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Somsen BA, Sijbesma E, Leysen S, Honzejkova K, Visser EJ, Cossar PJ, Obšil T, Brunsveld L, Ottmann C. Molecular basis and dual ligand regulation of tetrameric Estrogen Receptor α/14-3-3ζ protein complex. J Biol Chem 2023:104855. [PMID: 37224961 PMCID: PMC10302166 DOI: 10.1016/j.jbc.2023.104855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 05/15/2023] [Accepted: 05/16/2023] [Indexed: 05/26/2023] Open
Abstract
Therapeutic strategies targeting Nuclear Receptors (NRs) beyond their endogenous ligand binding pocket have gained significant scientific interest, driven by a need to circumvent problems associated with drug resistance and pharmacological profile. The hub protein 14-3-3 is an endogenous regulator of various NRs, providing a novel entry point for small molecule modulation of NR activity. Exemplified, 14-3-3 binding to the C-terminal F-domain of the Estrogen Receptor alpha (ERα), and small molecule stabilization of the ERα/14-3-3ζ protein complex by the natural product Fusicoccin A (FC-A), was demonstrated to downregulate ERα-mediated breast cancer proliferation. This presents a novel drug discovery approach to target ERα, however, structural and mechanistic insights into ERα/14-3-3 complex formation are lacking. Here, we provide an in-depth molecular understanding of the ERα/14-3-3ζ complex by isolating 14-3-3ζ in complex with an ERα protein construct comprising its Ligand Binding Domain (LBD) and phosphorylated F-domain. Bacterial co-expression and co-purification of the ERα/14-3-3ζ complex, followed by extensive biophysical and structural characterization, revealed a tetrameric complex between the ERα homodimer and the 14-3-3ζ homodimer. 14-3-3ζ binding to ERα, and ERα/14-3-3ζ complex stabilization by FC-A, appeared to be orthogonal to ERα endogenous agonist (E2) binding, E2-induced conformational changes, and cofactor recruitment. Similarly, the ERα antagonist 4-hydroxytamoxifen inhibited cofactor recruitment to the ERα LBD while ERα was bound to 14-3-3ζ. Furthermore, stabilization of the ERα/14-3-3ζ protein complex by FC-A was not influenced by the disease-associated and 4-hydroxytamoxifen resistant ERα-Y537S mutant. Together, these molecular and mechanistic insights provide direction for targeting ERα via the ERα/14-3-3 complex as an alternative drug discovery approach.
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Affiliation(s)
- Bente A Somsen
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, 5600 MB Eindhoven, The Netherlands
| | - Eline Sijbesma
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, 5600 MB Eindhoven, The Netherlands
| | - Seppe Leysen
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, 5600 MB Eindhoven, The Netherlands
| | - Karolina Honzejkova
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Prague, Czech Republic
| | - Emira J Visser
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, 5600 MB Eindhoven, The Netherlands
| | - Peter J Cossar
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, 5600 MB Eindhoven, The Netherlands
| | - Tomáš Obšil
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Prague, Czech Republic
| | - Luc Brunsveld
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, 5600 MB Eindhoven, The Netherlands.
| | - Christian Ottmann
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, 5600 MB Eindhoven, The Netherlands.
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Automated SSHHPS Analysis Predicts a Potential Host Protein Target Common to Several Neuroinvasive (+)ssRNA Viruses. Viruses 2023; 15:v15020542. [PMID: 36851756 PMCID: PMC9961674 DOI: 10.3390/v15020542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 01/24/2023] [Accepted: 02/01/2023] [Indexed: 02/18/2023] Open
Abstract
Within the viral genome, short stretches of homologous host pathogen sequences (SSHHPS) span the protease cleavage sites. To identify host proteins that may be cleaved during infection, we searched the human proteome for viral protease cleavage sites (~20 amino acids). We developed a sequence-to-symptom tool, automating the search and pairing process. We used the viral protein sequence, PHI-BLAST, and UniProt database for gene ontologies and disease relationships. We applied the tool to nine neuroinvasive viruses: Venezuelan and Eastern Equine encephalitis virus (VEEV, EEEV); severe acute respiratory syndrome (SARS, SARS-CoV-2); Middle East respiratory syndrome (MERS); EV-71; Japanese encephalitis virus (JEV); West Nile (WNV); and Zika (ZIKV). A comparison of the hits identified a protein common to all nine viruses called ADGRA2 (GPR124). ADGRA2 was a predicted hit of the 3CL main protease and papain-like protease (PLpro) of SARS-CoV-2. ADGRA2 is an adhesion G protein-coupled receptor and a key endothelial regulator of brain-specific angiogenesis. It is a Wnt7A/Wnt7B specific coactivator of beta-catenin signaling and is essential for blood-brain barrier (BBB) integrity in central nervous system (CNS) diseases. We show the cleavage of the predicted sequences in MYOM1, VWF by the SARS-CoV-2 PLpro; DNAH8 (dynein) by the MERS PLpro; ADGRA2 by the alphaviral VEEV nsP2 protease; and POT1 by the SARS-CoV-2 and MERS PLpro.
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3
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Zhao J, Zhuang M, Liu J, Zhang M, Zeng C, Jiang B, Wu J, Song X. pHisPred: a tool for the identification of histidine phosphorylation sites by integrating amino acid patterns and properties. BMC Bioinformatics 2022; 23:399. [PMID: 36171552 PMCID: PMC9520798 DOI: 10.1186/s12859-022-04938-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 09/16/2022] [Indexed: 11/17/2022] Open
Abstract
Background Protein histidine phosphorylation (pHis) plays critical roles in prokaryotic signal transduction pathways and various eukaryotic cellular processes. It is estimated to account for 6–10% of the phosphoproteome, however only hundreds of pHis sites have been discovered to date. Due to the inherent disadvantages of experimental methods, it is an urgent task for developing efficient computational approaches to identify pHis sites. Results Here, we present a novel tool, pHisPred, for accurately identifying pHis sites from protein sequences. We manually collected the largest number of experimental validated pHis sites to build benchmark datasets. Using randomized tenfold CV, the weighted SVM-RBF model shows the best performance than other four commonly used classification models (LR, KNN, RF, and MLP). From ten thousands of features, 140 and 150 most informative features were individually selected out for eukaryotic and prokaryotic models. The average AUC and F1-score values of pHisPred were (0.81, 0.40) and (0.78, 0.46) for tenfold CV on the eukaryotic and prokaryotic training datasets, respectively. In addition, pHisPred significantly outperforms other tools on testing datasets, in particular on the eukaryotic one. Conclusion We implemented a python program of pHisPred, which is freely available for non-commercial use at https://github.com/xiaofengsong/pHisPred. Moreover, users can use it to train new models with their own data. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-022-04938-x.
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Affiliation(s)
- Jian Zhao
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, 210016, China
| | - Minhui Zhuang
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, 210016, China
| | - Jingjing Liu
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, 210016, China
| | - Meng Zhang
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, 210016, China
| | - Cong Zeng
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, 210016, China
| | - Bin Jiang
- College of Automation Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, 211106, China
| | - Jing Wu
- School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing, 211166, China.
| | - Xiaofeng Song
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, 210016, China.
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Lin S, Wang C, Zhou J, Shi Y, Ruan C, Tu Y, Yao L, Peng D, Xue Y. EPSD: a well-annotated data resource of protein phosphorylation sites in eukaryotes. Brief Bioinform 2020; 22:298-307. [PMID: 32008039 DOI: 10.1093/bib/bbz169] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 11/25/2019] [Accepted: 12/10/2019] [Indexed: 12/16/2022] Open
Abstract
As an important post-translational modification (PTM), protein phosphorylation is involved in the regulation of almost all of biological processes in eukaryotes. Due to the rapid progress in mass spectrometry-based phosphoproteomics, a large number of phosphorylation sites (p-sites) have been characterized but remain to be curated. Here, we briefly summarized the current progresses in the development of data resources for the collection, curation, integration and annotation of p-sites in eukaryotic proteins. Also, we designed the eukaryotic phosphorylation site database (EPSD), which contained 1 616 804 experimentally identified p-sites in 209 326 phosphoproteins from 68 eukaryotic species. In EPSD, we not only collected 1 451 629 newly identified p-sites from high-throughput (HTP) phosphoproteomic studies, but also integrated known p-sites from 13 additional databases. Moreover, we carefully annotated the phosphoproteins and p-sites of eight model organisms by integrating the knowledge from 100 additional resources that covered 15 aspects, including phosphorylation regulator, genetic variation and mutation, functional annotation, structural annotation, physicochemical property, functional domain, disease-associated information, protein-protein interaction, drug-target relation, orthologous information, biological pathway, transcriptional regulator, mRNA expression, protein expression/proteomics and subcellular localization. We anticipate that the EPSD can serve as a useful resource for further analysis of eukaryotic phosphorylation. With a data volume of 14.1 GB, EPSD is free for all users at http://epsd.biocuckoo.cn/.
