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Man KY, Chan CO, Wan SW, Kwok KWH, Capozzi F, Dong NP, Wong KH, Mok DKW. Untargeted foodomics for authenticating the organic farming of water spinach (Ipomoea aquatica). Food Chem 2024; 453:139545. [PMID: 38772304 DOI: 10.1016/j.foodchem.2024.139545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 04/25/2024] [Accepted: 05/01/2024] [Indexed: 05/23/2024]
Abstract
This study aimed to conduct a comprehensive analysis of the primary and secondary metabolites of water spinach (Ipomoea aquatica) using hydrophilic interaction liquid chromatography coupled with Orbitrap high-resolution mass spectrometry (HILIC-Orbitrap-HRMS). Certified samples from two cultivars, Green stem water spinach (G) and White stem water spinach (W) cultivated using organic and conventional farming methods, were collected from the Hong Kong market. Multivariate analysis was used to differentiate water spinach of different cultivars and farming methods. We identified 12 metabolites to distinguish between G and W, 26 metabolites to identify G from organic farming and 8 metabolites to identify W from organic farming. Then, two metabolites, isorhamnetin and jasmonic acid, have been proposed to serve as biomarkers for organic farming (in both G and W). Our foodomics findings provide useful tools for improving the crop performance of water spinach under abiotic/biotic stressesand authentication of organic produce.
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Affiliation(s)
- Ka-Yi Man
- Department of Food Science and Nutrition, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China.
| | - Chi-On Chan
- Department of Food Science and Nutrition, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China.
| | - Siu-Wai Wan
- Department of Food Science and Nutrition, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China.
| | - Kevin Wing Hin Kwok
- Department of Food Science and Nutrition, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China; Research Institute for Future Food, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China.
| | - Francesco Capozzi
- Department of Agricultural and Food Sciences, Alma Mater Studiorum - University of Bologna, Piazza Goidanich 60, 47521 Cesena, FC, Italy.
| | - Nai-Ping Dong
- Department of Food Science and Nutrition, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China; State Key Laboratory of Chinese Medicine and Molecular Pharmacology (Incubation), Shenzhen Research Institute of The Hong Kong Polytechnic University, Shenzhen 518057, China.
| | - Ka-Hing Wong
- Department of Food Science and Nutrition, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China; Research Institute for Future Food, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China.
| | - Daniel Kam-Wah Mok
- Department of Food Science and Nutrition, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China; Research Institute for Future Food, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China.
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Komatsu S, Diniyah A, Zhu W, Nakano M, Rehman SU, Yamaguchi H, Hitachi K, Tsuchida K. Metabolomic and Proteomic Analyses to Reveal the Role of Plant-Derived Smoke Solution on Wheat under Salt Stress. Int J Mol Sci 2024; 25:8216. [PMID: 39125784 PMCID: PMC11311447 DOI: 10.3390/ijms25158216] [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: 06/25/2024] [Revised: 07/24/2024] [Accepted: 07/25/2024] [Indexed: 08/12/2024] Open
Abstract
Salt stress is a serious problem, because it reduces the plant growth and seed yield of wheat. To investigate the salt-tolerant mechanism of wheat caused by plant-derived smoke (PDS) solution, metabolomic and proteomic techniques were used. PDS solution, which repairs the growth inhibition of wheat under salt stress, contains metabolites related to flavonoid biosynthesis. Wheat was treated with PDS solution under salt stress and proteins were analyzed using a gel-free/label-free proteomic technique. Oppositely changed proteins were associated with protein metabolism and signal transduction in biological processes, as well as mitochondrion, endoplasmic reticulum/Golgi, and plasma membrane in cellular components with PDS solution under salt stress compared to control. Using immuno-blot analysis, proteomic results confirmed that ascorbate peroxidase increased with salt stress and decreased with additional PDS solution; however, H+-ATPase displayed opposite effects. Ubiquitin increased with salt stress and decreased with additional PDS solution; nevertheless, genomic DNA did not change. As part of mitochondrion-related events, the contents of ATP increased with salt stress and recovered with additional PDS solution. These results suggest that PDS solution enhances wheat growth suppressed by salt stress through the regulation of energy metabolism and the ubiquitin-proteasome system related to flavonoid metabolism.
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Affiliation(s)
- Setsuko Komatsu
- Faculty of Environment and Information Sciences, Fukui University of Technology, Fukui 910-8505, Japan
| | - Azzahrah Diniyah
- Faculty of Environment and Information Sciences, Fukui University of Technology, Fukui 910-8505, Japan
| | - Wei Zhu
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou 310018, China;
| | - Masataka Nakano
- Research Center for Experimental Modeling of Human Disease, Kanazawa University, Kanazawa 920-8640, Japan;
| | - Shafiq Ur Rehman
- Department of Biology, University of Haripur, Haripur 22620, Pakistan
| | - Hisateru Yamaguchi
- Department of Medical Technology, Yokkaichi Nursing and Medical Care University, Yokkaichi 512-8045, Japan
| | - Keisuke Hitachi
- Center for Medical Science, Fujita Health University, Toyoake 470-1192, Japan
| | - Kunihiro Tsuchida
- Center for Medical Science, Fujita Health University, Toyoake 470-1192, Japan
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Kausar R, Nishiuchi T, Komatsu S. Proteomic and molecular analyses to understand the promotive effect of safranal on soybean growth under salt stress. J Proteomics 2024; 294:105072. [PMID: 38218428 DOI: 10.1016/j.jprot.2024.105072] [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: 10/15/2023] [Revised: 01/01/2024] [Accepted: 01/03/2024] [Indexed: 01/15/2024]
Abstract
Safranal is a free radical scavenger and useful as an antioxidant molecule; however, its promotive role in soybean is not explored. Salt stress decreased soybean growth and safranal improved it even if under salt stress. To study the positive mechanism of safranal on soybean growth, a proteomic approach was used. According to functional categorization, oppositely changed proteins were further confirmed using biochemical techniques. Actin and calcium-dependent protein kinase decreased in soybean root and hypocotyl, respectively, under salt stress and increased with safranal application. Xyloglucan endotransglucosylase/ hydrolase increased in soybean root under salt stress but decreased with safranal application. Peroxidase increased under salt stress and further enhanced by safranal application in soybean root. Actin, RuvB-like helicase, and protein kinase domain-containing protein were upregulated under salt stress and further enhanced by safranal application under salt stress. Dynamin GTPase was downregulated under salt stress but recovered with safranal application under salt stress. Glutathione peroxidase and PfkB domain-containing protein were upregulated by safranal application under salt stress in soybean root. These results suggest that safranal improves soybean growth through the regulation of cell wall and nuclear proteins along with reactive‑oxygen species scavenging system. Furthermore, it might promote salt-stress tolerance through the regulation of membrane proteins involved in endocytosis and post-Golgi trafficking. SIGNIFICANCE: To study the positive mechanism of safranal on soybean growth, a proteomic approach was used. According to functional categorization, oppositely changed proteins were further confirmed using biochemical techniques. Actin and calcium-dependent protein kinase decreased in soybean root and hypocotyl, respectively, under salt stress and increased with safranal application. Xyloglucan endotransglucosylase/ hydrolase increased in soybean root under salt stress but decreased with safranal application. Peroxidase increased under salt stress and further enhanced by safranal application in soybean root. Actin, RuvB-like helicase, and protein kinase domain-containing protein were upregulated under salt stress and further enhanced by safranal application under salt stress. Dynamin GTPase was downregulated under salt stress but recovered with safranal application under salt stress. Glutathione peroxidase and PfkB domain-containing protein were upregulated by safranal application under salt stress in soybean root. These results suggest that safranal improves soybean growth through the regulation of cell wall and nuclear proteins along with reactive‑oxygen species scavenging system. Furthermore, it might promote salt-stress tolerance through the regulation of membrane proteins involved in endocytosis and post-Golgi trafficking.
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Affiliation(s)
- Rehana Kausar
- Department of Botany, University of Azad Jammu and Kashmir, Muzaffarabad 13100, Pakistan
| | - Takumi Nishiuchi
- Research Center for Experimental Modeling of Human Disease, Kanazawa University, Kanazawa 920-8640, Japan
| | - Setsuko Komatsu
- Faculty of Environment and Information Sciences, Fukui University of Technology, Fukui 910-8505, Japan.
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Komatsu S, Nishiuchi T, Furuya T, Tani M. Millmeter-wave irradiation regulates mRNA-expression and the ubiquitin-proteasome system in wheat exposed to flooding stress. J Proteomics 2024; 294:105073. [PMID: 38218429 DOI: 10.1016/j.jprot.2024.105073] [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: 12/31/2023] [Accepted: 01/03/2024] [Indexed: 01/15/2024]
Abstract
The irradiation with millimeter-wave (MMW) of wheat seeds promotes root growth under flooding stress; however, its role is not completely clarified. Nuclear proteomics was performed, to reveal the role of MMW irradiation in enhancing flooding tolerance. The purity of nuclear fractions purified from roots was verified. Histone, which is a protein marker for nuclear-purification efficiency, was enriched; and cytosolic ascorbate peroxidase was reduced in the nuclear fraction. The principal-component analysis of proteome displayed that the irradiation of seeds affected nuclear proteins in roots grown under flooding stress. Proteins detected using proteomic analysis were verified using immunoblot analysis. Histone H3 accumulated under flooding stress; however, it decreased to the control level by irradiation. Whereas the ubiquitin accumulated in roots grown under stress when seeds were irradiated. These results suggest that MMW irradiation improves wheat-root growth under flooding stress through the regulation of mRNA-expression level and the ubiquitin-proteasome system. SIGNIFICANCE: To reveal the role of millimeter-wave irradiation in enhancing flooding tolerance in wheat, nuclear proteomics was performed. The principal-component analysis of proteome displayed that irradiation of seeds affected nuclear proteins in roots grown under flooding stress. Proteins detected using proteomic analysis were verified using immunoblot analysis. Histone H3 accumulated under flooding stress; however, it decreased to the control level with irradiation. Whereas the ubiquitin accumulated in roots grown under stress when seeds were irradiated. These results suggest that millimeter-wave irradiation improves wheat-root growth under flooding stress through the regulation of mRNA-expression level and the ubiquitin-proteasome system.
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Affiliation(s)
- Setsuko Komatsu
- Department of Applied Chemistry and Food Science, Fukui University of Technology, Fukui 910-8505, Japan.
| | - Takumi Nishiuchi
- Research Center for Experimental Modeling of Human Disease, Kanazawa University, Kanazawa 920-8640, Japan
| | - Takashi Furuya
- Research Center for Development of Far-Infrared Region, University of Fukui, Fukui 910-8507, Japan
| | - Masahiko Tani
- Research Center for Development of Far-Infrared Region, University of Fukui, Fukui 910-8507, Japan
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Wang X, Komatsu S. Subcellular Proteomics to Elucidate Soybean Response to Abiotic Stress. PLANTS (BASEL, SWITZERLAND) 2023; 12:2865. [PMID: 37571018 PMCID: PMC10421527 DOI: 10.3390/plants12152865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/01/2023] [Accepted: 08/02/2023] [Indexed: 08/13/2023]
Abstract
Climate change jeopardizes soybean production by declining seed yield and quality. In this review, the morphophysiological alterations of soybean in response to abiotic stress are summarized, followed by illustrations of cellular metabolisms and regulatory mechanisms to organellar stress based on subcellular proteomics. This highlights the communications associated with reactive oxygen species scavenging, molecular chaperones, and phytohormone signals among subcellular compartments. Given the complexity of climate change and the limitations of plants in coping with multiple abiotic stresses, a generic response to environmental constraints is proposed between calcium and abscisic acid signals in subcellular organelles. This review summarizes the findings of subcellular proteomics in stressed soybean and discusses the future prospects of subcellular proteomics for promoting the improvement of climate-tolerant crops.
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Affiliation(s)
- Xin Wang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China;
| | - Setsuko Komatsu
- Faculty of Environmental and Information Sciences, Fukui University of Technology, Fukui 910-8505, Japan
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Komatsu S, Hamada K, Furuya T, Nishiuchi T, Tani M. Membrane Proteomics to Understand Enhancement Effects of Millimeter-Wave Irradiation on Wheat Root under Flooding Stress. Int J Mol Sci 2023; 24:ijms24109014. [PMID: 37240359 DOI: 10.3390/ijms24109014] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 05/13/2023] [Accepted: 05/16/2023] [Indexed: 05/28/2023] Open
Abstract
Millimeter-wave irradiation of wheat seeds enhances the growth of roots under flooding stress, but its mechanism is not clearly understood. To understand the role of millimeter-wave irradiation on root-growth enhancement, membrane proteomics was performed. Membrane fractions purified from wheat roots were evaluated for purity. H+-ATPase and calnexin, which are protein markers for membrane-purification efficiency, were enriched in a membrane fraction. A principal-component analysis of the proteomic results indicated that the millimeter-wave irradiation of seeds affects membrane proteins in grown roots. Proteins identified using proteomic analysis were confirmed using immunoblot or polymerase chain reaction analyses. The abundance of cellulose synthetase, which is a plasma-membrane protein, decreased under flooding stress; however, it increased with millimeter-wave irradiation. On the other hand, the abundance of calnexin and V-ATPase, which are proteins in the endoplasmic reticulum and vacuolar, increased under flooding stress; however, it decreased with millimeter-wave irradiation. Furthermore, NADH dehydrogenase, which is found in mitochondria membranes, was upregulated due to flooding stress but downregulated following millimeter-wave irradiation even under flooding stress. The ATP content showed a similar trend toward change in NADH dehydrogenase expression. These results suggest that millimeter-wave irradiation improves the root growth of wheat via the transitions of proteins in the plasma membrane, endoplasmic reticulum, vacuolar, and mitochondria.
