facing humanity. To address this challenge, modern crop breeding approaches are required to create plants that can cope with increased abiotic/biotic stress. Metabolomics is rapidly gaining traction in plant breeding by predicting the metabolic marker for plant performance under a stressful environment and has emerged as a powerful tool for guiding crop improvement. The advent of more sensitive, automated, and high-throughput analytical tools combined with advanced bioinformatics and other omics techniques has laid the foundation to broadly characterize the genetic traits for crop improvement. Progress in metabolomics allows scientists to rapidly map specific metabolites to the genes that encode their metabolic pathways and offer plant scientists an excellent opportunity to fully explore and rationally harness the wealth of metabolites that plants biosynthesize. Here, we outline the current application of advanced metabolomics tools integrated with other OMICS techniques that can be used to: dissect the details of plant genotype–metabolite–phenotype interactions facilitating metabolomics-assisted plant breeding for probing the stress-responsive metabolic markers, explore the hidden metabolic networks associated with abiotic/biotic stress resistance, facilitate screening and selection of climate-smart crops at the metabolite level, and enable accurate risk-assessment and characterization of gene edited/transgenic plants to assist the regulatory process. The basic concept behind metabolic editing is to identify specific genes that govern the crucial metabolic pathways followed by the editing of one or more genes associated with those pathways. Thus, metabolomics provides a superb platform for not only rapid assessment and commercialization of future genome-edited crops, but also for accelerated metabolomics-assisted plant breeding. Furthermore, metabolomics can be a useful tool to expedite the crop research if integrated with speed breeding in future.
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Pacifico D, Lanzanova C, Pagnotta E, Bassolino L, Mastrangelo AM, Marone D, Matteo R, Lo Scalzo R, Balconi C. Sustainable Use of Bioactive Compounds from Solanum Tuberosum and Brassicaceae Wastes and by-Products for Crop Protection-A Review. Molecules 2021; 26:2174. [PMID: 33918886 PMCID: PMC8070479 DOI: 10.3390/molecules26082174] [Citation(s) in RCA: 6] [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: 03/12/2021] [Revised: 03/31/2021] [Accepted: 04/01/2021] [Indexed: 12/24/2022] Open
Abstract
Defatted seed meals of oleaginous Brassicaceae, such as Eruca sativa, and potato peel are excellent plant matrices to recover potentially useful biomolecules from industrial processes in a circular strategy perspective aiming at crop protection. These biomolecules, mainly glycoalkaloids and phenols for potato and glucosinolates for Brassicaceae, have been proven to be effective against microbes, fungi, nematodes, insects, and even parasitic plants. Their role in plant protection is overviewed, together with the molecular basis of their synthesis in plant, and the description of their mechanisms of action. Possible genetic and biotechnological strategies are presented to increase their content in plants. Genetic mapping and identification of closely linked molecular markers are useful to identify the loci/genes responsible for their accumulation and transfer them to elite cultivars in breeding programs. Biotechnological approaches can be used to modify their allelic sequence and enhance the accumulation of the bioactive compounds. How the global challenges, such as reducing agri-food waste and increasing sustainability and food safety, could be addressed through bioprotector applications are discussed here.
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Affiliation(s)
- Daniela Pacifico
- CREA Council for Agricultural Research and Economics—Research Centre for Cereal and Industrial Crops, 00198 Rome, Italy; (C.L.); (E.P.); (L.B.); (A.M.M.); (D.M.); (C.B.); (R.M.)
| | - Chiara Lanzanova
- CREA Council for Agricultural Research and Economics—Research Centre for Cereal and Industrial Crops, 00198 Rome, Italy; (C.L.); (E.P.); (L.B.); (A.M.M.); (D.M.); (C.B.); (R.M.)
| | - Eleonora Pagnotta
- CREA Council for Agricultural Research and Economics—Research Centre for Cereal and Industrial Crops, 00198 Rome, Italy; (C.L.); (E.P.); (L.B.); (A.M.M.); (D.M.); (C.B.); (R.M.)
| | - Laura Bassolino
- CREA Council for Agricultural Research and Economics—Research Centre for Cereal and Industrial Crops, 00198 Rome, Italy; (C.L.); (E.P.); (L.B.); (A.M.M.); (D.M.); (C.B.); (R.M.)
