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DeMarco AG, Hall MC. Phosphoproteomic Approaches for Identifying Phosphatase and Kinase Substrates. Molecules 2023; 28:3675. [PMID: 37175085 PMCID: PMC10180314 DOI: 10.3390/molecules28093675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 04/21/2023] [Accepted: 04/22/2023] [Indexed: 05/15/2023] Open
Abstract
Protein phosphorylation is a ubiquitous post-translational modification controlled by the opposing activities of protein kinases and phosphatases, which regulate diverse biological processes in all kingdoms of life. One of the key challenges to a complete understanding of phosphoregulatory networks is the unambiguous identification of kinase and phosphatase substrates. Liquid chromatography-coupled mass spectrometry (LC-MS/MS) and associated phosphoproteomic tools enable global surveys of phosphoproteome changes in response to signaling events or perturbation of phosphoregulatory network components. Despite the power of LC-MS/MS, it is still challenging to directly link kinases and phosphatases to specific substrate phosphorylation sites in many experiments. Here, we survey common LC-MS/MS-based phosphoproteomic workflows for identifying protein kinase and phosphatase substrates, noting key advantages and limitations of each. We conclude by discussing the value of inducible degradation technologies coupled with phosphoproteomics as a new approach that overcomes some limitations of current methods for substrate identification of kinases, phosphatases, and other regulatory enzymes.
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Affiliation(s)
- Andrew G. DeMarco
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Mark C. Hall
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
- Institute for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
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2
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Dunphy K, Dowling P, Bazou D, O’Gorman P. Current Methods of Post-Translational Modification Analysis and Their Applications in Blood Cancers. Cancers (Basel) 2021; 13:1930. [PMID: 33923680 PMCID: PMC8072572 DOI: 10.3390/cancers13081930] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/04/2021] [Accepted: 04/14/2021] [Indexed: 12/12/2022] Open
Abstract
Post-translational modifications (PTMs) add a layer of complexity to the proteome through the addition of biochemical moieties to specific residues of proteins, altering their structure, function and/or localization. Mass spectrometry (MS)-based techniques are at the forefront of PTM analysis due to their ability to detect large numbers of modified proteins with a high level of sensitivity and specificity. The low stoichiometry of modified peptides means fractionation and enrichment techniques are often performed prior to MS to improve detection yields. Immuno-based techniques remain popular, with improvements in the quality of commercially available modification-specific antibodies facilitating the detection of modified proteins with high affinity. PTM-focused studies on blood cancers have provided information on altered cellular processes, including cell signaling, apoptosis and transcriptional regulation, that contribute to the malignant phenotype. Furthermore, the mechanism of action of many blood cancer therapies, such as kinase inhibitors, involves inhibiting or modulating protein modifications. Continued optimization of protocols and techniques for PTM analysis in blood cancer will undoubtedly lead to novel insights into mechanisms of malignant transformation, proliferation, and survival, in addition to the identification of novel biomarkers and therapeutic targets. This review discusses techniques used for PTM analysis and their applications in blood cancer research.
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Affiliation(s)
- Katie Dunphy
- Department of Biology, National University of Ireland, W23 F2K8 Maynooth, Ireland; (K.D.); (P.D.)
| | - Paul Dowling
- Department of Biology, National University of Ireland, W23 F2K8 Maynooth, Ireland; (K.D.); (P.D.)