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Affiliation(s)
- Setsuko Komatsu
- Faculty of Environment and Information Sciences, Fukui University of Technology, Fukui 910-8505, Japan
| | - Kazuna Hamada
- Faculty of Environment and Information Sciences, Fukui University of Technology, Fukui 910-8505, Japan
| | - Takashi Furuya
- Research Center for Development of Far-Infrared Region, University of Fukui, Fukui 910-8507, Japan
| | - Takumi Nishiuchi
- Institute for Gene Research, Kanazawa University, Kanazawa 920-8640, Japan
| | - Masahiko Tani
- Research Center for Development of Far-Infrared Region, University of Fukui, Fukui 910-8507, Japan
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7
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Abbey L, Ofoe R, Wang Z, Chada S. How Central Carbon Metabolites of Mexican Mint ( Plectranthus amboinicus) Plants Are Impacted under Different Watering Regimes. Metabolites 2023; 13:metabo13040539. [PMID: 37110197 PMCID: PMC10141017 DOI: 10.3390/metabo13040539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 04/02/2023] [Accepted: 04/08/2023] [Indexed: 04/29/2023] Open
Abstract
Plants are sessile, and their ability to reprogram their metabolism to adapt to fluctuations in soil water level is crucial but not clearly understood. A study was performed to determine alterations in intermediate metabolites involved in central carbon metabolism (CCM) following exposure of Mexican mint (Plectranthus amboinicus) to varying watering regimes. The water treatments were regular watering (RW), drought (DR), flooding (FL), and resumption of regular watering after flooding (DHFL) or after drought (RH). Leaf cluster formation and leaf greening were swift following the resumption of regular watering. A total of 68 key metabolites from the CCM routes were found to be significantly (p < 0.01) impacted by water stress. Calvin cycle metabolites in FL plants, glycolytic metabolites in DR plants, total tricarboxylic acid (TCA) cycle metabolites in DR and DHFL plants, and nucleotide biosynthetic molecules in FL and RH plants were significantly (p < 0.05) increased. Pentose phosphate pathway (PPP) metabolites were equally high in all the plants except DR plants. Total Calvin cycle metabolites had a significantly (p < 0.001) strong positive association with TCA cycle (r = 0.81) and PPP (r = 0.75) metabolites. Total PPP metabolites had a moderately positive association with total TCA cycle metabolites (r = 0.68; p < 0.01) and a negative correlation with total glycolytic metabolites (r = -0.70; p < 0.005). In conclusion, the metabolic alterations of Mexican mint plants under different watering regimes were revealed. Future studies will use transcriptomic and proteomic approaches to identify genes and proteins that regulate the CCM route.
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Affiliation(s)
- Lord Abbey
- Department of Plant, Food, and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS B2N 5E3, Canada
| | - Raphael Ofoe
- Department of Plant, Food, and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS B2N 5E3, Canada
| | - Zijing Wang
- Department of Plant, Food, and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS B2N 5E3, Canada
| | - Sparsha Chada
- Department of Plant, Food, and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS B2N 5E3, Canada
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Proteomic and Biochemical Approaches Elucidate the Role of Millimeter-Wave Irradiation in Wheat Growth under Flooding Stress. Int J Mol Sci 2022; 23:ijms231810360. [PMID: 36142271 PMCID: PMC9499361 DOI: 10.3390/ijms231810360] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/04/2022] [Accepted: 09/05/2022] [Indexed: 11/25/2022] Open
Abstract
Flooding impairs wheat growth and considerably affects yield productivity worldwide. On the other hand, irradiation with millimeter waves enhanced the growth of chickpea and soybean under flooding stress. In the current work, millimeter-wave irradiation notably enhanced wheat growth, even under flooding stress. To explore the protective mechanisms of millimeter-wave irradiation on wheat under flooding, quantitative proteomics was performed. According to functional categorization, proteins whose abundances were changed significantly with and without irradiation under flooding stress were correlated to glycolysis, reactive-oxygen species scavenging, cell organization, and hormonal metabolism. Immunoblot analysis confirmed that fructose-bisphosphate aldolase and β tubulin accumulated in root and leaf under flooding; however, even in such condition, their accumulations were recovered to the control level in irradiated wheat. The abundance of ascorbate peroxidase increased in leaf under flooding and recovered to the control level in irradiated wheat. Because the abundance of auxin-related proteins changed with millimeter-wave irradiation, auxin was applied to wheat under flooding, resulting in the application of auxin improving its growth, even in such condition. These results suggest that millimeter-wave irradiation on wheat seeds improves the recovery of plant growth from flooding via the regulation of glycolysis, reactive-oxygen species scavenging, and cell organization. Additionally, millimeter-wave irradiation could promote tolerance against flooding through the regulation of auxin contents in wheat.
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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; 23:5716. [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
| | - Xinyu Fu
- Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
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Komatsu S, Yamaguchi H, Hitachi K, Tsuchida K. Proteomic, Biochemical, and Morphological Analyses of the Effect of Silver Nanoparticles Mixed with Organic and Inorganic Chemicals on Wheat Growth. Cells 2022; 11:1579. [PMID: 35563885 PMCID: PMC9104970 DOI: 10.3390/cells11091579] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 05/04/2022] [Accepted: 05/05/2022] [Indexed: 12/04/2022] Open
Abstract
Wheat is vulnerable to numerous diseases; on the other hand, silver nanoparticles (AgNPs) exhibit a sterilizing action. To understand the combined effects of AgNPs with nicotinate and potassium nitrate (KNO3) for plant growth and sterilization, a gel- and label-free proteomics was performed. Root weight was promoted by the treatment of AgNPs mixed with nicotinate and KNO3. From a total of 5557 detected proteins, 90 proteins were changed by the mixture of AgNPs, nicotinate, and KNO3; among them, 25 and 65 proteins increased and decreased, respectively. The changed proteins were mainly associated with redox and biotic stress in the functional categorization. By immunoblot analysis, the abundance of glutathione reductase/peroxiredoxin and pathogen-related protein three significantly decreased with the mixture. Furthermore, from the changed proteins, the abundance of starch synthase and lipoxygenase significantly increased and decreased, respectively. Through biochemical analysis, the starch contents increased with the mixture. The application of esculetin, which is a lipoxygenase inhibitor, increased the weight and length of the root. These results suggest that the AgNPs mixed with nicotinate and KNO3 cause positive effects on wheat seedlings by regulating pathogen-related protein and reactive-oxygen species scavenging. Furthermore, increasing starch and decreasing lipoxygenase might improve wheat growth.
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Affiliation(s)
- Setsuko Komatsu
- Faculty of Environment and Information Sciences, Fukui University of Technology, Fukui 910-8505, Japan
| | - Hisateru Yamaguchi
- Department of Medical Technology, Yokkaichi Nursing and Medical Care University, Yokkaichi 512-8045, Japan;
| | - Keisuke Hitachi
- Institute for Comprehensive Medical Science, Fujita Health University, Toyoake 470-1192, Japan; (K.H.); (K.T.)
| | - Kunihiro Tsuchida
- Institute for Comprehensive Medical Science, Fujita Health University, Toyoake 470-1192, Japan; (K.H.); (K.T.)
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Zhang M, Liu S, Wang Z, Yuan Y, Zhang Z, Liang Q, Yang X, Duan Z, Liu Y, Kong F, Liu B, Ren B, Tian Z. Progress in soybean functional genomics over the past decade. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:256-282. [PMID: 34388296 PMCID: PMC8753368 DOI: 10.1111/pbi.13682] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 08/04/2021] [Accepted: 08/09/2021] [Indexed: 05/24/2023]
Abstract
Soybean is one of the most important oilseed and fodder crops. Benefiting from the efforts of soybean breeders and the development of breeding technology, large number of germplasm has been generated over the last 100 years. Nevertheless, soybean breeding needs to be accelerated to meet the needs of a growing world population, to promote sustainable agriculture and to address future environmental changes. The acceleration is highly reliant on the discoveries in gene functional studies. The release of the reference soybean genome in 2010 has significantly facilitated the advance in soybean functional genomics. Here, we review the research progress in soybean omics (genomics, transcriptomics, epigenomics and proteomics), germplasm development (germplasm resources and databases), gene discovery (genes that are responsible for important soybean traits including yield, flowering and maturity, seed quality, stress resistance, nodulation and domestication) and transformation technology during the past decade. At the end, we also briefly discuss current challenges and future directions.
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Affiliation(s)
- Min Zhang
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
| | - Shulin Liu
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
| | - Zhao Wang
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yaqin Yuan
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Zhifang Zhang
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Qianjin Liang
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Xia Yang
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Zongbiao Duan
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yucheng Liu
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
| | - Fanjiang Kong
- Innovative Center of Molecular Genetics and EvolutionSchool of Life SciencesGuangzhou UniversityGuangzhouChina
| | - Baohui Liu
- Innovative Center of Molecular Genetics and EvolutionSchool of Life SciencesGuangzhou UniversityGuangzhouChina
| | - Bo Ren
- State Key Laboratory of Plant GenomicsInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Zhixi Tian
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
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12
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Tao M, Zhu W, Han H, Liu S, Liu A, Li S, Fu H, Tian J. Mitochondrial proteomic analysis reveals the regulation of energy metabolism and reactive oxygen species production in Clematis terniflora DC. leaves under high-level UV-B radiation followed by dark treatment. J Proteomics 2021; 254:104410. [PMID: 34923174 DOI: 10.1016/j.jprot.2021.104410] [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: 07/25/2021] [Revised: 10/08/2021] [Accepted: 10/19/2021] [Indexed: 11/15/2022]
Abstract
Clematis terniflora DC. is an important medicinal plant from the family Ranunculaceae. A previous study has shown that active ingredients in C. terniflora, such as flavonoids and coumarins, are increased under ultraviolet B radiation (UV-B) and dark treatment and that the numbers of genes related to the tricarboxylic acid cycle and mitochondrial electron transport chain (mETC) are changed. To uncover the mechanism of the response to UV-B radiation and dark treatment in C. terniflora, mitochondrial proteomics was performed. The results showed that proteins related to photorespiration, mitochondrial membrane permeability, the tricarboxylic acid cycle, and the mETC mainly showed differential expression profiles. Moreover, the increase in alternative oxidase indicated that another oxygen-consuming respiratory pathway in plant mitochondria was induced to minimize mitochondrial reactive oxygen species production. These results suggested that respiration and mitochondrial membrane permeability were deeply influenced to avoid energy consumption and maintain energy balance under UV-B radiation and dark treatment in C. terniflora leaf mitochondria. Furthermore, oxidative phosphorylation was able to regulate intracellular oxygen balance to resist oxidative stress. This study improves understanding of the function of mitochondria in response to UV-B radiation and dark treatment in C. terniflora. SIGNIFICANCE: C. terniflora was an important traditional Chinese medicine for anti-inflammatory. Previous study showed that the contents of coumarins which were the main active ingredient in C. terniflora were induced by UV-B radiation and dark treatment. In the present study, to uncover the regulatory mechanism of metabolic changes in C. terniflora, mitochondrial proteomics analysis of leaves was performed. The results showed that photorespiration and oxidative phosphorylation pathways were influenced under UV-B radiation and dark treatment. Mitochondria in C. terniflora leaf played a crucial role in energy mechanism and regulation of cellular oxidation-reduction to maintain cell homeostasis under UV-B radiation followed with dark treatment.
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Affiliation(s)
- Minglei Tao
- College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou 310027, China; The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou 310022, China; College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Wei Zhu
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou 310022, China; Changshu Qiushi Technology Co. Ltd, Suzhou 215500, PR China
| | - Haote Han
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou 310022, China
| | - Shengzhi Liu
- College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou 310027, China
| | - Amin Liu
- College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou 310027, China
| | - Shouxin Li
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou 310022, China
| | - Hongwei Fu
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China.
| | - Jingkui Tian
- College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou 310027, China; The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou 310022, China.
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13
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Mustafa G, Komatsu S. Plant proteomic research for improvement of food crops under stresses: a review. Mol Omics 2021; 17:860-880. [PMID: 34870299 DOI: 10.1039/d1mo00151e] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Crop improvement approaches have been changed due to technological advancements in traditional plant-breeding methods. Abiotic and biotic stresses limit plant growth and development, which ultimately lead to reduced crop yield. Proteins encoded by genomes have a considerable role in the endurance and adaptation of plants to different environmental conditions. Biotechnological applications in plant breeding depend upon the information generated from proteomic studies. Proteomics has a specific advantage to contemplate post-translational modifications, which indicate the functional effects of protein modifications on crop production. Subcellular proteomics helps in exploring the precise cellular responses and investigating the networking among subcellular compartments during plant development and biotic/abiotic stress responses. Large-scale mass spectrometry-based plant proteomic studies with a more comprehensive overview are now possible due to dramatic improvements in mass spectrometry, sample preparation procedures, analytical software, and strengthened availability of genomes for numerous plant species. Development of stress-tolerant or resilient crops is essential to improve crop productivity and growth. Use of high throughput techniques with advanced instrumentation giving efficient results made this possible. In this review, the role of proteomic studies in identifying the stress-response processes in different crops is summarized. Advanced techniques and their possible utilization on plants are discussed in detail. Proteomic studies accelerate marker-assisted genetic augmentation studies on crops for developing high yielding stress-tolerant lines or varieties under stresses.
