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Yijun G, Zhiming X, Jianing G, Qian Z, Rasheed A, Hussain MI, Ali I, Shuheng Z, Hassan MU, Hashem M, Mostafa YS, Wang Y, Chen L, Xiaoxue W, Jian W. The intervention of classical and molecular breeding approaches to enhance flooding stress tolerance in soybean - An review. FRONTIERS IN PLANT SCIENCE 2022; 13:1085368. [PMID: 36643298 PMCID: PMC9835000 DOI: 10.3389/fpls.2022.1085368] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 11/28/2022] [Indexed: 05/27/2023]
Abstract
Abiotic stresses and climate changes cause severe loss of yield and quality of crops and reduce the production area worldwide. Flooding stress curtails soybean growth, yield, and quality and ultimately threatens the global food supply chain. Flooding tolerance is a multigenic trait. Tremendous research in molecular breeding explored the potential genomic regions governing flood tolerance in soybean. The most robust way to develop flooding tolerance in soybean is by using molecular methods, including quantitative trait loci (QTL) mapping, identification of transcriptomes, transcription factor analysis, CRISPR/Cas9, and to some extent, genome-wide association studies (GWAS), and multi-omics techniques. These powerful molecular tools have deepened our knowledge about the molecular mechanism of flooding stress tolerance. Besides all this, using conventional breeding methods (hybridization, introduction, and backcrossing) and other agronomic practices is also helpful in combating the rising flooding threats to the soybean crop. The current review aims to summarize recent advancements in breeding flood-tolerant soybean, mainly by using molecular and conventional tools and their prospects. This updated picture will be a treasure trove for future researchers to comprehend the foundation of flooding tolerance in soybean and cover the given research gaps to develop tolerant soybean cultivars able to sustain growth under extreme climatic changes.
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Affiliation(s)
- Guan Yijun
- College of Life Sciences, Northwest Agricultural and Forestry University, Yangling, Shanxi, China
| | - Xie Zhiming
- College of Life Sciences, Baicheng Normal University, Baicheng, Jilin, China
| | - Guan Jianing
- Rice Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Zhao Qian
- Changchun Normal University, College of Life Sciences, Changchun, China
| | - Adnan Rasheed
- Changchun Normal University, College of Life Sciences, Changchun, China
- Jilin Changfa Modern Agricultural Science and Technology Group Co., Ltd., Changchun, China
| | | | - Iftikhar Ali
- State Key Laboratory of Molecular Development Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Zhang Shuheng
- College of Agronomy, Jilin Agricultural University, Changchun, Jilin, China
| | - Muhammad Umair Hassan
- Research Center on Ecological Sciences , Jiangxi Agricultural University, Nanchang, China
| | - Mohamed Hashem
- Department of Biology, College of Science, King Khalid University, Abha, Saudi Arabia
- Botany and Microbiology Department, Faculty of Science, Asiut University, Assiut, Egypt
| | - Yasser S. Mostafa
- Department of Biology, College of Science, King Khalid University, Abha, Saudi Arabia
| | - Yueqiang Wang
- Jilin Academy of Agricultural Sciences and National Engineering Research Center for Soybean, Changchun, China
| | - Liang Chen
- Jilin Academy of Agricultural Sciences and National Engineering Research Center for Soybean, Changchun, China
| | - Wang Xiaoxue
- Rice Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Wei Jian
- Changchun Normal University, College of Life Sciences, Changchun, China
- Jilin Changfa Modern Agricultural Science and Technology Group Co., Ltd., Changchun, China
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Wang X, Komatsu S. The Role of Phytohormones in Plant Response to Flooding. Int J Mol Sci 2022; 23:6383. [PMID: 35742828 PMCID: PMC9223812 DOI: 10.3390/ijms23126383] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 06/05/2022] [Accepted: 06/06/2022] [Indexed: 02/07/2023] Open
Abstract
Climatic variations influence the morphological, physiological, biological, and biochemical states of plants. Plant responses to abiotic stress include biochemical adjustments, regulation of proteins, molecular mechanisms, and alteration of post-translational modifications, as well as signal transduction. Among the various abiotic stresses, flooding stress adversely affects the growth of plants, including various economically important crops. Biochemical and biological techniques, including proteomic techniques, provide a thorough understanding of the molecular mechanisms during flooding conditions. In particular, plants can cope with flooding conditions by embracing an orchestrated set of morphological adaptations and physiological adjustments that are regulated by an elaborate hormonal signaling network. With the help of these findings, the main objective is to identify plant responses to flooding and utilize that information for the development of flood-tolerant plants. This review provides an insight into the role of phytohormones in plant response mechanisms to flooding stress, as well as different mitigation strategies that can be successfully administered to improve plant growth during stress exposure. Ultimately, this review will expedite marker-assisted genetic enhancement studies in crops for developing high-yield lines or varieties with flood tolerance.