| | - Anna Maria Mastrangelo
- CREA Council for Agricultural Research and Economics—Research Centre for Cereal and Industrial Crops, 00198 Rome, Italy; (C.L.); (E.P.); (L.B.); (A.M.M.); (D.M.); (C.B.); (R.M.)
| | - Daniela Marone
- CREA Council for Agricultural Research and Economics—Research Centre for Cereal and Industrial Crops, 00198 Rome, Italy; (C.L.); (E.P.); (L.B.); (A.M.M.); (D.M.); (C.B.); (R.M.)
| | - Roberto Matteo
- CREA Council for Agricultural Research and Economics—Research Centre for Cereal and Industrial Crops, 00198 Rome, Italy; (C.L.); (E.P.); (L.B.); (A.M.M.); (D.M.); (C.B.); (R.M.)
| | - Roberto Lo Scalzo
- CREA Council for Agricultural Research and Economics—Research Centre for Engineering and Agro-Food Processing, 00198 Rome, Italy;
| | - Carlotta Balconi
- CREA Council for Agricultural Research and Economics—Research Centre for Cereal and Industrial Crops, 00198 Rome, Italy; (C.L.); (E.P.); (L.B.); (A.M.M.); (D.M.); (C.B.); (R.M.)
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Zhao DK, Zhao Y, Chen SY, Kennelly EJ. Solanum steroidal glycoalkaloids: structural diversity, biological activities, and biosynthesis. Nat Prod Rep 2021; 38:1423-1444. [DOI: 10.1039/d1np00001b] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Chemical structures of typical Solanum steroidal glycoalkaloids from eggplant, tomato, and potato.
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Affiliation(s)
- Da-Ke Zhao
- Biocontrol Engineering Research Center of Plant Disease and Pest, Biocontrol Engineering Research Center of Crop Disease and Pest, School of Ecology and Environment, Yunnan University, Kunming, 650504, P. R. China
| | - Yi Zhao
- Department of Biological Sciences, Lehman College, City University of New York, Bronx, New York, 10468, USA
- PhD Program in Biology, The Graduate Center, City University of New York, New York, 10016, USA
| | - Sui-Yun Chen
- Biocontrol Engineering Research Center of Plant Disease and Pest, Biocontrol Engineering Research Center of Crop Disease and Pest, School of Ecology and Environment, Yunnan University, Kunming, 650504, P. R. China
| | - Edward J. Kennelly
- Department of Biological Sciences, Lehman College, City University of New York, Bronx, New York, 10468, USA
- PhD Program in Biology, The Graduate Center, City University of New York, New York, 10016, USA
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Fraser PD, Aharoni A, Hall RD, Huang S, Giovannoni JJ, Sonnewald U, Fernie AR. Metabolomics should be deployed in the identification and characterization of gene-edited crops. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 102:897-902. [PMID: 31923321 DOI: 10.1111/tpj.14679] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 12/17/2019] [Accepted: 01/07/2020] [Indexed: 05/23/2023]
Abstract
Gene-editing techniques are currently revolutionizing biology, allowing far greater precision than previous mutagenic and transgenic approaches. They are becoming applicable to a wide range of plant species and biological processes. Gene editing can rapidly improve a range of crop traits, including disease resistance, abiotic stress tolerance, yield, nutritional quality and additional consumer traits. Unlike transgenic approaches, however, it is not facile to forensically detect gene-editing events at the molecular level, as no foreign DNA exists in the elite line. These limitations in molecular detection approaches are likely to focus more attention on the products generated from the technology than on the process in itself. Rapid advances in sequencing and genome assembly increasingly facilitate genome sequencing as a means of characterizing new varieties generated by gene-editing techniques. Nevertheless, subtle edits such as single base changes or small deletions may be difficult to distinguish from normal variation within a genotype. Given these emerging scenarios, downstream 'omics' technologies reflective of edited affects, such as metabolomics, need to be used in a more prominent manner to fully assess compositional changes in novel foodstuffs. To achieve this goal, metabolomics or 'non-targeted metabolite analysis' needs to make significant advances to deliver greater representation across the metabolome. With the emergence of new edited crop varieties, we advocate: (i) concerted efforts in the advancement of 'omics' technologies, such as metabolomics, and (ii) an effort to redress the use of the technology in the regulatory assessment for metabolically engineered biotech crops.
