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Lau H, Heng Tan L, Ying Ee L, Dayal H, Ying Lim S, Liu F, Yau Li SF. Application of 1H-NMR- and LC-MS based Metabolomic analysis for the evaluation of celery preservation methods. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.113938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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The Different Metabolic Responses of Resistant and Susceptible Wheats to Fusarium graminearum Inoculation. Metabolites 2022; 12:metabo12080727. [PMID: 36005599 PMCID: PMC9413380 DOI: 10.3390/metabo12080727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 07/29/2022] [Accepted: 07/31/2022] [Indexed: 11/23/2022] Open
Abstract
Fusarium head blight (FHB) is a serious wheat disease caused by Fusarium graminearum (Fg) Schwabe. FHB can cause huge loss in wheat yield. In addition, trichothecene mycotoxins produced by Fg are harmful to the environment and humans. In our previous study, we obtained two mutants TPS1− and TPS2−. Neither of these mutants could synthesize trehalose, and they produced fewer mycotoxins. To understand the complex interaction between Fg and wheat, we systematically analyzed the metabolic responses of FHB-susceptible and -resistant wheat to ddH2O, the TPS− mutants and wild type (WT) using NMR combined with multivariate analysis. More than 40 metabolites were identified in wheat extracts including sugars, amino acids, organic acids, choline metabolites and other metabolites. When infected by Fg, FHB-resistant and -susceptible wheat plants showed different metabolic responses. For FHB-resistant wheat, there were clear metabolic differences between inoculation with mutants (TPS1−/TPS2−) and with ddH2O/WT. For the susceptible wheat, there were obvious metabolic differences between inoculation with mutant (TPS1−/TPS2−) and inoculation with ddH2O; however, there were no significant metabolic differences between inoculation with TPS− mutants and with WT. Specifically, compared with ddH2O, resistant wheat increased the levels of Phe, p-hydroxy cinnamic acid (p-HCA), and chlorogenic acid in response to TPS− mutants; however, susceptible wheat did not. Shikimate-mediated secondary metabolism was activated in the FHB-resistant wheat to inhibit the growth of Fg and reduce the production of mycotoxins. These results can be helpful for the development of FHB-resistant wheat varieties, although the molecular relationship between the trehalose biosynthetic pathway in Fg and shikimate-mediated secondary metabolism in wheat remains to be further studied.
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Hu Q, Sun Y, Yuan P, Lei H, Zhong H, Wang Y, Tang H. Quantitative structure-retention relationship for reliable metabolite identification and quantification in metabolomics using ion-pair reversed-phase chromatography coupled with tandem mass spectrometry. Talanta 2022; 238:123059. [PMID: 34808567 DOI: 10.1016/j.talanta.2021.123059] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 11/09/2021] [Accepted: 11/10/2021] [Indexed: 10/19/2022]
Abstract
Hydrophilic metabolites are essential for all biological systems with multiple functions and their quantitative analysis forms an important part of metabolomics. However, poor retention of these metabolites on reversed-phase (RP) chromatographic column hinders their effective analysis with RPLC-MS methods. Herein, we developed a method for detecting hydrophilic metabolites using the ion-pair reversed-phase liquid-chromatography coupled with mass spectrometry (IPRP-LC-MS/MS) in scheduled multiple-reaction-monitoring (sMRM) mode. We first developed a hexylamine-based IPRP-UHPLC-QTOFMS method and experimentally measured retention time (tR) for 183 hydrophilic metabolites. We found that tRs of these metabolites were dominated by their electrostatic potential depending upon the numbers and types of their ionizable groups. We then systematically investigated the quantitative structure-retention relationship (QSRR) and constructed QSRR models using the measured tR. Subsequently, we developed a retention time predictive model using the random-forest regression algorithm (r2 = 0.93, q2 = 0.70, MAE = 1.28 min) for predicting metabolite retention time, which was applied in IPRP-UHPLC-MS/MS method in sMRM mode for quantitative metabolomic analysis. Our method can simultaneously quantify more than 260 metabolites. Moreover, we found that this method was applicable for multiple major biological matrices including biofluids and tissues. This approach offers an efficient method for large-scale quantitative hydrophilic metabolomic profiling even when metabolite standards are unavailable.
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Affiliation(s)
- Qingyu Hu
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Centre for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, China; State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Metabonomics and Systems Biology Laboratory at Shanghai International Centre for Molecular Phenomics, Zhongshan Hospital, Fudan University, Shanghai, 200032, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuting Sun
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Centre for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, China; State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Metabonomics and Systems Biology Laboratory at Shanghai International Centre for Molecular Phenomics, Zhongshan Hospital, Fudan University, Shanghai, 200032, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Peihong Yuan
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Centre for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, China; Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Hehua Lei
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Centre for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Huiqin Zhong
- Waters Technologies (Shanghai) Limited, 1000 Jinhai Road, Shanghai, 201206, China
| | - Yulan Wang
- Singapore Phenome Centre, Lee Kong Chian School of Medicine, Nanyang Technological University, 639798, Singapore.
| | - Huiru Tang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Metabonomics and Systems Biology Laboratory at Shanghai International Centre for Molecular Phenomics, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.
