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Yang N, Ren J, Dai S, Wang K, Leung M, Lu Y, An Y, Burlingame A, Xu S, Wang Z, Yu W, Li N. The Quantitative Biotinylproteomics Studies Reveal a WInd-Related Kinase 1 (Raf-Like Kinase 36) Functioning as an Early Signaling Component in Wind-Induced Thigmomorphogenesis and Gravitropism. Mol Cell Proteomics 2024; 23:100738. [PMID: 38364992 PMCID: PMC10951710 DOI: 10.1016/j.mcpro.2024.100738] [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: 08/04/2023] [Revised: 01/31/2024] [Accepted: 02/08/2024] [Indexed: 02/18/2024] Open
Abstract
Wind is one of the most prevalent environmental forces entraining plants to develop various mechano-responses, collectively called thigmomorphogenesis. Largely unknown is how plants transduce these versatile wind force signals downstream to nuclear events and to the development of thigmomorphogenic phenotype or anemotropic response. To identify molecular components at the early steps of the wind force signaling, two mechanical signaling-related phosphoproteins, identified from our previous phosphoproteomic study of Arabidopsis touch response, mitogen-activated protein kinase kinase 1 (MKK1) and 2 (MKK2), were selected for performing in planta TurboID (ID)-based quantitative proximity-labeling (PL) proteomics. This quantitative biotinylproteomics was separately performed on MKK1-ID and MKK2-ID transgenic plants, respectively, using the genetically engineered TurboID biotin ligase expression transgenics as a universal control. This unique PTM proteomics successfully identified 11 and 71 MKK1 and MKK2 putative interactors, respectively. Biotin occupancy ratio (BOR) was found to be an alternative parameter to measure the extent of proximity and specificity between the proximal target proteins and the bait fusion protein. Bioinformatics analysis of these biotinylprotein data also found that TurboID biotin ligase favorably labels the loop region of target proteins. A WInd-Related Kinase 1 (WIRK1), previously known as rapidly accelerated fibrosarcoma (Raf)-like kinase 36 (RAF36), was found to be a putative common interactor for both MKK1 and MKK2 and preferentially interacts with MKK2. Further molecular biology studies of the Arabidopsis RAF36 kinase found that it plays a role in wind regulation of the touch-responsive TCH3 and CML38 gene expression and the phosphorylation of a touch-regulated PATL3 phosphoprotein. Measurement of leaf morphology and shoot gravitropic response of wirk1 (raf36) mutant revealed that the WIRK1 gene is involved in both wind-triggered rosette thigmomorphogenesis and gravitropism of Arabidopsis stems, suggesting that the WIRK1 (RAF36) protein probably functioning upstream of both MKK1 and MKK2 and that it may serve as the crosstalk point among multiple mechano-signal transduction pathways mediating both wind mechano-response and gravitropism.
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Affiliation(s)
- Nan Yang
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Jia Ren
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Shuaijian Dai
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Kai Wang
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Manhin Leung
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Yinglin Lu
- Institute of Nanfan and Seed Industry, Guangdong Academy of Sciences, Guangzhou, Guangdong, China
| | - Yuxing An
- Institute of Nanfan and Seed Industry, Guangdong Academy of Sciences, Guangzhou, Guangdong, China
| | - Al Burlingame
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, USA
| | - Shouling Xu
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, USA
| | - Zhiyong Wang
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, USA
| | - Weichuan Yu
- Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China.
| | - Ning Li
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China; Shenzhen Research Institute, The Hong Kong University of Science and Technology, Shenzhen, Guangdong, China.
