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Sang T, Chen CW, Lin Z, Ma Y, Du Y, Lin PY, Hadisurya M, Zhu JK, Lang Z, Tao WA, Hsu CC, Wang P. DIA-Based Phosphoproteomics Identifies Early Phosphorylation Events in Response to EGTA and Mannitol in Arabidopsis. Mol Cell Proteomics 2024; 23:100804. [PMID: 38901673 DOI: 10.1016/j.mcpro.2024.100804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 04/19/2024] [Accepted: 06/12/2024] [Indexed: 06/22/2024] Open
Abstract
Osmotic stress significantly hampers plant growth and crop yields, emphasizing the need for a thorough comprehension of the underlying molecular responses. Previous research has demonstrated that osmotic stress rapidly induces calcium influx and signaling, along with the activation of a specific subset of protein kinases, notably the Raf-like protein (RAF)-sucrose nonfermenting-1-related protein kinase 2 (SnRK2) kinase cascades within minutes. However, the intricate interplay between calcium signaling and the activation of RAF-SnRK2 kinase cascades remains elusive. Here, in this study, we discovered that Raf-like protein (RAF) kinases undergo hyperphosphorylation in response to osmotic shocks. Intriguingly, treatment with the calcium chelator EGTA robustly activates RAF-SnRK2 cascades, mirroring the effects of osmotic treatment. Utilizing high-throughput data-independent acquisition-based phosphoproteomics, we unveiled the global impact of EGTA on protein phosphorylation. Beyond the activation of RAFs and SnRK2s, EGTA treatment also activates mitogen-activated protein kinase cascades, Calcium-dependent protein kinases, and receptor-like protein kinases, etc. Through overlapping assays, we identified potential roles of mitogen-activated protein kinase kinase kinase kinases and receptor-like protein kinases in the osmotic stress-induced activation of RAF-SnRK2 cascades. Our findings illuminate the regulation of phosphorylation and cellular events by Ca2+ signaling, offering insights into the (exocellular) Ca2+ deprivation during early hyperosmolality sensing and signaling.
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Affiliation(s)
- Tian Sang
- Institute of Advanced Biotechnology and School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Chin-Wen Chen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Zhen Lin
- Institute of Advanced Biotechnology and School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Yu Ma
- Institute of Advanced Biotechnology and School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Yanyan Du
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, USA
| | - Pei-Yi Lin
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Marco Hadisurya
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, USA
| | - Jian-Kang Zhu
- Institute of Advanced Biotechnology and School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Zhaobo Lang
- Institute of Advanced Biotechnology and School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - W Andy Tao
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, USA; Department of Chemistry, Purdue University, West Lafayette, Indiana, USA; Purdue Institute for Cancer Research, Purdue University, West Lafayette, Indiana, USA
| | - Chuan-Chih Hsu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan.
| | - Pengcheng Wang
- Institute of Advanced Biotechnology and School of Medicine, Southern University of Science and Technology, Shenzhen, China.
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Chen CW, Lin PY, Lai YM, Lin MH, Lin SY, Hsu CC. TIMAHAC: Streamlined Tandem IMAC-HILIC Workflow for Simultaneous and High-Throughput Plant Phosphoproteomics and N-glycoproteomics. Mol Cell Proteomics 2024; 23:100762. [PMID: 38608839 PMCID: PMC11098956 DOI: 10.1016/j.mcpro.2024.100762] [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: 11/30/2023] [Revised: 03/29/2024] [Accepted: 04/03/2024] [Indexed: 04/14/2024] Open
Abstract
Protein post-translational modifications (PTMs) are crucial in plant cellular processes, particularly in protein folding and signal transduction. N-glycosylation and phosphorylation are notably significant PTMs, playing essential roles in regulating plant responses to environmental stimuli. However, current sequential enrichment methods for simultaneous analysis of phosphoproteome and N-glycoproteome are labor-intensive and time-consuming, limiting their throughput. Addressing this challenge, this study introduces a novel tandem S-Trap-IMAC-HILIC (S-Trap: suspension trapping; IMAC: immobilized metal ion affinity chromatography; HILIC: hydrophilic interaction chromatography) strategy, termed TIMAHAC, for simultaneous analysis of plant phosphoproteomics and N-glycoproteomics. This approach integrates IMAC and HILIC into a tandem tip format, streamlining the enrichment process of phosphopeptides and N-glycopeptides. The key innovation lies in the use of a unified buffer system and an optimized enrichment sequence to enhance efficiency and reproducibility. The applicability of TIMAHAC was demonstrated by analyzing the Arabidopsis phosphoproteome and N-glycoproteome in response to abscisic acid (ABA) treatment. Up to 1954 N-glycopeptides and 11,255 phosphopeptides were identified from Arabidopsis, indicating its scalability for plant tissues. Notably, distinct perturbation patterns were observed in the phosphoproteome and N-glycoproteome, suggesting their unique contributions to ABA response. Our results reveal that TIMAHAC offers a comprehensive approach to studying complex regulatory mechanisms and PTM interplay in plant biology, paving the way for in-depth investigations into plant signaling networks.