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4
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Gut microbiome and metabolic response in non-alcoholic fatty liver disease. Clin Chim Acta 2021; 523:304-314. [PMID: 34666025 DOI: 10.1016/j.cca.2021.10.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 09/19/2021] [Accepted: 10/13/2021] [Indexed: 12/12/2022]
Abstract
Fatty liver disease (FLD) is one of the largest burdens to human health worldwide and is associated with gut microbiome and metabolite stability. Engineered liver tissues have shown promise in restoring liver functions in non-alcoholic FLD (NAFLD), hepatitis and cirrhosis. Fatty liver, largely noted in obesity and hepatic cancer, is highly fatal and has led to a global increase in death rates. It is associated with complex metabolic reprogramming too. A standard approach to therapy in the newly diagnosed setting includes surgery or identification of biomarkers/ metabolites for therapeutic purposes, which ultimately focus on improvement of liver health in patients. As such there are no standard procedures for patient care, but depending on the severity, systemic therapy with either genomic, proteomic or metabolomic profiling form potential options. Better comparisons and study of underlying mechanisms in gut microbiome-based metabolic functions in obesity are urgently required. Today, an emerging field, focusing on metabolomic approaches and metabolic phenotyping, involved in high-throughput identification of metabolome in obesity and gut disorders, is involved in biomarker and metabolite identification. There are supporting technologies and approaches in NAFLD that throw light on the metabolites and gut microbiome, and also on the understanding of the risk factors of obesity along with liver cancer metabolic reaction networks. We discuss the current state of NAFLD metabolites, gut micro-environmental changes, and the further challenges in digital metabolomics profiling. Innovative clinical trial designs, with biomarker-enrichment strategies that are required to improve the outcome of NAFLD in patients are also discussed.
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Wei G, Sun H, Dong K, Hu L, Wang Q, Zhuang Q, Zhu Y, Zhang X, Shao Y, Tang H, Li Z, Chen S, Lu J, Wang Y, Gan X, Zhong TP, Gui D, Hu X, Wang L, Liu J. The thermogenic activity of adjacent adipocytes fuels the progression of ccRCC and compromises anti-tumor therapeutic efficacy. Cell Metab 2021; 33:2021-2039.e8. [PMID: 34508696 DOI: 10.1016/j.cmet.2021.08.012] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 07/08/2021] [Accepted: 08/17/2021] [Indexed: 01/18/2023]
Abstract
Clear cell renal cell carcinoma (ccRCC) preferentially invades into perinephric adipose tissue (PAT), a process associated with poor prognosis. However, the detailed mechanisms underlying this interaction remain elusive. Here, we describe a bi-directional communication between ccRCC cells and the PAT. We found that ccRCC cells secrete parathyroid-hormone-related protein (PTHrP) to promote the browning of PAT by PKA activation, while PAT-mediated thermogenesis results in the release of excess lactate to enhance ccRCC growth, invasion, and metastasis. Further, tyrosine kinase inhibitors (TKIs) extensively used in the treatment of ccRCC enhanced this vicious cycle of ccRCC-PAT communication by promoting the browning of PAT. However, if this cross-communication was short circuited by the pharmacological suppression of adipocyte browning via H89 or KT5720, the anti-tumor efficacy of the TKI, sunitinib, was enhanced. These results suggest that ccRCC-PAT cross-communication has important clinical relevance, and use of combined therapy holds great promise in enhancing the efficacy of TKIs.
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Affiliation(s)
- Gang Wei
- Shanghai Diabetes Institute, Department of Endocrinology and Metabolism, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai 200032, China
| | - Honglin Sun
- Shanghai Diabetes Institute, Department of Endocrinology and Metabolism, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai 200032, China
| | - Kai Dong
- Department of Urology, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Libing Hu
- Department of Urology, Yan'an Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650051, China
| | - Qi Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Metabonomics and Systems Biology Laboratory at Shanghai International Centre for Molecular Phenomics, Zhongshan Hospital, Fudan University, Shanghai 200438, China
| | - Qian Zhuang
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yan Zhu
- Department of Urology, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Xianjing Zhang
- Shanghai Diabetes Institute, Department of Endocrinology and Metabolism, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai 200032, China
| | - Yaodi Shao
- Shanghai Diabetes Institute, Department of Endocrinology and Metabolism, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai 200032, China
| | - Huiru Tang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Metabonomics and Systems Biology Laboratory at Shanghai International Centre for Molecular Phenomics, Zhongshan Hospital, Fudan University, Shanghai 200438, China
| | - Zhenfei Li
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Suzhen Chen
- Shanghai Diabetes Institute, Department of Endocrinology and Metabolism, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai 200032, China
| | - Junxi Lu
- Shanghai Diabetes Institute, Department of Endocrinology and Metabolism, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai 200032, China
| | - Yibing Wang
- School of Kinesiology, Shanghai University of Sport, Shanghai 200438, China
| | - Xinxin Gan
- Department of Urology, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Tao P Zhong
- Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Dingkun Gui
- Shanghai Diabetes Institute, Department of Endocrinology and Metabolism, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai 200032, China
| | - Xiaoyong Hu
- Shanghai Diabetes Institute, Department of Endocrinology and Metabolism, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai 200032, China
| | - Linhui Wang
- Department of Urology, Changhai Hospital, Naval Medical University, Shanghai 200433, China.
| | - Junli Liu
- Shanghai Diabetes Institute, Department of Endocrinology and Metabolism, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai 200032, China.
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Kaur B, Sandhu KS, Kamal R, Kaur K, Singh J, Röder MS, Muqaddasi QH. Omics for the Improvement of Abiotic, Biotic, and Agronomic Traits in Major Cereal Crops: Applications, Challenges, and Prospects. PLANTS 2021; 10:plants10101989. [PMID: 34685799 PMCID: PMC8541486 DOI: 10.3390/plants10101989] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 09/17/2021] [Accepted: 09/18/2021] [Indexed: 12/22/2022]
Abstract
Omics technologies, namely genomics, transcriptomics, proteomics, metabolomics, and phenomics, are becoming an integral part of virtually every commercial cereal crop breeding program, as they provide substantial dividends per unit time in both pre-breeding and breeding phases. Continuous advances in omics assure time efficiency and cost benefits to improve cereal crops. This review provides a comprehensive overview of the established omics methods in five major cereals, namely rice, sorghum, maize, barley, and bread wheat. We cover the evolution of technologies in each omics section independently and concentrate on their use to improve economically important agronomic as well as biotic and abiotic stress-related traits. Advancements in the (1) identification, mapping, and sequencing of molecular/structural variants; (2) high-density transcriptomics data to study gene expression patterns; (3) global and targeted proteome profiling to study protein structure and interaction; (4) metabolomic profiling to quantify organ-level, small-density metabolites, and their composition; and (5) high-resolution, high-throughput, image-based phenomics approaches are surveyed in this review.
