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Liu J, Meng Z, Liu B, Wang J, Zhang H, Ai L, Guan J, Niu L. Application of a metabolomics method in the study of pear fruit storage. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024. [PMID: 39392403 DOI: 10.1039/d4ay01368a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/12/2024]
Abstract
The entire transportation process of 'crown' pears from harvest to consumption is primarily refrigerated. However, the impact of refrigeration time and temperature on fruit quality remains unclear. In this study, metabolites of 'crown' pears were analyzed using UHPLC-Q-Exactive and GC-MS/MS techniques under cold storage, at room temperature, and at different cold storage durations. A total of 372 substances were identified, including sugars, amino acids, and flavonoids, among others. Among these substances, 27 were identified as significant biomarkers affecting pear quality. An accurate quantitative method for amino acids was established to systematically verify the change trend of L-aspartic amide, glycine, glutamic acid, and other amino acids. The results indicated that after 30 days of storage at 0 °C, there was a relatively small change in the quality and substance content of 'crown' pears with little effect on their nutritional value. These findings could serve as a reference for optimizing the refrigeration time and temperature for pear fruit.
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Affiliation(s)
- Jing Liu
- School of Public Health, Hebei Medical University, Shijiazhuang 050017, China.
| | - Zixuan Meng
- School of Public Health, Hebei Medical University, Shijiazhuang 050017, China.
| | - Baoru Liu
- Shijiazhuang Customs Technology Center, Shijiazhuang 050051, China
| | - Jing Wang
- Shijiazhuang Customs Technology Center, Shijiazhuang 050051, China
| | - Haichao Zhang
- Shijiazhuang Customs Technology Center, Shijiazhuang 050051, China
| | - Lianfeng Ai
- School of Public Health, Hebei Medical University, Shijiazhuang 050017, China.
- Shijiazhuang Customs Technology Center, Shijiazhuang 050051, China
| | - Junfeng Guan
- Heibei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050017, China.
| | - Lingmei Niu
- School of Public Health, Hebei Medical University, Shijiazhuang 050017, China.
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2
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Estêvão C, Rodrigues L, Rato AE, Garcia R, Cardoso H, Campos C. Applicability of metabolomics to improve sustainable grapevine production. Front Mol Biosci 2024; 11:1395677. [PMID: 39310375 PMCID: PMC11413592 DOI: 10.3389/fmolb.2024.1395677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 08/12/2024] [Indexed: 09/25/2024] Open
Abstract
Metabolites represent the end product of gene expression, protein interaction and other regulatory mechanisms. The metabolome reflects a biological system's response to genetic and environmental changes, providing a more accurate description of plants' phenotype than the transcriptome or the proteome. Grapevine (Vitis vinifera L.), established for the production of wine grapes, table grapes, and raisins, holds immense agronomical and economic significance not only in the Mediterranean region but worldwide. As all plants, grapevines face the adverse impact of biotic and abiotic stresses that negatively affect multiple stages of grape and wine industry, including plant and berry development pre- and post-harvest, fresh grapes processing and consequently wine quality. In the present review we highlight the applicability of metabolome analysis in the understanding of the mechanisms involved in grapevine response and acclimatization upon the main biotic and abiotic constrains. The metabolome of induced morphogenic processes such as adventitious rooting and somatic embryogenesis is also explored, as it adds knowledge on the physiological and molecular phenomena occurring in the explants used, and on the successfully propagation of grapevines with desired traits. Finally, the microbiome-induced metabolites in grapevine are discussed in view of beneficial applications derived from the plant symbioses.
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Affiliation(s)
- Catarina Estêvão
- MED—Mediterranean Institute for Agriculture, Environment and Development & CHANGE—Global Change and Sustainability Institute, Institute for Advanced Studies and Research, Universidade de Évora, Pólo da Mitra, Évora, Portugal
| | - Lénia Rodrigues
- MED—Mediterranean Institute for Agriculture, Environment and Development & CHANGE—Global Change and Sustainability Institute, Institute for Advanced Studies and Research, Universidade de Évora, Pólo da Mitra, Évora, Portugal
| | - Ana Elisa Rato
- MED—Mediterranean Institute for Agriculture, Environment and Development & CHANGE—Global Change and Sustainability Institute, Departamento de Fitotecnia, Escola de Ciências e Tecnologia, Universidade de Évora, Pólo da Mitra, Évora, Portugal
| | - Raquel Garcia
- MED—Mediterranean Institute for Agriculture, Environment and Development & CHANGE—Global Change and Sustainability Institute, Departamento de Fitotecnia, Escola de Ciências e Tecnologia, Universidade de Évora, Pólo da Mitra, Évora, Portugal
| | - Hélia Cardoso
- MED—Mediterranean Institute for Agriculture, Environment and Development & CHANGE—Global Change and Sustainability Institute, Departamento de Biologia, Escola de Ciências e Tecnologia, Universidade de Évora, Pólo da Mitra, Évora, Portugal
| | - Catarina Campos
- MED—Mediterranean Institute for Agriculture, Environment and Development & CHANGE—Global Change and Sustainability Institute, Institute for Advanced Studies and Research, Universidade de Évora, Pólo da Mitra, Évora, Portugal
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Rolli E, Ghitti E, Mapelli F, Borin S. Polychlorinated biphenyls modify Arabidopsis root exudation pattern to accommodate degrading bacteria, showing strain and functional trait specificity. FRONTIERS IN PLANT SCIENCE 2024; 15:1429096. [PMID: 39036359 PMCID: PMC11258928 DOI: 10.3389/fpls.2024.1429096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 06/13/2024] [Indexed: 07/23/2024]
Abstract
Introduction The importance of plant rhizodeposition to sustain microbial growth and induce xenobiotic degradation in polluted environments is increasingly recognized. Methods Here the "cry-for-help" hypothesis, consisting in root chemistry remodeling upon stress, was investigated in the presence of polychlorinated biphenyls (PCBs), highly recalcitrant and phytotoxic compounds, highlighting its role in reshaping the nutritional and signaling features of the root niche to accommodate PCB-degrading microorganisms. Results Arabidopsis exposure to 70 µM PCB-18 triggered plant-detrimental effects, stress-related traits, and PCB-responsive gene expression, reproducing PCB phytotoxicity. The root exudates of plantlets exposed for 2 days to the pollutant were collected and characterized through untargeted metabolomics analysis by liquid chromatography-mass spectrometry. Principal component analysis disclosed a different root exudation fingerprint in PCB-18-exposed plants, potentially contributing to the "cry-for-help" event. To investigate this aspect, the five compounds identified in the exudate metabolomic analysis (i.e., scopoletin, N-hydroxyethyl-β-alanine, hypoxanthine, L-arginyl-L-valine, and L-seryl-L-phenylalanine) were assayed for their influence on the physiology and functionality of the PCB-degrading strains Pseudomonas alcaliphila JAB1, Paraburkholderia xenovorans LB400, and Acinetobacter calcoaceticus P320. Scopoletin, whose relative abundance decreased in PCB-18-stressed plant exudates, hampered the growth and proliferation of strains JAB1 and P320, presumably due to its antimicrobial activity, and reduced the beneficial effect of Acinetobacter P320, which showed a higher degree of growth promotion in the scopoletin-depleted mutant f6'h1 compared to Arabidopsis WT plants exposed to PCB. Nevertheless, scopoletin induced the expression of the bph catabolic operon in strains JAB1 and LB400. The primary metabolites hypoxanthine, L-arginyl-L-valine, and L-seryl-L-phenylalanine, which increased in relative abundance upon PCB-18 stress, were preferentially used as nutrients and growth-stimulating factors by the three degrading strains and showed a variable ability to affect rhizocompetence traits like motility and biofilm formation. Discussion These findings expand the knowledge on PCB-triggered "cry-for-help" and its role in steering the PCB-degrading microbiome to boost the holobiont fitness in polluted environments.
