1
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Song T, Yang Q, Qu P, Qiao L, Wang X. Attenphos: General Phosphorylation Site Prediction Model Based on Attention Mechanism. Int J Mol Sci 2024; 25:1526. [PMID: 38338804 PMCID: PMC10855885 DOI: 10.3390/ijms25031526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 01/18/2024] [Accepted: 01/23/2024] [Indexed: 02/12/2024] Open
Abstract
Phosphorylation site prediction has important application value in the field of bioinformatics. It can act as an important reference and help with protein function research, protein structure research, and drug discovery. So, it is of great significance to propose scientific and effective calculation methods to accurately predict phosphorylation sites. In this study, we propose a new method, Attenphos, based on the self-attention mechanism for predicting general phosphorylation sites in proteins. The method not only captures the long-range dependence information of proteins but also better represents the correlation between amino acids through feature vector encoding transformation. Attenphos takes advantage of the one-dimensional convolutional layer to reduce the number of model parameters, improve model efficiency and prediction accuracy, and enhance model generalization. Comparisons between our method and existing state-of-the-art prediction tools were made using balanced datasets from human proteins and unbalanced datasets from mouse proteins. We performed prediction comparisons using independent test sets. The results showed that Attenphos demonstrated the best overall performance in the prediction of Serine (S), Threonine (T), and Tyrosine (Y) sites on both balanced and unbalanced datasets. Compared to current state-of-the-art methods, Attenphos has significantly higher prediction accuracy. This proves the potential of Attenphos in accelerating the identification and functional analysis of protein phosphorylation sites and provides new tools and ideas for biological research and drug discovery.
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Affiliation(s)
| | | | | | | | - Xun Wang
- Qingdao Institute of Software, College of Computer Science and Technology, China University of Petroleum, Qingdao 266555, China; (T.S.); (Q.Y.); (P.Q.); (L.Q.)
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2
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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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3
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Pienkowski T, Kowalczyk T, Cysewski D, Kretowski A, Ciborowski M. Glioma and post-translational modifications: A complex relationship. Biochim Biophys Acta Rev Cancer 2023; 1878:189009. [PMID: 37913943 DOI: 10.1016/j.bbcan.2023.189009] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 10/17/2023] [Accepted: 10/17/2023] [Indexed: 11/03/2023]
Abstract
Post-translational modifications (PTMs) are common covalent processes in biochemical pathways that alter protein function and activity. These modifications occur through proteolytic cleavage or attachment of modifying groups, such as phosphoryl, methyl, glycosyl, or acetyl groups, with one or more amino acid residues of a single protein. Some PTMs also present crosstalk abilities that affect both protein functionality and structure, creating new proteoforms. Any alteration in organism homeostasis may be a cancer hallmark. Cataloging PTMs and consequently, emerging proteoforms, present new therapeutic targets, approaches, and opportunities to discover additional discriminatory biomarkers in disease diagnostics. In this review, we focus on experimentally confirmed PTMs and their potential crosstalk in glioma research to introduce new opportunities for this tumor type, which emerge within the PTMomics area.
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Affiliation(s)
- Tomasz Pienkowski
- Clinical Research Centre, Medical University of Bialystok, M. Sklodowskiej-Curie 24a, 15-276 Bialystok, Poland
| | - Tomasz Kowalczyk
- Clinical Research Centre, Medical University of Bialystok, M. Sklodowskiej-Curie 24a, 15-276 Bialystok, Poland; Department of Medical Microbiology and Nanobiomedical Engineering, Medical University of Bialystok, Mickiewicza 2C, 15-222 Bialystok, Poland
| | - Dominik Cysewski
- Clinical Research Centre, Medical University of Bialystok, M. Sklodowskiej-Curie 24a, 15-276 Bialystok, Poland
| | - Adam Kretowski
- Clinical Research Centre, Medical University of Bialystok, M. Sklodowskiej-Curie 24a, 15-276 Bialystok, Poland; Department of Endocrinology, Diabetology and Internal Medicine, Medical University of Bialystok, M. Sklodowskiej-Curie 24a, 15-276 Bialystok, Poland
| | - Michal Ciborowski
- Clinical Research Centre, Medical University of Bialystok, M. Sklodowskiej-Curie 24a, 15-276 Bialystok, Poland.
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4
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Keil L, Mehlmer N, Cavelius P, Garbe D, Haack M, Ritz M, Awad D, Brück T. The Time-Resolved Salt Stress Response of Dunaliella tertiolecta-A Comprehensive System Biology Perspective. Int J Mol Sci 2023; 24:15374. [PMID: 37895054 PMCID: PMC10607294 DOI: 10.3390/ijms242015374] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 10/12/2023] [Accepted: 10/17/2023] [Indexed: 10/29/2023] Open
Abstract
Algae-driven processes, such as direct CO2 fixation into glycerol, provide new routes for sustainable chemical production in synergy with greenhouse gas mitigation. The marine microalgae Dunaliella tertiolecta is reported to accumulate high amounts of intracellular glycerol upon exposure to high salt concentrations. We have conducted a comprehensive, time-resolved systems biology study to decipher the metabolic response of D. tertiolecta up to 24 h under continuous light conditions. Initially, due to a lack of reference sequences required for MS/MS-based protein identification, a high-quality draft genome of D. tertiolecta was generated. Subsequently, a database was designed by combining the genome with transcriptome data obtained before and after salt stress. This database allowed for detection of differentially expressed proteins and identification of phosphorylated proteins, which are involved in the short- and long-term adaptation to salt stress, respectively. Specifically, in the rapid salt adaptation response, proteins linked to the Ca2+ signaling pathway and ion channel proteins were significantly increased. While phosphorylation is key in maintaining ion homeostasis during the rapid adaptation to salt stress, phosphofructokinase is required for long-term adaption. Lacking β-carotene, synthesis under salt stress conditions might be substituted by the redox-sensitive protein CP12. Furthermore, salt stress induces upregulation of Calvin-Benson cycle-related proteins.
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Affiliation(s)
| | | | | | | | | | | | | | - Thomas Brück
- Werner Siemens Chair of Synthetic Biotechnology, Department of Chemistry, Technical University of Munich (TUM), 85748 Garching, Germany; (L.K.); (N.M.); (P.C.); (D.G.); (M.H.); (M.R.); (D.A.)
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5
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Siao W, Wang P, Zhao X, Vu LD, De Smet I, Russinova E. Phosphorylation of ADAPTOR PROTEIN-2 μ-adaptin by ADAPTOR-ASSOCIATED KINASE1 regulates the tropic growth of Arabidopsis roots. THE PLANT CELL 2023; 35:3504-3521. [PMID: 37440281 PMCID: PMC10473204 DOI: 10.1093/plcell/koad141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 04/21/2023] [Indexed: 07/14/2023]
Abstract
ADAPTOR-ASSOCIATED PROTEIN KINASE1 (AAK1) is a known regulator of clathrin-mediated endocytosis in mammals. Human AAK1 phosphorylates the μ2 subunit of the ADAPTOR PROTEIN-2 (AP-2) complex (AP2M) and plays important roles in cell differentiation and development. Previous interactome studies discovered the association of AAK1 with AP-2 in Arabidopsis (Arabidopsis thaliana), but its function was unclear. Here, genetic analysis revealed that the Arabidopsis aak1 and ap2m mutants both displayed altered root tropic growth, including impaired touch- and gravity-sensing responses. In Arabidopsis, AAK1-phosphorylated AP2M on Thr-163, and expression of the phospho-null version of AP2M in the ap2m mutant led to an aak1-like phenotype, whereas the phospho-mimic forms of AP2M rescued the aak1 mutant. In addition, we found that the AAK1-dependent phosphorylation state of AP2M modulates the frequency distribution of endocytosis. Our data indicate that the phosphorylation of AP2M on Thr-163 by AAK1 fine-tunes endocytosis in the Arabidopsis root to control its tropic growth.
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Affiliation(s)
- Wei Siao
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Peng Wang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Xiuyang Zhao
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Lam Dai Vu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Ive De Smet
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Eugenia Russinova
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
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6
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Chen Y, Wang Y, Liang X, Zhang Y, Fernie AR. Mass spectrometric exploration of phytohormone profiles and signaling networks. TRENDS IN PLANT SCIENCE 2023; 28:399-414. [PMID: 36585336 DOI: 10.1016/j.tplants.2022.12.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 12/03/2022] [Accepted: 12/07/2022] [Indexed: 06/17/2023]
Abstract
Phytohormones have crucial roles in plant growth, development, and acclimation to environmental stress; however, measuring phytohormone levels and unraveling their complex signaling networks and interactions remains challenging. Mass spectrometry (MS) has revolutionized the study of complex biological systems, enabling the comprehensive identification and quantification of phytohormones and their related targets. Here, we review recent advances in MS technologies and highlight studies that have used MS to discover and analyze phytohormone-mediated molecular events. In particular, we focus on the application of MS for profiling phytohormones, elucidating phosphorylation signaling, and mapping protein interactions in plants.
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Affiliation(s)
- Yanmei Chen
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, 100193, Beijing, China.
| | - Yi Wang
- State Key Laboratory of Wheat and Maize Crop Science, College of Resources and Environment, Henan Agricultural University, 450002, Zhengzhou, China
| | - Xinlin Liang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, 100193, Beijing, China
| | - Youjun Zhang
- Center of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria; Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Alisdair R Fernie
- Center of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria; Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
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7
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Hartman MD, Rojas BE, Ferrero DML, Leyva A, Durán R, Iglesias AA, Figueroa CM. Phosphorylation of aldose-6-phosphate reductase from Prunus persica leaves. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 194:461-469. [PMID: 36508780 DOI: 10.1016/j.plaphy.2022.12.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 11/04/2022] [Accepted: 12/05/2022] [Indexed: 06/17/2023]
Abstract
Sugar-alcohols are major photosynthates in plants from the Rosaceae family. Expression of the gene encoding aldose-6-phosphate reductase (Ald6PRase), the critical enzyme for glucitol synthesis in rosaceous species, is regulated by physiological and environmental cues. Additionally, Ald6PRase is inhibited by small molecules (hexose-phosphates and inorganic orthophosphate) and oxidizing compounds. This work demonstrates that Ald6PRase from peach leaves is phosphorylated in planta at the N-terminus. We also show in vitro phosphorylation of recombinant Ald6PRase by a partially purified kinase extract from peach leaves containing Ca2+-dependent protein kinases (CDPKs). Moreover, phosphorylation of recombinant Ald6PRase was inhibited by hexose-phosphates, phosphoenolpyruvate and pyrophosphate. We further show that phosphorylation of recombinant Ald6PRase was maximal using recombinant CDPKs. Overall, our results suggest that phosphorylation could fine-tune the activity of Ald6PRase.
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Affiliation(s)
- Matías D Hartman
- Instituto de Agrobiotecnología del Litoral, UNL, CONICET, FBCB, Santa Fe, Argentina
| | - Bruno E Rojas
- Instituto de Agrobiotecnología del Litoral, UNL, CONICET, FBCB, Santa Fe, Argentina
| | - Danisa M L Ferrero
- Instituto de Agrobiotecnología del Litoral, UNL, CONICET, FBCB, Santa Fe, Argentina
| | - Alejandro Leyva
- Unidad de Bioquímica y Proteómica Analíticas, Instituto de Investigaciones Biológicas Clemente Estable and Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Rosario Durán
- Unidad de Bioquímica y Proteómica Analíticas, Instituto de Investigaciones Biológicas Clemente Estable and Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Alberto A Iglesias
- Instituto de Agrobiotecnología del Litoral, UNL, CONICET, FBCB, Santa Fe, Argentina
| | - Carlos M Figueroa
- Instituto de Agrobiotecnología del Litoral, UNL, CONICET, FBCB, Santa Fe, Argentina.