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Affiliation(s)
- Balwinder Kaur
- Everglades Research and Education Center, University of Florida, 3200 E. Palm Beach Rd., Belle Glade, FL 33430, USA;
| | - Karansher S. Sandhu
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99163, USA;
| | - Roop Kamal
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466 Stadt Seeland, Germany; (R.K.); or (M.S.R.)
| | - Kawalpreet Kaur
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada;
| | - Jagmohan Singh
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India;
| | - Marion S. Röder
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466 Stadt Seeland, Germany; (R.K.); or (M.S.R.)
| | - Quddoos H. Muqaddasi
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466 Stadt Seeland, Germany; (R.K.); or (M.S.R.)
- Correspondence: or
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7
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Shi B, Ding H, Wang L, Wang C, Tian X, Fu Z, Zhang L, Han L. Investigation on the stability in plant metabolomics with a special focus on freeze-thaw cycles: LC-MS and NMR analysis to Cassiae Semen (Cassia obtusifolia L.) seeds as a case study. J Pharm Biomed Anal 2021; 204:114243. [PMID: 34273658 DOI: 10.1016/j.jpba.2021.114243] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 05/27/2021] [Accepted: 07/03/2021] [Indexed: 01/16/2023]
Abstract
Metabolomics is a rapid and sensitive tool for the detection of dynamic metabolic compositions in the study of systemic metabolic consequences. However, it is also susceptible to a tiny variation of pre-analytical handling procedures. To provide reproducible results, specific knowledge on metabolites perturbance along with different freeze-thaw cycles (FTCs) is needed for further metabolomics studies. In this paper, five FTCs of germinated Cassiae Semen (CS) were chosen as a case study to investigate the influence of FTC effect based on UHPLC-Q-Orbitrap-MS and NMR technologies. A total of 108 metabolites were relatively quantified by LC-MS and NMR analyses. Principal component analysis (PCA) showed that the first and second FTC samples are welly separated from the other groups; however, the extent of FTC-induced effects are smaller after the third cycle. Upon five consecutive FTCs, alterations which consisted of decreased stachyose, sucrose, norrubrofusarin-6-O-β-d-glucopyranoside, and quercetin 3-(3″-acetylgalactoside), as well as increased phenylalanine, leucine, isoleucine, methionine, phenylalanine, mannose, gluconic acid, and valine, could be observed. FTC does not exert the same effect on all metabolites. Although a large number of secondary metabolites were stable when subjected to five FTCs, FTC effects may lead to false-positive in the discovery of biomarker. In the case of reusing plant seed samples, no more than three consecutive freeze-thaw cycles were found advisable. This work provides unique perspectives on the FTC effects, which may fill in some existing gaps in the knowledge of the stability of plant metabolites during sample pre-handling.
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Affiliation(s)
- Biru Shi
- Tianjin State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai, Tianjin 301617, PR China
| | - Hui Ding
- Tianjin State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai, Tianjin 301617, PR China
| | - Liming Wang
- Tianjin State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai, Tianjin 301617, PR China; Tianjin Key Laboratory of TCM Chemistry and Analysis, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai, Tianjin 301617, PR China
| | - Chenxi Wang
- Tianjin State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai, Tianjin 301617, PR China; Tianjin Key Laboratory of TCM Chemistry and Analysis, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai, Tianjin 301617, PR China
| | - Xiaoxuan Tian
- Tianjin State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai, Tianjin 301617, PR China
| | - Zhifei Fu
- Tianjin State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai, Tianjin 301617, PR China; Tianjin Key Laboratory of TCM Chemistry and Analysis, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai, Tianjin 301617, PR China
| | - Lihua Zhang
- Tianjin State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai, Tianjin 301617, PR China; Tianjin Key Laboratory of TCM Chemistry and Analysis, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai, Tianjin 301617, PR China.
| | - Lifeng Han
- Tianjin State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai, Tianjin 301617, PR China; Tianjin Key Laboratory of TCM Chemistry and Analysis, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai, Tianjin 301617, PR China.
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Raja G, Jung Y, Jung SH, Kim TJ. 1H-NMR-based metabolomics for cancer targeting and metabolic engineering –A review. Process Biochem 2020. [DOI: 10.1016/j.procbio.2020.08.023] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Zuo J, Cai R, An Y, Tang H. Simultaneous Quantification of Five Stereoisomeric Hexoses in Nine Biological Matrices Using Ultrahigh Performance Liquid Chromatography with Tandem Mass Spectrometry. JOURNAL OF ANALYSIS AND TESTING 2020. [DOI: 10.1007/s41664-020-00142-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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Wang Y, Wu X, An Y, Xie H, Hao F, Tang H. Quantitative Metabonomic Phenotypes in Different Structures of Mung Bean ( Vigna radiata) Seeds and Their Germination-Associated Dynamic Changes. J Proteome Res 2020; 19:3352-3363. [PMID: 32498518 DOI: 10.1021/acs.jproteome.0c00236] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Plant seed germination involving dynamic water uptakes and biochemical changes is essential for preservation of plant germplasm resource and worldwide food supply. To understand the germination-associated compartmental biochemistry changes, we quantitatively analyzed the metabolite composition (metabonome) for embryonic axes, cotyledons, and testae of mung bean (Vigna radiata) seeds in three germination phases using the NMR-based metabonomics approach. We found that three structures of mung bean seeds had distinct metabonomic phenotypes dominated by 53 metabolites including amino acids, carbohydrates, organic acids, choline metabolites, nucleotides/nucleosides, and shikimate-mediated secondary metabolites together with calcium and magnesium cations. During germination, all three seed structures had outstanding but distinct metabonomic changes. Both embryonic axis and cotyledon showed remarkable metabolic changes related to degradation of carbohydrates and proteins, metabolism of amino acids, nucleotides/nucleosides, and choline together with energy metabolism and shikimate-mediated plant secondary metabolism. The metabonomic changes in these two structures were mostly related to multiple functions for biochemical activities in the former and nutrient mobilizations in the latter. In contrast, testa metabonomic changes mainly reflected the metabolite leakages from the other two structures. Phase 1 of germination was featured with degradation of oligosaccharides and proteins and recycling of stored nucleic acids together with anaerobic metabolisms, whereas phase 2 was dominated by energy metabolism, biosynthesis of osmolytes, and plant secondary metabolites. These provided essential metabolic information for understanding the biochemistry associated with early events of seed germination and possible metabolic functions of different seed structures for plant development.