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Chen CY, Selvaraj P, Naqvi NI. Functional analysis of auxin derived from a symbiotic mycobiont. FRONTIERS IN PLANT SCIENCE 2023; 14:1216680. [PMID: 37745999 PMCID: PMC10515717 DOI: 10.3389/fpls.2023.1216680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 08/16/2023] [Indexed: 09/26/2023]
Abstract
The biosynthesis of auxin or indole-3-acetic acid by microorganisms has a major impact on plant-microbe interactions. Several beneficial microbiota are known to produce auxin, which largely influences root development and growth in the host plants. Akin to findings in rhizobacteria, recent studies have confirmed the production of auxin by plant growth-promoting fungi too. Here, we show that Penicillium citrinum isolate B9 produces auxin as deduced by liquid chromatography tandem-mass spectrometry analysis. Such fungal auxin is secreted and contributes directly to enhanced root and shoot development and overall plant growth in Arabidopsis thaliana. Furthermore, auxin production by P. citrinum likely involves more than one tryptophan-dependent pathway. Using auxin biosynthesis inhibitor L-Kynurenine, we show that the indole-3-pyruvate pathway might be one of the key biosynthetic routes involved in such auxin production. Confocal microscopy of the DR5rev:GFP Arabidopsis reporter line helped demonstrate that P. citrunum B9-derived auxin is biologically active and is able to significantly enhance auxin signaling in roots during such improved root growth and plant development. Furthermore, the phenotypic growth defects arising from impaired auxin signaling in Arabidopsis taa1 mutant or upon L-Kynurenine treatment of wild-type Arabidopsis seedlings could be significantly alleviated by fungus B9-derived auxin, thus suggesting its positive role in plant growth promotion. Collectively, our results provide clear evidence that the production of auxin is one of the main mechanisms involved in induction of the beneficial plant growth by P. citrinum.
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Affiliation(s)
- Cheng-Yen Chen
- Fungal Patho-Biology, Temasek Life Sciences Laboratory, Singapore, Singapore
| | | | - Naweed I. Naqvi
- Fungal Patho-Biology, Temasek Life Sciences Laboratory, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
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Dai S, Liu S, Zhou C, Yu F, Zhu G, Zhang W, Deng H, Burlingame A, Yu W, Wang T, Li N. Capturing the hierarchically assorted modules of protein-protein interactions in the organized nucleome. MOLECULAR PLANT 2023; 16:930-961. [PMID: 36960533 DOI: 10.1016/j.molp.2023.03.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 02/16/2023] [Accepted: 03/21/2023] [Indexed: 05/04/2023]
Abstract
Nuclear proteins are major constituents and key regulators of nucleome topological organization and manipulators of nuclear events. To decipher the global connectivity of nuclear proteins and the hierarchically organized modules of their interactions, we conducted two rounds of cross-linking mass spectrometry (XL-MS) analysis, one of which followed a quantitative double chemical cross-linking mass spectrometry (in vivoqXL-MS) workflow, and identified 24,140 unique crosslinks in total from the nuclei of soybean seedlings. This in vivo quantitative interactomics enabled the identification of 5340 crosslinks that can be converted into 1297 nuclear protein-protein interactions (PPIs), 1220 (94%) of which were non-confirmative (or novel) nuclear PPIs compared with those in repositories. There were 250 and 26 novel interactors of histones and the nucleolar box C/D small nucleolar ribonucleoprotein complex, respectively. Modulomic analysis of orthologous Arabidopsis PPIs produced 27 and 24 master nuclear PPI modules (NPIMs) that contain the condensate-forming protein(s) and the intrinsically disordered region-containing proteins, respectively. These NPIMs successfully captured previously reported nuclear protein complexes and nuclear bodies in the nucleus. Surprisingly, these NPIMs were hierarchically assorted into four higher-order communities in a nucleomic graph, including genome and nucleolus communities. This combinatorial pipeline of 4C quantitative interactomics and PPI network modularization revealed 17 ethylene-specific module variants that participate in a broad range of nuclear events. The pipeline was able to capture both nuclear protein complexes and nuclear bodies, construct the topological architectures of PPI modules and module variants in the nucleome, and probably map the protein compositions of biomolecular condensates.
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Affiliation(s)
- Shuaijian Dai
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Shichang Liu
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Chen Zhou
- Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Fengchao Yu
- Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Guang Zhu
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Wenhao Zhang
- Tsinghua-Peking Joint Centre for Life Sciences, Centre for Structural Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China
| | - Haiteng Deng
- Tsinghua-Peking Joint Centre for Life Sciences, Centre for Structural Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China
| | - Al Burlingame
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - Weichuan Yu
- The HKUST Shenzhen-Hong Kong Collaborative Innovation Research Institute, Futian, Shenzhen, Guangdong 518057, China; Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China.
| | - Tingliang Wang
- Tsinghua-Peking Joint Centre for Life Sciences, Centre for Structural Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China.
| | - Ning Li
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China; Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Hong Kong, China; The HKUST Shenzhen-Hong Kong Collaborative Innovation Research Institute, Futian, Shenzhen, Guangdong 518057, China.