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Affiliation(s)
- Chin-Wen Chen
- Institution of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Pei-Yi Lin
- Institution of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Ying-Mi Lai
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Miao-Hsia Lin
- Department of Microbiology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Shu-Yu Lin
- Academia Sinica Common Mass Spectrometry Facilities for Proteomics and Protein Modification Analysis, Academia Sinica, Taipei, Taiwan
| | - Chuan-Chih Hsu
- Institution of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan.
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Bortel P, Piga I, Koenig C, Gerner C, Martinez-Val A, Olsen JV. Systematic Optimization of Automated Phosphopeptide Enrichment for High-Sensitivity Phosphoproteomics. Mol Cell Proteomics 2024; 23:100754. [PMID: 38548019 PMCID: PMC11087715 DOI: 10.1016/j.mcpro.2024.100754] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 03/08/2024] [Accepted: 03/22/2024] [Indexed: 05/05/2024] Open
Abstract
Improving coverage, robustness, and sensitivity is crucial for routine phosphoproteomics analysis by single-shot liquid chromatography-tandem mass spectrometry (LC-MS/MS) from minimal peptide inputs. Here, we systematically optimized key experimental parameters for automated on-bead phosphoproteomics sample preparation with a focus on low-input samples. Assessing the number of identified phosphopeptides, enrichment efficiency, site localization scores, and relative enrichment of multiply-phosphorylated peptides pinpointed critical variables influencing the resulting phosphoproteome. Optimizing glycolic acid concentration in the loading buffer, percentage of ammonium hydroxide in the elution buffer, peptide-to-beads ratio, binding time, sample, and loading buffer volumes allowed us to confidently identify >16,000 phosphopeptides in half-an-hour LC-MS/MS on an Orbitrap Exploris 480 using 30 μg of peptides as starting material. Furthermore, we evaluated how sequential enrichment can boost phosphoproteome coverage and showed that pooling fractions into a single LC-MS/MS analysis increased the depth. We also present an alternative phosphopeptide enrichment strategy based on stepwise addition of beads thereby boosting phosphoproteome coverage by 20%. Finally, we applied our optimized strategy to evaluate phosphoproteome depth with the Orbitrap Astral MS using a cell dilution series and were able to identify >32,000 phosphopeptides from 0.5 million HeLa cells in half-an-hour LC-MS/MS using narrow-window data-independent acquisition (nDIA).
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Affiliation(s)
- Patricia Bortel
- Faculty of Chemistry, Department of Analytical Chemistry, University of Vienna, Vienna, Austria; Vienna Doctoral School in Chemistry (DoSChem), University of Vienna, Vienna, Austria
| | - Ilaria Piga
- Proteomics Program, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Claire Koenig
- Proteomics Program, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Christopher Gerner
- Faculty of Chemistry, Department of Analytical Chemistry, University of Vienna, Vienna, Austria; Joint Metabolome Facility, University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Ana Martinez-Val
- Proteomics Program, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark.
| | - Jesper V Olsen
- Proteomics Program, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark.
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Duan X, Zhang Y, Huang X, Ma X, Gao H, Wang Y, Xiao Z, Huang C, Wang Z, Li B, Yang W, Wang Y. GreenPhos, a universal method for in-depth measurement of plant phosphoproteomes with high quantitative reproducibility. MOLECULAR PLANT 2024; 17:199-213. [PMID: 38018035 DOI: 10.1016/j.molp.2023.11.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 11/08/2023] [Accepted: 11/25/2023] [Indexed: 11/30/2023]
Abstract
Protein phosphorylation regulates a variety of important cellular and physiological processes in plants. In-depth profiling of plant phosphoproteomes has been more technically challenging than that of animal phosphoproteomes. This is largely due to the need to improve protein extraction efficiency from plant cells, which have a dense cell wall, and to minimize sample loss resulting from the stringent sample clean-up steps required for the removal of a large amount of biomolecules interfering with phosphopeptide purification and mass spectrometry analysis. To this end, we developed a method with a streamlined workflow for highly efficient purification of phosphopeptides from tissues of various green organisms including Arabidopsis, rice, tomato, and Chlamydomonas reinhardtii, enabling in-depth identification with high quantitative reproducibility of about 11 000 phosphosites, the greatest depth achieved so far with single liquid chromatography-mass spectrometry (LC-MS) runs operated in a data-dependent acquisition (DDA) mode. The mainstay features of the method are the minimal sample loss achieved through elimination of sample clean-up before protease digestion and of desalting before phosphopeptide enrichment and hence the dramatic increases of time- and cost-effectiveness. The method, named GreenPhos, combined with single-shot LC-MS, enabled in-depth quantitative identification of Arabidopsis phosphoproteins, including differentially phosphorylated spliceosomal proteins, at multiple time points during salt stress and a number of kinase substrate motifs. GreenPhos is expected to serve as a universal method for purification of plant phosphopeptides, which, if samples are further fractionated and analyzed by multiple LC-MS runs, could enable measurement of plant phosphoproteomes with an unprecedented depth using a given mass spectrometry technology.