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Affiliation(s)
- Yunlong Wang
- State Key Laboratory of Genetic Engineering, Zhongshan Hospital and School of Life Sciences, Human Phenome Institute, Metabonomics and Systems Biology Laboratory at Shanghai International Centre for Molecular Phenomics, Fudan University, Shanghai 200438, China
| | - Xiangyu Wu
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Yanpeng An
- State Key Laboratory of Genetic Engineering, Zhongshan Hospital and School of Life Sciences, Human Phenome Institute, Metabonomics and Systems Biology Laboratory at Shanghai International Centre for Molecular Phenomics, Fudan University, Shanghai 200438, China
| | - Hui Xie
- State Key Laboratory of Genetic Engineering, Zhongshan Hospital and School of Life Sciences, Human Phenome Institute, Metabonomics and Systems Biology Laboratory at Shanghai International Centre for Molecular Phenomics, Fudan University, Shanghai 200438, China
| | - Fuhua Hao
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Huiru Tang
- State Key Laboratory of Genetic Engineering, Zhongshan Hospital and School of Life Sciences, Human Phenome Institute, Metabonomics and Systems Biology Laboratory at Shanghai International Centre for Molecular Phenomics, Fudan University, Shanghai 200438, China.,State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China
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Wu X, Wang Y, Tang H. Quantitative Metabonomic Analysis Reveals the Germination-Associated Dynamic and Systemic Biochemical Changes for Mung-Bean ( Vigna radiata) Seeds. J Proteome Res 2020; 19:2457-2470. [PMID: 32393034 DOI: 10.1021/acs.jproteome.0c00181] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Seed germination is essential for plant survival, germplasm resource preservation, and worldwide food supplies, although the germination-associated seed biochemical variations are not fully understood. With the NMR-based metabonomics, we quantitatively analyzed the comprehensive metabolite composition (metabonome) of mung-bean (Vigna radiata) seeds at eight time points of germination covering all three phases. We found that mung-bean seed metabonomes were dominated by 63 metabolites including lipids, amino acids, oligo-/monosaccharides, cyclitols, cholines, organic acids, nucleotides/-sides, nicotinates, and the shikimate pathway-mediated secondary metabolites. During germination, metabolic changes included mainly the degradation of proteins and raffinose family oligosaccharides, glycolysis, tricarboxylic acid (TCA) cycle, anaerobic respiration, biosynthesis of osmolytes and antioxidants together with the metabolisms of nucleotides/-sides, nicotinates, and amino acids. Oligosaccharide degradation was the primary energy source for germination, which coupled with the mobilization of starch and protein storages to produce sugars and amino acids for biomaterial and energy generations. Osmotic and redox regulations were prerequisites for seed germination together with mitochondrial reparations and generations to enable TCA cycle. During the postgermination growth stage (phase-3), the use of small molecules including amino acids and saccharides was switched to meet the growth demands of radicle cells. Small metabolites passed freely through seed testa leaking into the culture media during early germination but were reabsorbed by seed cells around the postgermination growth stage. Extra after-ripening accelerated these metabolic processes of seeds in phase-1, especially the biosynthesis of cyclitols, choline, and nicotinates, increasing the germination uniformity in terms of speed and percentage. Germination-resistant seeds were incapable of activating the germination-associated metabolic processes.
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Affiliation(s)
- Xiangyu Wu
- State Key Laboratory of Genetic Engineering, Zhongshan Hospital and School of Life Sciences, Human Phenome Institute, Metabonomics and Systems Biology Laboratory at Shanghai International Centre for Molecular Phenomics, Fudan University, Shanghai 200438, P. R. China.,CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, CAS, Wuhan 430071, P. R. China
| | - Yunlong Wang
- State Key Laboratory of Genetic Engineering, Zhongshan Hospital and School of Life Sciences, Human Phenome Institute, Metabonomics and Systems Biology Laboratory at Shanghai International Centre for Molecular Phenomics, Fudan University, Shanghai 200438, P. R. China
| | - Huiru Tang
- State Key Laboratory of Genetic Engineering, Zhongshan Hospital and School of Life Sciences, Human Phenome Institute, Metabonomics and Systems Biology Laboratory at Shanghai International Centre for Molecular Phenomics, Fudan University, Shanghai 200438, P. R. China
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12
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Razzaq A, Sadia B, Raza A, Khalid Hameed M, Saleem F. Metabolomics: A Way Forward for Crop Improvement. Metabolites 2019; 9:E303. [PMID: 31847393 PMCID: PMC6969922 DOI: 10.3390/metabo9120303] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 12/02/2019] [Accepted: 12/11/2019] [Indexed: 12/15/2022] Open
Abstract
Metabolomics is an emerging branch of "omics" and it involves identification and quantification of metabolites and chemical footprints of cellular regulatory processes in different biological species. The metabolome is the total metabolite pool in an organism, which can be measured to characterize genetic or environmental variations. Metabolomics plays a significant role in exploring environment-gene interactions, mutant characterization, phenotyping, identification of biomarkers, and drug discovery. Metabolomics is a promising approach to decipher various metabolic networks that are linked with biotic and abiotic stress tolerance in plants. In this context, metabolomics-assisted breeding enables efficient screening for yield and stress tolerance of crops at the metabolic level. Advanced metabolomics analytical tools, like non-destructive nuclear magnetic resonance spectroscopy (NMR), liquid chromatography mass-spectroscopy (LC-MS), gas chromatography-mass spectrometry (GC-MS), high performance liquid chromatography (HPLC), and direct flow injection (DFI) mass spectrometry, have sped up metabolic profiling. Presently, integrating metabolomics with post-genomics tools has enabled efficient dissection of genetic and phenotypic association in crop plants. This review provides insight into the state-of-the-art plant metabolomics tools for crop improvement. Here, we describe the workflow of plant metabolomics research focusing on the elucidation of biotic and abiotic stress tolerance mechanisms in plants. Furthermore, the potential of metabolomics-assisted breeding for crop improvement and its future applications in speed breeding are also discussed. Mention has also been made of possible bottlenecks and future prospects of plant metabolomics.