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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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Tyagi A, Sharma S, Ali S, Gaikwad K. Crosstalk between H 2 S and NO: an emerging signalling pathway during waterlogging stress in legume crops. PLANT BIOLOGY (STUTTGART, GERMANY) 2022; 24:576-586. [PMID: 34693601 DOI: 10.1111/plb.13319] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 07/04/2021] [Indexed: 06/13/2023]
Abstract
In legumes, waterlogging is a major detrimental factor leading to huge yield losses. Generally, legumes lack tolerance to submergence, and conventional breeding to develop tolerant varieties are limited due to the lack of tolerant germplasm and potential target genes. Moreover, our understanding of the various signalling cascades, their interactions and key pathways induced during waterlogging is limited. Here, we focus on the role of two important plant signalling molecules, viz. hydrogen sulphide (H2 S) and nitric oxide (NO), during waterlogging stress in legumes. Plants and soil microbes produce these signalling molecules both endogenously and exogenously under various stresses, including waterlogging. NO and H2 S are known to regulate key physiological pathways, such as stomatal closure, leaf senescence and regulation of numerous stress signalling pathways, while NO plays a pivotal role in adventitious root formation during waterlogging. The crosstalk between H2 S and NO is synergistic because of the resemblance of their physiological effects and proteomic functions, which mainly operate through cysteine-dependent post-translational modifications via S-nitrosation and persulfidation. Such knowledge has provided novel platforms for researchers to unravel the complexity associated with H2 S-NO signalling and interactions with plant stress hormones. This review provides an overall summary on H2 S and NO, including biosynthesis, biological importance, crosstalk, transporter regulation as well as understanding their role during waterlogging using 'multi-omics' approach. Understanding H2 S and NO signalling will help in deciphering the metabolic interactions and identifying key regulatory genes that could be used for developing waterlogging tolerance in legumes.
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Affiliation(s)
- A Tyagi
- ICAR - National Institute for Plant Biotechnology, New Delhi, India
| | - S Sharma
- ICAR - National Institute for Plant Biotechnology, New Delhi, India
| | - S Ali
- Department of Biotechnology, Yeungnam University, Gyeongsan Gyeongbuk, Republic of Korea
| | - K Gaikwad
- ICAR - National Institute for Plant Biotechnology, New Delhi, India
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Komatsu S, Yamaguchi H, Hitachi K, Tsuchida K, Kono Y, Nishimura M. Proteomic and Biochemical Analyses of the Mechanism of Tolerance in Mutant Soybean Responding to Flooding Stress. Int J Mol Sci 2021; 22:9046. [PMID: 34445752 PMCID: PMC8396653 DOI: 10.3390/ijms22169046] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/13/2021] [Accepted: 08/19/2021] [Indexed: 11/16/2022] Open
Abstract
To investigate the mechanism of flooding tolerance of soybean, flooding-tolerant mutants derived from gamma-ray irradiated soybean were crossed with parent cultivar Enrei for removal of other factors besides the genes related to flooding tolerance in primary generated mutant soybean. Although the growth of the wild type was significantly suppressed by flooding compared with the non-flooding condition, that of the mutant lines was better than that of the wild type even if it was treated with flooding. A two-day-old mutant line was subjected to flooding for 2 days and proteins were analyzed using a gel-free/label-free proteomic technique. Oppositely changed proteins in abundance between the wild type and mutant line under flooding stress were associated in endoplasmic reticulum according to gene-ontology categorization. Immunoblot analysis confirmed that calnexin accumulation increased in both the wild type and mutant line; however, calreticulin accumulated in only the mutant line under flooding stress. Furthermore, although glycoproteins in the wild type decreased by flooding compared with the non-flooding condition, those in the mutant line increased even if it was under flooding stress. Alcohol dehydrogenase accumulated in the wild type and mutant line; however, this enzyme activity significantly increased and mildly increased in the wild type and mutant line, respectively, under flooding stress compared with the non-flooding condition. Cell death increased and decreased in the wild type and mutant line, respectively, by flooding stress. These results suggest that the regulation of cell death through the fermentation system and glycoprotein folding might be an important factor for the acquisition of flooding tolerance in mutant soybean.
