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Garnelo Gómez B, Holzwart E, Shi C, Lozano-Durán R, Wolf S. Phosphorylation-dependent routing of RLP44 towards brassinosteroid or phytosulfokine signalling. J Cell Sci 2021; 134:272537. [PMID: 34569597 PMCID: PMC8572011 DOI: 10.1242/jcs.259134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 09/20/2021] [Indexed: 12/14/2022] Open
Abstract
Plants rely on cell surface receptors to integrate developmental and environmental cues into behaviour adapted to the conditions. The largest group of these receptors, leucine-rich repeat receptor-like kinases, form a complex interaction network that is modulated and extended by receptor-like proteins. This raises the question of how specific outputs can be generated when receptor proteins are engaged in a plethora of promiscuous interactions. RECEPTOR-LIKE PROTEIN 44 (RLP44) acts to promote both brassinosteroid and phytosulfokine signalling, which orchestrate diverse cellular responses. However, it is unclear how these activities are coordinated. Here, we show that RLP44 is phosphorylated in its highly conserved cytosolic tail and that this post-translational modification governs its subcellular localization. Whereas phosphorylation is essential for brassinosteroid-associated functions of RLP44, its role in phytosulfokine signalling is not affected by phospho-status. Detailed mutational analysis suggests that phospho-charge, rather than modification of individual amino acids determines routing of RLP44 to its target receptor complexes, providing a framework to understand how a common component of different receptor complexes can get specifically engaged in a particular signalling pathway.
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Affiliation(s)
- Borja Garnelo Gómez
- Centre for Organismal Studies Heidelberg, University of Heidelberg, INF230, 69120 Heidelberg, Germany.,Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai 201602China
| | - Eleonore Holzwart
- Centre for Organismal Studies Heidelberg, University of Heidelberg, INF230, 69120 Heidelberg, Germany
| | - Chaonan Shi
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai 201602China
| | - Rosa Lozano-Durán
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai 201602China.,Department of Plant Biochemistry, Centre for Plant Molecular Biology (ZMBP), Eberhard Karls University, D-72076 Tübingen, Germany
| | - Sebastian Wolf
- Centre for Organismal Studies Heidelberg, University of Heidelberg, INF230, 69120 Heidelberg, Germany.,Department of Plant Biochemistry, Centre for Plant Molecular Biology (ZMBP), Eberhard Karls University, D-72076 Tübingen, Germany
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2
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Shi S, Wang L, Cao M, Chen G, Yu J. Proteomic analysis and prediction of amino acid variations that influence protein posttranslational modifications. Brief Bioinform 2018; 20:1597-1606. [DOI: 10.1093/bib/bby036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 03/07/2018] [Indexed: 12/18/2022] Open
Abstract
Abstract
Accumulative studies have indicated that amino acid variations through changing the type of residues of the target sites or key flanking residues could directly or indirectly influence protein posttranslational modifications (PTMs) and bring about a detrimental effect on protein function. Computational mutation analysis can greatly narrow down the efforts on experimental work. To increase the utilization of current computational resources, we first provide an overview of computational prediction of amino acid variations that influence protein PTMs and their functional analysis. We also discuss the challenges that are faced while developing novel in silico approaches in the future. The development of better methods for mutation analysis-related protein PTMs will help to facilitate the development of personalized precision medicine.