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8
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Zhou J, Zhao L, Wu Y, Zhang X, Cheng S, Wei F, Zhang Y, Zhu H, Zhou Y, Feng Z, Feng H. A DEK domain-containing protein GhDEK2D mediated Gossypium hirsutum enhanced resistance to Verticillium dahliae. PLANT SIGNALING & BEHAVIOR 2022; 17:2024738. [PMID: 35034577 PMCID: PMC9176258 DOI: 10.1080/15592324.2021.2024738] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
DEK is associated with DNA replication and break repair, mRNA splicing, and transcriptional regulation, which had been studied in humans and mammals. The function of DEK in plants was poorly understood. In this study, GhDEK2D was identified in Gossypium hirsutum by genome-wide and post-translational modifications. GhDEK2D had been phosphorylated, acetylated and ubiquitylated under Verticillium dahliae (Vd) challenge. The GhDEK2D-silenced cotton decreased resistance against Vd. In GhDEK2D-silenced cotton plants, the reactive oxygen species was activated, the callose, xylogen, hypersensitive reaction (HR) and expression levels of defense-related genes were reduced. Homozygous overexpressing-GhDEK2D transgenic Arabidopsis lines were more resistant to Verticillium wilt (Vw). We propose that GhDEK2D was a potential molecular target for improving resistance to Vw in cotton.
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Affiliation(s)
- Jinglong Zhou
- College of Agriculture, Yangtze University, Jingzhou, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
- Yi Zhou College of Agriculture, Yangtze University, Jingzhou, Hubei 434025, China
| | - Lihong Zhao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
- Yi Zhou College of Agriculture, Yangtze University, Jingzhou, Hubei 434025, China
| | - Yajie Wu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Xiaojian Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Sheng Cheng
- College of Agriculture, Yangtze University, Jingzhou, China
| | - Feng Wei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Yalin Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Heqin Zhu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Yi Zhou
- College of Agriculture, Yangtze University, Jingzhou, China
- Yi Zhou College of Agriculture, Yangtze University, Jingzhou, Hubei 434025, China
| | - Zili Feng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
- Zili Feng State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, Henan 455000, China
| | - Hongjie Feng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
- CONTACT Hongjie Feng
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9
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Weigle AT, Feng J, Shukla D. Thirty years of molecular dynamics simulations on posttranslational modifications of proteins. Phys Chem Chem Phys 2022; 24:26371-26397. [PMID: 36285789 PMCID: PMC9704509 DOI: 10.1039/d2cp02883b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
Abstract
Posttranslational modifications (PTMs) are an integral component to how cells respond to perturbation. While experimental advances have enabled improved PTM identification capabilities, the same throughput for characterizing how structural changes caused by PTMs equate to altered physiological function has not been maintained. In this Perspective, we cover the history of computational modeling and molecular dynamics simulations which have characterized the structural implications of PTMs. We distinguish results from different molecular dynamics studies based upon the timescales simulated and analysis approaches used for PTM characterization. Lastly, we offer insights into how opportunities for modern research efforts on in silico PTM characterization may proceed given current state-of-the-art computing capabilities and methodological advancements.
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Affiliation(s)
- Austin T Weigle
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Jiangyan Feng
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Diwakar Shukla
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.
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10
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Sun L, Qin J, Wu X, Zhang J, Zhang J. TOUCH 3 and CALMODULIN 1/4/6 cooperate with calcium-dependent protein kinases to trigger calcium-dependent activation of CAM-BINDING PROTEIN 60-LIKE G and regulate fungal resistance in plants. THE PLANT CELL 2022; 34:4088-4104. [PMID: 35863056 PMCID: PMC9516039 DOI: 10.1093/plcell/koac209] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 07/14/2022] [Indexed: 05/24/2023]
Abstract
Plants utilize localized cell-surface and intracellular receptors to sense microbes and activate the influx of calcium, which serves as an important second messenger in eukaryotes to regulate cellular responses. However, the mechanisms through which plants decipher calcium influx to activate immune responses remain largely unknown. Here, we show that pathogen-associated molecular patterns (PAMPs) trigger calcium-dependent phosphorylation of CAM-BINDING PROTEIN 60-LIKE G (CBP60g) in Arabidopsis (Arabidopsis thaliana). CALCIUM-DEPENDENT PROTEIN KINASE5 (CPK5) phosphorylates CBP60g directly, thereby enhancing its transcription factor activity. TOUCH 3 (TCH3) and its homologs CALMODULIN (CAM) 1/4/6 and CPK4/5/6/11 are required for PAMP-induced CBP60g phosphorylation. TCH3 interferes with the auto-inhibitory region of CPK5 and promotes CPK5-mediated CBP60g phosphorylation. Furthermore, CPKs-mediated CBP60g phosphorylation positively regulates plant resistance to soil-borne fungal pathogens. These lines of evidence uncover a novel calcium signal decoding mechanism during plant immunity through which TCH3 relieves auto-inhibition of CPK5 to phosphorylate and activate CBP60g. The findings reveal cooperative interconnections between different types of calcium sensors in eukaryotes.
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Affiliation(s)
- Lifan Sun
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jun Qin
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiaoyun Wu
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinghan Zhang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- School of Life Sciences, Hebei University, Baoding, Hebei 710023, China
| | - Jie Zhang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
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11
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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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12
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Wang X, Zhang Z, Zhang C, Meng X, Shi X, Qu P. TransPhos: A Deep-Learning Model for General Phosphorylation Site Prediction Based on Transformer-Encoder Architecture. Int J Mol Sci 2022; 23:ijms23084263. [PMID: 35457080 PMCID: PMC9029334 DOI: 10.3390/ijms23084263] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 04/04/2022] [Accepted: 04/09/2022] [Indexed: 02/06/2023] Open
Abstract
Protein phosphorylation is one of the most critical post-translational modifications of proteins in eukaryotes, which is essential for a variety of biological processes. Plenty of attempts have been made to improve the performance of computational predictors for phosphorylation site prediction. However, most of them are based on extra domain knowledge or feature selection. In this article, we present a novel deep learning-based predictor, named TransPhos, which is constructed using a transformer encoder and densely connected convolutional neural network blocks, for predicting phosphorylation sites. Data experiments are conducted on the datasets of PPA (version 3.0) and Phospho. ELM. The experimental results show that our TransPhos performs better than several deep learning models, including Convolutional Neural Networks (CNN), Long-term and short-term memory networks (LSTM), Recurrent neural networks (RNN) and Fully connected neural networks (FCNN), and some state-of-the-art deep learning-based prediction tools, including GPS2.1, NetPhos, PPRED, Musite, PhosphoSVM, SKIPHOS, and DeepPhos. Our model achieves a good performance on the training datasets of Serine (S), Threonine (T), and Tyrosine (Y), with AUC values of 0.8579, 0.8335, and 0.6953 using 10-fold cross-validation tests, respectively, and demonstrates that the presented TransPhos tool considerably outperforms competing predictors in general protein phosphorylation site prediction.
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Affiliation(s)
- Xun Wang
- College of Computer Science and Technology, China University of Petroleum, Qingdao 266555, China; (Z.Z.); (C.Z.); (X.M.); (X.S.); (P.Q.)
- State Key Laboratory of Computer Architecture, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100080, China
- Correspondence:
| | - Zhiyuan Zhang
- College of Computer Science and Technology, China University of Petroleum, Qingdao 266555, China; (Z.Z.); (C.Z.); (X.M.); (X.S.); (P.Q.)
| | - Chaogang Zhang
- College of Computer Science and Technology, China University of Petroleum, Qingdao 266555, China; (Z.Z.); (C.Z.); (X.M.); (X.S.); (P.Q.)
| | - Xiangyu Meng
- College of Computer Science and Technology, China University of Petroleum, Qingdao 266555, China; (Z.Z.); (C.Z.); (X.M.); (X.S.); (P.Q.)
| | - Xin Shi
- College of Computer Science and Technology, China University of Petroleum, Qingdao 266555, China; (Z.Z.); (C.Z.); (X.M.); (X.S.); (P.Q.)
| | - Peng Qu
- College of Computer Science and Technology, China University of Petroleum, Qingdao 266555, China; (Z.Z.); (C.Z.); (X.M.); (X.S.); (P.Q.)
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13
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Guo J, Chai X, Mei Y, Du J, Du H, Shi H, Zhu JK, Zhang H. Acetylproteomics analyses reveal critical features of lysine-ε-acetylation in Arabidopsis and a role of 14-3-3 protein acetylation in alkaline response. STRESS BIOLOGY 2022; 2:1. [PMID: 37676343 PMCID: PMC10442023 DOI: 10.1007/s44154-021-00024-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/07/2021] [Indexed: 09/08/2023]
Abstract
Lysine-ε-acetylation (Kac) is a post-translational modification (PTM) that is critical for metabolic regulation and cell signaling in mammals. However, its prevalence and importance in plants remain to be determined. Employing high-resolution tandem mass spectrometry, we analyzed protein lysine acetylation in five representative Arabidopsis organs with 2 ~ 3 biological replicates per organ. A total of 2887 Kac proteins and 5929 Kac sites were identified. This comprehensive catalog allows us to analyze proteome-wide features of lysine acetylation. We found that Kac proteins tend to be more uniformly expressed in different organs, and the acetylation status exhibits little correlation with the gene expression level, indicating that acetylation is unlikely caused by stochastic processes. Kac preferentially targets evolutionarily conserved proteins and lysine residues, but only a small percentage of Kac proteins are orthologous between rat and Arabidopsis. A large portion of Kac proteins overlap with proteins modified by other PTMs including ubiquitination, SUMOylation and phosphorylation. Although acetylation, ubiquitination and SUMOylation all modify lysine residues, our analyses show that they rarely target the same sites. In addition, we found that "reader" proteins for acetylation and phosphorylation, i.e., bromodomain-containing proteins and GRF (General Regulatory Factor)/14-3-3 proteins, are intensively modified by the two PTMs, suggesting that they are main crosstalk nodes between acetylation and phosphorylation signaling. Analyses of GRF6/14-3-3λ reveal that the Kac level of GRF6 is decreased under alkaline stress, suggesting that acetylation represses plant alkaline response. Indeed, K56ac of GRF6 inhibits its binding to and subsequent activation of the plasma membrane H+-ATPase AHA2, leading to hypersensitivity to alkaline stress. These results provide valuable resources for protein acetylation studies in plants and reveal that protein acetylation suppresses phosphorylation output by acetylating GRF/14-3-3 proteins.
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Affiliation(s)
- Jianfei Guo
- State Key Laboratory of Plant Molecular Genetics, Shanghai Center for Plant Stress Biology, Center for Excellence in Plant Molecular Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoqiang Chai
- State Key Laboratory of Plant Molecular Genetics, Shanghai Center for Plant Stress Biology, Center for Excellence in Plant Molecular Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
| | - Yuchao Mei
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Jiamu Du
- Department of Biology, Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen, 518055, Guangdong, China
| | - Haining Du
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Huazhong Shi
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Jian-Kang Zhu
- State Key Laboratory of Plant Molecular Genetics, Shanghai Center for Plant Stress Biology, Center for Excellence in Plant Molecular Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
| | - Heng Zhang
- State Key Laboratory of Plant Molecular Genetics, Shanghai Center for Plant Stress Biology, Center for Excellence in Plant Molecular Sciences, Chinese Academy of Sciences, Shanghai, 201602, China.
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14
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Blea MN, Wallace IS. Analysis of Posttranslational Modifications in Arabidopsis Proteins and Metabolic Pathways Using the FAT-PTM Database. Methods Mol Biol 2022; 2499:145-154. [PMID: 35696079 DOI: 10.1007/978-1-0716-2317-6_7] [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: 06/15/2023]
Abstract
Posttranslational modifications (PTMs) are critical regulators of protein behavior, and over 200 different types of PTMs have been identified. Recent developments in mass spectrometry technology and sample enrichment approaches have led to a massive expansion in the number of identified PTM types and sites within eukaryotic proteins. As these types of data become increasingly available, it is important to develop additional analysis tools and data repositories to investigate PTM cross talk and larger networks of PTMs. Recently, we developed the Functional Analysis Tools for Post-translational Modifications (FAT-PTM) database, which supports data from publicly available proteomic analyses encompassing eight different types of PTMs and over 49,000 PTM sites. In this chapter, we describe the utility of FAT-PTM for analysis of posttranslationally modified proteins in three different contexts. First, a simple protein search tool is available that allows users to investigate proteins in the Arabidopsis proteome to identify types of PTMs that are associated with the query protein as well as quantitative phosphorylation site changes associated with ten different experimental conditions. Second, FAT-PTM contains a metabolic pathway analysis tool to investigate PTMs in the broader context of over 600 different metabolic pathways compiled from the Plant Metabolic Network. Finally, FAT-PTM contains a comodification tool that can be used to identify groups of proteins that are subject to two or more user-defined PTMs. Overall, FAT-PTM provides a user-friendly platform to visualize posttranslationally modified proteins at the individual, metabolic pathway, and PTM cross-talk levels.