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Affiliation(s)
- Ghazala Mustafa
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Setsuko Komatsu
- Faculty of Environment and Information Sciences, Fukui University of Technology, Fukui 910-8505, Japan.
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14
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Subcellular Proteomics to Understand Promotive Effect of Plant-Derived Smoke Solution on Soybean Root. Proteomes 2021; 9:proteomes9040039. [PMID: 34698284 PMCID: PMC8544748 DOI: 10.3390/proteomes9040039] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 09/27/2021] [Accepted: 09/30/2021] [Indexed: 12/11/2022] Open
Abstract
Plant-derived smoke solution enhances soybean root growth; however, its mechanism is not clearly understood. Subcellular proteomics techniques were used for underlying roles of plant-derived smoke solution on soybean root growth. The fractions of membrane and nucleus were purified and evaluated for purity. ATPase and histone were enriched in the fractions of membrane and nucleus, respectively. Principal component analysis of proteomic results indicated that the plant-derived smoke solution affected the proteins in the membrane and nucleus. The proteins in the membrane and nucleus mainly increased and decreased, respectively, by the treatment of plant-derived smoke solution compared with control. In the proteins in the plasma membrane, ATPase increased, which was confirmed by immunoblot analysis, and ATP contents increased through the treatment of plant-derived smoke solution. Additionally, although the nuclear proteins mainly decreased, the expression of RNA polymerase II was up-regulated through the treatment of plant-derived smoke solution. These results indicate that plant-derived smoke solution enhanced soybean root growth through the transcriptional promotion with RNA polymerase II expression and the energy production with ATPase accumulation.
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15
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Rojas-Méndez KJ, Sánchez Segura L, Chagolla A, Lino B, González de la Vara LE. Voltage-Dependent Anion-Selective Channels and Other Mitochondrial Membrane Proteins Form Diverse Complexes in Beetroots Subjected to Flood-Induced Programmed Cell Death. FRONTIERS IN PLANT SCIENCE 2021; 12:714847. [PMID: 34567029 PMCID: PMC8457146 DOI: 10.3389/fpls.2021.714847] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 08/03/2021] [Indexed: 06/13/2023]
Abstract
In plants, programmed cell death (PCD) is involved in both the development and the response to biotic and abiotic aggressions. In early stages of PCD, mitochondrial membranes are made permeable by the formation of permeability transition pores, whose protein composition is debated. Cytochrome c (cyt c) is then released from mitochondria, inducing the degradation of chromatin characteristic of PCD. Since flooding stress can produce PCD in several plant species, the first goal of this study was to know if flooding stress could be used to induce PCD in Beta vulgaris roots. To do this, 2-month-old beet plants were flood-stressed from 1 to 5 days, and the alterations indicating PCD in stressed beetroot cells were observed with a confocal fluorescence microscope. As expected, nuclei were deformed, and chromatin was condensed and fragmented in flooded beetroots. In addition, cyt c was released from mitochondria. After assessing that flood stress induced PCD in beetroots, the composition of mitochondrial protein complexes was observed in control and flood-stressed beetroots. Protein complexes from isolated mitochondria were separated by native gel electrophoresis, and their proteins were identified by mass spectrometry. The spectra count of three isoforms of voltage-dependent anion-selective channels (VDACs) increased after 1 day of flooding. In addition, the size of the complexes formed by VDAC was higher in flood-stressed beetroots for 1 day (∼200 kDa) compared with non-stressed ones (∼100 kDa). Other proteins, such as chaperonin CPN60-2, also formed complexes with different masses in control and flood-stressed beetroots. Finally, possible interactions of VDAC with other proteins were found performing a cluster analysis. These results indicate that mitochondrial protein complexes formed by VDAC could be involved in the process of PCD in flood-stressed beetroots. Data are available via ProteomeXchange with identifier PXD027781.
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Affiliation(s)
- Karla J. Rojas-Méndez
- Laboratorio de Bioenergética y Biomembranas, Departamento de Biotecnología y Bioquímica, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Mexico
| | - Lino Sánchez Segura
- Laboratorio de Microscopía, Departamento de Ingeniería Genética, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Mexico
| | - Alicia Chagolla
- Laboratorio de Proteómica, Departamento de Biotecnología y Bioquímica, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Mexico
| | - Bárbara Lino
- Laboratorio de Bioenergética y Biomembranas, Departamento de Biotecnología y Bioquímica, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Mexico
| | - Luis E. González de la Vara
- Laboratorio de Bioenergética y Biomembranas, Departamento de Biotecnología y Bioquímica, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Mexico
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16
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Pazhamala LT, Kudapa H, Weckwerth W, Millar AH, Varshney RK. Systems biology for crop improvement. THE PLANT GENOME 2021; 14:e20098. [PMID: 33949787 DOI: 10.1002/tpg2.20098] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 03/09/2021] [Indexed: 05/19/2023]
Abstract
In recent years, generation of large-scale data from genome, transcriptome, proteome, metabolome, epigenome, and others, has become routine in several plant species. Most of these datasets in different crop species, however, were studied independently and as a result, full insight could not be gained on the molecular basis of complex traits and biological networks. A systems biology approach involving integration of multiple omics data, modeling, and prediction of the cellular functions is required to understand the flow of biological information that underlies complex traits. In this context, systems biology with multiomics data integration is crucial and allows a holistic understanding of the dynamic system with the different levels of biological organization interacting with external environment for a phenotypic expression. Here, we present recent progress made in the area of various omics studies-integrative and systems biology approaches with a special focus on application to crop improvement. We have also discussed the challenges and opportunities in multiomics data integration, modeling, and understanding of the biology of complex traits underpinning yield and stress tolerance in major cereals and legumes.
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Affiliation(s)
- Lekha T Pazhamala
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, 502 324, India
| | - Himabindu Kudapa
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, 502 324, India
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
- Vienna Metabolomics Center, University of Vienna, Vienna, Austria
| | - A Harvey Millar
- ARC Centre of Excellence in Plant Energy Biology and School of Molecular Sciences, The University of Western Australia, Perth, WA, Australia
| | - Rajeev K Varshney
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, 502 324, India
- State Agricultural Biotechnology Centre, Crop Research Innovation Centre, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
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17
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Wang X, Komatsu S. Review: Proteomic Techniques for the Development of Flood-Tolerant Soybean. Int J Mol Sci 2020; 21:E7497. [PMID: 33053653 PMCID: PMC7589014 DOI: 10.3390/ijms21207497] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 10/04/2020] [Accepted: 10/08/2020] [Indexed: 12/16/2022] Open
Abstract
Soybean, which is rich in protein and oil as well as phytochemicals, is cultivated in several climatic zones. However, its growth is markedly decreased by flooding stress, which is caused by climate change. Proteomic techniques were used for understanding the flood-response and -tolerant mechanisms in soybean. Subcellular proteomics has potential to elucidate localized cellular responses and investigate communications among subcellular components during plant growth and under stress stimuli. Furthermore, post-translational modifications play important roles in stress response and tolerance to flooding stress. Although many flood-response mechanisms have been reported, flood-tolerant mechanisms have not been fully clarified for soybean because of limitations in germplasm with flooding tolerance. This review provides an update on current biochemical and molecular networks involved in soybean tolerance against flooding stress, as well as recent developments in the area of functional genomics in terms of developing flood-tolerant soybeans. This work will expedite marker-assisted genetic enhancement studies in crops for developing high-yielding stress-tolerant lines or varieties under abiotic stress.
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Affiliation(s)
- Xin Wang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Setsuko Komatsu
- Faculty of Environmental and Information Sciences, Fukui University of Technology, Fukui 910-8505, Japan
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18
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Mustafa G, Hasan M, Yamaguchi H, Hitachi K, Tsuchida K, Komatsu S. A comparative proteomic analysis of engineered and bio synthesized silver nanoparticles on soybean seedlings. J Proteomics 2020; 224:103833. [PMID: 32450145 DOI: 10.1016/j.jprot.2020.103833] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 04/20/2020] [Accepted: 05/18/2020] [Indexed: 02/06/2023]
Abstract
Nanoparticles (NPs) are synthesized by different methods and response mechanism of plants varied towards NPs based on their origin. To study the effects of bio synthesized (BS) and chemically synthesized (CS) silver NPs on soybean, a gel-free/ label-free proteomic technique was used. Length of root and hypocotyl was enhanced by BS compared to CS silver NPs. 10 ppm BS silver NPs enhanced the length of root and hypocotyl compared to 1 and 50 ppm. A total of 190 and 173 differentially changed proteins were identified in BS and CS silver NPs treated soybean, respectively. Twenty proteins commonly changed between BS and CS silver NPs treated soybean. Differentially-changed proteins were associated with protein-degradation and stress according to functional categorization. From proteomics, abundances of peroxidases were increased under CS silver NPs. Immunoblot analysis depicted that accumulation of ascorbate peroxidase, glutathione reductase, and peroxiredoxin remained unchanged under both BS and CS silver NPs. ATP content decreased under CS silver NPs compared to BS silver NPs. ADH activity increased in CS silver NPs treated soybean. These results suggest that BS silver NPs enhanced the growth of soybean by regulating proteins related to protein-degradation and ATP contents, which are negatively affected by CS silver NPs. BIOLOGICAL SIGNIFICANCE: This study highlighted the response mechanism of soybean towards bio synthesized (BS) and chemically synthesized (CS) silver nanoparticles (NPs) using a gel-free/ label-free proteomics technique. Length of root and hypocotyl was enhanced by BS silver NPs compared to CS silver NPs. 10 ppm BS silver NPs enhanced the length of root and hypocotyl compared to other concentrations. Differentially changed proteins were associated with protein degradation and stress. From the proteomics, the abundances of peroxidases were increased under CS silver NPs. Immunoblot analysis depicted that accumulation of ascorbate peroxidase, glutathione reductase, and peroxiredoxin remained unchanged under both BS and CS silver NPs. ATP content decreased under CS silver NPs compared to BS silver NPs. ADH activity increased in CS silver NPs compared to BS silver NPs treated soybean. These results suggest that the BS silver NPs enhanced the growth of soybean by regulating the proteins related to protein degradation and ATP contents, which are negatively affected by the CS silver NPs.
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Affiliation(s)
- Ghazala Mustafa
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan; Faculty of Environment and Information Sciences, Fukui University of Technology, Fukui 910-8505, Japan.
| | - Murtaza Hasan
- Department of Biochemistry and Biotechnology, Islamia University of Bahawalpur, Bahawalpur 63100, Pakistan
| | - Hisateru Yamaguchi
- Department of Medical Technology, Yokkaichi Nursing and Medical Care University, Yokkaichi 512-8045, Japan
| | - Keisuke Hitachi
- Institute for Comprehensive Medical Science, Fujita Health University, Toyoake 470-1192, Japan
| | - Kunihiro Tsuchida
- Institute for Comprehensive Medical Science, Fujita Health University, Toyoake 470-1192, Japan
| | - Setsuko Komatsu
- Faculty of Environment and Information Sciences, Fukui University of Technology, Fukui 910-8505, Japan.
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19
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Ambrosino L, Colantuono C, Diretto G, Fiore A, Chiusano ML. Bioinformatics Resources for Plant Abiotic Stress Responses: State of the Art and Opportunities in the Fast Evolving -Omics Era. PLANTS 2020; 9:plants9050591. [PMID: 32384671 PMCID: PMC7285221 DOI: 10.3390/plants9050591] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 04/24/2020] [Accepted: 04/29/2020] [Indexed: 12/13/2022]
Abstract
Abiotic stresses are among the principal limiting factors for productivity in agriculture. In the current era of continuous climate changes, the understanding of the molecular aspects involved in abiotic stress response in plants is a priority. The rise of -omics approaches provides key strategies to promote effective research in the field, facilitating the investigations from reference models to an increasing number of species, tolerant and sensitive genotypes. Integrated multilevel approaches, based on molecular investigations at genomics, transcriptomics, proteomics and metabolomics levels, are now feasible, expanding the opportunities to clarify key molecular aspects involved in responses to abiotic stresses. To this aim, bioinformatics has become fundamental for data production, mining and integration, and necessary for extracting valuable information and for comparative efforts, paving the way to the modeling of the involved processes. We provide here an overview of bioinformatics resources for research on plant abiotic stresses, describing collections from -omics efforts in the field, ranging from raw data to complete databases or platforms, highlighting opportunities and still open challenges in abiotic stress research based on -omics technologies.
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Affiliation(s)
- Luca Ambrosino
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici (Na), Italy; (L.A.); (C.C.)
- Department of Research Infrastructures for Marine Biological Resources (RIMAR), 80121 Naples, Italy
| | - Chiara Colantuono
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici (Na), Italy; (L.A.); (C.C.)
- Department of Research Infrastructures for Marine Biological Resources (RIMAR), 80121 Naples, Italy
| | - Gianfranco Diretto
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), 00123 Rome, Italy; (G.D.); (A.F.)
| | - Alessia Fiore
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), 00123 Rome, Italy; (G.D.); (A.F.)
| | - Maria Luisa Chiusano
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici (Na), Italy; (L.A.); (C.C.)