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Affiliation(s)
- Ali Razzaq
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad 38040, Pakistan; (A.R.); (B.S.)
| | - Bushra Sadia
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad 38040, Pakistan; (A.R.); (B.S.)
| | - Ali Raza
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Wuhan 430062, China;
| | - Muhammad Khalid Hameed
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China;
| | - Fozia Saleem
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad 38040, Pakistan; (A.R.); (B.S.)
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13
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Mazzei P, Celano G, Palese AM, Lardo E, Drosos M, Piccolo A. HRMAS-NMR metabolomics of Aglianicone grapes pulp to evaluate terroir and vintage effects, and, as assessed by the electromagnetic induction (EMI) technique, spatial variability of vineyard soils. Food Chem 2019; 283:215-223. [DOI: 10.1016/j.foodchem.2019.01.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 01/04/2019] [Accepted: 01/06/2019] [Indexed: 12/21/2022]
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14
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Kumar D, Thakur K, Sharma S, Kumar S. NMR for metabolomics studies of Crataegus rhipidophylla Gand. Anal Bioanal Chem 2019; 411:2149-2159. [DOI: 10.1007/s00216-019-01646-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 01/21/2019] [Accepted: 01/25/2019] [Indexed: 01/01/2023]
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15
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Creydt M, Arndt M, Hudzik D, Fischer M. Plant Metabolomics: Evaluation of Different Extraction Parameters for Nontargeted UPLC-ESI-QTOF-Mass Spectrometry at the Example of White Asparagus officinalis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:12876-12887. [PMID: 30411896 DOI: 10.1021/acs.jafc.8b06037] [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] [Indexed: 05/19/2023]
Abstract
The extraction of metabolites turns out to be one of the most important key factors for nontargeted metabolomics approaches as this step can significantly affects the informative value of the successive measurements. Compared to metabolomics experiments of various matrices of bacterial or mammalian origins, there are only few studies, which focus on different extraction methods for plant metabolomics analyses. In this study, various solvent extraction compositions were compared and assessed using an UPLC-ESI-QTOF-MS strategy. Exemplary, white asparagus ( Asparagus officinalis) were employed as a low-fat-, low-protein-, high-water-content model commodity with the objective of designing an optimal nontargeted extraction protocol for polar and nonpolar metabolites. Furthermore, the influence of acid addition, mechanical cell disruption methods (ball mill, ultrasonic bath, vortex mixer), and extract stability have been systematically scrutinized too. The different extraction protocols were compared based on sum of features, sum of peak intensities, sum of peak areas, as well as by analyzing individual signals of as many different substance groups as possible to obtain a maximum overview.
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Affiliation(s)
- Marina Creydt
- Hamburg School of Food Science, Institute of Food Chemistry , University of Hamburg , Grindelallee 117 , 20146 Hamburg , Germany
| | - Maike Arndt
- Hamburg School of Food Science, Institute of Food Chemistry , University of Hamburg , Grindelallee 117 , 20146 Hamburg , Germany
| | - Daria Hudzik
- Hamburg School of Food Science, Institute of Food Chemistry , University of Hamburg , Grindelallee 117 , 20146 Hamburg , Germany
| | - Markus Fischer
- Hamburg School of Food Science, Institute of Food Chemistry , University of Hamburg , Grindelallee 117 , 20146 Hamburg , Germany
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16
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Wang Q, Zeng S, Wu X, Lei H, Wang Y, Tang H. Interspecies Developmental Differences in Metabonomic Phenotypes of Lycium ruthenicum and L. barbarum Fruits. J Proteome Res 2018; 17:3223-3236. [DOI: 10.1021/acs.jproteome.8b00349] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Qi Wang
- State Key Laboratory of Genetic Engineering, Zhongshan Hospital and School of Life Sciences, Human Phenome Institute, Metabonomics and Systems Biology Laboratory at Shanghai International Centre for Molecular Phenomics, Fudan University, Shanghai 200438, China
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, University of Chinese Academy of Sciences, Wuhan, Hubei 430071, China
| | - Shaohua Zeng
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong 510650, China
| | - Xiangyu Wu
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, University of Chinese Academy of Sciences, Wuhan, Hubei 430071, China
| | - Hehua Lei
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, University of Chinese Academy of Sciences, Wuhan, Hubei 430071, China
| | - Ying Wang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong 510650, China
| | - Huiru Tang
- State Key Laboratory of Genetic Engineering, Zhongshan Hospital and School of Life Sciences, Human Phenome Institute, Metabonomics and Systems Biology Laboratory at Shanghai International Centre for Molecular Phenomics, Fudan University, Shanghai 200438, China
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, University of Chinese Academy of Sciences, Wuhan, Hubei 430071, China
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17
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Transformed Root Culture: From Genetic Transformation to NMR-Based Metabolomics. Methods Mol Biol 2018. [PMID: 29981142 DOI: 10.1007/978-1-4939-8594-4_32] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Hairy root (HR) culture is considered as "green factory" for mass production of bioactive molecules with pharmaceutical relevance. As such, HR culture has an immense potential as a valuable platform to elucidate biosynthetic pathways and physiological processes, generate recombinant therapeutic proteins, assist molecular breeding, and enhance phytoremediation efforts. However, some plant species appear recalcitrant to the classical Agrobacterium rhizogenes transformation techniques. Sonication-assisted Agrobacterium-mediated transformation (SAArT) is a highly effective method to deliver bacteria to target plant tissues that includes exposure of the explants to short periods of ultrasound in the presence of the bacteria.Nuclear magnetic resonance (NMR)-based metabolomics is one of the most powerful and suitable platforms for identifying and obtaining structural information on a wide range of compounds with a high analytical precision. In terms of plant science, NMR metabolomics is used to determine the phytochemical variations of medicinal plants or commercial cultivars in certain environments and conditions, including biotic stress and plant biotic interaction, structural determination of natural products, quality control of herbal drugs or dietary supplements, and comparison of metabolite differences between plants and their respective in vitro cultures.In this chapter, we attempt to summarize our knowledge and expertise in induction of hairy roots from rare and recalcitrant plant species by SAArT technique and further methodology for extraction of secondary metabolites of moderate to high polarity and their identification by using NMR-based metabolomics.