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Affiliation(s)
| | | | - Jiaqi Zhou
- Huazhong University of Science and Technology
| | - Ying Shi
- Huazhong University of Science and Technology
| | - Chen Ruan
- Huazhong University of Science and Technology
| | - Yiran Tu
- Huazhong University of Science and Technology
| | - Lan Yao
- Huazhong University of Science and Technology
| | - Di Peng
- Huazhong University of Science and Technology
| | - Yu Xue
- Huazhong University of Science and Technology
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Gao Y, Hao W, Gu J, Liu D, Fan C, Chen Z, Deng L. PredPhos: an ensemble framework for structure-based prediction of phosphorylation sites. ACTA ACUST UNITED AC 2016; 23:12. [PMID: 27437197 PMCID: PMC4943517 DOI: 10.1186/s40709-016-0042-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Background Post-translational modifications (PTMs) occur on almost all proteins and often strongly affect the functions of modified proteins. Phosphorylation is a crucial PTM mechanism with important regulatory functions in biological systems. Identifying the potential phosphorylation sites of a target protein may increase our understanding of the molecular processes in which it takes part. Results In this paper, we propose PredPhos, a computational method that can accurately predict both kinase-specific and non-kinase-specific phosphorylation sites by using optimally selected properties. The optimal combination of features was selected from a set of 153 novel structural neighborhood properties by a two-step feature selection method consisting of a random forest algorithm and a sequential backward elimination method. To overcome the imbalanced problem, we adopt an ensemble method, which combines bootstrap resampling technique, support vector machine-based fusion classifiers and majority voting strategy. We evaluate the proposed method using both tenfold cross validation and independent test. Results show that our method achieves a significant improvement on the prediction performance for both kinase-specific and non-kinase-specific phosphorylation sites. Conclusions The experimental results demonstrate that the proposed method is quite effective in predicting phosphorylation sites. Promising results are derived from the new structural neighborhood properties, the novel way of feature selection, as well as the ensemble method.
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Affiliation(s)
- Yong Gao
- School of Software, Central South University, No. 22 Shaoshan South RD., Changsha, 410075 China
| | - Weilin Hao
- School of Software, Central South University, No. 22 Shaoshan South RD., Changsha, 410075 China.,School of Electronics Engineering and Computer Science, Peking University, No. 5 Yiheyuan Road, Beijing, 100871 China
| | - Jing Gu
- School of Software, Central South University, No. 22 Shaoshan South RD., Changsha, 410075 China
| | - Diwei Liu
- School of Software, Central South University, No. 22 Shaoshan South RD., Changsha, 410075 China
| | - Chao Fan
- School of Software, Central South University, No. 22 Shaoshan South RD., Changsha, 410075 China
| | - Zhigang Chen
- School of Software, Central South University, No. 22 Shaoshan South RD., Changsha, 410075 China
| | - Lei Deng
- School of Software, Central South University, No. 22 Shaoshan South RD., Changsha, 410075 China.,Shanghai Key Laboratory of Intelligent Information Processing, No. 220 Handan Road, Shanghai, 200433 China
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Ullah S, Lin S, Xu Y, Deng W, Ma L, Zhang Y, Liu Z, Xue Y. dbPAF: an integrative database of protein phosphorylation in animals and fungi. Sci Rep 2016; 6:23534. [PMID: 27010073 PMCID: PMC4806352 DOI: 10.1038/srep23534] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 03/08/2016] [Indexed: 12/26/2022] Open
Abstract
Protein phosphorylation is one of the most important post-translational modifications (PTMs) and regulates a broad spectrum of biological processes. Recent progresses in phosphoproteomic identifications have generated a flood of phosphorylation sites, while the integration of these sites is an urgent need. In this work, we developed a curated database of dbPAF, containing known phosphorylation sites in H. sapiens, M. musculus, R. norvegicus, D. melanogaster, C. elegans, S. pombe and S. cerevisiae. From the scientific literature and public databases, we totally collected and integrated 54,148 phosphoproteins with 483,001 phosphorylation sites. Multiple options were provided for accessing the data, while original references and other annotations were also present for each phosphoprotein. Based on the new data set, we computationally detected significantly over-represented sequence motifs around phosphorylation sites, predicted potential kinases that are responsible for the modification of collected phospho-sites, and evolutionarily analyzed phosphorylation conservation states across different species. Besides to be largely consistent with previous reports, our results also proposed new features of phospho-regulation. Taken together, our database can be useful for further analyses of protein phosphorylation in human and other model organisms. The dbPAF database was implemented in PHP + MySQL and freely available at http://dbpaf.biocuckoo.org.
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Affiliation(s)
- Shahid Ullah
- Department of Bioinformatics &Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Shaofeng Lin
- Department of Bioinformatics &Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Yang Xu
- Department of Bioinformatics &Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Wankun Deng
- Department of Bioinformatics &Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Lili Ma
- Department of Bioinformatics &Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Ying Zhang
- Department of Bioinformatics &Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Zexian Liu
- Department of Bioinformatics &Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Yu Xue
- Department of Bioinformatics &Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China.,Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
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7
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Accuracy of density functionals in the description of dispersion interactions and IR spectra of phosphates and phosphorylated compounds. J Mol Model 2014; 20:2426. [DOI: 10.1007/s00894-014-2426-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 08/07/2014] [Indexed: 10/24/2022]
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8
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Bugeja HE, Hynes MJ, Andrianopoulos A. HgrA is necessary and sufficient to drive hyphal growth in the dimorphic pathogen Penicillium marneffei. Mol Microbiol 2013; 88:998-1014. [PMID: 23656348 DOI: 10.1111/mmi.12239] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/14/2013] [Indexed: 12/17/2022]
Abstract
Fungi produce multiple morphological forms as part of developmental programs or in response to changing, often stressful, environmental conditions. An opportunistic pathogen of humans, Penicillium marneffei displays multicellular hyphal growth and asexual development (conidiation) in the environment at 25°C and unicellular yeast growth in macrophages at 37°C. We characterized the transcription factor, hgrA, which contains a C(2)H(2) DNA binding domain closely related to that of the stress-response regulators Msn2/4 of Saccharomyces cerevisiae. Northern hybridization analysis demonstrated that hgrA expression is specific to hyphal growth, and its constitutive overexpression prevents conidiation and yeast growth, even in the presence of inductive cues, and causes apical hyperbranching during hyphal growth. Consistent with its expression pattern, deletion of hgrA causes defects in hyphal morphogenesis and the dimorphic transition from yeast cells to hyphae. Specifically, loss of HgrA causes cell wall defects, reduced expression of cell wall biosynthetic enzymes and increased sensitvity to cell wall, oxidative, but not osmotic stress agents. These data suggest that HgrA does not have a direct role in the response to stress but is an inducer of the hyphal growth program and its activity must be downregulated to allow alternative developmental programs, including the morphogenesis of yeast cells in macrophages.
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Affiliation(s)
- Hayley E Bugeja
- Department of Genetics, University of Melbourne, Melbourne, Vic., 3010, Australia
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9
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Taouji S, Higa A, Delom F, Palcy S, Mahon FX, Pasquet JM, Bossé R, Ségui B, Chevet E. Phosphorylation of serine palmitoyltransferase long chain-1 (SPTLC1) on tyrosine 164 inhibits its activity and promotes cell survival. J Biol Chem 2013; 288:17190-201. [PMID: 23629659 DOI: 10.1074/jbc.m112.409185] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In BCR-ABL-expressing cells, sphingolipid metabolism is altered. Because the first step of sphingolipid biosynthesis occurs in the endoplasmic reticulum (ER), our objective was to identify ABL targets in the ER. A phosphoproteomic analysis of canine pancreatic ER microsomes identified 49 high scoring phosphotyrosine-containing peptides. These were then categorized in silico and validated in vitro. We demonstrated that the ER-resident human protein serine palmitoyltransferase long chain-1 (SPTLC1), which is the first enzyme of sphingolipid biosynthesis, is phosphorylated at Tyr(164) by the tyrosine kinase ABL. Inhibition of BCR-ABL using either imatinib or shRNA-mediated silencing led to the activation of SPTLC1 and to increased apoptosis in both K562 and LAMA-84 cells. Finally, we demonstrated that mutation of Tyr(164) to Phe in SPTLC1 increased serine palmitoyltransferase activity. The Y164F mutation also promoted the remodeling of cellular sphingolipid content, thereby sensitizing K562 cells to apoptosis. Our observations provide a mechanistic explanation for imatinib-mediated cell death and a novel avenue for therapeutic strategies.
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Peppelenbosch MP. Kinome profiling. SCIENTIFICA 2012; 2012:306798. [PMID: 24278683 PMCID: PMC3820527 DOI: 10.6064/2012/306798] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2012] [Accepted: 07/12/2012] [Indexed: 06/02/2023]
Abstract
The use of arrays in genomics has led to a fast and reliable way to screen the transcriptome of an organism. It can be automated and analysis tools have become available and hence the technique has become widely used within the past few years. Signal-transduction routes rely mainly on the phosphorylation status of already available proteins; therefore kinases are central players in signal-transduction routes. The array technology can now also be used for the analysis of the kinome. To enable array analysis, consensus peptides for kinases are spot on a solid support. After incubation with cell lysates and in the presence of radioactive ATP, radioactive peptides can be visualized and the kinases that are active in the cells can be determined. The present paper reviews comprehensively the different kinome array platforms available and results obtained hitherto using such platforms. It will appear that this technology does not disappoint its high expectations and is especially powerful because of its species independence. Nevertheless, improvements are still possible and I shall also sketch future possible directions.