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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.)
| | - Yuhi Kono
- Central Region Agricultural Research Center, National Agriculture and Food Research Organization, Joetsu 943-0193, Japan;
| | - Minoru Nishimura
- Graduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan;
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Yin X, Fan H, Chen Y, Li LZ, Song W, Fan Y, Zhou W, Ma G, Alolga RN, Li W, Zhang B, Li P, Tran LSP, Lu X, Qi LW. Integrative omic and transgenic analyses reveal the positive effect of ultraviolet-B irradiation on salvianolic acid biosynthesis through upregulation of SmNAC1. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:781-799. [PMID: 32772407 DOI: 10.1111/tpj.14952] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 07/21/2020] [Accepted: 07/30/2020] [Indexed: 06/11/2023]
Abstract
Salvianolic acids (SalAs), a group of secondary metabolites in Salvia miltiorrhiza, are widely used for treating cerebrovascular diseases. Their biosynthesis is modulated by a variety of abiotic factors, including ultraviolet-B (UV-B) irradiation; however, the underlying mechanisms remain largely unknown. Here, an integrated metabolomic, proteomic, and transcriptomic approach coupled with transgenic analyses was employed to dissect the mechanisms underlying UV-B irradiation-induced SalA biosynthesis. Results of metabolomics showed that 28 metabolites, including 12 SalAs, were elevated in leaves of UV-B-treated S. miltiorrhiza. Meanwhile, the contents of several phytohormones, including jasmonic acid and salicylic acid, which positively modulate the biosynthesis of SalAs, also increased in UV-B-treated S. miltiorrhiza. Consistently, 20 core biosynthetic enzymes and numerous transcription factors that are involved in SalA biosynthesis were elevated in treated samples as indicated by a comprehensive proteomic analysis. Correlation and gene expression analyses demonstrated that the NAC1 gene, encoding a NAC transcriptional factor, was positively involved in UV-B-induced SalA biosynthesis. Accordingly, overexpression and RNA interference of NAC1 increased and decreased SalA contents, respectively, through regulation of key biosynthetic enzymes. Furthermore, ChIP-qPCR and Dual-LUC assays showed that NAC1 could directly bind to the CATGTG and CATGTC motifs present in the promoters of the SalA biosynthesis-related genes PAL3 and TAT3, respectively, and activate their expression. Our results collectively demonstrate that NAC1 plays a crucial role in UV-B irradiation-induced SalA biosynthesis. Taken together, our findings provide mechanistic insights into the UV-B-induced SalA biosynthesis in S. miltiorrhiza, and shed light on a great potential for the development of SalA-abundant varieties through genetic engineering.