- Department of Research Infrastructures for Marine Biological Resources (RIMAR), 80121 Naples, Italy
- Correspondence: ; Tel.: +39-081-253-9492
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Feng Z, Ding C, Li W, Wang D, Cui D. Applications of metabolomics in the research of soybean plant under abiotic stress. Food Chem 2020; 310:125914. [PMID: 31835223 DOI: 10.1016/j.foodchem.2019.125914] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Revised: 09/19/2019] [Accepted: 11/14/2019] [Indexed: 12/25/2022]
Abstract
Qualitative and quantitative metabolomics analysis of all small-molecule metabolites in organisms is an emerging omics technology alongside genomics and proteomics. Plant metabolites are extremely diverse both within species and in terms of their physiological function. Plant metabolomics studies use mainly liquid/gas chromatography-mass spectrometry (LC/GC-MS) and nuclear magnetic resonance (NMR) techniques combined with chemometrics and multivariate statistical analysis to analyze plant metabolites, and metabolomics plays a key role in agricultural and food science research. In this review, we discuss the status of metabolomics in soybean in response to abiotic stresses such as drought, heat, salinity, flooding, chilling and heavy metal stresses and analyze the challenges and opportunities. Furthermore, the notable metabolites detected in response to different stresses are summarized to provide a reference for applications of metabolomics in soybean research.
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Affiliation(s)
- Zhe Feng
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, PR China
| | - Chengqiao Ding
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, PR China
| | - Weihao Li
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, PR China
| | - Dachen Wang
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, PR China
| | - Di Cui
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, PR China.
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21
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Andrzejczak OA, Havelund JF, Wang WQ, Kovalchuk S, Hagensen CE, Hasler-Sheetal H, Jensen ON, Rogowska-Wrzesinska A, Møller IM, Hebelstrup KH. The Hypoxic Proteome and Metabolome of Barley ( Hordeum vulgare L.) with and without Phytoglobin Priming. Int J Mol Sci 2020; 21:E1546. [PMID: 32102473 PMCID: PMC7073221 DOI: 10.3390/ijms21041546] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 02/20/2020] [Accepted: 02/21/2020] [Indexed: 12/13/2022] Open
Abstract
Overexpression of phytoglobins (formerly plant hemoglobins) increases the survival rate of plant tissues under hypoxia stress by the following two known mechanisms: (1) scavenging of nitric oxide (NO) in the phytoglobin/NO cycle and (2) mimicking ethylene priming to hypoxia when NO scavenging activates transcription factors that are regulated by levels of NO and O2 in the N-end rule pathway. To map the cellular and metabolic effects of hypoxia in barley (Hordeum vulgare L., cv. Golden Promise), with or without priming to hypoxia, we studied the proteome and metabolome of wild type (WT) and hemoglobin overexpressing (HO) plants in normoxia and after 24 h hypoxia (WT24, HO24). The WT plants were more susceptible to hypoxia than HO plants. The chlorophyll a + b content was lowered by 50% and biomass by 30% in WT24 compared to WT, while HO plants were unaffected. We observed an increase in ROS production during hypoxia treatment in WT seedlings that was not observed in HO seedlings. We identified and quantified 9694 proteins out of which 1107 changed significantly in abundance. Many proteins, such as ion transporters, Ca2+-signal transduction, and proteins related to protein degradation were downregulated in HO plants during hypoxia, but not in WT plants. Changes in the levels of histones indicates that chromatin restructuring plays a role in the priming of hypoxia. We also identified and quantified 1470 metabolites, of which the abundance of >500 changed significantly. In summary the data confirm known mechanisms of hypoxia priming by ethylene priming and N-end rule activation; however, the data also indicate the existence of other mechanisms for hypoxia priming in plants.
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Affiliation(s)
- Olga A. Andrzejczak
- Department of Agroecology, Section of Crop Genetics and Biotechnology, Aarhus University, Forsøgsvej 1, DK-4200 Slagelse, Denmark;
| | - Jesper F. Havelund
- Department of Biochemistry & Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark; (J.F.H.); (W.-Q.W.); (S.K.); (C.E.H.); (H.H.-S.); (O.N.J.); (A.R.-W.)
| | - Wei-Qing Wang
- Department of Biochemistry & Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark; (J.F.H.); (W.-Q.W.); (S.K.); (C.E.H.); (H.H.-S.); (O.N.J.); (A.R.-W.)
| | - Sergey Kovalchuk
- Department of Biochemistry & Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark; (J.F.H.); (W.-Q.W.); (S.K.); (C.E.H.); (H.H.-S.); (O.N.J.); (A.R.-W.)
| | - Christina E. Hagensen
- Department of Biochemistry & Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark; (J.F.H.); (W.-Q.W.); (S.K.); (C.E.H.); (H.H.-S.); (O.N.J.); (A.R.-W.)
| | - Harald Hasler-Sheetal
- Department of Biochemistry & Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark; (J.F.H.); (W.-Q.W.); (S.K.); (C.E.H.); (H.H.-S.); (O.N.J.); (A.R.-W.)
- Nordcee, Department of Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Ole N. Jensen
- Department of Biochemistry & Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark; (J.F.H.); (W.-Q.W.); (S.K.); (C.E.H.); (H.H.-S.); (O.N.J.); (A.R.-W.)
| | - Adelina Rogowska-Wrzesinska
- Department of Biochemistry & Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark; (J.F.H.); (W.-Q.W.); (S.K.); (C.E.H.); (H.H.-S.); (O.N.J.); (A.R.-W.)
| | - Ian Max Møller
- Department of Molecular Biology and Genetics, Aarhus University, Forsøgsvej 1, DK-4200 Slagelse, Denmark;
| | - Kim H. Hebelstrup
- Department of Agroecology, Section of Crop Genetics and Biotechnology, Aarhus University, Forsøgsvej 1, DK-4200 Slagelse, Denmark;
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22
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Zhong Z, Furuya T, Ueno K, Yamaguchi H, Hitachi K, Tsuchida K, Tani M, Tian J, Komatsu S. Proteomic Analysis of Irradiation with Millimeter Waves on Soybean Growth under Flooding Conditions. Int J Mol Sci 2020; 21:E486. [PMID: 31940953 PMCID: PMC7013696 DOI: 10.3390/ijms21020486] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 01/03/2020] [Accepted: 01/08/2020] [Indexed: 01/01/2023] Open
Abstract
Improving soybean growth and tolerance under environmental stress is crucial for sustainable development. Millimeter waves are a radio-frequency band with a wavelength range of 1-10 mm that has dynamic effects on organisms. To investigate the potential effects of millimeter-waves irradiation on soybean seedlings, morphological and proteomic analyses were performed. Millimeter-waves irradiation improved the growth of roots/hypocotyl and the tolerance of soybean to flooding stress. Proteomic analysis indicated that the irradiated soybean seedlings recovered under oxidative stress during growth, whereas proteins related to glycolysis and ascorbate/glutathione metabolism were not affected. Immunoblot analysis confirmed the promotive effect of millimeter waves to glycolysis- and redox-related pathways under flooding conditions. Sugar metabolism was suppressed under flooding in unirradiated soybean seedlings, whereas it was activated in the irradiated ones, especially trehalose synthesis. These results suggest that millimeter-waves irradiation on soybean seeds promotes the recovery of soybean seedlings under oxidative stress, which positively regulates soybean growth through the regulation of glycolysis and redox related pathways.
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Affiliation(s)
- Zhuoheng Zhong
- Faculty of Environment and Information Sciences, Fukui University of Technology, Fukui 910-8505, Japan; (Z.Z.); (K.U.)
- College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou 310027, China;
| | - Takashi Furuya
- Research Center for Development of Far-Infrared Region, University of Fukui, Fukui 910-8507, Japan; (T.F.); (M.T.)
| | - Kimitaka Ueno
- Faculty of Environment and Information Sciences, Fukui University of Technology, Fukui 910-8505, Japan; (Z.Z.); (K.U.)
| | - Hisateru Yamaguchi
- Institute for Comprehensive Medical Science, Fujita Health University, Toyoake 470-1192, Japan; (H.Y.); (K.H.); (K.T.)
| | - Keisuke Hitachi
- Institute for Comprehensive Medical Science, Fujita Health University, Toyoake 470-1192, Japan; (H.Y.); (K.H.); (K.T.)
| | - Kunihiro Tsuchida
- Institute for Comprehensive Medical Science, Fujita Health University, Toyoake 470-1192, Japan; (H.Y.); (K.H.); (K.T.)
| | - Masahiko Tani
- Research Center for Development of Far-Infrared Region, University of Fukui, Fukui 910-8507, Japan; (T.F.); (M.T.)
| | - Jingkui Tian
- College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou 310027, China;
| | - Setsuko Komatsu
- Faculty of Environment and Information Sciences, Fukui University of Technology, Fukui 910-8505, Japan; (Z.Z.); (K.U.)
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23
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Abstract
Subcellular proteomics include, in its experimental workflow, steps aimed at purifying organelles. The purity of the subcellular fraction should be assessed before mass spectrometry analysis, in order to confidently conclude the presence of associated specific proteoforms, deepening the knowledge of its biological function. In this chapter, a protocol for isolating endoplasmic reticulum (ER) and purity assessment is reported, and it precedes the proteomic analysis through a gel-free/label-free proteomic approach. Dysfunction of quality-control mechanisms of protein metabolism in ER leads to ER stress. Additionally, ER, which is a calcium-storage organelle, is responsible for signaling and homeostatic function, and calcium homeostasis is required for plant tolerance. With such predominant cell functions, effective protocols to fractionate highly purified ER are needed. Here, isolation methods and purity assessments of ER are described. In addition, a gel-free/label-free proteomic approach of ER is presented.
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Affiliation(s)
- Xin Wang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Setsuko Komatsu
- Faculty of Environmental and Information Sciences, Fukui University of Technology, Fukui, Japan.
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24
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Haq SU, Khan A, Ali M, Gai WX, Zhang HX, Yu QH, Yang SB, Wei AM, Gong ZH. Knockdown of CaHSP60-6 confers enhanced sensitivity to heat stress in pepper (Capsicum annuum L.). PLANTA 2019; 250:2127-2145. [PMID: 31606756 DOI: 10.1007/s00425-019-03290-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 09/26/2019] [Indexed: 05/24/2023]
Abstract
HSP60 gene family in pepper was analyzed through bioinformatics along with transcriptional regulation against multiple abiotic and hormonal stresses. Furthermore, the knockdown of CaHSP60-6 increased sensitivity to heat stress. The 60 kDa heat shock protein (HSP60) also known as chaperonin (cpn60) is encoded by multi-gene family that plays an important role in plant growth, development and in stress response as a molecular chaperone. However, little is known about the HSP60 gene family in pepper (Capsicum annuum L.). In this study, 16 putative pepper HSP60 genes were identified through bioinformatic tools. The phylogenetic tree revealed that eight of the pepper HSP60 genes (50%) clustered into group I, three (19%) into group II, and five (31%) into group III. Twelve (75%) CaHSP60 genes have more than 10 introns, while only a single gene contained no introns. Chromosomal mapping revealed that the tandem and segmental duplication events occurred in the process of evolution. Gene ontology enrichment analysis predicted that CaHSP60 genes were responsible for protein folding and refolding in an ATP-dependent manner in response to various stresses in the biological processes category. Multiple stress-related cis-regulatory elements were found in the promoter region of these CaHSP60 genes, which indicated that these genes were regulated in response to multiple stresses. Tissue-specific expression was studied under normal conditions and induced under 2 h of heat stress measured by RNA-Seq data and qRT-PCR in different tissues (roots, stems, leaves, and flowers). The data implied that HSP60 genes play a crucial role in pepper growth, development, and stress responses. Fifteen (93%) CaHSP60 genes were induced in both, thermo-sensitive B6 and thermo-tolerant R9 lines under heat treatment. The relative expression of nine representative CaHSP60 genes in response to other abiotic stresses (cold, NaCl, and mannitol) and hormonal applications [ABA, methyl jasmonate (MeJA), and salicylic acid (SA)] was also evaluated. Knockdown of CaHSP60-6 increased the sensitivity to heat shock treatment as documented by a higher relative electrolyte leakage, lipid peroxidation, and reactive oxygen species accumulation in silenced pepper plants along with a substantial lower chlorophyll content and antioxidant enzyme activity. These results suggested that HSP60 might act as a positive regulator in pepper defense against heat and other abiotic stresses. Our results provide a basis for further functional analysis of HSP60 genes in pepper.
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Affiliation(s)
- Saeed Ul Haq
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Abid Khan
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Muhammad Ali
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Wen-Xian Gai
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Huai-Xia Zhang
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Qing-Hui Yu
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, People's Republic of China
| | - Sheng-Bao Yang
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, People's Republic of China
| | - Ai-Min Wei
- Tianjin Vegetable Research Center, Tianjin, 300192, People's Republic of China
| | - Zhen-Hui Gong
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China.
- State Key Laboratory of Vegetable Germplasm Innovation, Tianjin, 300384, People's Republic of China.
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25
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Afzal M, Alghamdi SS, Migdadi HH, Khan MA, Nurmansyah, Mirza SB, El-Harty E. Legume genomics and transcriptomics: From classic breeding to modern technologies. Saudi J Biol Sci 2019; 27:543-555. [PMID: 31889880 PMCID: PMC6933173 DOI: 10.1016/j.sjbs.2019.11.018] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 11/16/2019] [Accepted: 11/17/2019] [Indexed: 02/06/2023] Open
Abstract
Legumes are essential and play a significant role in maintaining food standards and augmenting physiochemical soil properties through the biological nitrogen fixation process. Biotic and abiotic factors are the main factors limiting legume production. Classical breeding methodologies have been explored extensively about the problem of truncated yield in legumes but have not succeeded at the desired rate. Conventional breeding improved legume genotypes but with more resources and time. Recently, the invention of next-generation sequencing (NGS) and high-throughput methods for genotyping have opened new avenues for research and developments in legume studies. During the last decade, genome sequencing for many legume crops documented. Sequencing and re-sequencing of important legume species have made structural variation and functional genomics conceivable. NGS and other molecular techniques such as the development of markers; genotyping; high density genetic linkage maps; quantitative trait loci (QTLs) identification, expressed sequence tags (ESTs), single nucleotide polymorphisms (SNPs); and transcription factors incorporated into existing breeding technologies have made possible the accurate and accelerated delivery of information for researchers. The application of genome sequencing, RNA sequencing (transcriptome sequencing), and DNA sequencing (re-sequencing) provide considerable insights for legume development and improvement programs. Moreover, RNA-Seq helps to characterize genes, including differentially expressed genes, and can be applied for functional genomics studies, especially when there is limited information available for the studied genomes. Genome-based crop development studies and the availability of genomics data as well as decision-making gears look be specific for breeding programs. This review mainly presents an overview of the path from classical breeding to new emerging genomics tools, which will trigger and accelerate genomics-assisted breeding for recognition of novel genes for yield and quality characters for sustainable legume crop production.