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Affiliation(s)
- Maikel P. Peppelenbosch
- Department of Gastroenterology and Hepatology, Erasmus MC University Medical Center Rotterdam, L-459, P.O. Box 2040, NL-3000 CA Rotterdam, The Netherlands
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11
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Trost B, Kusalik A. Computational prediction of eukaryotic phosphorylation sites. Bioinformatics 2011; 27:2927-35. [DOI: 10.1093/bioinformatics/btr525] [Citation(s) in RCA: 121] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Stark C, Su TC, Breitkreutz A, Lourenco P, Dahabieh M, Breitkreutz BJ, Tyers M, Sadowski I. PhosphoGRID: a database of experimentally verified in vivo protein phosphorylation sites from the budding yeast Saccharomyces cerevisiae. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2010; 2010:bap026. [PMID: 20428315 PMCID: PMC2860897 DOI: 10.1093/database/bap026] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2009] [Revised: 12/07/2009] [Accepted: 12/23/2009] [Indexed: 12/17/2022]
Abstract
Protein phosphorylation plays a central role in cellular regulation. Recent proteomics strategies for identifying phosphopeptides have been developed using the model organism Saccharomyces cerevisiae, and consequently, when combined with studies of individual gene products, the number of reported specific phosphorylation sites for this organism has expanded enormously. In order to systematically document and integrate these various data types, we have developed a database of experimentally verified in vivo phosphorylation sites curated from the S. cerevisiae primary literature. PhosphoGRID (www.phosphogrid.org) records the positions of over 5000 specific phosphorylated residues on 1495 gene products. Nearly 900 phosphorylated residues are reported from detailed studies of individual proteins; these in vivo phosphorylation sites are documented by a hierarchy of experimental evidence codes. Where available for specific sites, we have also noted the relevant protein kinases and/or phosphatases, the specific condition(s) under which phosphorylation occurs, and the effect(s) that phosphorylation has on protein function. The unique features of PhosphoGRID that assign both function and specific physiological conditions to each phosphorylated residue will provide a valuable benchmark for proteome-level studies and will facilitate bioinformatic analysis of cellular signal transduction networks. Database URL: http://phosphogrid.org/
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Affiliation(s)
- Chris Stark
- Centre for Systems Biology, Samuel Lunenfeld Research Institute, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada
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Parikh K, Peppelenbosch MP, Ritsema T. Kinome profiling using peptide arrays in eukaryotic cells. Methods Mol Biol 2009; 527:269-80, x. [PMID: 19241020 DOI: 10.1007/978-1-60327-834-8_20] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Over the last 10 years array and mass spectrometry technologies have enabled the determination of the transcriptome and proteome of biological and in particular eukaryotic systems. This information will likely be of significant value to our elucidation of the molecular mechanisms that govern eukaryotic physiology. However, an equally, if not more important goal, is to define those proteins that participate in signalling pathways that ultimately control cell fate. Enzymes that phosphorylate tyrosine, serine, and threonine residues on other proteins play a major role in signalling cascades that determine cell-cycle entry, and survival and differentiation fate in the tissues across the eukaryotic kingdoms. Knowing which signalling pathways are being used in these cells is of critical importance. Traditional genetic and biochemical approaches can certainly provide answers here, but for technical and practical reasons there is typically pursued one gene or pathway at a time. Thus, a more comprehensive approach is needed in order to reveal signalling pathways active in nucleated cells. Towards this end, kinome analysis techniques using peptide arrays have begun to be applied with substantial success in a variety of organisms from all major branches of eukaryotic life, generating descriptions of cellular signalling without a priori assumptions as to possibly effected pathways. The general procedure and analysis methods are very similar disregarding whether the primary source of the material is animal, plant, or fungal of nature and will be described in this chapter. These studies will help us better understand what signalling pathways are critical to controlling eukaryotic cell function.
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Affiliation(s)
- Kaushal Parikh
- Department of Cell Biology, University Medical Center Groningen, Groningen, The Netherlands
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Correia CF, Clavaguera C, Erlekam U, Scuderi D, Ohanessian G. IRMPD Spectroscopy of a Protonated, Phosphorylated Dipeptide. Chemphyschem 2008; 9:2564-73. [DOI: 10.1002/cphc.200800469] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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15
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Cecconi D, Zamò A, Bianchi E, Parisi A, Barbi S, Milli A, Rinalducci S, Rosenwald A, Hartmann E, Zolla L, Chilosi M. Signal transduction pathways of mantle cell lymphoma: A phosphoproteome-based study. Proteomics 2008; 8:4495-506. [DOI: 10.1002/pmic.200800080] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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16
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Plewczynski D, Tkacz A, Wyrwicz LS, Rychlewski L, Ginalski K. AutoMotif Server for prediction of phosphorylation sites in proteins using support vector machine: 2007 update. J Mol Model 2007; 14:69-76. [PMID: 17994256 DOI: 10.1007/s00894-007-0250-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2007] [Accepted: 10/12/2007] [Indexed: 10/22/2022]
Abstract
We present here the recent update of AutoMotif Server (AMS 2.0) that predicts post-translational modification sites in protein sequences. The support vector machine (SVM) algorithm was trained on data gathered in 2007 from various sets of proteins containing experimentally verified chemical modifications of proteins. Short sequence segments around a modification site were dissected from a parent protein, and represented in the training set as binary or profile vectors. The updated efficiency of the SVM classification for each type of modification and the predictive power of both representations were estimated using leave-one-out tests for model of general phosphorylation and for modifications catalyzed by several specific protein kinases. The accuracy of the method was improved in comparison to the previous version of the service (Plewczynski et al., "AutoMotif server: prediction of single residue post-translational modifications in proteins", Bioinformatics 21: 2525-7, 2005). The precision of the updated version reached over 90% for selected types of phosphorylation and was optimized in trade of lower recall value of the classification model. The AutoMotif Server version 2007 is freely available at http://ams2.bioinfo.pl/ . Additionally, the reference dataset for optimization of prediction of phosphorylation sites, collected from the UniProtKB was also provided and can be accessed at http://ams2.bioinfo.pl/data/ .
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Affiliation(s)
- Dariusz Plewczynski
- Interdisciplinary Centre for Mathematical and Computational Modeling, University of Warsaw, Pawinskiego 5a, 02-106, Warsaw, Poland.
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17
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Mapping phosphoproteins in Mycoplasma genitalium and Mycoplasma pneumoniae. BMC Microbiol 2007; 7:63. [PMID: 17605819 PMCID: PMC1947986 DOI: 10.1186/1471-2180-7-63] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2006] [Accepted: 07/02/2007] [Indexed: 12/04/2022] Open
Abstract
Background Little is known regarding the extent or targets of phosphorylation in mycoplasmas, yet in many other bacterial species phosphorylation is known to play an important role in signaling and regulation of cellular processes. To determine the prevalence of phosphorylation in mycoplasmas, we examined the CHAPS-soluble protein fractions of Mycoplasma genitalium and Mycoplasma pneumoniae by two-dimensional gel electrophoresis (2-DE), using a combination of Pro-Q Diamond phosphoprotein stain and 33P labeling. Protein spots that were positive for phosphorylation were identified by peptide mass fingerprinting using MALDI-TOF-TOF mass spectrometry. Results We identified a total of 24 distinct phosphoproteins, about 3% and 5% of the total protein complement in M. pneumoniae and M. genitalium, respectively, indicating that phosphorylation occurs with prevalence similar to many other bacterial species. Identified phosphoproteins include pyruvate dehydrogenase E1 alpha and beta subunits, enolase, heat shock proteins DnaK and GroEL, elongation factor Tu, cytadherence accessory protein HMW3, P65, and several hypothetical proteins. These proteins are involved in energy metabolism, carbohydrate metabolism, translation/transcription and cytadherence. Interestingly, fourteen of the 24 phosphoproteins we identified (58%) were previously reported as putatively associated with a cytoskeleton-like structure that is present in the mycoplasmas, indicating a potential regulatory role for phosphorylation in this structure. Conclusion This study has shown that phosphorylation in mycoplasmas is comparable to that of other bacterial species. Our evidence supports a link between phosphorylation and cytadherence and/or a cytoskeleton-like structure, since over half of the proteins identified as phosphorylated have been previously associated with these functions. This opens the door to further research into the purposes and mechanisms of phosphorylation for mycoplasmas.
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18
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Kelley-Hickie LP, O'Keeffe MB, Reid HM, Kinsella BT. Homologous desensitization of signalling by the alpha (alpha) isoform of the human thromboxane A2 receptor: a specific role for nitric oxide signalling. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2007; 1773:970-89. [PMID: 17466390 PMCID: PMC2680961 DOI: 10.1016/j.bbamcr.2007.03.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2007] [Revised: 03/14/2007] [Accepted: 03/15/2007] [Indexed: 01/16/2023]
Abstract
Thromboxane (TX) A2 plays a central role in hemostasis, regulating platelet activation status and vascular tone. We have recently established that the TPβ isoform of the human TXA2 receptor (TP) undergoes rapid, agonist-induced homologous desensitization of signalling largely through a G protein-coupled receptor kinase (GRK) 2/3-dependent mechanism with a lesser role for protein kinase (PK) C. Herein, we investigated the mechanism of desensitization of signalling by the TPα isoform. TPα undergoes profound agonist-induced desensitization of signalling (intracellular calcium mobilization and inositol 1,4,5 trisphosphate generation) in response to the TXA2 mimetic U46619 but, unlike that of TPβ, this is independent of GRKs. Similar to TPβ, TPα undergoes partial agonist-induced desensitization that occurs through a GF 109203X-sensitive, PKC mechanism where Ser145 within intracellular domain (IC)2 represents the key phospho-target. TPα also undergoes more profound sustained PKC- and PKG-dependent desensitization where Thr337 and Ser331, respectively, within its unique C-tail domain were identified as the phospho-targets. Desensitization was impaired by the nitric oxide synthase (NOS), soluble guanylyl cyclase (sGC) and PKG inhibitors l-NAME, LY 83583 and KT5823, respectively, indicating that homologous desensitization of TPα involves nitric oxide generation and signalling. Consistent with this, U46619 led to rapid phosphorylation/activation of endogenous eNOS. Collectively, data herein suggest a mechanism whereby agonist-induced PKC phosphorylation of Ser145 partially and transiently impairs TPα signalling while PKG- and PKC-phosphorylation at both Ser331 and Thr337, respectively, within its C-tail domain profoundly desensitizes TPα, effectively terminating its signalling. Hence, in addition to the agonist-mediated PKC feedback mechanism, U46619-activation of the NOS/sGC/PKG pathway plays a significant role in inducing homologous desensitization of TPα.