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Affiliation(s)
- Shaoping Shi
- Department of Mathematics and Numerical Simulation and High-Performance Computing Laboratory, School of Sciences, Nanchang University, Nanchang, Jiangxi 330031, China
| | - Lina Wang
- Department of Science, Nanchang Institute of Technology, Nanchang, Jiangxi 330031, China
| | - Man Cao
- Department of Mathematics, School of Sciences, Nanchang University, Nanchang, Jiangxi 330031, China
| | - Guodong Chen
- Department of Mathematics, School of Sciences, Nanchang University, Nanchang, Jiangxi 330031, China
| | - Jialin Yu
- Department of Mathematics, School of Sciences, Nanchang University, Nanchang, Jiangxi 330031, China
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3
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MIMP: predicting the impact of mutations on kinase-substrate phosphorylation. Nat Methods 2015; 12:531-3. [DOI: 10.1038/nmeth.3396] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 03/30/2015] [Indexed: 12/14/2022]
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4
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Fang X, Chen J, Dai L, Ma H, Zhang H, Yang J, Wang F, Yan C. Proteomic dissection of plant responses to various pathogens. Proteomics 2015; 15:1525-43. [DOI: 10.1002/pmic.201400384] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2014] [Revised: 11/28/2014] [Accepted: 01/12/2015] [Indexed: 01/15/2023]
Affiliation(s)
- Xianping Fang
- Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization and Hunan Provincial Key Laboratory of Biology and Control of Plant Diseases and Insect Pests; Hunan Agricultural University; Changsha Hunan P. R. China
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control; Institute of Virology and Biotechnology; Zhejiang Academy of Agricultural Sciences; Hangzhou P. R. China
- Institute of Biology; Hangzhou Academy of Agricultural Sciences; Hangzhou P. R. China
| | - Jianping Chen
- Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization and Hunan Provincial Key Laboratory of Biology and Control of Plant Diseases and Insect Pests; Hunan Agricultural University; Changsha Hunan P. R. China
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control; Institute of Virology and Biotechnology; Zhejiang Academy of Agricultural Sciences; Hangzhou P. R. China
| | - Liangying Dai
- Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization and Hunan Provincial Key Laboratory of Biology and Control of Plant Diseases and Insect Pests; Hunan Agricultural University; Changsha Hunan P. R. China
| | - Huasheng Ma
- Institute of Biology; Hangzhou Academy of Agricultural Sciences; Hangzhou P. R. China
| | - Hengmu Zhang
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control; Institute of Virology and Biotechnology; Zhejiang Academy of Agricultural Sciences; Hangzhou P. R. China
| | - Jian Yang
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control; Institute of Virology and Biotechnology; Zhejiang Academy of Agricultural Sciences; Hangzhou P. R. China
| | - Fang Wang
- Laboratory of Biotechnology; Institute of Biotechnology; Ningbo Academy of Agricultural Sciences; Ningbo P. R. China
| | - Chengqi Yan
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control; Institute of Virology and Biotechnology; Zhejiang Academy of Agricultural Sciences; Hangzhou P. R. China
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5
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Abstract
Protein phosphorylation events on serine, threonine, and tyrosine residues are the most pervasive protein covalent bond modifications in plant signaling. Both low and high throughput studies reveal the importance of phosphorylation in plant molecular biology. Although becoming more and more common, the proteome-wide screening on phosphorylation by experiments remains time consuming and costly. Therefore, in silico prediction methods are proposed as a complementary analysis tool to enhance the phosphorylation site identification, develop biological hypothesis, or help experimental design. These methods build statistical models based on the experimental data, and they do not have some of the technical-specific bias, which may have advantage in proteome-wide analysis. More importantly computational methods are very fast and cheap to run, which makes large-scale phosphorylation identifications very practical for any types of biological study. Thus, the phosphorylation prediction tools become more and more popular. In this chapter, we will focus on plant specific phosphorylation site prediction tools, with essential illustration of technical details and application guidelines. We will use Musite, PhosPhAt and PlantPhos as the representative tools. We will present the results on the prediction of the Arabidopsis protein phosphorylation events to give users a general idea of the performance range of the three tools, together with their strengths and limitations. We believe these prediction tools will contribute more and more to the plant phosphorylation research community.