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Affiliation(s)
- Muhammad Afzal
- Department of Plant Production, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Salem S Alghamdi
- Department of Plant Production, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Hussein H Migdadi
- Department of Plant Production, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Muhammad Altaf Khan
- Department of Plant Production, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Nurmansyah
- Department of Plant Production, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Shaher Bano Mirza
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University (BAU), Istanbul, Turkey.,Department of Biosciences, COMSATS Institute of Information Technology (CIIT), Chak Shahzad, Islamabad, Pakistan
| | - Ehab El-Harty
- Department of Plant Production, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
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26
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ul Haq S, Khan A, Ali M, Khattak AM, Gai WX, Zhang HX, Wei AM, Gong ZH. Heat Shock Proteins: Dynamic Biomolecules to Counter Plant Biotic and Abiotic Stresses. Int J Mol Sci 2019; 20:E5321. [PMID: 31731530 PMCID: PMC6862505 DOI: 10.3390/ijms20215321] [Citation(s) in RCA: 213] [Impact Index Per Article: 42.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Revised: 10/15/2019] [Accepted: 10/23/2019] [Indexed: 12/13/2022] Open
Abstract
Due to the present scenario of climate change, plants have to evolve strategies to survive and perform under a plethora of biotic and abiotic stresses, which restrict plant productivity. Maintenance of plant protein functional conformation and preventing non-native proteins from aggregation, which leads to metabolic disruption, are of prime importance. Plant heat shock proteins (HSPs), as chaperones, play a pivotal role in conferring biotic and abiotic stress tolerance. Moreover, HSP also enhances membrane stability and detoxifies the reactive oxygen species (ROS) by positively regulating the antioxidant enzymes system. Additionally, it uses ROS as a signal to molecules to induce HSP production. HSP also enhances plant immunity by the accumulation and stability of pathogenesis-related (PR) proteins under various biotic stresses. Thus, to unravel the entire plant defense system, the role of HSPs are discussed with a special focus on plant response to biotic and abiotic stresses, which will be helpful in the development of stress tolerance in plant crops.
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Affiliation(s)
- Saeed ul Haq
- College of Horticulture, Northwest A&F University, Yangling 712100, China; (S.u.H.); (A.K.); (M.A.); (W.-X.G.); (H.-X.Z.)
- Department of Horticulture, University of Agriculture Peshawar, Peshawar 25130, Pakistan;
| | - Abid Khan
- College of Horticulture, Northwest A&F University, Yangling 712100, China; (S.u.H.); (A.K.); (M.A.); (W.-X.G.); (H.-X.Z.)
| | - Muhammad Ali
- College of Horticulture, Northwest A&F University, Yangling 712100, China; (S.u.H.); (A.K.); (M.A.); (W.-X.G.); (H.-X.Z.)
| | - Abdul Mateen Khattak
- Department of Horticulture, University of Agriculture Peshawar, Peshawar 25130, Pakistan;
- College of Information and Electrical Engineering, China Agricultural University, Beijing 100083, China
| | - Wen-Xian Gai
- College of Horticulture, Northwest A&F University, Yangling 712100, China; (S.u.H.); (A.K.); (M.A.); (W.-X.G.); (H.-X.Z.)
| | - Huai-Xia Zhang
- College of Horticulture, Northwest A&F University, Yangling 712100, China; (S.u.H.); (A.K.); (M.A.); (W.-X.G.); (H.-X.Z.)
| | - Ai-Min Wei
- Tianjin Vegetable Research Center, Tianjin 300192, China;
| | - Zhen-Hui Gong
- College of Horticulture, Northwest A&F University, Yangling 712100, China; (S.u.H.); (A.K.); (M.A.); (W.-X.G.); (H.-X.Z.)
- State Key Laboratory of Vegetable Germplasm Innovation, Tianjin 300384, China
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27
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Zhong Z, Liu S, Zhu W, Ou Y, Yamaguchi H, Hitachi K, Tsuchida K, Tian J, Komatsu S. Phosphoproteomics Reveals the Biosynthesis of Secondary Metabolites in Catharanthus roseus under Ultraviolet-B Radiation. J Proteome Res 2019; 18:3328-3341. [PMID: 31356092 DOI: 10.1021/acs.jproteome.9b00267] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Ultraviolet (UV)-B radiation acts as an elicitor to enhance the production of secondary metabolites in medicinal plants. To investigate the mechanisms, which lead to secondary metabolites in Catharanthus roseus under UVB radiation, a phosphoproteomic technique was used. ATP content increased in the leaves of C. roseus under UVB radiation. Phosphoproteins related to calcium such as calmodulin, calcium-dependent kinase, and heat shock proteins increased. Phosphoproteins related to protein synthesis/modification/degradation and signaling intensively changed. Metabolomic analysis indicated that the metabolites classified with pentoses, aromatic amino acids, and phenylpropanoids accumulated under UVB radiation. Phosphoproteomic and immunoblot analyses indicated that proteins related to glycolysis and the reactive-oxygen species scavenging system were changed under UVB radiation. These results suggest that UVB radiation activates the calcium-related pathway and reactive-oxygen species scavenging system in C. roseus. These changes lead to the upregulation of proteins, which are responsible for the redox reactions in secondary metabolism and are important for the accumulation of secondary metabolites in C. roseus under UVB radiation.
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Affiliation(s)
- Zhuoheng Zhong
- College of Biomedical Engineering & Instrument Science , Zhejiang University , Hangzhou 310027 , P. R. China.,Faculty of Life and Environmental and Information Sciences , Fukui University of Technology , Fukui 910-8505 , Japan
| | - Shengzhi Liu
- College of Biomedical Engineering & Instrument Science , Zhejiang University , Hangzhou 310027 , P. R. China
| | - Wei Zhu
- College of Biomedical Engineering & Instrument Science , Zhejiang University , Hangzhou 310027 , P. R. China
| | - Yuting Ou
- College of Biomedical Engineering & Instrument Science , Zhejiang University , Hangzhou 310027 , P. R. China
| | - Hisateru Yamaguchi
- Institute for Comprehensive Medical Science , Fujita Health University , Toyoake 470-1192 , Japan
| | - Keisuke Hitachi
- Institute for Comprehensive Medical Science , Fujita Health University , Toyoake 470-1192 , Japan
| | - Kunihiro Tsuchida
- Institute for Comprehensive Medical Science , Fujita Health University , Toyoake 470-1192 , Japan
| | - Jingkui Tian
- College of Biomedical Engineering & Instrument Science , Zhejiang University , Hangzhou 310027 , P. R. China
| | - Setsuko Komatsu
- Faculty of Life and Environmental and Information Sciences , Fukui University of Technology , Fukui 910-8505 , Japan
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28
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Ghatak A, Chaturvedi P, Weckwerth W. Metabolomics in Plant Stress Physiology. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2019; 164:187-236. [PMID: 29470599 DOI: 10.1007/10_2017_55] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Metabolomics is an essential technology for functional genomics and systems biology. It plays a key role in functional annotation of genes and understanding towards cellular and molecular, biotic and abiotic stress responses. Different analytical techniques are used to extend the coverage of a full metabolome. The commonly used techniques are NMR, CE-MS, LC-MS, and GC-MS. The choice of a suitable technique depends on the speed, sensitivity, and accuracy. This chapter provides insight into plant metabolomic techniques, databases used in the analysis, data mining and processing, compound identification, and limitations in metabolomics. It also describes the workflow of measuring metabolites in plants. Metabolomic studies in plant responses to stress are a key research topic in many laboratories worldwide. We summarize different approaches and provide a generic overview of stress responsive metabolite markers and processes compiled from a broad range of different studies. Graphical Abstract.
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Affiliation(s)
- Arindam Ghatak
- Department of Ecogenomics and Systems Biology, Faculty of Sciences, University of Vienna, Vienna, Austria
| | - Palak Chaturvedi
- Department of Ecogenomics and Systems Biology, Faculty of Sciences, University of Vienna, Vienna, Austria
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology, Faculty of Sciences, University of Vienna, Vienna, Austria. .,Vienna Metabolomics Center (VIME), University of Vienna, Althanstrasse 14, 1090, Vienna, Austria.
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29
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Aslam MM, Rehman S, Khatoon A, Jamil M, Yamaguchi H, Hitachi K, Tsuchida K, Li X, Sunohara Y, Matsumoto H, Komatsu S. Molecular Responses of Maize Shoot to a Plant Derived Smoke Solution. Int J Mol Sci 2019; 20:E1319. [PMID: 30875914 PMCID: PMC6471572 DOI: 10.3390/ijms20061319] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Revised: 02/14/2019] [Accepted: 03/05/2019] [Indexed: 11/16/2022] Open
Abstract
Plant-derived smoke has effects on plant growth. To find the molecular mechanism of plant-derived smoke on maize, a gel-free/label-free proteomic technique was used. The length of root and shoot were increased in maize by plant-derived smoke. Proteomic analysis revealed that 2000 ppm plant-derived smoke changed the abundance of 69 proteins in 4-days old maize shoot. Proteins in cytoplasm, chloroplast, and cell membrane were altered by plant-derived smoke. Catalytic, signaling, and nucleotide binding proteins were changed. Proteins related to sucrose synthase, nucleotides, signaling, and glutathione were significantly increased; however, cell wall, lipids, photosynthetic, and amino acid degradations related proteins were decreased. Based on proteomic and immunoblot analyses, ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) was decreased; however, RuBisCO activase was not changed by plant-derived smoke in maize shoot. Ascorbate peroxidase was not affected; however, peroxiredoxin was decreased by plant-derived smoke. Furthermore, the results from enzyme-activity and mRNA-expression analyses confirmed regulation of ascorbate peroxidase and the peroxiredoxinin reactive oxygen scavenging system. These results suggest that increases in sucrose synthase, nucleotides, signaling, and glutathione related proteins combined with regulation of reactive oxygen species and their scavenging system in response to plant-derived smoke may improve maize growth.
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Affiliation(s)
- Muhammad Mudasar Aslam
- Department of Botany, Kohat University of Science and Technology, Kohat 26000, Pakistan.
- Faculty of Environmental and Information Sciences, Fukui University of Technology, Fukui 910-8505, Japan.
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan.
| | - Shafiq Rehman
- Department of Botany, Kohat University of Science and Technology, Kohat 26000, Pakistan.
| | - Amana Khatoon
- Department of Botany, Kohat University of Science and Technology, Kohat 26000, Pakistan.
| | - Muhammad Jamil
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology, Kohat 26000, Pakistan.
| | - Hisateru Yamaguchi
- Institute for Comprehensive Medical Science, Fujita Health University, Toyoake 470-1192, Japan.
| | - Keisuke Hitachi
- Institute for Comprehensive Medical Science, Fujita Health University, Toyoake 470-1192, Japan.
| | - Kunihiro Tsuchida
- Institute for Comprehensive Medical Science, Fujita Health University, Toyoake 470-1192, Japan.
| | - Xinyue Li
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan.
| | - Yukari Sunohara
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan.
| | - Hiroshi Matsumoto
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan.
| | - Setsuko Komatsu
- Faculty of Environmental and Information Sciences, Fukui University of Technology, Fukui 910-8505, Japan.
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30
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Jha UC, Bohra A, Jha R, Parida SK. Salinity stress response and 'omics' approaches for improving salinity stress tolerance in major grain legumes. PLANT CELL REPORTS 2019; 38:255-277. [PMID: 30637478 DOI: 10.1007/s00299-019-02374-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 01/04/2019] [Indexed: 05/21/2023]
Abstract
Sustaining yield gains of grain legume crops under growing salt-stressed conditions demands a thorough understanding of plant salinity response and more efficient breeding techniques that effectively integrate modern omics knowledge. Grain legume crops are important to global food security being an affordable source of dietary protein and essential mineral nutrients to human population, especially in the developing countries. The global productivity of grain legume crops is severely challenged by the salinity stress particularly in the face of changing climates coupled with injudicious use of irrigation water and improper agricultural land management. Plants adapt to sustain under salinity-challenged conditions through evoking complex molecular mechanisms. Elucidating the underlying complex mechanisms remains pivotal to our knowledge about plant salinity response. Improving salinity tolerance of plants demand enriching cultivated gene pool of grain legume crops through capitalizing on 'adaptive traits' that contribute to salinity stress tolerance. Here, we review the current progress in understanding the genetic makeup of salinity tolerance and highlight the role of germplasm resources and omics advances in improving salt tolerance of grain legumes. In parallel, scope of next generation phenotyping platforms that efficiently bridge the phenotyping-genotyping gap and latest research advances including epigenetics is also discussed in context to salt stress tolerance. Breeding salt-tolerant cultivars of grain legumes will require an integrated "omics-assisted" approach enabling accelerated improvement of salt-tolerance traits in crop breeding programs.