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MESH Headings
- 15-Hydroxy-11 alpha,9 alpha-(epoxymethano)prosta-5,13-dienoic Acid/pharmacology
- Calcium Signaling/drug effects
- Calcium Signaling/physiology
- Cell Line
- Cyclic GMP-Dependent Protein Kinases/antagonists & inhibitors
- Cyclic GMP-Dependent Protein Kinases/metabolism
- Enzyme Inhibitors/pharmacology
- G-Protein-Coupled Receptor Kinase 2
- G-Protein-Coupled Receptor Kinase 3
- Hemostasis/drug effects
- Hemostasis/physiology
- Humans
- Indoles/pharmacology
- Inositol 1,4,5-Trisphosphate/metabolism
- Maleimides/pharmacology
- Nitric Oxide/metabolism
- Nitric Oxide Synthase Type III/metabolism
- Platelet Activation/drug effects
- Platelet Activation/physiology
- Protein Isoforms/agonists
- Protein Isoforms/genetics
- Protein Isoforms/metabolism
- Protein Kinase C/antagonists & inhibitors
- Protein Kinase C/metabolism
- Protein Structure, Tertiary/genetics
- Receptors, Thromboxane A2, Prostaglandin H2/agonists
- Receptors, Thromboxane A2, Prostaglandin H2/genetics
- Receptors, Thromboxane A2, Prostaglandin H2/metabolism
- Thromboxane A2/metabolism
- Vasoconstrictor Agents/pharmacology
- beta-Adrenergic Receptor Kinases/metabolism
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19
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Ingrell CR, Miller ML, Jensen ON, Blom N. NetPhosYeast: prediction of protein phosphorylation sites in yeast. Bioinformatics 2007; 23:895-7. [PMID: 17282998 DOI: 10.1093/bioinformatics/btm020] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
UNLABELLED We here present a neural network-based method for the prediction of protein phosphorylation sites in yeast--an important model organism for basic research. Existing protein phosphorylation site predictors are primarily based on mammalian data and show reduced sensitivity on yeast phosphorylation sites compared to those in humans, suggesting the need for an yeast-specific phosphorylation site predictor. NetPhosYeast achieves a correlation coefficient close to 0.75 with a sensitivity of 0.84 and specificity of 0.90 and outperforms existing predictors in the identification of phosphorylation sites in yeast. AVAILABILITY The NetPhosYeast prediction service is available as a public web server at http://www.cbs.dtu.dk/services/NetPhosYeast/.
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20
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Baroudi G, Qu Y, Ramadan O, Chahine M, Boutjdir M. Protein kinase C activation inhibits Cav1.3 calcium channel at NH2-terminal serine 81 phosphorylation site. Am J Physiol Heart Circ Physiol 2006; 291:H1614-22. [PMID: 16973824 DOI: 10.1152/ajpheart.00095.2006] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The Cav1.3 (α1D) variant of L-type Ca2+ channels plays a vital role in the function of neuroendocrine and cardiovascular systems. In this article, we report on the molecular and functional basis of α1D Ca2+ channel modulation by protein kinase C (PKC). Specifically, we show that the serine 81 (S81) phosphorylation site at the NH2-terminal region plays a critical role in α1D Ca2+ channel modulation by PKC. The introduction of a negatively charged residue at position 81, by converting serine to aspartate, mimicked the PKC phosphorylation effect on α1D Ca2+ channel. The modulation of α1D Ca2+ channel by PKC was prevented by dialyzing cells with a 35-amino acid peptide mimicking the α1D NH2-terminal region comprising S81. In addition, the data revealed that only βII- and εPKC isozymes are implicated in this regulation. These novel findings have significant implications in the pathophysiology of α1D Ca2+ channel and in the development of PKC isozyme-targeted therapeutics.
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Affiliation(s)
- Ghayath Baroudi
- Veterans Affairs New York Harbor Healthcare System, Research and Development (151 800 Poly Place, Brooklyn, NY 11209, USA
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21
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Kelley-Hickie LP, Kinsella BT. Homologous desensitization of signalling by the beta (β) isoform of the human thromboxane A2 receptor. Biochim Biophys Acta Mol Cell Biol Lipids 2006; 1761:1114-31. [PMID: 16956790 DOI: 10.1016/j.bbalip.2006.07.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2006] [Revised: 07/26/2006] [Accepted: 07/27/2006] [Indexed: 10/24/2022]
Abstract
Thromboxane (TX) A(2) is a potent stimulator of platelet activation/aggregation and smooth muscle contraction and contributes to a variety of pathologies within the vasculature. In this study, we investigated the mechanism whereby the cellular responses to TXA(2) mediated through the TPbeta isoform of the human TXA(2) receptor (TP) are dynamically regulated by examining the mechanism of agonist-induced desensitization of intracellular signalling and second messenger generation by TPbeta. It was established that TPbeta is subject to profound agonist-induced homologous desensitization of signalling (intracellular calcium mobilization and inositol 1,3,5 trisphosphate generation) in response to stimulation with the TXA(2) mimetic U46619 and this occurs through two key mechanisms: TPbeta undergoes partial agonist-induced desensitization that occurs through a GF 109203X-sensitive, protein kinase (PK)C mechanism whereby Ser(145) within intracellular domain (IC)(2) has been identified as the key phospho-target. In addition, TPbeta also undergoes more profound and sustained agonist-induced desensitization involving G protein-coupled receptor kinase (GRK)2/3-phosphorylation of both Ser(239) and Ser(357) within its IC(3) and carboxyl-terminal C-tail domains, respectively. Inhibition of phosphorylation of either Ser(239) or Ser(357), through site directed mutagenesis, impaired desensitization while mutation of both Ser(239) and Ser(357) almost completely abolished desensitization of signalling, GRK phosphorylation and beta-arrestin association, thereby blocking TPbeta internalization. These data suggest a model whereby agonist-induced PKC phosphorylation of Ser(145) partially impairs. TPbeta signalling while GRK2/3 phosphorylation at both Ser(239) and Ser(357) within its IC(3) and C-tail domains, respectively, sterically inhibits G-protein coupling, profoundly desensitizing signalling, and promotes beta-arrestin association and, in turn, facilitates TPbeta internalization. Thromboxane (TX) A(2) is a potent stimulator of platelet aggregation and smooth muscle contraction and contributes to a variety of vascular pathologies. Herein the mechanism whereby the cellular responses to TXA(2) mediated through the TPbeta isoform of the human TXA(2) receptor (TP) are dynamically regulated was investigated by examining the mechanism of its agonist-induced desensitization of intracellular signalling and second messenger generation. TPbeta is subject to profound agonist-induced homologous desensitization of signalling (intracellular calcium mobilization and inositol 1,3,5 trisphosphate generation) in response to stimulation with the TXA(2) mimetic U46619 and this occurs through two key mechanisms: TPbeta undergoes partial agonist-induced desensitization that occurs through a GF 109203X-sensitive, protein kinase (PK)C mechanism whereby Ser(145) within intracellular domain (IC)(2) was identified as the key phospho-target. In addition, TPbeta also undergoes more profound and sustained agonist-induced desensitization involving G protein-coupled receptor kinase (GRK)2/3-phosphorylation of both Ser(239) and Ser(357) within its IC(3) and carboxyl-terminal C-tail domains, respectively. Inhibition of phosphorylation of either Ser(239) or Ser(357), through site directed mutagenesis, impaired desensitization while mutation of both Ser(239) and Ser(357) almost completely abolished desensitization of signalling, GRK phosphorylation and beta-arrestin association, thereby blocking TPbeta internalization. These data suggest a model whereby agonist-induced PKC phosphorylation of Ser(145) partially impairs TPbeta signalling while GRK2/3 phosphorylation at both Ser(239) and Ser(357) within its IC(3) and C-tail domains, respectively, sterically inhibits G-protein coupling, profoundly desensitizing signalling, and promotes beta-arrestin association and, in turn, facilitates TPbeta internalization.
