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Hachem M, Ahmmed MK, Nacir-Delord H. Phospholipidomics in Clinical Trials for Brain Disorders: Advancing our Understanding and Therapeutic Potentials. Mol Neurobiol 2024; 61:3272-3295. [PMID: 37981628 PMCID: PMC11087356 DOI: 10.1007/s12035-023-03793-y] [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: 05/19/2023] [Accepted: 10/31/2023] [Indexed: 11/21/2023]
Abstract
Phospholipidomics is a specialized branch of lipidomics that focuses on the characterization and quantification of phospholipids. By using sensitive analytical techniques, phospholipidomics enables researchers to better understand the metabolism and activities of phospholipids in brain disorders such as Alzheimer's and Parkinson's diseases. In the brain, identifying specific phospholipid biomarkers can offer valuable insights into the underlying molecular features and biochemistry of these diseases through a variety of sensitive analytical techniques. Phospholipidomics has emerged as a promising tool in clinical studies, with immense potential to advance our knowledge of neurological diseases and enhance diagnosis and treatment options for patients. In the present review paper, we discussed numerous applications of phospholipidomics tools in clinical studies, with a particular focus on the neurological field. By exploring phospholipids' functions in neurological diseases and the potential of phospholipidomics in clinical research, we provided valuable insights that could aid researchers and clinicians in harnessing the full prospective of this innovative practice and improve patient outcomes by providing more potent treatments for neurological diseases.
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Affiliation(s)
- Mayssa Hachem
- Department of Chemistry and Healthcare Engineering Innovation Center, Khalifa University of Sciences and Technology, P.O. Box 127788, Abu Dhabi, United Arab Emirates.
| | - Mirja Kaizer Ahmmed
- Department of Fishing and Post-Harvest Technology, Chattogram Veterinary and Animal Sciences University, Chattogram, Bangladesh
- Riddet Institute, Massey University, Palmerston North, New Zealand
| | - Houda Nacir-Delord
- Department of Chemistry, Khalifa University of Sciences and Technology, P.O. Box 127788, Abu Dhabi, United Arab Emirates
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2
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Wei H, Chen J, Zhang X, Lu Z, Liu G, Lian B, Yu C, Chen Y, Zhong F, Zhang J. Characterization, expression pattern, and function analysis of gibberellin oxidases in Salix matsudana. Int J Biol Macromol 2024; 266:131095. [PMID: 38537859 DOI: 10.1016/j.ijbiomac.2024.131095] [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: 10/24/2023] [Revised: 03/06/2024] [Accepted: 03/20/2024] [Indexed: 05/01/2024]
Abstract
Gibberellin oxidases (GAoxs) identified from many species play indispensable roles in GA biosynthesis and GA signal transduction. However, there has been limited research conducted on the GAox family of Salix matsudana, a tetraploid ornamental tree species. Here, 54 GAox genes were identified from S. matsudana and renamed as SmGA20ox1-22, SmGA2ox1-24, SmGA3ox1-6, and SmGAox-like1/2. Gene structure and conserved motif analysis showed that SmGA3ox members possess the 1 intron and other SmGAoxs contain 2-3 introns, and motif 1/2/7 universally present in all SmGAoxs. A total of 69 gene pairs were identified from SmGAox family members, and the Ka/Ks values indicated the SmGAoxs experience the purifying selection. The intra species collinearity analysis implied S. matsudana, S. purpurea, and Populus trichocarpa have the close genetic relationship. The GO analysis suggested SmGAoxs are dominantly involved in GA metabolic process, ion binding, and oxidoreductase activity. RNA-sequencing demonstrated that some SmGAoxs may play an essential role in salt and submergence stresses. In addition, the SmGA20ox13/21 displayed the dominant vitality of GA20 oxidase, but the SmGA20ox13/21 still possessed low activities of GA2 and GA3 oxidases. This study can contribute to reveal the regulatory mechanism of salt and submergence tolerance in willow.
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Affiliation(s)
- Hui Wei
- Key Laboratory of Landscape Plant Genetics and Breeding, School of Life Sciences, Nantong University, Nantong, China; Key Lab of Landscape Plant Genetics and Breeding, Nantong 226000, China
| | - Jinxin Chen
- Key Laboratory of Landscape Plant Genetics and Breeding, School of Life Sciences, Nantong University, Nantong, China; Key Lab of Landscape Plant Genetics and Breeding, Nantong 226000, China
| | - Xingyue Zhang
- Key Laboratory of Landscape Plant Genetics and Breeding, School of Life Sciences, Nantong University, Nantong, China; Key Lab of Landscape Plant Genetics and Breeding, Nantong 226000, China.
| | - Zixuan Lu
- Key Laboratory of Landscape Plant Genetics and Breeding, School of Life Sciences, Nantong University, Nantong, China; Key Lab of Landscape Plant Genetics and Breeding, Nantong 226000, China
| | - Guoyuan Liu
- Key Laboratory of Landscape Plant Genetics and Breeding, School of Life Sciences, Nantong University, Nantong, China; Key Lab of Landscape Plant Genetics and Breeding, Nantong 226000, China
| | - Bolin Lian
- Key Laboratory of Landscape Plant Genetics and Breeding, School of Life Sciences, Nantong University, Nantong, China; Key Lab of Landscape Plant Genetics and Breeding, Nantong 226000, China.
| | - Chunmei Yu
- Key Laboratory of Landscape Plant Genetics and Breeding, School of Life Sciences, Nantong University, Nantong, China; Key Lab of Landscape Plant Genetics and Breeding, Nantong 226000, China.
| | - Yanhong Chen
- Key Laboratory of Landscape Plant Genetics and Breeding, School of Life Sciences, Nantong University, Nantong, China; Key Lab of Landscape Plant Genetics and Breeding, Nantong 226000, China.
| | - Fei Zhong
- Key Laboratory of Landscape Plant Genetics and Breeding, School of Life Sciences, Nantong University, Nantong, China; Key Lab of Landscape Plant Genetics and Breeding, Nantong 226000, China.
| | - Jian Zhang
- Key Laboratory of Landscape Plant Genetics and Breeding, School of Life Sciences, Nantong University, Nantong, China; Key Lab of Landscape Plant Genetics and Breeding, Nantong 226000, China.
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He D, Yao X, Zhang P, Liu W, Huang J, Sun H, Wang N, Zhang X, Wang H, Zhang H, Ao X, Xie F. Effects of continuous cropping on fungal community diversity and soil metabolites in soybean roots. Microbiol Spectr 2023; 11:e0178623. [PMID: 37811990 PMCID: PMC10715103 DOI: 10.1128/spectrum.01786-23] [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: 04/28/2023] [Accepted: 08/11/2023] [Indexed: 10/10/2023] Open
Abstract
IMPORTANCE Soybean yield can be affected by soybean soil fungal communities in different tillage patterns. Soybean is an important food crop with great significance worldwide. Continuous cultivation resulted in soil nutrient deficiencies, disordered metabolism of root exudates, fungal pathogen accumulation, and an altered microbial community, which brought a drop in soybean output. In this study, taking the soybean agroecosystem in northeast China, we revealed the microbial ecology and soil metabolites spectrum, especially the diversity and composition of soil fungi and the correlation of pathogenic fungi, and discussed the mechanisms and the measures of alleviating the obstacles.
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Affiliation(s)
- Dexin He
- Soybean Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Xingdong Yao
- Soybean Research Institute, Shenyang Agricultural University, Shenyang, China
- Postdoctoral Station of Agricultural Resources and Environment, Land and Environment College, Shenyang Agricultural University, Shenyang, China
| | - Pengyu Zhang
- Inner Mongolia Agronomy and Animal Husbandry Technology Extension Center, Hohhot, Inner Mongolia, China
| | - Wenbo Liu
- Soybean Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Junxia Huang
- Soybean Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Hexiang Sun
- Soybean Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Nan Wang
- Soybean Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Xuejing Zhang
- Soybean Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Haiying Wang
- Soybean Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Huijun Zhang
- Soybean Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Xue Ao
- Soybean Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Futi Xie
- Soybean Research Institute, Shenyang Agricultural University, Shenyang, China
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4
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Fatimawali, Tallei TE, Kepel BJ, Bodhi W, Manampiring AE, Nainu F. Molecular Insight into the Pharmacological Potential of Clerodendrum minahassae Leaf Extract for Type-2 Diabetes Management Using the Network Pharmacology Approach. MEDICINA (KAUNAS, LITHUANIA) 2023; 59:1899. [PMID: 38003949 PMCID: PMC10673377 DOI: 10.3390/medicina59111899] [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: 09/16/2023] [Revised: 10/18/2023] [Accepted: 10/23/2023] [Indexed: 11/26/2023]
Abstract
Background and Objectives: The increasing occurrence and prevalence of type-2 diabetes mellitus (T2DM) have led to a growing interest in researching available treatment alternatives. Clerodendrum minahassae, a native plant species of North Sulawesi, has been a focus of ethnopharmacological studies due to its significance contributions to drug development, particularly its potential antidiabetic properties. This study investigated the pharmacological potential of Clerodendrum minahassae (CM) leaf extract for managing type-2 diabetes (T2DM) using a network pharmacology approach. Materials and Methods: Active compounds were extracted from CM leaves, and their interactions with target proteins in T2DM were explored through various in silico analyses. Results: SAR analysis using Way2Drug Pass Online identified 29 bioactive CM leaf extract compounds with promise as T2DM treatments. Additionally, 26 of these met Ro5 criteria for favorable drug-likeness. Most compounds exhibited positive pharmacodynamic and pharmacokinetic profiles, with 22 considered safe, while 7 posed potential toxicity risks when ingested individually. CM leaf extract targeted 60 T2DM-related proteins, potentially affecting T2DM via cytokine regulation, particularly in proteins linked to metabolic processes, cellular response to angiotensin, and the sphingosine-1-phosphate signaling pathway. The network pharmacology analysis identified five genes targeted by CM leaf extract, namely, STAT3, MAPK1, ESR1, PIK3R1, and NFKB1. Among these genes, PIK3R1's interaction with the insulin receptor (INSR) positions it as a crucial candidate gene due to its pivotal role in insulin signal transduction during T2DM development. Conclusions: This research sheds light on the therapeutic potential of CM leaf extract for treating T2DM. This potential is attributed to the diverse array of bioactive compounds present in the extract, which have the capacity to interact with and inhibit proteins participating in the insulin signal transduction pathway crucial for the progression of T2DM. The findings of this study may open up possibilities for future applications of CM leaf extract in the development of novel T2DM treatments.
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Affiliation(s)
- Fatimawali
- Department of Pharmacy, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University, Manado 95115, North Sulawesi, Indonesia
| | - Trina Ekawati Tallei
- Department of Biology, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University, Manado 95115, North Sulawesi, Indonesia
- Department of Biology, Faculty of Medicine, Sam Ratulangi University, Manado 95115, North Sulawesi, Indonesia
| | - Billy Johnson Kepel
- Department of Chemistry, Faculty of Medicine, Sam Ratulangi University, Manado 95115, North Sulawesi, Indonesia; (B.J.K.); (W.B.); (A.E.M.)
| | - Widdhi Bodhi
- Department of Chemistry, Faculty of Medicine, Sam Ratulangi University, Manado 95115, North Sulawesi, Indonesia; (B.J.K.); (W.B.); (A.E.M.)
| | - Aaltje Ellen Manampiring
- Department of Chemistry, Faculty of Medicine, Sam Ratulangi University, Manado 95115, North Sulawesi, Indonesia; (B.J.K.); (W.B.); (A.E.M.)
| | - Firzan Nainu
- Department of Pharmacy, Faculty of Pharmacy, Hasanuddin University, Makassar 90245, South Sulawesi, Indonesia;
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Singh U, Alsuhaymi S, Al-Nemi R, Emwas AH, Jaremko M. Compound-Specific 1D 1H NMR Pulse Sequence Selection for Metabolomics Analyses. ACS OMEGA 2023; 8:23651-23663. [PMID: 37426221 PMCID: PMC10324067 DOI: 10.1021/acsomega.3c01688] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 04/13/2023] [Indexed: 07/11/2023]
Abstract
NMR-based metabolomics approaches have been used in a wide range of applications, for example, with medical, plant, and marine samples. One-dimensional (1D) 1H NMR is routinely used to find out biomarkers in biofluids such as urine, blood plasma, and serum. To mimic biological conditions, most NMR studies have been carried out in an aqueous solution where the high intensity of the water peak is a major problem in obtaining a meaningful spectrum. Different methods have been used to suppress the water signal, including 1D Carr-Purcell-Meiboom-Gill (CPMG) presat, consisting of a T2 filter to suppress macromolecule signals and reduce the humped curve in the spectrum. 1D nuclear Overhauser enhancement spectroscopy (NOESY) is another method for water suppression that is used routinely in plant samples with fewer macromolecules than in biofluid samples. Other common 1D 1H NMR methods such as 1D 1H presat and 1D 1H ES have simple pulse sequences; their acquisition parameters can be set easily. The proton with presat has just one pulse and the presat block causes water suppression, while other 1D 1H NMR methods including those mentioned above have more pulses. However, it is not well known in metabolomics studies because it is used only occasionally and in a few types of samples by metabolomics experts. Another effective method is excitation sculpting to suppress water. Herein, we evaluate the effect of method selection on signal intensities of commonly detected metabolites. Different classes of samples including biofluid, plant, and marine samples were investigated, and recommendations on the advantages and limitations of each method are presented.