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18
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Mazzei P, Cozzolino V, Piccolo A. High-Resolution Magic-Angle-Spinning NMR and Magnetic Resonance Imaging Spectroscopies Distinguish Metabolome and Structural Properties of Maize Seeds from Plants Treated with Different Fertilizers and Arbuscular mycorrhizal fungi. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:2580-2588. [PMID: 29323890 DOI: 10.1021/acs.jafc.7b04340] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Both high-resolution magic-angle-spinning (HRMAS) and magnetic resonance imaging (MRI) NMR spectroscopies were applied here to identify the changes of metabolome, morphology, and structural properties induced in seeds (caryopses) of maize plants grown at field level under either mineral or compost fertilization in combination with the inoculation by arbuscular mycorrhizal fungi (AMF). The metabolome of intact caryopses was examined by HRMAS-NMR, while the morphological aspects, endosperm properties and seed water distribution were investigated by MRI. Principal component analysis (PCA) was applied to evaluate 1H CPMG (Carr-Purcel-Meiboom-Gill) HRMAS spectra as well as several MRI-derived parameters ( T1, T2, and self-diffusion coefficients) of intact maize caryopses. PCA score-plots from spectral results indicated that both seeds metabolome and structural properties depended on the specific field treatment undergone by maize plants. Our findings show that a combination of multivariate statistical analyses with advanced and nondestructive NMR techniques, such as HRMAS and MRI, enables the evaluation of the effects induced on maize caryopses by different fertilization and management practices at field level. The spectroscopic approach adopted here may become useful for the objective appraisal of the quality of seeds produced under a sustainable agriculture.
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19
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Longobardi F, Innamorato V, Di Gioia A, Ventrella A, Lippolis V, Logrieco AF, Catucci L, Agostiano A. Geographical origin discrimination of lentils (Lens culinaris Medik.) using 1H NMR fingerprinting and multivariate statistical analyses. Food Chem 2017; 237:743-748. [DOI: 10.1016/j.foodchem.2017.05.159] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 05/25/2017] [Accepted: 05/31/2017] [Indexed: 11/27/2022]
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20
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Mumtaz MW, Hamid AA, Akhtar MT, Anwar F, Rashid U, AL-Zuaidy MH. An overview of recent developments in metabolomics and proteomics – phytotherapic research perspectives. FRONTIERS IN LIFE SCIENCE 2017. [DOI: 10.1080/21553769.2017.1279573] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Muhammad Waseem Mumtaz
- Department of Food Science, Faculty of Food Science and Technology, Universiti Putra Malaysia, Serdang, Malaysia
- Department of Chemistry, Faculty of Science, University of Gujrat, Gujrat, Pakistan
| | - Azizah Abdul Hamid
- Department of Food Science, Faculty of Food Science and Technology, Universiti Putra Malaysia, Serdang, Malaysia
| | - Muhammad Tayyab Akhtar
- Institute of Bioscience, Laboratory of Natural Products, Universiti Putra Malaysia, Serdang, Malaysia
| | - Farooq Anwar
- Department of Chemistry, University of Sargodha, Sargodha, Pakistan
| | - Umer Rashid
- Institute of Advanced Technology, Universiti Putra Malaysia, Serdang, Malaysia
| | - Mizher Hezam AL-Zuaidy
- Department of Food Science, Faculty of Food Science and Technology, Universiti Putra Malaysia, Serdang, Malaysia
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21
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Klein-Júnior LC, Viaene J, Salton J, Koetz M, Gasper AL, Henriques AT, Vander Heyden Y. The use of chemometrics to study multifunctional indole alkaloids from Psychotria nemorosa (Palicourea comb. nov.). Part I: Extraction and fractionation optimization based on metabolic profiling. J Chromatogr A 2016; 1463:60-70. [DOI: 10.1016/j.chroma.2016.07.030] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 07/08/2016] [Accepted: 07/11/2016] [Indexed: 12/24/2022]
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22
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Mazzei P, Vinale F, Woo SL, Pascale A, Lorito M, Piccolo A. Metabolomics by Proton High-Resolution Magic-Angle-Spinning Nuclear Magnetic Resonance of Tomato Plants Treated with Two Secondary Metabolites Isolated from Trichoderma. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2016; 64:3538-45. [PMID: 27088924 DOI: 10.1021/acs.jafc.6b00801] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Trichoderma fungi release 6-pentyl-2H-pyran-2-one (1) and harzianic acid (2) secondary metabolites to improve plant growth and health protection. We isolated metabolites 1 and 2 from Trichoderma strains, whose different concentrations were used to treat seeds of Solanum lycopersicum. The metabolic profile in the resulting 15 day old tomato leaves was studied by high-resolution magic-angle-spinning nuclear magnetic resonance (HRMAS NMR) spectroscopy directly on the whole samples without any preliminary extraction. Principal component analysis (PCA) of HRMAS NMR showed significantly enhanced acetylcholine and γ-aminobutyric acid (GABA) content accompanied by variable amount of amino acids in samples treated with both Trichoderma secondary metabolites. Seed germination rates, seedling fresh weight, and the metabolome of tomato leaves were also dependent upon doses of metabolites 1 and 2 treatments. HRMAS NMR spectroscopy was proven to represent a rapid and reliable technique for evaluating specific changes in the metabolome of plant leaves and calibrating the best concentration of bioactive compounds required to stimulate plant growth.