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Lee K, O'Reilly FJ. Cross-linking mass spectrometry for mapping protein complex topologies in situ. Essays Biochem 2023; 67:215-228. [PMID: 36734207 PMCID: PMC10070479 DOI: 10.1042/ebc20220168] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 01/03/2023] [Accepted: 01/05/2023] [Indexed: 02/04/2023]
Abstract
Cross-linking mass spectrometry has become an established technology to provide structural information on the topology and dynamics of protein complexes. Readily accessible workflows can provide detailed data on simplified systems, such as purified complexes. However, using this technology to study the structure of protein complexes in situ, such as in organelles, cells, and even tissues, is still a technological frontier. The complexity of these systems remains a considerable challenge, but there have been dramatic improvements in sample handling, data acquisition, and data processing. Here, we summarise these developments and describe the paths towards comprehensive and comparative structural interactomes by cross-linking mass spectrometry.
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Affiliation(s)
- Kitaik Lee
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute (NCI), Frederick, MD 21702-1201, U.S.A
| | - Francis J O'Reilly
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute (NCI), Frederick, MD 21702-1201, U.S.A
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Yan S, Bhawal R, Yin Z, Thannhauser TW, Zhang S. Recent advances in proteomics and metabolomics in plants. MOLECULAR HORTICULTURE 2022; 2:17. [PMID: 37789425 PMCID: PMC10514990 DOI: 10.1186/s43897-022-00038-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 06/20/2022] [Indexed: 10/05/2023]
Abstract
Over the past decade, systems biology and plant-omics have increasingly become the main stream in plant biology research. New developments in mass spectrometry and bioinformatics tools, and methodological schema to integrate multi-omics data have leveraged recent advances in proteomics and metabolomics. These progresses are driving a rapid evolution in the field of plant research, greatly facilitating our understanding of the mechanistic aspects of plant metabolisms and the interactions of plants with their external environment. Here, we review the recent progresses in MS-based proteomics and metabolomics tools and workflows with a special focus on their applications to plant biology research using several case studies related to mechanistic understanding of stress response, gene/protein function characterization, metabolic and signaling pathways exploration, and natural product discovery. We also present a projection concerning future perspectives in MS-based proteomics and metabolomics development including their applications to and challenges for system biology. This review is intended to provide readers with an overview of how advanced MS technology, and integrated application of proteomics and metabolomics can be used to advance plant system biology research.
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Affiliation(s)
- Shijuan Yan
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Ruchika Bhawal
- Proteomics and Metabolomics Facility, Institute of Biotechnology, Cornell University, 139 Biotechnology Building, 526 Campus Road, Ithaca, NY, 14853, USA
| | - Zhibin Yin
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | | | - Sheng Zhang
- Proteomics and Metabolomics Facility, Institute of Biotechnology, Cornell University, 139 Biotechnology Building, 526 Campus Road, Ithaca, NY, 14853, USA.
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Jiang P, Wang C, Diehl A, Viner R, Etienne C, Nandhikonda P, Foster L, Bomgarden RD, Liu F. A Membrane-Permeable and Immobilized Metal Affinity Chromatography (IMAC) Enrichable Cross-Linking Reagent to Advance In Vivo Cross-Linking Mass Spectrometry. Angew Chem Int Ed Engl 2022; 61:e202113937. [PMID: 34927332 PMCID: PMC9303249 DOI: 10.1002/anie.202113937] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Indexed: 11/29/2022]
Abstract
Cross-linking mass spectrometry (XL-MS) is an attractive method for the proteome-wide characterization of protein structures and interactions. Currently, the depth of in vivo XL-MS studies is lagging behind the established applications to cell lysates, because cross-linking reagents that can penetrate intact cells and strategies to enrich cross-linked peptides lack efficiency. To tackle these limitations, we have developed a phosphonate-containing cross-linker, tBu-PhoX, that efficiently permeates various biological membranes and can be robustly enriched using routine immobilized metal ion affinity chromatography. We have established a tBu-PhoX-based in vivo XL-MS approach that enables cross-links in intact human cells to be identified in high numbers with substantially reduced analysis time. Collectively, the developed cross-linker and XL-MS approach pave the way for the comprehensive XL-MS characterization of living systems.