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Affiliation(s)
- Upendra Singh
- Smart-Health
Initiative (SHI) and Red Sea Research Center (RSRC), Division of Biological
and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Makkah 23955-6900, Saudi
Arabia
| | - Shuruq Alsuhaymi
- Smart-Health
Initiative (SHI) and Red Sea Research Center (RSRC), Division of Biological
and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Makkah 23955-6900, Saudi
Arabia
| | - Ruba Al-Nemi
- Smart-Health
Initiative (SHI) and Red Sea Research Center (RSRC), Division of Biological
and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Makkah 23955-6900, Saudi
Arabia
| | - Abdul-Hamid Emwas
- Core
Lab of NMR, King Abdullah University of
Science and Technology (KAUST), Thuwal, Makkah 23955-6900, Saudi Arabia
| | - Mariusz Jaremko
- Smart-Health
Initiative (SHI) and Red Sea Research Center (RSRC), Division of Biological
and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Makkah 23955-6900, Saudi
Arabia
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6
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Nicoleti JL, Braga ES, Stanisic D, Jadranin M, Façanha DAE, Barral TD, Hanna SA, Azevedo V, Meyer R, Tasic L, Portela RW. A serum NMR metabolomic analysis of the Corynebacterium pseudotuberculosis infection in goats. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12595-0. [PMID: 37219572 DOI: 10.1007/s00253-023-12595-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 05/10/2023] [Accepted: 05/15/2023] [Indexed: 05/24/2023]
Abstract
Caseous lymphadenitis (CLA), an infectious disease caused by Corynebacterium pseudotuberculosis in small ruminants, is highly prevalent worldwide. Economic losses have already been associated with the disease, and little is known about the host-pathogen relationship associated with the disease. The present study aimed to perform a metabolomic study of the C. pseudotuberculosis infection in goats. Serum samples were collected from a herd of 173 goats. The animals were classified as controls (not infected), asymptomatic (seropositives but without detectable CLA clinical signs), and symptomatic (seropositive animals presenting CLA lesions), according to microbiological isolation and immunodiagnosis. The serum samples were analyzed using nuclear magnetic resonance (1H-NMR), nuclear Overhauser effect spectroscopy (NOESY), and Carr-Purcell-Meiboom-Gill (CPMG) sequences. The NMR data were analyzed using chemometrics, and principal component analysis (PCA) and partial least square discriminant analysis (PLS-DA) were performed to discover specific biomarkers responsible for discrimination between the groups. A high dissemination of the infection by C. pseudotuberculosis was observed, being 74.57% asymptomatic and 11.56% symptomatic. In the evaluation of 62 serum samples by NMR, the techniques were satisfactory in the discrimination of the groups, being also complementary and mutually confirming, demonstrating possible biomarkers for the infection by the bacterium. Twenty metabolites of interest were identified by NOESY and 29 by CPMG, such as tryptophan, polyunsaturated fatty acids, formic acid, NAD+, and 3-hydroxybutyrate, opening promising possibilities for the use of these results in new therapeutic, immunodiagnosis, and immunoprophylactic tools, as well as for studies of the immune response against C. pseudotuberculosis. KEY POINTS: • Sixty-two samples from healthy, CLA asymptomatic, and symptomatic goats were screened • Twenty metabolites of interest were identified by NOESY and 29 by CPMG • 1H-NMR NOESY and CPMG were complementary and mutually confirming.
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Affiliation(s)
- Jorge Luis Nicoleti
- Laboratório de Imunologia E Biologia Molecular, Instituto de Ciências da Saúde, Universidade Federal da Bahia, Salvador, Bahia State, 40231-300, Brazil
| | - Erik Sobrinho Braga
- Laboratório de Química Biológica, Instituto de Química, Universidade Estadual de Campinas, Campinas, São Paulo State, 13083-970, Brazil
| | - Danijela Stanisic
- Laboratório de Química Biológica, Instituto de Química, Universidade Estadual de Campinas, Campinas, São Paulo State, 13083-970, Brazil
| | - Milka Jadranin
- Laboratório de Química Biológica, Instituto de Química, Universidade Estadual de Campinas, Campinas, São Paulo State, 13083-970, Brazil
- Institute of Chemistry, Technology and Metallurgy, University of Belgrade, 11000, Belgrade, Serbia
| | - Débora Andréa Evangelista Façanha
- Institute of Rural Development, Universidade da Integração Internacional da Lusofonia Afro-Brasileira, Redenção, Ceará State, 62790-000, Brazil
| | - Thiago Doria Barral
- Laboratório de Imunologia E Biologia Molecular, Instituto de Ciências da Saúde, Universidade Federal da Bahia, Salvador, Bahia State, 40231-300, Brazil
| | - Samira Abdallah Hanna
- Laboratório de Imunologia E Biologia Molecular, Instituto de Ciências da Saúde, Universidade Federal da Bahia, Salvador, Bahia State, 40231-300, Brazil
| | - Vasco Azevedo
- Laboratório de Genética Celular e Molecular, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais State, 31270-901, Brazil
| | - Roberto Meyer
- Laboratório de Imunologia E Biologia Molecular, Instituto de Ciências da Saúde, Universidade Federal da Bahia, Salvador, Bahia State, 40231-300, Brazil
| | - Ljubica Tasic
- Laboratório de Química Biológica, Instituto de Química, Universidade Estadual de Campinas, Campinas, São Paulo State, 13083-970, Brazil
| | - Ricardo Wagner Portela
- Laboratório de Imunologia E Biologia Molecular, Instituto de Ciências da Saúde, Universidade Federal da Bahia, Salvador, Bahia State, 40231-300, Brazil.
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Integrated Transcriptomic and Metabolomics Analysis of the Root Responses of Orchardgrass to Submergence Stress. Int J Mol Sci 2023; 24:ijms24032089. [PMID: 36768412 PMCID: PMC9916531 DOI: 10.3390/ijms24032089] [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: 11/29/2022] [Revised: 01/07/2023] [Accepted: 01/16/2023] [Indexed: 01/21/2023] Open
Abstract
Submergence stress can severely affect plant growth. Orchardgrass (Dactylis glomerata L.) is an important forage grass, and the molecular mechanisms of orchardgrass to submergence stress are not well understood. The roots of the flood-tolerant cultivar "Dian Bei" were harvested at 0 h, 8 h and 24 h of submergence stress. The combined transcriptomic and metabolomic analyses showed that β-alanine metabolism, flavonoid biosynthesis, and biosynthesis of amino acid pathways were significantly enriched at 8 h and 24 h of submergence stress and were more pronounced at 24 h. Most of the flavonoid biosynthesis-related genes were down-regulated for the synthesis of metabolites such as naringenin, apigenin, naringin, neohesperidin, naringenin chalcone, and liquiritigenin in response to submergence stress. Metabolites such as phenylalanine, tyrosine, and tryptophan were up-regulated under stress. The predominant response of flavonoid and amino acids biosynthesis to submergence stress suggests an important role of these pathways in the submergence tolerance of orchardgrass.
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8
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Skin Cancer Metabolic Profile Assessed by Different Analytical Platforms. Int J Mol Sci 2023; 24:ijms24021604. [PMID: 36675128 PMCID: PMC9866771 DOI: 10.3390/ijms24021604] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/03/2023] [Accepted: 01/10/2023] [Indexed: 01/17/2023] Open
Abstract
Skin cancer, including malignant melanoma (MM) and keratinocyte carcinoma (KC), historically named non-melanoma skin cancers (NMSC), represents the most common type of cancer among the white skin population. Despite decades of clinical research, the incidence rate of melanoma is increasing globally. Therefore, a better understanding of disease pathogenesis and resistance mechanisms is considered vital to accomplish early diagnosis and satisfactory control. The "Omics" field has recently gained attention, as it can help in identifying and exploring metabolites and metabolic pathways that assist cancer cells in proliferation, which can be further utilized to improve the diagnosis and treatment of skin cancer. Although skin tissues contain diverse metabolic enzymes, it remains challenging to fully characterize these metabolites. Metabolomics is a powerful omics technique that allows us to measure and compare a vast array of metabolites in a biological sample. This technology enables us to study the dermal metabolic effects and get a clear explanation of the pathogenesis of skin diseases. The purpose of this literature review is to illustrate how metabolomics technology can be used to evaluate the metabolic profile of human skin cancer, using a variety of analytical platforms including gas chromatography-mass spectrometry (GC-MS), liquid chromatography-mass spectrometry (LC-MS), and nuclear magnetic resonance (NMR). Data collection has not been based on any analytical method.
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Park E, Yu H, Lim JH, Hee Choi J, Park KJ, Lee J. Seaweed metabolomics: A review on its nutrients, bioactive compounds and changes in climate change. Food Res Int 2023; 163:112221. [PMID: 36596150 DOI: 10.1016/j.foodres.2022.112221] [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: 08/22/2022] [Revised: 11/15/2022] [Accepted: 11/20/2022] [Indexed: 11/25/2022]
Abstract
Seaweed, an important food resource in several Asian countries, contains various metabolites, including sugars, organic acids, and amino acids; however, their content is affected by prevailing environmental conditions. This review discusses seaweed metabolomics, especially the distribution of primary and functional secondary metabolites (e.g., carotenoids, polyphenols) in seaweed. Additionally, the effects of global warming on seaweed metabolite profile changes are discussed. For example, high temperatures can increase amino acid levels in seaweeds. Overall, understanding the effects of global warming on seaweed metabolite profiles can be useful for evaluating the nutritional composition of seaweeds as food. This review provides an overview of recent applications of metabolomics in seaweed research as well as a perspective on the nutrient content and cultivation of seaweeds under climate change scenarios.
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Affiliation(s)
- Eunyoung Park
- Department of Food Science and Technology, Chung-Ang University, Anseong 17546, Republic of Korea
| | - Hahyeong Yu
- Department of Food Science and Technology, Chung-Ang University, Anseong 17546, Republic of Korea
| | - Jeong-Ho Lim
- Research Group of Consumer Safety, Korea Food Research Institute, Wanju 55365, Republic of Korea
| | - Jeong Hee Choi
- Research Group of Consumer Safety, Korea Food Research Institute, Wanju 55365, Republic of Korea
| | - Kee-Jai Park
- Research Group of Consumer Safety, Korea Food Research Institute, Wanju 55365, Republic of Korea.
| | - Jihyun Lee
- Department of Food Science and Technology, Chung-Ang University, Anseong 17546, Republic of Korea.
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10
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Rao SW, Duan YY, Zhao DS, Liu CJ, Xu SH, Liang D, Zhang FX, Shi W. Integrative Analysis of Transcriptomic and Metabolomic Data for Identification of Pathways Related to Matrine-Induced Hepatotoxicity. Chem Res Toxicol 2022; 35:2271-2284. [PMID: 36440846 DOI: 10.1021/acs.chemrestox.2c00264] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Matrine (MT) is a major bioactive compound extracted from Sophorae tonkinensis. However, the clinical application of MT is relatively restricted due to its potentially toxic effects, especially hepatotoxicity. Although MT-induced liver injury has been reported, little is known about the underlying molecular mechanisms. In this study, transcriptomics and metabolomics were applied to investigate the hepatotoxicity of MT in mice. The results indicated that liver injury occurred when the administration of MT (30 or 60 mg/kg, i.g) lasted for 2 weeks, including dramatically increased alanine aminotransferase (ALT), aspartate aminotransferase (AST), etc. The metabolomic results revealed that steroid biosynthesis, purine metabolism, glutathione metabolism, and pyruvate metabolism were involved in the occurrence and development of MT-induced hepatotoxicity. Further, the transcriptomic data indicated that the downregulation of NSDHL with CYP51, FDFT1, and DHCR7, involved in steroid biosynthesis, resulted in a lower level of cholic acid. Besides, Gstps and Nat8f1 were related to the disorder of glutathione metabolism, and HMGCS1 could be treated as the marker gene of the development of MT-induced hepatotoxicity. In addition, other metabolites, such as taurine, flavin mononucleotide (FMN), and inosine monophosphate (IMP), also made a contribution to the boosting of MT-induced hepatotoxicity. In this work, our results provide clues for the mechanism investigation of MT-induced hepatotoxicity, and several biomarkers (metabolites and genes) closely related to the liver injury caused by MT are also provided. Meanwhile, new insights into the understanding of the development of MT-induced hepatotoxicity or other monomer-induced hepatotoxicity were also provided.
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Affiliation(s)
- Si-Wei Rao
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Science, Guangxi Normal University, Guilin 541004, P. R. China
| | - Yuan-Yuan Duan
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Science, Guangxi Normal University, Guilin 541004, P. R. China
| | - Dong-Sheng Zhao
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, P. R. China
| | - Cheng-Jun Liu
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Science, Guangxi Normal University, Guilin 541004, P. R. China
| | - Shao-Hua Xu
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Science, Guangxi Normal University, Guilin 541004, P. R. China
| | - Dong Liang
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Science, Guangxi Normal University, Guilin 541004, P. R. China
| | - Feng-Xiang Zhang
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Science, Guangxi Normal University, Guilin 541004, P. R. China
| | - Wei Shi
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Science, Guangxi Normal University, Guilin 541004, P. R. China
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11
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Huo L, Wang H, Wang Q, Gao Y, Xu K, Sun X. Exogenous treatment with melatonin enhances waterlogging tolerance of kiwifruit plants. FRONTIERS IN PLANT SCIENCE 2022; 13:1081787. [PMID: 36570925 PMCID: PMC9780670 DOI: 10.3389/fpls.2022.1081787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 11/25/2022] [Indexed: 06/17/2023]
Abstract
Waterlogging stress has an enormous negative impact on the kiwifruit yield and quality. The protective role of exogenous melatonin on water stress has been widely studied, especially in drought stress. However, the research on melatonin-induced waterlogging tolerance is scarce. Here, we found that treatment with exogenous melatonin could effectively alleviate the damage on kiwifruit plants in response to waterlogging treatment. This was accompanied by higher antioxidant activity and lower ROS accumulation in kiwifruit roots during stress period. The detection of changes in amino acid levels of kiwifruit roots during waterlogging stress showed a possible interaction between melatonin and amino acid metabolism, which promoted the tolerance of kiwifruit plants to waterlogging. The higher levels of GABA and Pro in the roots of melatonin-treated kiwifruit plants partly contributed to their improved waterlogging tolerance. In addition, some plant hormones were also involved in the melatonin-mediated waterlogging tolerance, such as the enhancement of ACC accumulation. This study discussed the melatonin-mediated water stress tolerance of plants from the perspective of amino acid metabolism for the first time.