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Affiliation(s)
- Pierluigi Mazzei
- Centro Interdipartimentale per la Risonanza Magnetica Nucleare per l'Ambiente, l'Agro-Alimentare ed i Nuovi Materiali (CERMANU), Università di Napoli Federico II , Via Università 100, 80055 Portici, Città Metropolitana di Napoli, Italy
| | - Francesco Vinale
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche (CNR) , Via Università 133, 80055 Portici, Città Metropolitana di Napoli, Italy
| | - Sheridan Lois Woo
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche (CNR) , Via Università 133, 80055 Portici, Città Metropolitana di Napoli, Italy
- Dipartimento di Agraria, Università degli Studi di Napoli Federico II , Via Università 100, 80055 Portici, Città Metropolitana di Napoli, Italy
| | - Alberto Pascale
- Dipartimento di Agraria, Università degli Studi di Napoli Federico II , Via Università 100, 80055 Portici, Città Metropolitana di Napoli, Italy
| | - Matteo Lorito
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche (CNR) , Via Università 133, 80055 Portici, Città Metropolitana di Napoli, Italy
- Dipartimento di Agraria, Università degli Studi di Napoli Federico II , Via Università 100, 80055 Portici, Città Metropolitana di Napoli, Italy
| | - Alessandro Piccolo
- Centro Interdipartimentale per la Risonanza Magnetica Nucleare per l'Ambiente, l'Agro-Alimentare ed i Nuovi Materiali (CERMANU), Università di Napoli Federico II , Via Università 100, 80055 Portici, Città Metropolitana di Napoli, Italy
- Dipartimento di Agraria, Università degli Studi di Napoli Federico II , Via Università 100, 80055 Portici, Città Metropolitana di Napoli, Italy
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23
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Liu C, Ding F, Hao F, Yu M, Lei H, Wu X, Zhao Z, Guo H, Yin J, Wang Y, Tang H. Reprogramming of Seed Metabolism Facilitates Pre-harvest Sprouting Resistance of Wheat. Sci Rep 2016; 6:20593. [PMID: 26860057 PMCID: PMC4748292 DOI: 10.1038/srep20593] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 01/07/2016] [Indexed: 12/14/2022] Open
Abstract
Pre-harvest sprouting (PHS) is a worldwide problem for wheat production and transgene antisense-thioredoxin-s (anti-trx-s) facilitates outstanding resistance. To understand the molecular details of PHS resistance, we analyzed the metabonomes of the transgenic and wild-type (control) wheat seeds at various stages using NMR and GC-FID/MS. 60 metabolites were dominant in these seeds including sugars, organic acids, amino acids, choline metabolites and fatty acids. At day-20 post-anthesis, only malate level in transgenic wheat differed significantly from that in controls whereas at day-30 post-anthesis, levels of amino acids and sucrose were significantly different between these two groups. For mature seeds, most metabolites in glycolysis, TCA cycle, choline metabolism, biosynthesis of proteins, nucleotides and fatty acids had significantly lower levels in transgenic seeds than in controls. After 30-days post-harvest ripening, most metabolites in transgenic seeds had higher levels than in controls including amino acids, sugars, organic acids, fatty acids, choline metabolites and NAD+. These indicated that anti-trx-s lowered overall metabolic activities of mature seeds eliminating pre-harvest sprouting potential. Post-harvest ripening reactivated the metabolic activities of transgenic seeds to restore their germination vigor. These findings provided essential molecular phenomic information for PHS resistance of anti-trx-s and a credible strategy for future developing PHS resistant crops.
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Affiliation(s)
- Caixiang Liu
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Centre for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, the Chinese Academy of Sciences, Wuhan 430071, China
| | - Feng Ding
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Fuhua Hao
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Centre for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, the Chinese Academy of Sciences, Wuhan 430071, China
| | - Men Yu
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Centre for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, the Chinese Academy of Sciences, Wuhan 430071, China.,Wuhan Zhongke Metaboss Ltd, 128 Guang-Gu-Qi-Lu, Wuhan 430074, China
| | - Hehua Lei
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Centre for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, the Chinese Academy of Sciences, Wuhan 430071, China
| | - Xiangyu Wu
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Centre for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, the Chinese Academy of Sciences, Wuhan 430071, China
| | - Zhengxi Zhao
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Hongxiang Guo
- National Engineering Research Center for Wheat, Henan Agricultural University, Zhengzhou 450002, China
| | - Jun Yin
- National Engineering Research Center for Wheat, Henan Agricultural University, Zhengzhou 450002, China
| | - Yulan Wang
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Centre for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, the Chinese Academy of Sciences, Wuhan 430071, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou 310058, China
| | - Huiru Tang
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Centre for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, the Chinese Academy of Sciences, Wuhan 430071, China.,State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Developmental Biology, Metabonomics and Systems Biology Laboratory, School of Life Sciences, Fudan University, Shanghai 200438, China
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24
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Wei D, Chen D, Lou Y, Ye Y, Yang R. Metabolomic Profile Characteristics of Pyropia haitanensis as Affected by Harvest Time. FOOD SCIENCE AND TECHNOLOGY RESEARCH 2016. [DOI: 10.3136/fstr.22.529] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Dandan Wei
- School of Marine Sciences, Ningbo University
| | - Daian Chen
- School of Marine Sciences, Ningbo University
| | | | - Yangfang Ye
- School of Marine Sciences, Ningbo University
| | - Rui Yang
- School of Marine Sciences, Ningbo University
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25
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Kumar D. Nuclear Magnetic Resonance (NMR) Spectroscopy For Metabolic Profiling of Medicinal Plants and Their Products. Crit Rev Anal Chem 2015; 46:400-12. [PMID: 26575437 DOI: 10.1080/10408347.2015.1106932] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
NMR spectroscopy has multidisciplinary applications, including excellent impact in metabolomics. The analytical capacity of NMR spectroscopy provides information for easy qualitative and quantitative assessment of both endogenous and exogenous metabolites present in biological samples. The complexity of a particular metabolite and its contribution in a biological system are critically important for understanding the functional state that governs the organism's phenotypes. This review covers historical aspects of developments in the NMR field, its applications in chemical profiling, metabolomics, and quality control of plants and their derived medicines, foods, and other products. The bottlenecks of NMR in metabolic profiling are also discussed, keeping in view the future scope and further technological interventions.