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Affiliation(s)
| | | | | | - Sara Borin
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Milan, Italy
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Yang L, Teng Y, Bu S, Ma B, Guo S, Liang M, Huang L. Effect of SlSAHH2 on metabolites in over-expressed and wild-type tomato fruit. PeerJ 2024; 12:e17466. [PMID: 38827284 PMCID: PMC11143970 DOI: 10.7717/peerj.17466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 05/05/2024] [Indexed: 06/04/2024] Open
Abstract
Background Tomato (Solanum lycopersicum) is an annual or perennial herb that occupies an important position in daily agricultural production. It is an essential food crop for humans and its ripening process is regulated by a number of genes. S-adenosyl-l-homocysteine hydrolase (AdoHcyase, EC 3.3.1.1) is widespread in organisms and plays an important role in regulating biological methylation reactions. Previous studies have revealed that transgenic tomato that over-express SlSAHH2 ripen earlier than the wild-type (WT). However, the differences in metabolites and the mechanisms driving how these differences affect the ripening cycle are unclear. Objective To investigate the effects of SlSAHH2 on metabolites in over-expressed tomato and WT tomato. Methods SlSAHH2 over-expressed tomato fruit (OE-5# and OE-6#) and WT tomato fruit at the breaker stage (Br) were selected for non-targeted metabolome analysis. Results A total of 733 metabolites were identified by mass spectrometry using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database and the Human Metabolome database (HMDB). The metabolites were divided into 12 categories based on the superclass results and a comparison with the HMDB. The differences between the two databases were analyzed by PLS-DA. Based on a variable important in projection value >1 and P < 0.05, 103 differential metabolites were found between tomato variety OE-5# and WT and 63 differential metabolites were found between OE-6# and WT. These included dehydrotomatine, L-serine, and gallic acid amongst others. Many metabolites are associated with fruit ripening and eight common metabolites were found between the OE-5# vs. WT and OE-6# vs. WT comparison groups. The low L-tryptophan expression in OE-5# and OE-6# is consistent with previous reports that its content decreases with fruit ripening. A KEGG pathway enrichment analysis of the significantly different metabolites revealed that in the OE-5# and WT groups, up-regulated metabolites were enriched in 23 metabolic pathways and down-regulated metabolites were enriched in 11 metabolic pathways. In the OE-6# and WT groups, up-regulated metabolites were enriched in 29 pathways and down-regulated metabolites were enriched in six metabolic pathways. In addition, the differential metabolite changes in the L-serine to flavonoid transformation metabolic pathway also provide evidence that there is a phenotypic explanation for the changes in transgenic tomato. Discussion The metabolomic mechanism controlling SlSAHH2 promotion of tomato fruit ripening has been further elucidated.
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Affiliation(s)
- Lu Yang
- College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Yue Teng
- College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Sijia Bu
- College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Ben Ma
- College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Shijia Guo
- College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Mengxiao Liang
- College of Life Sciences, Nankai University, Tianjin, China
| | - Lifen Huang
- Majorbio Bio-PharmTechnology Co. Ltd., Shanghai, China
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Mascellani Bergo A, Leiss K, Havlik J. Twenty Years of 1H NMR Plant Metabolomics: A Way Forward toward Assessment of Plant Metabolites for Constitutive and Inducible Defenses to Biotic Stress. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:8332-8346. [PMID: 38501393 DOI: 10.1021/acs.jafc.3c09362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
Metabolomics has become an important tool in elucidating the complex relationship between a plant genotype and phenotype. For over 20 years, nuclear magnetic resonance (NMR) spectroscopy has been known for its robustness, quantitative capabilities, simplicity, and cost-efficiency. 1H NMR is the method of choice for analyzing a broad range of relatively abundant metabolites, which can be used for both capturing the plant chemical profile at one point in time and understanding the pathways that underpin plant defense. This systematic Review explores how 1H NMR-based plant metabolomics has contributed to understanding the role of various compounds in plant responses to biotic stress, focusing on both primary and secondary metabolites. It clarifies the challenges and advantages of using 1H NMR in plant metabolomics, interprets common trends observed, and suggests guidelines for method development and establishing standard procedures.
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Affiliation(s)
- Anna Mascellani Bergo
- Department of Food Science, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, 16500 Prague, Czechia
| | - Kirsten Leiss
- Business Unit Greenhouse Horticulture, Wageningen University & Research, 2665MV Bleiswijk, Netherlands
| | - Jaroslav Havlik
- Department of Food Science, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, 16500 Prague, Czechia
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Bernal-Gallardo JJ, de Folter S. Plant genome information facilitates plant functional genomics. PLANTA 2024; 259:117. [PMID: 38592421 PMCID: PMC11004055 DOI: 10.1007/s00425-024-04397-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 03/20/2024] [Indexed: 04/10/2024]
Abstract
MAIN CONCLUSION In this review, we give an overview of plant sequencing efforts and how this impacts plant functional genomics research. Plant genome sequence information greatly facilitates the studies of plant biology, functional genomics, evolution of genomes and genes, domestication processes, phylogenetic relationships, among many others. More than two decades of sequencing efforts have boosted the number of available sequenced plant genomes. The first plant genome, of Arabidopsis, was published in the year 2000 and currently, 4604 plant genomes from 1482 plant species have been published. Various large sequence initiatives are running, which are planning to produce tens of thousands of sequenced plant genomes in the near future. In this review, we give an overview on the status of sequenced plant genomes and on the use of genome information in different research areas.
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Affiliation(s)
- Judith Jazmin Bernal-Gallardo
- Unidad de Genómica Avanzada (UGA-Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Irapuato, Mexico
| | - Stefan de Folter
- Unidad de Genómica Avanzada (UGA-Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Irapuato, Mexico.
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Santiago KAA, Wong WC, Goh YK, Tey SH, Ting ASY. Pathogenicity of monokaryotic and dikaryotic mycelia of Ganoderma boninense revealed via LC-MS-based metabolomics. Sci Rep 2024; 14:5330. [PMID: 38438519 PMCID: PMC10912678 DOI: 10.1038/s41598-024-56129-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 03/01/2024] [Indexed: 03/06/2024] Open
Abstract
This study compared the pathogenicity of monokaryotic (monokaryon) and dikaryotic (dikaryon) mycelia of the oil palm pathogen Ganoderma boninense via metabolomics approach. Ethyl acetate crude extracts of monokaryon and dikaryon were analysed by liquid chromatography quadrupole/time-of-flight-mass spectrometry (LC-Q/TOF-MS) coupled with multivariate data analysis using MetaboAnalyst. The mummichog algorithm was also used to identify the functional activities of monokaryon and dikaryon without a priori identification of all their secondary metabolites. Results revealed that monokaryon produced lesser fungal metabolites than dikaryon, suggesting that monokaryon had a lower possibility of inducing plant infection. These findings were further supported by the identified functional activities. Monokaryon exhibits tyrosine, phenylalanine, and tryptophan metabolism, which are important for fungal growth and development and to produce toxin precursors. In contrast, dikaryon exhibits the metabolism of cysteine and methionine, arginine and proline, and phenylalanine, which are important for fungal growth, development, virulence, and pathogenicity. As such, monokaryon is rendered non-pathogenic as it produces growth metabolites and toxin precursors, whereas dikaryon is pathogenic as it produces metabolites that are involved in fungal growth and pathogenicity. The LC-MS-based metabolomics approach contributes significantly to our understanding of the pathogenesis of Ganoderma boninense, which is essential for disease management in oil palm plantations.
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Affiliation(s)
- Krystle Angelique A Santiago
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia
| | - Wei Chee Wong
- Advanced Agriecological Research Sdn. Bhd., 11 Jalan Teknologi 3/6, Taman Sains Selangor 1, Kota Damansara, 47810, Petaling Jaya, Selangor Darul Ehsan, Malaysia
| | - You Keng Goh
- Advanced Agriecological Research Sdn. Bhd., 11 Jalan Teknologi 3/6, Taman Sains Selangor 1, Kota Damansara, 47810, Petaling Jaya, Selangor Darul Ehsan, Malaysia
| | - Seng Heng Tey
- Advanced Agriecological Research Sdn. Bhd., 11 Jalan Teknologi 3/6, Taman Sains Selangor 1, Kota Damansara, 47810, Petaling Jaya, Selangor Darul Ehsan, Malaysia
| | - Adeline Su Yien Ting
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia.
