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Kang BH, Chowdhury S, Kang SH, Shin SY, Lee WH, Lee HS, Ha BK. Transcriptome Profiling of a Soybean Mutant with Salt Tolerance Induced by Gamma-ray Irradiation. PLANTS (BASEL, SWITZERLAND) 2024; 13:254. [PMID: 38256807 PMCID: PMC10818854 DOI: 10.3390/plants13020254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 12/21/2023] [Accepted: 01/11/2024] [Indexed: 01/24/2024]
Abstract
Salt stress is a significant abiotic stress that reduces crop yield and quality globally. In this study, we utilized RNA sequencing (RNA-Seq) to identify differentially expressed genes (DEGs) in response to salt stress induced by gamma-ray irradiation in a salt-tolerant soybean mutant. The total RNA library samples were obtained from the salt-sensitive soybean cultivar Kwangan and the salt-tolerant mutant KA-1285. Samples were taken at three time points (0, 24, and 72 h) from two tissues (leaves and roots) under 200 mM NaCl. A total of 967,719,358 clean reads were generated using the Illumina NovaSeq 6000 platform, and 94.48% of these reads were mapped to 56,044 gene models of the soybean reference genome (Glycine_max_Wm82.a2.v1). The DEGs with expression values were compared at each time point within each tissue between the two soybeans. As a result, 296 DEGs were identified in the leaves, while 170 DEGs were identified in the roots. In the case of the leaves, eight DEGs were related to the phenylpropanoid biosynthesis pathway; however, in the roots, Glyma.03G171700 within GmSalt3, a major QTL associated with salt tolerance in soybean plants, was differentially expressed. Overall, these differences may explain the mechanisms through which mutants exhibit enhanced tolerance to salt stress, and they may provide a basic understanding of salt tolerance in soybean plants.
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Affiliation(s)
- Byeong Hee Kang
- Department of Applied Plant Science, Chonnam National University, Gwangju 61186, Republic of Korea; (B.H.K.); (S.C.); (S.-H.K.); (S.-Y.S.); (W.-H.L.)
- BK21 Interdisciplinary Program in IT-Bio Convergence System, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Sreeparna Chowdhury
- Department of Applied Plant Science, Chonnam National University, Gwangju 61186, Republic of Korea; (B.H.K.); (S.C.); (S.-H.K.); (S.-Y.S.); (W.-H.L.)
| | - Se-Hee Kang
- Department of Applied Plant Science, Chonnam National University, Gwangju 61186, Republic of Korea; (B.H.K.); (S.C.); (S.-H.K.); (S.-Y.S.); (W.-H.L.)
- BK21 Interdisciplinary Program in IT-Bio Convergence System, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Seo-Young Shin
- Department of Applied Plant Science, Chonnam National University, Gwangju 61186, Republic of Korea; (B.H.K.); (S.C.); (S.-H.K.); (S.-Y.S.); (W.-H.L.)
- BK21 Interdisciplinary Program in IT-Bio Convergence System, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Won-Ho Lee
- Department of Applied Plant Science, Chonnam National University, Gwangju 61186, Republic of Korea; (B.H.K.); (S.C.); (S.-H.K.); (S.-Y.S.); (W.-H.L.)
- BK21 Interdisciplinary Program in IT-Bio Convergence System, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Hyeon-Seok Lee
- National Institute of Crop Science, RDA, Wanju 55365, Republic of Korea
| | - Bo-Keun Ha
- Department of Applied Plant Science, Chonnam National University, Gwangju 61186, Republic of Korea; (B.H.K.); (S.C.); (S.-H.K.); (S.-Y.S.); (W.-H.L.)
- BK21 Interdisciplinary Program in IT-Bio Convergence System, Chonnam National University, Gwangju 61186, Republic of Korea
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2
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Dong X, Gao Y, Bao X, Wang R, Ma X, Zhang H, Liu Y, Jin L, Lin G. Multi-Omics Revealed Peanut Root Metabolism Regulated by Exogenous Calcium under Salt Stress. PLANTS (BASEL, SWITZERLAND) 2023; 12:3130. [PMID: 37687376 PMCID: PMC10490012 DOI: 10.3390/plants12173130] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 08/28/2023] [Accepted: 08/30/2023] [Indexed: 09/10/2023]
Abstract
High salinity severely inhibits plant seedling root development and metabolism. Although plant salt tolerance can be improved by exogenous calcium supplementation, the metabolism molecular mechanisms involved remain unclear. In this study, we integrated three types of omics data (transcriptome, metabolome, and phytohormone absolute quantification) to analyze the metabolic profiles of peanut seedling roots as regulated by exogenous calcium under salt stress. (1) exogenous calcium supplementation enhanced the allocation of carbohydrates to the TCA cycle and plant cell wall biosynthesis rather than the shikimate pathway influenced by up-regulating the gene expression of antioxidant enzymes under salt stress; (2) exogenous calcium induced further ABA accumulation under salt stress by up-regulating the gene expression of ABA biosynthesis key enzymes AAO2 and AAO3 while down-regulating ABA glycosylation enzyme UGT71C5 expression; (3) exogenous calcium supplementation under salt stress restored the trans-zeatin absolute content to unstressed levels while inhibiting the root cis-zeatin biosynthesis.
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Affiliation(s)
- Xuan Dong
- College of Land and Environment, Shenyang Agricultural University, No. 120 Dongling Road, Shenhe District, Shenyang 110866, China; (X.D.); (Y.G.); (X.B.); (R.W.); (H.Z.); (Y.L.); (L.J.)
| | - Yan Gao
- College of Land and Environment, Shenyang Agricultural University, No. 120 Dongling Road, Shenhe District, Shenyang 110866, China; (X.D.); (Y.G.); (X.B.); (R.W.); (H.Z.); (Y.L.); (L.J.)
| | - Xuefeng Bao
- College of Land and Environment, Shenyang Agricultural University, No. 120 Dongling Road, Shenhe District, Shenyang 110866, China; (X.D.); (Y.G.); (X.B.); (R.W.); (H.Z.); (Y.L.); (L.J.)
| | - Rongjin Wang
- College of Land and Environment, Shenyang Agricultural University, No. 120 Dongling Road, Shenhe District, Shenyang 110866, China; (X.D.); (Y.G.); (X.B.); (R.W.); (H.Z.); (Y.L.); (L.J.)
| | - Xinyu Ma
- Testing Center for Agricultural Product Safety and Environmental Quality, Shenyang Institute of Applied Ecology, Chinese Academy of Sciences, No. 72, Culture Road, Shenhe District, Shenyang 110017, China
| | - Hui Zhang
- College of Land and Environment, Shenyang Agricultural University, No. 120 Dongling Road, Shenhe District, Shenyang 110866, China; (X.D.); (Y.G.); (X.B.); (R.W.); (H.Z.); (Y.L.); (L.J.)
| | - Yifei Liu
- College of Land and Environment, Shenyang Agricultural University, No. 120 Dongling Road, Shenhe District, Shenyang 110866, China; (X.D.); (Y.G.); (X.B.); (R.W.); (H.Z.); (Y.L.); (L.J.)
| | - Lanshu Jin
- College of Land and Environment, Shenyang Agricultural University, No. 120 Dongling Road, Shenhe District, Shenyang 110866, China; (X.D.); (Y.G.); (X.B.); (R.W.); (H.Z.); (Y.L.); (L.J.)
| | - Guolin Lin
- College of Land and Environment, Shenyang Agricultural University, No. 120 Dongling Road, Shenhe District, Shenyang 110866, China; (X.D.); (Y.G.); (X.B.); (R.W.); (H.Z.); (Y.L.); (L.J.)
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3
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Leung HS, Chan LY, Law CH, Li MW, Lam HM. Twenty years of mining salt tolerance genes in soybean. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:45. [PMID: 37313223 PMCID: PMC10248715 DOI: 10.1007/s11032-023-01383-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 04/12/2023] [Indexed: 06/15/2023]
Abstract
Current combined challenges of rising food demand, climate change and farmland degradation exert enormous pressure on agricultural production. Worldwide soil salinization, in particular, necessitates the development of salt-tolerant crops. Soybean, being a globally important produce, has its genetic resources increasingly examined to facilitate crop improvement based on functional genomics. In response to the multifaceted physiological challenge that salt stress imposes, soybean has evolved an array of defences against salinity. These include maintaining cell homeostasis by ion transportation, osmoregulation, and restoring oxidative balance. Other adaptations include cell wall alterations, transcriptomic reprogramming, and efficient signal transduction for detecting and responding to salt stress. Here, we reviewed functionally verified genes that underly different salt tolerance mechanisms employed by soybean in the past two decades, and discussed the strategy in selecting salt tolerance genes for crop improvement. Future studies could adopt an integrated multi-omic approach in characterizing soybean salt tolerance adaptations and put our existing knowledge into practice via omic-assisted breeding and gene editing. This review serves as a guide and inspiration for crop developers in enhancing soybean tolerance against abiotic stresses, thereby fulfilling the role of science in solving real-life problems. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-023-01383-3.