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Affiliation(s)
- Dinesh Kumar
- a Natural Product Chemistry and Process Development Division, CSIR-Institute of Himalayan Bioresource Technology , Palampur , India
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26
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Li N, Song YP, Tang H, Wang Y. Recent developments in sample preparation and data pre-treatment in metabonomics research. Arch Biochem Biophys 2015; 589:4-9. [PMID: 26342458 DOI: 10.1016/j.abb.2015.08.024] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 08/27/2015] [Accepted: 08/30/2015] [Indexed: 12/13/2022]
Abstract
Metabonomics is a powerful approach for biomarker discovery and an effective tool for pinpointing endpoint metabolic effects of external stimuli, such as pathogens and disease development. Due to its wide applications, metabonomics is required to deal with various biological samples of different properties. Hence sample preparation and corresponding data pre-treatment become important factors in ensuring validity of an investigation. In this review, we summarize some recent developments in metabonomics sample preparation and data-pretreatment procedures.
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Affiliation(s)
- Ning Li
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Centre for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, PR China
| | - Yi peng Song
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Centre for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, PR China
| | - Huiru Tang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Centre for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, PR China; State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Metabolomics and Systems Biology Laboratory, School of Life Sciences, Fudan University, Shanghai 200433, PR China
| | - Yulan Wang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Centre for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, PR China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, PR China.
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27
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Lesiak AD, Cody RB, Dane AJ, Musah RA. Plant Seed Species Identification from Chemical Fingerprints: A High-Throughput Application of Direct Analysis in Real Time Mass Spectrometry. Anal Chem 2015; 87:8748-57. [DOI: 10.1021/acs.analchem.5b01611] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Ashton D. Lesiak
- Department
of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States
| | - Robert B. Cody
- JEOL USA Inc., 11 Dearborn
Road, Peabody, Massachusetts 01960, United States
| | - A. John Dane
- JEOL USA Inc., 11 Dearborn
Road, Peabody, Massachusetts 01960, United States
| | - Rabi A. Musah
- Department
of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States
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28
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Tsogtbaatar E, Cocuron JC, Sonera MC, Alonso AP. Metabolite fingerprinting of pennycress (Thlaspi arvense L.) embryos to assess active pathways during oil synthesis. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:4267-77. [PMID: 25711705 PMCID: PMC4493779 DOI: 10.1093/jxb/erv020] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Pennycress (Thlaspi arvense L.), a plant naturalized to North America, accumulates high levels of erucic acid in its seeds, which makes it a promising biodiesel and industrial crop. The main carbon sinks in pennycress embryos were found to be proteins, fatty acids, and cell wall, which respectively represented 38.5, 33.2, and 27.0% of the biomass at 21 days after pollination. Erucic acid reached a maximum of 36% of the total fatty acids. Together these results indicate that total oil and erucic acid contents could be increased to boost the economic competitiveness of this crop. Understanding the biochemical basis of oil synthesis in pennycress embryos is therefore timely and relevant to guide future breeding and/or metabolic engineering efforts. For this purpose, a combination of metabolomics approaches was conducted to assess the active biochemical pathways during oil synthesis. First, gas chromatography-mass spectrometry (GC-MS) profiling of intracellular metabolites highlighted three main families of compounds: organic acids, amino acids, and sugars/sugar alcohols. Secondly, these intermediates were quantified in developing pennycress embryos by liquid chromatography-tandem mass spectrometry (LC-MS/MS) in multiple reaction monitoring mode. Finally, partitional clustering analysis grouped the intracellular metabolites that shared a similar pattern of accumulation over time into eight clusters. This study underlined that: (i) sucrose might be stored rather than cleaved into hexoses; (ii) glucose and glutamine would be the main sources of carbon and nitrogen, respectively; and (iii) glycolysis, the oxidative pentose phosphate pathway, the tricarboxylic acid cycle, and the Calvin cycle were active in developing pennycress embryos.
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Affiliation(s)
- Enkhtuul Tsogtbaatar
- The Ohio State University, Department of Molecular Genetics, Columbus, OH 43210, USA
| | - Jean-Christophe Cocuron
- The Ohio State University, Department of Molecular Genetics, Columbus, OH 43210, USA The Ohio State University, Center for Applied Plant Sciences, Columbus, OH 43210, USA
| | - Marcos Corchado Sonera
- University of Puerto Rico, Mechanical Engineering Department, Mayagüez, 00681-9000, Puerto Rico
| | - Ana Paula Alonso
- The Ohio State University, Department of Molecular Genetics, Columbus, OH 43210, USA
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