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Affiliation(s)
| | | | | | | | - Kai Xu
- *Correspondence: Kai Xu, ; Liuqing Huo,
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12
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Advances in Plant Metabolomics and Its Applications in Stress and Single-Cell Biology. Int J Mol Sci 2022; 23:ijms23136985. [PMID: 35805979 PMCID: PMC9266571 DOI: 10.3390/ijms23136985] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 06/19/2022] [Accepted: 06/19/2022] [Indexed: 02/04/2023] Open
Abstract
In the past two decades, the post-genomic era envisaged high-throughput technologies, resulting in more species with available genome sequences. In-depth multi-omics approaches have evolved to integrate cellular processes at various levels into a systems biology knowledge base. Metabolomics plays a crucial role in molecular networking to bridge the gaps between genotypes and phenotypes. However, the greater complexity of metabolites with diverse chemical and physical properties has limited the advances in plant metabolomics. For several years, applications of liquid/gas chromatography (LC/GC)-mass spectrometry (MS) and nuclear magnetic resonance (NMR) have been constantly developed. Recently, ion mobility spectrometry (IMS)-MS has shown utility in resolving isomeric and isobaric metabolites. Both MS and NMR combined metabolomics significantly increased the identification and quantification of metabolites in an untargeted and targeted manner. Thus, hyphenated metabolomics tools will narrow the gap between the number of metabolite features and the identified metabolites. Metabolites change in response to environmental conditions, including biotic and abiotic stress factors. The spatial distribution of metabolites across different organs, tissues, cells and cellular compartments is a trending research area in metabolomics. Herein, we review recent technological advancements in metabolomics and their applications in understanding plant stress biology and different levels of spatial organization. In addition, we discuss the opportunities and challenges in multiple stress interactions, multi-omics, and single-cell metabolomics.
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13
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Xu Y, Fu X. Reprogramming of Plant Central Metabolism in Response to Abiotic Stresses: A Metabolomics View. Int J Mol Sci 2022; 23:ijms23105716. [PMID: 35628526 PMCID: PMC9143615 DOI: 10.3390/ijms23105716] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Revised: 05/15/2022] [Accepted: 05/18/2022] [Indexed: 12/15/2022] Open
Abstract
Abiotic stresses rewire plant central metabolism to maintain metabolic and energy homeostasis. Metabolites involved in the plant central metabolic network serve as a hub for regulating carbon and energy metabolism under various stress conditions. In this review, we introduce recent metabolomics techniques used to investigate the dynamics of metabolic responses to abiotic stresses and analyze the trend of publications in this field. We provide an updated overview of the changing patterns in central metabolic pathways related to the metabolic responses to common stresses, including flooding, drought, cold, heat, and salinity. We extensively review the common and unique metabolic changes in central metabolism in response to major abiotic stresses. Finally, we discuss the challenges and some emerging insights in the future application of metabolomics to study plant responses to abiotic stresses.
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Affiliation(s)
- Yuan Xu
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
- Correspondence: (Y.X.); (X.F.)
| | - Xinyu Fu
- Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
- Correspondence: (Y.X.); (X.F.)
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14
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Alpuerto JB, Fukuda M, Li S, Hussain RMF, Sakane K, Fukao T. The submergence tolerance regulator SUB1A differentially coordinates molecular adaptation to submergence in mature and growing leaves of rice (Oryza sativa L.). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:71-87. [PMID: 34978355 DOI: 10.1111/tpj.15654] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 12/06/2021] [Accepted: 12/20/2021] [Indexed: 06/14/2023]
Abstract
A typical adaptive response to submergence regulated by SUB1A, the ethylene-responsive transcription factor gene, is the restricted elongation of the uppermost leaves. However, the molecular and physiological functions of SUB1A have been characterized using entire shoot tissues, most of which are mature leaves that do not elongate under submergence. We aimed to identify leaf-type-specific and overlapping adaptations coordinated in SUB1A-dependent and -independent manners. To this end, we compared the transcriptomic and hormonal responses to submergence between mature and growing leaves using rice genotypes with and without SUB1A. Monosaccharide, branched-chain amino acid, and nucleoside metabolism, associated with ATP synthesis, were commonly activated in both leaf types regardless of genotype. In both leaf types, pathways involved in carbohydrate and nitrogen metabolism were suppressed by SUB1A, with more severe restriction in growing leaves that have a greater energy demand if SUB1A is absent. In growing leaves, accumulation of and responsiveness to growth-regulating hormones were properly modulated by SUB1A, which correlated with restricted elongation. In mature leaves, submergence-induced auxin accumulation was suppressed by SUB1A. This study demonstrates that different sets of hormonal pathways, both of which are modulated by SUB1A, contribute to distinct adaptive responses to submergence in mature and growing rice leaves.
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Affiliation(s)
- Jasper B Alpuerto
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Mika Fukuda
- Department of Bioscience and Biotechnology, Fukui Prefectural University, Eiheiji, Fukui, 910-1195, Japan
| | - Song Li
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Rana M F Hussain
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Kodai Sakane
- Department of Bioscience and Biotechnology, Fukui Prefectural University, Eiheiji, Fukui, 910-1195, Japan
| | - Takeshi Fukao
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, 24061, USA
- Department of Bioscience and Biotechnology, Fukui Prefectural University, Eiheiji, Fukui, 910-1195, Japan
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15
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Jethva J, Schmidt RR, Sauter M, Selinski J. Try or Die: Dynamics of Plant Respiration and How to Survive Low Oxygen Conditions. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11020205. [PMID: 35050092 PMCID: PMC8780655 DOI: 10.3390/plants11020205] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/07/2022] [Accepted: 01/11/2022] [Indexed: 05/09/2023]
Abstract
Fluctuations in oxygen (O2) availability occur as a result of flooding, which is periodically encountered by terrestrial plants. Plant respiration and mitochondrial energy generation rely on O2 availability. Therefore, decreased O2 concentrations severely affect mitochondrial function. Low O2 concentrations (hypoxia) induce cellular stress due to decreased ATP production, depletion of energy reserves and accumulation of metabolic intermediates. In addition, the transition from low to high O2 in combination with light changes-as experienced during re-oxygenation-leads to the excess formation of reactive oxygen species (ROS). In this review, we will update our current knowledge about the mechanisms enabling plants to adapt to low-O2 environments, and how to survive re-oxygenation. New insights into the role of mitochondrial retrograde signaling, chromatin modification, as well as moonlighting proteins and mitochondrial alternative electron transport pathways (and their contribution to low O2 tolerance and survival of re-oxygenation), are presented.
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Affiliation(s)
- Jay Jethva
- Department of Plant Developmental Biology and Plant Physiology, Faculty of Mathematics and Natural Sciences, Botanical Institute, Christian-Albrechts University, D-24118 Kiel, Germany; (J.J.); (M.S.)
| | - Romy R. Schmidt
- Department of Plant Biotechnology, Faculty of Biology, University of Bielefeld, D-33615 Bielefeld, Germany;
| | - Margret Sauter
- Department of Plant Developmental Biology and Plant Physiology, Faculty of Mathematics and Natural Sciences, Botanical Institute, Christian-Albrechts University, D-24118 Kiel, Germany; (J.J.); (M.S.)
| | - Jennifer Selinski
- Department of Plant Cell Biology, Botanical Institute, Faculty of Mathematics and Natural Sciences, Christian-Albrechts University, D-24118 Kiel, Germany
- Correspondence: ; Tel.: +49-(0)431-880-4245
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16
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Zemaitis KJ, Ye H, Nguyen HT, Wood TD. Direct Infusion Metabolomics of the Photosystem and Chlorophyll Related Metabolites within a Drought Tolerant Plant Introduction of Glycine max. Metabolites 2021; 11:metabo11120843. [PMID: 34940601 PMCID: PMC8706224 DOI: 10.3390/metabo11120843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 11/29/2021] [Accepted: 11/30/2021] [Indexed: 11/16/2022] Open
Abstract
Drought is the most prolific form of abiotic stress that legumes and cereal plants alike can endure, and the planting of an improper cultivar at the beginning of a season can cause unexpected losses up to fifty percent under water deficient conditions. Herein, a plant introduction (PI) of an exotic cultivar of soybean (Glycine max), PI 567731, which demonstrates a slow wilting (SW) canopy phenotype in maturity group III, was profiled under drought conditions in field trials in Missouri against a drought susceptible check cultivar, Pana. Metabolomic profiling was carried out on samples of leaves from each of these cultivars at V5 and R2 growth stages both while irrigated and while under drought stress for three weeks. PI 567731 was observed to have differential phytochemical content, and enhanced levels of chlorophyll (Chl) a/b and pheophytin (Pheo) were profiled by direct infusion electrospray Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). Indicating drought induced changes of the photosystem and photosynthetic capabilities alongside water preservation strategies are important within the SW phenotype drought response. Subsequent multivariate analysis was able to form predictive models, encompassing the variance of growth and drought stress of the cultivar. Moreover, the existence of unique Chl-related metabolites (CRM) (m/z > 900) were confirmed through tandem mass spectrometry. The resultant coordination of fatty acids to the core of the porphyrin ring was observed and played an unknown role in the proliferation of the photosynthesis. However, the relative ratio of the most abundant CRM is undisturbed by drought stress in PI 567731, in contrast to the drought susceptible cultivar. These results provide key insights into drought related metabolic mechanisms.
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Affiliation(s)
- Kevin J. Zemaitis
- Department of Chemistry, Natural Sciences Complex, University at Buffalo, State University of New York, Buffalo, NY 14260, USA;
| | - Heng Ye
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO 65211, USA; (H.Y.); (H.T.N.)
| | - Henry T. Nguyen
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO 65211, USA; (H.Y.); (H.T.N.)
| | - Troy D. Wood
- Department of Chemistry, Natural Sciences Complex, University at Buffalo, State University of New York, Buffalo, NY 14260, USA;
- Correspondence:
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17
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Metabolomics and Molecular Approaches Reveal Drought Stress Tolerance in Plants. Int J Mol Sci 2021; 22:ijms22179108. [PMID: 34502020 PMCID: PMC8431676 DOI: 10.3390/ijms22179108] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/17/2021] [Accepted: 08/20/2021] [Indexed: 01/21/2023] Open
Abstract
Metabolic regulation is the key mechanism implicated in plants maintaining cell osmotic potential under drought stress. Understanding drought stress tolerance in plants will have a significant impact on food security in the face of increasingly harsh climatic conditions. Plant primary and secondary metabolites and metabolic genes are key factors in drought tolerance through their involvement in diverse metabolic pathways. Physio-biochemical and molecular strategies involved in plant tolerance mechanisms could be exploited to increase plant survival under drought stress. This review summarizes the most updated findings on primary and secondary metabolites involved in drought stress. We also examine the application of useful metabolic genes and their molecular responses to drought tolerance in plants and discuss possible strategies to help plants to counteract unfavorable drought periods.
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18
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Ackah M, Shi Y, Wu M, Wang L, Guo P, Guo L, Jin X, Li S, Zhang Q, Qiu C, Lin Q, Zhao W. Metabolomics Response to Drought Stress in Morus alba L. Variety Yu-711. PLANTS (BASEL, SWITZERLAND) 2021; 10:1636. [PMID: 34451681 PMCID: PMC8400578 DOI: 10.3390/plants10081636] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/04/2021] [Accepted: 08/05/2021] [Indexed: 11/16/2022]
Abstract
Mulberry is an economically significant crop for the sericulture industry worldwide. Stresses such as drought exposure have a significant influence on plant survival. Because metabolome directly reflects plant physiological condition, performing a global metabolomic analysis is one technique to examine this influence. Using a liquid chromatography-mass spectrometry (LC-MS) technique based on an untargeted metabolomic approach, the effect of drought stress on mulberry Yu-711 metabolic balance was examined. For this objective, Yu-711 leaves were subjected to two weeks of drought stress treatment and control without drought stress. Numerous differentially accumulated metabolic components in response to drought stress treatment were revealed by multivariate and univariate statistical analysis. Drought stress treatment (EG) revealed a more differentiated metabolite response than the control (CK). We found that the levels of total lipids, galactolipids, and phospholipids (PC, PA, PE) were significantly altered, producing 48% of the total differentially expressed metabolites. Fatty acyls components were the most abundant lipids expressed and decreased considerably by 73.6%. On the other hand, the prenol lipids class of lipids increased in drought leaves. Other classes of metabolites, including polyphenols (flavonoids and cinnamic acid), organic acid (amino acids), carbohydrates, benzenoids, and organoheterocyclic, had a dynamic trend in response to the drought stress. However, their levels under drought stress decreased significantly compared to the control. These findings give an overview for the understanding of global plant metabolic changes in defense mechanisms by revealing the mulberry plant metabolic profile through differentially accumulated compounds.
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Affiliation(s)
- Michael Ackah
- School of Biology and Technology, Jiangsu University of Science and Technology, Sibaidu, Zhenjiang 212018, China; (Y.S.); (M.W.); (L.W.); (P.G.); (L.G.); (X.J.); (S.L.); (Q.Z.)
| | - Yisu Shi
- School of Biology and Technology, Jiangsu University of Science and Technology, Sibaidu, Zhenjiang 212018, China; (Y.S.); (M.W.); (L.W.); (P.G.); (L.G.); (X.J.); (S.L.); (Q.Z.)
| | - Mengmeng Wu
- School of Biology and Technology, Jiangsu University of Science and Technology, Sibaidu, Zhenjiang 212018, China; (Y.S.); (M.W.); (L.W.); (P.G.); (L.G.); (X.J.); (S.L.); (Q.Z.)
| | - Lei Wang
- School of Biology and Technology, Jiangsu University of Science and Technology, Sibaidu, Zhenjiang 212018, China; (Y.S.); (M.W.); (L.W.); (P.G.); (L.G.); (X.J.); (S.L.); (Q.Z.)
| | - Peng Guo
- School of Biology and Technology, Jiangsu University of Science and Technology, Sibaidu, Zhenjiang 212018, China; (Y.S.); (M.W.); (L.W.); (P.G.); (L.G.); (X.J.); (S.L.); (Q.Z.)
| | - Liangliang Guo
- School of Biology and Technology, Jiangsu University of Science and Technology, Sibaidu, Zhenjiang 212018, China; (Y.S.); (M.W.); (L.W.); (P.G.); (L.G.); (X.J.); (S.L.); (Q.Z.)
| | - Xin Jin
- School of Biology and Technology, Jiangsu University of Science and Technology, Sibaidu, Zhenjiang 212018, China; (Y.S.); (M.W.); (L.W.); (P.G.); (L.G.); (X.J.); (S.L.); (Q.Z.)
| | - Shaocong Li
- School of Biology and Technology, Jiangsu University of Science and Technology, Sibaidu, Zhenjiang 212018, China; (Y.S.); (M.W.); (L.W.); (P.G.); (L.G.); (X.J.); (S.L.); (Q.Z.)
| | - Qiaonan Zhang
- School of Biology and Technology, Jiangsu University of Science and Technology, Sibaidu, Zhenjiang 212018, China; (Y.S.); (M.W.); (L.W.); (P.G.); (L.G.); (X.J.); (S.L.); (Q.Z.)
| | - Changyu Qiu
- Sericulture Research Institute, Guangxi Zhuang Autonomous Region, Nanning 530007, China; (C.Q.); (Q.L.)
| | - Qiang Lin
- Sericulture Research Institute, Guangxi Zhuang Autonomous Region, Nanning 530007, China; (C.Q.); (Q.L.)
| | - Weiguo Zhao
- School of Biology and Technology, Jiangsu University of Science and Technology, Sibaidu, Zhenjiang 212018, China; (Y.S.); (M.W.); (L.W.); (P.G.); (L.G.); (X.J.); (S.L.); (Q.Z.)