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Affiliation(s)
- Hoi-Sze Leung
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR People’s Republic of China
| | - Long-Yiu Chan
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR People’s Republic of China
| | - Cheuk-Hin Law
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR People’s Republic of China
| | - Man-Wah Li
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR People’s Republic of China
| | - Hon-Ming Lam
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR People’s Republic of China
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, 518000 People’s Republic of China
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4
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You Y, Luo B, Wang C, Dong H, Wang X, Hou P, Sun L, Li A. An ultrasensitive probe-free electrochemical immunosensor for gibberellins employing polydopamine-antibody nanoparticles modified electrode. Bioelectrochemistry 2023; 150:108331. [PMID: 36446196 DOI: 10.1016/j.bioelechem.2022.108331] [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: 08/30/2022] [Revised: 11/14/2022] [Accepted: 11/21/2022] [Indexed: 11/27/2022]
Abstract
Gibberellins (GA3) is an ubiquitous plant hormone, which plays a regulatory role in different growth stages of plants, so it is of great significance to develop a sensitive quantitative analysis method for GA3. In this study, carboxylated graphene oxide- carboxylated multi-walled carbon nanotubes-Fc (GO-MWNT-Fc) composite material and PDANPs-antibody (PDANPs-Ab) were sequentially modified to screen-printed electrodes (SPEs), and an ultrasensitive probe-free immunosensor for GA3 was developed. Fc was applied to generate electrochemical signals. GO-COOH and MWNT-COOH can increase the catalytic ability of the sensor and bind the PDANPs-Ab nanoparticles. PDANPs nanomaterial were synthetized by a facile self-polymerization and used to bind with antibody, so as to increase the antibody loading of the sensor. The as-prepared immunosensor has the widest detection range (100 aM-1 mM) and lowest detection limit (17.4 aM) for GA3 up to date. To our knowledge, it is the first electrochemical immunosensor for GA3. By changing the GA3 antibody to ABA antibody, a sensitive and selective immunosensor for ABA was also fabricated. This immunosensor platform is simple, sensitive, and low cost. It opens broad prospect in on-site applications for biosensors in detecting of various biomolecules in precision agriculture.
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Affiliation(s)
- Yang You
- Research Center of Intelligent Equipment, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; College of Landscape and Ecological Engineering, Hebei University of Engineering, Handan 056038, China
| | - Bin Luo
- Research Center of Intelligent Equipment, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Cheng Wang
- Research Center of Intelligent Equipment, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Hongtu Dong
- Research Center of Intelligent Equipment, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Xiaodong Wang
- Research Center of Intelligent Equipment, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Peichen Hou
- Research Center of Intelligent Equipment, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Lijun Sun
- School of Life Sciences, Nantong University, 9 Seyuan Rd, Nantong, Jiangsu 226019, China.
| | - Aixue Li
- Research Center of Intelligent Equipment, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.
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5
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Lu Y, Liu H, Chen Y, Zhang L, Kudusi K, Song J. Effects of drought and salt stress on seed germination of ephemeral plants in desert of northwest China. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.1026095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Seed germination is the most sensitive stage of plant life history. Studying its response to drought and salinity can analysis the response and adaptation characteristics of desert plants to the environment. In this experiment, the seeds of four common desert ephemeral plants in Xinjiang (Ixiolirion tataricum, Nepeta micrantha, Lepidium apetalum, and Plantago minuta) were used as materials. To study the germination characteristics of seeds under drought, we used salt stress, and coupled salt-drought stress under treatments and explored the germination recovery ability of rehydrated seeds after salt and drought stress treatments. The results showed that: (1) Under salt stress, the germination ability of four plant seeds was inhibited in different degrees. Overall, the degree of inhibition was proportional to the concentration of NaCl solution. (2) Drought stress slowed the seed germination process, and the greater the degree of stress, the more pronounced the slowdown; PEG treatment showed no significant effect on the germination of the four seeds at low concentrations and significant inhibition at medium and high concentrations. (3) The coupled salt-drought treatment significantly alleviated the stress effect of one factor and improved the germination characteristics of seeds. (4) Seeds that did not germinate under different concentrations of salt stress, drought stress, and coupled stresses rapidly recover germination when the stress was relieved or lifted. Ephemeral plants are sensitive to environmental changes, and this study aims to provide a reference basis for vegetation restoration and ecological rehabilitation in arid and semi-arid areas.
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Ben Youssef R, Jelali N, Boukari N, Albacete A, Martinez C, Alfocea FP, Abdelly C. The Efficiency of Different Priming Agents for Improving Germination and Early Seedling Growth of Local Tunisian Barley under Salinity Stress. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10112264. [PMID: 34834627 PMCID: PMC8623335 DOI: 10.3390/plants10112264] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 09/23/2021] [Accepted: 10/06/2021] [Indexed: 06/13/2023]
Abstract
The current work aimed to investigate the effect of seed priming with different agents (CaCl2, KCl, and KNO3) on germination and seedling establishment in seeds of the barley species of both Hordeum vulgare (L. Manel) and Hordeum maritimum germinated with three salt concentrations (0, 100, and 200 mM NaCl). The results showed that under unprimed conditions, salt stress significantly reduced the final germination rate, the mean daily germination, and the seedling length and dry weight. It led to a decrease in the essential nutrient content (iron, calcium, magnesium, and potassium) against an increase in sodium level in both of the barley species. Moreover, this environmental constraint provoked a membrane injury caused by a considerable increase in electrolyte leakage and the malondialdehyde content (MDA). Data analysis proved that seed priming with CaCl2, KCl, and KNO3 was an effective method for alleviating barley seed germination caused by salt stress to varying degrees. Different priming treatments clearly stimulated germination parameters and the essential nutrient concentration, in addition to increasing the seedling growth rate. The application of seed priming reduced the accumulation of sodium ions and mitigated the oxidative stress of seeds caused by salt. This mitigation was traduced by the maintenance of low levels of MDA and electrolyte leakage. We conclude that the priming agents can be classed into three ranges based on their efficacy on the different parameters analyzed; CaCl2 was placed in the first range, followed closely by KNO3, while the least effective was KCl, which placed in the third range.
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Affiliation(s)
- Rim Ben Youssef
- Laboratory of Extremophile Plants, Biotechnology Center of Borj-Cedria, P.O. Box 901, Hammam-Lif 2050, Tunisia; (N.J.); (N.B.); (C.A.)
- Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis 1060, Tunisia
- Centro de Edafología y Biología Aplicada del Segura, Spanish National Research Council (CEBAS-CSIC), Departameno Nutricion Vegetal, 30100 Murcia, Spain; (A.A.); (C.M.); (F.P.A.)
| | - Nahida Jelali
- Laboratory of Extremophile Plants, Biotechnology Center of Borj-Cedria, P.O. Box 901, Hammam-Lif 2050, Tunisia; (N.J.); (N.B.); (C.A.)
| | - Nadia Boukari
- Laboratory of Extremophile Plants, Biotechnology Center of Borj-Cedria, P.O. Box 901, Hammam-Lif 2050, Tunisia; (N.J.); (N.B.); (C.A.)
- Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis 1060, Tunisia
| | - Alfonso Albacete
- Centro de Edafología y Biología Aplicada del Segura, Spanish National Research Council (CEBAS-CSIC), Departameno Nutricion Vegetal, 30100 Murcia, Spain; (A.A.); (C.M.); (F.P.A.)
| | - Cristina Martinez
- Centro de Edafología y Biología Aplicada del Segura, Spanish National Research Council (CEBAS-CSIC), Departameno Nutricion Vegetal, 30100 Murcia, Spain; (A.A.); (C.M.); (F.P.A.)
| | - Francisco Perez Alfocea
- Centro de Edafología y Biología Aplicada del Segura, Spanish National Research Council (CEBAS-CSIC), Departameno Nutricion Vegetal, 30100 Murcia, Spain; (A.A.); (C.M.); (F.P.A.)
| | - Chedly Abdelly
- Laboratory of Extremophile Plants, Biotechnology Center of Borj-Cedria, P.O. Box 901, Hammam-Lif 2050, Tunisia; (N.J.); (N.B.); (C.A.)