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Roy A, Mandal M, Das S, Popek R, Rakwal R, Agrawal GK, Awasthi A, Sarkar A. The cellular consequences of particulate matter pollutants in plants: Safeguarding the harmonious integration of structure and function. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 914:169763. [PMID: 38181950 DOI: 10.1016/j.scitotenv.2023.169763] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 12/19/2023] [Accepted: 12/28/2023] [Indexed: 01/07/2024]
Abstract
Particulate matter (PM) pollution is one of the pressing environmental concerns confronting human civilization in the face of the Anthropocene era. Plants are continuously exposed to an accelerating PM, threatening their growth and productivity. Although plants and plant-based infrastructures can potentially reduce ambient air pollutants, PM still affects them morphologically, anatomically, and physiologically. This review comprehensively summarizes an up-to-date review of plant-PM interaction among different functional plant groups, PM deposition and penetration through aboveground and belowground plant parts, and plants' cellular strategies. Upon exposure, PM represses lipid desaturases, eventually leading to modification of cell wall and membrane and altering cell fluidity; consequently, plants can sense the pollutants and, thus, adapt different cellular strategies. The PM also causes a reduction in the photosynthetically active radiation. The study demonstrated that plants reduce stomatal density to avoid PM uptake and increase stomatal index to compensate for decreased gaseous exchange efficiency and transpiration rates. Furthermore, genes and gene sets associated with photosynthesis, glycolysis, gluconeogenesis, and the TCA cycle were dramatically lowered by PM stress. Several transcription factors, including MYB, C2H2, C3H, G2-like, and WRKY were induced, and metabolites such as proline and soluble sugar were accumulated to increase resistance against stressors. In addition, enzymatic and non-enzymatic antioxidants were also accumulated to scavenge the PM-induced reactive oxygen species (ROS). Taken together, this review provides an insight into plants' underlying cellular mechanisms and gene regulatory networks in response to the PM to determine strategies to preserve their structural and functional blend in the face of particulate pollution. The study concludes by recommending that future research should precisely focus on plants' response to short- and long-term PM exposure.
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Affiliation(s)
- Anamika Roy
- Laboratory of Applied Stress Biology, Department of Botany, University of Gour Banga, Malda 732 103, West Bengal, India
| | - Mamun Mandal
- Laboratory of Applied Stress Biology, Department of Botany, University of Gour Banga, Malda 732 103, West Bengal, India
| | - Sujit Das
- Laboratory of Applied Stress Biology, Department of Botany, University of Gour Banga, Malda 732 103, West Bengal, India
| | - Robert Popek
- Section of Basic Research in Horticulture, Department of Plant Protection, Institute of Horticultural Sciences, Warsaw University of Life Sciences - SGGW (WULS-SGGW), Nowoursynowska 159, Warsaw, Poland
| | - Randeep Rakwal
- Institute of Health and Sport Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8574, Japan; GRADE Academy (Pvt.) Ltd., Birgunj, Nepal
| | | | - Amit Awasthi
- Department of Applied Sciences, University of Petroleum and Energy Studies, Dehradun, India
| | - Abhijit Sarkar
- Laboratory of Applied Stress Biology, Department of Botany, University of Gour Banga, Malda 732 103, West Bengal, India.
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Mosley JD, Schock TB, Beecher CW, Dunn WB, Kuligowski J, Lewis MR, Theodoridis G, Ulmer Holland CZ, Vuckovic D, Wilson ID, Zanetti KA. Establishing a framework for best practices for quality assurance and quality control in untargeted metabolomics. Metabolomics 2024; 20:20. [PMID: 38345679 PMCID: PMC10861687 DOI: 10.1007/s11306-023-02080-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 12/11/2023] [Indexed: 02/15/2024]
Abstract
BACKGROUND Quality assurance (QA) and quality control (QC) practices are key tenets that facilitate study and data quality across all applications of untargeted metabolomics. These important practices will strengthen this field and accelerate its success. The Best Practices Working Group (WG) within the Metabolomics Quality Assurance and Quality Control Consortium (mQACC) focuses on community use of QA/QC practices and protocols and aims to identify, catalogue, harmonize, and disseminate current best practices in untargeted metabolomics through community-driven activities. AIM OF REVIEW A present goal of the Best Practices WG is to develop a working strategy, or roadmap, that guides the actions of practitioners and progress in the field. The framework in which mQACC operates promotes the harmonization and dissemination of current best QA/QC practice guidance and encourages widespread adoption of these essential QA/QC activities for liquid chromatography-mass spectrometry. KEY SCIENTIFIC CONCEPTS OF REVIEW Community engagement and QA/QC information gathering activities have been occurring through conference workshops, virtual and in-person interactive forum discussions, and community surveys. Seven principal QC stages prioritized by internal discussions of the Best Practices WG have received participant input, feedback and discussion. We outline these stages, each involving a multitude of activities, as the framework for identifying QA/QC best practices. The ultimate planned product of these endeavors is a "living guidance" document of current QA/QC best practices for untargeted metabolomics that will grow and change with the evolution of the field.
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Affiliation(s)
- Jonathan D Mosley
- Center for Environmental Measurement and Modeling, Environmental Protection Agency, Athens, GA, 30605, USA.
| | - Tracey B Schock
- Chemical Sciences Division, National Institute of Standards and Technology (NIST), Charleston, SC, 29412, USA
| | | | - Warwick B Dunn
- Centre for Metabolomics Research, Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Julia Kuligowski
- Neonatal Research Group, Health Research Institute La Fe, 46026, Valencia, Spain
| | - Matthew R Lewis
- Life Sciences Mass Spectrometry Division, Bruker UK Limited, Coventry, CV4 8HZ, UK
- National Phenome Centre & Division of Systems Medicine, Department of Metabolism, Digestion & Reproduction, Imperial College London, London, W12 0NN, UK
| | - Georgios Theodoridis
- BIOMIC_Auth, Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Aristotle University Thessaloniki, 57001, Thermi, Greece
| | - Candice Z Ulmer Holland
- Eastern Laboratory, Office of Public Health Science (OPHS), Food Safety and Inspection Service (FSIS), Department of Agriculture (USDA), Athens, GA, 30605, USA
| | - Dajana Vuckovic
- Department of Chemistry and Biochemistry, Concordia University, Montreal, QC, H4B 1R6, Canada
| | - Ian D Wilson
- Centre for Metabolomics Research, Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
- Division of Systems Medicine, Department of Metabolism Department of Metabolism, Digestion and Reproduction, Imperial College, London, W12 0NN, UK
| | - Krista A Zanetti
- Office of Nutrition Research, Office of the Director, Division of Program Coordination, Planning, and Strategic Initiatives, National Institutes of Health, Bethesda, MD, USA
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10
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Eshawu AB, Ghalsasi VV. Metabolomics of natural samples: A tutorial review on the latest technologies. J Sep Sci 2024; 47:e2300588. [PMID: 37942863 DOI: 10.1002/jssc.202300588] [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: 08/13/2023] [Revised: 10/29/2023] [Accepted: 11/06/2023] [Indexed: 11/10/2023]
Abstract
Metabolomics is the study of metabolites present in a living system. It is a rapidly growing field aimed at discovering novel compounds, studying biological processes, diagnosing diseases, and ensuring the quality of food products. Recently, the analysis of natural samples has become important to explore novel bioactive compounds and to study how environment and genetics affect living systems. Various metabolomics techniques, databases, and data analysis tools are available for natural sample metabolomics. However, choosing the right method can be a daunting exercise because natural samples are heterogeneous and require untargeted approaches. This tutorial review aims to compile the latest technologies to guide an early-career scientist on natural sample metabolomics. First, different extraction methods and their pros and cons are reviewed. Second, currently available metabolomics databases and data analysis tools are summarized. Next, recent research on metabolomics of milk, honey, and microbial samples is reviewed. Finally, after reviewing the latest trends in technologies, a checklist is presented to guide an early-career researcher on how to design a metabolomics project. In conclusion, this review is a comprehensive resource for a researcher planning to conduct their first metabolomics analysis. It is also useful for experienced researchers to update themselves on the latest trends in metabolomics.