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MESH Headings
- 15-Hydroxy-11 alpha,9 alpha-(epoxymethano)prosta-5,13-dienoic Acid/pharmacology
- Amino Acid Sequence
- Arrestins/metabolism
- Calcium/metabolism
- Cell Line
- G-Protein-Coupled Receptor Kinase 3
- Humans
- Indoles/pharmacology
- Inositol 1,4,5-Trisphosphate/analogs & derivatives
- Inositol 1,4,5-Trisphosphate/metabolism
- Maleimides/pharmacology
- Molecular Sequence Data
- Mutagenesis, Site-Directed
- Phosphorylation
- Protein Isoforms/agonists
- Protein Isoforms/antagonists & inhibitors
- Protein Isoforms/metabolism
- Protein Kinase C/antagonists & inhibitors
- Protein Kinase C/metabolism
- Protein Serine-Threonine Kinases/metabolism
- Protein Structure, Tertiary
- Receptors, Thromboxane A2, Prostaglandin H2/agonists
- Receptors, Thromboxane A2, Prostaglandin H2/antagonists & inhibitors
- Receptors, Thromboxane A2, Prostaglandin H2/metabolism
- Second Messenger Systems
- Serine/metabolism
- Signal Transduction
- beta-Arrestins
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Affiliation(s)
- Leanne P Kelley-Hickie
- School of Biomolecular and Biomedical Science, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
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22
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Boehm J, Kang MG, Johnson RC, Esteban J, Huganir RL, Malinow R. Synaptic Incorporation of AMPA Receptors during LTP Is Controlled by a PKC Phosphorylation Site on GluR1. Neuron 2006; 51:213-25. [PMID: 16846856 DOI: 10.1016/j.neuron.2006.06.013] [Citation(s) in RCA: 284] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2005] [Revised: 05/08/2006] [Accepted: 06/16/2006] [Indexed: 11/17/2022]
Abstract
Incorporation of GluR1-containing AMPA receptors into synapses is essential to several forms of neural plasticity, including long-term potentiation (LTP). Numerous signaling pathways that trigger this process have been identified, but the direct modifications of GluR1 that control its incorporation into synapses are unclear. Here, we show that phosphorylation of GluR1 by PKC at a highly conserved serine 818 residue is increased during LTP and critical for LTP expression. GluR1 is phosphorylated by PKC at this site in vitro and in vivo. In addition, acute phosphorylation at GluR1 S818 by PKC, as well as a phosphomimetic mutation, promotes GluR1 synaptic incorporation. Conversely, preventing GluR1 S818 phosphorylation reduces LTP and blocks PKC-driven synaptic incorporation of GluR1. We conclude that the phosphorylation of GluR1 S818 by PKC is a critical event in the plasticity-driven synaptic incorporation of AMPA receptors.
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Affiliation(s)
- Jannic Boehm
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
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23
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Lin JM, Schroeder A, Allada R. In vivo circadian function of casein kinase 2 phosphorylation sites in Drosophila PERIOD. J Neurosci 2006; 25:11175-83. [PMID: 16319317 PMCID: PMC6725653 DOI: 10.1523/jneurosci.2159-05.2005] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Phosphorylation plays a key role in the precise timing of circadian clocks. Daily rhythms of phosphorylation of the Drosophila circadian clock component PERIOD (PER) were first described more than a decade ago, yet little is known about their phosphorylation sites and their function in circadian behavior. Here we show that serines 151 and 153 in PER are required for robust in vitro phosphorylation by the casein kinase 2 (CK2) holoenzyme, a cytoplasmic kinase shown to be involved in circadian rhythms. Mutation of these sites in transgenic flies results in significant period lengthening of behavioral rhythms, altered PER rhythms, and delayed PER nuclear localization in circadian pacemaker neurons. In many respects, mutation of these phosphorylation sites phenocopies mutation of the catalytic subunit of CK2. We propose that CK2 phosphorylation at these sites triggers PER nuclear localization.
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Affiliation(s)
- Jui-Ming Lin
- Department of Neurobiology and Physiology, Northwestern University, Evanston, Illinois 60208, USA
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24
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Huang HD, Lee TY, Tzeng SW, Horng JT. KinasePhos: a web tool for identifying protein kinase-specific phosphorylation sites. Nucleic Acids Res 2005; 33:W226-9. [PMID: 15980458 PMCID: PMC1160232 DOI: 10.1093/nar/gki471] [Citation(s) in RCA: 265] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
KinasePhos is a novel web server for computationally identifying catalytic kinase-specific phosphorylation sites. The known phosphorylation sites from public domain data sources are categorized by their annotated protein kinases. Based on the profile hidden Markov model, computational models are learned from the kinase-specific groups of the phosphorylation sites. After evaluating the learned models, the model with highest accuracy was selected from each kinase-specific group, for use in a web-based prediction tool for identifying protein phosphorylation sites. Therefore, this work developed a kinase-specific phosphorylation site prediction tool with both high sensitivity and specificity. The prediction tool is freely available at http://KinasePhos.mbc.nctu.edu.tw/.
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Affiliation(s)
- Hsien-Da Huang
- To whom correspondence should be addressed. Tel: +886 3 5712121, ext. 56952; Fax: +886 3 5729288;
| | | | - Shih-Wei Tzeng
- Department of Life Science, National Central UniversityChung-Li 320, Taiwan
| | - Jorng-Tzong Horng
- Department of Life Science, National Central UniversityChung-Li 320, Taiwan
- Department of Computer Science and Information Engineering, National Central UniversityChung-Li 320, Taiwan
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25
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Huang HD, Lee TY, Tzeng SW, Wu LC, Horng JT, Tsou AP, Huang KT. Incorporating hidden Markov models for identifying protein kinase-specific phosphorylation sites. J Comput Chem 2005; 26:1032-41. [PMID: 15889432 DOI: 10.1002/jcc.20235] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Protein phosphorylation, which is an important mechanism in posttranslational modification, affects essential cellular processes such as metabolism, cell signaling, differentiation, and membrane transportation. Proteins are phosphorylated by a variety of protein kinases. In this investigation, we develop a novel tool to computationally predict catalytic kinase-specific phosphorylation sites. The known phosphorylation sites from public domain data sources are categorized by their annotated protein kinases. Based on the concepts of profile Hidden Markov Models (HMM), computational models are trained from the kinase-specific groups of phosphorylation sites. After evaluating the trained models, we select the model with highest accuracy in each kinase-specific group and provide a Web-based prediction tool for identifying protein phosphorylation sites. The main contribution here is that we have developed a kinase-specific phosphorylation site prediction tool with both high sensitivity and specificity.
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Affiliation(s)
- Hsien-Da Huang
- Department of Biological Science and Technology, Institute of Bioinformatics, National Chiao Tung University, Hsin-Chu 300, Taiwan, Republic of China.
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26
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Habran L, Bontems S, Di Valentin E, Sadzot-Delvaux C, Piette J. Varicella-zoster virus IE63 protein phosphorylation by roscovitine-sensitive cyclin-dependent kinases modulates its cellular localization and activity. J Biol Chem 2005; 280:29135-43. [PMID: 15955820 DOI: 10.1074/jbc.m503312200] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
During the first stage of Varicella-Zoster virus (VZV) infection, IE63 (immediate early 63 protein) is mostly expressed in the nucleus and also slightly in the cytoplasm, and during latency, IE63 localizes in the cytoplasm quite exclusively. Because phosphorylation is known to regulate various cellular mechanisms, we investigated the impact of phosphorylation by roscovitine-sensitive cyclin-dependent kinase (RSC) on the localization and functional properties of IE63. We demonstrated first that IE63 was phosphorylated on Ser-224 in vitro by CDK1 and CDK5 but not by CDK2, CDK7, or CDK9. Furthermore, by using roscovitine and CDK1 inhibitor III (CiIII), we showed that CDK1 phosphorylated IE63 on Ser-224 in vivo. By mutagenesis and the use of inhibitors, we demonstrated that phosphorylation on Ser-224 was important for the correct localization of the protein. Indeed, the substitution of these residues by alanine led to an exclusive nuclear localization of the protein, whereas mutations into glutamic acid did not modify its subcellular distribution. When transfected or VZV-infected cells were treated with roscovitine or CiIII, an exclusive nuclear localization of IE63 was also observed. By using a transfection assay, we also showed that phosphorylation on Ser-224 and Thr-222 was essential for the down-regulation of the basal activity of the VZV DNA polymerase gene promoter. Similarly, roscovitine and CiIII impaired these properties of the wild-type form of IE63. These observations clearly demonstrated the importance of CDK1-mediated IE63 phosphorylation for a correct distribution of IE63 between both cellular compartments and for its repressive activity toward the promoter tested.
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Affiliation(s)
- Lionel Habran
- Laboratory of Virology and Immunology, Center for Biomedical Genoproteomics, Institute of Pathology B23, University of Liège, B-4000, Liège, Belgium
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27
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Loog M, Ek B, Oskolkov N, Närvänen A, Järv J, Ek P. Screening for the optimal specificity profile of protein kinase C using electrospray mass-spectrometry. JOURNAL OF BIOMOLECULAR SCREENING 2005; 10:320-8. [PMID: 15964933 DOI: 10.1177/1087057104274353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
A peptide library approach based on electrospray mass-spectrometric (ESI-MS) detection of phosphopeptides was designed for rapid and quantitative characterization of protein kinase specificity. The k(cat)/K(m) values for the protein kinase Cbeta (PKCbeta) were determined for a systematically varied set of individual substrate peptides in library mixtures by the ESI-MS method. The analysis revealed a complex structural specificity profile in positions around the phosphorylated serine with hydrophobic and/or basic residues being mostly preferred. On the basis of the kinetic parameters, a highly efficient peptide substrate for PKCbeta (K(m)value below 100 nM) FRRRRSFRRR and its alanine substituted pseudosubstrate-analog inhibitor (K(i) value of 76 nM) were designed. The quantitative specificity profiles obtained by the new approach contained more information about kinase specificity than the conventional substrate consensus motifs. The new method presents a promising basis for design of substrate-site directed peptide or peptidomimetic inhibitors of protein kinases. Second, highly specific substrates could be designed for novel applications such as high-throughput protein kinase activity screens on protein kinase chips.