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Jin T, Sun Y, Shan Z, He J, Wang N, Gai J, Li Y. Natural variation in the promoter of GsERD15B affects salt tolerance in soybean. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:1155-1169. [PMID: 33368860 PMCID: PMC8196659 DOI: 10.1111/pbi.13536] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 12/11/2020] [Accepted: 12/16/2020] [Indexed: 05/24/2023]
Abstract
Salt stress has detrimental effects on crop growth and yield, and the area of salt-affected land is increasing. Soybean is a major source of vegetable protein, oil and feed, but considered as a salt-sensitive crop. Cultivated soybean (Glycine max) is domesticated from wild soybean (G. soja) but lost considerable amount of genetic diversity during the artificial selection. Therefore, it is important to exploit the gene pool of wild soybean. In this study, we identified 34 salt-tolerant accessions from wild soybean germplasm and found that a 7-bp insertion/deletion (InDel) in the promoter of GsERD15B (early responsive to dehydration 15B) significantly affects the salt tolerance of soybean. GsERD15B encodes a protein with transcriptional activation function and contains a PAM2 domain to mediate its interaction with poly(A)-binding (PAB) proteins. The 7-bp deletion in GsERD15B promoter enhanced the salt tolerance of soybean, with increased up-regulation of GsERD15B, two GmPAB genes, the known stress-related genes including GmABI1, GmABI2, GmbZIP1, GmP5CS, GmCAT4, GmPIP1:6, GmMYB84 and GmSOS1 in response to salt stress. We propose that natural variation in GsERD15B promoter affects soybean salt tolerance, and overexpression of GsERD15B enhanced salt tolerance probably by increasing the expression levels of genes related to ABA-signalling, proline content, catalase peroxidase, dehydration response and cation transport.
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Affiliation(s)
- Ting Jin
- National Key Laboratory of Crop Genetics and Germplasm EnhancementNational Center for Soybean ImprovementKey Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture)Jiangsu Collaborative Innovation Center for Modern Crop ProductionNanjing Agricultural UniversityNanjingChina
| | - Yangyang Sun
- National Key Laboratory of Crop Genetics and Germplasm EnhancementNational Center for Soybean ImprovementKey Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture)Jiangsu Collaborative Innovation Center for Modern Crop ProductionNanjing Agricultural UniversityNanjingChina
| | - Zhong Shan
- National Key Laboratory of Crop Genetics and Germplasm EnhancementNational Center for Soybean ImprovementKey Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture)Jiangsu Collaborative Innovation Center for Modern Crop ProductionNanjing Agricultural UniversityNanjingChina
| | - Jianbo He
- National Key Laboratory of Crop Genetics and Germplasm EnhancementNational Center for Soybean ImprovementKey Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture)Jiangsu Collaborative Innovation Center for Modern Crop ProductionNanjing Agricultural UniversityNanjingChina
| | - Ning Wang
- National Key Laboratory of Crop Genetics and Germplasm EnhancementNational Center for Soybean ImprovementKey Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture)Jiangsu Collaborative Innovation Center for Modern Crop ProductionNanjing Agricultural UniversityNanjingChina
| | - Junyi Gai
- National Key Laboratory of Crop Genetics and Germplasm EnhancementNational Center for Soybean ImprovementKey Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture)Jiangsu Collaborative Innovation Center for Modern Crop ProductionNanjing Agricultural UniversityNanjingChina
| | - Yan Li
- National Key Laboratory of Crop Genetics and Germplasm EnhancementNational Center for Soybean ImprovementKey Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture)Jiangsu Collaborative Innovation Center for Modern Crop ProductionNanjing Agricultural UniversityNanjingChina
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8
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Smolikova G, Gorbach D, Lukasheva E, Mavropolo-Stolyarenko G, Bilova T, Soboleva A, Tsarev A, Romanovskaya E, Podolskaya E, Zhukov V, Tikhonovich I, Medvedev S, Hoehenwarter W, Frolov A. Bringing New Methods to the Seed Proteomics Platform: Challenges and Perspectives. Int J Mol Sci 2020; 21:E9162. [PMID: 33271881 PMCID: PMC7729594 DOI: 10.3390/ijms21239162] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 11/26/2020] [Accepted: 11/27/2020] [Indexed: 12/14/2022] Open
Abstract
For centuries, crop plants have represented the basis of the daily human diet. Among them, cereals and legumes, accumulating oils, proteins, and carbohydrates in their seeds, distinctly dominate modern agriculture, thus play an essential role in food industry and fuel production. Therefore, seeds of crop plants are intensively studied by food chemists, biologists, biochemists, and nutritional physiologists. Accordingly, seed development and germination as well as age- and stress-related alterations in seed vigor, longevity, nutritional value, and safety can be addressed by a broad panel of analytical, biochemical, and physiological methods. Currently, functional genomics is one of the most powerful tools, giving direct access to characteristic metabolic changes accompanying plant development, senescence, and response to biotic or abiotic stress. Among individual post-genomic methodological platforms, proteomics represents one of the most effective ones, giving access to cellular metabolism at the level of proteins. During the recent decades, multiple methodological advances were introduced in different branches of life science, although only some of them were established in seed proteomics so far. Therefore, here we discuss main methodological approaches already employed in seed proteomics, as well as those still waiting for implementation in this field of plant research, with a special emphasis on sample preparation, data acquisition, processing, and post-processing. Thereby, the overall goal of this review is to bring new methodologies emerging in different areas of proteomics research (clinical, food, ecological, microbial, and plant proteomics) to the broad society of seed biologists.
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Affiliation(s)
- Galina Smolikova
- Department of Plant Physiology and Biochemistry, St. Petersburg State University; 199034 St. Petersburg, Russia; (G.S.); (T.B.); (S.M.)
| | - Daria Gorbach
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
| | - Elena Lukasheva
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
| | - Gregory Mavropolo-Stolyarenko
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
| | - Tatiana Bilova
- Department of Plant Physiology and Biochemistry, St. Petersburg State University; 199034 St. Petersburg, Russia; (G.S.); (T.B.); (S.M.)
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry; 06120 Halle (Saale), Germany
| | - Alena Soboleva
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry; 06120 Halle (Saale), Germany
| | - Alexander Tsarev
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry; 06120 Halle (Saale), Germany
| | - Ekaterina Romanovskaya
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
| | - Ekaterina Podolskaya
- Institute of Analytical Instrumentation, Russian Academy of Science; 190103 St. Petersburg, Russia;
- Institute of Toxicology, Russian Federal Medical Agency; 192019 St. Petersburg, Russia
| | - Vladimir Zhukov
- All-Russia Research Institute for Agricultural Microbiology; 196608 St. Petersburg, Russia; (V.Z.); (I.T.)
| | - Igor Tikhonovich
- All-Russia Research Institute for Agricultural Microbiology; 196608 St. Petersburg, Russia; (V.Z.); (I.T.)
- Department of Genetics and Biotechnology, St. Petersburg State University; 199034 St. Petersburg, Russia
| | - Sergei Medvedev
- Department of Plant Physiology and Biochemistry, St. Petersburg State University; 199034 St. Petersburg, Russia; (G.S.); (T.B.); (S.M.)
| | - Wolfgang Hoehenwarter
- Proteome Analytics Research Group, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany;
| | - Andrej Frolov
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry; 06120 Halle (Saale), Germany
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9
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Proteomics analysis of Cyclobalanopsis gilva provides new insights of low seed germination. Biochimie 2020; 180:68-78. [PMID: 33250447 DOI: 10.1016/j.biochi.2020.10.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 10/18/2020] [Accepted: 10/19/2020] [Indexed: 12/27/2022]
Abstract
A valuable plant, Cyclobalanopsis gilva, (C. gilva) has a low germination rate (below 50%) under its natural habitations. In order to examine the reasons for the low germination rate, the seeds of C. gilva (germinated and non-germinated) were evaluated using comparative proteomics analysis. A total of 3078 differentially abundant proteins (DAPs) were identified through a label-free method; most DAPs up-accumulated in germinated seeds were related to carbohydrates metabolism. Furthermore the proteins related to the signals, stress, and protein metabolism showed up-accumulation in germinated and no abundance or down-accumulation in non-germinated seeds. Enzyme activity of HK, PGK, PFK, and PK from glycolysis in SG-Control samples were 1.7-, 1.1-, 1.4-, and 1.3-times higher compared with those in control ones while CS, NAD-MDH, α-KGDH, and ICDH from the TCA cycle in SG-Control samples were 3, 1.1, 1.2, and 1.2 times higher than those in NG-Control ones. The β-amylase activity was 4-fold higher in successfully germinated seeds compared to non-germinated seeds. Interestingly, α-amylase did not show significant changes in protein abundance and enzyme activity among the three samples. The present findings reveal that unsuccessful germination of C. gilva seeds is due to lack of energy.