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Affiliation(s)
- Paul D Fraser
- School of Biological Sciences, Royal Holloway, University of London, Egham Hill, Egham, Surrey, TW20 0EX, UK
| | - Asaph Aharoni
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Robert D Hall
- Wageningen Research, Wageningen University and Research, Droevendaalsesteeg 1, Wageningen, the Netherlands
- Laboratory of Plant Physiology, Wageningen University and Research, Droevendaalsesteeg 1, Wageningen, the Netherlands
- Netherlands Metabolomics Centre, Einsteinweg 55, Leiden, the Netherlands
| | - Sanwen Huang
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100084, China
| | - James J Giovannoni
- USDA-ARS, Robert W. Holley Center and Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY, 14853, USA
| | - Uwe Sonnewald
- Department of Biology, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
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Li S, Tian Y, Jiang P, Lin Y, Liu X, Yang H. Recent advances in the application of metabolomics for food safety control and food quality analyses. Crit Rev Food Sci Nutr 2020; 61:1448-1469. [PMID: 32441547 DOI: 10.1080/10408398.2020.1761287] [Citation(s) in RCA: 145] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
As one of the omics fields, metabolomics has unique advantages in facilitating the understanding of physiological and pathological activities in biology, physiology, pathology, and food science. In this review, based on developments in analytical chemistry tools, cheminformatics, and bioinformatics methods, we highlight the current applications of metabolomics in food safety, food authenticity and quality, and food traceability. Additionally, the combined use of metabolomics with other omics techniques for "foodomics" is comprehensively described. Finally, the latest developments and advances, practical challenges and limitations, and requirements related to the application of metabolomics are critically discussed, providing new insight into the application of metabolomics in food analysis.
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Affiliation(s)
- Shubo Li
- College of Light Industry and Food Engineering, Guangxi University, Nanning, China
| | - Yufeng Tian
- College of Light Industry and Food Engineering, Guangxi University, Nanning, China
| | - Pingyingzi Jiang
- College of Light Industry and Food Engineering, Guangxi University, Nanning, China
| | - Ying Lin
- College of Light Industry and Food Engineering, Guangxi University, Nanning, China
| | - Xiaoling Liu
- College of Light Industry and Food Engineering, Guangxi University, Nanning, China
| | - Hongshun Yang
- Department of Food Science & Technology, National University of Singapore, Singapore, Singapore
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Christ B, Pluskal T, Aubry S, Weng JK. Contribution of Untargeted Metabolomics for Future Assessment of Biotech Crops. TRENDS IN PLANT SCIENCE 2018; 23:1047-1056. [PMID: 30361071 DOI: 10.1016/j.tplants.2018.09.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 08/14/2018] [Accepted: 09/24/2018] [Indexed: 05/20/2023]
Abstract
The nutritional value and safety of food crops are ultimately determined by their chemical composition. Recent developments in the field of metabolomics have made it possible to characterize the metabolic profile of crops in a comprehensive and high-throughput manner. Here, we propose that state-of-the-art untargeted metabolomics technology should be leveraged for safety assessment of new crop products. We suggest generally applicable experimental design principles that facilitate the efficient and rigorous identification of both intended and unintended metabolic alterations associated with a newly engineered trait. Our proposition could contribute to increased transparency of the safety assessment process for new biotech crops.
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Affiliation(s)
- Bastien Christ
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Tomáš Pluskal
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Sylvain Aubry
- Federal Office for Agriculture, 3003 Bern, Switzerland; Department of Plant and Microbial Biology, University of Zurich, 8008 Zurich, Switzerland.