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Affiliation(s)
- Ali Baba Eshawu
- School of Biotechnology, Faculty of Applied Sciences and Biotechnology, Shoolini University of Biotechnology and Management Sciences, Solan, India
| | - Vihang Vivek Ghalsasi
- School of Biotechnology, Faculty of Applied Sciences and Biotechnology, Shoolini University of Biotechnology and Management Sciences, Solan, India
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11
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Timilsina AP, Raut BK, Huo C, Khadayat K, Budhathoki P, Ghimire M, Budhathoki R, Aryal N, Kim KH, Parajuli N. Metabolomics and molecular networking approach for exploring the anti-diabetic activity of medicinal plants. RSC Adv 2023; 13:30665-30679. [PMID: 37869390 PMCID: PMC10585453 DOI: 10.1039/d3ra04037b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 10/04/2023] [Indexed: 10/24/2023] Open
Abstract
Metabolomics and molecular networking approaches have expanded rapidly in the field of biological sciences and involve the systematic identification, visualization, and high-throughput characterization of bioactive metabolites in natural products using sophisticated mass spectrometry-based techniques. The popularity of natural products in pharmaceutical therapies has been influenced by medicinal plants with a long history of ethnobotany and a vast collection of bioactive compounds. Here, we selected four medicinal plants Cleistocalyx operculatus, Terminalia chebula, Ficus lacor, and Ficus semicordata, the biochemical characteristics of which remain unclear owing to the inherent complexity of their plant metabolites. In this study, we aimed to evaluate the potential of these aforementioned plant extracts in inhibiting the enzymatic activity of α-amylase and α-glucosidase, respectively, followed by the annotation of secondary metabolites. The methanol extract of Ficus semicordata exhibited the highest α-amylase inhibition with an IC50 of 46.8 ± 1.8 μg mL-1, whereas the water fraction of Terminalia chebula fruits demonstrated the most significant α-glucosidase inhibition with an IC50 value of 1.07 ± 0.01 μg mL-1. The metabolic profiling of plant extracts was analyzed through Liquid Chromatography-Mass Spectrometry (LC-HRMS) of the active fractions, resulting in the annotation of 32 secondary metabolites. Furthermore, we applied the Global Natural Product Social Molecular Networking (GNPS) platform to evaluate the MS/MS data of Terminalia chebula (bark), revealing that there were 205 and 160 individual ion species observed as nodes in the methanol and ethyl acetate fractions, respectively. Twenty-two metabolites were tentatively identified from the network map, of which 11 compounds were unidentified during manual annotation.
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Affiliation(s)
- Arjun Prasad Timilsina
- Biological Chemistry Lab, Central Department of Chemistry, Tribhuvan University Kirtipur Kathmandu 44618 Nepal +977-1-4332034
| | - Bimal Kumar Raut
- Biological Chemistry Lab, Central Department of Chemistry, Tribhuvan University Kirtipur Kathmandu 44618 Nepal +977-1-4332034
| | - Chen Huo
- School of Pharmacy, Sungkyunkwan University Suwon 16419 Republic of Korea +82-31-290-7700
| | - Karan Khadayat
- Biological Chemistry Lab, Central Department of Chemistry, Tribhuvan University Kirtipur Kathmandu 44618 Nepal +977-1-4332034
| | - Prakriti Budhathoki
- Biological Chemistry Lab, Central Department of Chemistry, Tribhuvan University Kirtipur Kathmandu 44618 Nepal +977-1-4332034
| | - Mandira Ghimire
- Biological Chemistry Lab, Central Department of Chemistry, Tribhuvan University Kirtipur Kathmandu 44618 Nepal +977-1-4332034
| | - Rabin Budhathoki
- Biological Chemistry Lab, Central Department of Chemistry, Tribhuvan University Kirtipur Kathmandu 44618 Nepal +977-1-4332034
| | - Niraj Aryal
- Department of Biology, University of Florida Gainesville FL 32611 USA
| | - Ki Hyun Kim
- School of Pharmacy, Sungkyunkwan University Suwon 16419 Republic of Korea +82-31-290-7700
| | - Niranjan Parajuli
- Biological Chemistry Lab, Central Department of Chemistry, Tribhuvan University Kirtipur Kathmandu 44618 Nepal +977-1-4332034
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12
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Pandian K, Matsui M, Hankemeier T, Ali A, Okubo-Kurihara E. Advances in single-cell metabolomics to unravel cellular heterogeneity in plant biology. PLANT PHYSIOLOGY 2023; 193:949-965. [PMID: 37338502 PMCID: PMC10517197 DOI: 10.1093/plphys/kiad357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 05/03/2023] [Accepted: 05/17/2023] [Indexed: 06/21/2023]
Abstract
Single-cell metabolomics is a powerful tool that can reveal cellular heterogeneity and can elucidate the mechanisms of biological phenomena in detail. It is a promising approach in studying plants, especially when cellular heterogeneity has an impact on different biological processes. In addition, metabolomics, which can be regarded as a detailed phenotypic analysis, is expected to answer previously unrequited questions which will lead to expansion of crop production, increased understanding of resistance to diseases, and in other applications as well. In this review, we will introduce the flow of sample acquisition and single-cell techniques to facilitate the adoption of single-cell metabolomics. Furthermore, the applications of single-cell metabolomics will be summarized and reviewed.
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Affiliation(s)
- Kanchana Pandian
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, Einstein Road 55, 2333 CC Leiden, The Netherlands
| | - Minami Matsui
- RIKEN, Center for Sustainable Resource Science, Kanagawa 230-0045, Japan
| | - Thomas Hankemeier
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, Einstein Road 55, 2333 CC Leiden, The Netherlands
| | - Ahmed Ali
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, Einstein Road 55, 2333 CC Leiden, The Netherlands
| | - Emiko Okubo-Kurihara
- RIKEN, Center for Sustainable Resource Science, Kanagawa 230-0045, Japan
- College of Science, Rikkyo University, Tokyo 171-8501, Japan
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13
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Grazina L, Mafra I, Monaci L, Amaral JS. Mass spectrometry-based approaches to assess the botanical authenticity of dietary supplements. Compr Rev Food Sci Food Saf 2023; 22:3870-3909. [PMID: 37548598 DOI: 10.1111/1541-4337.13222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 07/05/2023] [Accepted: 07/18/2023] [Indexed: 08/08/2023]
Abstract
Dietary supplements are legally considered foods despite frequently including medicinal plants as ingredients. Currently, the consumption of herbal dietary supplements, also known as plant food supplements (PFS), is increasing worldwide and some raw botanicals, highly demanded due to their popularity, extensive use, and/or well-established pharmacological effects, have been attaining high prices in the international markets. Therefore, botanical adulteration for profit increase can occur along the whole PFS industry chain, from raw botanicals to plant extracts, until final PFS. Besides the substitution of high-value species, unintentional mislabeling can happen in morphologically similar species. Both cases represent a health risk for consumers, prompting the development of numerous works to access botanical adulterations in PFS. Among different approaches proposed for this purpose, mass spectrometry (MS)-based techniques have often been reported as the most promising, particularly when hyphenated with chromatographic techniques. Thus, this review aims at describing an overview of the developments in this field, focusing on the applications of MS-based techniques to targeted and untargeted analysis to detect botanical adulterations in plant materials, extracts, and PFS.
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Affiliation(s)
- Liliana Grazina
- REQUIMTE-LAQV, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Isabel Mafra
- REQUIMTE-LAQV, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Linda Monaci
- ISPA-CNR, Institute of Sciences of Food Production of National Research Council of Italy, Bari, Italy
| | - Joana S Amaral
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Bragança, Portugal
- Laboratório Associado para a Sustentabilidade e Tecnologia em Regiões de Montanha (SusTEC), Instituto Politécnico de Bragança, Bragança, Portugal
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14
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Rogers HJ. How far can omics go in unveiling the mechanisms of floral senescence? Biochem Soc Trans 2023; 51:1485-1493. [PMID: 37387359 PMCID: PMC10586764 DOI: 10.1042/bst20221097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 06/12/2023] [Accepted: 06/13/2023] [Indexed: 07/01/2023]
Abstract
Floral senescence is of fundamental interest in understanding plant developmental regulation, it is of ecological and agricultural interest in relation to seed production, and is of key importance to the production of cut flowers. The biochemical changes occurring are well-studied and involve macromolecular breakdown and remobilisation of nutrients to developing seeds or other young organs in the plant. However, the initiation and regulation of the process and inter-organ communication remain to be fully elucidated. Although ethylene emission, which becomes autocatalytic, is a key regulator in some species, in other species it appears not to be as important. Other plant growth regulators such as cytokinins, however, seem to be important in floral senescence across both ethylene sensitive and insensitive species. Other plant growth regulators are also likely involved. Omics approaches have provided a wealth of data especially in ornamental species where genome data is lacking. Two families of transcription factors: NAC and WRKY emerge as major regulators, and omics information has been critical in understanding their functions. Future progress would greatly benefit from a single model species for understanding floral senescence; however, this is challenging due to the diversity of regulatory mechanisms. Combining omics data sets can be powerful in understanding different layers of regulation, but in vitro biochemical and or genetic analysis through transgenics or mutants is still needed to fully verify mechanisms and interactions between regulators.