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Vaish S, Gupta D, Mehrotra R, Mehrotra S, Basantani MK. Glutathione S-transferase: a versatile protein family. 3 Biotech 2020; 10:321. [PMID: 32656054 PMCID: PMC7320970 DOI: 10.1007/s13205-020-02312-3] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 06/19/2020] [Indexed: 12/20/2022] Open
Abstract
Glutathione-S transferase (GST) is a most ancient protein superfamily of multipurpose roles and evolved principally from gene duplication of an ancestral GSH binding protein. They have implemented in diverse plant functions such as detoxification of xenobiotic, secondary metabolism, growth and development, and majorly against biotic and abiotic stresses. The vital structural features of GSTs like highly divergent functional topographies, conserved integrated architecture with separate binding pockets for substrates and ligand, the stringent structural fidelity with high Tm values (50º-60º), and stress-responsive cis-regulatory elements in the promoter region offer this protein as most flexible plant protein for plant breeding approaches, biotechnological applications, etc. This review article summarizes the recent information of GST evolution, and their distribution and structural features with emphasis on the assorted roles of Ser and Cys GSTs with the signature motifs in their active sites, alongside their recent biotechnological application in the area of agriculture, environment, and nanotechnology have been highlighted.
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Affiliation(s)
- Swati Vaish
- Institute of Bioscience and Technology, Shri Ramswaroop Memorial University, Lucknow Deva Road, Barabanki, Uttar Pradesh 225003 India
| | - Divya Gupta
- Institute of Bioscience and Technology, Shri Ramswaroop Memorial University, Lucknow Deva Road, Barabanki, Uttar Pradesh 225003 India
| | - Rajesh Mehrotra
- Department of Biological Sciences, Birla Institute of Technology and Science, KK Birla Goa Campus, NH-17B, Zuarinagar, Goa 403726 India
| | - Sandhya Mehrotra
- Department of Biological Sciences, Birla Institute of Technology and Science, KK Birla Goa Campus, NH-17B, Zuarinagar, Goa 403726 India
| | - Mahesh Kumar Basantani
- Faculty of Bioscience, Institute of Bioscience and Technology, Shri Ramswaroop Memorial University, Lucknow-Deva Road, Barabanki, Uttar Pradesh India
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Liu D, Han C, Deng X, Liu Y, Liu N, Yan Y. Integrated physiological and proteomic analysis of embryo and endosperm reveals central salt stress response proteins during seed germination of winter wheat cultivar Zhengmai 366. BMC PLANT BIOLOGY 2019; 19:29. [PMID: 30658564 PMCID: PMC6339335 DOI: 10.1186/s12870-019-1643-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 01/09/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND Salinity is a major abiotic stressor that affects seed germination, plant growth, and crop production. Seed germination represents the beginning of plant growth and is closely linked with subsequent crop development and ultimate yield formation. This study attempted to extend findings regarding the potential proteomic dynamics during wheat seed germination under salt stress and to explore the mechanism of crop salt response. RESULTS Salt stress significantly affected seed physiological activities during the germination process, resulting in significant decreases in phytohormone and α-amylase activity and significant increases in soluble sugar, starch, and ADP glucose pyrophosphorylase activity. A comparative proteomics approach was applied to analyze the dynamic proteome changes of embryo and endosperm during seed germination in Chinese winter wheat cultivar Zhengmai 366 under salt stress. Two-dimensional electrophoresis identified 92 and 61 differentially accumulated proteins (DAPs) in response to salt stress in embryo and endosperm, respectively. Both organs contained a high proportion of DAPs involved in stress defense, energy metabolism, and protein/amino acid metabolism. The endosperm had more DAPs related to storage proteins and starch metabolism than the embryo, and 2% of DAPs participating in lipid and sterol metabolism were specifically detected in the embryo. CONCLUSIONS Seed physiological activities were significantly affected during the germination process when subjected to salt stress. The DAPs involved in stress defense and energy metabolism were upregulated whereas those related to reserve substance degradation and protein/amino acid metabolism were significantly downregulated, leading to delayed seed germination under salt stress. Our proteomic results revealed synergistic regulation of the response to salt stress during seed germination.
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Affiliation(s)
- Dongmiao Liu
- Laboratory of Molecular Genetics and Proteomics, College of Life Science, Capital Normal University, Beijing, 100048 China
| | - Caixia Han
- Laboratory of Molecular Genetics and Proteomics, College of Life Science, Capital Normal University, Beijing, 100048 China
| | - Xiong Deng
- Laboratory of Molecular Genetics and Proteomics, College of Life Science, Capital Normal University, Beijing, 100048 China
| | - Yue Liu
- Laboratory of Molecular Genetics and Proteomics, College of Life Science, Capital Normal University, Beijing, 100048 China
| | - Nannan Liu
- Laboratory of Molecular Genetics and Proteomics, College of Life Science, Capital Normal University, Beijing, 100048 China
| | - Yueming Yan
- Laboratory of Molecular Genetics and Proteomics, College of Life Science, Capital Normal University, Beijing, 100048 China
- Hubei Collaborative Innovation Center for Grain Industry (HCICGI), Yangtze University, Jingzhou, 434025 China
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Gu J, Hou D, Li Y, Chao H, Zhang K, Wang H, Xiang J, Raboanatahiry N, Wang B, Li M. Integration of proteomic and genomic approaches to dissect seed germination vigor in Brassica napus seeds differing in oil content. BMC PLANT BIOLOGY 2019; 19:21. [PMID: 30634904 PMCID: PMC6329107 DOI: 10.1186/s12870-018-1624-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 12/28/2018] [Indexed: 05/23/2023]
Abstract
BACKGROUND Rapeseed (Brassica napus, B. napus) is an important oil seed crop in the world. Previous studies showed that seed germination vigor might be correlated with seed oil content in B. napus, but the regulation mechanism for seed germination has not yet been explained clearly. Dissecting the regulation mechanism of seed germination and germination vigor is necessary. RESULTS Here, proteomic and genomic approaches were used to analyze the germination process in B. napus seeds with different oil content. The identification of 165 differentially expressed proteins (DEPs) in the germinating seeds of B. napus with high and low oil content was accomplished by two-dimensional fluorescence difference in gel electrophoresis (2D-DIGE). The comparative proteomic results revealed that seeds with high oil content had higher metabolic activity, especially for sulfur amino acid metabolism. Thirty-one unique genes were shown to be significantly changed during germination between the seeds with high and low oil content, and thirteen of these genes were located within the confidence interval of germination-related quantitative trait locus (QTLs), which might play an important role in regulating seed germination vigor. CONCLUSIONS The present results are of importance for the understanding of the regulation mechanism for seed germination vigor in B. napus.
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Affiliation(s)
- Jianwei Gu
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
- Hubei Institute of New Socialist Countryside Development, Hubei Engineering University, Xiaogan, China
| | - Dalin Hou
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
- Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, Huanggang, China
| | - Yonghong Li
- Hybrid Rapeseed Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, China
| | - Hongbo Chao
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Kai Zhang
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Hao Wang
- Hybrid Rapeseed Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, China
| | - Jun Xiang
- Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, Huanggang, China
| | - Nadia Raboanatahiry
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Baoshan Wang
- College of Life Science, Shandong Normal University, Jinan, China
| | - Maoteng Li
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
- Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, Huanggang, China
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Shu K, Qi Y, Chen F, Meng Y, Luo X, Shuai H, Zhou W, Ding J, Du J, Liu J, Yang F, Wang Q, Liu W, Yong T, Wang X, Feng Y, Yang W. Salt Stress Represses Soybean Seed Germination by Negatively Regulating GA Biosynthesis While Positively Mediating ABA Biosynthesis. FRONTIERS IN PLANT SCIENCE 2017; 8:1372. [PMID: 28848576 PMCID: PMC5554363 DOI: 10.3389/fpls.2017.01372] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 07/24/2017] [Indexed: 05/20/2023]
Abstract
Soybean is an important and staple oilseed crop worldwide. Salinity stress has adverse effects on soybean development periods, especially on seed germination and post-germinative growth. Improving seed germination and emergence will have positive effects under salt stress conditions on agricultural production. Here we report that NaCl delays soybean seed germination by negatively regulating gibberellin (GA) while positively mediating abscisic acid (ABA) biogenesis, which leads to a decrease in the GA/ABA ratio. This study suggests that fluridone (FLUN), an ABA biogenesis inhibitor, might be a potential plant growth regulator that can promote soybean seed germination under saline stress. Different soybean cultivars, which possessed distinct genetic backgrounds, showed a similar repressed phenotype during seed germination under exogenous NaCl application. Biochemical analysis revealed that NaCl treatment led to high MDA (malondialdehyde) level during germination and the post-germinative growth stages. Furthermore, catalase, superoxide dismutase, and peroxidase activities also changed after NaCl treatment. Subsequent quantitative Real-Time Polymerase Chain Reaction analysis showed that the transcription levels of ABA and GA biogenesis and signaling genes were altered after NaCl treatment. In line with this, phytohormone measurement also revealed that NaCl considerably down-regulated active GA1, GA3, and GA4 levels, whereas the ABA content was up-regulated; and therefore ratios, such as GA1/ABA, GA3/ABA, and GA4/ABA, are decreased. Consistent with the hormonal quantification, FLUN partially rescued the delayed-germination phenotype caused by NaCl-treatment. Altogether, these results demonstrate that NaCl stress inhibits soybean seed germination by decreasing the GA/ABA ratio, and that FLUN might be a potential plant growth regulator that could promote soybean seed germination under salinity stress.