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19
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Tamang BG, Li S, Rajasundaram D, Lamichhane S, Fukao T. Overlapping and stress-specific transcriptomic and hormonal responses to flooding and drought in soybean. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:100-117. [PMID: 33864651 DOI: 10.1111/tpj.15276] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 02/19/2021] [Accepted: 04/08/2021] [Indexed: 06/12/2023]
Abstract
Flooding and drought are serious constraints that reduce crop productivity worldwide. Previous studies identified genes conferring tolerance to both water extremes in various plants. However, overlapping responses to flooding and drought at the genome-scale remain obscure. Here, we defined overlapping and stress-specific transcriptomic and hormonal responses to submergence, drought and recovery from these stresses in soybean (Glycine max). We performed comparative RNA-sequencing and hormone profiling, identifying genes, hormones and biological processes that are differentially regulated in an overlapping or stress-specific manner. Overlapping responses included positive regulation of trehalose and sucrose metabolism and negative regulation of cellulose, tubulin, photosystem II and I, and chlorophyll biosynthesis, facilitating the economization of energy reserves under both submergence and drought. Additional energy-consuming pathways were restricted in a stress-specific manner. Downregulation of distinct pathways for energy saving under each stress suggests energy-consuming processes that are relatively unnecessary for each stress adaptation are turned down. Our newly developed transcriptomic-response analysis revealed that abscisic acid and ethylene responses were activated in common under both stresses, whereas stimulated auxin response was submergence-specific. The energy-saving strategy is the key overlapping mechanism that underpins adaptation to both submergence and drought in soybean. Abscisic acid and ethylene are candidate hormones that coordinate transcriptomic energy-saving processes under both stresses. Auxin may be a signaling component that distinguishes submergence-specific regulation of the stress response.
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Affiliation(s)
- Bishal G Tamang
- Virginia Tech, School of Plant and Environmental Sciences, Blacksburg, VA, 24061, USA
- Department of Plant Biology and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Song Li
- Virginia Tech, School of Plant and Environmental Sciences, Blacksburg, VA, 24061, USA
| | - Dhivyaa Rajasundaram
- Virginia Tech, School of Plant and Environmental Sciences, Blacksburg, VA, 24061, USA
- Department of Pediatrics, University of Pittsburg, Pittsburg, PA, 15224, USA
| | - Suman Lamichhane
- Virginia Tech, School of Plant and Environmental Sciences, Blacksburg, VA, 24061, USA
| | - Takeshi Fukao
- Virginia Tech, School of Plant and Environmental Sciences, Blacksburg, VA, 24061, USA
- Department of Bioscience and Biotechnology, Fukui Prefectural University, Eiheiji, Fukui, 910-1195, Japan
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20
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Yadav B, Jogawat A, Rahman MS, Narayan OP. Secondary metabolites in the drought stress tolerance of crop plants: A review. GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2021.101040] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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21
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Bian X, Zhao Y, Xiao S, Yang H, Han Y, Zhang L. Metabolome and transcriptome analysis reveals the molecular profiles underlying the ginseng response to rusty root symptoms. BMC PLANT BIOLOGY 2021; 21:215. [PMID: 33985437 PMCID: PMC8117609 DOI: 10.1186/s12870-021-03001-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Accepted: 04/27/2021] [Indexed: 05/04/2023]
Abstract
BACKGROUND Ginseng rusty root symptoms (GRS) is one of the primary diseases of ginseng. This disease leads to a severe decline in the quality of ginseng. It has been shown that the occurrence of GRS is associated with soil environmental degradation, which may involve changes in soil microbiology and physicochemical properties. RESULTS In this study, GRS and healthy ginseng (HG) samples were used as experimental materials for comparative analysis of transcriptome and metabolome. Compared with those in HG samples, 949 metabolites and 9451 genes were significantly changed at the metabolic and transcriptional levels in diseased samples. The diseased tissues' metabolic patterns changed, and the accumulation of various organic acids, alkaloids, alcohols and phenols in diseased tissues increased significantly. There were significant differences in the expression of genes involved in plant hormone signal transduction, phenylpropanoid biosynthesis, the peroxidase pathway, and the plant-pathogen interaction pathway. CONCLUSION The current study involved a comparative metabolome and transcriptome analysis of GRS and HG samples. Based on the findings at the transcriptional and metabolic levels, a mechanism model of the ginseng response to GRS was established. Our results provide new insights into ginseng's response to GRS, which will reveal the potential molecular mechanisms of this disease in ginseng.
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Affiliation(s)
- Xingbo Bian
- College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun, 130118, Jilin Province, China
- State Local Joint Engineering Research Center of Ginseng Breeding and Application, Changchun, China
| | - Yan Zhao
- College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun, 130118, Jilin Province, China
| | - Shengyuan Xiao
- College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun, 130118, Jilin Province, China.
- State Local Joint Engineering Research Center of Ginseng Breeding and Application, Changchun, China.
| | - He Yang
- College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun, 130118, Jilin Province, China
- State Local Joint Engineering Research Center of Ginseng Breeding and Application, Changchun, China
| | - Yongzhong Han
- Jilin Provincial Ginseng and Pilose Antler Office, Changchun, China
| | - Lianxue Zhang
- College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun, 130118, Jilin Province, China.
- State Local Joint Engineering Research Center of Ginseng Breeding and Application, Changchun, China.
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22
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Identification of Bioactive Compounds of Asparagus officinalis L.: Permutation Test Allows Differentiation among "Triguero" and Hybrid Green Varieties. Molecules 2021; 26:molecules26061640. [PMID: 33804205 PMCID: PMC7999721 DOI: 10.3390/molecules26061640] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 03/11/2021] [Accepted: 03/12/2021] [Indexed: 11/17/2022] Open
Abstract
In this study, we determined the phytochemical profile of the Spanish “triguero” asparagus landrace “verde-morado” (Asparagus officinalis L.), a wild traditional landrace, and the improved “triguero” HT-801, together with two commercial green asparagus varieties. For comparison, we used reverse-phase high-performance liquid chromatography coupled with diode array electrospray time-of-flight mass spectrometry (RP-HPLC-DAD-ESI-TOF/MS) followed by a permutation test applied using a resampling methodology valid under a relaxed set of assumptions, such as i.i.d. errors (not necessarily normal) that are exchangeable under the null hypothesis. As a result, we postulate that “triguero” varieties (the improved HT-801 followed by its parent “verde-morado”) have a significantly different phytochemical profile from that of the other two commercial hybrid green varieties. In particular, we found compounds specific to the “triguero” varieties, such as feruloylhexosylhexose isomers, or isorhamnetin-3-O-glucoside, which was found only in the “triguero” variety HT-801. Although studies relating the phytochemical content of “triguero” asparagus varieties to its health-promoting effects are required, this characteristic phytochemical profile can be used for differentiating and revalorizating these asparagus cultivars.
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23
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Lee HK, Kim K, Lee J, Lee J, Lee J, Kim S, Lee SE, Kim JH. Targeted toxicometabolomics of endosulfan sulfate in adult zebrafish (Danio rerio) using GC-MS/MS in multiple reaction monitoring mode. JOURNAL OF HAZARDOUS MATERIALS 2020; 389:122056. [PMID: 32000124 DOI: 10.1016/j.jhazmat.2020.122056] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 12/16/2019] [Accepted: 01/08/2020] [Indexed: 06/10/2023]
Abstract
Endosulfan sulfate is a major oxidative metabolite of the chlorinated insecticide endosulfan. In this study, a targeted metabolomics approach was used to investigate the toxic mechanisms of endosulfan sulfate in adult zebrafish using the multiple reaction monitoring mode of a GC-MS/MS. The LC50 of endosulfan sulfate in adult zebrafish was determined and then zebrafish were exposed to endosulfan sulfate at one-tenth the LC50 (0.1LC50) or the LC50 for 24 and 48 h. After exposure, the fish were extracted, derivatized and analyzed by GC-MS/MS for 379 metabolites to identify 170 metabolites. Three experimental groups (control, 0.1LC50 and LC50) were clearly separated in PLS-DA score plots. Based on the VIP, ANOVA, and fold change results, 40 metabolites were selected as biomarkers. Metabolic pathways associated with those metabolites were identified using MetaboAnalyst 4.0 as follows: aminoacyl-tRNA biosynthesis, valine/leucine/isoleucine biosynthesis, citrate cycle, glycerolipid metabolism, and arginine/proline metabolism. Gene expression studies confirmed the activation of citrate cycle and glycerolipids metabolism. MDA levels of the exposed group significantly increased in oxidative toxicity assay tests. Such significant perturbations of important metabolites within key biochemical pathways must result in biologically hazardous effects in zebrafish.
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Affiliation(s)
- Hwa-Kyung Lee
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Kyeongnam Kim
- School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Junghak Lee
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jonghwa Lee
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, MA, 01003, USA
| | - Jiho Lee
- Environmental Medical Center, Korea Conformity Laboratories, Incheon, 21999, Republic of Korea
| | - Sooyeon Kim
- Gyeongnam Department of Environmental Toxicology and Chemistry, Korea Institute of Toxicology, Gyeongsangnam-do, 52834, Republic of Korea
| | - Sung-Eun Lee
- School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea.
| | - Jeong-Han Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea.
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Nakamura M, Noguchi K. Tolerant mechanisms to O 2 deficiency under submergence conditions in plants. JOURNAL OF PLANT RESEARCH 2020; 133:343-371. [PMID: 32185673 PMCID: PMC7214491 DOI: 10.1007/s10265-020-01176-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 03/06/2020] [Indexed: 05/02/2023]
Abstract
Wetland plants can tolerate long-term strict hypoxia and anoxic conditions and the subsequent re-oxidative stress compared to terrestrial plants. During O2 deficiency, both wetland and terrestrial plants use NAD(P)+ and ATP that are produced during ethanol fermentation, sucrose degradation, and major amino acid metabolisms. The oxidation of NADH by non-phosphorylating pathways in the mitochondrial respiratory chain is common in both terrestrial and wetland plants. As the wetland plants enhance and combine these traits especially in their roots, they can survive under long-term hypoxic and anoxic stresses. Wetland plants show two contrasting strategies, low O2 escape and low O2 quiescence strategies (LOES and LOQS, respectively). Differences between two strategies are ascribed to the different signaling networks related to phytohormones. During O2 deficiency, LOES-type plants show several unique traits such as shoot elongation, aerenchyma formation and leaf acclimation, whereas the LOQS-type plants cease their growth and save carbohydrate reserves. Many wetland plants utilize NH4+ as the nitrogen (N) source without NH4+-dependent respiratory increase, leading to efficient respiratory O2 consumption in roots. In contrast, some wetland plants with high O2 supply system efficiently use NO3- from the soil where nitrification occurs. The differences in the N utilization strategies relate to the different systems of anaerobic ATP production, the NO2--driven ATP production and fermentation. The different N utilization strategies are functionally related to the hypoxia or anoxia tolerance in the wetland plants.
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Affiliation(s)
- Motoka Nakamura
- Department of Bio-Production, Faculty of Bio-Industry, Tokyo University of Agriculture, 196 Yasaka, Abashiri, Hokkaido, 099-2493, Japan.
| | - Ko Noguchi
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan.
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Guo X, Xin Z, Yang T, Ma X, Zhang Y, Wang Z, Ren Y, Lin T. Metabolomics Response for Drought Stress Tolerance in Chinese Wheat Genotypes ( Triticum aestivum). PLANTS (BASEL, SWITZERLAND) 2020; 9:E520. [PMID: 32316652 PMCID: PMC7238273 DOI: 10.3390/plants9040520] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 03/29/2020] [Accepted: 04/08/2020] [Indexed: 01/15/2023]
Abstract
Metabolomics is an effective biotechnological tool that can be used to attain comprehensive information on metabolites. In this study, the profiles of metabolites produced by wheat seedlings in response to drought stress were investigated using an untargeted approach with ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) to determine various physiological processes related to drought tolerance from the cross between drought-tolerant genotype (HX10) and drought-sensitive genotype (YN211). The current study results showed that under drought stress, HX10 exhibited higher growth indices than YN211. After drought stress treatment, a series of phenolics accumulated higher in HX10 than in YN211, whereas the amount of thymine, a pyrimidine, is almost 13 folds of that in YN211. These metabolites, as well as high levels of different amino acids, alkaloids, organic acids, and flavonoids in the drought treated HX10 could help to explain its strong drought-tolerant capacity. The current study explored the understanding of the mechanisms involved in the drought response of wheat seedling; these metabolome data could also be used for potential QTL or GWAS studies to identify locus (loci) or gene(s) associated with these metabolic traits for the crop improvement.