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Affiliation(s)
- Madison N Blea
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Reno, NV, USA
| | - Ian S Wallace
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Reno, NV, USA.
- Department of Chemistry, University of Nevada, Reno, Reno, NV, USA.
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15
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Arico DS, Beati P, Wengier DL, Mazzella MA. A novel strategy to uncover specific GO terms/phosphorylation pathways in phosphoproteomic data in Arabidopsis thaliana. BMC PLANT BIOLOGY 2021; 21:592. [PMID: 34906086 PMCID: PMC8670200 DOI: 10.1186/s12870-021-03377-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 11/29/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND Proteins are the workforce of the cell and their phosphorylation status tailors specific responses efficiently. One of the main challenges of phosphoproteomic approaches is to deconvolute biological processes that specifically respond to an experimental query from a list of phosphoproteins. Comparison of the frequency distribution of GO (Gene Ontology) terms in a given phosphoproteome set with that observed in the genome reference set (GenRS) is the most widely used tool to infer biological significance. Yet, this comparison assumes that GO term distribution between the phosphoproteome and the genome are identical. However, this hypothesis has not been tested due to the lack of a comprehensive phosphoproteome database. RESULTS In this study, we test this hypothesis by constructing three phosphoproteome databases in Arabidopsis thaliana: one based in experimental data (ExpRS), another based in in silico phosphorylation protein prediction (PredRS) and a third that is the union of both (UnRS). Our results show that the three phosphoproteome reference sets show default enrichment of several GO terms compared to GenRS, indicating that GO term distribution in the phosphoproteomes does not match that of the genome. Moreover, these differences overshadow the identification of GO terms that are specifically enriched in a particular condition. To overcome this limitation, we present an additional comparison of the sample of interest with UnRS to uncover GO terms specifically enriched in a particular phosphoproteome experiment. Using this strategy, we found that mRNA splicing and cytoplasmic microtubule compounds are important processes specifically enriched in the phosphoproteome of dark-grown Arabidopsis seedlings. CONCLUSIONS This study provides a novel strategy to uncover GO specific terms in phosphoproteome data of Arabidopsis that could be applied to any other organism. We also highlight the importance of specific phosphorylation pathways that take place during dark-grown Arabidopsis development.
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Affiliation(s)
- Denise S Arico
- INGEBI-CONICET Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor Torres", Vuelta de Obligado 2490, 1428, CABA, Argentina
| | - Paula Beati
- INGEBI-CONICET Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor Torres", Vuelta de Obligado 2490, 1428, CABA, Argentina
| | - Diego L Wengier
- INGEBI-CONICET Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor Torres", Vuelta de Obligado 2490, 1428, CABA, Argentina
- Department of Chemical Engineering, Stanford University, 443 Via Ortega, Stanford, CA, 94305, USA
| | - Maria Agustina Mazzella
- INGEBI-CONICET Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor Torres", Vuelta de Obligado 2490, 1428, CABA, Argentina.
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16
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Subba P, Prasad TSK. Plant Phosphoproteomics: Known Knowns, Known Unknowns, and Unknown Unknowns of an Emerging Systems Science Frontier. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2021; 25:750-769. [PMID: 34882020 DOI: 10.1089/omi.2021.0192] [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] [Indexed: 06/13/2023]
Abstract
Plant systems science research depends on the dynamic functional maps of the biological substrates of plant phenotypes and host/environment interactions in diverse ecologies. In this context, high-resolution mass spectrometry platforms offer comprehensive insights into the molecular pathways regulated by protein phosphorylation. Reversible protein phosphorylation is a ubiquitous reaction in signal transduction mechanisms in biological systems. In contrast to human and animal biology research, a plethora of experimental options for functional mapping and regulation of plant biology are, however, not currently available. Plant phosphoproteomics is an emerging field of research that aims at addressing this gap in systems science and plant omics, and thus has a large scope to empower fundamental discoveries. To date, large-scale data-intensive identification of phosphorylation events in plants remained technically challenging. In this expert review, we present a critical analysis and overview of phosphoproteomic studies performed in the model plant Arabidopsis thaliana. We discuss the technical strategies used for the enrichment of phosphopeptides and methods used for their quantitative assessment. Various types of mass spectrometry data acquisition and fragmentation methods are also discussed. The insights gathered here can allow plant biology and systems science researchers to design high-throughput function-oriented experimental workflows that elucidate the regulatory signaling mechanisms impacting plant physiology and plant diseases.
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Affiliation(s)
- Pratigya Subba
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
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17
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Xue H, Zhang Q, Wang P, Cao B, Jia C, Cheng B, Shi Y, Guo WF, Wang Z, Liu ZX, Cheng H. qPTMplants: an integrative database of quantitative post-translational modifications in plants. Nucleic Acids Res 2021; 50:D1491-D1499. [PMID: 34718741 PMCID: PMC8728288 DOI: 10.1093/nar/gkab945] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 09/28/2021] [Accepted: 10/06/2021] [Indexed: 12/13/2022] Open
Abstract
As a crucial molecular mechanism, post-translational modifications (PTMs) play critical roles in a wide range of biological processes in plants. Recent advances in mass spectrometry-based proteomic technologies have greatly accelerated the profiling and quantification of plant PTM events. Although several databases have been constructed to store plant PTM data, a resource including more plant species and more PTM types with quantitative dynamics still remains to be developed. In this paper, we present an integrative database of quantitative PTMs in plants named qPTMplants (http://qptmplants.omicsbio.info), which hosts 1 242 365 experimentally identified PTM events for 429 821 nonredundant sites on 123 551 proteins under 583 conditions for 23 PTM types in 43 plant species from 293 published studies, with 620 509 quantification events for 136 700 PTM sites on 55 361 proteins under 354 conditions. Moreover, the experimental details, such as conditions, samples, instruments and methods, were manually curated, while a variety of annotations, including the sequence and structural characteristics, were integrated into qPTMplants. Then, various search and browse functions were implemented to access the qPTMplants data in a user-friendly manner. Overall, we anticipate that the qPTMplants database will be a valuable resource for further research on PTMs in plants.
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Affiliation(s)
- Han Xue
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Qingfeng Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Panqin Wang
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Bijin Cao
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Chongchong Jia
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Ben Cheng
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Yuhua Shi
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Wei-Feng Guo
- School of Electrical Engineering, Zhengzhou University, Zhengzhou 450001, China
| | - Zhenlong Wang
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Ze-Xian Liu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Han Cheng
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
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18
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Vega A, Fredes I, O'Brien J, Shen Z, Ötvös K, Abualia R, Benkova E, Briggs SP, Gutiérrez RA. Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture. EMBO Rep 2021; 22:e51813. [PMID: 34357701 PMCID: PMC8447600 DOI: 10.15252/embr.202051813] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 05/13/2021] [Accepted: 06/23/2021] [Indexed: 01/04/2023] Open
Abstract
Nitrate commands genome‐wide gene expression changes that impact metabolism, physiology, plant growth, and development. In an effort to identify new components involved in nitrate responses in plants, we analyze the Arabidopsis thaliana root phosphoproteome in response to nitrate treatments via liquid chromatography coupled to tandem mass spectrometry. 176 phosphoproteins show significant changes at 5 or 20 min after nitrate treatments. Proteins identified by 5 min include signaling components such as kinases or transcription factors. In contrast, by 20 min, proteins identified were associated with transporter activity or hormone metabolism functions, among others. The phosphorylation profile of NITRATE TRANSPORTER 1.1 (NRT1.1) mutant plants was significantly altered as compared to wild‐type plants, confirming its key role in nitrate signaling pathways that involves phosphorylation changes. Integrative bioinformatics analysis highlights auxin transport as an important mechanism modulated by nitrate signaling at the post‐translational level. We validated a new phosphorylation site in PIN2 and provide evidence that it functions in primary and lateral root growth responses to nitrate.
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Affiliation(s)
- Andrea Vega
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile.,FONDAP Center for Genome Regulation, ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Isabel Fredes
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile.,FONDAP Center for Genome Regulation, ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - José O'Brien
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile.,FONDAP Center for Genome Regulation, ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio), Santiago, Chile.,Departamento de Fruticultura y Enología, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Zhouxin Shen
- Cell and Developmental Biology, University of California San Diego. San Diego, CA, USA
| | - Krisztina Ötvös
- Institute of Science and Technology (IST) Austria, Klosterneuburg, Austria.,Bioresources Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | - Rashed Abualia
- Institute of Science and Technology (IST) Austria, Klosterneuburg, Austria
| | - Eva Benkova
- Institute of Science and Technology (IST) Austria, Klosterneuburg, Austria
| | - Steven P Briggs
- Cell and Developmental Biology, University of California San Diego. San Diego, CA, USA
| | - Rodrigo A Gutiérrez
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile.,FONDAP Center for Genome Regulation, ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio), Santiago, Chile
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19
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Computational Phosphorylation Network Reconstruction: An Update on Methods and Resources. Methods Mol Biol 2021. [PMID: 34270057 DOI: 10.1007/978-1-0716-1625-3_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
Most proteins undergo some form of modification after translation, and phosphorylation is one of the most relevant and ubiquitous post-translational modifications. The succession of protein phosphorylation and dephosphorylation catalyzed by protein kinase and phosphatase, respectively, constitutes a key mechanism of molecular information flow in cellular systems. The protein interactions of kinases, phosphatases, and their regulatory subunits and substrates are the main part of phosphorylation networks. To elucidate the landscape of phosphorylation events has been a central goal pursued by both experimental and computational approaches. Substrate specificity (e.g., sequence, structure) or the phosphoproteome has been utilized in an array of different statistical learning methods to infer phosphorylation networks. In this chapter, different computational phosphorylation network inference-related methods and resources are summarized and discussed.
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20
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Zhang Y, Giese J, Kerbler SM, Siemiatkowska B, Perez de Souza L, Alpers J, Medeiros DB, Hincha DK, Daloso DM, Stitt M, Finkemeier I, Fernie AR. Two mitochondrial phosphatases, PP2c63 and Sal2, are required for posttranslational regulation of the TCA cycle in Arabidopsis. MOLECULAR PLANT 2021; 14:1104-1118. [PMID: 33798747 DOI: 10.1016/j.molp.2021.03.023] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 01/26/2021] [Accepted: 03/29/2021] [Indexed: 05/22/2023]
Abstract
Protein phosphorylation is a well-established post-translational mechanism that regulates protein functions and metabolic pathways. It is known that several plant mitochondrial proteins are phosphorylated in a reversible manner. However, the identities of the protein kinases/phosphatases involved in this mechanism and their roles in the regulation of the tricarboxylic acid (TCA) cycle remain unclear. In this study, we isolated and characterized plants lacking two mitochondrially targeted phosphatases (Sal2 and PP2c63) along with pyruvate dehydrogenase kinase (PDK). Protein-protein interaction analysis, quantitative phosphoproteomics, and enzymatic analyses revealed that PDK specifically regulates pyruvate dehydrogenase complex (PDC), while PP2c63 nonspecifically regulates PDC. When recombinant PP2c63 and Sal2 proteins were added to mitochondria isolated from mutant plants, protein-protein interaction and enzymatic analyses showed that PP2c63 directly phosphorylates and modulates the activity of PDC, while Sal2 only indirectly affects TCA cycle enzymes. Characterization of steady-state metabolite levels and fluxes in the mutant lines further revealed that these phosphatases regulate flux through the TCA cycle, and that altered metabolism in the sal2 pp2c63 double mutant compromises plant growth. These results are discussed in the context of current models of the control of respiration in plants.