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Affiliation(s)
- Kai Shu
- Key Laboratory of Crop Ecophysiology and Farming System in Southwest China, Sichuan Engineering Research Center for Crop Strip Intercropping System, Institute of Ecological Agriculture, Sichuan Agricultural UniversityChengdu, China
- *Correspondence: Kai Shu, Wenyu Yang,
| | - Ying Qi
- Key Laboratory of Crop Ecophysiology and Farming System in Southwest China, Sichuan Engineering Research Center for Crop Strip Intercropping System, Institute of Ecological Agriculture, Sichuan Agricultural UniversityChengdu, China
| | - Feng Chen
- Key Laboratory of Crop Ecophysiology and Farming System in Southwest China, Sichuan Engineering Research Center for Crop Strip Intercropping System, Institute of Ecological Agriculture, Sichuan Agricultural UniversityChengdu, China
| | - Yongjie Meng
- Key Laboratory of Crop Ecophysiology and Farming System in Southwest China, Sichuan Engineering Research Center for Crop Strip Intercropping System, Institute of Ecological Agriculture, Sichuan Agricultural UniversityChengdu, China
| | - Xiaofeng Luo
- Key Laboratory of Crop Ecophysiology and Farming System in Southwest China, Sichuan Engineering Research Center for Crop Strip Intercropping System, Institute of Ecological Agriculture, Sichuan Agricultural UniversityChengdu, China
| | - Haiwei Shuai
- Key Laboratory of Crop Ecophysiology and Farming System in Southwest China, Sichuan Engineering Research Center for Crop Strip Intercropping System, Institute of Ecological Agriculture, Sichuan Agricultural UniversityChengdu, China
| | - Wenguan Zhou
- Key Laboratory of Crop Ecophysiology and Farming System in Southwest China, Sichuan Engineering Research Center for Crop Strip Intercropping System, Institute of Ecological Agriculture, Sichuan Agricultural UniversityChengdu, China
| | - Jun Ding
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan UniversityWuhan, China
| | - Junbo Du
- Key Laboratory of Crop Ecophysiology and Farming System in Southwest China, Sichuan Engineering Research Center for Crop Strip Intercropping System, Institute of Ecological Agriculture, Sichuan Agricultural UniversityChengdu, China
| | - Jiang Liu
- Key Laboratory of Crop Ecophysiology and Farming System in Southwest China, Sichuan Engineering Research Center for Crop Strip Intercropping System, Institute of Ecological Agriculture, Sichuan Agricultural UniversityChengdu, China
| | - Feng Yang
- Key Laboratory of Crop Ecophysiology and Farming System in Southwest China, Sichuan Engineering Research Center for Crop Strip Intercropping System, Institute of Ecological Agriculture, Sichuan Agricultural UniversityChengdu, China
| | - Qiang Wang
- Key Laboratory of Crop Ecophysiology and Farming System in Southwest China, Sichuan Engineering Research Center for Crop Strip Intercropping System, Institute of Ecological Agriculture, Sichuan Agricultural UniversityChengdu, China
| | - Weiguo Liu
- Key Laboratory of Crop Ecophysiology and Farming System in Southwest China, Sichuan Engineering Research Center for Crop Strip Intercropping System, Institute of Ecological Agriculture, Sichuan Agricultural UniversityChengdu, China
| | - Taiwen Yong
- Key Laboratory of Crop Ecophysiology and Farming System in Southwest China, Sichuan Engineering Research Center for Crop Strip Intercropping System, Institute of Ecological Agriculture, Sichuan Agricultural UniversityChengdu, China
| | - Xiaochun Wang
- Key Laboratory of Crop Ecophysiology and Farming System in Southwest China, Sichuan Engineering Research Center for Crop Strip Intercropping System, Institute of Ecological Agriculture, Sichuan Agricultural UniversityChengdu, China
| | - Yuqi Feng
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan UniversityWuhan, China
| | - Wenyu Yang
- Key Laboratory of Crop Ecophysiology and Farming System in Southwest China, Sichuan Engineering Research Center for Crop Strip Intercropping System, Institute of Ecological Agriculture, Sichuan Agricultural UniversityChengdu, China
- *Correspondence: Kai Shu, Wenyu Yang,
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Subramanian S, Ricci E, Souleimanov A, Smith DL. A Proteomic Approach to Lipo-Chitooligosaccharide and Thuricin 17 Effects on Soybean GerminationUnstressed and Salt Stress. PLoS One 2016; 11:e0160660. [PMID: 27560934 PMCID: PMC4999219 DOI: 10.1371/journal.pone.0160660] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 07/23/2016] [Indexed: 12/13/2022] Open
Abstract
Salt stress is an important abiotic stressor affecting crop growth and productivity. Of the 20 percent of the terrestrial earth's surface available as agricultural land, 50 percent is estimated by the United Nations Environment Program to be salinized to the level that crops growing on it will be salt-stressed. Increased soil salinity has profound effects on seed germination and germinating seedlings as they are frequently confronted with much higher salinities than vigorously growing plants, because germination usually occurs in surface soils, the site of greatest soluble salt accumulation. The growth of soybean exposed to 40 mM NaCl is negatively affected, while an exposure to 80 mM NaCl is often lethal. When treated with the bacterial signal compounds lipo-chitooligosaccharide (LCO) and thuricin 17 (Th17), soybean seeds (variety Absolute RR) responded positively at salt stress of up to 150 mM NaCl. Shotgun proteomics of unstressed and 100 mM NaCl stressed seeds (48 h) in combination with the LCO and Th17 revealed many known, predicted, hypothetical and unknown proteins. In all, carbon, nitrogen and energy metabolic pathways were affected under both unstressed and salt stressed conditions when treated with signals. PEP carboxylase, Rubisco oxygenase large subunit, pyruvate kinase, and isocitrate lyase were some of the noteworthy proteins enhanced by the signals, along with antioxidant glutathione-S-transferase and other stress related proteins. These findings suggest that the germinating seeds alter their proteome based on bacterial signals and on stress, the specificity of this response plays a crucial role in organ maturation and transition from one stage to another in the plants' life cycle; understanding this response is of fundamental importance in agriculture and, as a result, global food security. The mass spectrometry proteomics data have been deposited to the ProteomeXchange with identifier PXD004106.
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Affiliation(s)
- Sowmyalakshmi Subramanian
- Department of Plant Sciences, Macdonald Campus, McGill University, 21111 Lakeshore Road, Sainte Anne de Bellevue, Quebec, H9X3V9, Canada
| | - Emily Ricci
- Department of Plant Sciences, Macdonald Campus, McGill University, 21111 Lakeshore Road, Sainte Anne de Bellevue, Quebec, H9X3V9, Canada
| | - Alfred Souleimanov
- Department of Plant Sciences, Macdonald Campus, McGill University, 21111 Lakeshore Road, Sainte Anne de Bellevue, Quebec, H9X3V9, Canada
| | - Donald L. Smith
- Department of Plant Sciences, Macdonald Campus, McGill University, 21111 Lakeshore Road, Sainte Anne de Bellevue, Quebec, H9X3V9, Canada
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15
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Fercha A, Capriotti AL, Caruso G, Cavaliere C, Stampachiacchiere S, Zenezini Chiozzi R, Laganà A. Shotgun proteomic analysis of soybean embryonic axes during germination under salt stress. Proteomics 2016; 16:1537-46. [PMID: 26969838 DOI: 10.1002/pmic.201500283] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 01/19/2016] [Accepted: 03/08/2016] [Indexed: 12/21/2022]
Abstract
Seed imbibition and radicle emergence are generally less affected by salinity in soybean than in other crop plants. In order to unveil the mechanisms underlying this remarkable salt tolerance of soybean at seed germination, a comparative label-free shotgun proteomic analysis of embryonic axes exposed to salinity during germination sensu stricto (GSS) was conducted. The results revealed that the application of 100 and 200 mmol/L NaCl stress was accompanied by significant changes (>2-fold, P<0.05) of 97 and 75 proteins, respectively. Most of these salt-responsive proteins (70%) were classified into three major functional categories: disease/defense response, protein destination and storage and primary metabolism. The involvement of these proteins in salt tolerance of soybean was discussed, and some of them were suggested to be potential salt-tolerant proteins. Furthermore, our results suggest that the cross-protection against aldehydes, oxidative as well as osmotic stress, is the major adaptive response to salinity in soybean.