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Affiliation(s)
- Uday Chand Jha
- ICAR-Indian Institute of Pulses Research (IIPR), Kanpur, 208024, India.
| | - Abhishek Bohra
- ICAR-Indian Institute of Pulses Research (IIPR), Kanpur, 208024, India.
| | - Rintu Jha
- ICAR-Indian Institute of Pulses Research (IIPR), Kanpur, 208024, India
| | - Swarup Kumar Parida
- National Institute of Plant Genome Research (NIPGR), New Delhi, 110067, India
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31
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Wang X, Sakata K, Komatsu S. An Integrated Approach of Proteomics and Computational Genetic Modification Effectiveness Analysis to Uncover the Mechanisms of Flood Tolerance in Soybeans. Int J Mol Sci 2018; 19:E1301. [PMID: 29701710 PMCID: PMC5983631 DOI: 10.3390/ijms19051301] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 04/20/2018] [Accepted: 04/22/2018] [Indexed: 12/21/2022] Open
Abstract
Flooding negatively affects the growth of soybeans. Recently, omic approaches have been used to study abiotic stress responses in plants. To explore flood-tolerant genes in soybeans, an integrated approach of proteomics and computational genetic modification effectiveness analysis was applied to the soybean (Glycine max L. (Merrill)). Flood-tolerant mutant and abscisic acid (ABA)-treated soybean plants were used as the flood-tolerant materials. Among the primary metabolism, glycolysis, fermentation, and tricarboxylic acid cycle were markedly affected under flooding. Fifteen proteins, which were related to the affected processes, displayed similar protein profiles in the mutant and ABA-treated soybean plants. Protein levels of glyceraldehyde-3-phosphate dehydrogenase (GAPDH), aconitase 1, and 2-oxoglutarate dehydrogenase were higher in flood-tolerant materials than in wild-type soybean plants under flood conditions. These three proteins were positioned in each of the three enzyme groups revealed by our computational genetic modification effectiveness analysis, and the three proteins configured a candidate set of genes to promote flood tolerance. Additionally, transcript levels of GAPDH were similar in flood-tolerant materials and in unstressed plants. These results suggest that proteins related to energy metabolism might play an essential role to confer flood tolerance in soybeans.
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Affiliation(s)
- Xin Wang
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan.
- National Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba 305-8518, Japan.
| | - Katsumi Sakata
- Department of Life Science and Informatics, Maebashi Institute of Technology, Maebashi 371-0816, Japan.
| | - Setsuko Komatsu
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan.
- National Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba 305-8518, Japan.
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32
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Rurek M, Czołpińska M, Pawłowski TA, Krzesiński W, Spiżewski T. Cold and Heat Stress Diversely Alter Both Cauliflower Respiration and Distinct Mitochondrial Proteins Including OXPHOS Components and Matrix Enzymes. Int J Mol Sci 2018; 19:ijms19030877. [PMID: 29547512 PMCID: PMC5877738 DOI: 10.3390/ijms19030877] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 03/07/2018] [Accepted: 03/09/2018] [Indexed: 12/11/2022] Open
Abstract
Complex proteomic and physiological approaches for studying cold and heat stress responses in plant mitochondria are still limited. Variations in the mitochondrial proteome of cauliflower (Brassica oleracea var. botrytis) curds after cold and heat and after stress recovery were assayed by two-dimensional polyacrylamide gel electrophoresis (2D PAGE) in relation to mRNA abundance and respiratory parameters. Quantitative analysis of the mitochondrial proteome revealed numerous stress-affected protein spots. In cold, major downregulations in the level of photorespiratory enzymes, porine isoforms, oxidative phosphorylation (OXPHOS) and some low-abundant proteins were observed. In contrast, carbohydrate metabolism enzymes, heat-shock proteins, translation, protein import, and OXPHOS components were involved in heat response and recovery. Several transcriptomic and metabolic regulation mechanisms are also suggested. Cauliflower plants appeared less susceptible to heat; closed stomata in heat stress resulted in moderate photosynthetic, but only minor respiratory impairments, however, photosystem II performance was unaffected. Decreased photorespiration corresponded with proteomic alterations in cold. Our results show that cold and heat stress not only operate in diverse modes (exemplified by cold-specific accumulation of some heat shock proteins), but exert some associations at molecular and physiological levels. This implies a more complex model of action of investigated stresses on plant mitochondria.
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Affiliation(s)
- Michał Rurek
- Department of Molecular and Cellular Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Umultowska 89, 61-614 Poznań, Poland.
| | - Magdalena Czołpińska
- Department of Molecular and Cellular Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Umultowska 89, 61-614 Poznań, Poland.
| | | | - Włodzimierz Krzesiński
- Department of Vegetable Crops, Poznan University of Life Sciences, Dąbrowskiego 159, 60-594 Poznań, Poland.
| | - Tomasz Spiżewski
- Department of Vegetable Crops, Poznan University of Life Sciences, Dąbrowskiego 159, 60-594 Poznań, Poland.
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Komatsu S, Hashiguchi A. Subcellular Proteomics: Application to Elucidation of Flooding-Response Mechanisms in Soybean. Proteomes 2018; 6:E13. [PMID: 29495455 PMCID: PMC5874772 DOI: 10.3390/proteomes6010013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 02/13/2018] [Accepted: 02/23/2018] [Indexed: 02/06/2023] Open
Abstract
Soybean, which is rich in protein and oil, is cultivated in several climatic zones; however, its growth is markedly decreased by flooding. Proteomics is a useful tool for understanding the flooding-response mechanism in soybean. Subcellular proteomics has the potential to elucidate localized cellular responses and investigate communications among subcellular components during plant growth and during stress. Under flooding, proteins related to signaling, stress and the antioxidative system are increased in the plasma membrane; scavenging enzymes for reactive-oxygen species are suppressed in the cell wall; protein translation is suppressed through inhibition of proteins related to preribosome biogenesis and mRNA processing in the nucleus; levels of proteins involved in the electron transport chain are reduced in the mitochondrion; and levels of proteins related to protein folding are decreased in the endoplasmic reticulum. This review discusses the advantages of a gel-free/label-free proteomic technique and methods of plant subcellular purification. It also summarizes cellular events in soybean under flooding and discusses future prospects for generation of flooding-tolerant soybean.
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Affiliation(s)
- Setsuko Komatsu
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan.
| | - Akiko Hashiguchi
- Faculty of Medicine, University of Tsukuba, Tsukuba 305-8577, Japan.
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Wang X, Komatsu S. Proteomic approaches to uncover the flooding and drought stress response mechanisms in soybean. J Proteomics 2018; 172:201-215. [PMID: 29133124 DOI: 10.1016/j.jprot.2017.11.006] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 10/13/2017] [Accepted: 11/08/2017] [Indexed: 12/20/2022]
Abstract
Soybean is the important crop with abundant protein, vegetable oil, and several phytochemicals. With such predominant values, soybean is cultivated with a long history. However, flooding and drought stresses exert deleterious effects on soybean growth. The present review summarizes the morphological changes and affected events in soybean exposed to such extreme-water conditions. Sensitive organ in stressed soybean at different-developmental stages is presented based on protein profiles. Protein quality control and calcium homeostasis in the endoplasmic reticulum are discussed in soybean under both stresses. In addition, the way of calcium homeostasis in mediating protein folding and energy metabolism is addressed. Finally, stress response to flooding and drought is systematically demonstrated. This review concludes the recent findings of plant response to flooding and drought stresses in soybean employed proteomic approaches. BIOLOGICAL SIGNIFICANCE Soybean is considered as traditional-health food because of nutritional elements and pharmacological values. Flooding and drought exert deleterious effects to soybean growth. Proteomic approaches have been employed to elucidate stress response in soybean exposed to flooding and drought stresses. In this review, stress response is presented on organ-specific manner in the early-stage plant and soybean seedling exposed to combined stresses. The endoplasmic reticulum (ER) stress is induced by both stresses; and stress-response in the ER is addressed in the root tip of early-stage soybean. Moreover, calcium-response processes in stressed plant are described in the ER and in the cytosol. Additionally, stress-dependent response was discussed in flooded and drought-stressed plant. This review depicts stress response in the sensitive organ of stressed soybean and forms the basis to develop molecular markers related to plant defense under flooding and drought stresses.
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Affiliation(s)
- Xin Wang
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan
| | - Setsuko Komatsu
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan.
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Kosová K, Vítámvás P, Urban MO, Prášil IT, Renaut J. Plant Abiotic Stress Proteomics: The Major Factors Determining Alterations in Cellular Proteome. FRONTIERS IN PLANT SCIENCE 2018; 9:122. [PMID: 29472941 PMCID: PMC5810178 DOI: 10.3389/fpls.2018.00122] [Citation(s) in RCA: 137] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 01/23/2018] [Indexed: 05/19/2023]
Abstract
HIGHLIGHTS: Major environmental and genetic factors determining stress-related protein abundance are discussed.Major aspects of protein biological function including protein isoforms and PTMs, cellular localization and protein interactions are discussed.Functional diversity of protein isoforms and PTMs is discussed. Abiotic stresses reveal profound impacts on plant proteomes including alterations in protein relative abundance, cellular localization, post-transcriptional and post-translational modifications (PTMs), protein interactions with other protein partners, and, finally, protein biological functions. The main aim of the present review is to discuss the major factors determining stress-related protein accumulation and their final biological functions. A dynamics of stress response including stress acclimation to altered ambient conditions and recovery after the stress treatment is discussed. The results of proteomic studies aimed at a comparison of stress response in plant genotypes differing in stress adaptability reveal constitutively enhanced levels of several stress-related proteins (protective proteins, chaperones, ROS scavenging- and detoxification-related enzymes) in the tolerant genotypes with respect to the susceptible ones. Tolerant genotypes can efficiently adjust energy metabolism to enhanced needs during stress acclimation. Stress tolerance vs. stress susceptibility are relative terms which can reflect different stress-coping strategies depending on the given stress treatment. The role of differential protein isoforms and PTMs with respect to their biological functions in different physiological constraints (cellular compartments and interacting partners) is discussed. The importance of protein functional studies following high-throughput proteome analyses is presented in a broader context of plant biology. In summary, the manuscript tries to provide an overview of the major factors which have to be considered when interpreting data from proteomic studies on stress-treated plants.
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Affiliation(s)
- Klára Kosová
- Division of Crop Genetics and Breeding, Laboratory of Plant Stress Biology and Biotechnology, Crop Research Institute, Prague, Czechia
- Department of Experimental Plant Biology, Faculty of Science, Charles University in Prague, Prague, Czechia
| | - Pavel Vítámvás
- Division of Crop Genetics and Breeding, Laboratory of Plant Stress Biology and Biotechnology, Crop Research Institute, Prague, Czechia
- Department of Experimental Plant Biology, Faculty of Science, Charles University in Prague, Prague, Czechia
| | - Milan O. Urban
- Division of Crop Genetics and Breeding, Laboratory of Plant Stress Biology and Biotechnology, Crop Research Institute, Prague, Czechia
- Department of Experimental Plant Biology, Faculty of Science, Charles University in Prague, Prague, Czechia
| | - Ilja T. Prášil
- Division of Crop Genetics and Breeding, Laboratory of Plant Stress Biology and Biotechnology, Crop Research Institute, Prague, Czechia
| | - Jenny Renaut
- Environmental Research and Technology Platform, Environmental Research and Innovation, Luxembourg Institute of Science and Technology (LIST), Esch-sur-Alzette, Luxembourg
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Rehman A, Rehman SU, Khatoon A, Qasim M, Itoh T, Iwasaki Y, Wang X, Sunohara Y, Matsumoto H, Komatsu S. Proteomic analysis of the promotive effect of plant-derived smoke on plant growth of chickpea. J Proteomics 2018; 176:56-70. [PMID: 29391210 DOI: 10.1016/j.jprot.2018.01.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 01/10/2018] [Accepted: 01/24/2018] [Indexed: 12/29/2022]
Abstract
Plant-derived smoke plays a key role in seed germination and plant growth. To investigate the effect of plant-derived smoke on chickpea, a gel-free/label-free proteomic technique was used. Germination percentage, root/shoot length, and fresh biomass were increased in chickpea treated with 2000 ppm plant-derived smoke within 6 days. On treatment with 2000 ppm plant-derived smoke for 6 days, the abundance of 90 proteins including glycolysis-related proteins significantly changed in chickpea root. Proteins related to signaling and transport were increased; however, protein metabolism, cell, and cell wall were decreased. The sucrose synthase for starch degradation was increased and total soluble sugar was induced. The proteins for nitrate pathway were increased and nitrate content was improved. On the other hand, although secondary metabolism related proteins were decreased, flavonoid contents were increased. Based on proteomic and immuno-blot analyses, proteins related to redox homeostasis were decreased and increased in root and shoot, respectively. Furthermore, fructose‑bisphosphate aldolase was increased; while, phosphotransferase and phosphoglycero mutase were decreased in glycolysis. In addition, phosphoglyceraldehyde‑3‑phosphate dehydrogenase and glutamine synthetase related genes were up-regulated. These results suggest that plant-derived smoke improves early stage of growth in chickpea with the balance of many cascades such as glycolysis, redox homeostasis, and secondary metabolism. BIOLOGICAL SIGNIFICANCE The current study examined the effects of plant-derived smoke on root of chickpea seedlings using a gel-free/label-free proteomic technique. Based on functional categorization of results from proteomics, proteins related to glycolysis, signaling, transport, protein metabolism, cell wall, and cell were predominantly changed in chickpea. The proteins related to carbohydrate and nitrate pathways were increased, while, those of secondary metabolism were decreased. Physiological analysis indicated that flavonoid, total soluble sugar, and nitrate content were increased in root of chickpea treated with plant-derived smoke for 6 days. Moreover, accumulated protein abundance of glyceraldehyde‑3‑phosphate dehydrogenase and fructose-bisphosphate aldolase was in agreement with immuno-blot results, which suggests that glycolysis process might be enhanced in root of chickpea in response to plant-derived smoke.