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Affiliation(s)
- Qiuming Yao
- Department of Computer Science and Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
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6
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Bigeard J, Rayapuram N, Bonhomme L, Hirt H, Pflieger D. Proteomic and phosphoproteomic analyses of chromatin-associated proteins from Arabidopsis thaliana. Proteomics 2014; 14:2141-55. [PMID: 24889360 DOI: 10.1002/pmic.201400072] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 04/28/2014] [Accepted: 05/26/2014] [Indexed: 11/09/2022]
Abstract
The nucleus is the organelle where basically all DNA-related processes take place in eukaryotes, such as replication, transcription, and splicing as well as epigenetic regulation. The identification and description of the nuclear proteins is one of the requisites toward a comprehensive understanding of the biological functions accomplished in the nucleus. Many of the regulatory mechanisms of protein functions rely on their PTMs among which phosphorylation is probably one of the most important properties affecting enzymatic activity, interaction with other molecules, localization, or stability. So far, the nuclear and subnuclear proteome and phosphoproteome of the model plant Arabidopsis thaliana have been the subject of very few studies. In this work, we developed a purification protocol of Arabidopsis chromatin-associated proteins and performed proteomic and phosphoproteomic analyses identifying a total of 879 proteins of which 198 were phosphoproteins that were mainly involved in chromatin remodeling, transcriptional regulation, and RNA processing. From 230 precisely localized phosphorylation sites (phosphosites), 52 correspond to hitherto unidentified sites. This protocol and data thereby obtained should be a valuable resource for many domains of plant research.
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Affiliation(s)
- Jean Bigeard
- Unité de Recherche en Génomique Végétale (URGV), UMR INRA/CNRS/Université d'Evry Val d'Essonne/Saclay Plant Sciences, Evry, France
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7
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Bigeard J, Rayapuram N, Pflieger D, Hirt H. Phosphorylation-dependent regulation of plant chromatin and chromatin-associated proteins. Proteomics 2014; 14:2127-40. [PMID: 24889195 DOI: 10.1002/pmic.201400073] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 04/28/2014] [Accepted: 05/26/2014] [Indexed: 12/25/2022]
Abstract
In eukaryotes, most of the DNA is located in the nucleus where it is organized with histone proteins in a higher order structure as chromatin. Chromatin and chromatin-associated proteins contribute to DNA-related processes such as replication and transcription as well as epigenetic regulation. Protein functions are often regulated by PTMs among which phosphorylation is one of the most abundant PTM. Phosphorylation of proteins affects important properties, such as enzyme activity, protein stability, or subcellular localization. We here describe the main specificities of protein phosphorylation in plants and review the current knowledge on phosphorylation-dependent regulation of plant chromatin and chromatin-associated proteins. We also outline some future challenges to further elucidate protein phosphorylation and chromatin regulation.
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Affiliation(s)
- Jean Bigeard
- Unité de Recherche en Génomique Végétale (URGV), UMR INRA/CNRS/Université d'Evry Val d'Essonne/Saclay Plant Sciences, Evry, France
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8
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Zulawski M, Schulze G, Braginets R, Hartmann S, Schulze WX. The Arabidopsis Kinome: phylogeny and evolutionary insights into functional diversification. BMC Genomics 2014; 15:548. [PMID: 24984858 PMCID: PMC4112214 DOI: 10.1186/1471-2164-15-548] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2014] [Accepted: 06/25/2014] [Indexed: 12/14/2022] Open
Abstract
Background Protein kinases constitute a particularly large protein family in Arabidopsis with important functions in cellular signal transduction networks. At the same time Arabidopsis is a model plant with high frequencies of gene duplications. Here, we have conducted a systematic analysis of the Arabidopsis kinase complement, the kinome, with particular focus on gene duplication events. We matched Arabidopsis proteins to a Hidden-Markov Model of eukaryotic kinases and computed a phylogeny of 942 Arabidopsis protein kinase domains and mapped their origin by gene duplication. Results The phylogeny showed two major clades of receptor kinases and soluble kinases, each of which was divided into functional subclades. Based on this phylogeny, association of yet uncharacterized kinases to families was possible which extended functional annotation of unknowns. Classification of gene duplications within these protein kinases revealed that representatives of cytosolic subfamilies showed a tendency to maintain segmentally duplicated genes, while some subfamilies of the receptor kinases were enriched for tandem duplicates. Although functional diversification is observed throughout most subfamilies, some instances of functional conservation among genes transposed from the same ancestor were observed. In general, a significant enrichment of essential genes was found among genes encoding for protein kinases. Conclusions The inferred phylogeny allowed classification and annotation of yet uncharacterized kinases. The prediction and analysis of syntenic blocks and duplication events within gene families of interest can be used to link functional biology to insights from an evolutionary viewpoint. The approach undertaken here can be applied to any gene family in any organism with an annotated genome. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-548) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | - Waltraud X Schulze
- Department of Plant Systems Biology, University of Hohenheim, Garbenstraße 30, Stuttgart 70599, Germany.