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Affiliation(s)
- Mart Loog
- Department of Medical Biochemistry and Microbiology, Uppsala University, 75123 Uppsala, Sweden.
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28
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Walther RF, Atlas E, Carrigan A, Rouleau Y, Edgecombe A, Visentin L, Lamprecht C, Addicks GC, Haché RJG, Lefebvre YA. A Serine/Threonine-rich Motif Is One of Three Nuclear Localization Signals That Determine Unidirectional Transport of the Mineralocorticoid Receptor to the Nucleus. J Biol Chem 2005; 280:17549-61. [PMID: 15737989 DOI: 10.1074/jbc.m501548200] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The mineralocorticoid receptor (MR) is a tightly regulated nuclear hormone receptor that selectively transmits corticosteroid signals. Steroid treatment transforms MR from a transcriptionally inert state, in which it is distributed equally between the nucleus and cytoplasm, to an active completely nuclear transcription factor. We report here that MR is an atypical nuclear hormone receptor that moves unidirectionally from the cytoplasm to the nucleus. We show that nuclear import of MR is controlled through three nuclear localization signals (NLSs) of distinct types. Nuclear localization of naive MR was mediated primarily through a novel serine/threonine-rich NLS (NL0) in the receptor N terminus. Specific amino acid substitutions that mimicked phosphorylation selectively enhanced or repressed NL0 activity, highlighting the potential for active regulation of this new type of NLS. The second NLS (NL2) within the ligand-binding domain also lacks a recognizable basic motif. Nuclear transfer through this signal was strictly dependent on steroid agonist, but was independent of the interaction of MR with coactivator proteins. The third MR NLS (NL1) is a bipartite basic motif localized to the C terminus of the MR DNA-binding domain with properties distinct from those of NL1 of the closely related glucocorticoid receptor. NL1 acted in concert with NL0 and NL2 to stimulate nuclear uptake of the agonist-treated receptor, but also directed the complete nuclear localization of MR in response to treatment with steroid antagonist. These results present MR as a nuclear hormone receptor whose unidirectional transfer to the nucleus may be regulated through multiple pathways.
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Affiliation(s)
- Rhian F Walther
- Department of Medicine and Biochemistry, Graduate Program in Biochemistry, Ottawa Health Research Institute, Ottawa Hospital, University of Ottawa, Ontario, Canada
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29
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Rasmussen TN, Novak I, Nielsen SM. Internalization of the human CRF receptor 1 is independent of classical phosphorylation sites and of beta-arrestin 1 recruitment. ACTA ACUST UNITED AC 2004; 271:4366-74. [PMID: 15560778 DOI: 10.1111/j.1432-1033.2004.04371.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The corticotropin releasing factor receptor 1 (CRFR1) belongs to the superfamily of G-protein coupled receptors. Though CRF is involved in the aetiology of several stress-related disorders, including depression and anxiety, details of CRFR1 regulation such as internalization remain uncharacterized. In the present study, agonist-induced internalization of CRFR1 in HEK293 cells was visualized by confocal microscopy and quantified using the radioligand 125I-labelled sauvagine. Recruitment of beta-arrestin 1 in response to receptor activation was demonstrated by confocal microscopy. The extent of 125I-labelled sauvagine stimulated internalization was significantly impaired by sucrose, indicating the involvement of clathrin-coated pits. No effect on the extent of internalization was observed in the presence of the second messenger dependent kinase inhibitors H-89 and staurosporine, indicating that cAMP-dependent protein kinase and protein kinase C are not prerequisites for CRFR1 internalization. Surprisingly, deletion of all putative phosphorylation sites in the C-terminal tail, as well as a cluster of putative phosphorylation sites in the third intracellular loop, did not affect receptor internalization. However, these mutations almost abolished the recruitment of beta-arrestin 1 following receptor activation. In conclusion, we demonstrate that CRFR1 internalization is independent of phosphorylation sites in the C-terminal tail and third intracellular loop, and the degree of beta-arrestin 1 recruitment.
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30
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Diks SH, Kok K, O'Toole T, Hommes DW, van Dijken P, Joore J, Peppelenbosch MP. Kinome profiling for studying lipopolysaccharide signal transduction in human peripheral blood mononuclear cells. J Biol Chem 2004; 279:49206-13. [PMID: 15355981 DOI: 10.1074/jbc.m405028200] [Citation(s) in RCA: 107] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The DNA array technique allows comprehensive analysis of the genome and transcriptome, but the high throughput array-based assessment of intracellular signal transduction remains troublesome. The goal of this study was to test a new peptide array technology for studying the activity of all kinases of whole cell lysates, the kinome. Cell lysates from human peripheral blood mononuclear cells before and after stimulation with lipopolysaccharide were used for in vitro phosphorylation with [gamma-33P]ATP arrays consisting of 192 peptides (substrates for kinases) spotted on glass. The usefulness of peptide arrays for studying signal transduction was demonstrated by the generation of the first comprehensive description of the temporal kinetics of phosphorylation events induced by lipopolysaccharide stimulation. Furthermore analysis of the signals obtained suggested activation of p21Ras by lipopolysaccharide, and this was confirmed by direct measurement of p21Ras GTP levels in lipopolysaccharide-stimulated human peripheral blood mononuclear cells, which represents the first direct demonstration of p21Ras activation by stimulation of a Toll receptor family member. Further confidence in the usefulness of peptide array technology for studying signal transduction came from Western blot analysis of lipopolysaccharide-stimulated cells, which corroborated the signals obtained using peptide arrays as well as from the demonstration that kinase inhibitors effected peptide array phosphorylation patterns consistent with the expected action of these inhibitors. We conclude that this first metabolic array is a useful method to determine the enzymatic activities of a large group of kinases, offering high throughput analysis of cellular metabolism and signal transduction.
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Affiliation(s)
- Sander H Diks
- Department of Cell Biology, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
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Kelley-Hickie LP, Kinsella BT. EP1- and FP-mediated cross-desensitization of the alpha (alpha) and beta (beta) isoforms of the human thromboxane A2 receptor. Br J Pharmacol 2004; 142:203-21. [PMID: 15100160 PMCID: PMC1574916 DOI: 10.1038/sj.bjp.0705695] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
1. Heterologous desensitization or intermolecular cross-talk plays a critical role in regulating intracellular signalling by diverse members of the G-protein-coupled receptor superfamily. We have previously established that the alpha and beta isoforms of the human thromboxane A(2) receptor (TP) undergo differential desensitization of signalling in response to 17 phenyl trinor prostaglandin (PG)E(2), an agonist of the EP(1) subtype of the PGE(2) receptor (EP) family. 2. Herein, we investigated the molecular basis of TPalpha and TPbeta desensitization in human embryonic kidney (HEK) 293 cells and in renal mesangial cells in response to 17 phenyl trinor PGE(2) and in response to the PGF(2alpha) receptor (FP) agonist PGF(2alpha), and sought to identify the target site(s) of those desensitizations. 3. Our results demonstrated that TPalpha and TPbeta receptors are subject to desensitization in response to both EP(1) and FP receptor activation and that these effects are mediated by direct protein kinase (PK)C phosphorylation of the individual TP isoforms within their unique carboxyl-terminal (C)-tail domains. 4. Moreover, deletion/site-directed mutagenesis and metabolic labelling studies identified Thr(337), within TPalpha, and Thr(399), within TPbeta, as the specific target residues for PKC phosphorylation and EP(1)- and FP-mediated desensitization of TPalpha and TPbeta signalling, respectively. 5. Hence, in conclusion, while the TPalpha and TPbeta diverge within their C-tail domains, they have evolved to share a similar mechanism of PKC-induced phosphorylation and desensitization in response to EP(1) and FP receptor activation, though it occurs at sites unique to the individual TP isoforms.