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Affiliation(s)
- Xiaojian Yin
- State Key Laboratory of Natural Medicines, Department of Pharmacognosy, Institute of Pharmaceutical Science, China Pharmaceutical University, Nanjing, 210009, China
- Clinical Metabolomics Center, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Hui Fan
- State Key Laboratory of Natural Medicines, Department of Pharmacognosy, Institute of Pharmaceutical Science, China Pharmaceutical University, Nanjing, 210009, China
| | - Yan Chen
- Clinical Metabolomics Center, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Lan-Zhu Li
- Clinical Metabolomics Center, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Wei Song
- State Key Laboratory of Natural Medicines, Department of Pharmacognosy, Institute of Pharmaceutical Science, China Pharmaceutical University, Nanjing, 210009, China
| | - Yuanming Fan
- Clinical Metabolomics Center, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Wei Zhou
- Clinical Metabolomics Center, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Gaoxiang Ma
- Clinical Metabolomics Center, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Raphael N Alolga
- Clinical Metabolomics Center, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Weiqiang Li
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, 85 Minglun Street, Kaifeng, 475001, China
| | - Baolong Zhang
- Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Science, Nanjing, 210014, China
| | - Ping Li
- Clinical Metabolomics Center, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Lam-Son P Tran
- Institute of Research and Development, Duy Tan University, 03 Quang Trung, Da Nang, Vietnam
- Stress Adaptation Research Unit, RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro-cho, Tsurumi, 230-0045, Japan
| | - Xu Lu
- Clinical Metabolomics Center, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Lian-Wen Qi
- Clinical Metabolomics Center, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
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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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Yin X, Komatsu S. Comprehensive analysis of response and tolerant mechanisms in early-stage soybean at initial-flooding stress. J Proteomics 2017; 169:225-232. [PMID: 28137666 DOI: 10.1016/j.jprot.2017.01.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 01/17/2017] [Accepted: 01/23/2017] [Indexed: 12/31/2022]
Abstract
Soybean is one of the most cultivated crops in the world; however, it is very sensitive to flooding stress, which markedly reduces its growth and yield. Morphological and biochemical changes such as an increase of fresh weight and a decrease of ATP content happen in early-stage soybean at initial-flooding stress, indicating that soybean responses to flooding stress are keys for its survival and seedling growth. Phosphoproteomics and nuclear proteomics are useful tools to detect protein-phosphorylation status and to identify transcriptional factors. In the review, the effect of flooding on soybean response to initial flooding stress is discussed based on recent results of proteomic, phosphoproteomic, nuclear proteomic, and nuclear phosphoproteomic studies. In addition, soybean survival under flooding stress, which is defined as tolerance mechanism, is discussed with the results of comprehensive analysis in flooding-tolerant mutant line and abscisic acid-treated soybean. BIOLOGICAL SIGNIFICANCE Soybean is one of the most cultivated crops in the world; however, it is very sensitive to flooding stress, especially soybean responses to initial flooding stress is key for its survival and seedling growth. Recently, proteomic techniques are applied to investigate the response and tolerant mechanisms of soybean at initial flooding condition. In this review, the progress in proteomic, phosphoproteomic, nuclear proteomic, and nuclear phosphoproteomic studies about the initial-flooding response mechanism in early-stage soybean is presented. In addition, the tolerant mechanism in soybean is discussed with the results of comprehensive analysis in flooding-tolerant mutant line and abscisic acid-treated soybean. Through this review, the key proteins and genes involved in initial flooding response and tolerance at early stage soybean are summarized and they contribute greatly to uncover response and tolerance mechanism at early stage under stressful environmental conditions in soybean.
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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. Improvement of Soybean Products Through the Response Mechanism Analysis Using Proteomic Technique. ADVANCES IN FOOD AND NUTRITION RESEARCH 2017; 82:117-148. [PMID: 28427531 DOI: 10.1016/bs.afnr.2016.12.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Soybean is rich in protein/vegetable oil and contains several phytochemicals such as isoflavones and phenolic compounds. Because of the predominated nutritional values, soybean is considered as traditional health benefit food. Soybean is a widely cultivated crop; however, its growth and yield are markedly affected by adverse environmental conditions. Proteomic techniques make it feasible to map protein profiles both during soybean growth and under unfavorable conditions. The stress-responsive mechanisms during soybean growth have been uncovered with the help of proteomic studies. In this review, the history of soybean as food and the morphology/physiology of soybean are described. The utilization of proteomics during soybean germination and development is summarized. In addition, the stress-responsive mechanisms explored using proteomic techniques are reviewed in soybean.
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Affiliation(s)
- Xin Wang
- National Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan; Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Setsuko Komatsu
- National Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan; Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan.
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9
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Yin X, Komatsu S. Plant nuclear proteomics for unraveling physiological function. N Biotechnol 2016; 33:644-654. [PMID: 27004615 DOI: 10.1016/j.nbt.2016.03.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 03/09/2016] [Accepted: 03/10/2016] [Indexed: 10/22/2022]
Abstract
The nucleus is the subcellular organelle that functions as the regulatory hub of the cell and is responsible for regulating several critical cellular functions, including cell proliferation, gene expression, and cell survival. Nuclear proteomics is a useful approach for investigating the mechanisms underlying plant responses to abiotic stresses, including protein-protein interactions, enzyme activities, and post-translational modifications. Among abiotic stresses, flooding is a major limiting factor for plant growth and yields, particularly for soybean. In this review, plant nuclei purification methods, modifications of plant nuclear proteins, and recent contributions to the field of plant nuclear proteomics are summarized. In addition, to reveal the upstream regulating mechanisms controlling soybean responses to flooding stress, the functions of flooding-responsive nuclear proteins are reviewed based on the results of nuclear proteomic analysis of soybean in the early stages of flooding stress.