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Affiliation(s)
- Ali Rehman
- Department of Botany, Kohat University of Science and Technology, Kohat 26000, Pakistan; Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan
| | - Shafiq Ur Rehman
- Department of Botany, Kohat University of Science and Technology, Kohat 26000, Pakistan
| | - Amana Khatoon
- Department of Botany, Kohat University of Science and Technology, Kohat 26000, Pakistan
| | - Muhammad Qasim
- Department of Microbiology, Kohat University of Science and Technology, Kohat 26000, Pakistan
| | - Takafumi Itoh
- Faculty of Biotechnology, Fukui Prefectural University, Fukui 910-1195, Japan
| | - Yukimoto Iwasaki
- Faculty of Biotechnology, Fukui Prefectural University, Fukui 910-1195, Japan
| | - Xin Wang
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan
| | - Yukari Sunohara
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan
| | - Hiroshi Matsumoto
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan
| | - Setsuko Komatsu
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan.
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Mishra D, Shekhar S, Singh D, Chakraborty S, Chakraborty N. Heat Shock Proteins and Abiotic Stress Tolerance in Plants. REGULATION OF HEAT SHOCK PROTEIN RESPONSES 2018. [DOI: 10.1007/978-3-319-74715-6_3] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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Liu X, Xu G. Recent advances in using mass spectrometry for mitochondrial metabolomics and lipidomics - A review. Anal Chim Acta 2017; 1037:3-12. [PMID: 30292306 DOI: 10.1016/j.aca.2017.11.080] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 11/28/2017] [Accepted: 11/29/2017] [Indexed: 01/09/2023]
Abstract
Metabolomics and lipidomics generally targets a huge number of intermediate and end products of cellular metabolism in body fluids, tissues, and cells etc. At present, mass spectrometry (MS) based metabolic or lipid profiling of routine biological specimens including the whole cells, tissues, plasma, serum and urine etc., can cover hundreds of metabolites or lipid species in one analysis, which has qualified deep elucidation of global metabolic and lipid networks. Mitochondria are important intracellular organelles and many critical biochemical reactions occur here, they provide building block for new cells, control redox balance, participate in apoptosis and behave as a signalling platform. Evidence suggests high prevalence of mitochondrial dysfunction occurs in a variety of cancers and other diseases, thus there is an urgent demand for investigating and clarifying mitochondrial metabolic and lipid alterations induced by diseases. Nevertheless, mitochondria contribute a small fraction to cellular contents, profiling of whole cell is probably unsuitable for monitoring alterations in mitochondria. Therefore, metabolomics and lipidomics analyses specially for mitochondria are necessary to understand disturbed metabolic and lipid pathways induced by environment and diseases. However, methods for comprehensively profiling metabolites and lipids in mitochondria have been limited at present. This review summarizes the current states and progress of MS-based mitochondrial metabolomics and lipidomics study. Details of mitochondrial isolation procedure, analytical methods and their applications are described. The challenges and opportunities are also given.
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Affiliation(s)
- Xinyu Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Guowang Xu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
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Kumar R, Bohra A, Pandey AK, Pandey MK, Kumar A. Metabolomics for Plant Improvement: Status and Prospects. FRONTIERS IN PLANT SCIENCE 2017; 8:1302. [PMID: 28824660 PMCID: PMC5545584 DOI: 10.3389/fpls.2017.01302] [Citation(s) in RCA: 129] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 07/11/2017] [Indexed: 05/12/2023]
Abstract
Post-genomics era has witnessed the development of cutting-edge technologies that have offered cost-efficient and high-throughput ways for molecular characterization of the function of a cell or organism. Large-scale metabolite profiling assays have allowed researchers to access the global data sets of metabolites and the corresponding metabolic pathways in an unprecedented way. Recent efforts in metabolomics have been directed to improve the quality along with a major focus on yield related traits. Importantly, an integration of metabolomics with other approaches such as quantitative genetics, transcriptomics and genetic modification has established its immense relevance to plant improvement. An effective combination of these modern approaches guides researchers to pinpoint the functional gene(s) and the characterization of massive metabolites, in order to prioritize the candidate genes for downstream analyses and ultimately, offering trait specific markers to improve commercially important traits. This in turn will improve the ability of a plant breeder by allowing him to make more informed decisions. Given this, the present review captures the significant leads gained in the past decade in the field of plant metabolomics accompanied by a brief discussion on the current contribution and the future scope of metabolomics to accelerate plant improvement.
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Affiliation(s)
- Rakesh Kumar
- Department of Plant Sciences, University of Hyderabad (UoH)Hyderabad, India
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Hyderabad, India
| | - Abhishek Bohra
- Crop Improvement Division, Indian Institute of Pulses Research (IIPR)Kanpur, India
| | - Arun K. Pandey
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Hyderabad, India
| | - Manish K. Pandey
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Hyderabad, India
| | - Anirudh Kumar
- Department of Botany, Indira Gandhi National Tribal University (IGNTU)Amarkantak, India
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Wang X, Zhu W, Hashiguchi A, Nishimura M, Tian J, Komatsu S. Metabolic profiles of flooding-tolerant mechanism in early-stage soybean responding to initial stress. PLANT MOLECULAR BIOLOGY 2017; 94:669-685. [PMID: 28733872 DOI: 10.1007/s11103-017-0635-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 07/14/2017] [Indexed: 06/07/2023]
Abstract
KEY MESSAGE Metabolomic analysis of flooding-tolerant mutant and abscisic acid-treated soybeans suggests that accumulated fructose might play a role in initial flooding tolerance through regulation of hexokinase and phosphofructokinase. Soybean is sensitive to flooding stress, which markedly reduces plant growth. To explore the mechanism underlying initial-flooding tolerance in soybean, mass spectrometry-based metabolomic analysis was performed using flooding-tolerant mutant and abscisic-acid treated soybeans. Among the commonly-identified metabolites in both flooding-tolerant materials, metabolites involved in carbohydrate and organic acid displayed same profile at initial-flooding stress. Sugar metabolism was highlighted in both flooding-tolerant materials with the decreased and increased accumulation of sucrose and fructose, respectively, compared to flooded soybeans. Gene expression of hexokinase 1 was upregulated in flooded soybean; however, it was downregulated in both flooding-tolerant materials. Metabolites involved in carbohydrate/organic acid and proteins related to glycolysis/tricarboxylic acid cycle were integrated. Increased protein abundance of phosphofructokinase was identified in both flooding-tolerant materials, which was in agreement with its enzyme activity. Furthermore, sugar metabolism was pointed out as the tolerant-responsive process at initial-flooding stress with the integration of metabolomics, proteomics, and transcriptomics. Moreover, application of fructose declined the increased fresh weight of plant induced by flooding stress. These results suggest that fructose might be the critical metabolite through regulation of hexokinase and phosphofructokinase to confer initial-flooding stress in soybean.
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Affiliation(s)
- Xin Wang
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tennodai 1-1-1, Tsukuba, 305-8572, Japan
- National Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, 305-8518, Japan
| | - Wei Zhu
- College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou, 310027, China
| | - Akiko Hashiguchi
- National Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, 305-8518, Japan
| | - Minoru Nishimura
- Graduate School of Life and Food Sciences, Niigata University, Niigata, 950-2181, Japan
| | - Jingkui Tian
- College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou, 310027, China
| | - Setsuko Komatsu
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tennodai 1-1-1, Tsukuba, 305-8572, Japan.
- National Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, 305-8518, Japan.
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Wang X, Komatsu S. Proteomic Analysis of Calcium Effects on Soybean Root Tip under Flooding and Drought Stresses. PLANT & CELL PHYSIOLOGY 2017; 58:1405-1420. [PMID: 28586431 DOI: 10.1093/pcp/pcx078] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 05/18/2017] [Indexed: 06/07/2023]
Abstract
Flooding and drought are disadvantageous environmental conditions that induce cytosolic calcium in soybean. To explore the effects of flooding- and drought-induced increases in calcium, a gel-free/label-free proteomic analysis was performed. Cytosolic calcium was decreased by blocking calcium channels in the endoplasmic reticulum (ER) and plasma membrane under both stresses. Calnexin, protein disulfide isomerase, heat shock proteins and thioredoxin were predominantly affected as the ER proteins in response to calcium, and ER-associated degradation-related proteins of HCP-like superfamily protein were up-regulated under stress exposure and then down-regulated. Glycolysis, fermentation, the tricarboxylic acid cycle and amino acid metabolism were mainly induced as the types of cellular metabolism in response to calcium under both stresses. Pyruvate decarboxylase was increased and decreased under flooding and drought, respectively, and was further decreased by the reduction of cytosolic calcium; however, it was recovered by exogenous calcium under both stresses. Furthermore, pyruvate decarboxylase activity was increased under flooding, but decreased under drought. These results suggest that calcium is involved in protein folding in the ER, and ER-associated degradation might alleviate ER stress during the early stage of both stresses. Furthermore, calcium appears to modify energy metabolism, and pyruvate decarboxylase may be a key enzyme in this process under flooding and drought.
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Affiliation(s)
- Xin Wang
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan
- National Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba 305-8518, Japan
| | - Setsuko Komatsu
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan
- National Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba 305-8518, Japan
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Wang X, Khodadadi E, Fakheri B, Komatsu S. Organ-specific proteomics of soybean seedlings under flooding and drought stresses. J Proteomics 2017; 162:62-72. [PMID: 28435105 DOI: 10.1016/j.jprot.2017.04.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 03/30/2017] [Accepted: 04/05/2017] [Indexed: 01/15/2023]
Abstract
Organ-specific analyses enrich the understanding of plant growth and development under abiotic stresses. To elucidate the cellular responses in soybean seedlings exposed to flooding and drought stresses, organ-specific analysis was performed using a gel-free/label-free proteomic technique. Physiological analysis indicated that enzyme activities of alcohol dehydrogenase and delta-1-pyrroline-5-carboxylate synthase were markedly increased in leaf and root of plants treated with 6days of flooding and drought stresses, respectively. Proteins related to photosynthesis, RNA, DNA, signaling, and the tricarboxylic acid cycle were predominately affected in leaf, hypocotyl, and root in response to flooding and drought. Notably, the tricarboxylic acid cycle was suppressed in leaf and root under both stresses. Moreover, 17 proteins, including beta-glucosidase 31 and beta-amylase 5, were identified in soybean seedlings under both stresses. The protein abundances of beta-glucosidase 31 and beta-amylase 5 were increased in leaf and root under both stresses. Additionally, the gene expression of beta-amylase 5 was upregulated in leaf exposed to the flooding and drought, and the expression level was highly correlated with the protein abundance. These results suggest that beta-amylase 5 may be involved in carbohydrate mobilization to provide energy to the leaf of soybean seedlings exposed to flooding and drought. BIOLOGICAL SIGNIFICANCE This study examined the effects of flooding and drought on soybean seedlings in different organs using a gel-free/label-free proteomic approach. Physiological responses indicated that enzyme activities of alcohol dehydrogenase and delta-1-pyrroline-5-carboxylate synthase were increased in leaf and root of soybean seedlings exposed to flooding and drought for 6days. Functional analysis of acquired protein profiles exhibited that proteins related to photosynthesis, RNA, DNA, signaling, and the tricarboxylic acid cycle were predominated affected in leaf, hypocotyl, and root under both stresses. Moreover, the tricarboxylic acid cycle was suppressed in leaf and root of stressed soybean seedlings. Additionally, increased protein abundance of beta-amylase 5 was consistent with upregulated gene expression in the leaf under both stresses, suggesting that carbohydrate metabolism might be governed in response to flooding and drought of soybean seedlings.
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Affiliation(s)
- Xin Wang
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan; National Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba 305-8518, Japan
| | - Ehsaneh Khodadadi
- National Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba 305-8518, Japan; Department of Plant Breeding and Biotechnology, University of Zabol, Zabol 98613-35856, Iran
| | - Baratali Fakheri
- Department of Plant Breeding and Biotechnology, University of Zabol, Zabol 98613-35856, Iran
| | - Setsuko Komatsu
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan; National Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba 305-8518, Japan.