| | - Jing-Ke Weng
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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Comparative compositional analysis of transgenic potato resistant to potato tuber moth (PTM) and its non-transformed counterpart. Transgenic Res 2018; 27:301-313. [PMID: 29728958 DOI: 10.1007/s11248-018-0075-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 04/27/2018] [Indexed: 10/17/2022]
Abstract
In this study, the compositions of transgenic potatoes (TPs) resistant to potato tuber moth (Phthorimaea operculella) were compared with those of its non-transgenic (NTP) counterparts. The light inducible promoter, phosphoenolpyruvate carboxylase led to the expression of Cry1Ab only in the leaves and light-treated tubers of the TPs. No significant differences were found in the moisture, ash, dry weight, total soluble protein, carbohydrate, starch, fiber, ascorbate, cations, anions, fatty acids, and glycoalkaloids contents of TP and NTP. Moreover, light treatment significantly affected the contents of ascorbate, acetate and nitrite anions, palmitic, stearic and linolenic fatty acids, α-haconine and α-solanine glycoalkaloids in TP and NTP tubers. While, significant differences were observed in the amino acid contents in light-treated tubers of TPs than the NTP ones. Although, light treatment in potato tubers resulted in marked metabolic changes, all the variations observed in the metabolites compositions were found to be within the desired reference ranges for potato plants. In conclusion, the results indicated that the TPs were substantially and nutritionally equivalent to the NTP counterparts.
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Mesnage R, Arno M, Séralini GE, Antoniou MN. Transcriptome and metabolome analysis of liver and kidneys of rats chronically fed NK603 Roundup-tolerant genetically modified maize. ENVIRONMENTAL SCIENCES EUROPE 2017; 29:6. [PMID: 28239534 PMCID: PMC5306156 DOI: 10.1186/s12302-017-0105-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 01/27/2017] [Indexed: 05/08/2023]
Abstract
BACKGROUND A previous 2-year rat feeding trial assessing potential toxicity of NK603 Roundup-tolerant genetically modified maize revealed blood and urine biochemical changes indicative of liver and kidney pathology. In an effort to obtain deeper insight into these findings, molecular profiling of the liver and kidneys from the same animals was undertaken. RESULTS Transcriptomics showed no segregation of NK603 maize and control feed groups with false discovery rates ranging from 43 to 83% at a cut-off p value of 1%. Changes in gene expression were not reflective of liver and kidney toxic effects. Metabolomics identified 692 and 673 metabolites in kidney and liver, respectively. None of the statistically significant disturbances detected (12-56 for different test groups) survived a false discovery rate analysis. Differences in these metabolites between individual animals within a group were greater than the effect of test diets, which prevents a definitive conclusion on either pathology or safety. CONCLUSIONS Even if the biological relevance of the statistical differences presented in this study is unclear, our results are made available for scrutiny by the scientific community and for comparison in future studies investigating potential toxicological properties of the NK603 corn.
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Affiliation(s)
- Robin Mesnage
- Department of Medical and Molecular Genetics, Gene Expression and Therapy Group, Faculty of Life Sciences & Medicine, King’s College London, 8th Floor, Tower Wing, Guy’s Hospital, Great Maze Pond, London, SE1 9RT UK
| | - Matthew Arno
- Genomics Centre, King’s College London, Waterloo Campus, 150 Stamford Street, London, SE1 9NH UK
| | - Gilles-Eric Séralini
- Institute of Biology, EA 2608 and Risk Pole, MRSH-CNRS, University of Caen, Esplanade de la Paix, 14032 Caen Cedex, France
| | - Michael N. Antoniou
- Department of Medical and Molecular Genetics, Gene Expression and Therapy Group, Faculty of Life Sciences & Medicine, King’s College London, 8th Floor, Tower Wing, Guy’s Hospital, Great Maze Pond, London, SE1 9RT UK
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Zhu M, Liu T, Guo M. Current Advances in the Metabolomics Study on Lotus Seeds. FRONTIERS IN PLANT SCIENCE 2016; 7:891. [PMID: 27379154 PMCID: PMC4913082 DOI: 10.3389/fpls.2016.00891] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2016] [Accepted: 06/06/2016] [Indexed: 05/08/2023]
Abstract
Lotus (Nelumbo nucifera), which is distributed widely throughout Asia, Australia and North America, is an aquatic perennial that has been cultivated for over 2,000 years. It is very stimulating that almost all parts of lotus have been consumed as vegetable as well as food, especially the seeds. Except for the nutritive values of lotus, there has been increasing interest in its potential as functional food due to its rich secondary metabolites, such as flavonoids and alkaloids. Not only have these metabolites greatly contributed to the biological process of lotus seeds, but also have been reported to possess multiple health-promoting effects, including antioxidant, anti-amnesic, anti-inflammatory, and anti-tumor activities. Thus, comprehensive metabolomic profiling of these metabolites is of key importance to help understand their biological activities, and other chemical biology features. In this context, this review will provide an update on the current technological platforms, and workflow associated with metabolomic studies on lotus seeds, as well as insights into the application of metabolomics for the improvement of food safety and quality, assisting breeding, and promotion of the study of metabolism and pharmacokinetics of lotus seeds; meanwhile it will also help explore new perspectives and outline future challenges in this fast-growing research subject.