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Affiliation(s)
- Xiaoxiao Duan
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuanya Zhang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiahe Huang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiao Ma
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hui Gao
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yan Wang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhen Xiao
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chengcheng Huang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhongshu Wang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bolong Li
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenqiang Yang
- University of Chinese Academy of Sciences, Beijing 100049, China; Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Yingchun Wang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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5
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Tsai CF, Hsu CC, Wang YT, Kim H, Liu T. A Tip-Based Workflow for Sensitive IMAC-Based Low Nanogram Level Phosphoproteomics. Methods Mol Biol 2024; 2823:129-140. [PMID: 39052218 DOI: 10.1007/978-1-0716-3922-1_9] [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] [Indexed: 07/27/2024]
Abstract
Analyzing the phosphoproteome at nanoscale poses a significant challenge, mainly due to the substantial sample loss from nonspecific surface adsorption during the enrichment of low stoichiometric phosphopeptides. Here, we describe a tandem tip-based phosphoproteomics sample preparation method capable of sequential sample cleanup and enrichment without the need for additional sample transfer, thereby minimizing sample loss. Integration of this method to our recently developed SOP (surfactant-assisted one-pot sample preparation) and iBASIL (improved boosting to amplify signal with isobaric labeling) approaches creates a streamlined workflow, enabling sensitive, high-throughput nanoscale phosphoproteomics measurements.
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Affiliation(s)
- Chia-Feng Tsai
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Chuan-Chih Hsu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Yi-Ting Wang
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Hyeyoon Kim
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.
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Lin YH, Xu MY, Hsu CC, Damei FA, Lee HC, Tsai WL, Hoang CV, Chiang YR, Ma LS. Ustilago maydis PR-1-like protein has evolved two distinct domains for dual virulence activities. Nat Commun 2023; 14:5755. [PMID: 37716995 PMCID: PMC10505147 DOI: 10.1038/s41467-023-41459-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 09/05/2023] [Indexed: 09/18/2023] Open
Abstract
The diversification of effector function, driven by a co-evolutionary arms race, enables pathogens to establish compatible interactions with hosts. Structurally conserved plant pathogenesis-related PR-1 and PR-1-like (PR-1L) proteins are involved in plant defense and fungal virulence, respectively. It is unclear how fungal PR-1L counters plant defense. Here, we show that Ustilago maydis UmPR-1La and yeast ScPRY1, with conserved phenolic resistance functions, are Ser/Thr-rich region mediated cell-surface localization proteins. However, UmPR-1La has gained specialized activity in sensing phenolics and eliciting hyphal-like formation to guide fungal growth in plants. Additionally, U. maydis hijacks maize cathepsin B-like 3 (CatB3) to release functional CAPE-like peptides by cleaving UmPR-1La's conserved CNYD motif, subverting plant CAPE-primed immunity and promoting fungal virulence. Surprisingly, CatB3 avoids cleavage of plant PR-1s, despite the presence of the same conserved CNYD motif. Our work highlights that UmPR-1La has acquired additional dual roles to suppress plant defense and sustain the infection process of fungal pathogens.
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Affiliation(s)
- Yu-Han Lin
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 115201, Taiwan
| | - Meng-Yun Xu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 115201, Taiwan
| | - Chuan-Chih Hsu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 115201, Taiwan
| | | | - Hui-Chun Lee
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 115201, Taiwan
| | - Wei-Lun Tsai
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 115201, Taiwan
| | - Cuong V Hoang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 115201, Taiwan
| | - Yin-Ru Chiang
- Biodiversity Research Center, Academia Sinica, Taipei, 115201, Taiwan
| | - Lay-Sun Ma
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 115201, Taiwan.
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