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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. 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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Yasmeen F, Raja NI, Mustafa G, Sakata K, Komatsu S. Quantitative proteomic analysis of post-flooding recovery in soybean root exposed to aluminum oxide nanoparticles. J Proteomics 2016; 143:136-150. [PMID: 27079982 DOI: 10.1016/j.jprot.2016.03.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 03/02/2016] [Accepted: 03/03/2016] [Indexed: 12/22/2022]
Abstract
UNLABELLED Aluminum oxide nanoparticles (Al2O3 NPs) are used in various commercial and agricultural products. Soybean exhibits severe reduction in growth under flooding condition. To examine the effects of Al2O3 NPs on the recovery of soybean from flooding, proteomic analysis was performed. Survival percentage and weight/length of root including hypocotyl were improved after 2 and 4days of flooding with 50ppm Al2O3 NPs leading to recovery as compared to flooding. A total of 211 common proteins were changed in abundance during the recovery period after treatment without or with Al2O3 NPs. These proteins were related to protein synthesis, stress, cell wall, and signaling. Among the identified stress-related proteins, S-adenosyl-l-methionine dependent methyltransferases were recovered from flooding with Al2O3 NPs. Hierarchical clustering divided the identified proteins into three clusters. Cluster II exhibited the greatest change in proteins related to protein synthesis, transport, and development during the recovery from flooding with Al2O3 NPs. However, activity of enolase remained unchanged during flooding leading to subsequent recovery with Al2O3 NPs. These results suggest that S-adenosyl-l-methionine dependent methyltransferases and enolase might be involved in mediating recovery responses by Al2O3 NPs. BIOLOGICAL SIGNIFICANCE This study highlighted the role of Al2O3 NPs in recovery of soybean seedlings from flooding stress using gel-free proteomic technique. The key findings of this study are as follows: (i) survival percentage was enhanced at 50ppm Al2O3 NPs during the recovery stage; (ii) seedling weight and weight/length of root including hypocotyl improved at 50ppm Al2O3 NPs during the period of recovery; (iii) protein synthesis and stress related proteins were increased on recovery after flooding without or with Al2O3 NPs; (iv) the abundance of S-adenosyl-l-methionine dependent methyltransferases recovered from flooding with Al2O3 NPs; (v) glycolysis related proteins amplified under flooding with Al2O3 NPs; (vi) enolase enzyme remained unchanged during flooding leading to subsequent recovery from flooding with Al2O3 NPs. Collectively, these results suggest that S-adenosyl-l-methionine dependent methyltransferases and enolase are involved in response to flooding with Al2O3 NPs and might be helpful in recovery from flooding stress.
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Affiliation(s)
- Farhat Yasmeen
- Department of Botany, PMAS-Arid Agriculture University, Rawalpindi 46300, Pakistan; National Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba 305-8518, Japan
| | - Naveed Iqbal Raja
- Department of Botany, PMAS-Arid Agriculture University, Rawalpindi 46300, Pakistan
| | - Ghazala Mustafa
- National Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba 305-8518, Japan
| | - Katsumi Sakata
- Maebashi Institute of Technology, Maebashi 371-0816, Japan
| | - Setsuko Komatsu
- National Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba 305-8518, Japan.