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15
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Joshi R, Sirikantaramas S, Kumar D. Editorial: Integrative analysis approaches for understanding plant metabolism, metabolite, chemodiversity and their respective regulation. FRONTIERS IN PLANT SCIENCE 2023; 14:1248983. [PMID: 37575933 PMCID: PMC10415068 DOI: 10.3389/fpls.2023.1248983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 07/17/2023] [Indexed: 08/15/2023]
Affiliation(s)
- Robin Joshi
- Chemical Technology Division, Council of Scientific and Industrial Research (CSIR)-Institute of Himalayan Bioresource Technology, Palampur, India
- Perelman School of Medicine, Institute for Translational Medicine and Therapeutics (ITMAT), University of Pennsylvania (UPenn), Philadelphia, PA, United States
| | - Supaart Sirikantaramas
- Center of Excellence in Molecular Crop, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Dinesh Kumar
- Chemical Technology Division, Council of Scientific and Industrial Research (CSIR)-Institute of Himalayan Bioresource Technology, Palampur, India
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16
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Elessawy FM, Hughes J, Khazaei H, Vandenberg A, El-Aneed A, Purves RW. A comparative metabolomics investigation of flavonoid variation in faba bean flowers. Metabolomics 2023; 19:52. [PMID: 37249718 DOI: 10.1007/s11306-023-02014-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 04/28/2023] [Indexed: 05/31/2023]
Abstract
INTRODUCTION Faba bean (Vicia faba L.) flowers are edible and used as garnishes because of their aroma, sweet flavor and attractive colors. Anthocyanins are the common plant pigments that give flowers their vivid colors, whereas non-anthocyanin flavonoids can serve as co-pigments that can modify the color intensity of flowers. OBJECTIVES To explore the polyphenol diversity and differences in standard and wing petals of faba bean flowers; and identify glycosylated flavonoids that contribute to flower color. METHODS Flower standard and wing petals from 30 faba bean genotypes (eight color groups with a total of 60 samples) were used for polyphenol extraction. Samples were analyzed using a targeted method and a semi-untargeted analysis using liquid chromatography-high resolution mass spectrometry (LC-HRMS) combined with photodiode array (PDA) detection. Compound Discoverer software was used for polyphenol identification and multivariate analysis. RESULTS The semi-untargeted analysis guided by the PDA detected 90 flavonoid metabolites present in faba bean flower petals. Ten anthocyanins largely influenced the flower colors, but other flavonoids (63 flavonols and 12 flavones) found with variable levels in different flower color groups appeared to also influence color, especially in mixed colors. CONCLUSION Analysis of the different colored faba bean flowers confirmed that the color variation between the flowers was mainly controlled by anthocyanins in brown, red and purple-red flowers. Of the other flavonoids, multiglycosylated kaempferols were abundant in white and brown flowers, monoglycosylated kaempferols were common in red and purple-red flowers, and quercetin and apigenin glycosides were abundant co-pigments in purple-red flowers.
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Affiliation(s)
- Fatma M Elessawy
- College of Pharmacy and Nutrition, University of Saskatchewan, Saskatoon, SK, Canada
| | - Jessa Hughes
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Hamid Khazaei
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
- Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Albert Vandenberg
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Anas El-Aneed
- College of Pharmacy and Nutrition, University of Saskatchewan, Saskatoon, SK, Canada
| | - Randy W Purves
- College of Pharmacy and Nutrition, University of Saskatchewan, Saskatoon, SK, Canada.
- Centre for Veterinary Drug Residues, Canadian Food Inspection Agency, Saskatoon, SK, Canada.
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17
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Tran TLC, Callahan DL, Islam MT, Wang Y, Arioli T, Cahill D. Comparative metabolomic profiling of Arabidopsis thaliana roots and leaves reveals complex response mechanisms induced by a seaweed extract. FRONTIERS IN PLANT SCIENCE 2023; 14:1114172. [PMID: 36968386 PMCID: PMC10035662 DOI: 10.3389/fpls.2023.1114172] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 02/15/2023] [Indexed: 06/18/2023]
Abstract
Seaweed extracts are a prominent class of biostimulants that enhance plant health and tolerance to biotic and abiotic stresses due to their unique bioactive components. However, the mechanisms of action of biostimulants are still unknown. Here, we have used a metabolomic approach, a UHPLC-MS method, to uncover the mechanisms induced following application to Arabidopsis thaliana of a seaweed extract derived from Durvillaea potatorum and Ascophyllum nodosum. We have identified, following the application of the extract, key metabolites and systemic responses in roots and leaves across 3 timepoints (0, 3, 5 days). Significant alterations in metabolite accumulation or reduction were found for those belonging to broad groups of compounds such as lipids, amino acids, and phytohormones; and secondary metabolites such as phenylpropanoids, glucosinolates, and organic acids. Strong accumulations of TCA cycle and N-containing and defensive metabolites such as glucosinolates were also found revealing the enhancement of carbon and nitrogen metabolism and defence systems. Our study has demonstrated that application of seaweed extract dramatically altered the metabolomic profiles of Arabidopsis and revealed differences in roots and leaves that varied across the timepoints tested. We also show clear evidence of systemic responses that were initiated in the roots and resulted in metabolic alterations in the leaves. Collectively, our results suggest that this seaweed extract promotes plant growth and activates defence systems by altering various physiological processes at the individual metabolite level.
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Affiliation(s)
- Thi Linh Chi Tran
- School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia
| | - Damien L. Callahan
- School of Life and Environmental Sciences, Centre for Cellular and Molecular Biology, Deakin University, Burwood, VIC, Australia
| | - Md Tohidul Islam
- School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia
| | - Yichao Wang
- School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia
| | - Tony Arioli
- School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia
- Seasol International R&D Department, Bayswater, VIC, Australia
| | - David Cahill
- School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia
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Ni B, Feussner K. Ex vivo metabolomics-A hypothesis-free approach to identify native substrate(s) and product(s) of orphan enzymes. Methods Enzymol 2023; 680:303-323. [PMID: 36710016 DOI: 10.1016/bs.mie.2022.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Over the past decade, the number of fully sequenced genomes has increased at an awe-inspiring pace. Similarly, the quality and scope of tools for the prediction of both protein structure and function has seen vast improvements. However, to pinpoint the exact function of a protein, for instance the exact reaction catalyzed by an enzyme, experimental evidence is crucial. At the same time, this step is the main bottleneck when generating a conclusive model for the function of an enzyme and to interpret its function in a physiological context. Hence, a comprehensive experimental strategy for functional annotation of enzymes that is as efficient as possible is required. Ex vivo metabolomics is a powerful non-targeted approach that overcomes several of the challenges inherent to in vitro characterization of enzymes with unknown functions. By incubating the recombinant enzyme of interest in a quasi-native metabolite extract from its tissue of origin under specific environmental and developmental conditions, the complete native substrate range can be tested in a single assay. This unlocks compounds that are commercially unavailable or otherwise difficult to procure. Coupled with non-targeted metabolomics analysis, ex vivo has the capability to test for and identify even unexpected substrates and assign the respective products of the enzymatic reaction.
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Affiliation(s)
- Benedikt Ni
- University of Goettingen, Albrecht-von-Haller-Institute for Plant Sciences, Department of Plant Biochemistry, Goettingen, Germany
| | - Kirstin Feussner
- University of Goettingen, Albrecht-von-Haller-Institute for Plant Sciences, Department of Plant Biochemistry, Goettingen, Germany; University of Goettingen, Goettingen Center for Molecular Biosciences (GZMB), Service Unit for Metabolomics and Lipidomics, Goettingen, Germany.