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Affiliation(s)
- Youjun Zhang
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; Center of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria.
| | - Jonas Giese
- Institute of Plant Biology and Biotechnology, University of Muenster, Schlossplatz 7, 48149 Muenster, Germany
| | - Sandra M Kerbler
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Beata Siemiatkowska
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Leonardo Perez de Souza
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Jessica Alpers
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - David Barbosa Medeiros
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Dirk K Hincha
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Danilo M Daloso
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza, Ceará, Brasil
| | - Mark Stitt
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Iris Finkemeier
- Institute of Plant Biology and Biotechnology, University of Muenster, Schlossplatz 7, 48149 Muenster, Germany.
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; Center of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria.
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21
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Niehaus TD. Phosphatases are involved in modulating the TCA cycle in plants. MOLECULAR PLANT 2021; 14:1036-1037. [PMID: 34020053 DOI: 10.1016/j.molp.2021.05.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 05/13/2021] [Accepted: 05/13/2021] [Indexed: 06/12/2023]
Affiliation(s)
- Thomas D Niehaus
- Department of Plant and Microbial Biology, University of Minnesota Twin Cities, Saint Paul, MN, USA.
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22
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Ródenas R, Ragel P, Nieves-Cordones M, Martínez-Martínez A, Amo J, Lara A, Martínez V, Quintero FJ, Pardo JM, Rubio F. Insights into the mechanisms of transport and regulation of the arabidopsis high-affinity K+ transporter HAK51. PLANT PHYSIOLOGY 2021; 185:1860-1874. [PMID: 33595056 PMCID: PMC8133630 DOI: 10.1093/plphys/kiab028] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 01/11/2021] [Indexed: 05/02/2023]
Abstract
The high-affinity K+ transporter HAK5 from Arabidopsis (Arabidopsis thaliana) is essential for K+ acquisition and plant growth at low micromolar K+ concentrations. Despite its functional relevance in plant nutrition, information about functional domains of HAK5 is scarce. Its activity is enhanced by phosphorylation via the AtCIPK23/AtCBL1-9 complex. Based on the recently published three-dimensionalstructure of the bacterial ortholog KimA from Bacillus subtilis, we have modeled AtHAK5 and, by a mutational approach, identified residues G67, Y70, G71, D72, D201, and E312 as essential for transporter function. According to the structural model, residues D72, D201, and E312 may bind K+, whereas residues G67, Y70, and G71 may shape the selective filter for K+, which resembles that of K+shaker-like channels. In addition, we show that phosphorylation of residue S35 by AtCIPK23 is required for reaching maximal transport activity. Serial deletions of the AtHAK5 C-terminus disclosed the presence of an autoinhibitory domain located between residues 571 and 633 together with an AtCIPK23-dependent activation domain downstream of position 633. Presumably, autoinhibition of AtHAK5 is counteracted by phosphorylation of S35 by AtCIPK23. Our results provide a molecular model for K+ transport and describe CIPK-CBL-mediated regulation of plant HAK transporters.
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Affiliation(s)
- Reyes Ródenas
- Departamento de Nutrición Vegetal, Centro de Edafología y Biología Aplicada del Segura, Consejo Superior de Investigaciones Científicas, Campus de Espinardo, 30100 Murcia, Spain
- Present address: Plant Science Research Laboratory (LRSV), UMR5546 CNRS/Université Toulouse 3, 24 chemin de Borde Rouge, 31320 Auzeville-Tolosane, France
| | - Paula Ragel
- Instituto de Bioquímica Vegetal y Fotosíntesis, cic-Cartuja, Consejo Superior de Investigaciones Científicas-Universidad de Sevilla, 41092 Sevilla, Spain
- Present address: Centre for Organismal Studies (COS), Department of Cell Biology, Heidelberg University, Heidelberg, Germany
| | - Manuel Nieves-Cordones
- Departamento de Nutrición Vegetal, Centro de Edafología y Biología Aplicada del Segura, Consejo Superior de Investigaciones Científicas, Campus de Espinardo, 30100 Murcia, Spain
| | - Almudena Martínez-Martínez
- Departamento de Nutrición Vegetal, Centro de Edafología y Biología Aplicada del Segura, Consejo Superior de Investigaciones Científicas, Campus de Espinardo, 30100 Murcia, Spain
| | - Jesús Amo
- Departamento de Nutrición Vegetal, Centro de Edafología y Biología Aplicada del Segura, Consejo Superior de Investigaciones Científicas, Campus de Espinardo, 30100 Murcia, Spain
| | - Alberto Lara
- Departamento de Nutrición Vegetal, Centro de Edafología y Biología Aplicada del Segura, Consejo Superior de Investigaciones Científicas, Campus de Espinardo, 30100 Murcia, Spain
| | - Vicente Martínez
- Departamento de Nutrición Vegetal, Centro de Edafología y Biología Aplicada del Segura, Consejo Superior de Investigaciones Científicas, Campus de Espinardo, 30100 Murcia, Spain
| | - Francisco J Quintero
- Instituto de Bioquímica Vegetal y Fotosíntesis, cic-Cartuja, Consejo Superior de Investigaciones Científicas-Universidad de Sevilla, 41092 Sevilla, Spain
| | - Jose M Pardo
- Instituto de Bioquímica Vegetal y Fotosíntesis, cic-Cartuja, Consejo Superior de Investigaciones Científicas-Universidad de Sevilla, 41092 Sevilla, Spain
| | - Francisco Rubio
- Departamento de Nutrición Vegetal, Centro de Edafología y Biología Aplicada del Segura, Consejo Superior de Investigaciones Científicas, Campus de Espinardo, 30100 Murcia, Spain
- Author for communication:
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Genome-Wide Analysis of Ribosomal Protein GhRPS6 and Its Role in Cotton Verticillium Wilt Resistance. Int J Mol Sci 2021; 22:ijms22041795. [PMID: 33670294 PMCID: PMC7918698 DOI: 10.3390/ijms22041795] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/06/2021] [Accepted: 02/08/2021] [Indexed: 01/02/2023] Open
Abstract
Verticillium wilt is threatening the world’s cotton production. The pathogenic fungus Verticillium dahliae can survive in the soil in the form of microsclerotia for a long time, colonize through the root of cotton, and invade into vascular bundles, causing yellowing and wilting of cotton leaves, and in serious cases, leading to plant death. Breeding resistant varieties is the most economical and effective method to control Verticillium wilt. In previous studies, proteomic analysis was carried out on different cotton varieties inoculated with V. dahliae strain Vd080. It was found that GhRPS6 was phosphorylated after inoculation, and the phosphorylation level in resistant cultivars was 1.5 times than that in susceptible cultivars. In this study, knockdown of GhRPS6 expression results in the reduction of SA and JA content, and suppresses a series of defensive response, enhancing cotton plants susceptibility to V. dahliae. Overexpression in Arabidopsis thaliana transgenic plants was found to be more resistant to V. dahliae. Further, serines at 237 and 240 were mutated to phenylalanine, respectively and jointly. The transgenic Arabidopsis plants demonstrated that seri-237 compromised the plant resistance to V. dahliae. Subcellular localization in Nicotiana benthamiana showed that GhRPS6 was localized in the nucleus. Additionally, the pathogen inoculation and phosphorylation site mutation did not change its localization. These results indicate that GhRPS6 is a potential molecular target for improving resistance to Verticillium wilt in cotton. This lays a foundation for breeding disease-resistant varieties.
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Dvořák P, Krasylenko Y, Zeiner A, Šamaj J, Takáč T. Signaling Toward Reactive Oxygen Species-Scavenging Enzymes in Plants. FRONTIERS IN PLANT SCIENCE 2021; 11:618835. [PMID: 33597960 PMCID: PMC7882706 DOI: 10.3389/fpls.2020.618835] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Accepted: 12/11/2020] [Indexed: 05/26/2023]
Abstract
Reactive oxygen species (ROS) are signaling molecules essential for plant responses to abiotic and biotic stimuli as well as for multiple developmental processes. They are produced as byproducts of aerobic metabolism and are affected by adverse environmental conditions. The ROS content is controlled on the side of their production but also by scavenging machinery. Antioxidant enzymes represent a major ROS-scavenging force and are crucial for stress tolerance in plants. Enzymatic antioxidant defense occurs as a series of redox reactions for ROS elimination. Therefore, the deregulation of the antioxidant machinery may lead to the overaccumulation of ROS in plants, with negative consequences both in terms of plant development and resistance to environmental challenges. The transcriptional activation of antioxidant enzymes accompanies the long-term exposure of plants to unfavorable environmental conditions. Fast ROS production requires the immediate mobilization of the antioxidant defense system, which may occur via retrograde signaling, redox-based modifications, and the phosphorylation of ROS detoxifying enzymes. This review aimed to summarize the current knowledge on signaling processes regulating the enzymatic antioxidant capacity of plants.
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25
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Xi L, Zhang Z, Herold S, Kassem S, Wu XN, Schulze WX. Phosphorylation Site Motifs in Plant Protein Kinases and Their Substrates. Methods Mol Biol 2021; 2358:1-16. [PMID: 34270043 DOI: 10.1007/978-1-0716-1625-3_1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Protein phosphorylation is an important cellular regulatory mechanism affecting the activity, localization, conformation, and interaction of proteins. Protein phosphorylation is catalyzed by kinases, and thus kinases are the enzymes regulating cellular signaling cascades. In the model plant Arabidopsis, 940 genes encode for kinases. The substrate proteins of kinases are phosphorylated at defined sites, which consist of common patterns around the phosphorylation site, known as phosphorylation motifs. The discovery of kinase specificity with a preference of phosphorylation of certain motifs and application of such motifs in deducing signaling cascades helped to reveal underlying regulation mechanisms, and facilitated the prediction of kinase-target pairs. In this mini-review, we took advantage of retrieved data as examples to present the functions of kinase families along with their commonly found phosphorylation motifs from their substrates.
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Affiliation(s)
- Lin Xi
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany.
| | - Zhaoxia Zhang
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany
| | - Sandra Herold
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany
| | - Sarah Kassem
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany
| | - Xu Na Wu
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan and Center for Life Science, School of Life Sciences, Yunnan University, Kunming, China
| | - Waltraud X Schulze
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany
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26
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PhosPhAt 4.0: An Updated Arabidopsis Database for Searching Phosphorylation Sites and Kinase-Target Interactions. Methods Mol Biol 2021; 2358:189-202. [PMID: 34270056 DOI: 10.1007/978-1-0716-1625-3_14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The PhosPhAt 4.0 database contains information on Arabidopsis phosphorylation sites identified by mass spectrometry in large-scale experiments from different research groups. So far PhosPhAt 4.0 has been one of the most significant large-scale data resources for plant phosphorylation studies. Functionalities of the web application, besides display of phosphorylation sites, include phosphorylation site prediction and kinase-target relationships retrieval. Here, we present an overview and user instructions for the PhosPhAt 4.0 database, with strong emphasis on recent renewals regarding protein annotation by SUBA4.0 and Mapman4, and additional phosphorylation site information imported from other databases, such as UniProt. Here, we provide a user guide for the retrieval of phosphorylation motifs from the kinase-target database and how to visualize these results. The improvements incorporated into the PhosPhAt 4.0 database have produced much more functionality and user flexibility for phosphoproteomic analysis.
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27
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Abstract
Plants are an important part of nature because as photoautotrophs, they provide a nutrient source for many other living organisms. Due to their sessile nature, to overcome both biotic and abiotic stresses, plants have developed intricate mechanisms for perception of and reaction to these stresses, both on an external level (perception) and on an internal level (reaction). Specific proteins found within cells play crucial roles in stress mitigation by enhancing cellular processes that facilitate the plants survival during the unfavorable conditions. Well before plants are able to synthesize nascent proteins in response to stress, proteins which already exist in the cell can be subjected to an array of posttranslation modifications (PTMs) that permit a rapid response. These activated proteins can, in turn, aid in further stress responses. Different PTMs have different functions in growth and development of plants. Protein phosphorylation, a reversible form of modification has been well elucidated, and its role in signaling cascades is well documented. In this mini-review, we discuss the integration of protein phosphorylation with other components of abiotic stress-responsive pathways including phytohormones and ion homeostasis. Overall, this review demonstrates the high interconnectivity of the stress response system in plants and how readily plants are able to toggle between various signaling pathways in order to survive harsh conditions. Most notably, fluctuations of the cytosolic calcium levels seem to be a linking component of the various signaling pathways.