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12
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Yang B, Wang X, Gao C, Chen M, Guan Q, Tian J, Komatsu S. Proteomic and Metabolomic Analyses of Leaf from Clematis terniflora DC. Exposed to High-Level Ultraviolet-B Irradiation with Dark Treatment. J Proteome Res 2016; 15:2643-57. [PMID: 27323210 DOI: 10.1021/acs.jproteome.6b00206] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Clematis terniflora DC. has potential pharmaceutical value; on the contrary, high-level UV-B irradiation with dark treatment led to the accumulation of secondary metabolites. Metabolomic and proteomic analyses of leaf of C. terniflora were performed to investigate the systematic response mechanisms to high-level UV-B irradiation with dark treatment. Metabolites related to carbohydrates, fatty acids, and amino acids and/or proteins related to stress, cell wall, and amino acid metabolism were gradually increased in response to high-level UV-B irradiation with dark treatment. On the basis of cluster analysis and mapping of proteins related to amino acid metabolism, the abundances of S-adenosylmethionine synthetase and cysteine synthase as well as 1,1-diphenyl-2-picrylhydrazyl scavenging activity were gradually increased in response to high-level UV-B irradiation with dark treatment. Furthermore, the abundance of dihydrolipoyl dehydrogenase/glutamate dehydrogenase and the content of γ-aminobutyric acid were also increased following high-level UV-B irradiation with dark treatment. Taken together, these results suggest that high-level UV-B irradiation with dark treatment induces the activation of reactive oxygen species scavenging system and γ-aminobutyric acid shunt pathway in leaf of C. terniflora.
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Affiliation(s)
- Bingxian Yang
- College of Biomedical Engineering & Instrument Science, Zhejiang University , Zheda Road 38, Hangzhou 310027, China.,National Institute of Crop Science, National Agriculture and Food Research Organization, Kannondai 2-1-18, Tsukuba 305-8518, Japan
| | - Xin Wang
- National Institute of Crop Science, National Agriculture and Food Research Organization, Kannondai 2-1-18, Tsukuba 305-8518, Japan
| | - Cuixia Gao
- College of Biomedical Engineering & Instrument Science, Zhejiang University , Zheda Road 38, Hangzhou 310027, China
| | - Meng Chen
- College of Biomedical Engineering & Instrument Science, Zhejiang University , Zheda Road 38, Hangzhou 310027, China
| | - Qijie Guan
- College of Biomedical Engineering & Instrument Science, Zhejiang University , Zheda Road 38, Hangzhou 310027, China
| | - Jingkui Tian
- College of Biomedical Engineering & Instrument Science, Zhejiang University , Zheda Road 38, Hangzhou 310027, China
| | - Setsuko Komatsu
- National Institute of Crop Science, National Agriculture and Food Research Organization, Kannondai 2-1-18, Tsukuba 305-8518, Japan
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13
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Yin X, Nishimura M, Hajika M, Komatsu S. Quantitative Proteomics Reveals the Flooding-Tolerance Mechanism in Mutant and Abscisic Acid-Treated Soybean. J Proteome Res 2016; 15:2008-25. [PMID: 27132649 DOI: 10.1021/acs.jproteome.6b00196] [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: 01/01/2023]
Abstract
Flooding negatively affects the growth of soybean, and several flooding-specific stress responses have been identified; however, the mechanisms underlying flooding tolerance in soybean remain unclear. To explore the initial flooding tolerance mechanisms in soybean, flooding-tolerant mutant and abscisic acid (ABA)-treated plants were analyzed. In the mutant and ABA-treated soybeans, 146 proteins were commonly changed at the initial flooding stress. Among the identified proteins, protein synthesis-related proteins, including nascent polypeptide-associated complex and chaperonin 20, and RNA regulation-related proteins were increased in abundance both at protein and mRNA expression. However, these proteins identified at the initial flooding stress were not significantly changed during survival stages under continuous flooding. Cluster analysis indicated that glycolysis- and cell wall-related proteins, such as enolase and polygalacturonase inhibiting protein, were increased in abundance during survival stages. Furthermore, lignification of root tissue was improved even under flooding stress. Taken together, these results suggest that protein synthesis- and RNA regulation-related proteins play a key role in triggering tolerance to the initial flooding stress in soybean. Furthermore, the integrity of cell wall and balance of glycolysis might be important factors for promoting tolerance of soybean root to flooding stress during survival stages.