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MESH Headings
- 15-Hydroxy-11 alpha,9 alpha-(epoxymethano)prosta-5,13-dienoic Acid/pharmacology
- Amino Acid Sequence
- Cell Line
- Humans
- Molecular Sequence Data
- Protein Isoforms/genetics
- Protein Isoforms/metabolism
- Receptors, Prostaglandin/genetics
- Receptors, Prostaglandin/metabolism
- Receptors, Prostaglandin E/genetics
- Receptors, Prostaglandin E/metabolism
- Receptors, Prostaglandin E, EP1 Subtype
- Receptors, Thromboxane A2, Prostaglandin H2/genetics
- Receptors, Thromboxane A2, Prostaglandin H2/metabolism
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Affiliation(s)
- Leanne P Kelley-Hickie
- Department of Biochemistry, Conway Institute of Biomolecular and Biomedical Research, Merville House, University College Dublin, Belfield, Dublin 4, Ireland
| | - B Therese Kinsella
- Department of Biochemistry, Conway Institute of Biomolecular and Biomedical Research, Merville House, University College Dublin, Belfield, Dublin 4, Ireland
- Author for correspondence:
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Abramovitch RB, Yang G, Kronstad JW. The ukb1 gene encodes a putative protein kinase required for bud site selection and pathogenicity in Ustilago maydis. Fungal Genet Biol 2002; 37:98-108. [PMID: 12223194 DOI: 10.1016/s1087-1845(02)00030-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Morphogenesis and pathogenesis are closely associated aspects of the life cycle of the fungal pathogen Ustilago maydis. In this fungus, the dimorphic switch from budding to filamentous growth coincides with the transition from non-pathogenic to pathogenic growth on maize. We have cloned and characterized the ukb1 gene that encodes a putative serine/threonine protein kinase with a role in budding and filamentous growth. Mutants defective in ukb1 were altered in bud site selection and produced lateral buds at a greater frequency than wild-type cells. Dikaryotic cells defective in ukb1 were capable of colonizing host tissue and growing with a filamentous morphology in planta. However, the mutants were incapable of inducing tumor formation and they failed to complete sexual development. In addition, the ukb1 gene influenced the ability of colonies to form aerial mycelia in response to environmental stimuli. Overall, the discovery of ukb1 reinforces the connection between morphogenesis and pathogenesis in U. maydis.
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Affiliation(s)
- R B Abramovitch
- Biotechnology Laboratory, Department of Microbiology and Immunology, Faculty of Agricultural Sciences, University of British Columbia, 237-6174 University Blvd., Vancouver, BC, Canada
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33
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Miggin SM, Kinsella BT. Investigation of the mechanisms of G protein: effector coupling by the human and mouse prostacyclin receptors. Identification of critical species-dependent differences. J Biol Chem 2002; 277:27053-64. [PMID: 12016224 DOI: 10.1074/jbc.m203353200] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We recently identified a novel mechanism explaining how the mouse (m) prostacyclin receptor (IP) couples to Galpha(s), Galpha(i), and Galpha(q) (Lawler, O. A., Miggin, S. M., and Kinsella, B. T. (2001) J. Biol. Chem. 276, 33596-33607) whereby mIP coupling to Galpha(i) and Galpha(q) is dependent on its initial coupling to Galpha(s) and subsequent phosphorylation by cAMP-dependent protein kinase A (PKA) on Ser(357). In the current study, the generality of that mechanism was investigated by examining the G protein coupling specificity of the human (h) IP. The hIP efficiently coupled to Galpha(s)/adenylyl cyclase and to Galpha(q)/phospholipase C activation but failed to couple to Galpha(i). Coupling of the hIP to Galpha(q), or indeed to Galpha(s) or Galpha(i), was unaffected by the PKA or protein kinase C (PKC) inhibitors H-89 and GF 109203X, respectively. Thus, mIP and hIP exhibit essential differences in their coupling to Galpha(i) and in their dependence on PKA in regulating their coupling to Galpha(q). Analysis of their primary sequences revealed that the critical PKA phosphorylation site within the mIP, at Ser(357), is replaced by a PKC site within the hIP, at Ser(328). Conversion of the PKC site of the hIP to a PKA site generated hIP(QL325,326RP) that efficiently coupled to Galpha(s) and to Galpha(i) and Galpha(q); coupling of hIP(QL325,326RP) to Galpha(i) but not to Galpha(s) or Galpha(q) was inhibited by H-89. Abolition of the PKC site of the hIP generated hIP(S328A) that efficiently coupled to Galpha(s) and Galpha(q) but failed to couple to Galpha(i). Finally, conversion of the PKA site at Ser(357) within the mIP to a PKC site generated mIP(RP354,355QL) that efficiently coupled to Galpha(s) but not to Galpha(i) or Galpha(q). Collectively, our data highlight critical differences in signaling by the mIP and hIP that are regulated by their differential phosphorylation by PKA and PKC together with contextual sequence differences surrounding those sites.
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Affiliation(s)
- Sinead M Miggin
- Department of Biochemistry, Conway Institute of Biomolecular and Biomedical Research, Merville House, University College Dublin, Belfield, Dublin 4, Ireland
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34
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Bontems S, Di Valentin E, Baudoux L, Rentier B, Sadzot-Delvaux C, Piette J. Phosphorylation of varicella-zoster virus IE63 protein by casein kinases influences its cellular localization and gene regulation activity. J Biol Chem 2002; 277:21050-60. [PMID: 11912195 DOI: 10.1074/jbc.m111872200] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
During the early phase of varicella-zoster virus (VZV) infection, Immediate Early protein 63 (IE63) is expressed rapidly and abundantly in the nucleus, while during latency, this protein is confined mostly to the cytoplasm. Because phosphorylation is known to regulate many cellular events, we investigated the importance of this modification on the cellular localization of IE63 and on its regulatory properties. We demonstrate here that cellular casein kinases I and II are implicated in the in vitro and in vivo phosphorylation of IE63. A mutational approach also indicated that phosphorylation of the protein is important for its correct cellular localization in a cell type-dependent fashion. Using an activity test, we demonstrated that IE63 was able to repress the gene expression driven by two VZV promoters and that phosphorylation of the protein was required for its full repressive properties. Finally, we showed that IE63 was capable of exerting its repressive activity in the cytoplasm, as well as in the nucleus, suggesting a regulation at the transcriptional and/or post-transcriptional level.
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Affiliation(s)
- Sébastien Bontems
- Laboratory of Virology and Immunology, University of Liège, B-4000 Liège, Belgium
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35
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Lawler OA, Miggin SM, Kinsella BT. Protein kinase A-mediated phosphorylation of serine 357 of the mouse prostacyclin receptor regulates its coupling to G(s)-, to G(i)-, and to G(q)-coupled effector signaling. J Biol Chem 2001; 276:33596-607. [PMID: 11443126 DOI: 10.1074/jbc.m104434200] [Citation(s) in RCA: 95] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The prostacyclin receptor (IP) is primarily coupled to G alpha(s)-dependent activation of adenylyl cyclase; however, a number of studies indicate that the IP may couple to other secondary effector systems perhaps in a species-specific manner. In the current study, we investigated the specificity of G protein:effector coupling by the mouse (m) IP overexpressed in human embryonic kidney 293 cells and endogenously expressed in murine erythroleukemia cells. The mIP exhibited efficient G alpha(s) coupling and concentration-dependent increases in cAMP generation in response to the IP agonist cicaprost; however, mIP also coupled to G alpha(i) decreasing the levels of cAMP in forskolin-treated cells. mIP coupling to G alpha(i) was pertussis toxin-sensitive and was dependent on protein kinase (PK) A activation status. In addition, the mIP coupled to phospholipase C (PLC) activation in a pertussis toxin-insensitive, G alpha(i)-, G beta gamma-, and PKC-independent but in a G alpha(q)- and PKA-dependent manner. Whole cell phosphorylation assays demonstrated that the mIP undergoes cicaprost-induced PKA phosphorylation. mIP(S357A), a site-directed mutant of mIP, efficiently coupled to G alpha(s) but failed to couple to G alpha(i) or to efficiently couple to G alpha(q):PLC. Moreover, mIP(S357A) did not undergo cicaprost-induced phosphorylation confirming that Ser(357) is the target residue for PKA-dependent phosphorylation. Finally, co-precipitation experiments permitted the detection of G alpha(s), G alpha(i), and G alpha(q) in the immunoprecipitates of mIP, whereas only G alpha(s) was co-precipitated with mIP(S357A) indicating that Ser(357) of mIP is essential for G alpha(i) and G alpha(q) interaction. Moreover, inhibition of PKA blocked co-precipitation of mIP with G alpha(i) or G alpha(q). Taken together our data indicate that the mIP, in addition to coupling to G alpha(s), couples to G alpha(i) and G alpha(q); however, G alpha(i) and G alpha(q) coupling is dependent on initial cicaprost-induced mIP:G alpha(s) coupling and phosphorylation of mIP by cAMP-dependent PKA where Ser(357) was identified as the target residue for PKA phosphorylation.
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Affiliation(s)
- O A Lawler
- Department of Biochemistry, Conway Institute of Biomolecular and Biomedical Research, Merville House, University College Dublin, Belfield, Dublin 4, Ireland
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36
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Foley JF, Kelley LP, Kinsella BT. Prostaglandin D(2) receptor-mediated desensitization of the alpha isoform of the human thromboxane A(2) receptor. Biochem Pharmacol 2001; 62:229-39. [PMID: 11389883 DOI: 10.1016/s0006-2952(01)00661-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Thromboxane (TX) A(2) and prostaglandin (PG) D(2) mediate opposing actions in platelets and in vascular and non-vascular smooth muscle. Here, we investigated the effects of stimulation of the PGD(2) receptor (DP) on signaling by the TXA(2) receptor (TP) expressed in human platelets and in human embryonic kidney (HEK) 293 cells over-expressing the individual TP alpha and TP beta isoforms. In platelets, the selective DP agonist BW245C abolished TP-mediated mobilization of intracellular calcium ([Ca(2+)](i)) and inhibited platelet aggregation in response to the TXA(2) mimetic U46619. DP-mediated desensitization of TP signaling in platelets was prevented by pretreatment with the cAMP-dependent PKA inhibitor, H-89, but was unaffected by the PKC inhibitor GF 109203X. In HEK 293 cells, signaling by TP alpha, but not TP beta, was subject to DP-mediated desensitization in a PKA-dependent, PKC-independent manner. U46619-induced signaling by TP(Delta 328), a truncated variant of TP containing only those residues common to TP alpha and TP beta, was insensitive to prior DP stimulation, indicating that the carboxyl terminal tail of TPalpha contains the target site(s) for DP-mediated desensitization. Mutation of Ser(329) to Ala(329) within a consensus PKA site in TP alpha rendered the mutant TP alpha(S329A) insensitive to BW245C-mediated desensitization. Whole cell phosphorylation assays established that TP alpha, but not TP beta or TP alpha(S329A), was subject to DP-mediated phosphorylation and that TP alpha phosphorylation was blocked by the PKA inhibitor H-89. These data establish that TP alpha, but not TP beta, is subject to DP-mediated cross desensitization, which occurs through direct PKA-mediated phosphorylation of TP alpha at Ser(329).