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Affiliation(s)
- Rebecca Njeri Damaris
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Science, Hubei University, Wuhan, China
| | - Pingfang Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Science, Hubei University, Wuhan, China.
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28
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Kamal MM, Ishikawa S, Takahashi F, Suzuki K, Kamo M, Umezawa T, Shinozaki K, Kawamura Y, Uemura M. Large-Scale Phosphoproteomic Study of Arabidopsis Membrane Proteins Reveals Early Signaling Events in Response to Cold. Int J Mol Sci 2020; 21:E8631. [PMID: 33207747 PMCID: PMC7696906 DOI: 10.3390/ijms21228631] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/12/2020] [Accepted: 11/13/2020] [Indexed: 12/22/2022] Open
Abstract
Cold stress is one of the major factors limiting global crop production. For survival at low temperatures, plants need to sense temperature changes in the surrounding environment. How plants sense and respond to the earliest drop in temperature is still not clearly understood. The plasma membrane and its adjacent extracellular and cytoplasmic sites are the first checkpoints for sensing temperature changes and the subsequent events, such as signal generation and solute transport. To understand how plants respond to early cold exposure, we used a mass spectrometry-based phosphoproteomic method to study the temporal changes in protein phosphorylation events in Arabidopsis membranes during 5 to 60 min of cold exposure. The results revealed that brief cold exposures led to rapid phosphorylation changes in the proteins involved in cellular ion homeostasis, solute and protein transport, cytoskeleton organization, vesical trafficking, protein modification, and signal transduction processes. The phosphorylation motif and kinase-substrate network analysis also revealed that multiple protein kinases, including RLKs, MAPKs, CDPKs, and their substrates, could be involved in early cold signaling. Taken together, our results provide a first look at the cold-responsive phosphoproteome changes of Arabidopsis membrane proteins that can be a significant resource to understand how plants respond to an early temperature drop.
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Affiliation(s)
- Md Mostafa Kamal
- United Graduate School of Agricultural Sciences, Iwate University, Morioka 020-8550, Japan; (M.M.K.); (Y.K.)
| | - Shinnosuke Ishikawa
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Koganei 184-8588, Japan; (S.I.); (T.U.)
| | - Fuminori Takahashi
- Gene Discovery Research Group, RIKEN Center for Sustainable Resource Science, 3-1-1 Koyadai, Tsukuba 305-0074, Japan; (F.T.); (K.S.)
| | - Ko Suzuki
- Department of Biochemistry, Iwate Medical University, Yahaba 028-3694, Japan; (K.S.); (M.K.)
| | - Masaharu Kamo
- Department of Biochemistry, Iwate Medical University, Yahaba 028-3694, Japan; (K.S.); (M.K.)
| | - Taishi Umezawa
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Koganei 184-8588, Japan; (S.I.); (T.U.)
| | - Kazuo Shinozaki
- Gene Discovery Research Group, RIKEN Center for Sustainable Resource Science, 3-1-1 Koyadai, Tsukuba 305-0074, Japan; (F.T.); (K.S.)
| | - Yukio Kawamura
- United Graduate School of Agricultural Sciences, Iwate University, Morioka 020-8550, Japan; (M.M.K.); (Y.K.)
- Department of Plant-Bioscience, Faculty of Agriculture, Iwate University, Morioka 020-8550, Japan
| | - Matsuo Uemura
- United Graduate School of Agricultural Sciences, Iwate University, Morioka 020-8550, Japan; (M.M.K.); (Y.K.)
- Department of Plant-Bioscience, Faculty of Agriculture, Iwate University, Morioka 020-8550, Japan
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Kong Q, Singh SK, Mantyla JJ, Pattanaik S, Guo L, Yuan L, Benning C, Ma W. TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR4 Interacts with WRINKLED1 to Mediate Seed Oil Biosynthesis. PLANT PHYSIOLOGY 2020; 184:658-665. [PMID: 32663164 PMCID: PMC7536675 DOI: 10.1104/pp.20.00547] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 06/27/2020] [Indexed: 05/20/2023]
Abstract
Cross-family transcription factor (TF) interactions play critical roles in the regulation of plant developmental and metabolic pathways. WRINKLED1 (WRI1) is a key TF governing oil biosynthesis in plants. However, little is known about WRI1-interacting factors and their roles in oil biosynthesis. We screened a TF library using Arabidopsis (Arabidopsis thaliana) WRI1 (AtWRI1) as bait in yeast two-hybrid assays and identified three TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR (TCP) family TFs, namely TCP4, TCP10, and TCP24, as AtWRI1-interacting partners. The physical interaction between AtWRI1 and TCPs was further validated using bimolecular fluorescence complementation assays. TCPs play important roles in various plant developmental processes; however, their involvement in fatty acid biosynthesis was not previously known. Coexpression of TCP4, but not TCP10 or TCP24, with AtWRI1 reduced AtWRI1-mediated oil biosynthesis in Nicotiana benthamiana leaves. Transcriptomic analysis in transgenic Arabidopsis plants with enhanced TCP4 activity engineered by expressing rTCP4 (i.e. miR319-resistant TCP4) revealed that AtWRI1 target genes were significantly repressed. TCP4 expression is strongly correlated with AtWRI1 during embryo development. A tcp4 loss-of-function mutant, the jaw-D mutant with a strong reduction of TCP4 expression, and a tcp2 tcp4 tcp10 triple mutant accumulated more seed oil than wild-type Arabidopsis. In addition, TCP4 repressed the AtWRI1-mediated transactivation of the promoters of fatty acid biosynthetic genes. Collectively, our findings suggest that TCP4 represses fatty acid biosynthetic gene expression through interaction with AtWRI1, leading to a reduction of AtWRI1-mediated seed oil accumulation.
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Affiliation(s)
- Que Kong
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, Michigan 48824
| | - Sanjay K Singh
- Department of Plant and Soil Sciences, Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, Kentucky 40546
| | - Jenny J Mantyla
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
| | - Sitakanta Pattanaik
- Department of Plant and Soil Sciences, Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, Kentucky 40546
| | - Liang Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Ling Yuan
- Department of Plant and Soil Sciences, Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, Kentucky 40546
| | - Christoph Benning
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, Michigan 48824
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Wei Ma
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, Michigan 48824
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30
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Xiao Z, Yang C, Liu C, Yang L, Yang S, Zhou J, Li F, Jiang L, Xiao S, Gao C, Shen W. SINAT E3 ligases regulate the stability of the ESCRT component FREE1 in response to iron deficiency in plants. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2020; 62:1399-1417. [PMID: 32786047 DOI: 10.1111/jipb.13005] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 08/12/2020] [Indexed: 05/18/2023]
Abstract
The endosomal sorting complex required for transport (ESCRT) machinery is an ancient, evolutionarily conserved membrane remodeling complex that is essential for multivesicular body (MVB) biogenesis in eukaryotes. FYVE DOMAIN PROTEIN REQUIRED FOR ENDOSOMAL SORTING 1 (FREE1), which was previously identified as a plant-specific ESCRT component, modulates MVB-mediated endosomal sorting and autophagic degradation. Although the basic cellular functions of FREE1 as an ESCRT component have been described, the regulators that control FREE1 turnover remain unknown. Here, we analyzed how FREE1 homeostasis is mediated by the RING-finger E3 ubiquitin ligases, SINA of Arabidopsis thaliana (SINATs), in response to iron deficiency. Under iron-deficient growth conditions, SINAT1-4 were induced and ubiquitinated FREE1, thereby promoting its degradation and relieving the repressive effect of FREE1 on iron absorption. By contrast, SINAT5, another SINAT member that lacks ubiquitin ligase activity due to the absence of the RING domain, functions as a protector protein which stabilizes FREE1. Collectively, our findings uncover a hitherto unknown mechanism of homeostatic regulation of FREE1, and demonstrate a unique regulatory SINAT-FREE1 module that subtly regulates plant response to iron deficiency stress.
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Affiliation(s)
- Zhidan Xiao
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Chao Yang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Chuanliang Liu
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Lianming Yang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Shuhong Yang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Jun Zhou
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, 510631, China
| | - Faqiang Li
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Liwen Jiang
- School of Life Sciences, Center for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, New Territories, Hong Kong, China
| | - Shi Xiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Caiji Gao
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Wenjin Shen
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
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31
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Lu J, Fu Y, Li M, Wang S, Wang J, Yang Q, Ye J, Zhang X, Ma H, Chang F. Global Quantitative Proteomics Studies Revealed Tissue-Preferential Expression and Phosphorylation of Regulatory Proteins in Arabidopsis. Int J Mol Sci 2020; 21:ijms21176116. [PMID: 32854314 PMCID: PMC7503369 DOI: 10.3390/ijms21176116] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 08/18/2020] [Accepted: 08/21/2020] [Indexed: 12/24/2022] Open
Abstract
Organogenesis in plants occurs across all stages of the life cycle. Although previous studies have identified many genes as important for either vegetative or reproductive development at the RNA level, global information on translational and post-translational levels remains limited. In this study, six Arabidopsis stages/organs were analyzed using quantitative proteomics and phosphoproteomics, identifying 2187 non-redundant proteins and evidence for 1194 phosphoproteins. Compared to the expression observed in cauline leaves, the expression of 1445, 1644, and 1377 proteins showed greater than 1.5-fold alterations in stage 1–9 flowers, stage 10–12 flowers, and open flowers, respectively. Among these, 294 phosphoproteins with 472 phosphorylation sites were newly uncovered, including 275 phosphoproteins showing differential expression patterns, providing molecular markers and possible candidates for functional studies. Proteins encoded by genes preferentially expressed in anther (15), meiocyte (4), or pollen (15) were enriched in reproductive organs, and mutants of two anther-preferentially expressed proteins, acos5 and mee48, showed obviously reduced male fertility with abnormally organized pollen exine. In addition, more phosphorylated proteins were identified in reproductive stages (1149) than in the vegetative organs (995). The floral organ-preferential phosphorylation of GRP17, CDC2/CDKA.1, and ATSK11 was confirmed with western blot analysis. Moreover, phosphorylation levels of CDPK6 and MAPK6 and their interacting proteins were elevated in reproductive tissues. Overall, our study yielded extensive data on protein expression and phosphorylation at six stages/organs and provides an important resource for future studies investigating the regulatory mechanisms governing plant development.
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Affiliation(s)
- Jianan Lu
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and Institute of Biodiversity Sciences, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China; (J.L.); (Y.F.); (M.L.); (S.W.); (J.W.); (Q.Y.); (J.Y.); (X.Z.)
| | - Ying Fu
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and Institute of Biodiversity Sciences, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China; (J.L.); (Y.F.); (M.L.); (S.W.); (J.W.); (Q.Y.); (J.Y.); (X.Z.)
| | - Mengyu Li
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and Institute of Biodiversity Sciences, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China; (J.L.); (Y.F.); (M.L.); (S.W.); (J.W.); (Q.Y.); (J.Y.); (X.Z.)
| | - Shuangshuang Wang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and Institute of Biodiversity Sciences, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China; (J.L.); (Y.F.); (M.L.); (S.W.); (J.W.); (Q.Y.); (J.Y.); (X.Z.)
| | - Jingya Wang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and Institute of Biodiversity Sciences, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China; (J.L.); (Y.F.); (M.L.); (S.W.); (J.W.); (Q.Y.); (J.Y.); (X.Z.)
| | - Qi Yang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and Institute of Biodiversity Sciences, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China; (J.L.); (Y.F.); (M.L.); (S.W.); (J.W.); (Q.Y.); (J.Y.); (X.Z.)
| | - Juanying Ye
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and Institute of Biodiversity Sciences, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China; (J.L.); (Y.F.); (M.L.); (S.W.); (J.W.); (Q.Y.); (J.Y.); (X.Z.)
| | - Xumin Zhang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and Institute of Biodiversity Sciences, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China; (J.L.); (Y.F.); (M.L.); (S.W.); (J.W.); (Q.Y.); (J.Y.); (X.Z.)
| | - Hong Ma
- Department of Biology, the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Correspondence: (H.M.); (F.C.); Tel.: +86-021-51630534 (H.M.); +1-814-865-5343 (F.C.)
| | - Fang Chang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and Institute of Biodiversity Sciences, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China; (J.L.); (Y.F.); (M.L.); (S.W.); (J.W.); (Q.Y.); (J.Y.); (X.Z.)
