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Chen CW, Tsai CF, Lin MH, Lin SY, Hsu CC. Suspension Trapping-Based Sample Preparation Workflow for In-Depth Plant Phosphoproteomics. Anal Chem 2023; 95:12232-12239. [PMID: 37552764 DOI: 10.1021/acs.analchem.3c00786] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2023]
Abstract
Plant phosphoproteomics provides a global view of phosphorylation-mediated signaling in plants; however, it demands high-throughput methods with sensitive detection and accurate quantification. Despite the widespread use of protein precipitation for removing contaminants and improving sample purity, it limits the sensitivity and throughput of plant phosphoproteomic analysis. The multiple handling steps involved in protein precipitation lead to sample loss and process variability. Herein, we developed an approach based on suspension trapping (S-Trap), termed tandem S-Trap-IMAC (immobilized metal ion affinity chromatography), by integrating an S-Trap micro-column with a Fe-IMAC tip. Compared with a precipitation-based workflow, the tandem S-Trap-IMAC method deepened the coverage of the Arabidopsis (Arabidopsis thaliana) phosphoproteome by more than 30%, with improved number of multiply phosphorylated peptides, quantification accuracy, and short sample processing time. We applied the tandem S-Trap-IMAC method for studying abscisic acid (ABA) signaling in Arabidopsis seedlings. We thus discovered that a significant proportion of the phosphopeptides induced by ABA are multiply phosphorylated peptides, indicating their importance in early ABA signaling and quantified several key phosphorylation sites on core ABA signaling components across four time points. Our results show that the optimized workflow aids high-throughput phosphoproteome profiling of low-input plant samples.
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Affiliation(s)
- Chin-Wen Chen
- Institution of Plant and Microbial Biology, Academia Sinica, Taipei 115201, Taiwan
| | - Chia-Feng Tsai
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Miao-Hsia Lin
- Department of Microbiology, College of Medicine, National Taiwan University, Taipei 100233, Taiwan
| | - Shu-Yu Lin
- Academia Sinica Common Mass Spectrometry Facilities for Proteomics and Protein Modification Analysis, Academia Sinica, Taipei 115201, Taiwan
| | - Chuan-Chih Hsu
- Institution of Plant and Microbial Biology, Academia Sinica, Taipei 115201, Taiwan
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Ni L, Wang Q, Chen C, Wang S, Shen T, Jiang J, Cui Z, Li K, Yang Q, Jiang M. OsDMI3-mediated OsUXS3 phosphorylation improves oxidative stress tolerance by modulating OsCATB protein abundance in rice. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:1087-1101. [PMID: 35348292 DOI: 10.1111/jipb.13255] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 03/27/2022] [Indexed: 06/14/2023]
Abstract
Calcium (Ca2+ )/calmodulin (CaM)-dependent protein kinase (CCaMK) is an important positive regulator of antioxidant defenses and tolerance against oxidative stress. However, the underlying molecular mechanisms are largely unknown. Here, we report that the rice (Oryza sativa) CCaMK (OsDMI3) physically interacts with and phosphorylates OsUXS3, a cytosol-localized UDP-xylose synthase. Genetic and biochemical evidence demonstrated that OsUXS3 acts downstream of OsDMI3 to enhance the oxidative stress tolerance conferred by higher catalase (CAT) activity. Indeed, OsUXS3 interacted with CAT isozyme B (OsCATB), and this interaction was required to increase OsCATB protein abundance under oxidative stress conditions. Furthermore, we showed that OsDMI3 phosphorylates OsUXS3 on residue Ser-245, thereby further promoting the interaction between OsUXS3 and OsCATB. Our results indicate that OsDMI3 promotes the association of OsUXS3 with OsCATB to enhance CAT activity under oxidative stress. These findings reveal OsUXS3 as a direct target of OsDMI3 and demonstrate its involvement in antioxidant defense.