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MESH Headings
- 15-Hydroxy-11 alpha,9 alpha-(epoxymethano)prosta-5,13-dienoic Acid/pharmacology
- Blood Platelets/drug effects
- Blood Platelets/metabolism
- Cells, Cultured
- Humans
- Hydantoins/pharmacology
- Inositol 1,4,5-Trisphosphate/metabolism
- Phosphorylation
- Protein Isoforms/physiology
- Receptor Cross-Talk/physiology
- Receptors, Immunologic
- Receptors, Prostaglandin/antagonists & inhibitors
- Receptors, Prostaglandin/metabolism
- Receptors, Prostaglandin/physiology
- Receptors, Thromboxane/physiology
- Signal Transduction
- Vasoconstrictor Agents/pharmacology
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Affiliation(s)
- J F Foley
- Department of Biochemistry, Conway Institute of Biomolecular and Biomedical Research, Merville House, University College Dublin, Belfield, Dublin 4, Ireland
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37
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Walsh MT, Foley JF, Kinsella BT. The alpha, but not the beta, isoform of the human thromboxane A2 receptor is a target for prostacyclin-mediated desensitization. J Biol Chem 2000; 275:20412-23. [PMID: 10827090 DOI: 10.1074/jbc.m907881199] [Citation(s) in RCA: 87] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In this study, we examined the effects the prostacyclin receptor (IP) agonist cicaprost exhibited on U46619-mediated thromboxane A(2) receptor (TP) signaling in platelets and compared it to that which occurs in human embryonic kidney (HEK) 293 cells stably overexpressing the individual TPalpha or TPbeta isoforms. Consistent with previous studies, cicaprost abrogated U46619-mediated platelet aggregation and mobilization of intracellular calcium ([Ca(2+)](i)). In HEK 293 cells, signaling by TPalpha, but not TPbeta, was subject to IP-mediated desensitization in a protein kinase A-dependent, protein kinase C-independent manner. Desensitization of TPalpha signaling was independent of the nature of the IP agonist used, the level of IP expression, or the subtype of G(q) protein. Signaling by TP(Delta)(328), a truncated variant of TP devoid of the divergent residues of the TPs, or by TPalpha(S329A), a site-directed mutant of TPalpha, were insensitive to IP agonist activation. Whole cell phosphorylations established that TPalpha, but not TPbeta or TPalpha(S329A), is subject to IP-mediated phosphorylation and that TPalpha phosphorylation is inhibited by H-89. Thus, we conclude that TPalpha, but not TPbeta, is subject to cross-desensitization by IP mediated through direct protein kinase A phosphorylation at Ser(329) and propose that TPalpha may be the isoform physiologically relevant to TP:IP-mediated vascular hemostasis.
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Affiliation(s)
- M T Walsh
- Department of Biochemistry, Conway Institute of Biomolecular and Biomedical Research, Merville House, University College Dublin, Belfield, Dublin 4, Ireland
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38
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Yaguchi S, Mitsui K, Iha H, Tsurugi K. Phosphorylation of the GTS1 gene product of the yeast Saccharomyces cerevisiae and its effect on heat tolerance and flocculation. FEMS Microbiol Lett 2000; 187:179-84. [PMID: 10856654 DOI: 10.1111/j.1574-6968.2000.tb09157.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The GTS1 gene from the yeast Saccharomyces cerevisiae showed pleiotropic effects on yeast phenotypes, including an increase of heat tolerance in stationary-phase cells and an induction of flocculation. Here, we found that the GTS1 product, Gts1p, was partially phosphorylated at some serine residue(s) in cells grown on glucose. Studies using mutants of protein kinase A (PKA) and CDC25, the Ras-GTP exchange activator, showed that PKA positively regulated the phosphorylation level of Gts1p. Overexpression of Gts1p in a mutant with attenuated PKA activity did not show any increase of heat tolerance and partially decreased flocculation inducibility, suggesting that phosphorylation of Gts1p is required for induction of these phenomena.
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Affiliation(s)
- S Yaguchi
- Department of Biochemistry 2, Yamanashi Medical University, 1110 Shimokato, Tamaho, Nakakoma, 409-3898, Yamanashi, Japan
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39
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Pevzner V, Kraft R, Kostka S, Lipp M. Phosphorylation of Oct-2 at sites located in the POU domain induces differential down-regulation of Oct-2 DNA-binding ability. Biochem J 2000; 347 Pt 1:29-35. [PMID: 10727398 PMCID: PMC1220927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
We compared the effects of phosphorylation of Oct-2 protein on its binding to the consensus octamer sequence (ATGCAAAT) and two non-canonical sequences present in human (AAGCAAAT) and murine (AAACAAAT) promoters of the BLR1 (Burkitts' lymphoma receptor 1) gene encoding chemokine receptor CXCR5 (CXC-chemokine receptor 5). The latter cis-acting elements represent low-affinity recognition sequences for the octamer transcription factors. Okadaic acid was found to induce hyperphosphorylation of Oct-2 specifically in cells of lymphoid lineage. Potentially phosphorylated amino acid residues localized to the POU-specific domain of Oct-2. Whereas binding of Oct-2 to the octamer site from the human BLR1 promoter or to the consensus octamer sequence was unaffected by phosphorylation of this factor, a strong reduction of Oct-2 binding to the octamer site from the murine BLR1 promoter was observed. This finding correlates well with the down-regulation of expression of the BLR1 gene in murine splenic cells but not in lymphoid cells of human origin treated with okadaic acid. These data support the hypothesis that phosphorylation of Oct-2 may be a mechanism by which activities of the promoters containing non-canonical octamer sequences are differentially regulated in response to extracellular stimuli.
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Affiliation(s)
- V Pevzner
- Department of Tumorgenetics, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, D-13092 Berlin, Germany
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40
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Wera S. An EXCEL-based method to search for potential Ser/Thr-phosphorylation sites in proteins. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 1999; 58:65-68. [PMID: 10195647 DOI: 10.1016/s0169-2607(98)00068-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
A user-friendly, inexpensive EXCEL-based program to find potential phosphorylation sites in proteins is presented. The input of the program is a protein sequence in single letter code. The program searches for 93 different protein kinase recognition sites from 30 different protein kinases. The output is a list of these sites and their position in the sequence. The program can easily be updated in case new recognition sites are described. With a few adaptations, the tool can also be used to find other patterns in a protein sequence.
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Affiliation(s)
- S Wera
- Laboratorium voor Moleculaire Celbiologie, Katholieke Universiteit Leuven, Leuven-Heverlee, Belgium.
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41
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Kreegipuu A, Blom N, Brunak S. PhosphoBase, a database of phosphorylation sites: release 2.0. Nucleic Acids Res 1999; 27:237-9. [PMID: 9847189 PMCID: PMC148144 DOI: 10.1093/nar/27.1.237] [Citation(s) in RCA: 212] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
PhosphoBase contains information about phosphorylated residues in proteins and data about peptide phosphorylation by a variety of protein kinases. The data are collected from literature and compiled into a common format. The current release of PhosphoBase (October 1998, version 2.0) comprises 414 phosphoprotein entries covering 1052 phosphorylatable serine, threonine and tyrosine residues. The kinetic data from peptide phosphorylation assays for approximately 330 oligopeptides is also included. The database entries are cross-referenced to the corresponding records in the Swiss-Prot protein database and literature references are linked to MedLine records. PhosphoBase is available via the WWW at http://www.cbs.dtu. dk/databases/PhosphoBase/
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Affiliation(s)
- A Kreegipuu
- Institute of Chemical Physics, University of Tartu, 2 Jakobi St., EE2400 Tartu, Estonia
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42
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Abstract
The site and sequence specificity of protein kinases, as well as the role of the secondary structure and surface accessibility of the phosphorylation sites on substrate proteins, was statistically analyzed. The experimental data were collected from the literature and are available on the World Wide Web at http://www.cbs.dtu.dk/databases/PhosphoBase/. The set of data involved 1008 phosphorylatable sites in 406 proteins, which were phosphorylated by 58 protein kinases. It was found that there exists almost absolute Ser/Thr or Tyr specificity, with rare exceptions. The sequence specificity determinants were less strict and were located between positions -4 and +4 relative to the phosphorylation site. Secondary structure and surface accessibility predictions revealed that most of the phosphorylation sites were located on the surface of the target proteins.
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Affiliation(s)
- A Kreegipuu
- Institute of Chemical Physics, University of Tartu, Estonia
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