- Correspondence: (H.M.); (F.C.); Tel.: +86-021-51630534 (H.M.); +1-814-865-5343 (F.C.)
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32
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Shi XX, Wu FX, Mei LC, Wang YL, Hao GF, Yang GF. Bioinformatics toolbox for exploring protein phosphorylation network. Brief Bioinform 2020; 22:5871447. [PMID: 32666116 DOI: 10.1093/bib/bbaa134] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 05/15/2020] [Accepted: 06/02/2020] [Indexed: 01/23/2023] Open
Abstract
A clear systematic delineation of the interactions between phosphorylation sites on substrates and their effector kinases plays a fundamental role in revealing cellular activities, understanding signaling modulation mechanisms and proposing novel hypotheses. The emergence of bioinformatics tools contributes to studying phosphorylation network. Some of them feature the visualization of network, enabling more effective trace of the underlying biological problems in a clear and succinct way. In this review, we aimed to provide a toolbox for exploring phosphorylation network. We first systematically surveyed 19 tools that are available for exploring phosphorylation networks, and subsequently comparatively analyzed and summarized these tools to guide tool selection in terms of functionality, data sources, performance, network visualization and implementation, and finally briefly discussed the application cases of these tools. In different scenarios, the conclusion on the suitability of a tool for a specific user may vary. Nevertheless, easily accessible bioinformatics tools are proved to facilitate biological findings. Hopefully, this work might also assist non-specialists, students, as well as computational scientists who aim at developing novel tools in the field of phosphorylation modification.
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Affiliation(s)
- Xing-Xing Shi
- College of Chemistry, Central China Normal University (CCNU)
| | | | | | - Yu-Liang Wang
- College of Chemistry, Central China Normal University (CCNU)
| | - Ge-Fei Hao
- Bioinformatics in State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering of GZU and College of Chemistry of CCNU
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33
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Facciuolo A, Denomy C, Lipsit S, Kusalik A, Napper S. From Beef to Bees: High-Throughput Kinome Analysis to Understand Host Responses of Livestock Species to Infectious Diseases and Industry-Associated Stress. Front Immunol 2020; 11:765. [PMID: 32499776 PMCID: PMC7243914 DOI: 10.3389/fimmu.2020.00765] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 04/06/2020] [Indexed: 11/13/2022] Open
Abstract
Within human health research, the remarkable utility of kinase inhibitors as therapeutics has motivated efforts to understand biology at the level of global cellular kinase activity (the kinome). In contrast, the diminished potential for using kinase inhibitors in food animals has dampened efforts to translate this research approach to livestock species. This, in our opinion, was a lost opportunity for livestock researchers given the unique potential of kinome analysis to offer insight into complex biology. To remedy this situation, our lab developed user-friendly, cost-effective approaches for kinome analysis that can be readily incorporated into most research programs but with a specific priority to enable the technology to livestock researchers. These contributions include the development of custom software programs for the creation of species-specific kinome arrays as well as comprehensive deconvolution and analysis of kinome array data. Presented in this review are examples of the application of kinome analysis to highlight the utility of the technology to further our understanding of two key complex biological events of priority to the livestock industry: host immune responses to infectious diseases and animal stress responses. These advances and examples of application aim to provide both mechanisms and motivation for researchers, particularly livestock researchers, to incorporate kinome analysis into their research programs.
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Affiliation(s)
- Antonio Facciuolo
- Vaccine and Infectious Disease Organization - International Vaccine Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Connor Denomy
- Vaccine and Infectious Disease Organization - International Vaccine Centre, University of Saskatchewan, Saskatoon, SK, Canada.,Department of Computer Science, University of Saskatchewan, Saskatoon, SK, Canada
| | - Sean Lipsit
- Vaccine and Infectious Disease Organization - International Vaccine Centre, University of Saskatchewan, Saskatoon, SK, Canada.,Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Anthony Kusalik
- Department of Computer Science, University of Saskatchewan, Saskatoon, SK, Canada
| | - Scott Napper
- Vaccine and Infectious Disease Organization - International Vaccine Centre, University of Saskatchewan, Saskatoon, SK, Canada.,Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, Canada
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Ambrosino L, Colantuono C, Diretto G, Fiore A, Chiusano ML. Bioinformatics Resources for Plant Abiotic Stress Responses: State of the Art and Opportunities in the Fast Evolving -Omics Era. PLANTS 2020; 9:plants9050591. [PMID: 32384671 PMCID: PMC7285221 DOI: 10.3390/plants9050591] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 04/24/2020] [Accepted: 04/29/2020] [Indexed: 12/13/2022]
Abstract
Abiotic stresses are among the principal limiting factors for productivity in agriculture. In the current era of continuous climate changes, the understanding of the molecular aspects involved in abiotic stress response in plants is a priority. The rise of -omics approaches provides key strategies to promote effective research in the field, facilitating the investigations from reference models to an increasing number of species, tolerant and sensitive genotypes. Integrated multilevel approaches, based on molecular investigations at genomics, transcriptomics, proteomics and metabolomics levels, are now feasible, expanding the opportunities to clarify key molecular aspects involved in responses to abiotic stresses. To this aim, bioinformatics has become fundamental for data production, mining and integration, and necessary for extracting valuable information and for comparative efforts, paving the way to the modeling of the involved processes. We provide here an overview of bioinformatics resources for research on plant abiotic stresses, describing collections from -omics efforts in the field, ranging from raw data to complete databases or platforms, highlighting opportunities and still open challenges in abiotic stress research based on -omics technologies.
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Affiliation(s)
- Luca Ambrosino
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici (Na), Italy; (L.A.); (C.C.)
- Department of Research Infrastructures for Marine Biological Resources (RIMAR), 80121 Naples, Italy
| | - Chiara Colantuono
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici (Na), Italy; (L.A.); (C.C.)
- Department of Research Infrastructures for Marine Biological Resources (RIMAR), 80121 Naples, Italy
| | - Gianfranco Diretto
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), 00123 Rome, Italy; (G.D.); (A.F.)
| | - Alessia Fiore
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), 00123 Rome, Italy; (G.D.); (A.F.)
| | - Maria Luisa Chiusano
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici (Na), Italy; (L.A.); (C.C.)
- Department of Research Infrastructures for Marine Biological Resources (RIMAR), 80121 Naples, Italy
- Correspondence: ; Tel.: +39-081-253-9492
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Baune MC, Lansing H, Fischer K, Meyer T, Charton L, Linka N, von Schaewen A. The Arabidopsis Plastidial Glucose-6-Phosphate Transporter GPT1 is Dually Targeted to Peroxisomes via the Endoplasmic Reticulum. THE PLANT CELL 2020; 32:1703-1726. [PMID: 32111666 PMCID: PMC7203913 DOI: 10.1105/tpc.19.00959] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 01/28/2020] [Accepted: 02/28/2020] [Indexed: 05/22/2023]
Abstract
Studies on Glucose-6-phosphate (G6P)/phosphate translocator isoforms GPT1 and GPT2 reported the viability of Arabidopsis (Arabidopsis thaliana) gpt2 mutants, whereas heterozygous gpt1 mutants exhibited a variety of defects during fertilization/seed set, indicating that GPT1 is essential for this process. Among other functions, GPT1 was shown to be important for pollen and embryo-sac development. Because our previous work on the irreversible part of the oxidative pentose phosphate pathway (OPPP) revealed comparable effects, we investigated whether GPT1 may dually localize to plastids and peroxisomes. In reporter fusions, GPT2 localized to plastids, but GPT1 also localized to the endoplasmic reticulum (ER) and around peroxisomes. GPT1 contacted two oxidoreductases and also peroxins that mediate import of peroxisomal membrane proteins from the ER, hinting at dual localization. Reconstitution in yeast (Saccharomyces cerevisiae) proteoliposomes revealed that GPT1 preferentially exchanges G6P for ribulose-5-phosphate (Ru5P). Complementation analyses of heterozygous +/gpt1 plants demonstrated that GPT2 is unable to compensate for GPT1 in plastids, whereas GPT1 without the transit peptide (enforcing ER/peroxisomal localization) increased gpt1 transmission significantly. Because OPPP activity in peroxisomes is essential for fertilization, and immunoblot analyses hinted at the presence of unprocessed GPT1-specific bands, our findings suggest that GPT1 is indispensable in both plastids and peroxisomes. Together with its G6P-Ru5P exchange preference, GPT1 appears to play a role distinct from that of GPT2 due to dual targeting.
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Affiliation(s)
- Marie-Christin Baune
- Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität Münster, 48149 Münster, Germany
| | - Hannes Lansing
- Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität Münster, 48149 Münster, Germany
| | - Kerstin Fischer
- Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität Münster, 48149 Münster, Germany
| | - Tanja Meyer
- Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität Münster, 48149 Münster, Germany
| | - Lennart Charton
- Biochemie der Pflanzen, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Nicole Linka
- Biochemie der Pflanzen, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Antje von Schaewen
- Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität Münster, 48149 Münster, Germany
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Zhang Y, Shi Y, Zhao L, Wei F, Feng Z, Feng H. Phosphoproteomics Profiling of Cotton ( Gossypium hirsutum L.) Roots in Response to Verticillium dahliae Inoculation. ACS OMEGA 2019; 4:18434-18443. [PMID: 31720547 PMCID: PMC6844108 DOI: 10.1021/acsomega.9b02634] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 10/11/2019] [Indexed: 06/10/2023]
Abstract
Verticillium wilt is a plant vascular disease causing severe yield and quality losses in many crops and is caused by the soil-borne plant pathogenic fungus Verticillium dahliae. To investigate the molecular mechanisms of the cotton-V. dahliae interaction, a time-course phosphoproteomic analysis of roots of susceptible and resistant cotton lines in response to V. dahliae was performed. In total, 1716 unique phosphoproteins were identified in the susceptible (S) and resistant (R) cotton lines. Of these, 359 phosphoproteins were significantly different in R1 (1 day after V. dahliae inoculation) vs R0 (mock) group and 287 phosphoproteins in R2 (3 days after V. dahliae inoculation) vs R0 group. Moreover, 263 proteins of V. dahliae-regulated phosphoproteins were significantly changed in S1 (1 day after V. dahliae inoculation) vs S0 (mock) group and 197 proteins in S2 (3 days after V. dahliae inoculation) vs S0 group. Thirty phosphoproteins were significantly changed and common to the resistant and susceptible cotton lines following inoculation with V. dahliae. Specifically, 92 phosphoproteins were shared in both in R1 vs R0 and R2 vs R0 but not in susceptible cotton lines. There were 38 common phosphoproteins shared in both S1 vs S0 and S2 vs S0 but not in resistant cotton lines. GO terms and Kyoto Encyclopedia of Genes and Genomes pathway analyses displayed an abundance of known and novel phosphoproteins related to plant-pathogen interactions, signal transduction, and metabolic processes, which were correlated with resistance against fungal infection. These data provide new perspectives and inspiration for understanding molecular defense mechanisms of cotton roots against V. dahliae infection.