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9
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van Wijk KJ, Friso G, Walther D, Schulze WX. Meta-Analysis of Arabidopsis thaliana Phospho-Proteomics Data Reveals Compartmentalization of Phosphorylation Motifs. THE PLANT CELL 2014; 26:2367-2389. [PMID: 24894044 PMCID: PMC4114939 DOI: 10.1105/tpc.114.125815] [Citation(s) in RCA: 125] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Revised: 03/27/2014] [Accepted: 05/09/2014] [Indexed: 05/18/2023]
Abstract
Protein (de)phosphorylation plays an important role in plants. To provide a robust foundation for subcellular phosphorylation signaling network analysis and kinase-substrate relationships, we performed a meta-analysis of 27 published and unpublished in-house mass spectrometry-based phospho-proteome data sets for Arabidopsis thaliana covering a range of processes, (non)photosynthetic tissue types, and cell cultures. This resulted in an assembly of 60,366 phospho-peptides matching to 8141 nonredundant proteins. Filtering the data for quality and consistency generated a set of medium and a set of high confidence phospho-proteins and their assigned phospho-sites. The relation between single and multiphosphorylated peptides is discussed. The distribution of p-proteins across cellular functions and subcellular compartments was determined and showed overrepresentation of protein kinases. Extensive differences in frequency of pY were found between individual studies due to proteomics and mass spectrometry workflows. Interestingly, pY was underrepresented in peroxisomes but overrepresented in mitochondria. Using motif-finding algorithms motif-x and MMFPh at high stringency, we identified compartmentalization of phosphorylation motifs likely reflecting localized kinase activity. The filtering of the data assembly improved signal/noise ratio for such motifs. Identified motifs were linked to kinases through (bioinformatic) enrichment analysis. This study also provides insight into the challenges/pitfalls of using large-scale phospho-proteomic data sets to nonexperts.
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Affiliation(s)
- Klaas J van Wijk
- Department of Plant Biology, Cornell University, Ithaca, New York 14850
| | - Giulia Friso
- Department of Plant Biology, Cornell University, Ithaca, New York 14850
| | - Dirk Walther
- Max Planck Institute of Molecular Plant Physiology, 14476 Golm, Germany
| | - Waltraud X Schulze
- Department of Plant Systems Biology, University of Hohenheim, 70593 Stuttgart, Germany
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10
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Kissoudis C, van de Wiel C, Visser RGF, van der Linden G. Enhancing crop resilience to combined abiotic and biotic stress through the dissection of physiological and molecular crosstalk. FRONTIERS IN PLANT SCIENCE 2014; 5:207. [PMID: 24904607 PMCID: PMC4032886 DOI: 10.3389/fpls.2014.00207] [Citation(s) in RCA: 146] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 04/28/2014] [Indexed: 05/18/2023]
Abstract
Plants growing in their natural habitats are often challenged simultaneously by multiple stress factors, both abiotic and biotic. Research has so far been limited to responses to individual stresses, and understanding of adaptation to combinatorial stress is limited, but indicative of non-additive interactions. Omics data analysis and functional characterization of individual genes has revealed a convergence of signaling pathways for abiotic and biotic stress adaptation. Taking into account that most data originate from imposition of individual stress factors, this review summarizes these findings in a physiological context, following the pathogenesis timeline and highlighting potential differential interactions occurring between abiotic and biotic stress signaling across the different cellular compartments and at the whole plant level. Potential effects of abiotic stress on resistance components such as extracellular receptor proteins, R-genes and systemic acquired resistance will be elaborated, as well as crosstalk at the levels of hormone, reactive oxygen species, and redox signaling. Breeding targets and strategies are proposed focusing on either manipulation and deployment of individual common regulators such as transcription factors or pyramiding of non- (negatively) interacting components such as R-genes with abiotic stress resistance genes. We propose that dissection of broad spectrum stress tolerance conferred by priming chemicals may provide an insight on stress cross regulation and additional candidate genes for improving crop performance under combined stress. Validation of the proposed strategies in lab and field experiments is a first step toward the goal of achieving tolerance to combinatorial stress in crops.