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19
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Shen S, Zhan C, Yang C, Fernie AR, Luo J. Metabolomics-centered mining of plant metabolic diversity and function: Past decade and future perspectives. MOLECULAR PLANT 2023; 16:43-63. [PMID: 36114669 DOI: 10.1016/j.molp.2022.09.007] [Citation(s) in RCA: 49] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 09/06/2022] [Accepted: 09/11/2022] [Indexed: 06/15/2023]
Abstract
Plants are natural experts in organic synthesis, being able to generate large numbers of specific metabolites with widely varying structures that help them adapt to variable survival challenges. Metabolomics is a research discipline that integrates the capabilities of several types of research including analytical chemistry, statistics, and biochemistry. Its ongoing development provides strategies for gaining a systematic understanding of quantitative changes in the levels of metabolites. Metabolomics is usually performed by targeting either a specific cell, a specific tissue, or the entire organism. Considerable advances in science and technology over the last three decades have propelled us into the era of multi-omics, in which metabolomics, despite at an earlier developmental stage than genomics, transcriptomics, and proteomics, offers the distinct advantage of studying the cellular entities that have the greatest influence on end phenotype. Here, we summarize the state of the art of metabolite detection and identification, and illustrate these techniques with four case study applications: (i) comparing metabolite composition within and between species, (ii) assessing spatio-temporal metabolic changes during plant development, (iii) mining characteristic metabolites of plants in different ecological environments and upon exposure to various stresses, and (iv) assessing the performance of metabolomics as a means of functional gene identification , metabolic pathway elucidation, and metabolomics-assisted breeding through analyzing plant populations with diverse genetic variations. In addition, we highlight the prominent contributions of joint analyses of plant metabolomics and other omics datasets, including those from genomics, transcriptomics, proteomics, epigenomics, phenomics, microbiomes, and ion-omics studies. Finally, we discuss future directions and challenges exploiting metabolomics-centered approaches in understanding plant metabolic diversity.
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Affiliation(s)
- Shuangqian Shen
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China; College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Chuansong Zhan
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China; College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Chenkun Yang
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China; College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany
| | - Jie Luo
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China; College of Tropical Crops, Hainan University, Haikou 570228, China.
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20
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Popoola JO, Ojuederie OB, Aworunse OS, Adelekan A, Oyelakin AS, Oyesola OL, Akinduti PA, Dahunsi SO, Adegboyega TT, Oranusi SU, Ayilara MS, Omonhinmin CA. Nutritional, functional, and bioactive properties of african underutilized legumes. FRONTIERS IN PLANT SCIENCE 2023; 14:1105364. [PMID: 37123863 PMCID: PMC10141332 DOI: 10.3389/fpls.2023.1105364] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 03/16/2023] [Indexed: 05/03/2023]
Abstract
Globally, legumes are vital constituents of diet and perform critical roles in maintaining well-being owing to the dense nutritional contents and functional properties of their seeds. While much emphasis has been placed on the major grain legumes over the years, the neglected and underutilized legumes (NULs) are gaining significant recognition as probable crops to alleviate malnutrition and give a boost to food security in Africa. Consumption of these underutilized legumes has been associated with several health-promoting benefits and can be utilized as functional foods due to their rich dietary fibers, vitamins, polyunsaturated fatty acids (PUFAs), proteins/essential amino acids, micro-nutrients, and bioactive compounds. Despite the plethora of nutritional benefits, the underutilized legumes have not received much research attention compared to common mainstream grain legumes, thus hindering their adoption and utilization. Consequently, research efforts geared toward improvement, utilization, and incorporation into mainstream agriculture in Africa are more convincing than ever. This work reviews some selected NULs of Africa (Adzuki beans (Vigna angularis), African yam bean (Sphenostylis stenocarpa), Bambara groundnut (Vigna subterranea), Jack bean (Canavalia ensiformis), Kidney bean (Phaseolus vulgaris), Lima bean (Phaseolus lunatus), Marama bean (Tylosema esculentum), Mung bean, (Vigna radiata), Rice bean (Vigna Umbellata), and Winged bean (Psophocarpus tetragonolobus)), and their nutritional, and functional properties. Furthermore, we highlight the prospects and current challenges associated with the utilization of the NULs and discusses the strategies to facilitate their exploitation as not only sources of vital nutrients, but also their integration for the development of cheap and accessible functional foods.
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Affiliation(s)
- Jacob Olagbenro Popoola
- Pure and Applied Biology Programme, College of Agriculture, Engineering and Science, Bowen University, Iwo, Osun, Nigeria
- Department of Biological Sciences/Biotechnology Cluster, Covenant University, Ota, Ogun, Nigeria
- *Correspondence: Jacob Olagbenro Popoola, ; Omena B. Ojuederie,
| | - Omena B. Ojuederie
- Department of Biological Sciences, Kings University, Ode-Omu, Osun, Nigeria
- Food Security and Safety Focus, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, South Africa
- *Correspondence: Jacob Olagbenro Popoola, ; Omena B. Ojuederie,
| | | | - Aminat Adelekan
- Department of Chemical and Food Sciences, College of Natural and Applied Sciences, Bells University of Technology, Ota, Ogun, Nigeria
| | - Abiodun S. Oyelakin
- Department of Pure and Applied Botany, College of Biosciences, Federal University of Agriculture, Abeokuta, Nigeria
| | - Olusola Luke Oyesola
- Department of Biological Sciences/Biotechnology Cluster, Covenant University, Ota, Ogun, Nigeria
| | - Paul A. Akinduti
- Department of Biological Sciences/Biotechnology Cluster, Covenant University, Ota, Ogun, Nigeria
| | - Samuel Olatunde Dahunsi
- Microbiology Programme, College of Agriculture, Engineering and Science, Bowen University, Iwo, Osun, Nigeria
- The Radcliffe Institute for Advanced Study, Harvard University, Cambridge, MA, United States
| | - Taofeek T. Adegboyega
- Food Security and Safety Focus, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, South Africa
- Biology Unit, Faculty of Science, Air Force Institute of Technology, Kaduna, Nigeria
| | - Solomon U. Oranusi
- Department of Biological Sciences/Biotechnology Cluster, Covenant University, Ota, Ogun, Nigeria
| | - Modupe S. Ayilara
- Department of Biological Sciences, Kings University, Ode-Omu, Osun, Nigeria
- Food Security and Safety Focus, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, South Africa
| | - Conrad A. Omonhinmin
- Department of Biological Sciences/Biotechnology Cluster, Covenant University, Ota, Ogun, Nigeria
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21
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Primary Investigation of Phenotypic Plasticity in Fritillaria cirrhosa Based on Metabolome and Transcriptome Analyses. Cells 2022; 11:cells11233844. [PMID: 36497104 PMCID: PMC9736200 DOI: 10.3390/cells11233844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/06/2022] [Accepted: 11/26/2022] [Indexed: 12/05/2022] Open
Abstract
Phenotypic plasticity refers to the adaptability of an organism to a heterogeneous environment. In this study, the differential gene expression and compositional changes in Fritillaria cirrhosa during phenotypic plasticity were evaluated using transcriptomic and metabolomic analyses. The annotation profiles of 1696 differentially expressed genes from the transcriptome between abnormal and normal phenotypes revealed that the main annotation pathways were related to the biosynthesis of amino acids, ABC transporters, and plant-pathogen interactions. According to the metabolome, the abnormal phenotype had 36 upregulated amino acids, including tryptophan, proline, and valine, which had a 3.77-fold higher relative content than the normal phenotype. However, saccharides and vitamins were found to be deficient in the abnormal phenotypes. The combination profiles demonstrated that phenotypic plasticity may be an effective strategy for overcoming potential stress via the accumulation of amino acids and regulation of the corresponding genes and transcription factors. In conclusion, a pathogen attack on F. cirrhosa may promote the synthesis of numerous amino acids and transport them into the bulbs through ABC transporters, which may further result in phenotypic variation. Our results provide new insights into the potential mechanism of phenotypic changes.
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22
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Mishra AK, Sudalaimuthuasari N, Hazzouri KM, Saeed EE, Shah I, Amiri KMA. Tapping into Plant-Microbiome Interactions through the Lens of Multi-Omics Techniques. Cells 2022; 11:3254. [PMID: 36291121 PMCID: PMC9600287 DOI: 10.3390/cells11203254] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/27/2022] [Accepted: 09/29/2022] [Indexed: 10/21/2023] Open
Abstract
This review highlights the pivotal role of root exudates in the rhizosphere, especially the interactions between plants and microbes and between plants and plants. Root exudates determine soil nutrient mobilization, plant nutritional status, and the communication of plant roots with microbes. Root exudates contain diverse specialized signaling metabolites (primary and secondary). The spatial behavior of these metabolites around the root zone strongly influences rhizosphere microorganisms through an intimate compatible interaction, thereby regulating complex biological and ecological mechanisms. In this context, we reviewed the current understanding of the biological phenomenon of allelopathy, which is mediated by phytotoxic compounds (called allelochemicals) released by plants into the soil that affect the growth, survival, development, ecological infestation, and intensification of other plant species and microbes in natural communities or agricultural systems. Advances in next-generation sequencing (NGS), such as metagenomics and metatranscriptomics, have opened the possibility of better understanding the effects of secreted metabolites on the composition and activity of root-associated microbial communities. Nevertheless, understanding the role of secretory metabolites in microbiome manipulation can assist in designing next-generation microbial inoculants for targeted disease mitigation and improved plant growth using the synthetic microbial communities (SynComs) tool. Besides a discussion on different approaches, we highlighted the advantages of conjugation of metabolomic approaches with genetic design (metabolite-based genome-wide association studies) in dissecting metabolome diversity and understanding the genetic components of metabolite accumulation. Recent advances in the field of metabolomics have expedited comprehensive and rapid profiling and discovery of novel bioactive compounds in root exudates. In this context, we discussed the expanding array of metabolomics platforms for metabolome profiling and their integration with multivariate data analysis, which is crucial to explore the biosynthesis pathway, as well as the regulation of associated pathways at the gene, transcript, and protein levels, and finally their role in determining and shaping the rhizomicrobiome.
