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Krishnamoorthy S, Liu Z, Hong A, Zhu R, Chen H, Li T, Zhou X, Gao X. A Novel Phosphopeptide Microarray Based Interactome Map in Breast Cancer Cells Reveals Phosphoprotein-GRB2 Cell Signaling Networks. PLoS One 2013; 8:e67634. [PMID: 23826330 PMCID: PMC3694890 DOI: 10.1371/journal.pone.0067634] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2012] [Accepted: 05/21/2013] [Indexed: 11/23/2022] Open
Abstract
The architecture of cellular proteins connected to form signaling pathways in response to internal and external cues is much more complex than a group of simple protein-protein interactions. Post translational modifications on proteins (e.g., phosphorylation of serine, threonine and tyrosine residues on proteins) initiate many downstream signaling events leading to protein-protein interactions and subsequent activation of signaling cascades leading to cell proliferation, cell differentiation and cell death. As evidenced by a rapidly expanding mass spectrometry database demonstrating protein phosphorylation at specific motifs, there is currently a large gap in understanding the functional significance of phosphoproteins with respect to their specific protein connections in the signaling cascades. A comprehensive map that interconnects phospho-motifs in pathways will enable identification of nodal protein interactions that are sensitive signatures indicating a disease phenotype from the physiological hemostasis and provide clues into control of disease. Using a novel phosphopeptide microarray technology, we have mapped endogenous tyrosine-phosphoproteome interaction networks in breast cancer cells mediated by signaling adaptor protein GRB2, which transduces cellular responses downstream of several RTKs through the Ras-ERK signaling cascade. We have identified several previously reported motif specific interactions and novel interactions. The peptide microarray data indicate that various phospho-motifs on a single protein are differentially regulated in various cell types and shows global downregulation of phosphoprotein interactions specifically in cells with metastatic potential. The study has revealed novel phosphoprotein mediated signaling networks, which warrants further detailed analysis of the nodes of protein-protein interaction to uncover their biomarker or therapeutic potential.
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Affiliation(s)
- Srinivasan Krishnamoorthy
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
- * E-mail: (SK); (XG)
| | - Zhonghua Liu
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
| | - Ailing Hong
- LC Sciences, Houston, Texas, United States of America
| | - Ruijuan Zhu
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
| | - Haosi Chen
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
| | - Tongbin Li
- LC Sciences, Houston, Texas, United States of America
| | | | - Xiaolian Gao
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
- * E-mail: (SK); (XG)
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Condina MR, Gustafsson JOR, Klingler-Hoffmann M, Bagley CJ, McColl SR, Hoffmann P. EZYprep LC-coupled MALDI-TOF/TOF MS: an improved matrix spray application for phosphopeptide characterisation. Proteomics 2010; 10:2516-30. [PMID: 20432483 DOI: 10.1002/pmic.200900800] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The quality of MALDI-TOF mass spectrometric analysis is highly dependent on the matrix and its deposition strategy. Although different matrix-deposition methods have specific advantages, one major problem in the field of proteomics, particularly with respect to quantitation, is reproducibility between users or laboratories. Compounding this is the varying crystal homogeneity of matrices depending on the deposition strategy used. Here, we describe a novel optimised matrix-deposition strategy for LC-MALDI-TOF/TOF MS using an automated instrument that produces a nebulised matrix "mist" under controlled atmospheric conditions. Comparisons of this with previously reported strategies showed the method to be advantageous for the atypical matrix, 2,5-DHB, and improved phosphopeptide ionisation when compared with deposition strategies for CHCA. This optimised DHB matrix-deposition strategy with LC-MALDI-TOF/TOF MS, termed EZYprep LC, was subsequently optimised for phosphoproteome analysis and compared to LC-ESI-IT-MS and a previously reported approach for phosphotyrosine identification and characterisation. These methods were used to map phosphorylation on epidermal growth factor-stimulated epidermal growth factor receptor to gauge the sensitivity of the proposed method. EZYprep DHB LC-MALDI-TOF/TOF MS was able to identify more phosphopeptides and characterise more phosphorylation sites than the other two proteomic strategies, thus proving to be a sensitive approach for phosphoproteome analysis.