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11
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Duan G, Walther D, Schulze WX. Reconstruction and analysis of nutrient-induced phosphorylation networks in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2013; 4:540. [PMID: 24400017 PMCID: PMC3872036 DOI: 10.3389/fpls.2013.00540] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Accepted: 12/12/2013] [Indexed: 05/23/2023]
Abstract
Elucidating the dynamics of molecular processes in living organisms in response to external perturbations is a central goal in modern systems biology. We investigated the dynamics of protein phosphorylation events in Arabidopsis thaliana exposed to changing nutrient conditions. Phosphopeptide expression levels were detected at five consecutive time points over a time interval of 30 min after nutrient resupply following prior starvation. The three tested inorganic, ionic nutrients NH(+) 4, NO(-) 3, PO(3-) 4 elicited similar phosphosignaling responses that were distinguishable from those invoked by the sugars mannitol, sucrose. When embedded in the protein-protein interaction network of Arabidopsis thaliana, phosphoproteins were found to exhibit a higher degree compared to average proteins. Based on the time-series data, we reconstructed a network of regulatory interactions mediated by phosphorylation. The performance of different network inference methods was evaluated by the observed likelihood of physical interactions within and across different subcellular compartments and based on gene ontology semantic similarity. The dynamic phosphorylation network was then reconstructed using a Pearson correlation method with added directionality based on partial variance differences. The topology of the inferred integrated network corresponds to an information dissemination architecture, in which the phosphorylation signal is passed on to an increasing number of phosphoproteins stratified into an initiation, processing, and effector layer. Specific phosphorylation peptide motifs associated with the distinct layers were identified indicating the action of layer-specific kinases. Despite the limited temporal resolution, combined with information on subcellular location, the available time-series data proved useful for reconstructing the dynamics of the molecular signaling cascade in response to nutrient stress conditions in the plant Arabidopsis thaliana.
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Affiliation(s)
- Guangyou Duan
- Max Planck Institute of Molecular Plant PhysiologyPotsdam, Germany
| | - Dirk Walther
- Max Planck Institute of Molecular Plant PhysiologyPotsdam, Germany
| | - Waltraud X. Schulze
- Max Planck Institute of Molecular Plant PhysiologyPotsdam, Germany
- Department of Plant Systems Biology, Universität HohenheimStuttgart, Germany
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12
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Zulawski M, Braginets R, Schulze WX. PhosPhAt goes kinases--searchable protein kinase target information in the plant phosphorylation site database PhosPhAt. Nucleic Acids Res 2012; 41:D1176-84. [PMID: 23172287 PMCID: PMC3531128 DOI: 10.1093/nar/gks1081] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Reversible phosphorylation is a key mechanism for regulating protein function. Thus it is of high interest to know which kinase can phosphorylate which proteins. Comprehensive information about phosphorylation sites in Arabidopsis proteins is hosted within the PhosPhAt database (http://phosphat.mpimp-golm.mpg.de). However, our knowledge of the kinases that phosphorylate those sites is dispersed throughout the literature and very difficult to access, particularly for investigators seeking to interpret large scale and high-throughput experiments. Therefore, we aimed to compile information on kinase–substrate interactions and kinase-specific regulatory information and make this available via a new functionality embedded in PhosPhAt. Our approach involved systematic surveying of the literature for regulatory information on the members of the major kinase families in Arabidopsis thaliana, such as CDPKs, MPK(KK)s, AGC kinases and SnRKs, as well as individual kinases from other families. To date, we have researched more than 4450 kinase-related publications, which collectively contain information on about 289 kinases. Users can now query the PhosPhAt database not only for experimental and predicted phosphorylation sites of individual proteins, but also for known substrates for a given kinase or kinase family. Further developments include addition of new phosphorylation sites and visualization of clustered phosphorylation events, known as phosphorylation hotspots.