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Affiliation(s)
- Ajay Kumar Mishra
- Khalifa Centre for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Naganeeswaran Sudalaimuthuasari
- Khalifa Centre for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Khaled M. Hazzouri
- Khalifa Centre for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Esam Eldin Saeed
- Khalifa Centre for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Iltaf Shah
- Department of Chemistry (Biochemistry), College of Science, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Khaled M. A. Amiri
- Khalifa Centre for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
- Department of Biology, College of Science, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
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23
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Singh DP, Bisen MS, Shukla R, Prabha R, Maurya S, Reddy YS, Singh PM, Rai N, Chaubey T, Chaturvedi KK, Srivastava S, Farooqi MS, Gupta VK, Sarma BK, Rai A, Behera TK. Metabolomics-Driven Mining of Metabolite Resources: Applications and Prospects for Improving Vegetable Crops. Int J Mol Sci 2022; 23:ijms232012062. [PMID: 36292920 PMCID: PMC9603451 DOI: 10.3390/ijms232012062] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 09/13/2022] [Accepted: 09/23/2022] [Indexed: 11/16/2022] Open
Abstract
Vegetable crops possess a prominent nutri-metabolite pool that not only contributes to the crop performance in the fields, but also offers nutritional security for humans. In the pursuit of identifying, quantifying and functionally characterizing the cellular metabolome pool, biomolecule separation technologies, data acquisition platforms, chemical libraries, bioinformatics tools, databases and visualization techniques have come to play significant role. High-throughput metabolomics unravels structurally diverse nutrition-rich metabolites and their entangled interactions in vegetable plants. It has helped to link identified phytometabolites with unique phenotypic traits, nutri-functional characters, defense mechanisms and crop productivity. In this study, we explore mining diverse metabolites, localizing cellular metabolic pathways, classifying functional biomolecules and establishing linkages between metabolic fluxes and genomic regulations, using comprehensive metabolomics deciphers of the plant’s performance in the environment. We discuss exemplary reports covering the implications of metabolomics, addressing metabolic changes in vegetable plants during crop domestication, stage-dependent growth, fruit development, nutri-metabolic capabilities, climatic impacts, plant-microbe-pest interactions and anthropogenic activities. Efforts leading to identify biomarker metabolites, candidate proteins and the genes responsible for plant health, defense mechanisms and nutri-rich crop produce are documented. With the insights on metabolite-QTL (mQTL) driven genetic architecture, molecular breeding in vegetable crops can be revolutionized for developing better nutritional capabilities, improved tolerance against diseases/pests and enhanced climate resilience in plants.
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Affiliation(s)
- Dhananjaya Pratap Singh
- ICAR-Indian Institute of Vegetable Research, Jakhini, Shahanshahpur, Varanasi 221305, India
- Correspondence:
| | - Mansi Singh Bisen
- ICAR-Indian Institute of Vegetable Research, Jakhini, Shahanshahpur, Varanasi 221305, India
| | - Renu Shukla
- Indian Council of Agricultural Research (ICAR), Krishi Bhawan, Dr. Rajendra Prasad Road, New Delhi 110001, India
| | - Ratna Prabha
- ICAR-Indian Agricultural Statistics Research Institute, Centre for Agricultural Bioinformatics, Library Avenue, Pusa, New Delhi 110012, India
| | - Sudarshan Maurya
- ICAR-Indian Institute of Vegetable Research, Jakhini, Shahanshahpur, Varanasi 221305, India
| | - Yesaru S. Reddy
- ICAR-Indian Institute of Vegetable Research, Jakhini, Shahanshahpur, Varanasi 221305, India
| | - Prabhakar Mohan Singh
- ICAR-Indian Institute of Vegetable Research, Jakhini, Shahanshahpur, Varanasi 221305, India
| | - Nagendra Rai
- ICAR-Indian Institute of Vegetable Research, Jakhini, Shahanshahpur, Varanasi 221305, India
| | - Tribhuwan Chaubey
- ICAR-Indian Institute of Vegetable Research, Jakhini, Shahanshahpur, Varanasi 221305, India
| | - Krishna Kumar Chaturvedi
- ICAR-Indian Agricultural Statistics Research Institute, Centre for Agricultural Bioinformatics, Library Avenue, Pusa, New Delhi 110012, India
| | - Sudhir Srivastava
- ICAR-Indian Agricultural Statistics Research Institute, Centre for Agricultural Bioinformatics, Library Avenue, Pusa, New Delhi 110012, India
| | - Mohammad Samir Farooqi
- ICAR-Indian Agricultural Statistics Research Institute, Centre for Agricultural Bioinformatics, Library Avenue, Pusa, New Delhi 110012, India
| | - Vijai Kumar Gupta
- Biorefining and Advanced Materials Research Centre, Scotland’s Rural College, Kings Buildings, West Mains Road, Edinburgh EH9 3JG, UK
| | - Birinchi K. Sarma
- Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi 221005, India
| | - Anil Rai
- ICAR-Indian Agricultural Statistics Research Institute, Centre for Agricultural Bioinformatics, Library Avenue, Pusa, New Delhi 110012, India
| | - Tusar Kanti Behera
- ICAR-Indian Institute of Vegetable Research, Jakhini, Shahanshahpur, Varanasi 221305, India
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Maldonado-Alconada AM, Castillejo MÁ, Rey MD, Labella-Ortega M, Tienda-Parrilla M, Hernández-Lao T, Honrubia-Gómez I, Ramírez-García J, Guerrero-Sanchez VM, López-Hidalgo C, Valledor L, Navarro-Cerrillo RM, Jorrin-Novo JV. Multiomics Molecular Research into the Recalcitrant and Orphan Quercus ilex Tree Species: Why, What for, and How. Int J Mol Sci 2022; 23:9980. [PMID: 36077370 PMCID: PMC9456323 DOI: 10.3390/ijms23179980] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/29/2022] [Accepted: 08/30/2022] [Indexed: 11/17/2022] Open
Abstract
The holm oak (Quercus ilex L.) is the dominant tree species of the Mediterranean forest and the Spanish agrosilvopastoral ecosystem, "dehesa." It has been, since the prehistoric period, an important part of the Iberian population from a social, cultural, and religious point of view, providing an ample variety of goods and services, and forming the basis of the economy in rural areas. Currently, there is renewed interest in its use for dietary diversification and sustainable food production. It is part of cultural richness, both economically (tangible) and environmentally (intangible), and must be preserved for future generations. However, a worrisome degradation of the species and associated ecosystems is occurring, observed in an increase in tree decline and mortality, which requires urgent action. Breeding programs based on the selection of elite genotypes by molecular markers is the only plausible biotechnological approach. To this end, the authors' group started, in 2004, a research line aimed at characterizing the molecular biology of Q. ilex. It has been a challenging task due to its biological characteristics (long life cycle, allogamous, high phenotypic variability) and recalcitrant nature. The biology of this species has been characterized following the central dogma of molecular biology using the omics cascade. Molecular responses to biotic and abiotic stresses, as well as seed maturation and germination, are the two main objectives of our research. The contributions of the group to the knowledge of the species at the level of DNA-based markers, genomics, epigenomics, transcriptomics, proteomics, and metabolomics are discussed here. Moreover, data are compared with those reported for Quercus spp. All omics data generated, and the genome of Q. ilex available, will be integrated with morphological and physiological data in the systems biology direction. Thus, we will propose possible molecular markers related to resilient and productive genotypes to be used in reforestation programs. In addition, possible markers related to the nutritional value of acorn and derivate products, as well as bioactive compounds (peptides and phenolics) and allergens, will be suggested. Subsequently, the selected molecular markers will be validated by both genome-wide association and functional genomic analyses.