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Affiliation(s)
- Pin‐Lian Jiang
- Department of Structural BiologyLeibniz-Forschungsinstitut für Molekulare Pharmakologie im Forschungsverbund Berlin e.V. (FMP)Campus Berlin-BuchRobert-Roessle-Str. 1013125BerlinGermany
| | - Cong Wang
- Department of Structural BiologyLeibniz-Forschungsinstitut für Molekulare Pharmakologie im Forschungsverbund Berlin e.V. (FMP)Campus Berlin-BuchRobert-Roessle-Str. 1013125BerlinGermany
| | - Anne Diehl
- Department of Structural BiologyLeibniz-Forschungsinstitut für Molekulare Pharmakologie im Forschungsverbund Berlin e.V. (FMP)Campus Berlin-BuchRobert-Roessle-Str. 1013125BerlinGermany
| | - Rosa Viner
- Thermo Fisher Scientific355 River Oaks PkwySan JoseCA 95134USA
| | - Chris Etienne
- Thermo Fisher Scientific3747N Meridian RdRockfordIL 61101USA
| | | | - Leigh Foster
- Thermo Fisher Scientific3747N Meridian RdRockfordIL 61101USA
| | | | - Fan Liu
- Department of Structural BiologyLeibniz-Forschungsinstitut für Molekulare Pharmakologie im Forschungsverbund Berlin e.V. (FMP)Campus Berlin-BuchRobert-Roessle-Str. 1013125BerlinGermany
- PCharité—Universitätsmedizin BerlinCharitépl. 110117BerlinGermany
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7
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Jiang P, Wang C, Diehl A, Viner R, Etienne C, Nandhikonda P, Foster L, Bomgarden RD, Liu F. A Membrane‐Permeable and Immobilized Metal Affinity Chromatography (IMAC) Enrichable Cross‐Linking Reagent to Advance In Vivo Cross‐Linking Mass Spectrometry. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202113937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Pin‐Lian Jiang
- Department of Structural Biology Leibniz-Forschungsinstitut für Molekulare Pharmakologie im Forschungsverbund Berlin e.V. (FMP) Campus Berlin-Buch Robert-Roessle-Str. 10 13125 Berlin Germany
| | - Cong Wang
- Department of Structural Biology Leibniz-Forschungsinstitut für Molekulare Pharmakologie im Forschungsverbund Berlin e.V. (FMP) Campus Berlin-Buch Robert-Roessle-Str. 10 13125 Berlin Germany
| | - Anne Diehl
- Department of Structural Biology Leibniz-Forschungsinstitut für Molekulare Pharmakologie im Forschungsverbund Berlin e.V. (FMP) Campus Berlin-Buch Robert-Roessle-Str. 10 13125 Berlin Germany
| | - Rosa Viner
- Thermo Fisher Scientific 355 River Oaks Pkwy San Jose CA 95134 USA
| | - Chris Etienne
- Thermo Fisher Scientific 3747N Meridian Rd Rockford IL 61101 USA
| | | | - Leigh Foster
- Thermo Fisher Scientific 3747N Meridian Rd Rockford IL 61101 USA
| | | | - Fan Liu
- Department of Structural Biology Leibniz-Forschungsinstitut für Molekulare Pharmakologie im Forschungsverbund Berlin e.V. (FMP) Campus Berlin-Buch Robert-Roessle-Str. 10 13125 Berlin Germany
- PCharité—Universitätsmedizin Berlin Charitépl. 1 10117 Berlin Germany
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Balotf S, Wilson R, Tegg RS, Nichols DS, Wilson CR. Shotgun Proteomics as a Powerful Tool for the Study of the Proteomes of Plants, Their Pathogens, and Plant-Pathogen Interactions. Proteomes 2022; 10:5. [PMID: 35225985 PMCID: PMC8883913 DOI: 10.3390/proteomes10010005] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/12/2022] [Accepted: 01/17/2022] [Indexed: 12/31/2022] Open
Abstract
The interaction between plants and pathogenic microorganisms is a multifaceted process mediated by both plant- and pathogen-derived molecules, including proteins, metabolites, and lipids. Large-scale proteome analysis can quantify the dynamics of proteins, biological pathways, and posttranslational modifications (PTMs) involved in the plant-pathogen interaction. Mass spectrometry (MS)-based proteomics has become the preferred method for characterizing proteins at the proteome and sub-proteome (e.g., the phosphoproteome) levels. MS-based proteomics can reveal changes in the quantitative state of a proteome and provide a foundation for understanding the mechanisms involved in plant-pathogen interactions. This review is intended as a primer for biologists that may be unfamiliar with the diverse range of methodology for MS-based shotgun proteomics, with a focus on techniques that have been used to investigate plant-pathogen interactions. We provide a summary of the essential steps required for shotgun proteomic studies of plants, pathogens and plant-pathogen interactions, including methods for protein digestion, identification, separation, and quantification. Finally, we discuss how protein PTMs may directly participate in the interaction between a pathogen and its host plant.