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Affiliation(s)
- Azzedine Fercha
- Department of Biology, University of Abbès Laghrour Khenchela, Khenchela, Algeria
| | | | - Giuseppe Caruso
- Department of Chemistry, Sapienza Università di Roma, Rome, Italy
| | - Chiara Cavaliere
- Department of Chemistry, Sapienza Università di Roma, Rome, Italy
| | | | | | - Aldo Laganà
- Department of Chemistry, Sapienza Università di Roma, Rome, Italy
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16
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Gu J, Chao H, Gan L, Guo L, Zhang K, Li Y, Wang H, Raboanatahiry N, Li M. Proteomic Dissection of Seed Germination and Seedling Establishment in Brassica napus. FRONTIERS IN PLANT SCIENCE 2016; 7:1482. [PMID: 27822216 PMCID: PMC5075573 DOI: 10.3389/fpls.2016.01482] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 09/20/2016] [Indexed: 05/22/2023]
Abstract
The success of seed germination and establishment of a normal seedling are key determinants of plant species propagation. At present, only a few studies have focused on the genetic control of seed germination by using a proteomic approach in Brassica napus. In the present study, the protein expression pattern of seed germination was investigated using differential fluorescence two-dimensional gel electrophoresis in B. napus. One hundred and thirteen differentially expressed proteins (DEPs) that were mainly involved in storage (23.4%), energy metabolism (18.9%), protein metabolism (16.2%), defense/disease (12.6%), seed maturation (11.7%), carbohydrate metabolism (4.5%), lipid metabolism (4.5%), amino acids metabolism (3.6%), cell growth/division (3.6%), and some unclear functions (2.7%) were observed by proteomic analysis. Seventeen genes corresponding to 11 DEPs were identified within or near the associated linkage disequilibrium regions related to seed germination and vigor quantitative traits reported in B. napus in previous studies. The expression pattern of proteins showed that heterotrophic metabolism could be activated in the process of seed germination and that the onset of defense mechanisms might start during seed germination. These findings will help generate a more in-depth understanding of the mobilization of seed storage reserves and regulation mechanisms of the germination process in B. napus.
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Affiliation(s)
- Jianwei Gu
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
- Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal UniversityHuanggang, China
| | - Hongbo Chao
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
| | - Lu Gan
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
| | - Liangxing Guo
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
| | - Kai Zhang
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
| | - Yonghong Li
- Hybrid Rapeseed Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic ImprovementYangling, China
| | - Hao Wang
- Hybrid Rapeseed Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic ImprovementYangling, China
| | - Nadia Raboanatahiry
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
| | - Maoteng Li
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
- Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal UniversityHuanggang, China
- *Correspondence: Maoteng Li
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Rathi D, Gayen D, Gayali S, Chakraborty S, Chakraborty N. Legume proteomics: Progress, prospects, and challenges. Proteomics 2015; 16:310-27. [DOI: 10.1002/pmic.201500257] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 09/19/2015] [Accepted: 11/05/2015] [Indexed: 11/10/2022]
Affiliation(s)
- Divya Rathi
- National Institute of Plant Genome Research; Aruna Asaf Ali Marg New Delhi India
| | - Dipak Gayen
- National Institute of Plant Genome Research; Aruna Asaf Ali Marg New Delhi India
| | - Saurabh Gayali
- National Institute of Plant Genome Research; Aruna Asaf Ali Marg New Delhi India
| | - Subhra Chakraborty
- National Institute of Plant Genome Research; Aruna Asaf Ali Marg New Delhi India
| | - Niranjan Chakraborty
- National Institute of Plant Genome Research; Aruna Asaf Ali Marg New Delhi India
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18
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Kan G, Zhang W, Yang W, Ma D, Zhang D, Hao D, Hu Z, Yu D. Association mapping of soybean seed germination under salt stress. Mol Genet Genomics 2015; 290:2147-62. [PMID: 26001372 DOI: 10.1007/s00438-015-1066-y] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Accepted: 05/12/2015] [Indexed: 01/31/2023]
Abstract
Soil salinity is a serious threat to agriculture sustainability worldwide. Seed germination is a critical phase that ensures the successful establishment and productivity of soybeans in saline soils. However, little information is available regarding soybean salt tolerance at the germination stage. The objective of this study was to identify the genetic mechanisms of soybean seed germination under salt stress. One natural population consisting of 191 soybean landraces was used in this study. Soybean seeds produced in four environments were used to evaluate the salt tolerance at their germination stage. Using 1142 single-nucleotide polymorphisms (SNPs), the molecular markers associated with salt tolerance were detected by genome-wide association analysis. Eight SNP-trait associations and 13 suggestive SNP-trait associations were identified using a mixed linear model and the TASSEL 4.0 software. Eight SNPs or suggestive SNPs were co-associated with two salt tolerance indices, namely (1) the ratio of the germination index under salt conditions to the germination index under no-salt conditions (ST-GI) and (2) the ratio of the germination rate under salt conditions to the germination rate under no-salt conditions (ST-GR). One SNP (BARC-021347-04042) was significantly associated with these two traits (ST-GI and ST-GR). In addition, nine possible candidate genes were located in or near the genetic region where the above markers were mapped. Of these, five genes, Glyma08g12400.1, Glyma08g09730.1, Glyma18g47140.1, Glyma09g00460.1, and Glyma09g00490.3, were verified in response to salt stress at the germination stage. The SNPs detected could facilitate a better understanding of the genetic basis of soybean salt tolerance at the germination stage, and the marker BARC-021347-04042 could contribute to future breeding for soybean salt tolerance by marker-assisted selection.
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Affiliation(s)
- Guizhen Kan
- National Center for Soybean Improvement/National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Wei Zhang
- National Center for Soybean Improvement/National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Wenming Yang
- National Center for Soybean Improvement/National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Deyuan Ma
- National Center for Soybean Improvement/National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Dan Zhang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Derong Hao
- Jiangsu Yanjiang Institute of Agricultural Sciences, Nantong, 226541, China
| | - Zhenbin Hu
- National Center for Soybean Improvement/National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Deyue Yu
- National Center for Soybean Improvement/National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
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Chakraborty S, Salekdeh GH, Yang P, Woo SH, Chin CF, Gehring C, Haynes PA, Mirzaei M, Komatsu S. Proteomics of Important Food Crops in the Asia Oceania Region: Current Status and Future Perspectives. J Proteome Res 2015; 14:2723-44. [DOI: 10.1021/acs.jproteome.5b00211] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
| | | | - Pingfang Yang
- Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Sun Hee Woo
- Chungbuk National University, Cheongju 362-763, Korea
| | - Chiew Foan Chin
- University of Nottingham Malaysia Campus, 43500 Semenyih, Selangor, Malaysia
| | - Chris Gehring
- King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | | | | | - Setsuko Komatsu
- National Institute of Crop Science, Tsukuba, Ibaraki 305-8518, Japan
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Subramanian S, Han L, Dutilleul P, Smith DL. Computed tomography scanning can monitor the effects of soil medium on root system development: an example of salt stress in corn. FRONTIERS IN PLANT SCIENCE 2015; 6:256. [PMID: 25972876 PMCID: PMC4411998 DOI: 10.3389/fpls.2015.00256] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 04/01/2015] [Indexed: 05/25/2023]
Abstract
Seeds and young seedlings often encounter high soluble salt levels in the upmost soil layers, impeding vigorous growth by affecting root establishment. Computed tomography (CT) scanning used at low X-ray doses can help study root development in such conditions non-destructively, because plants are allowed to grow throughout the experiment. Using a high-resolution Toshiba XVision CT scanner, we studied corn (Zea mays L.) root growth under optimal and salt-stressed conditions in 3D and on a weekly basis over 3 weeks. Two groups of three corn plants were grown in the controlled environment of a growth chamber, in mid-sized plastic pots filled with sieved and autoclaved sand. Seedlings were subjected to first CT scanning 1 week after seed planting. Our main research objectives concerning root systems were: (i) to quantify structural complexity from fractal dimensions estimated on skeletal 3-D images built from CT scanning data; (ii) to measure growth from volumes and lengths and the derived relative rates and increments, after isolating primary and secondary roots from the soil medium in CT scanning data; and (iii) to assess differences in complexity and growth per week and over Weeks 1-3 for groups of corn plants. Differences between groups were present from Week 1; starting in Week 2 secondary roots were present and could be isolated, which refined the complexity and growth analyses of root systems. Besides expected Week main effects (P < 0.01 or 0.05), Week × Group interaction (P < 0.05 or 0.10), and Group main effects were observed. Graphical, quantitative, and statistical analyses of CT scanning data were thus completed at an unprecedented level, and provided new and important insights regarding root system development. Repeated CT scanning is the key to a better understanding of the establishment in the soil medium of crop plants such as corn and the assessment of salt stress effects on developing root systems, in complexity, volume, and length.