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Affiliation(s)
- Yihao Zhang
- Zhengzhou
Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou 450001, China
| | - Yongqiang Shi
- State
Key Laboratory of Cotton Biology, Institute
of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, Henan 455000, China
| | - Lihong Zhao
- State
Key Laboratory of Cotton Biology, Institute
of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, Henan 455000, China
| | - Feng Wei
- Zhengzhou
Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou 450001, China
- State
Key Laboratory of Cotton Biology, Institute
of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, Henan 455000, China
| | - Zili Feng
- State
Key Laboratory of Cotton Biology, Institute
of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, Henan 455000, China
| | - Hongjie Feng
- Zhengzhou
Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou 450001, China
- State
Key Laboratory of Cotton Biology, Institute
of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, Henan 455000, China
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Cheng G, Chen Q, Zhang R. Prediction of phosphorylation sites based on granular support vector machine. GRANULAR COMPUTING 2019. [DOI: 10.1007/s41066-019-00202-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Cruz ER, Nguyen H, Nguyen T, Wallace IS. Functional analysis tools for post-translational modification: a post-translational modification database for analysis of proteins and metabolic pathways. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 99:1003-1013. [PMID: 31034103 DOI: 10.1111/tpj.14372] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 04/03/2019] [Accepted: 04/17/2019] [Indexed: 05/23/2023]
Abstract
Post-translational modifications (PTMs) are critical regulators of protein function, and nearly 200 different types of PTM have been identified. Advances in high-resolution mass spectrometry have led to the identification of an unprecedented number of PTM sites in numerous organisms, potentially facilitating a more complete understanding of how PTMs regulate cellular behavior. While databases have been created to house the resulting data, most of these resources focus on individual types of PTM, do not consider quantitative PTM analyses or do not provide tools for the visualization and analysis of PTM data. Here, we describe the Functional Analysis Tools for Post-Translational Modifications (FAT-PTM) database (https://bioinformatics.cse.unr.edu/fat-ptm/), which currently supports eight different types of PTM and over 49 000 PTM sites identified in large-scale proteomic surveys of the model organism Arabidopsis thaliana. The FAT-PTM database currently supports tools to visualize protein-centric PTM networks, quantitative phosphorylation site data from over 10 different quantitative phosphoproteomic studies, PTM information displayed in protein-centric metabolic pathways and groups of proteins that are co-modified by multiple PTMs. Overall, the FAT-PTM database provides users with a robust platform to share and visualize experimentally supported PTM data, develop hypotheses related to target proteins or identify emergent patterns in PTM data for signaling and metabolic pathways.
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Affiliation(s)
- Edward R Cruz
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Reno, NV, 89557, USA
| | - Hung Nguyen
- Department of Computer Science and Engineering, University of Nevada, Reno, Reno, NV, 89557, USA
| | - Tin Nguyen
- Department of Computer Science and Engineering, University of Nevada, Reno, Reno, NV, 89557, USA
| | - Ian S Wallace
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Reno, NV, 89557, USA
- Department of Chemistry, University of Nevada, Reno, Reno, NV, 89557, USA
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Geng F, Liu X, Wang J, He R, Zhao J, Xiang D, Zou L, Peng L, Zhao G. In-depth mapping of the seed phosphoproteome and N-glycoproteome of Tartary buckwheat (Fagopyrum tataricum) using off-line high pH RPLC fractionation and nLC-MS/MS. Int J Biol Macromol 2019; 137:688-696. [DOI: 10.1016/j.ijbiomac.2019.07.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 03/21/2019] [Accepted: 07/03/2019] [Indexed: 12/18/2022]
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40
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Hunter K, Kimura S, Rokka A, Tran HC, Toyota M, Kukkonen JP, Wrzaczek M. CRK2 Enhances Salt Tolerance by Regulating Callose Deposition in Connection with PLD α1. PLANT PHYSIOLOGY 2019; 180:2004-2021. [PMID: 31118265 PMCID: PMC6670071 DOI: 10.1104/pp.19.00560] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 05/15/2019] [Indexed: 05/03/2023]
Abstract
High salinity is an increasingly prevalent source of stress to which plants must adapt. The receptor-like protein kinases, including members of the Cys-rich receptor-like kinase (CRK) subfamily, are a highly expanded family of transmembrane proteins in plants that are largely responsible for communication between cells and the extracellular environment. Various CRKs have been implicated in biotic and abiotic stress responses; however, their functions on a cellular level remain largely uncharacterized. Here we have shown that CRK2 enhances salt tolerance at the germination stage in Arabidopsis (Arabidopsis thaliana) and also modulates root length. We established that functional CRK2 is required for salt-induced callose deposition. In doing so, we revealed a role for callose deposition in response to increased salinity and demonstrated its importance for salt tolerance during germination. Using fluorescently tagged proteins, we observed specific changes in the subcellular localization of CRK2 in response to various stress treatments. Many of CRK2's cellular functions were dependent on phospholipase D activity, as were the subcellular localization changes. Thus, we propose that CRK2 acts downstream of phospholipase D during salt stress, promoting callose deposition and regulating plasmodesmal permeability, and that CRK2 adopts specific stress-dependent subcellular localization patterns that allow it to carry out its functions.
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Affiliation(s)
- Kerri Hunter
- Viikki Plant Science Centre, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Sachie Kimura
- Viikki Plant Science Centre, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Anne Rokka
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
| | - Huy Cuong Tran
- Viikki Plant Science Centre, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Masatsugu Toyota
- Department of Biochemistry and Molecular Biology, Saitama University, Saitama, Japan
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin
| | - Jyrki P Kukkonen
- Biochemistry and Cell Biology, Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
- Department of Physiology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Michael Wrzaczek
- Viikki Plant Science Centre, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
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Haj Ahmad F, Wu XN, Stintzi A, Schaller A, Schulze WX. The Systemin Signaling Cascade As Derived from Time Course Analyses of the Systemin-responsive Phosphoproteome. Mol Cell Proteomics 2019; 18:1526-1542. [PMID: 31138643 PMCID: PMC6683004 DOI: 10.1074/mcp.ra119.001367] [Citation(s) in RCA: 20] [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: 01/30/2019] [Revised: 05/20/2019] [Indexed: 11/06/2022] Open
Abstract
Systemin is a small peptide with important functions in plant wound response signaling. Although the transcriptional responses of systemin action are well described, the signaling cascades involved in systemin perception and signal transduction at the protein level are poorly understood. Here we used a tomato cell suspension culture system to profile phosphoproteomic responses induced by systemin and its inactive Thr17Ala analog, allowing us to reconstruct a systemin-specific kinase/phosphatase signaling network. Our time-course analysis revealed early phosphorylation events at the plasma membrane, such as dephosphorylation of H+-ATPase, rapid phosphorylation of NADPH-oxidase and Ca2+-ATPase. Later responses involved transient phosphorylation of small GTPases, vesicle trafficking proteins and transcription factors. Based on a correlation analysis of systemin-induced phosphorylation profiles, we predicted substrate candidates for 44 early systemin-responsive kinases, which includes receptor kinases and downstream kinases such as MAP kinases, as well as nine phosphatases. We propose a regulatory module in which H+-ATPase LHA1 is rapidly de-phosphorylated at its C-terminal regulatory residue T955 by phosphatase PLL5, resulting in the alkalization of the growth medium within 2 mins of systemin treatment. We found the MAP kinase MPK2 to have increased phosphorylation level at its activating TEY-motif at 15 min post-treatment. The predicted interaction of MPK2 with LHA1 was confirmed by in vitro kinase assays, suggesting that the H+-ATPase LHA1 is re-activated by MPK2 later in the systemin response. Our data set provides a resource of proteomic events involved in systemin signaling that will be valuable for further in-depth functional studies in elucidation of systemin signaling cascades.
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Affiliation(s)
- Fatima Haj Ahmad
- ‡University of Hohenheim, Institute of Molecular Plant Physiology, 70593 Stuttgart, Germany
| | - Xu Na Wu
- ‡University of Hohenheim, Institute of Molecular Plant Physiology, 70593 Stuttgart, Germany
| | - Annick Stintzi
- ‡University of Hohenheim, Institute of Molecular Plant Physiology, 70593 Stuttgart, Germany
| | - Andreas Schaller
- ‡University of Hohenheim, Institute of Molecular Plant Physiology, 70593 Stuttgart, Germany
| | - Waltraud X Schulze
- ‡University of Hohenheim, Institute of Molecular Plant Physiology, 70593 Stuttgart, Germany.
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Zhang Z, Ke D, Hu M, Zhang C, Deng L, Li Y, Li J, Zhao H, Cheng L, Wang L, Yuan H. Quantitative phosphoproteomic analyses provide evidence for extensive phosphorylation of regulatory proteins in the rhizobia-legume symbiosis. PLANT MOLECULAR BIOLOGY 2019; 100:265-283. [PMID: 30989446 DOI: 10.1007/s11103-019-00857-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 03/18/2019] [Indexed: 06/09/2023]
Abstract
Symbiotic nitrogen fixation in root nodules of grain legumes is essential for high yielding. Protein phosphorylation/dephosphorylation plays important role in root nodule development. Differences in the phosphoproteomes may either be developmental specific and related to nitrogen fixation activity. An iTRAQ-based quantitative phosphoproteomic analyses during nodule development enables identification of specific phosphorylation signaling in the Lotus-rhizobia symbiosis. During evolution, legumes (Fabaceae) have evolved a symbiotic relationship with rhizobia, which fix atmospheric nitrogen and produce ammonia that host plants can then absorb. Root nodule development depends on the activation of protein phosphorylation-mediated signal transduction cascades. To investigate possible molecular mechanisms of protein modulation during nodule development, we used iTRAQ-based quantitative proteomic analyses to identify root phosphoproteins during rhizobial colonization and infection of Lotus japonicus. 1154 phosphoproteins with 2957 high-confidence phosphorylation sites were identified. Gene ontology enrichment analysis of functional groups of these genes revealed that the biological processes mediated by these proteins included cellular processes, signal transduction, and transporter activity. Quantitative data highlighted the dynamics of protein phosphorylation during nodule development and, based on regulatory trends, seven groups were identified. RNA splicing and brassinosteroid (BR) signaling pathways were extensively affected by phosphorylation, and most Ser/Arg-rich (SR) proteins were multiply phosphorylated. In addition, many proposed kinase-substrate pairs were predicted, and in these MAPK6 substrates were found to be highly enriched. This study offers insights into the regulatory processes underlying nodule development, provides an accessible resource cataloging the phosphorylation status of thousands of Lotus proteins during nodule development, and develops our understanding of post-translational regulatory mechanisms in the Lotus-rhizobia symbiosis.
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Affiliation(s)
- Zaibao Zhang
- Henan Key Laboratory of Tea Plant Biology, Xinyang Normal University, Xinyang, Henan, China
- College of Life Science, Xinyang Normal University, Xinyang, Henan, China
| | - Danxia Ke
- Henan Key Laboratory of Tea Plant Biology, Xinyang Normal University, Xinyang, Henan, China
- College of Life Science, Xinyang Normal University, Xinyang, Henan, China
| | - Menghui Hu
- College of Life Science, Xinyang Normal University, Xinyang, Henan, China
| | - Chi Zhang
- College of Life Science, Xinyang Normal University, Xinyang, Henan, China
| | - Lijun Deng
- College of Life Science, Xinyang Normal University, Xinyang, Henan, China
| | - Yuting Li
- College of Life Science, Xinyang Normal University, Xinyang, Henan, China
| | - Jiuli Li
- College of Life Science, Xinyang Normal University, Xinyang, Henan, China
| | - Hai Zhao
- College of Life Science, Xinyang Normal University, Xinyang, Henan, China
| | - Lin Cheng
- College of Life Science, Xinyang Normal University, Xinyang, Henan, China
| | - Lei Wang
- Henan Key Laboratory of Tea Plant Biology, Xinyang Normal University, Xinyang, Henan, China.
- College of Life Science, Xinyang Normal University, Xinyang, Henan, China.
| | - Hongyu Yuan
- Henan Key Laboratory of Tea Plant Biology, Xinyang Normal University, Xinyang, Henan, China.
- College of Life Science, Xinyang Normal University, Xinyang, Henan, China.