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Affiliation(s)
- Xiaoyang Guo
- College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China; (X.G.); (Z.X.); (X.M.); (Z.W.); (Y.R.)
| | - Zeyu Xin
- College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China; (X.G.); (Z.X.); (X.M.); (Z.W.); (Y.R.)
| | - Tiegang Yang
- Industrial Crops Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China;
| | - Xingli Ma
- College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China; (X.G.); (Z.X.); (X.M.); (Z.W.); (Y.R.)
| | - Yang Zhang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 10081, China;
| | - Zhiqiang Wang
- College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China; (X.G.); (Z.X.); (X.M.); (Z.W.); (Y.R.)
| | - Yongzhe Ren
- College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China; (X.G.); (Z.X.); (X.M.); (Z.W.); (Y.R.)
| | - Tongbao Lin
- College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China; (X.G.); (Z.X.); (X.M.); (Z.W.); (Y.R.)
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Oleic Acid Is not the Only Relevant Mono-Unsaturated Fatty Ester in Olive Oil. Foods 2020; 9:foods9040384. [PMID: 32224949 PMCID: PMC7230673 DOI: 10.3390/foods9040384] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 03/13/2020] [Accepted: 03/19/2020] [Indexed: 01/04/2023] Open
Abstract
(1) Background: Extra-virgin olive oil (EVOO) is a precious and universally studied food matrix. Recently, the quantitative chemical composition was investigated by an innovative processing method for the nuclear magnetic resonance (NMR) experiments called Multi-Assignment Recovered Analysis (MARA)-NMR. (2) Methods: Any EVOO 13-carbon NMR (13C-NMR) profile displayed inconsistent signals. This mismatch was resolved by comparing NMR data to the official gas-chromatographic flame ionization detection (GC-FID) experiments: the analyses concerned many EVOOs but also the "exotic" Capparis spinosa oil (CSO). (3) Results: NMR and GC-FID evidenced the overwhelming presence of cis-vaccenic esters in the CSO and, more importantly, cis-vaccenic 13C-NMR resonances unequivocally matched the misunderstood 13C-NMR signals of EVOOs. The updated assignment revealed the unexpected relevant presence of cis-vaccenic ester (around 3%) in EVOOs; it was neglected, so far, because routine and official GC-FID profiles did not resolve oleic and cis-vaccenic signals leading to the total quantification of both monounsaturated fatty esters. (4) Conclusions: The rebuilt MARA-NMR and GC-FID interpretations consistently show a meaningful presence of cis-vaccenic esters in EVOOs, whose content could be a discrimination factor featuring specific cultivar or geographical origin. The study paves the way toward new quantification panels and scientific research concerning vegetable oils.
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Fukushima A, Kuroha T, Nagai K, Hattori Y, Kobayashi M, Nishizawa T, Kojima M, Utsumi Y, Oikawa A, Seki M, Sakakibara H, Saito K, Ashikari M, Kusano M. Metabolite and Phytohormone Profiling Illustrates Metabolic Reprogramming as an Escape Strategy of Deepwater Rice during Partially Submerged Stress. Metabolites 2020; 10:metabo10020068. [PMID: 32075002 PMCID: PMC7074043 DOI: 10.3390/metabo10020068] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Revised: 02/03/2020] [Accepted: 02/11/2020] [Indexed: 02/02/2023] Open
Abstract
Rice varieties that can survive under submergence conditions respond to flooding either by enhancing internode elongation or by quiescence of shoot elongation. Despite extensive efforts to identify key metabolites triggered by complete submergence of rice possessing SUBMERGENCE 1 (SUB1) locus, metabolic responses of internode elongation of deepwater rice governed by the SNORKEL 1 and 2 genes remain elusive. This study investigated specific metabolomic responses under partial submergence (PS) to deepwater- (C9285) and non-deepwater rice cultivars (Taichung 65 (T65)). In addition, we examined the response in a near-isogenic line (NIL-12) that has a C9285 genomic fragment on chromosome 12 introgressed into the genetic background of T65. Under short-term submergence (0-24 h), metabolite profiles of C9285, NIL-12, and T65 were compared to extract significantly changed metabolites in deepwater rice under PS conditions. Comprehensive metabolite and phytohormone profiling revealed increases in metabolite levels in the glycolysis pathway in NIL-12 plants. Under long-term submergence (0-288 h), we found decreased amino acid levels. These metabolomic changes were opposite when compared to those in flood-tolerant rice with SUB1 locus. Auxin conjugate levels related to stress response decreased in NIL-12 lines relative to T65. Our analysis helped clarify the complex metabolic reprogramming in deepwater rice as an escape strategy.
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Affiliation(s)
- Atsushi Fukushima
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan; (A.F.); (M.K.); (T.N.); (M.K.); (Y.U.); (A.O.); (M.S.); (H.S.); (K.S.)
| | - Takeshi Kuroha
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan; (T.K.); (K.N.); (Y.H.); (M.A.)
| | - Keisuke Nagai
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan; (T.K.); (K.N.); (Y.H.); (M.A.)
| | - Yoko Hattori
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan; (T.K.); (K.N.); (Y.H.); (M.A.)
| | - Makoto Kobayashi
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan; (A.F.); (M.K.); (T.N.); (M.K.); (Y.U.); (A.O.); (M.S.); (H.S.); (K.S.)
| | - Tomoko Nishizawa
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan; (A.F.); (M.K.); (T.N.); (M.K.); (Y.U.); (A.O.); (M.S.); (H.S.); (K.S.)
| | - Mikiko Kojima
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan; (A.F.); (M.K.); (T.N.); (M.K.); (Y.U.); (A.O.); (M.S.); (H.S.); (K.S.)
| | - Yoshinori Utsumi
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan; (A.F.); (M.K.); (T.N.); (M.K.); (Y.U.); (A.O.); (M.S.); (H.S.); (K.S.)
| | - Akira Oikawa
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan; (A.F.); (M.K.); (T.N.); (M.K.); (Y.U.); (A.O.); (M.S.); (H.S.); (K.S.)
- Faculty of Agriculture, Yamagata University, Tsuruoka, Yamagata 997-8555, Japan
| | - Motoaki Seki
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan; (A.F.); (M.K.); (T.N.); (M.K.); (Y.U.); (A.O.); (M.S.); (H.S.); (K.S.)
| | - Hitoshi Sakakibara
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan; (A.F.); (M.K.); (T.N.); (M.K.); (Y.U.); (A.O.); (M.S.); (H.S.); (K.S.)
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Kazuki Saito
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan; (A.F.); (M.K.); (T.N.); (M.K.); (Y.U.); (A.O.); (M.S.); (H.S.); (K.S.)
- Graduate School of Pharmaceutical Sciences, Chiba University, Chuo-ku, Chiba 263-8522, Japan
| | - Motoyuki Ashikari
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan; (T.K.); (K.N.); (Y.H.); (M.A.)
| | - Miyako Kusano
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan; (A.F.); (M.K.); (T.N.); (M.K.); (Y.U.); (A.O.); (M.S.); (H.S.); (K.S.)
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
- Tsukuba Plant Innovation Research Center, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
- Correspondence:
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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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Morgan MA, Griffith CM, Volz DC, Larive CK. TDCIPP exposure affects Artemia franciscana growth and osmoregulation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 694:133486. [PMID: 31401516 PMCID: PMC6868324 DOI: 10.1016/j.scitotenv.2019.07.292] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 07/15/2019] [Accepted: 07/18/2019] [Indexed: 05/18/2023]
Abstract
Environmental monitoring has demonstrated widespread occurrence of the flame-retardant tris(1,3-dichloro-2-propyl) phosphate (TDCIPP), raising concerns about the impact on aquatic life. Using 1H NMR and GC-MS metabolomics and 20-day body length experiments, we have determined that exposure to TDCIPP affects Artemia franciscana. The LC50 for a 48 h TDCIPP exposure was determined to be 37.1 ± 1.3 μM. Acute exposure (48 h) to 20.0 μM did not affect A. franciscana body length but did elicit a metabolic change. Chronic exposure to 0.50 μM TDCIPP caused decreased body length in A. franciscana exposed for 20 days and elicited a metabolic response. Principal component analysis revealed variance between acute and chronic exposure along PC1 (36.4%) and between control and TDCIPP along PC2 (17.4%). One-way ANOVA indicated that 19 metabolites were significantly affected by TDCIPP exposure; namely metabolites of the osmolyte class, including betaine, phosphocholine, gadusol, taurine, glycerol and trehalose - metabolites that are essential osmoprotectants in extremophile species. Other pathways that may be perturbed by TDCIPP exposure include one carbon, glycine, serine, threonine, and glycerophospholipid metabolism.
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Affiliation(s)
- Melissa A Morgan
- Department of Chemistry, University of California, Riverside, CA 92521, United States
| | - Corey M Griffith
- Environmental Toxicology Graduate Program, University of California, Riverside, CA 92521, United States
| | - David C Volz
- Department of Environmental Sciences, University of California, Riverside, CA 92521, United States
| | - Cynthia K Larive
- Department of Chemistry, University of California, Riverside, CA 92521, United States.
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30
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Di Giovanni N, Meuwis MA, Louis E, Focant JF. Untargeted Serum Metabolic Profiling by Comprehensive Two-Dimensional Gas Chromatography–High-Resolution Time-of-Flight Mass Spectrometry. J Proteome Res 2019; 19:1013-1028. [DOI: 10.1021/acs.jproteome.9b00535] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Nicolas Di Giovanni
- Department of Chemistry, Organic and Biological Analytical Chemistry Group, Quartier Agora, University of Liège, Allée du Six Août, B6c, B-4000 Liège (Sart Tilman), Belgium
| | - Marie-Alice Meuwis
- GIGA institute, Translational Gastroenterology and CHU de Liège, Hepato-Gastroenterology and Digestive Oncology, Quartier Hôpital, University of Liège, Avenue de l’Hôpital 13, B34-35, B-4000 Liège, Belgium
| | - Edouard Louis
- GIGA institute, Translational Gastroenterology and CHU de Liège, Hepato-Gastroenterology and Digestive Oncology, Quartier Hôpital, University of Liège, Avenue de l’Hôpital 13, B34-35, B-4000 Liège, Belgium
| | - Jean-François Focant
- Department of Chemistry, Organic and Biological Analytical Chemistry Group, Quartier Agora, University of Liège, Allée du Six Août, B6c, B-4000 Liège (Sart Tilman), Belgium
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Felline S, Del Coco L, Kaleb S, Guarnieri G, Fraschetti S, Terlizzi A, Fanizzi FP, Falace A. The response of the algae Fucus virsoides (Fucales, Ochrophyta) to Roundup® solution exposure: A metabolomics approach. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 254:112977. [PMID: 31377326 DOI: 10.1016/j.envpol.2019.112977] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 06/28/2019] [Accepted: 07/27/2019] [Indexed: 06/10/2023]
Abstract
Glyphosate, as a broad-spectrum herbicide, is frequently detected in water and several studies have investigated its effects on several freshwater aquatic organisms. Yet, only few investigations have been performed on marine macroalgae. Here, we studied both the metabolomics responses and the effect on primary production in the endemic brown algae Fucus virsoides exposed to different concentration (0, 0.5, 1.5 and 2.5 mg L-1) of a commercial glyphosate-based herbicide, namely Roundup®. Our results show that Roundup® significantly reduced quantum yield of photosynthesis (Fv/Fm) and caused alteration in the metabolomic profiles of exposed thalli compared to controls. Together with the decrease in the aromatic amino acids (phenylalanine and tyrosine), an increase in shikimate content was detected. The branched-amino acids differently varied according to levels of herbicide exposure, as well as observed for the content of choline, formate, glucose, malonate and fumarate. Our results suggest that marine primary producers could be largely affected by the agricultural land use, this asking for further studies addressing the ecosystem-level effects of glyphosate-based herbicides in coastal waters.
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Affiliation(s)
- S Felline
- CoNISMa, Piazzale Flaminio 9, 00196, Roma, Italy
| | - L Del Coco
- Department of Biology, Environmental Sciences and Technologies, University of Salento, 73100, Lecce, Italy
| | - S Kaleb
- Department of Life Sciences, University of Trieste, 34127, Trieste, Italy
| | - G Guarnieri
- CoNISMa, Piazzale Flaminio 9, 00196, Roma, Italy; Department of Biology, Environmental Sciences and Technologies, University of Salento, 73100, Lecce, Italy
| | - S Fraschetti
- Department of Biology, University of Naples Federico II, 80926, Napoli, Italy; Stazione Zoologica Anton Dohrn, 80121, Napoli, Italy
| | - A Terlizzi
- Department of Life Sciences, University of Trieste, 34127, Trieste, Italy; Stazione Zoologica Anton Dohrn, 80121, Napoli, Italy
| | - F P Fanizzi
- Department of Biology, Environmental Sciences and Technologies, University of Salento, 73100, Lecce, Italy.
| | - A Falace
- Department of Life Sciences, University of Trieste, 34127, Trieste, Italy
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Oakey LA, Fletcher RS, Elhassan YS, Cartwright DM, Doig CL, Garten A, Thakker A, Maddocks ODK, Zhang T, Tennant DA, Ludwig C, Lavery GG. Metabolic tracing reveals novel adaptations to skeletal muscle cell energy production pathways in response to NAD + depletion. Wellcome Open Res 2019; 3:147. [PMID: 30607371 PMCID: PMC6305244 DOI: 10.12688/wellcomeopenres.14898.2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/09/2019] [Indexed: 12/23/2022] Open
Abstract
Background: Skeletal muscle is central to whole body metabolic homeostasis, with age and disease impairing its ability to function appropriately to maintain health. Inadequate NAD + availability is proposed to contribute to pathophysiology by impairing metabolic energy pathway use. Despite the importance of NAD + as a vital redox cofactor in energy production pathways being well-established, the wider impact of disrupted NAD + homeostasis on these pathways is unknown. Methods: We utilised skeletal muscle myotube models to induce NAD + depletion, repletion and excess and conducted metabolic tracing to provide comprehensive and detailed analysis of the consequences of altered NAD + metabolism on central carbon metabolic pathways. We used stable isotope tracers, [1,2-13C] D-glucose and [U- 13C] glutamine, and conducted combined 2D-1H,13C-heteronuclear single quantum coherence (HSQC) NMR spectroscopy and GC-MS analysis. Results: NAD + excess driven by nicotinamide riboside (NR) supplementation within skeletal muscle cells resulted in enhanced nicotinamide clearance, but had no effect on energy homeostasis or central carbon metabolism. Nicotinamide phosphoribosyltransferase (NAMPT) inhibition induced NAD + depletion and resulted in equilibration of metabolites upstream of glyceraldehyde phosphate dehydrogenase (GAPDH). Aspartate production through glycolysis and TCA cycle activity was increased in response to low NAD +, which was rapidly reversed with repletion of the NAD + pool using NR. NAD + depletion reversibly inhibits cytosolic GAPDH activity, but retains mitochondrial oxidative metabolism, suggesting differential effects of this treatment on sub-cellular pyridine pools. When supplemented, NR efficiently reversed these metabolic consequences. However, the functional relevance of increased aspartate levels after NAD + depletion remains unclear, and requires further investigation. Conclusions: These data highlight the need to consider carbon metabolism and clearance pathways when investigating NAD + precursor usage in models of skeletal muscle physiology.