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Affiliation(s)
- Mingzhi Zhu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden – Chinese Academy of SciencesWuhan, China
| | - Ting Liu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden – Chinese Academy of SciencesWuhan, China
| | - Mingquan Guo
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden – Chinese Academy of SciencesWuhan, China
- Sino-Africa Joint Research Center – Chinese Academy of SciencesWuhan, China
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Mariot RF, de Oliveira LA, Voorhuijzen MM, Staats M, Hutten RCB, van Dijk JP, Kok EJ, Frazzon J. Characterization and Transcriptional Profile of Genes Involved in Glycoalkaloid Biosynthesis in New Varieties of Solanum tuberosum L. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2016; 64:988-96. [PMID: 26768994 DOI: 10.1021/acs.jafc.5b05519] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Before commercial release, new potato (Solanum tuberosum) varieties must be evaluated for content of toxic compounds such as glycoalkaloids (GAs), which are potent poisons. GA biosynthesis proceeds via the cholesterol pathway to α-chaconine and α-solanine. The goal of this study was to evaluate the relationship between total glycoalkaloid (TGA) content and the expression of GAME, SGT1, and SGT3 genes in potato tubers. TGA content was measured by HPLC-MS, and reverse transcription quantitative polymerase chain reactions were performed to determine the relative expression of GAME, SGT1, and SGT3 genes. We searched for cis-elements of the transcription start site using the PlantPAN database. There was a relationship between TGA content and the relative expression of GAME, SGT1, and SGT3 genes in potato tubers. Putative promoter regions showed the presence of several cis-elements related to biotic and abiotic stresses and light. These findings provide an important step toward understanding TGA regulation and variation in potato tubers.
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Affiliation(s)
| | | | - Marleen M Voorhuijzen
- RIKILT Food Safety Institute, Wageningen University , 6708 PB Wageningen, The Netherlands
| | - Martijn Staats
- RIKILT Food Safety Institute, Wageningen University , 6708 PB Wageningen, The Netherlands
| | | | - Jeroen P van Dijk
- RIKILT Food Safety Institute, Wageningen University , 6708 PB Wageningen, The Netherlands
| | - Esther J Kok
- RIKILT Food Safety Institute, Wageningen University , 6708 PB Wageningen, The Netherlands
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Gayen D, Ghosh S, Paul S, Sarkar SN, Datta SK, Datta K. Metabolic Regulation of Carotenoid-Enriched Golden Rice Line. FRONTIERS IN PLANT SCIENCE 2016; 7:1622. [PMID: 27840631 PMCID: PMC5083848 DOI: 10.3389/fpls.2016.01622] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 10/13/2016] [Indexed: 05/21/2023]
Abstract
Vitamin A deficiency (VAD) is the leading cause of blindness among children and is associated with high risk of maternal mortality. In order to enhance the bioavailability of vitamin A, high carotenoid transgenic golden rice has been developed by manipulating enzymes, such as phytoene synthase (psy) and phytoene desaturase (crtI). In this study, proteome and metabolite analyses were carried out to comprehend metabolic regulation and adaptation of transgenic golden rice after the manipulation of endosperm specific carotenoid pathways. The main alteration was observed in carbohydrate metabolism pathways of the transgenic seeds. The 2D based proteomic studies demonstrated that carbohydrate metabolism-related enzymes, such as pullulanase, UDP-glucose pyrophosphorylase, and glucose-1-phosphate adenylyltransferase, were primarily up-regulated in transgenic rice seeds. In addition, the enzyme PPDK was also elevated in transgenic seeds thus enhancing pyruvate biosynthesis, which is the precursor in the carotenoids biosynthetic pathway. GC-MS based metabolite profiling demonstrated an increase in the levels of glyceric acid, fructo-furanose, and galactose, while decrease in galactonic acid and gentiobiose in the transgenic rice compared to WT. It is noteworthy to mention that the carotenoid content, especially β-carotene level in transgenic rice (4.3 μg/g) was significantly enhanced. The present study highlights the metabolic adaptation process of a transgenic golden rice line (homozygous T4 progeny of SKBR-244) after enhancing carotenoid biosynthesis. The presented information would be helpful in the development of crops enriched in carotenoids by expressing metabolic flux of pyruvate biosynthesis.