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Affiliation(s)
- Lan Ni
- College of Life Sciences, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qingwen Wang
- College of Life Sciences, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Chao Chen
- College of Life Sciences, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shuang Wang
- College of Life Sciences, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Tao Shen
- College of Life Sciences, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jingjing Jiang
- College of Life Sciences, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhenzhen Cui
- College of Life Sciences, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Kaiyue Li
- College of Life Sciences, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qiqing Yang
- College of Life Sciences, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Mingyi Jiang
- College of Life Sciences, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Hunan Agricultural University, Changsha, 410128, China
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Abstract
Mass spectrometry (MS)-based phosphoproteomics is a powerful tool for investigating cell signaling, yet it remains challenging to study plant phosphoproteomes due to the low yield of cell lysis and high complexity of plant lysate. Here we report a streamlined sample preparation workflow to analyze plant phosphoproteomes in a high-throughput manner. This workflow addresses the problem of low yield in the lysis step and eliminates the interferences of pigments and metabolites in plant lysate. Integrating chemical labeling and high pH reverse phase fractionation with this workflow achieves in-depth phosphoproteomic coverage. Notably, the scalability of this approach is demonstrated by systematically analyzing the effect of long-term cold stress in the perturbation of the tomato phosphoproteome. Identification of more than 30,000 phosphopeptides from tomato leaves and more than 5000 kinase-substrate pairs from Arabidopsis create the largest phosphoproteomic and signaling network resource to date.
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Chen M, Ni L, Chen J, Sun M, Qin C, Zhang G, Zhang A, Jiang M. Rice calcium/calmodulin-dependent protein kinase directly phosphorylates a mitogen-activated protein kinase kinase to regulate abscisic acid responses. THE PLANT CELL 2021; 33:1790-1812. [PMID: 33630095 PMCID: PMC8254507 DOI: 10.1093/plcell/koab071] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 02/15/2021] [Indexed: 05/05/2023]
Abstract
Calcium (Ca2+)/calmodulin (CaM)-dependent protein kinase (CCaMK) is an important positive regulator of abscisic acid (ABA) and abiotic stress signaling in plants and is believed to act upstream of mitogen-activated protein kinase (MAPK) in ABA signaling. However, it is unclear how CCaMK activates MAPK in ABA signaling. Here, we show that OsDMI3, a rice (Oryza sativa) CCaMK, directly interacts with and phosphorylates OsMKK1, a MAPK kinase (MKK) in rice, in vitro and in vivo. OsDMI3 was found to directly phosphorylate Thr-25 in the N-terminus of OsMKK1, and this Thr-25 phosphorylation is OsDMI3-specific in ABA signaling. The activation of OsMKK1 and its downstream kinase OsMPK1 is dependent on Thr-25 phosphorylation of OsMKK1 in ABA signaling. Moreover, ABA treatment induces phosphorylation in the activation loop of OsMKK1, and the two phosphorylations, in the N-terminus and in the activation loop, are independent. Further analyses revealed that OsDMI3-mediated phosphorylation of OsMKK1 positively regulates ABA responses in seed germination, root growth, and tolerance to both water stress and oxidative stress. Our results indicate that OsMKK1 is a direct target of OsDMI3, and OsDMI3-mediated phosphorylation of OsMKK1 plays an important role in activating the MAPK cascade and ABA signaling.
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Affiliation(s)
- Min Chen
- College of Life Sciences, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Lan Ni
- College of Life Sciences, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Jing Chen
- College of Life Sciences, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Manman Sun
- College of Life Sciences, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Caihua Qin
- College of Life Sciences, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Gang Zhang
- College of Life Sciences, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Aying Zhang
- College of Life Sciences, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Mingyi Jiang
- College of Life Sciences, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Hunan Agricultural University, Changsha 410128, China
- Author for correspondence:
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Ghatak A, Chaturvedi P, Weckwerth W. Cereal Crop Proteomics: Systemic Analysis of Crop Drought Stress Responses Towards Marker-Assisted Selection Breeding. FRONTIERS IN PLANT SCIENCE 2017; 8:757. [PMID: 28626463 PMCID: PMC5454074 DOI: 10.3389/fpls.2017.00757] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Sustainable crop production is the major challenge in the current global climate change scenario. Drought stress is one of the most critical abiotic factors which negatively impact crop productivity. In recent years, knowledge about molecular regulation has been generated to understand drought stress responses. For example, information obtained by transcriptome analysis has enhanced our knowledge and facilitated the identification of candidate genes which can be utilized for plant breeding. On the other hand, it becomes more and more evident that the translational and post-translational machinery plays a major role in stress adaptation, especially for immediate molecular processes during stress adaptation. Therefore, it is essential to measure protein levels and post-translational protein modifications to reveal information about stress inducible signal perception and transduction, translational activity and induced protein levels. This information cannot be revealed by genomic or transcriptomic analysis. Eventually, these processes will provide more direct insight into stress perception then genetic markers and might build a complementary basis for future marker-assisted selection of drought resistance. In this review, we survey the role of proteomic studies to illustrate their applications in crop stress adaptation analysis with respect to productivity. Cereal crops such as wheat, rice, maize, barley, sorghum and pearl millet are discussed in detail. We provide a comprehensive and comparative overview of all detected protein changes involved in drought stress in these crops and have summarized existing knowledge into a proposed scheme of drought response. Based on a recent proteome study of pearl millet under drought stress we compare our findings with wheat proteomes and another recent study which defined genetic marker in pearl millet.