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Affiliation(s)
| | | | | | - Donald L. Smith
- Department of Plant Science, McGill UniversityMontréal, QC, Canada
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Biochemical and proteomic analysis of soybean sprouts at different germination temperatures. ACTA ACUST UNITED AC 2015. [DOI: 10.1007/s13765-015-0053-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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22
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Skopelitou K, Muleta AW, Papageorgiou AC, Chronopoulou E, Labrou NE. Catalytic features and crystal structure of a tau class glutathione transferase from Glycine max specifically upregulated in response to soybean mosaic virus infections. BIOCHIMICA ET BIOPHYSICA ACTA 2015; 1854:166-77. [PMID: 25479053 DOI: 10.1016/j.bbapap.2014.11.008] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Revised: 11/09/2014] [Accepted: 11/21/2014] [Indexed: 01/09/2023]
Abstract
The plant tau class glutathione transferases (GSTs) play important roles in biotic and abiotic stress tolerance in crops and weeds. In this study, we systematically examined the catalytic and structural features of a GST isoenzyme from Glycine max (GmGSTU10-10). GmGSTU10-10 is a unique isoenzyme in soybean that is specifically expressed in response to biotic stress caused by soybean mosaic virus (SMV) infections. GmGSTU10-10 was cloned, expressed in Escherichia coli, purified and characterized. The results showed that GmGSTU10-10 catalyzes several different reactions and exhibits wide substrate specificity. Of particular importance is the finding that the enzyme shows high antioxidant catalytic function and acts as hydroperoxidase. In addition, its Km for GSH is significantly lower, compared to other plant GSTs, suggesting that GmGSTU10-10 is able to perform efficient catalysis under conditions where the concentration of reduced glutathione is low (e.g. oxidative stress). The crystal structure of GmGSTU10-10 was solved by molecular replacement at 1.6Å resolution in complex with glutathione sulfenic acid (GSOH). Structural analysis showed that GmGSTU10-10 shares the same overall fold and domain organization as other plant cytosolic GSTs; however, major variations were identified in helix H9 and the upper part of helix H4 that affect the size of the active site pockets, substrate recognition and the catalytic mechanism. The results of the present study provide new information into GST diversity and give further insights into the complex regulation and enzymatic functions of this plant gene superfamily.
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Affiliation(s)
- Katholiki Skopelitou
- Laboratory of Enzyme Technology, Department of Biotechnology, School of Food, Biotechnology and Development, Agricultural University of Athens, 75 Iera Odos Street, GR-11855-Athens, Greece
| | - Abdi W Muleta
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku 20521, Finland
| | | | - Evangelia Chronopoulou
- Laboratory of Enzyme Technology, Department of Biotechnology, School of Food, Biotechnology and Development, Agricultural University of Athens, 75 Iera Odos Street, GR-11855-Athens, Greece
| | - Nikolaos E Labrou
- Laboratory of Enzyme Technology, Department of Biotechnology, School of Food, Biotechnology and Development, Agricultural University of Athens, 75 Iera Odos Street, GR-11855-Athens, Greece.
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23
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Yin Y, Yang R, Han Y, Gu Z. Comparative proteomic and physiological analyses reveal the protective effect of exogenous calcium on the germinating soybean response to salt stress. J Proteomics 2015; 113:110-26. [PMID: 25284050 DOI: 10.1016/j.jprot.2014.09.023] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 09/22/2014] [Accepted: 09/26/2014] [Indexed: 01/16/2023]
Abstract
Calcium enhances salt stress tolerance of soybeans. Nevertheless, the molecular mechanism of calcium's involvement in resistance to salt stress is unclear. A comparative proteomic approach was used to investigate protein profiles in germinating soybeans under NaCl-CaCl2 and NaCl-LaCl3 treatments. A total of 80 proteins affected by calcium in 4-day-old germinating soybean cotyledons and 71 in embryos were confidently identified. The clustering analysis showed proteins were subdivided into 5 and 6 clusters in cotyledon and embryo, respectively. Among them, proteins involved in signal transduction and energy pathways, in transportation, and in protein biosynthesis were largely enriched while those involved in proteolysis were decreased. Abundance of nucleoside diphosphate kinase and three antioxidant enzymes were visibly increased by calcium. Accumulation of gamma-aminobutyric acid and polyamines was also detected after application of exogenous calcium. This was consistent with proteomic results, which showed that proteins involved in the glutamate and methionine metabolism were mediated by calcium. Calcium could increase the salt stress tolerance of germinating soybeans via enriching signal transduction, energy pathway and transportation, promoting protein biosynthesis, inhibiting proteolysis, redistributing storage proteins, regulating protein processing in endoplasmic reticulum, enriching antioxidant enzymes and activating their activities, accumulating secondary metabolites and osmolytes, and other adaptive responses. Biological significance Soybean (Glycine max L.), as a traditional edible legume, is being targeted for designing functional foods. During soybean germination under stressful conditions especially salt stress, newly discovered functional components such as gamma-aminobutyric acid (GABA) are rapidly accumulated. However, soybean plants are relatively salt-sensitive and the growth, development and biomass of germinating soybeans are significantly suppressed under salt stress condition. According to previous studies, exogenous calcium counters the harmful effect of salt stress and increases the biomass and GABA content of germinating soybeans. Nevertheless, the precise molecular mechanism underlying the role of calcium in resistance to salt stress is still unknown. This paper is the first study employing comparative proteomic and physiological analyses to reveal the protective effect of exogenous calcium in the germinating soybean response to salt stress. Our study links the biological events with proteomic information and provides detailed peptide information on all identified proteins. The functions of those significantly changed proteins are also analyzed. The physiological and comparative proteomic analyses revealed the putative molecular mechanism of exogenous calcium treatment induced salt stress responses. The findings from this paper are beneficial to high GABA-rich germinating soybean biomass. Additionally, these findings also might be applicable to the genetic engineering of soybean plants to improve stress tolerance.
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Affiliation(s)
- Yongqi Yin
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China; College of Food Science and Technology, Yangzhou University, Yangzhou, Jiangsu 225127, PR China
| | - Runqiang Yang
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Yongbin Han
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Zhenxin Gu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China.
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24
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Comparative proteomic analysis reveals molecular mechanism of seedling roots of different salt tolerant soybean genotypes in responses to salinity stress. EUPA OPEN PROTEOMICS 2014. [DOI: 10.1016/j.euprot.2014.05.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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25
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Yin Y, Yang R, Gu Z. Organ-specific proteomic analysis of NaCl-stressed germinating soybeans. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2014; 62:7233-44. [PMID: 24960070 DOI: 10.1021/jf500851r] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
A comparative proteomic approach was employed to explore proteome expression patterns in germinating soybeans under NaCl stress and NaCl-aminoguanidine treatment. The proteins were extracted from 4-day-old germinating soybean cotyledons and noncotyledons (hypocotyl and radicle) and were separated using two-dimensional polyacrylamide gel electrophoresis. A total of 63 and 72 differentially expressed proteins were confidently identified by MALDI-TOF/TOF in the noncotyledons and cotyledons, respectively. These identified proteins were divided into ten functional groups and most of them were predicted to be cytoplasmic proteins in noncotyledons. Moreover, γ-aminobutyric acid was accumulated while the major allergen (Bd 30K protein) was reduced in the germinating soybeans. The proteins involved in energy metabolism and in protein processing in endoplasmic reticulum were enriched under NaCl stress. Meanwhile, the negative effect of stress was aggravated once polyamine degradation was inhibited. Redistribution of storage proteins under stress indicated that storage proteins might not only function as seed storage reserves but also have additional roles in plant defense.
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Affiliation(s)
- Yongqi Yin
- College of Food Science and Technology, Nanjing Agricultural University , Nanjing, Jiangsu 210095, People's Republic of China
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26
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Barkla BJ, Vera-Estrella R, Pantoja O. Progress and challenges for abiotic stress proteomics of crop plants. Proteomics 2014; 13:1801-15. [PMID: 23512887 DOI: 10.1002/pmic.201200401] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Revised: 01/07/2013] [Accepted: 01/08/2013] [Indexed: 12/12/2022]
Abstract
Plants are continually challenged to recognize and respond to adverse changes in their environment to avoid detrimental effects on growth and development. Understanding the mechanisms that crop plants employ to resist and tolerate abiotic stress is of considerable interest for designing agriculture breeding strategies to ensure sustainable productivity. The application of proteomics technologies to advance our knowledge in crop plant abiotic stress tolerance has increased dramatically in the past few years as evidenced by the large amount of publications in this area. This is attributed to advances in various technology platforms associated with MS-based techniques as well as the accessibility of proteomics units to a wider plant research community. This review summarizes the work which has been reported for major crop plants and evaluates the findings in context of the approaches that are widely employed with the aim to encourage broadening the strategies used to increase coverage of the proteome.
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Affiliation(s)
- Bronwyn J Barkla
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México.