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Affiliation(s)
- Dipak Gayen
- Laboratory for Translational Research on Transgenic Crops, Department of Botany, University of CalcuttaKolkata, India
- National Institute of Plant Genome ResearchNew Delhi, India
| | - Subhrajyoti Ghosh
- Laboratory for Translational Research on Transgenic Crops, Department of Botany, University of CalcuttaKolkata, India
| | - Soumitra Paul
- Laboratory for Translational Research on Transgenic Crops, Department of Botany, University of CalcuttaKolkata, India
| | - Sailendra N. Sarkar
- Laboratory for Translational Research on Transgenic Crops, Department of Botany, University of CalcuttaKolkata, India
| | - Swapan K. Datta
- Laboratory for Translational Research on Transgenic Crops, Department of Botany, University of CalcuttaKolkata, India
- Department of Crop Sciences, Institute of Agriculture, Visva Bharati UniversitySantiniketan, India
| | - Karabi Datta
- Laboratory for Translational Research on Transgenic Crops, Department of Botany, University of CalcuttaKolkata, India
- *Correspondence: Karabi Datta
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Shepherd LVT, Hackett CA, Alexander CJ, McNicol JW, Sungurtas JA, McRae D, McCue KF, Belknap WR, Davies HV. Impact of light-exposure on the metabolite balance of transgenic potato tubers with modified glycoalkaloid biosynthesis. Food Chem 2015; 200:263-73. [PMID: 26830588 DOI: 10.1016/j.foodchem.2015.12.095] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 12/11/2015] [Accepted: 12/31/2015] [Indexed: 11/24/2022]
Abstract
Metabolite profiling (liquid chromatography-mass spectrometry (LC-MS) and gas chromatography (GC-MS)) was used to assess the impact of light on the composition of transgenic potato (Solanum tuberosum L. cv. Desirée) with reduced glycoalkaloid content via the down-regulation of the SGT1 gene. Transgenic tubers exhibited an almost complete knock-out of α-solanine production and light had little impact on its accumulation. Levels of α-chaconine increased significantly in the peel of both the control and transgenic lines when exposed to light, particularly in the transgenic line. Major differences in metabolite profiles existed between outer and inner tuber tissues, and between light and dark-treated tubers. Many of the light-induced changes are explicable in terms of pathways known to be affected by stress responses. The impact of transgenesis on profiles was much less than that of tissue type or light and most differences were explicable in terms of the modification to the glycoalkaloid pathway.
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Affiliation(s)
- Louise Vida Traill Shepherd
- Environmental and Biochemical Sciences Group, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, Scotland, United Kingdom.
| | - Christine Anne Hackett
- Biomathematics and Statistics Scotland, Invergowrie, Dundee DD2 5DA, Scotland, United Kingdom
| | - Colin James Alexander
- Biomathematics and Statistics Scotland, Invergowrie, Dundee DD2 5DA, Scotland, United Kingdom
| | - James William McNicol
- Biomathematics and Statistics Scotland, Invergowrie, Dundee DD2 5DA, Scotland, United Kingdom
| | - Julia Anne Sungurtas
- Environmental and Biochemical Sciences Group, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, Scotland, United Kingdom
| | - Diane McRae
- Environmental and Biochemical Sciences Group, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, Scotland, United Kingdom
| | - Kent Frank McCue
- USDA, Agricultural Research Service, Crop Improvement and Genetics, Western Regional Research Centre, 800 Buchanan St, Albany, CA 94710-1105, USA
| | - William Richardson Belknap
- USDA, Agricultural Research Service, Crop Improvement and Genetics, Western Regional Research Centre, 800 Buchanan St, Albany, CA 94710-1105, USA
| | - Howard Vivian Davies
- Environmental and Biochemical Sciences Group, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, Scotland, United Kingdom
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