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Affiliation(s)
- Mark R Condina
- School of Molecular and Biomedical Science, The University of Adelaide, Adelaide, SA, Australia
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Przybylski C, Jünger MA, Aubertin J, Radvanyi F, Aebersold R, Pflieger D. Quantitative Analysis of Protein Complex Constituents and Their Phosphorylation States on a LTQ-Orbitrap Instrument. J Proteome Res 2010; 9:5118-32. [DOI: 10.1021/pr1003888] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Cédric Przybylski
- Laboratoire Analyse et Modélisation pour la Biologie et l’Environnement, Université d’Evry-Val-d’Essonne, 91025 Evry, France, CNRS UMR 8587, Laboratoire d’Analyse et de Modélisation pour la Biologie et l’Environnement, Université d’Evry-Val-d’Essonne, 91025 Evry, France, Institute for Molecular Systems Biology, ETH, Zürich, Switzerland and Faculty of Science, University of Zurich, Zurich, Switzerland, and Équipe Oncologie Moléculaire, UMR 144 - CNRS, Institut Curie, 75248 Paris, France
| | - Martin A. Jünger
- Laboratoire Analyse et Modélisation pour la Biologie et l’Environnement, Université d’Evry-Val-d’Essonne, 91025 Evry, France, CNRS UMR 8587, Laboratoire d’Analyse et de Modélisation pour la Biologie et l’Environnement, Université d’Evry-Val-d’Essonne, 91025 Evry, France, Institute for Molecular Systems Biology, ETH, Zürich, Switzerland and Faculty of Science, University of Zurich, Zurich, Switzerland, and Équipe Oncologie Moléculaire, UMR 144 - CNRS, Institut Curie, 75248 Paris, France
| | - Johannes Aubertin
- Laboratoire Analyse et Modélisation pour la Biologie et l’Environnement, Université d’Evry-Val-d’Essonne, 91025 Evry, France, CNRS UMR 8587, Laboratoire d’Analyse et de Modélisation pour la Biologie et l’Environnement, Université d’Evry-Val-d’Essonne, 91025 Evry, France, Institute for Molecular Systems Biology, ETH, Zürich, Switzerland and Faculty of Science, University of Zurich, Zurich, Switzerland, and Équipe Oncologie Moléculaire, UMR 144 - CNRS, Institut Curie, 75248 Paris, France
| | - François Radvanyi
- Laboratoire Analyse et Modélisation pour la Biologie et l’Environnement, Université d’Evry-Val-d’Essonne, 91025 Evry, France, CNRS UMR 8587, Laboratoire d’Analyse et de Modélisation pour la Biologie et l’Environnement, Université d’Evry-Val-d’Essonne, 91025 Evry, France, Institute for Molecular Systems Biology, ETH, Zürich, Switzerland and Faculty of Science, University of Zurich, Zurich, Switzerland, and Équipe Oncologie Moléculaire, UMR 144 - CNRS, Institut Curie, 75248 Paris, France
| | - Ruedi Aebersold
- Laboratoire Analyse et Modélisation pour la Biologie et l’Environnement, Université d’Evry-Val-d’Essonne, 91025 Evry, France, CNRS UMR 8587, Laboratoire d’Analyse et de Modélisation pour la Biologie et l’Environnement, Université d’Evry-Val-d’Essonne, 91025 Evry, France, Institute for Molecular Systems Biology, ETH, Zürich, Switzerland and Faculty of Science, University of Zurich, Zurich, Switzerland, and Équipe Oncologie Moléculaire, UMR 144 - CNRS, Institut Curie, 75248 Paris, France
| | - Delphine Pflieger
- Laboratoire Analyse et Modélisation pour la Biologie et l’Environnement, Université d’Evry-Val-d’Essonne, 91025 Evry, France, CNRS UMR 8587, Laboratoire d’Analyse et de Modélisation pour la Biologie et l’Environnement, Université d’Evry-Val-d’Essonne, 91025 Evry, France, Institute for Molecular Systems Biology, ETH, Zürich, Switzerland and Faculty of Science, University of Zurich, Zurich, Switzerland, and Équipe Oncologie Moléculaire, UMR 144 - CNRS, Institut Curie, 75248 Paris, France
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Veraksa A. When peptides fly: advances in Drosophila proteomics. J Proteomics 2010; 73:2158-70. [PMID: 20580952 DOI: 10.1016/j.jprot.2010.05.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2010] [Accepted: 05/11/2010] [Indexed: 10/25/2022]
Abstract
In the past decade, improvements in genome annotation, protein fractionation methods and mass spectrometry instrumentation resulted in rapid growth of Drosophila proteomics. This review presents the current status of proteomics research in the fly. Areas that have seen major advances in recent years include efforts to map and catalog the Drosophila proteome and high-throughput as well as targeted studies to analyze protein-protein interactions and post-translational modifications. Stable isotope labeling of flies and other applications of quantitative proteomics have opened up new possibilities for functional analyses. It is clear that proteomics is becoming an indispensable tool in Drosophila systems biology research that adds a unique dimension to studying gene function.
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Affiliation(s)
- Alexey Veraksa
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125, USA.
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Eybishtz A, Peretz Y, Sade D, Akad F, Czosnek H. Silencing of a single gene in tomato plants resistant to Tomato yellow leaf curl virus renders them susceptible to the virus. PLANT MOLECULAR BIOLOGY 2009; 71:157-71. [PMID: 19533378 DOI: 10.1007/s11103-009-9515-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2008] [Accepted: 06/08/2009] [Indexed: 05/21/2023]
Abstract
A reverse-genetics approach was applied to identify genes involved in Tomato yellow leaf curl virus (TYLCV) resistance, taking advantage of two tomato inbred lines from the same breeding program-one susceptible (S), one resistant (R-that used Solanum habrochaites as the source of resistance. cDNA libraries from inoculated and non-inoculated R and S plants were compared, postulating that genes preferentially expressed in the R line may be part of the network sustaining resistance to TYLCV. Further, we assumed that silencing genes located at important nodes of the network would lead to collapse of resistance. Approximately 70 different cDNAs representing genes preferentially expressed in R plants were isolated and their genes identified by comparison with public databases. A Permease I-like protein gene encoding a transmembranal transporter was further studied: it was preferentially expressed in R plants and its expression was enhanced several-fold following TYLCV inoculation. Silencing of the Permease gene of R plants using Tobacco rattle virus-induced gene silencing led to loss of resistance, expressed as development of disease symptoms typical of infected susceptible plants and accumulation of large amounts of virus. Silencing of another membrane protein gene preferentially expressed in R plants, Pectin methylesterase, previously shown to be involved in Tobacco mosaic virus translocation, did not lead to collapse of resistance of R plants. Thus, silencing of a single gene can lead to collapse of resistance, but not every gene preferentially expressed in the R line has the same effect, upon silencing, on resistance.
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Affiliation(s)
- Assaf Eybishtz
- The Otto Warburg Minerva Center for Agricultural Biotechnology and the Robert H. Smith Institute of Plant Science and Genetics in Agriculture, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
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