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Affiliation(s)
- Sadegh Balotf
- New Town Research Laboratories, Tasmanian Institute of Agriculture, University of Tasmania, New Town, TAS 7008, Australia; (S.B.); (R.S.T.)
| | - Richard Wilson
- Central Science Laboratory, University of Tasmania, Hobart, TAS 7001, Australia;
| | - Robert S. Tegg
- New Town Research Laboratories, Tasmanian Institute of Agriculture, University of Tasmania, New Town, TAS 7008, Australia; (S.B.); (R.S.T.)
| | - David S. Nichols
- Central Science Laboratory, University of Tasmania, Hobart, TAS 7001, Australia;
| | - Calum R. Wilson
- New Town Research Laboratories, Tasmanian Institute of Agriculture, University of Tasmania, New Town, TAS 7008, Australia; (S.B.); (R.S.T.)
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Sun T, Zhou X, Rao S, Liu J, Li L. Protein–protein interaction techniques to investigate post-translational regulation of carotenogenesis. Methods Enzymol 2022; 671:301-325. [DOI: 10.1016/bs.mie.2022.02.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Wang X, Jin S, Chang X, Li G, Zhang L, Jin S. Two interaction proteins between AtPHB6 and AtSOT12 regulate plant salt resistance through ROS signaling. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 169:70-80. [PMID: 34773804 DOI: 10.1016/j.plaphy.2021.11.001] [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: 08/11/2021] [Revised: 10/12/2021] [Accepted: 11/02/2021] [Indexed: 06/13/2023]
Abstract
In the past, the PHB gene function was mainly focused on anti-cell proliferation and antitumor effects. But the molecular mechanism of the PHB gene regarding saline and oxidative stresses is unclear. To study the role of AtPHB6 in salt and oxidative stress, AtPHB6 was cloned from A. thaliana. Bioinformatics analysis showed that AtPHB6 was closely related to AtPHB1 and AtPHB2, which are both type II PHB. RT-qPCR results indicated that the AtPHB6 in the leaves and roots of A. thaliana was obviously induced under different stress treatments. AtPHB6-overexpressing plants were larger and more lush than wild-type and mutant plants when placed under stress treatments during seed germination. The root length and fresh weight of AtPHB6 transgenic plants showed the best resistance compared to wild-type plants under different treatments, in contrast, the AtPHB6 mutants had the worst resistance during the seedling stage. AtSOT12 was an interacting protein of AtPHB6, which screened by yeast two-hybrid system. The interaction between the two proteins were further confirmed using in vitro pull-down experiments and in vivo BiFC experiments. Subcellular localization showed both AtPHB6 and AtSOT12 protein expressed in the nucleus and cytoplasm. The H2O2 content in both the transgenic AtPHB6 and AtSOT12 plants were lower than that in the wild type under stresses. Thus, AtPHB6 increased plant resistance to salt stress and interacted with the AtSOT12 protein.
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Affiliation(s)
- Xiaolu Wang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, 150040, China
| | - Shengxuan Jin
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, 150040, China; College of Forestry, Northeast Forestry University, Harbin, 150040, China
| | - Xu Chang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, 150040, China
| | - Guanrong Li
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, 150040, China
| | - Ling Zhang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, 150040, China
| | - Shumei Jin
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, 150040, China.