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Affiliation(s)
- Monika Zulawski
- Max Planck Institut für molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Golm, Germany
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13
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Christian JO, Braginets R, Schulze WX, Walther D. Characterization and Prediction of Protein Phosphorylation Hotspots in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2012; 3:207. [PMID: 22973286 PMCID: PMC3433687 DOI: 10.3389/fpls.2012.00207] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Accepted: 08/14/2012] [Indexed: 05/23/2023]
Abstract
The regulation of protein function by modulating the surface charge status via sequence-locally enriched phosphorylation sites (P-sites) in so called phosphorylation "hotspots" has gained increased attention in recent years. We set out to identify P-hotspots in the model plant Arabidopsis thaliana. We analyzed the spacing of experimentally detected P-sites within peptide-covered regions along Arabidopsis protein sequences as available from the PhosPhAt database. Confirming earlier reports (Schweiger and Linial, 2010), we found that, indeed, P-sites tend to cluster and that distributions between serine and threonine P-sites to their respected closest next P-site differ significantly from those for tyrosine P-sites. The ability to predict P-hotspots by applying available computational P-site prediction programs that focus on identifying single P-sites was observed to be severely compromised by the inevitable interference of nearby P-sites. We devised a new approach, named HotSPotter, for the prediction of phosphorylation hotspots. HotSPotter is based primarily on local amino acid compositional preferences rather than sequence position-specific motifs and uses support vector machines as the underlying classification engine. HotSPotter correctly identified experimentally determined phosphorylation hotspots in A. thaliana with high accuracy. Applied to the Arabidopsis proteome, HotSPotter-predicted 13,677 candidate P-hotspots in 9,599 proteins corresponding to 7,847 unique genes. Hotspot containing proteins are involved predominantly in signaling processes confirming the surmised modulating role of hotspots in signaling and interaction events. Our study provides new bioinformatics means to identify phosphorylation hotspots and lays the basis for further investigating novel candidate P-hotspots. All phosphorylation hotspot annotations and predictions have been made available as part of the PhosPhAt database at http://phosphat.mpimp-golm.mpg.de.
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Affiliation(s)
- Jan-Ole Christian
- Max Planck Institute for Molecular Plant PhysiologyPotsdam-Golm, Brandenburg, Germany
- Bioinformatics, Universität PotsdamPotsdam-Golm, Germany
| | - Rostyslav Braginets
- Max Planck Institute for Molecular Plant PhysiologyPotsdam-Golm, Brandenburg, Germany
| | - Waltraud X. Schulze
- Max Planck Institute for Molecular Plant PhysiologyPotsdam-Golm, Brandenburg, Germany
| | - Dirk Walther
- Max Planck Institute for Molecular Plant PhysiologyPotsdam-Golm, Brandenburg, Germany
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Rampitsch C, Bykova NV. The beginnings of crop phosphoproteomics: exploring early warning systems of stress. FRONTIERS IN PLANT SCIENCE 2012; 3:144. [PMID: 22783265 PMCID: PMC3387783 DOI: 10.3389/fpls.2012.00144] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Accepted: 06/13/2012] [Indexed: 05/22/2023]
Abstract
This review examines why a knowledge of plant protein phosphorylation events is important in devising strategies to protect crops from both biotic and abiotic stresses, and why proteomics should be included when studying stress pathways. Most of the achievements in elucidating phospho-signaling pathways in biotic and abiotic stress are reported from model systems: while these are discussed, this review attempts mainly to focus on work done with crops, with examples of achievements reported from rice, maize, wheat, grape, Brassica, tomato, and soy bean after cold acclimation, hormonal and oxidative hydrogen peroxide treatment, salt stress, mechanical wounding, or pathogen challenge. The challenges that remain to transfer this information into a format that can be used to protect crops against biotic and abiotic stresses are enormous. The tremendous increase in the speed and ease of DNA sequencing is poised to reveal the whole genomes of many crop species in the near future, which will facilitate phosphoproteomics and phosphogenomics research.