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Affiliation(s)
- Arindam Ghatak
- Department of Ecogenomics and Systems Biology, University of ViennaVienna, Austria
| | - Palak Chaturvedi
- Department of Ecogenomics and Systems Biology, University of ViennaVienna, Austria
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology, University of ViennaVienna, Austria
- Vienna Metabolomics Center, University of ViennaVienna, Austria
- *Correspondence: Wolfram Weckwerth
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Quantitative iTRAQ-based proteomic analysis of phosphoproteins and ABA-regulated phosphoproteins in maize leaves under osmotic stress. Sci Rep 2015; 5:15626. [PMID: 26503333 PMCID: PMC4650667 DOI: 10.1038/srep15626] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 09/29/2015] [Indexed: 11/18/2022] Open
Abstract
Abscisic acid (ABA) regulates various developmental processes and stress responses in plants.
Protein phosphorylation/dephosphorylation is a central post-translational modification (PTM) in ABA
signaling. However, the phosphoproteins regulated by ABA under osmotic stress remain unknown in
maize. In this study, maize mutant vp5 (deficient in ABA biosynthesis) and wild-type
Vp5 were used to identify leaf phosphoproteins regulated by ABA under osmotic stress. Up to
4052 phosphopeptides, corresponding to 3017 phosphoproteins, were identified by Multiplex run
iTRAQ-based quantitative proteomic and LC-MS/MS methods. The 4052 phosphopeptides contained 5723
non-redundant phosphosites; 512 phosphopeptides (379 in Vp5, 133 in vp5) displayed at
least a 1.5-fold change of phosphorylation level under osmotic stress, of which 40 shared common in
both genotypes and were differentially regulated by ABA. Comparing the signaling pathways involved
in vp5 response to osmotic stress and those that in Vp5, indicated that ABA played a
vital role in regulating these pathways related to mRNA synthesis, protein synthesis and
photosynthesis. Our results provide a comprehensive dataset of phosphopeptides and phosphorylation
sites regulated by ABA in maize adaptation to osmotic stress. This will be helpful to elucidate the
ABA-mediate mechanism of maize endurance to drought by triggering phosphorylation or
dephosphorylation cascades.
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Yoshida T, Mogami J, Yamaguchi-Shinozaki K. Omics Approaches Toward Defining the Comprehensive Abscisic Acid Signaling Network in Plants. PLANT & CELL PHYSIOLOGY 2015; 56:1043-52. [PMID: 25917608 DOI: 10.1093/pcp/pcv060] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 04/13/2015] [Indexed: 05/19/2023]
Abstract
ABA is a plant hormone that plays crucial roles in controlling cellular and physiological responses to osmotic stress and in developmental processes. Endogenous ABA levels are increased in response to a decrease in water availability in cells, and ABA sensing and signaling are thought to be mediated according to the current model established in Arabidopsis thaliana, which involves pyrabactin resistance 1 (PYR)/PYR1-like (PYL)/regulatory components of ABA receptor (RCAR), protein phosphatase 2C (PP2C) and sucrose non-fermenting-1 (SNF1)-related protein kinase 2 (SnRK2). These core components of ABA signaling have a pivotal role in stress-responsive gene expression and stomatal regulation. However, because a limited number of their upstream and downstream factors have been characterized, it is still difficult to define the comprehensive network of ABA signaling in plants. This review focuses on current progress in the study of PYR/PYL/RCARs, PP2Cs and SnRK2s, with particular emphasis on omics approaches, such as interactome and phosphoproteome studies. Moreover, the role of ABA in plant growth and development is discussed based on recent metabolomic profiling studies.
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Affiliation(s)
- Takuya Yoshida
- Laboratory of Plant Molecular Physiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-8657 Japan
| | - Junro Mogami
- Laboratory of Plant Molecular Physiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-8657 Japan
| | - Kazuko Yamaguchi-Shinozaki
- Laboratory of Plant Molecular Physiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-8657 Japan
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