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Moradi A, Dai S, Wong EOY, Zhu G, Yu F, Lam HM, Wang Z, Burlingame A, Lin C, Afsharifar A, Yu W, Wang T, Li N. Isotopically Dimethyl Labeling-Based Quantitative Proteomic Analysis of Phosphoproteomes of Soybean Cultivars. Biomolecules 2021; 11:1218. [PMID: 34439883 PMCID: PMC8393417 DOI: 10.3390/biom11081218] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 08/05/2021] [Accepted: 08/06/2021] [Indexed: 12/29/2022] Open
Abstract
Isotopically dimethyl labeling was applied in a quantitative post-translational modification (PTM) proteomic study of phosphoproteomic changes in the drought responses of two contrasting soybean cultivars. A total of 9457 phosphopeptides were identified subsequently, corresponding to 4571 phosphoprotein groups and 3889 leading phosphoproteins, which contained nine kinase families consisting of 279 kinases. These phosphoproteins contained a total of 8087 phosphosites, 6106 of which were newly identified and constituted 54% of the current soybean phosphosite repository. These phosphosites were converted into the highly conserved kinase docking sites by bioinformatics analysis, which predicted six kinase families that matched with those newly found nine kinase families. The overly post-translationally modified proteins (OPP) occupies 2.1% of these leading phosphoproteins. Most of these OPPs are photoreceptors, mRNA-, histone-, and phospholipid-binding proteins, as well as protein kinase/phosphatases. The subgroup population distribution of phosphoproteins over the number of phosphosites of phosphoproteins follows the exponential decay law, Y = 4.13e-0.098X - 0.04. Out of 218 significantly regulated unique phosphopeptide groups, 188 phosphoproteins were regulated by the drought-tolerant cultivar under the water loss condition. These significantly regulated phosphoproteins (SRP) are mainly enriched in the biological functions of water transport and deprivation, methionine metabolic processes, photosynthesis/light reaction, and response to cadmium ion, osmotic stress, and ABA response. Seventeen and 15 SRPs are protein kinases/phosphatases and transcription factors, respectively. Bioinformatics analysis again revealed that three members of the calcium dependent protein kinase family (CAMK family), GmSRK2I, GmCIPK25, and GmAKINβ1 kinases, constitute a phosphor-relay-mediated signal transduction network, regulating ion channel activities and many nuclear events in this drought-tolerant cultivar, which presumably contributes to the development of the soybean drought tolerance under water deprivation process.
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Affiliation(s)
- Atieh Moradi
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong, China; (A.M.); (E.O.Y.W.); (G.Z.)
- Institute of Biotechnology, School of Agriculture, Shiraz University, Shiraz 71946-84471, Iran
| | - Shuaijian Dai
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Hong Kong, China;
| | - Emily Oi Ying Wong
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong, China; (A.M.); (E.O.Y.W.); (G.Z.)
| | - Guang Zhu
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong, China; (A.M.); (E.O.Y.W.); (G.Z.)
| | - Fengchao Yu
- Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Hong Kong, China;
| | - Hon-Ming Lam
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China;
| | - Zhiyong Wang
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA;
| | - Al Burlingame
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143, USA;
| | - Chengtao Lin
- Department of Molecular, Cell & Developmental Biology, University of California, Los Angeles, CA 90095, USA;
| | - Alireza Afsharifar
- Plant Virology Research Centre, School of Agriculture, Shiraz University, Shiraz 71946-84471, Iran;
| | - Weichuan Yu
- Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Hong Kong, China;
| | - Tingliang Wang
- Tsinghua-Peking Joint Centre for Life Sciences, Centre for Structural Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China
| | - Ning Li
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong, China; (A.M.); (E.O.Y.W.); (G.Z.)
- The HKUST Shenzhen Research Institut, Shenzhen 518057, China
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Mehta D, Krahmer J, Uhrig RG. Closing the protein gap in plant chronobiology. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:1509-1522. [PMID: 33783885 DOI: 10.1111/tpj.15254] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/19/2021] [Accepted: 03/23/2021] [Indexed: 06/12/2023]
Abstract
Our modern understanding of diel cell regulation in plants stems from foundational work in the late 1990s that analysed the dynamics of selected genes and mutants in Arabidopsis thaliana. The subsequent rise of transcriptomics technologies such as microarrays and RNA sequencing has substantially increased our understanding of anticipatory (circadian) and reactive (light- or dark-triggered) diel events in plants. However, it is also becoming clear that gene expression data fail to capture critical events in diel regulation that can only be explained by studying protein-level dynamics. Over the past decade, mass spectrometry technologies and quantitative proteomic workflows have significantly advanced, finally allowing scientists to characterise diel protein regulation at high throughput. Initial proteomic investigations suggest that the diel transcriptome and proteome generally lack synchrony and that the timing of daily regulatory events in plants is impacted by multiple levels of protein regulation (e.g., post-translational modifications [PTMs] and protein-protein interactions [PPIs]). Here, we highlight and summarise how the use of quantitative proteomics to elucidate diel plant cell regulation has advanced our understanding of these processes. We argue that this new understanding, coupled with the extraordinary developments in mass spectrometry technologies, demands greater focus on protein-level regulation of, and by, the circadian clock. This includes hitherto unexplored diel dynamics of protein turnover, PTMs, protein subcellular localisation and PPIs that can be masked by simple transcript- and protein-level changes. Finally, we propose new directions for how the latest advancements in quantitative proteomics can be utilised to answer outstanding questions in plant chronobiology.