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27
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Komatsu S, Han C, Nanjo Y, Altaf-Un-Nahar M, Wang K, He D, Yang P. Label-free quantitative proteomic analysis of abscisic acid effect in early-stage soybean under flooding. J Proteome Res 2013; 12:4769-84. [PMID: 23808807 DOI: 10.1021/pr4001898] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Flooding is a serious problem for soybean cultivation because it markedly reduces growth. To investigate the role of phytohormones in soybean under flooding stress, gel-free proteomic technique was used. When 2-day-old soybeans were flooded, the content of abscisic acid (ABA) did not decrease in the root, though its content decreased in untreated plant. When ABA was added during flooding treatment, survival ratio was improved compared with that of soybeans flooded without ABA. When 2-day-old soybeans were flooded with ABA, the abundance of proteins related to cell organization, vesicle transport and glycolysis decreased compared with those in root of soybeans flooded without ABA. Furthermore, the nuclear proteins were analyzed to identify the transcriptional regulation. The abundance of 34 nuclear proteins such as histone deacetylase and U2 small nuclear ribonucleoprotein increased by ABA supplementation under flooding; however, 35 nuclear proteins such as importin alpha, chromatin remodeling factor, zinc finger protein, transducin, and cell division 5 protein decreased. Of them, the mRNA expression levels of cell division cycle 5 protein, C2H2 zinc finger protein SERRATE, CCCH type zinc finger family protein, and transducin were significantly down-regulated under the ABA treatment. These results suggest that ABA might be involved in the enhancement of flooding tolerance of soybean through the control of energy conservation via glycolytic system and the regulation on zinc finger proteins, cell division cycle 5 protein and transducin.
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Affiliation(s)
- Setsuko Komatsu
- National Institute of Crop Science, National Agriculture and Food Research Organization , Tsukuba 305-8518, Japan
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28
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Hossain Z, Khatoon A, Komatsu S. Soybean proteomics for unraveling abiotic stress response mechanism. J Proteome Res 2013; 12:4670-84. [PMID: 24016329 DOI: 10.1021/pr400604b] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Plant response to abiotic stresses depends upon the fast activation of molecular cascades involving stress perception, signal transduction, changes in gene and protein expression and post-translational modification of stress-induced proteins. Legumes are extremely sensitive to flooding, drought, salinity and heavy metal stresses, and soybean is not an exception of that. Invention of immobilized pH gradient strips followed by advancement in mass spectrometry has made proteomics a fast, sensitive and reliable technique for separation, identification and characterization of stress-induced proteins. As the functional translated portion of the genome plays an essential role in plant stress response, proteomic studies provide us a finer picture of protein networks and metabolic pathways primarily involved in stress tolerance mechanism. Identifying master regulator proteins that play key roles in the abiotic stress response pathway is fundamental in providing opportunities for developing genetically engineered stress-tolerant crop plants. This review highlights recent contributions in the field of soybean biology to comprehend the complex mechanism of abiotic stress acclimation. Furthermore, strengths and weaknesses of different proteomic methodologies of extracting complete proteome and challenges and future prospects of soybean proteome study both at organ and whole plant levels are discussed in detail to get new insights into the plant abiotic stress response mechanism.
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Affiliation(s)
- Zahed Hossain
- Plant Stress Biology Lab, Department of Botany, West Bengal State University , Kolkata 700126, West Bengal, India
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29
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Lu Y, Lam H, Pi E, Zhan Q, Tsai S, Wang C, Kwan Y, Ngai S. Comparative metabolomics in Glycine max and Glycine soja under salt stress to reveal the phenotypes of their offspring. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2013; 61:8711-21. [PMID: 23930713 DOI: 10.1021/jf402043m] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Metabolomics is developing as an important functional genomics tool for understanding plant systems' response to genetic and environmental changes. Here, we characterized the metabolic changes of cultivated soybean C08 (Glycine max L. Merr) and wild soybean W05 (Glycine soja Sieb.et Zucc.) under salt stress using MS-based metabolomics, in order to reveal the phenotypes of their eight hybrid offspring (9H0086, 9H0124, 9H0391, 9H0736, 9H0380, 9H0400, 9H0434, and 9H0590). Total small molecule extracts of soybean seedling leaves were profiled by gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-Fourier transform mass spectrometry (LC-FT/MS). We found that wild soybean contained higher amounts of disaccharides, sugar alcohols, and acetylated amino acids than cultivated soybean, but with lower amounts of monosaccharides, carboxylic acids, and unsaturated fatty acids. Further investigations demonstrated that the ability of soybean to tolerate salt was mainly based on synthesis of compatible solutes, induction of reactive oxygen species (ROS) scavengers, cell membrane modifications, and induction of plant hormones. On the basis of metabolic phenotype, the salt-tolerance abilities of 9H0086, 9H0124, 9H0391, 9H0736, 9H0380, 9H0400, 9H0434, and 9H0590 were discriminated. Our results demonstrated that MS-based metabolomics provides a fast and powerful approach to discriminate the salt-tolerance characteristics of soybeans.
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Affiliation(s)
- Yonghai Lu
- Centre for Soybean Research of Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences and ‡School of Biomedical Sciences, The Chinese University of Hong Kong , Hong Kong
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30
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Han C, Yin X, He D, Yang P. Analysis of proteome profile in germinating soybean seed, and its comparison with rice showing the styles of reserves mobilization in different crops. PLoS One 2013; 8:e56947. [PMID: 23460823 PMCID: PMC3584108 DOI: 10.1371/journal.pone.0056947] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Accepted: 01/16/2013] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Seed germination is a complex physiological process during which mobilization of nutrient reserves happens. In different crops, this event might be mediated by different regulatory and metabolic pathways. Proteome profiling has been proved to be an efficient way that can help us to construct these pathways. However, no such studies have been performed in soybean germinating seeds up to date. RESULTS Proteome profiling was conducted through one-dimensional gel electrophoresis followed by liquid chromatography and tandem mass spectrometry strategy in the germinating seeds of soybean (glycine max). Comprehensive comparisons were also carried out between rice and soybean germinating seeds. 764 proteins belonging to 14 functional groups were identified and metabolism related proteins were the largest group. Deep analyses of the proteins and pathways showed that lipids were degraded through lipoxygenase dependent pathway and proteins were degraded through both protease and 26S proteosome system, and the lipoxygenase could also help to remove the reactive oxygen species during the rapid mobilization of reserves of soybean germinating seeds. The differences between rice and soybean germinating seeds proteome profiles indicate that each crop species has distinct mechanism for reserves mobilization during germination. Different reserves could be converted into starches before they are totally utilized during the germination in different crops seeds. CONCLUSIONS This study is the first comprehensive analysis of proteome profile in germinating soybean seeds to date. The data presented in this paper will improve our understanding of the physiological and biochemical status in the imbibed soybean seeds just prior to germination. Comparison of the protein profile with that of germinating rice seeds gives us new insights on mobilization of nutrient reserves during the germination of crops seeds.
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Affiliation(s)
- Chao Han
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Graduate University of Chinese Academy of Sciences, Beijing, China
| | - Xiaojian Yin
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Graduate University of Chinese Academy of Sciences, Beijing, China
| | - Dongli He
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Pingfang Yang
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
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Dinamarca J, Sandoval-Alvarez A, Gidekel M, Gutiérrez-Moraga A. Differentially expressed genes induced by cold and UV-B in Deschampsia antarctica Desv. Polar Biol 2012. [DOI: 10.1007/s00300-012-1271-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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32
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Ma H, Song L, Shu Y, Wang S, Niu J, Wang Z, Yu T, Gu W, Ma H. Comparative proteomic analysis of seedling leaves of different salt tolerant soybean genotypes. J Proteomics 2012; 75:1529-46. [PMID: 22155470 DOI: 10.1016/j.jprot.2011.11.026] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2011] [Revised: 11/18/2011] [Accepted: 11/21/2011] [Indexed: 12/12/2022]
Abstract
Salinity is one of the major environmental constraints limiting yield of crop plants in many semi-arid and arid regions around the world. To understand responses in soybean seedling to salt stress at proteomic level, the extracted proteins from seedling leaves of salt-sensitive genotype Jackson and salt-tolerant genotype Lee 68 under 150 mM NaCl stress for 1, 12, 72 and 144 h, respectively, were analyzed by 2-DE. Approximately 800 protein spots were detected on 2-DE gels. Among them, 91 were found to be differently expressed, with 78 being successfully identified by MALDI-TOF-TOF. The identified proteins were involved in 14 metabolic pathways and cellular processes. Based on most of the 78 salt-responsive proteins, a salt stress-responsive protein network was proposed. This network consisted of several functional components, including balancing between ROS production and scavenging, accelerated proteolysis and reduced biosynthesis of proteins, impaired photosynthesis, abundant energy supply and enhanced biosynthesis of ethylene. Salt-tolerant genotype Lee 68 possessed the ability of higher ROS scavenging, more abundant energy supply and ethylene production, and stronger photosynthesis than salt-sensitive genotype Jackson under salt stress, which may be the major reasons why it is more salt-tolerant than Jackson.
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Affiliation(s)
- Hongyu Ma
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, Jiangsu Province 210095, PR China.
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