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Das A, Rushton PJ, Rohila JS. Metabolomic Profiling of Soybeans (Glycine max L.) Reveals the Importance of Sugar and Nitrogen Metabolism under Drought and Heat Stress. PLANTS (BASEL, SWITZERLAND) 2017; 6:E21. [PMID: 28587097 PMCID: PMC5489793 DOI: 10.3390/plants6020021] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 05/15/2017] [Accepted: 05/22/2017] [Indexed: 02/01/2023]
Abstract
Soybean is an important crop that is continually threatened by abiotic stresses, especially drought and heat stress. At molecular levels, reduced yields due to drought and heat stress can be seen as a result of alterations in metabolic homeostasis of vegetative tissues. At present an incomplete understanding of abiotic stress-associated metabolism and identification of associated metabolites remains a major gap in soybean stress research. A study with a goal to profile leaf metabolites under control conditions (28/24 °C), drought [28/24 °C, 10% volumetric water content (VWC)], and heat stress (43/35 °C) was conducted in a controlled environment. Analyses of non-targeted metabolomic data showed that in response to drought and heat stress, key metabolites (carbohydrates, amino acids, lipids, cofactors, nucleotides, peptides and secondary metabolites) were differentially accumulated in soybean leaves. The metabolites for various cellular processes, such as glycolysis, the tricarboxylic acid (TCA) cycle, the pentose phosphate pathway, and starch biosynthesis, that regulate carbohydrate metabolism, amino acid metabolism, peptide metabolism, and purine and pyrimidine biosynthesis, were found to be affected by drought as well as heat stress. Computationally based regulatory networks predicted additional compounds that address the possibility of other metabolites and metabolic pathways that could also be important for soybean under drought and heat stress conditions. Metabolomic profiling demonstrated that in soybeans, keeping up with sugar and nitrogen metabolism is of prime significance, along with phytochemical metabolism under drought and heat stress conditions.
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Affiliation(s)
- Aayudh Das
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA.
- Department of Plant Biology, University of Vermont, Burlington, VT 05405, USA.
| | - Paul J Rushton
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA.
- 22nd Century Group Inc., Clarence, NY 14031, USA.
| | - Jai S Rohila
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA.
- Dale Bumpers National Rice Research Center, USDA-ARS, Stuttgart, AR 72160, USA.
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Zadražnik T, Egge-Jacobsen W, Meglič V, Šuštar-Vozlič J. Proteomic analysis of common bean stem under drought stress using in-gel stable isotope labeling. JOURNAL OF PLANT PHYSIOLOGY 2017; 209:42-50. [PMID: 28013170 DOI: 10.1016/j.jplph.2016.10.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 10/26/2016] [Accepted: 10/30/2016] [Indexed: 05/10/2023]
Abstract
Drought is an abiotic stress that strongly influences plant growth, development and productivity. Proteome changes in the stem of the drought-tolerant common bean (Phaseolus vulgaris L.) cultivar Tiber have were when the plants were exposed to drought. Five-week-old plants were subjected to water deficit by withholding irrigation for 7, 12 and 17days, whereas control plants were regularly irrigated. Relative water content (RWC) of leaves, as an indicator of the degree of cell and tissue hydration, showed the highest statistically significant differences between control and drought-stressed plants after 17days of treatment, where RWC remained at 90% for control and declined to 45% for stressed plants. Plants exposed to drought for 17days and control plants at the same developmental stage were included in quantitative proteomic analysis using in-gel stable isotope labeling of proteins in combination with mass spectrometry. The quantified proteins were grouped into several functional groups, mainly into energy metabolism, photosynthesis, proteolysis, protein synthesis and proteins related to defense and stress. 70kDa heat shock protein showed the greatest increase in abundance under drought of all the proteins, suggesting its role in protecting plants against stress by re-establishing normal protein conformations and thus cellular homeostasis. The abundance of proteins involved in protein synthesis also increased under drought stress, important for recovery of damaged proteins involved in the plant cell's metabolic activities. Other important proteins in this study were related to proteolysis and folding, which are necessary for maintaining proper cellular protein homeostasis. Taken together, these results reveal the complexity of pathways involved in the drought stress response in common bean stems and enable comparison with the results of proteomic analysis of leaves, thus providing important information to further understand the biochemical and molecular mechanisms of drought response in this important legume.
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Affiliation(s)
- Tanja Zadražnik
- Agricultural Institute of Slovenia, 1000, Ljubljana, Slovenia.
| | | | - Vladimir Meglič
- Agricultural Institute of Slovenia, 1000, Ljubljana, Slovenia
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Mustafa G, Komatsu S. Insights into the Response of Soybean Mitochondrial Proteins to Various Sizes of Aluminum Oxide Nanoparticles under Flooding Stress. J Proteome Res 2016; 15:4464-4475. [PMID: 27780359 DOI: 10.1021/acs.jproteome.6b00572] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Rapid developments in nanotechnology have led to the increasing use of nanoparticles (NPs) in the agricultural sector. For possible interactions between NPs and crops under flooding stress to be investigated, the molecular mechanisms in soybeans affected by exposure to various sizes of Al2O3 NPs were analyzed using a proteomic technique. In plants exposed to 30-60 nm Al2O3 NPs, the length of the root including hypocotyl was increased, and proteins related to glycolysis were suppressed. Exposure to 30-60 nm Al2O3 NPs mediated the scavenging activity of cells by regulating the ascorbate/glutathione pathway. Hierarchical clustering analysis indicated that ribosomal proteins were also increased upon exposure to flooding-stressed plants with 30-60 nm Al2O3 NPs. Mitochondrion was the target organelle of Al2O3 NPs under flooding-stress conditions. Mitochondrial proteomic analysis revealed that the abundance of voltage-dependent anion channel protein was increased upon exposure to flooding-stressed soybeans with 135 nm Al2O3 NPs, indicating the permeability of the mitochondrial membrane was increased. Furthermore, isocitrate dehydrogenase was increased upon exposure of plants to 5 nm Al2O3 NPs under flooding conditions. These results suggest that Al2O3 NPs of various sizes affect mitochondrial proteins under flooding stress by regulating membrane permeability and tricarboxylic acid cycle activity.
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Affiliation(s)
- Ghazala Mustafa
- Graduate School of Life and Environmental Science, University of Tsukuba , Tsukuba 305-8572, Japan
- National Institute of Crop Science, National Agriculture and Food Research Organization , Tsukuba 305-8518, Japan
| | - Setsuko Komatsu
- Graduate School of Life and Environmental Science, University of Tsukuba , Tsukuba 305-8572, Japan
- National Institute of Crop Science, National Agriculture and Food Research Organization , Tsukuba 305-8518, Japan
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Yin X, Komatsu S. Nuclear Proteomics Reveals the Role of Protein Synthesis and Chromatin Structure in Root Tip of Soybean during the Initial Stage of Flooding Stress. J Proteome Res 2016; 15:2283-98. [PMID: 27291164 DOI: 10.1021/acs.jproteome.6b00330] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
To identify the upstream events controlling the regulation of flooding-responsive proteins in soybean, proteomic analysis of nuclear proteins in root tip was performed. By using nuclear fractions, which were highly enriched, a total of 365 nuclear proteins were changed in soybean root tip at initial stage of flooding stress. Four exon-junction complex-related proteins and NOP1/NOP56, which function in upstream of 60S preribosome biogenesis, were decreased in flooded soybean. Furthermore, proteomic analysis of crude protein extract revealed that the protein translation was suppressed by continuous flooding stress. Seventeen chromatin structure-related nuclear proteins were decreased in response to flooding stress. Out of them, histone H3 was clearly decreased with protein abundance and mRNA expression levels at the initial flooding stress. Additionally, a number of protein synthesis-, RNA-, and DNA-related nuclear proteins were decreased in a time-dependent manner. mRNA expressions of genes encoding the significantly changed flooding-responsive nuclear proteins were inhibited by the transcriptional inhibitor, actinomycin D. These results suggest that protein translation is suppressed through inhibition of preribosome biogenesis- and mRNA processing-related proteins in nuclei of soybean root tip at initial flooding stress. In addition, flooding stress may regulate histone variants with gene expression in root tip.
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Affiliation(s)
- Xiaojian Yin
- Graduate School of Life and Environmental Sciences, University of Tsukuba , Tsukuba 305-8572, Japan
- National Institute of Crop Science, National Agriculture and Food Research Organization , Tsukuba 305-8518, Japan
| | - Setsuko Komatsu
- Graduate School of Life and Environmental Sciences, University of Tsukuba , Tsukuba 305-8572, Japan
- National Institute of Crop Science, National Agriculture and Food Research Organization , Tsukuba 305-8518, Japan
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Wang X, Komatsu S. Gel-Free/Label-Free Proteomic Analysis of Endoplasmic Reticulum Proteins in Soybean Root Tips under Flooding and Drought Stresses. J Proteome Res 2016; 15:2211-27. [PMID: 27224218 DOI: 10.1021/acs.jproteome.6b00190] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Soybean is a widely cultivated crop; however, it is sensitive to flooding and drought stresses. The adverse environmental cues cause the endoplasmic reticulum (ER) stress due to accumulation of unfolded or misfolded proteins. To investigate the mechanisms in response to flooding and drought stresses, ER proteomics was performed in soybean root tips. The enzyme activity of NADH cytochrome c reductase was two-fold higher in the ER than other fractions, indicating that the ER was isolated with high purity. Protein abundance of ribosomal proteins was decreased under both stresses compared to control condition; however, the percentage of increased ribosomes was two-fold higher in flooding compared to drought. The ER proteins related to protein glycosylation and signaling were in response to both stresses. Compared to control condition, calnexin was decreased under both stresses; however, protein disulfide isomerase-like proteins and heat shock proteins were markedly decreased under flooding and drought conditions, respectively. Furthermore, fewer glycoproteins and higher levels of cytosolic calcium were identified under both stresses compared to control condition. These results suggest that reduced accumulation of glycoproteins in response to both stresses might be due to dysfunction of protein folding through calnexin/calreticulin cycle. Additionally, the increased cytosolic calcium levels induced by flooding and drought stresses might disturb the ER environment for proper protein folding in soybean root tips.
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Affiliation(s)
- Xin Wang
- Graduate School of Life and Environmental Sciences, University of Tsukuba , Tsukuba 305-8572, Japan
- National Institute of Crop Science, National Agriculture and Food Research Organization , Tsukuba 305-8518, Japan
| | - Setsuko Komatsu
- Graduate School of Life and Environmental Sciences, University of Tsukuba , Tsukuba 305-8572, Japan
- National Institute of Crop Science, National Agriculture and Food Research Organization , Tsukuba 305-8518, Japan
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Wang X, Komatsu S. Plant subcellular proteomics: Application for exploring optimal cell function in soybean. J Proteomics 2016; 143:45-56. [PMID: 26808589 DOI: 10.1016/j.jprot.2016.01.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Revised: 01/06/2016] [Accepted: 01/13/2016] [Indexed: 01/11/2023]
Abstract
UNLABELLED Plants have evolved complicated responses to developmental changes and stressful environmental conditions. Subcellular proteomics has the potential to elucidate localized cellular responses and investigate communications among subcellular compartments during plant development and in response to biotic and abiotic stresses. Soybean, which is a valuable legume crop rich in protein and vegetable oil, can grow in several climatic zones; however, the growth and yield of soybean are markedly decreased under stresses. To date, numerous proteomic studies have been performed in soybean to examine the specific protein profiles of cell wall, plasma membrane, nucleus, mitochondrion, chloroplast, and endoplasmic reticulum. In this review, methods for the purification and purity assessment of subcellular organelles from soybean are summarized. In addition, the findings from subcellular proteomic analyses of soybean during development and under stresses, particularly flooding stress, are presented and the proteins regulated among subcellular compartments are discussed. Continued advances in subcellular proteomics are expected to greatly contribute to the understanding of the responses and interactions that occur within and among subcellular compartments during development and under stressful environmental conditions. BIOLOGICAL SIGNIFICANCE Subcellular proteomics has the potential to investigate the cellular events and interactions among subcellular compartments in response to development and stresses in plants. Soybean could grow in several climatic zones; however, the growth and yield of soybean are markedly decreased under stresses. Numerous proteomics of cell wall, plasma membrane, nucleus, mitochondrion, chloroplast, and endoplasmic reticulum was carried out to investigate the respecting proteins and their functions in soybean during development or under stresses. In this review, methods of subcellular-organelle enrichment and purity assessment are summarized. In addition, previous findings of subcellular proteomics are presented, and functional proteins regulated among different subcellular are discussed. Subcellular proteomics contributes greatly to uncovering responses and interactions among subcellular compartments during development and under stressful environmental conditions in soybean.
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Affiliation(s)
- Xin Wang
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan; National Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba 305-8518, Japan
| | - Setsuko Komatsu
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan; National Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba 305-8518, Japan.
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Alqurashi M, Gehring C, Marondedze C. Changes in the Arabidopsis thaliana Proteome Implicate cAMP in Biotic and Abiotic Stress Responses and Changes in Energy Metabolism. Int J Mol Sci 2016; 17:E852. [PMID: 27258261 PMCID: PMC4926386 DOI: 10.3390/ijms17060852] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 05/18/2016] [Accepted: 05/24/2016] [Indexed: 11/23/2022] Open
Abstract
The second messenger 3',5'-cyclic adenosine monophosphate (cAMP) is increasingly recognized as having many different roles in plant responses to environmental stimuli. To gain further insights into these roles, Arabidopsis thaliana cell suspension culture was treated with 100 nM of cell permeant 8-bromo-cAMP for 5 or 10 min. Here, applying mass spectrometry and comparative proteomics, 20 proteins were identified as differentially expressed and we noted a specific bias in proteins with a role in abiotic stress, particularly cold and salinity, biotic stress as well as proteins with a role in glycolysis. These findings suggest that cAMP is sufficient to elicit specific stress responses that may in turn induce complex changes to cellular energy homeostasis.
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Affiliation(s)
- May Alqurashi
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia.
- Cambridge Centre for Proteomics, Cambridge System Biology, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK.
| | - Chris Gehring
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia.
| | - Claudius Marondedze
- Cambridge Centre for Proteomics, Cambridge System Biology, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK.
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Latef AAHA, Jan S, Abd‐Allah EF, Rashid B, John R, Ahmad P. Soybean under abiotic stress. PLANT‐ENVIRONMENT INTERACTION 2016:28-42. [DOI: 10.1002/9781119081005.ch2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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