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Affiliation(s)
- Devang Mehta
- Department of Biological Sciences, University of Alberta, Edmonton, Canada
| | - Johanna Krahmer
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - R Glen Uhrig
- Department of Biological Sciences, University of Alberta, Edmonton, Canada
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Armony G, Heck AJR, Wu W. Extracellular crosslinking mass spectrometry reveals HLA class I - HLA class II interactions on the cell surface. Mol Immunol 2021; 136:16-25. [PMID: 34052579 DOI: 10.1016/j.molimm.2021.05.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 04/23/2021] [Accepted: 05/19/2021] [Indexed: 01/26/2023]
Abstract
Human Leukocyte Antigen (HLA) complexes are critical cell-surface protein assemblies that facilitate T-cell surveillance of almost all cell types in the body. While T-cell receptor binding to HLA class I and class II complexes is well-described with detailed structural information, the nature of cis HLA interactions within the plasma membrane of the surveyed cells remains to be better characterized, as protein-protein interactions in the membrane environment are technically challenging to profile. Here we performed extracellular chemical crosslinking on intact antigen presenting cells to specifically elucidate protein-protein interactions present in the external plasma membrane. We found that the crosslink dataset was dominated by inter- and intra-protein crosslinks involving HLA molecules, which enabled not only the construction of an HLA-centric plasma membrane protein interaction map, but also revealed multiple modes of HLA class I - HLA class II interactions with further structural modeling based on crosslinker distance restraints. Collectively, our data demonstrate that HLA molecules colocalize and can be densely packed on the plasma membrane.
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Affiliation(s)
- Gad Armony
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands; Netherlands Proteomics Centre, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands; Netherlands Proteomics Centre, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
| | - Wei Wu
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands; Netherlands Proteomics Centre, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
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Smythers AL, Hicks LM. Mapping the plant proteome: tools for surveying coordinating pathways. Emerg Top Life Sci 2021; 5:203-220. [PMID: 33620075 PMCID: PMC8166341 DOI: 10.1042/etls20200270] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 02/07/2021] [Accepted: 02/09/2021] [Indexed: 12/14/2022]
Abstract
Plants rapidly respond to environmental fluctuations through coordinated, multi-scalar regulation, enabling complex reactions despite their inherently sessile nature. In particular, protein post-translational signaling and protein-protein interactions combine to manipulate cellular responses and regulate plant homeostasis with precise temporal and spatial control. Understanding these proteomic networks are essential to addressing ongoing global crises, including those of food security, rising global temperatures, and the need for renewable materials and fuels. Technological advances in mass spectrometry-based proteomics are enabling investigations of unprecedented depth, and are increasingly being optimized for and applied to plant systems. This review highlights recent advances in plant proteomics, with an emphasis on spatially and temporally resolved analysis of post-translational modifications and protein interactions. It also details the necessity for generation of a comprehensive plant cell atlas while highlighting recent accomplishments within the field.
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Affiliation(s)
- Amanda L Smythers
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, U.S.A
| | - Leslie M Hicks
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, U.S.A
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Huang R, Yang C, Zhang S. The Arabidopsis PHB3 is a pleiotropic regulator for plant development. PLANT SIGNALING & BEHAVIOR 2019; 14:1656036. [PMID: 31429630 PMCID: PMC6804698 DOI: 10.1080/15592324.2019.1656036] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 08/08/2019] [Indexed: 06/01/2023]
Abstract
Prohibitins (PHBs) are composed of an obviously conserved protein family in eukaryotic cells. Despite the extensive and in-depth research of mammalian PHB1 and PHB2, the plant prohibitins functions are not completely elucidated and little is known about their mechanism of action. This review focuses on the current knowledge about the protein subcellular localization, interaction proteins and target genes of PHB3. Furthermore, we discussed the roles of PHB3 protein in plant growth and development, plant responses to abiotic or biotic stresses and its participation in phytohormonal signaling.
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Affiliation(s)
- Ruihua Huang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Chengwei Yang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Shengchun Zhang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
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