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Affiliation(s)
- Lucy A. Oakey
- Institute of Metabolism and Systems Research, University of Birmingham, UK, Birmingham, B15 2TT, UK
| | - Rachel S. Fletcher
- Institute of Metabolism and Systems Research, University of Birmingham, UK, Birmingham, B15 2TT, UK
| | - Yasir S. Elhassan
- Institute of Metabolism and Systems Research, University of Birmingham, UK, Birmingham, B15 2TT, UK
| | - David M. Cartwright
- Institute of Metabolism and Systems Research, University of Birmingham, UK, Birmingham, B15 2TT, UK
| | - Craig L. Doig
- Institute of Metabolism and Systems Research, University of Birmingham, UK, Birmingham, B15 2TT, UK
| | - Antje Garten
- Institute of Metabolism and Systems Research, University of Birmingham, UK, Birmingham, B15 2TT, UK
| | - Alpesh Thakker
- Institute of Metabolism and Systems Research, University of Birmingham, UK, Birmingham, B15 2TT, UK
| | | | - Tong Zhang
- Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1QH, UK
| | - Daniel A. Tennant
- Institute of Metabolism and Systems Research, University of Birmingham, UK, Birmingham, B15 2TT, UK
| | - Christian Ludwig
- Institute of Metabolism and Systems Research, University of Birmingham, UK, Birmingham, B15 2TT, UK
| | - Gareth G. Lavery
- Institute of Metabolism and Systems Research, University of Birmingham, UK, Birmingham, B15 2TT, UK
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Griffith CM, Thai AC, Larive CK. Metabolite biomarkers of chlorothalonil exposure in earthworms, coelomic fluid, and coelomocytes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 681:435-443. [PMID: 31112921 PMCID: PMC6613798 DOI: 10.1016/j.scitotenv.2019.04.312] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Revised: 04/18/2019] [Accepted: 04/20/2019] [Indexed: 04/14/2023]
Abstract
Earthworm (Eisenia fetida) metabolomics is a useful indicator of toxicant exposure. Extracts of whole earthworms are most commonly used to measure metabolic perturbations, in addition to coelomic fluid which has been used on a more limited basis. Coelomocytes are free moving cells found within earthworm coelomic fluid, and the potential of this compartment has not been evaluated for its utility in earthworm metabolomics. In this study, earthworms were exposed to 18.5 and 37.0 mg/kg chlorothalonil, a commonly used fungicide that targets glutathione. The metabolic impacts of a 14-day chlorothalonil exposure were assessed using 1H NMR and targeted LC-MS measurements of earthworm, coelomic fluid, and coelomocyte extracts. Coelomic fluid was identified as the most sensitive matrix for measuring the effects of chlorothalonil exposure, where an increase in glutamine levels was the only biomarker observed at both doses. At the high dose, multiblocked-orthogonal partial least squares-discriminant analysis (MB-OPLS-DA) supported increased N-acetylserine and ophthalmic acid levels as additional biomarkers of exposure in coelomic fluid. These perturbations may indicate increased oxidative stress, although no changes in glutathione were observed in any matrix.
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Affiliation(s)
- Corey M Griffith
- Environmental Toxicology Graduate Program, University of California, Riverside, CA 92521, United States
| | - Andrew C Thai
- Department of Chemistry, University of California, Riverside, CA 92521, United States
| | - Cynthia K Larive
- Environmental Toxicology Graduate Program, University of California, Riverside, CA 92521, United States; Department of Chemistry, University of California, Riverside, CA 92521, United States.
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Morgan MA, Griffith CM, Dinges MM, Lyon YA, Julian RR, Larive CK. Evaluating sub-lethal stress from Roundup ® exposure in Artemia franciscana using 1H NMR and GC-MS. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2019; 212:77-87. [PMID: 31077969 PMCID: PMC6581565 DOI: 10.1016/j.aquatox.2019.04.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 04/30/2019] [Accepted: 04/30/2019] [Indexed: 05/04/2023]
Abstract
Global salinization trends present an urgent need for methods to monitor aquatic ecosystem health and characterize known and emerging stressors for water bodies that are becoming increasingly saline. Environmental metabolomics methods that combine quantitative measurements of metabolite levels and multivariate statistical analysis are powerful tools for ascertaining biological impacts and identifying potential biomarkers of exposure. We propose the use of the saltwater aquatic crustacean, Artemia franciscana, as a model organism for environmental metabolomics in saltwater ecosystems. Artemia are a good choice for ecotoxicity assays and metabolomics analysis because they have a short life cycle, their hemolymph is rich in metabolites and they tolerate a wide salinity range. In this work we explore the potential of Artemia franciscana for environmental metabolomics through exposure to the broad-spectrum herbicide, glyphosate. The LC50 for a 48 h exposure of Roundup® was determined to be 237 ± 23 ppm glyphosate in the Roundup® formulation. Artemia cysts were hatched and exposed to sub-lethal glyphosate concentrations of 1.00, 10.0, 50.0, or 100 ppm glyphosate in Roundup®. We profiled 48 h old Artemia extracts using 1H NMR and GC-MS. Dose-dependent metabolic perturbation was evident for several metabolites using univariate and multivariate analyses. Metabolites significantly affected by Roundup® exposure included aspartate, formate, betaine, glucose, tyrosine, phenylalanine, gadusol, and isopropylamine. Biochemical pathway analysis with the KEGG database suggests impairment of carbohydrate and energy metabolism, folate-mediated one-carbon metabolism, Artemia molting and development, and microbial metabolism.
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Affiliation(s)
- Melissa A Morgan
- Department of Chemistry, University of California - Riverside, Riverside, CA, 92521, United States
| | - Corey M Griffith
- Environmental Toxicology Graduate Program, University of California - Riverside, Riverside, CA, 92521, United States
| | - Meredith M Dinges
- Department of Chemistry, University of California - Riverside, Riverside, CA, 92521, United States
| | - Yana A Lyon
- Department of Chemistry, University of California - Riverside, Riverside, CA, 92521, United States
| | - Ryan R Julian
- Department of Chemistry, University of California - Riverside, Riverside, CA, 92521, United States
| | - Cynthia K Larive
- Department of Chemistry, University of California - Riverside, Riverside, CA, 92521, United States.
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Guo R, Jiao D, Zhou J, Zhong X, Gu F, Liu Q. Metabolic response and correlations between ions and metabolites in Phragmites communis under long-term salinity toxicity. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 139:651-659. [PMID: 31048122 DOI: 10.1016/j.plaphy.2019.04.027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 04/18/2019] [Accepted: 04/19/2019] [Indexed: 06/09/2023]
Abstract
Phragmites communis has a long history in Songnen grassland of China and has a series of biological, ecological as well as genetic characteristics contributing to its adaptation to the specific local climatic and edaphic conditions. The aim of the present study was to investigate the ions balance and their relationship to metabolites in P. communis under three salinity stress conditions. Results showed that the contents of Na+, Cl-, and SO42- significantly increased in P. communis leaves, while K+, Mg2+, and Mn2+ decreased. Moreover, Na+ and Cl- had significant negative correlations with metabolites involved in the tricarboxylic acid cycle (TCA cycle), and significant positive correlations with glycolysis. The metabolite results showed that high contents of sugars and proline played important roles in developing salinity tolerance, indicating that glycolysis and proline biosynthesis were enhanced; however, this consumes large amounts of energy and likely caused the TCA cycle to be inhibited. The results suggested that P. communis might enhance its salinity tolerance mainly through increased glycolysis and energy consumption. In addition, restricting Na+ accumulation and increasing of Cl-, and rearrangement of metabolite production in P. communis tissues are possible causes of salinity tolerance. Therefore, salinity caused systems alterations in widespread metabolic networks involving TCA cycle, glycolysis and proline biosynthesis. These findings provided new insights for the P. communis metabolic adaptation to salinity and demonstrated the ions balance and metabolites in P. communis are possibly attributable to development of salinity tolerance.
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Affiliation(s)
- Rui Guo
- Key Laboratory of Dryland Agriculture, Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Dezhi Jiao
- College of Life Science and Agriculture, Forestry, Qiqihar University, Qiqihar, 161006, Heilongjiang, China
| | - Ji Zhou
- Land Consolidation and Rehabilitation Centre, The Ministry of Land and Resources, Beijing, 100000, PR China
| | - XiuLi Zhong
- Key Laboratory of Dryland Agriculture, Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - FengXue Gu
- Key Laboratory of Dryland Agriculture, Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Qi Liu
- Key Laboratory of Dryland Agriculture, Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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Yeung E, Bailey-Serres J, Sasidharan R. After The Deluge: Plant Revival Post-Flooding. TRENDS IN PLANT SCIENCE 2019; 24:443-454. [PMID: 30857921 DOI: 10.1016/j.tplants.2019.02.007] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 02/06/2019] [Accepted: 02/08/2019] [Indexed: 05/22/2023]
Abstract
Increasing flooding events have detrimentally impacted food security amid a growing global population. Complete submergence of plants represents the most severe flooding stress and studies have identified underwater responses to low oxygen and light availability. However, knowledge on plant responses during the post-submergence phase is limited. It is important to consider how plants can resume vegetative growth after enduring submergence and post-submergence stress. This review highlights current knowledge on physiological and molecular adaptations following desubmergence. Interplays of reactive oxygen species (ROS), energy depletion, photoinhibition, desiccation stress, and hormonal signaling have been characterized as components of the post-submergence stress response. Active elucidation of key genes and traits enhancing post-submergence adaptations is highly relevant for the improvement of submergence tolerance and ultimately crop yield.
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Affiliation(s)
- Elaine Yeung
- Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, Utrecht, The Netherlands; Plant Sciences Department, Rothamsted Research, Harpenden, UK
| | - Julia Bailey-Serres
- Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, Utrecht, The Netherlands; Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of Riverside, CA, USA. https://twitter.com/@jnbserres
| | - Rashmi Sasidharan
- Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, Utrecht, The Netherlands. https://twitter.com/@R_Sasidharan
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Fukao T, Barrera-Figueroa BE, Juntawong P, Peña-Castro JM. Submergence and Waterlogging Stress in Plants: A Review Highlighting Research Opportunities and Understudied Aspects. FRONTIERS IN PLANT SCIENCE 2019; 10:340. [PMID: 30967888 PMCID: PMC6439527 DOI: 10.3389/fpls.2019.00340] [Citation(s) in RCA: 121] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Accepted: 03/05/2019] [Indexed: 05/20/2023]
Abstract
Soil flooding creates composite and complex stress in plants known as either submergence or waterlogging stress depending on the depth of the water table. In nature, these stresses are important factors dictating the species composition of the ecosystem. On agricultural land, they cause economic damage associated with long-term social consequences. The understanding of the plant molecular responses to these two stresses has benefited from research studying individual components of the stress, in particular low-oxygen stress. To a lesser extent, other associated stresses and plant responses have been incorporated into the molecular framework, such as ion and ROS signaling, pathogen susceptibility, and organ-specific expression and development. In this review, we aim to highlight known or suspected components of submergence/waterlogging stress that have not yet been thoroughly studied at the molecular level in this context, such as miRNA and retrotransposon expression, the influence of light/dark cycles, protein isoforms, root architecture, sugar sensing and signaling, post-stress molecular events, heavy-metal and salinity stress, and mRNA dynamics (splicing, sequestering, and ribosome loading). Finally, we explore biotechnological strategies that have applied this molecular knowledge to develop cultivars resistant to flooding or to offer alternative uses of flooding-prone soils, like bioethanol and biomass production.
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Affiliation(s)
- Takeshi Fukao
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
| | | | - Piyada Juntawong
- Center for Advanced Studies in Tropical Natural Resources, National Research University – Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Julián Mario Peña-Castro
- Laboratorio de Biotecnología Vegetal, Instituto de Biotecnología, Universidad del Papaloapan, Tuxtepec, Mexico
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Clugston RD, Gao MA, Blaner WS. The Hepatic Lipidome: A Gateway to Understanding the Pathogenes is of Alcohol-Induced Fatty Liver. Curr Mol Pharmacol 2019; 10:195-206. [PMID: 26278391 DOI: 10.2174/1874467208666150817111419] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Revised: 08/07/2015] [Accepted: 08/07/2015] [Indexed: 12/30/2022]
Abstract
Chronic alcohol consumption can lead to the development of alcoholic fatty liver disease. The underlying pathogenic mechanisms however, have not been fully elucidated. Here, we review the current state of the art regarding the application of lipidomics to study alcohol's effect on hepatic lipids. It is clear that alcohol has a profound effect on the hepatic lipidome, with documented changes in the major lipid categories (i.e. fatty acyls, glycerolipids, glycerophospholipids, sphingolipids, sterol lipids and prenol lipids). Alcohol's most striking effect is the marked change in the hepatic fatty acyl pool. This effect includes increased levels of 18-carbon fatty acyl chains incorporated into multiple lipid species, as well as a general shift toward increased unsaturation of fatty acyl moieties. In addition to our literature review, we also make several recommendations to consider when designing lipidomic studies into alcohol's effects. These recommendations include integration of lipidomic data with other measures of lipid metabolism, inclusion of multiple experimental time points, and presentation of quantitative data. We believe rigorous analysis of the hepatic lipidome can yield new insight into the pathogenesis of alcohol-induced fatty liver. While the existing literature has been largely descriptive, the field is poised to apply lipidomics to yield a new level of understanding on alcohol's effects on hepatic lipid metabolism.