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15
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Phosphorylation in protein-protein binding: effect on stability and function. Structure 2012; 19:1807-15. [PMID: 22153503 DOI: 10.1016/j.str.2011.09.021] [Citation(s) in RCA: 209] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2011] [Revised: 09/21/2011] [Accepted: 09/24/2011] [Indexed: 01/23/2023]
Abstract
Posttranslational modifications offer a dynamic way to regulate protein activity, subcellular localization, and stability. Here we estimate the effect of phosphorylation on protein binding and function for different types of complexes from human proteome. We find that phosphorylation sites tend to be located on binding interfaces in heterooligomeric and weak transient homooligomeric complexes. Analysis of molecular mechanisms of phosphorylation shows that phosphorylation may modulate the strength of interactions directly on interfaces and that binding hotspots tend to be phosphorylated in heterooligomers. Although the majority of complexes do not show significant estimated stability differences upon phosphorylation or dephosphorylation, for about one-third of all complexes it causes relatively large changes in binding energy. We discuss the cases where phosphorylation mediates the complex formation and regulates the function. We show that phosphorylation sites are more likely to be evolutionary conserved than other interfacial residues.
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16
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Joshi HJ, Christiansen KM, Fitz J, Cao J, Lipzen A, Martin J, Smith-Moritz AM, Pennacchio LA, Schackwitz WS, Weigel D, Heazlewood JL. 1001 Proteomes: a functional proteomics portal for the analysis of Arabidopsis thaliana accessions. ACTA ACUST UNITED AC 2012; 28:1303-6. [PMID: 22451271 DOI: 10.1093/bioinformatics/bts133] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
MOTIVATION The sequencing of over a thousand natural strains of the model plant Arabidopsis thaliana is producing unparalleled information at the genetic level for plant researchers. To enable the rapid exploitation of these data for functional proteomics studies, we have created a resource for the visualization of protein information and proteomic datasets for sequenced natural strains of A. thaliana. RESULTS The 1001 Proteomes portal can be used to visualize amino acid substitutions or non-synonymous single-nucleotide polymorphisms in individual proteins of A. thaliana based on the reference genome Col-0. We have used the available processed sequence information to analyze the conservation of known residues subject to protein phosphorylation among these natural strains. The substitution of amino acids in A. thaliana natural strains is heavily constrained and is likely a result of the conservation of functional attributes within proteins. At a practical level, we demonstrate that this information can be used to clarify ambiguously defined phosphorylation sites from phosphoproteomic studies. Protein sets of available natural variants are available for download to enable proteomic studies on these accessions. Together this information can be used to uncover the possible roles of specific amino acids in determining the structure and function of proteins in the model plant A. thaliana. An online portal to enable the community to exploit these data can be accessed at http://1001proteomes.masc-proteomics.org/
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Affiliation(s)
- Hiren J Joshi
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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Nakagami H, Sugiyama N, Ishihama Y, Shirasu K. Shotguns in the front line: phosphoproteomics in plants. PLANT & CELL PHYSIOLOGY 2012; 53:118-24. [PMID: 22039104 DOI: 10.1093/pcp/pcr148] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The emergence of 'shotgun proteomics' has paved the way for high-throughput proteome analysis, by which thousands of proteins can be identified simultaneously from complex samples. Although the shotgun approach has the potential to monitor many different post-translational modifications, further technological development is needed to enrich each post-translational 'modificome'. Large-scale in vivo phosphorylation site mapping, so-called shotgun phosphoproteomics, has become feasible in various organisms, including plants, owing to recent technological breakthroughs. Shotgun phosphoproteomics is not a mature technology, but progress has been rapid. In this review, we highlight the scope and limitations of current methods, and some key technological issues in this field.