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Subba P, Narayana Kotimoole C, Prasad TSK. Plant Proteome Databases and Bioinformatic Tools: An Expert Review and Comparative Insights. ACTA ACUST UNITED AC 2019; 23:190-206. [DOI: 10.1089/omi.2019.0024] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Pratigya Subba
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Chinmaya Narayana Kotimoole
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Thottethodi Subrahmanya Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
- Institute of Bioinformatics, International Technology Park, Bangalore, India
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Polko JK, Kieber JJ. The Regulation of Cellulose Biosynthesis in Plants. THE PLANT CELL 2019; 31:282-296. [PMID: 30647077 PMCID: PMC6447023 DOI: 10.1105/tpc.18.00760] [Citation(s) in RCA: 130] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 11/26/2018] [Accepted: 01/09/2019] [Indexed: 05/18/2023]
Abstract
Cell walls define the shape of plant cells, controlling the extent and orientation of cell elongation, and hence organ growth. The main load-bearing component of plant cell walls is cellulose, and how plants regulate its biosynthesis during development and in response to various environmental perturbations is a central question in plant biology. Cellulose is synthesized by cellulose synthase (CESA) complexes (CSCs) that are assembled in the Golgi apparatus and then delivered to the plasma membrane (PM), where they actively synthesize cellulose. CSCs travel along cortical microtubule paths that define the orientation of synthesis of the cellulose microfibrils. CSCs recycle between the PM and various intracellular compartments, and this trafficking plays an important role in determining the level of cellulose synthesized. In this review, we summarize recent findings in CESA complex organization, CESA posttranslational modifications and trafficking, and other components that interact with CESAs. We also discuss cell wall integrity maintenance, with a focus on how this impacts cellulose biosynthesis.
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Affiliation(s)
- Joanna K Polko
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Joseph J Kieber
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599
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Arsova B, Watt M, Usadel B. Monitoring of Plant Protein Post-translational Modifications Using Targeted Proteomics. FRONTIERS IN PLANT SCIENCE 2018; 9:1168. [PMID: 30174677 PMCID: PMC6107839 DOI: 10.3389/fpls.2018.01168] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 07/23/2018] [Indexed: 05/19/2023]
Abstract
Protein post-translational modifications (PTMs) are among the fastest and earliest of plant responses to changes in the environment, making the mechanisms and dynamics of PTMs an important area of plant science. One of the most studied PTMs is protein phosphorylation. This review summarizes the use of targeted proteomics for the elucidation of the biological functioning of plant PTMs, and focuses primarily on phosphorylation. Since phosphorylated peptides have a low abundance, usually complex enrichment protocols are required for their research. Initial identification is usually performed with discovery phosphoproteomics, using high sensitivity mass spectrometers, where as many phosphopeptides are measured as possible. Once a PTM site is identified, biological characterization can be addressed with targeted proteomics. In targeted proteomics, Selected/Multiple Reaction Monitoring (S/MRM) is traditionally coupled to simple, standard protein digestion protocols, often omitting the enrichment step, and relying on triple-quadruple mass spectrometer. The use of synthetic peptides as internal standards allows accurate identification, avoiding cross-reactivity typical for some antibody based approaches. Importantly, internal standards allow absolute peptide quantitation, reported down to 0.1 femtomoles, also useful for determination of phospho-site occupancy. S/MRM is advantageous in situations where monitoring and diagnostics of peptide PTM status is needed for many samples, as it has faster sample processing times, higher throughput than other approaches, and excellent quantitation and reproducibility. Furthermore, the number of publicly available data-bases with plant PTM discovery data is growing, facilitating selection of modified peptides and design of targeted proteomics workflows. Recent instrument developments result in faster scanning times, inclusion of ion-trap instruments leading to parallel reaction monitoring- which further facilitates S/MRM experimental design. Finally, recent combination of data independent and data dependent spectra acquisition means that in addition to anticipated targeted data, spectra can now be queried for unanticipated information. The potential for future applications in plant biology is outlined.
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Affiliation(s)
- Borjana Arsova
- Institut für Bio- und Geowissenschaften, IBG-2–Plant Sciences, Forschungszentrum Jülich, Jülich, Germany
| | - Michelle Watt
- Institut für Bio- und Geowissenschaften, IBG-2–Plant Sciences, Forschungszentrum Jülich, Jülich, Germany
| | - Björn Usadel
- Institut für Bio- und Geowissenschaften, IBG-2–Plant Sciences, Forschungszentrum Jülich, Jülich, Germany
- IBMG: Institute for Biology I, RWTH Aachen University, Aachen, Germany
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Li L, Aro EM, Millar AH. Mechanisms of Photodamage and Protein Turnover in Photoinhibition. TRENDS IN PLANT SCIENCE 2018; 23:667-676. [PMID: 29887276 DOI: 10.1016/j.tplants.2018.05.004] [Citation(s) in RCA: 116] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 05/05/2018] [Accepted: 05/08/2018] [Indexed: 05/05/2023]
Abstract
Rapid protein degradation and replacement is an important response to photodamage and a means of photoprotection by recovering proteostasis. Protein turnover and translation efficiency studies have discovered fast turnover subunits in cytochrome b6f and the NAD(P)H dehydrogenase (NDH) complex, in addition to PSII subunit D1. Mutations of these complexes have been linked to enhanced photodamage at least partially via cyclic electron flow. Photodamage and photoprotection involving cytochrome b6f, NDH complex, cyclic electron flow, PSI, and nonphotochemical quenching proteins have been reported. Here, we propose that the rapid turnover of specific proteins in cytochrome b6f and the NDH complex need to be characterised and compared with the inhibition of PSII by excess excitation energy and PSI by excess electron flux to expand our understanding of photoinhibition mechanisms.
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Affiliation(s)
- Lei Li
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, 35 Stirling Hwy, 6009, Perth, WA, Australia
| | - Eva-Mari Aro
- Finnish Centre of Excellence in Molecular Biology of Primary Producers, Department of Biochemistry, Molecular Plant Biology, University of Turku, FI-20014, Turku, Finland
| | - A Harvey Millar
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, 35 Stirling Hwy, 6009, Perth, WA, Australia.
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Nucleolar GTP-Binding Protein 1-2 (NOG1-2) Interacts with Jasmonate-ZIMDomain Protein 9 (JAZ9) to Regulate Stomatal Aperture during Plant Immunity. Int J Mol Sci 2018; 19:ijms19071922. [PMID: 29966336 PMCID: PMC6073727 DOI: 10.3390/ijms19071922] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 06/24/2018] [Accepted: 06/26/2018] [Indexed: 02/07/2023] Open
Abstract
Plant defense responses at stomata and apoplast are the most important early events during plant–bacteria interactions. The key components of stomatal defense responses have not been fully characterized. A GTPase encoding gene, NOG1-2, which is required for stomatal innate immunity against bacterial pathogens, was recently identified. Functional studies in Arabidopsis revealed that NOG1-2 regulates guard cell signaling in response to biotic and abiotic stimulus through jasmonic acid (JA)- and abscisic acid (ABA)-mediated pathways. Interestingly, in this study, Jasmonate-ZIM-domain protein 9 (JAZ9) was identified to interact with NOG1-2 for the regulation of stomatal closure. Upon interaction, JAZ9 reduces GTPase activity of NOG1-2. We explored the role of NOG1-2 binding with JAZ9 for COI1-mediated JA signaling and hypothesized that its function may be closely linked to MYC2 transcription factor in the regulation of the JA-signaling cascade in stomatal defense against bacterial pathogens. Our study provides valuable information on the function of a small GTPase, NOG1-2, in guard cell signaling and early plant defense in response to bacterial pathogens.
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Speicher TL, Li PZ, Wallace IS. Phosphoregulation of the Plant Cellulose Synthase Complex and Cellulose Synthase-Like Proteins. PLANTS (BASEL, SWITZERLAND) 2018; 7:E52. [PMID: 29966291 PMCID: PMC6161211 DOI: 10.3390/plants7030052] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 06/26/2018] [Accepted: 06/26/2018] [Indexed: 02/04/2023]
Abstract
Cellulose, the most abundant biopolymer on the planet, is synthesized at the plasma membrane of plant cells by the cellulose synthase complex (CSC). Cellulose is the primary load-bearing polysaccharide of plant cell walls and enables cell walls to maintain cellular shape and rigidity. The CSC is comprised of functionally distinct cellulose synthase A (CESA) proteins, which are responsible for synthesizing cellulose, and additional accessory proteins. Moreover, CESA-like (CSL) proteins are proposed to synthesize other essential non-cellulosic polysaccharides that comprise plant cell walls. The deposition of cell-wall polysaccharides is dynamically regulated in response to a variety of developmental and environmental stimuli, and post-translational phosphorylation has been proposed as one mechanism to mediate this dynamic regulation. In this review, we discuss CSC composition, the dynamics of CSCs in vivo, critical studies that highlight the post-translational control of CESAs and CSLs, and the receptor kinases implicated in plant cell-wall biosynthesis. Furthermore, we highlight the emerging importance of post-translational phosphorylation-based regulation of CSCs on the basis of current knowledge in the field.
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Affiliation(s)
- Tori L Speicher
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV 89557, USA.
| | - Patrick Ziqiang Li
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV 89557, USA.
| | - Ian S Wallace
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV 89557, USA.
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Prediction of Protein Phosphorylation Sites by Integrating Secondary Structure Information and Other One-Dimensional Structural Properties. Methods Mol Biol 2018; 1484:265-274. [PMID: 27787832 DOI: 10.1007/978-1-4939-6406-2_18] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Studies on phosphorylation are important but challenging for both wet-bench experiments and computational studies, and accurate non-kinase-specific prediction tools are highly desirable for whole-genome annotation in a wide variety of species. Here, we describe a phosphorylation site prediction webserver, PhosphoSVM, that employs Support Vector Machine to combine protein secondary structure information and seven other one-dimensional structural properties, including Shannon entropy, relative entropy, predicted protein disorder information, predicted solvent accessible area, amino acid overlapping properties, averaged cumulative hydrophobicity, and subsequence k-nearest neighbor profiles. This method achieved AUC values of 0.8405/0.8183/0.7383 for serine (S), threonine (T), and tyrosine (Y) phosphorylation sites, respectively, in animals with a tenfold cross-validation. The model trained by the animal phosphorylation sites was also applied to a plant phosphorylation site dataset as an independent test. The AUC values for the independent test data set were 0.7761/0.6652/0.5958 for S/T/Y phosphorylation sites, respectively. This algorithm with the optimally trained model was implemented as a webserver. The webserver, trained model, and all datasets used in the current study are available at http://sysbio.unl.edu/PhosphoSVM .
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50
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Law YS, Ngan L, Yan J, Kwok LY, Sun Y, Cheng S, Schwenkert S, Lim BL. Multiple Kinases Can Phosphorylate the N-Terminal Sequences of Mitochondrial Proteins in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2018; 9:982. [PMID: 30042778 PMCID: PMC6048449 DOI: 10.3389/fpls.2018.00982] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 06/18/2018] [Indexed: 05/06/2023]
Abstract
Phosphorylation of the transit peptides of nuclear-encoded preprotein is a well-known regulatory process of protein import in plant chloroplasts. In the Arabidopsis Protein Phosphorylation Site Database, 103 out of 802 mitochondrial proteins were found to contain one or more experimentally proven phosphorylation sites in their first 60 amino acid residues. Analysis of the N-terminal sequences of selected mitochondrial preproteins and their homologs from 64 plant species showed high conservation among phosphorylation sites. The ability of kinases from various sources including leaf extract (LE), root extract (RE), wheat germ lysate (WGL), and STY kinases to phosphorylate N-terminal sequences of several respiratory chain proteins were examined by in vitro kinase assays. The three STY kinases were shown to phosphorylate the N-terminal sequences of some proteins we tested but exhibited different specificities. Interestingly, the N-terminal sequences of two mitochondrial ATP synthase beta subunit 1/3 (pF1β-1/3) could be phosphorylated by LE and RE but not by STY kinases, suggesting that there are uncharacterized presequence-phosphorylating kinases other than STY kinases present in RE and LE. Mitochondrial import studies showed that the import of RRL-synthesized pF1βs was impeded by the treatment of LE, and the addition of a short SSU transit peptide containing a phosphorylatable 14-3-3 binding site could enhance the import of LE-treated pF1βs. Our results suggested that the transit peptide of pSSU can compete with the presequences of pF1βs for an uncharacterized kinase(s) in leaf. Altogether, our data showed that phosphorylation of transit peptides/presequences are not uncommon for chloroplast-targeted and mitochondria-targeted proteins, albeit possibly differentially regulated.
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Affiliation(s)
- Yee-Song Law
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Ling Ngan
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Junran Yan
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Lok Y. Kwok
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Yuzhe Sun
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Shifeng Cheng
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Serena Schwenkert
- Department of Biology I, Botany, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Boon L. Lim
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
- *Correspondence: Boon L. Lim,
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