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Affiliation(s)
- Robin D Clugston
- Department of Physiology, University of Alberta, Edmonton, AB, T6G 2H7. Canada
| | - Madeleine A Gao
- Department of Medicine, Columbia University, New York, NY, 10032. United States
| | - William S Blaner
- Department of Medicine, Columbia University, New York, NY, 10032. United States
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Li P, Liao ST, Wang JS, Zhang Q, Lv Y, Yang MH, Kong LY. Pharmacokinetic and NMR metabolomics approach to evaluate therapeutic effect of berberine and Coptidis Rhizoma for sepsis. CHINESE HERBAL MEDICINES 2019. [DOI: 10.1016/j.chmed.2018.05.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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40
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Chai F, Liu W, Xiang Y, Meng X, Sun X, Cheng C, Liu G, Duan L, Xin H, Li S. Comparative metabolic profiling of Vitis amurensis and Vitis vinifera during cold acclimation. HORTICULTURE RESEARCH 2019; 6:8. [PMID: 30603094 PMCID: PMC6312538 DOI: 10.1038/s41438-018-0083-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 07/19/2018] [Accepted: 08/01/2018] [Indexed: 05/20/2023]
Abstract
Vitis amurensis is a wild Vitis plant that can withstand extreme cold temperatures. However, the accumulation of metabolites during cold acclimation (CA) in V. amurensis remains largely unknown. In this study, plantlets of V. amurensis and V. vinifera cv. Muscat of Hamburg were treated at 4 °C for 24 and 72 h, and changes of metabolites in leaves were detected by gas chromatography coupled with time-of-flight mass spectrometry. Most of the identified metabolites, including carbohydrates, amino acids, and organic acids, accumulated in the two types of grape after CA. Galactinol, raffinose, fructose, mannose, glycine, and ascorbate were continuously induced by cold in V. amurensis, but not in Muscat of Hamburg. Twelve metabolites, including isoleucine, valine, proline, 2-oxoglutarate, and putrescine, increased in V. amurensis during CA. More galactinol, ascorbate, 2-oxoglutarate, and putrescine, accumulated in V. amurensis, but not in Muscat of Hamburg, during CA, which may be responsible for the excellent cold tolerance in V. amurensis. The expression levels of the genes encoding β-amylase (BAMY), galactinol synthase (GolS), and raffinose synthase (RafS) were evaluated by quantitative reverse transcription-PCR. The expression BAMY (VIT_02s0012 g00170) and RafS (VIT_05s0077 g00840) were primarily responsible for the accumulation of maltose and raffinose, respectively. The accumulation of galactinol was attributed to different members of GolS in the two grapes. In conclusion, these results show the inherent differences in metabolites between V. amurensis and V. vinifera under CA.
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Affiliation(s)
- Fengmei Chai
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, P.R. China
- Beijing Key Laboratory of Grape Sciences and Enology, CAS Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, P.R. China
- University of Chinese Academy of Sciences, Beijing, P.R. China
| | - Wenwen Liu
- Beijing Key Laboratory of Grape Sciences and Enology, CAS Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, P.R. China
- University of Chinese Academy of Sciences, Beijing, P.R. China
| | - Yue Xiang
- University of Chinese Academy of Sciences, Beijing, P.R. China
| | - Xianbin Meng
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, P.R. China
| | - Xiaoming Sun
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, P.R. China
- Beijing Key Laboratory of Grape Sciences and Enology, CAS Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, P.R. China
| | - Cheng Cheng
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, P.R. China
- University of Chinese Academy of Sciences, Beijing, P.R. China
| | - Guotian Liu
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi P.R. China
| | - Lixin Duan
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, P.R. China
| | - Haiping Xin
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, P.R. China
| | - Shaohua Li
- Beijing Key Laboratory of Grape Sciences and Enology, CAS Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, P.R. China
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Schwechheimer SK, Becker J, Wittmann C. Towards better understanding of industrial cell factories: novel approaches for 13C metabolic flux analysis in complex nutrient environments. Curr Opin Biotechnol 2018; 54:128-137. [DOI: 10.1016/j.copbio.2018.07.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 07/10/2018] [Accepted: 07/12/2018] [Indexed: 12/13/2022]
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Mogul R, Barding GA, Lalla S, Lee S, Madrid S, Baki R, Ahmed M, Brasali H, Cepeda I, Gornick T, Gunadi S, Hearn N, Jain C, Kim EJ, Nguyen T, Nguyen VB, Oei A, Perkins N, Rodriguez J, Rodriguez V, Savla G, Schmitz M, Tedjakesuma N, Walker J. Metabolism and Biodegradation of Spacecraft Cleaning Reagents by Strains of Spacecraft-Associated Acinetobacter. ASTROBIOLOGY 2018; 18:1517-1527. [PMID: 29672134 PMCID: PMC6276816 DOI: 10.1089/ast.2017.1814] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Accepted: 03/23/2018] [Indexed: 05/17/2023]
Abstract
Spacecraft assembly facilities are oligotrophic and low-humidity environments, which are routinely cleaned using alcohol wipes for benchtops and spacecraft materials, and alkaline detergents for floors. Despite these cleaning protocols, spacecraft assembly facilities possess a persistent, diverse, dynamic, and low abundant core microbiome, where the Acinetobacter are among the dominant members of the community. In this report, we show that several spacecraft-associated Acinetobacter metabolize or biodegrade the spacecraft cleaning reagents of ethanol (ethyl alcohol), 2-propanol (isopropyl alcohol), and Kleenol 30 (floor detergent) under ultraminimal conditions. Using cultivation and stable isotope labeling studies, we show that ethanol is a sole carbon source when cultivating in 0.2 × M9 minimal medium containing 26 μM Fe(NH4)2(SO4)2. Although cultures expectedly did not grow solely on 2-propanol, cultivations on mixtures of ethanol and 2-propanol exhibited enhanced plate counts at mole ratios of ≤0.50. In support, enzymology experiments on cellular extracts were consistent with oxidation of ethanol and 2-propanol by a membrane-bound alcohol dehydrogenase. In the presence of Kleenol 30, untargeted metabolite profiling on ultraminimal cultures of Acinetobacter radioresistens 50v1 indicated (1) biodegradation of Kleenol 30 into products including ethylene glycols, (2) the potential metabolism of decanoate (formed during incubation of Kleenol 30 in 0.2 × M9), and (3) decreases in the abundances of several hydroxy- and ketoacids in the extracellular metabolome. In ultraminimal medium (when using ethanol as a sole carbon source), A. radioresistens 50v1 also exhibits a remarkable survival against hydrogen peroxide (∼1.5-log loss, ∼108 colony forming units (cfu)/mL, 10 mM H2O2), indicating a considerable tolerance toward oxidative stress under nutrient-restricted conditions. Together, these results suggest that the spacecraft cleaning reagents may (1) serve as nutrient sources under oligotrophic conditions and (2) sustain extremotolerances against the oxidative stresses associated with low-humidity environments. In perspective, this study provides a plausible biochemical rationale to the observed microbial ecology dynamics of spacecraft-associated environments.
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Affiliation(s)
- Rakesh Mogul
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Gregory A. Barding
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Sidharth Lalla
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Sooji Lee
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Steve Madrid
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Ryan Baki
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Mahjabeen Ahmed
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Hania Brasali
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Ivonne Cepeda
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Trevor Gornick
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Shawn Gunadi
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Nicole Hearn
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Chirag Jain
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Eun Jin Kim
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Thi Nguyen
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Vinh Bao Nguyen
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Alex Oei
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Nicole Perkins
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Joseph Rodriguez
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Veronica Rodriguez
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Gautam Savla
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Megan Schmitz
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Nicholas Tedjakesuma
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Jillian Walker
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
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Zhao DS, Wu ZT, Li ZQ, Wang LL, Jiang LL, Shi W, Li P, Li HJ. Liver-specific metabolomics characterizes the hepatotoxicity of Dioscorea bulbifera rhizome in rats by integration of GC-MS and 1H-NMR. JOURNAL OF ETHNOPHARMACOLOGY 2018; 226:111-119. [PMID: 30114519 DOI: 10.1016/j.jep.2018.08.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 08/01/2018] [Accepted: 08/12/2018] [Indexed: 06/08/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Dioscorea bulbifera rhizome (DBR), one type of herbal medicine, is extensively used in both Indian and Chinese system of traditional medicine. It has been effective in treating various diseases, such as sore throat, struma, and tumors. However, more and more clinical investigations have suggested that DBR can cause liver injury. AIM OF THE STUDY In the present study, we aimed to characterize the corresponding molecular changes of liver dysfunction and reveal overall metabolic and physiological mechanisms of the subchronic toxic effect of DBR. MATERIALS AND METHODS A liver-specific metabolomics approach integrating GC-MS and 1H-NMR was developed to assess the hepatotoxicity in rats after DBR exposure for 12 weeks. Multivariate statistical analysis and pattern recognition were employed to examine different metabolic profiles of liver in DBR-challenged rats. RESULTS A total of 61 metabolites were screened as significantly altered metabolites, which were distributed in 43 metabolic pathways. The correlation network analysis indicated that the hub metabolites of hepatotoxicity could be mainly linked to amino acid, lipid, purine, pyrimidine, bile acid, gut microflora, and energy metabolisms. Notably, purine, pyrimidine, and gut microflora metabolisms might be novel pathways participating in metabolic abnormalities in rats with DBR-triggered hepatic damage. CONCLUSIONS Our results primarily showed that the liver-specific metabolic information provided by the different analytical platforms was essential for identifying more biomarkers and metabolic pathways, and our findings provided novel insights into understand the mechanistic complexity of herb-induced liver injury.
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Affiliation(s)
- Dong-Sheng Zhao
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, No. 24 Tongjia Lane, Nanjing 210009, China
| | - Zi-Tian Wu
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, No. 24 Tongjia Lane, Nanjing 210009, China
| | - Zhuo-Qing Li
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, No. 24 Tongjia Lane, Nanjing 210009, China
| | - Ling-Li Wang
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, No. 24 Tongjia Lane, Nanjing 210009, China
| | - Li-Long Jiang
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, No. 24 Tongjia Lane, Nanjing 210009, China
| | - Wei Shi
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, No. 24 Tongjia Lane, Nanjing 210009, China
| | - Ping Li
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, No. 24 Tongjia Lane, Nanjing 210009, China
| | - Hui-Jun Li
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, No. 24 Tongjia Lane, Nanjing 210009, China.
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Oakey LA, Fletcher RS, Elhassan YS, Cartwright DM, Doig CL, Garten A, Thakker A, Maddocks ODK, Zhang T, Tennant DA, Ludwig C, Lavery GG. Metabolic tracing reveals novel adaptations to skeletal muscle cell energy production pathways in response to NAD + depletion. Wellcome Open Res 2018; 3:147. [PMID: 30607371 PMCID: PMC6305244 DOI: 10.12688/wellcomeopenres.14898.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/02/2018] [Indexed: 11/15/2023] Open
Abstract
Background: Skeletal muscle is central to whole body metabolic homeostasis, with age and disease impairing its ability to function appropriately to maintain health. Inadequate NAD + availability is proposed to contribute to pathophysiology by impairing metabolic energy pathway use. Despite the importance of NAD + as a vital redox cofactor in energy production pathways being well-established, the wider impact of disrupted NAD + homeostasis on these pathways is unknown. Methods: We utilised skeletal muscle myotube models to induce NAD + depletion, repletion and excess and conducted metabolic tracing to provide comprehensive and detailed analysis of the consequences of altered NAD + metabolism on central carbon metabolic pathways. We used stable isotope tracers, [1,2-13C] D-glucose and [U- 13C] glutamine, and conducted combined 2D-1H,13C-heteronuclear single quantum coherence (HSQC) NMR spectroscopy and GC-MS analysis. Results: NAD + excess driven by nicotinamide riboside (NR) supplementation within skeletal muscle cells results in enhanced nicotinamide clearance, but had no effect on energy homeostasis or central carbon metabolism. Nicotinamide phosphoribosyltransferase (NAMPT) inhibition induced NAD + depletion and resulted in equilibration of metabolites upstream of glyceraldehyde phosphate dehydrogenase (GAPDH). Aspartate production through glycolysis and TCA cycle activity is increased in response to low NAD +, which is rapidly reversed with repletion of the NAD + pool using NR. NAD + depletion reversibly inhibits cytosolic GAPDH activity, but retains mitochondrial oxidative metabolism, suggesting differential effects of this treatment on sub-cellular pyridine pools. When supplemented, NR efficiently reverses these metabolic consequences. However, the functional relevance of increased aspartate levels after NAD + depletion remains unclear, and requires further investigation. Conclusions: These data highlight the need to consider carbon metabolism and clearance pathways when investigating NAD + precursor usage in models of skeletal muscle physiology.