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Usadel B, Schwacke R, Nagel A, Kersten B. GabiPD - The GABI Primary Database integrates plant proteomic data with gene-centric information. FRONTIERS IN PLANT SCIENCE 2012; 3:154. [PMID: 23293643 PMCID: PMC3391694 DOI: 10.3389/fpls.2012.00154] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Accepted: 06/20/2012] [Indexed: 05/08/2023]
Abstract
GabiPD is an integrative plant "omics" database that has been established as part of the German initiative for Genome Analysis of the Plant Biological System (GABI). Data from different "omics" disciplines are integrated and interactively visualized. Proteomics is represented by data and tools aiding studies on the identification of post-translational modification and function of proteins. Annotated 2D electrophoresis-gel images are offered to inspect protein sets expressed in different tissues of Arabidopsis thaliana and Brassica napus. From a given protein spot, a link will direct the user to the related GreenCard Gene entry where detailed gene-centric information will support the functional annotation. Beside MapMan- and GO-classification, information on conserved protein domains and on orthologs is integrated in this GreenCard service. Moreover, all other GabiPD data related to the gene, including transcriptomic data, as well as gene-specific links to external resources are provided. Researches interested in plant protein phosphorylation will find information on potential MAP kinase substrates identified in different protein microarray studies integrated in GabiPD's Phosphoproteomics page. These data can be easily compared to experimentally identified or predicted phosphorylation sites in PhosPhAt via the related Gene GreenCard. This will allow the selection of interesting candidates for further experimental validation of their phosphorylation.
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Affiliation(s)
- Björn Usadel
- Max Planck Institute of Molecular Plant Physiology,Potsdam, Germany
- Department of Botany, RWTH Aachen University,Aachen, Germany
- IBG-2: Plant Sciences, Institute of Bio- and Geosciences, Forschungszentrum Jülich,Jülich, Germany
| | - Rainer Schwacke
- IBG-2: Plant Sciences, Institute of Bio- and Geosciences, Forschungszentrum Jülich,Jülich, Germany
| | - Axel Nagel
- Max Planck Institute of Molecular Plant Physiology,Potsdam, Germany
| | - Birgit Kersten
- Max Planck Institute of Molecular Plant Physiology,Potsdam, Germany
- Department of Genome Research, Institute of Forest Genetics, Johann Heinrich von Thünen Institute,Großhansdorf, Germany
- *Correspondence: Birgit Kersten, Department of Genome Research, Institute of Forest Genetics, Johann Heinrich von Thünen Institute, Sieker Landstr. 2, D-22927 Großhansdorf, Germany. e-mail:
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Abstract
Major progress has been made in unravelling of regulatory mechanisms in eukaryotic cells. Modification of target protein properties by reversible phosphorylation events has been found to be one of the most prominent cellular control processes in all organisms. The phospho-status of a protein is dynamically controlled by protein kinases and counteracting phosphatases. Therefore, monitoring of kinase and phosphatase activities, identification of specific phosphorylation sites, and assessment of their functional significance are of crucial importance to understand development and homeostasis. Recent advances in the area of molecular biology and biochemistry, for instance, mass spectrometry-based phosphoproteomics or fluorescence spectroscopical methods, open new possibilities to reach an unprecidented depth and a proteome-wide understanding of phosphorylation processes in plants and other species. In addition, the growing number of model species allows now deepening evolutionary insights into signal transduction cascades and the use of kinase/phosphatase systems. Thus, this is the age where we move from an understanding of the structure and function of individual protein modules to insights how these proteins are organized into pathways and networks. In this introductory chapter, we briefly review general definitions, methodology, and current concepts of the molecular mechanisms of protein kinase function as a foundation for this methods book. We briefly review biochemistry and structural biology of kinases and provide selected examples for the role of kinases in biological systems.
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