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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
| | - Minoru Nishimura
- Graduate School of Life and Food Sciences, Niigata University , Niigata 950-2181, Japan
| | - Makita Hajika
- 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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14
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Abstract
Climate change is considered a major threat to world agriculture and food security. To improve the agricultural productivity and sustainability, the development of high-yielding stress-tolerant, and climate-resilient crops is essential. Of the abiotic stresses, flooding stress is a very serious hazard because it markedly reduces plant growth and grain yield. Proteomic analyses indicate that the effects of flooding stress are not limited to oxygen deprivation but include many other factors. Although many flooding response mechanisms have been reported, flooding tolerance mechanisms have not been fully clarified for soybean. There were limitations in soybean materials, such as mutants and varieties, while they were abundant in rice and Arabidopsis. In this review, plant proteomic technologies are introduced and flooding tolerance mechanisms of soybeans are summarized to assist in the improvement of flooding tolerance in soybeans. This work will expedite transgenic or 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)
- Setsuko Komatsu
- National Institute of Crop Science, National Agriculture and Food Research Organization, Kannondai 2-1-18, Tsukuba 305-8518, Japan
| | - Makoto Tougou
- National Institute of Crop Science, National Agriculture and Food Research Organization, Kannondai 2-1-18, Tsukuba 305-8518, Japan
| | - Yohei Nanjo
- National Institute of Crop Science, National Agriculture and Food Research Organization, Kannondai 2-1-18, Tsukuba 305-8518, Japan
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15
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Kosová K, Vítámvás P, Urban MO, Klíma M, Roy A, Prášil IT. Biological Networks Underlying Abiotic Stress Tolerance in Temperate Crops--A Proteomic Perspective. Int J Mol Sci 2015; 16:20913-42. [PMID: 26340626 PMCID: PMC4613235 DOI: 10.3390/ijms160920913] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 07/16/2015] [Accepted: 08/10/2015] [Indexed: 12/26/2022] Open
Abstract
Abiotic stress factors, especially low temperatures, drought, and salinity, represent the major constraints limiting agricultural production in temperate climate. Under the conditions of global climate change, the risk of damaging effects of abiotic stresses on crop production increases. Plant stress response represents an active process aimed at an establishment of novel homeostasis under altered environmental conditions. Proteins play a crucial role in plant stress response since they are directly involved in shaping the final phenotype. In the review, results of proteomic studies focused on stress response of major crops grown in temperate climate including cereals: common wheat (Triticum aestivum), durum wheat (Triticum durum), barley (Hordeum vulgare), maize (Zea mays); leguminous plants: alfalfa (Medicago sativa), soybean (Glycine max), common bean (Phaseolus vulgaris), pea (Pisum sativum); oilseed rape (Brassica napus); potato (Solanum tuberosum); tobacco (Nicotiana tabaccum); tomato (Lycopersicon esculentum); and others, to a wide range of abiotic stresses (cold, drought, salinity, heat, imbalances in mineral nutrition and heavy metals) are summarized. The dynamics of changes in various protein functional groups including signaling and regulatory proteins, transcription factors, proteins involved in protein metabolism, amino acid metabolism, metabolism of several stress-related compounds, proteins with chaperone and protective functions as well as structural proteins (cell wall components, cytoskeleton) are briefly overviewed. Attention is paid to the differences found between differentially tolerant genotypes. In addition, proteomic studies aimed at proteomic investigation of multiple stress factors are discussed. In conclusion, contribution of proteomic studies to understanding the complexity of crop response to abiotic stresses as well as possibilities to identify and utilize protein markers in crop breeding processes are discussed.
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Affiliation(s)
- Klára Kosová
- Laboratory of Plant Stress Biology and Biotechnology, Division of Crop Genetics and Breeding, Crop Research Institute, Drnovská 507/73, 16106 Prague, Czech Republic.
| | - Pavel Vítámvás
- Laboratory of Plant Stress Biology and Biotechnology, Division of Crop Genetics and Breeding, Crop Research Institute, Drnovská 507/73, 16106 Prague, Czech Republic.
| | - Milan Oldřich Urban
- Laboratory of Plant Stress Biology and Biotechnology, Division of Crop Genetics and Breeding, Crop Research Institute, Drnovská 507/73, 16106 Prague, Czech Republic.
| | - Miroslav Klíma
- Laboratory of Plant Stress Biology and Biotechnology, Division of Crop Genetics and Breeding, Crop Research Institute, Drnovská 507/73, 16106 Prague, Czech Republic.
| | - Amitava Roy
- Research Institute of Agricultural Engineering, Drnovská 507, 16106 Prague, Czech Republic.
| | - Ilja Tom Prášil
- Laboratory of Plant Stress Biology and Biotechnology, Division of Crop Genetics and Breeding, Crop Research Institute, Drnovská 507/73, 16106 Prague, Czech Republic.
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