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Affiliation(s)
- Lucy A. Oakey
- Institute of Metabolism and Systems Research, University of Birmingham, UK, Birmingham, B15 2TT, UK
| | - Rachel S. Fletcher
- Institute of Metabolism and Systems Research, University of Birmingham, UK, Birmingham, B15 2TT, UK
| | - Yasir S. Elhassan
- Institute of Metabolism and Systems Research, University of Birmingham, UK, Birmingham, B15 2TT, UK
| | - David M. Cartwright
- Institute of Metabolism and Systems Research, University of Birmingham, UK, Birmingham, B15 2TT, UK
| | - Craig L. Doig
- Institute of Metabolism and Systems Research, University of Birmingham, UK, Birmingham, B15 2TT, UK
| | - Antje Garten
- Institute of Metabolism and Systems Research, University of Birmingham, UK, Birmingham, B15 2TT, UK
| | - Alpesh Thakker
- Institute of Metabolism and Systems Research, University of Birmingham, UK, Birmingham, B15 2TT, UK
| | | | - Tong Zhang
- Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1QH, UK
| | - Daniel A. Tennant
- Institute of Metabolism and Systems Research, University of Birmingham, UK, Birmingham, B15 2TT, UK
| | - Christian Ludwig
- Institute of Metabolism and Systems Research, University of Birmingham, UK, Birmingham, B15 2TT, UK
| | - Gareth G. Lavery
- Institute of Metabolism and Systems Research, University of Birmingham, UK, Birmingham, B15 2TT, UK
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Wen B, Jin SR, Chen ZZ, Gao JZ. Physiological responses to cold stress in the gills of discus fish (Symphysodon aequifasciatus) revealed by conventional biochemical assays and GC-TOF-MS metabolomics. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 640-641:1372-1381. [PMID: 30021304 DOI: 10.1016/j.scitotenv.2018.05.401] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Revised: 05/31/2018] [Accepted: 05/31/2018] [Indexed: 05/18/2023]
Abstract
Discus fish (Symphysodon aequifasciatus) is a cichlid that is among the most popular fish for warm-water aquaria and also frequently used as the model animal for environmental science. However, little is known about the responses of S. aequifasciatus to low temperatures caused by environmental variation. Here, by using conventional biochemical assays and gas chromatography time-of-flight mass spectrometry metabolomics, we investigated the physiological responses of S. aequifasciatus gills exposed for 30 days to two temperature regimes: 28 °C and 20 °C. Low temperature resulted in elevated production of reactive oxygen species but not increased malondialdehyde. This might be partially related to protective responses in the antioxidant system, revealed by increased activities of superoxide dismutase and glutathione peroxidase, and level of reduced glutathione (GSH), compensating for the depletion of catalase activity. A total of 35 metabolites were identified as potential biomarkers of cold stress, showing the most influenced pathways including starch and sucrose metabolism, pentose phosphate pathway, glycerolipid metabolism, sphingolipid metabolism, glutathione metabolism, and arginine and proline metabolism. Moreover, the activation of glutathione metabolism agreed with the increased GSH level detected by biochemical assays. Overall, the results of this study suggest that low temperature can activate a protective antioxidant defence response and modify the metabolic pathways in gills of S. aequifasciatus, providing insights into the physiological regulation in response to cold stress in this tropical fish.
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Affiliation(s)
- Bin Wen
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai 201306, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China; Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai 201306, China
| | - Shi-Rong Jin
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai 201306, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China; Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai 201306, China
| | - Zai-Zhong Chen
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai 201306, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China; Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai 201306, China.
| | - Jian-Zhong Gao
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai 201306, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China; Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai 201306, China.
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Çatav ŞS, Elgin ES, Dağ Ç, Stark JL, Küçükakyüz K. NMR-based metabolomics reveals that plant-derived smoke stimulates root growth via affecting carbohydrate and energy metabolism in maize. Metabolomics 2018; 14:143. [PMID: 30830436 DOI: 10.1007/s11306-018-1440-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 10/05/2018] [Indexed: 01/01/2023]
Abstract
INTRODUCTION It is well known that plant-derived smoke stimulates seed germination and seedling growth in many plants. Although a number of transcriptomics and proteomics studies have been carried out to understand the mode of action of smoke, less is known about the biochemical alterations associated with smoke exposure in plants. OBJECTIVES The aims of this study were (1) to determine the metabolic alterations in maize roots pre-treated with various concentrations of smoke solution, and (2) to identify the smoke-responsive metabolic pathways during early root growth period. METHODS Maize seeds were pre-treated with different concentrations of smoke solutions for 24 h and then grown for 10 days. 600-MHz 1H NMR spectroscopy was performed on the aqueous root extracts of maize seedlings. The metabolite data obtained from the NMR spectra were analyzed by several statistical and functional methods, including one-way ANOVA, PCA, PLS-DA and pathway analysis. RESULTS Our study identified a total of 29 metabolites belonging to various chemical groups. Concentrations of 20 out of these 29 metabolites displayed significant (p < 0.05) changes after at least one smoke pre-treatment compared to the control. Moreover, functional analyses revealed that smoke pre-treatments markedly affected the carbohydrate- and energy-related metabolic pathways, such as galactose metabolism, glycolysis, glyoxylate metabolism, tricarboxylic acid cycle, and starch/sucrose metabolism. CONCLUSIONS To our knowledge, this is the first study that investigates smoke-induced biochemical alterations in early root growth period using NMR spectroscopy. Our findings clearly indicate that smoke either directly or indirectly influences many metabolic processes in maize roots.
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Affiliation(s)
- Şükrü Serter Çatav
- Division of Botany, Department of Biology, Muğla Sıtkı Koçman University, Kötekli, 48000, Muğla, Turkey
| | - Emine Sonay Elgin
- Division of Biochemistry, Department of Chemistry, Muğla Sıtkı Koçman University, Kötekli, 48000, Muğla, Turkey
| | - Çağdaş Dağ
- Division of Biochemistry, Department of Chemistry, Muğla Sıtkı Koçman University, Kötekli, 48000, Muğla, Turkey
- Department of Molecular and Cellular Biochemistry, Indiana University Bloomington, Bloomington, IN, 47403, USA
| | - Jaime L Stark
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Köksal Küçükakyüz
- Division of Botany, Department of Biology, Muğla Sıtkı Koçman University, Kötekli, 48000, Muğla, Turkey.
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Bhinderwala F, Wase N, DiRusso C, Powers R. Combining Mass Spectrometry and NMR Improves Metabolite Detection and Annotation. J Proteome Res 2018; 17:4017-4022. [PMID: 30303385 DOI: 10.1021/acs.jproteome.8b00567] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Despite inherent complementarity, nuclear magnetic resonance spectroscopy (NMR) and mass spectrometry (MS) are routinely separately employed to characterize metabolomics samples. More troubling is the erroneous view that metabolomics is better served by exclusively utilizing MS. Instead, we demonstrate the importance of combining NMR and MS for metabolomics by using small chemical compound treatments of Chlamydomonas reinhardtii as an illustrative example. A total of 102 metabolites were detected (82 by gas chromatography-MS, 20 by NMR, and 22 by both techniques). Out of these, 47 metabolites of interest were identified: 14 metabolites were uniquely identified by NMR, and 16 metabolites were uniquely identified by GC-MS. A total of 17 metabolites were identified by both NMR and GC-MS. In general, metabolites identified by both techniques exhibited similar changes upon compound treatment. In effect, NMR identified key metabolites that were missed by MS and enhanced the overall coverage of the oxidative pentose phosphate pathway, Calvin cycle, tricarboxylic acid cycle, and amino acid biosynthetic pathways that informed on pathway activity in central carbon metabolism, leading to fatty-acid and complex-lipid synthesis. Our study emphasizes a prime advantage of combining multiple analytical techniques: the improved detection and annotation of metabolites.
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Affiliation(s)
- Fatema Bhinderwala
- Department of Chemistry , University of Nebraska , Lincoln , Nebraska 68588-0304 , United States.,Nebraska Center for Integrated Biomolecular Communication , Lincoln , Nebraska 68588-0304 , United States
| | - Nishikant Wase
- Department of Biochemistry , University of Nebraska , Lincoln , Nebraska 68588-0664 , United States
| | - Concetta DiRusso
- Department of Biochemistry , University of Nebraska , Lincoln , Nebraska 68588-0664 , United States.,Nebraska Center for Integrated Biomolecular Communication , Lincoln , Nebraska 68588-0304 , United States
| | - Robert Powers
- Department of Chemistry , University of Nebraska , Lincoln , Nebraska 68588-0304 , United States.,Nebraska Center for Integrated Biomolecular Communication , Lincoln , Nebraska 68588-0304 , United States
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Richards LA, Oliveira C, Dyer LA, Rumbaugh A, Urbano-Muñoz F, Wallace IS, Dodson CD, Jeffrey CS. Shedding Light on Chemically Mediated Tri-Trophic Interactions: A 1H-NMR Network Approach to Identify Compound Structural Features and Associated Biological Activity. FRONTIERS IN PLANT SCIENCE 2018; 9:1155. [PMID: 30174676 PMCID: PMC6107749 DOI: 10.3389/fpls.2018.01155] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 07/20/2018] [Indexed: 06/08/2023]
Abstract
Diverse mixtures of plant natural products play an important role in plant-herbivore-parasitoid interactions. In the pursuit of understanding these chemically-mediated interactions, we are often faced with the challenge of determining ecologically and biologically relevant compounds present in complex phytochemical mixtures. Using a network-based approach, we analyzed binned 1H-NMR data from 196 prepared mixtures of commonly studied secondary metabolites including alkaloids, amides, terpenes, iridoid glycosides, saponins, phenylpropanoids, flavonoids and phytosterols. The mixtures included multiple dimensions of chemical diversity, including molecular complexity, mixture complexity and differences in relative compound concentrations. This approach yielded modules of co-occurring chemical shifts that were correlated with specific compounds or common structural features shared across compounds. This approach was then applied to crude phytochemical extracts of 31 species in the phytochemically diverse tropical plant genus Piper (Piperaceae). Combining the activity of crude plant extracts in an array of bioassays with our 1H-NMR network approach, we identified a potential prenylated benzoic acid from these mixtures that exhibits antifungal properties and identified small structural differences that were potentially responsible for antifungal activity. In an intraspecific analysis of individual Piper kelleyi plants, we also found ontogenetic differences in chemistry that may affect natural plant enemies. In sum, this approach allowed us to characterize mixtures as useful network modules and to combine chemical and ecological datasets to identify biologically important compounds from crude extracts.
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Affiliation(s)
- Lora A. Richards
- Department of Biology, University of Nevada, Reno, NV, United States
| | - Celso Oliveira
- Department of Chemistry, University of Nevada, Reno, NV, United States
| | - Lee A. Dyer
- Department of Biology, University of Nevada, Reno, NV, United States
| | - Arran Rumbaugh
- Department of Chemistry, University of Nevada, Reno, NV, United States
| | - Federico Urbano-Muñoz
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, United States
| | - Ian S. Wallace
- Department of Chemistry, University of Nevada, Reno, NV, United States
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, United States
| | - Craig D. Dodson
- Department of Chemistry, University of Nevada, Reno, NV, United States
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Griffith CM, Morgan MA, Dinges MM, Mathon C, Larive CK. Metabolic Profiling of Chloroacetanilide Herbicides in Earthworm Coelomic Fluid Using 1H NMR and GC-MS. J Proteome Res 2018; 17:2611-2622. [PMID: 29939029 DOI: 10.1021/acs.jproteome.8b00081] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Earthworms ( Eisenia fetida) are vital members of the soil environment. Because of their sensitivity to many contaminants, monitoring earthworm metabolism may be a useful indicator of environmental stressors. Here, metabolic profiles of exposure to five chloroacetanilide herbicides and one enantiomer (acetochlor, alachlor, butachlor, racemic metolachlor, S-metolachlor, and propachlor) are observed in earthworm coelomic fluid using proton nuclear magnetic resonance spectroscopy (NMR) and gas chromatography-mass spectrometry (GC-MS). Multiblocked-orthogonal partial least-squares-discriminant analysis (MB-OPLS-DA) and univariate analysis were used to identify metabolic perturbations in carnitine biosynthesis, carbohydrate metabolism, lipid metabolism, nitrogen metabolism, and the tricarboxylic acid cycle. Intriguingly, stereospecific metabolic responses were observed between racemic metolachlor and S-metolachlor exposed worms. These findings support the utility of coelomic fluid in monitoring metabolic perturbations induced by chloroacetanilide herbicides in nontarget organisms and reveal specificity in the metabolic impacts of herbicide analogues in earthworms.
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50
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Guo R, Bai Z, Zhou J, Zhong X, Gu F, Liu Q, Li H. Tissue physiological metabolic adaptability in young and old leaves of reed (Phragmites communis) in Songnen grassland. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 128:99-105. [PMID: 29772493 DOI: 10.1016/j.plaphy.2018.05.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 05/08/2018] [Accepted: 05/08/2018] [Indexed: 06/08/2023]
Abstract
Common reed (Phragmites communis) is widely distributed as the dominant plant species in the Songnen Plain of China. The aim of this study was to investigate different physiological adaptive mechanisms to salinity tolerance between young and old leaves. The profiles of 68 metabolites were measured and studied in reed leaves by gas chromatography-mass spectrometer. The nitrogen, carbon, and pigment contents showed stronger growth inhibition for older leaves with salinity stress. In young leaves, high K+ contents not only promoted cell growth, but also prevented influx of superfluous Na+ ions in cells; the Ca2+ accumulation in old leaves implied that Ca2+ triggered the SOS-Na+ exclusion system and reduced Na+ toxicity. Thus, the mechanism of enhanced tolerance differed between young and old leaves. The metabolite results indicated that the young and old leaves had different mechanisms of osmotic regulation; sugars/polyols and amino acids played important roles in developing salinity tolerance in young leaves but high contents of fatty acids were important for old leaves. These results implied dramatically enhanced sugars and amino acid synthesis but inhibited energy metabolism in young leaves. In contrast, fatty acid synthesis was enhanced in old leaves. The results extended our understanding of the differences in physiological metabolism in adaptive to the salt-alkalization of soil in Songnen grassland between young and old leaves of reeds.
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Affiliation(s)
- Rui Guo
- Key Laboratory of Dryland Agriculture, Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Zhenzi Bai
- Department of Infectious Diseases, China-Japan Union Hospital of Jilin University, Changchun 130033, China
| | - Ji Zhou
- Land Consolidation and Rehabilitation Centre, The Ministry of Land and Resources, Beijing 100000, China
| | - XiuLi Zhong
- Key Laboratory of Dryland Agriculture, Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - FengXue Gu
- Key Laboratory of Dryland Agriculture, Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Qi Liu
- Key Laboratory of Dryland Agriculture, Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - HaoRu Li
- Key Laboratory of Dryland Agriculture, Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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