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Affiliation(s)
- Ana María Maldonado-Alconada
- Agroforestry and Plant Biochemistry, Proteomics and Systems Biology, Department of Biochemistry and Molecular Biology, University of Cordoba, UCO-CeiA3, 14014 Cordoba, Spain
| | - María Ángeles Castillejo
- Agroforestry and Plant Biochemistry, Proteomics and Systems Biology, Department of Biochemistry and Molecular Biology, University of Cordoba, UCO-CeiA3, 14014 Cordoba, Spain
| | - María-Dolores Rey
- Agroforestry and Plant Biochemistry, Proteomics and Systems Biology, Department of Biochemistry and Molecular Biology, University of Cordoba, UCO-CeiA3, 14014 Cordoba, Spain
| | - Mónica Labella-Ortega
- Agroforestry and Plant Biochemistry, Proteomics and Systems Biology, Department of Biochemistry and Molecular Biology, University of Cordoba, UCO-CeiA3, 14014 Cordoba, Spain
| | - Marta Tienda-Parrilla
- Agroforestry and Plant Biochemistry, Proteomics and Systems Biology, Department of Biochemistry and Molecular Biology, University of Cordoba, UCO-CeiA3, 14014 Cordoba, Spain
| | - Tamara Hernández-Lao
- Agroforestry and Plant Biochemistry, Proteomics and Systems Biology, Department of Biochemistry and Molecular Biology, University of Cordoba, UCO-CeiA3, 14014 Cordoba, Spain
| | - Irene Honrubia-Gómez
- Agroforestry and Plant Biochemistry, Proteomics and Systems Biology, Department of Biochemistry and Molecular Biology, University of Cordoba, UCO-CeiA3, 14014 Cordoba, Spain
| | - Javier Ramírez-García
- Agroforestry and Plant Biochemistry, Proteomics and Systems Biology, Department of Biochemistry and Molecular Biology, University of Cordoba, UCO-CeiA3, 14014 Cordoba, Spain
| | - Víctor M. Guerrero-Sanchez
- Agroforestry and Plant Biochemistry, Proteomics and Systems Biology, Department of Biochemistry and Molecular Biology, University of Cordoba, UCO-CeiA3, 14014 Cordoba, Spain
- Cardiovascular Proteomics Laboratory, Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029 Madrid, Spain
| | - Cristina López-Hidalgo
- Agroforestry and Plant Biochemistry, Proteomics and Systems Biology, Department of Biochemistry and Molecular Biology, University of Cordoba, UCO-CeiA3, 14014 Cordoba, Spain
- Plant Physiology, Department of Organisms and Systems Biology, University Institute of Biotechnology of Asturias (IUBA), University of Oviedo, 33006 Asturias, Spain
| | - Luis Valledor
- Plant Physiology, Department of Organisms and Systems Biology, University Institute of Biotechnology of Asturias (IUBA), University of Oviedo, 33006 Asturias, Spain
| | - Rafael M. Navarro-Cerrillo
- Evaluation and Restoration of Agronomic and Forest Systems ERSAF, Department of Forest Engineering, University of Córdoba, 14014 Cordoba, Spain
| | - Jesús V. Jorrin-Novo
- Agroforestry and Plant Biochemistry, Proteomics and Systems Biology, Department of Biochemistry and Molecular Biology, University of Cordoba, UCO-CeiA3, 14014 Cordoba, Spain
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Zhu H, Liu C, Qian H. Pharmaceutical Potential of High-Altitude Plants for Fatigue-Related Disorders: A Review. PLANTS 2022; 11:plants11152004. [PMID: 35956482 PMCID: PMC9370126 DOI: 10.3390/plants11152004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 07/22/2022] [Accepted: 07/26/2022] [Indexed: 11/17/2022]
Abstract
Natural plants from plateaus have been the richest source of secondary metabolites extensively used in traditional and modern health care systems. They were submitted to years of natural selection, co-evolved within that habitat, and show significant anti-fatigue-related pharmacological effects. However, currently, no review on high-altitude plants with anti-fatigue related properties has been published yet. This study summarized several Chinese traditional high-altitude plants, including Rhodiola rosea L., Crocus sativus L., Lepidium meyenii W., Hippophaerhamnoides L., which are widely used in the Qinghai–Tibet Plateau and surrounding mountains, as well as herbal markets in the plains. Based on phytopharmacology studies, deeper questions can be further revealed regarding how these plants regulate fatigue and related mental or physical disease conditions. Many active derivatives in high-altitude medical plants show therapeutic potential for the management of fatigue and related disorders. Therefore, high-altitude plants significantly relieve central or peripheral fatigue by acting as neuroprotective agents, energy supplements, metabolism regulators, antioxidant, and inflammatory response inhibitors. Their applications on the highland or flatland and prospects in natural medicine are further forecast, which may open treatments to reduce or prevent fatigue-related disorders in populations with sub-optimal health.
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Affiliation(s)
- Hongkang Zhu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (H.Z.); (C.L.)
- Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Chang Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (H.Z.); (C.L.)
- Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - He Qian
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (H.Z.); (C.L.)
- Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Correspondence:
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26
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Makhumbila P, Rauwane M, Muedi H, Figlan S. Metabolome Profiling: A Breeding Prediction Tool for Legume Performance under Biotic Stress Conditions. PLANTS 2022; 11:plants11131756. [PMID: 35807708 PMCID: PMC9268993 DOI: 10.3390/plants11131756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/17/2022] [Accepted: 06/22/2022] [Indexed: 11/16/2022]
Abstract
Legume crops such as common bean, pea, alfalfa, cowpea, peanut, soybean and others contribute significantly to the diet of both humans and animals. They are also important in the improvement of cropping systems that employ rotation and fix atmospheric nitrogen. Biotic stresses hinder the production of leguminous crops, significantly limiting their yield potential. There is a need to understand the molecular and biochemical mechanisms involved in the response of these crops to biotic stressors. Simultaneous expressions of a number of genes responsible for specific traits of interest in legumes under biotic stress conditions have been reported, often with the functions of the identified genes unknown. Metabolomics can, therefore, be a complementary tool to understand the pathways involved in biotic stress response in legumes. Reports on legume metabolomic studies in response to biotic stress have paved the way in understanding stress-signalling pathways. This review provides a progress update on metabolomic studies of legumes in response to different biotic stresses. Metabolome annotation and data analysis platforms are discussed together with future prospects. The integration of metabolomics with other “omics” tools in breeding programmes can aid greatly in ensuring food security through the production of stress tolerant cultivars.
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Affiliation(s)
- Penny Makhumbila
- Department of Agriculture and Animal Health, School of Agriculture and Life Sciences, College of Agriculture and Environmental Sciences, University of South Africa, 28 Pioneer Ave, Florida Park, Roodeport 1709, South Africa; (M.R.); (S.F.)
- Correspondence:
| | - Molemi Rauwane
- Department of Agriculture and Animal Health, School of Agriculture and Life Sciences, College of Agriculture and Environmental Sciences, University of South Africa, 28 Pioneer Ave, Florida Park, Roodeport 1709, South Africa; (M.R.); (S.F.)
| | - Hangwani Muedi
- Research Support Services, North West Provincial Department of Agriculture and Rural Development, 114 Chris Hani Street, Potchefstroom 2531, South Africa;
| | - Sandiswa Figlan
- Department of Agriculture and Animal Health, School of Agriculture and Life Sciences, College of Agriculture and Environmental Sciences, University of South Africa, 28 Pioneer Ave, Florida Park, Roodeport 1709, South Africa; (M.R.); (S.F.)
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27
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Kang JS, Yadav NS. Special Issue Editorial: Isolation and Analysis of Characteristic Compounds from Herbal and Plant Extracts. PLANTS 2021; 10:plants10122775. [PMID: 34961245 PMCID: PMC8709148 DOI: 10.3390/plants10122775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 12/07/2021] [Indexed: 11/16/2022]
Affiliation(s)
- Jong-Seong Kang
- College of Pharmacy, Chungnam National University, Daejeon 34134, Korea
- Correspondence: (J.-S.K.); (N.S.Y.)
| | - Narendra Singh Yadav
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
- Correspondence: (J.-S.K.); (N.S.Y.)
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