| | - Despina Bazou
- Department of Haematology, Mater Misericordiae University Hospital, D07 WKW8 Dublin, Ireland;
| | - Peter O’Gorman
- Department of Haematology, Mater Misericordiae University Hospital, D07 WKW8 Dublin, Ireland;
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Zhou S, Appleman VA, Rose CM, Jun HJ, Yang J, Zhou Y, Bronson RT, Gygi SP, Charest A. Chronic platelet-derived growth factor receptor signaling exerts control over initiation of protein translation in glioma. Life Sci Alliance 2018; 1:e201800029. [PMID: 30456354 PMCID: PMC6238596 DOI: 10.26508/lsa.201800029] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 05/29/2018] [Accepted: 05/29/2018] [Indexed: 01/23/2023] Open
Abstract
Using phospho-proteomics in a new model of malignant glioma, we reveal that clinically relevant, chronic PDGFRα signaling differs considerably from acute receptor stimulation and unveils previously unrecognized control over key elements of the translation initiation machinery. Activation of the platelet-derived growth factor receptors (PDGFRs) gives rise to some of the most important signaling pathways that regulate mammalian cellular growth, survival, proliferation, and differentiation and their misregulation is common in a variety of diseases. Herein, we present a comprehensive and detailed map of PDGFR signaling pathways assembled from literature and integrate this map in a bioinformatics protocol designed to extract meaningful information from large-scale quantitative proteomics mass spectrometry data. We demonstrate the usefulness of this approach using a new genetically engineered mouse model of PDGFRα-driven glioma. We discovered that acute PDGFRα stimulation differs considerably from chronic receptor activation in the regulation of protein translation initiation. Transient stimulation activates several key components of the translation initiation machinery, whereas the clinically relevant chronic activity of PDGFRα is associated with a significant shutdown of translational members. Our work defines a step-by-step approach to extract biologically relevant insights from global unbiased phospho-protein datasets to uncover targets for therapeutic assessment.
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Affiliation(s)
- Shuang Zhou
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Vicky A Appleman
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | | | - Hyun Jung Jun
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Juechen Yang
- Department of Computer Science, North Dakota State University, Fargo, ND, USA
| | - Yue Zhou
- Department of Statistics, North Dakota State University, Fargo, ND, USA
| | - Roderick T Bronson
- Rodent Histopathology Core, Dana-Farber/Harvard Cancer Center, Boston, MA, USA
| | - Steve P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Al Charest
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
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Junker S, Maaβ S, Otto A, Michalik S, Morgenroth F, Gerth U, Hecker M, Becher D. Spectral Library Based Analysis of Arginine Phosphorylations in Staphylococcus aureus. Mol Cell Proteomics 2018; 17:335-348. [PMID: 29183913 PMCID: PMC5795395 DOI: 10.1074/mcp.ra117.000378] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Indexed: 12/19/2022] Open
Abstract
Reversible protein phosphorylation is one of the major mechanisms in the regulation of protein expression and protein activity, controlling physiological functions of the important human pathogen Staphylococcus aureus Phosphorylations at serine, threonine and tyrosine are known to influence for example protein activity in central metabolic pathways and the more energy-rich phosphorylations at histidine, aspartate or cysteine can be found as part of two component system sensor domains or mediating bacterial virulence. In addition to these well-known phosphorylations, the phosphorylation at arginine residues plays an essential role. Hence, the deletion mutant S. aureus COL ΔptpB (protein tyrosine phosphatase B) was studied because the protein PtpB is assumed to be an arginine phosphatase. A gel-free approach was applied to analyze the changes in the phosphoproteome of the deletion mutant ΔptpB and the wild type in growing cells, thereby focusing on the occurrence of phosphorylation on arginine residues. In order to enhance the reliability of identified phosphorylation sites at arginine residues, a subset of arginine phosphorylated peptides was chemically synthesized. Combined spectral libraries based on phosphoenriched samples, synthetic arginine phosphorylated peptides and classical proteome samples provide a sophisticated tool for the analysis of arginine phosphorylations. This way, 212 proteins phosphorylated on serine, threonine, tyrosine or arginine residues were identified within the mutant ΔptpB and 102 in wild type samples. Among them, 207 arginine phosphosites were identified exclusively within the mutant ΔptpB, widely distributed along the whole bacterial metabolism. This identification of putative targets of PtpB allows further investigation of the physiological relevance of arginine phosphorylations and provides the basis for reliable quantification of arginine phosphorylations in bacteria.
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Affiliation(s)
- Sabryna Junker
- From the ‡Institute for Microbiology, University of Greifswald, Germany
| | - Sandra Maaβ
- From the ‡Institute for Microbiology, University of Greifswald, Germany
| | - Andreas Otto
- From the ‡Institute for Microbiology, University of Greifswald, Germany
| | - Stephan Michalik
- From the ‡Institute for Microbiology, University of Greifswald, Germany
| | | | - Ulf Gerth
- From the ‡Institute for Microbiology, University of Greifswald, Germany
| | - Michael Hecker
- From the ‡Institute for Microbiology, University of Greifswald, Germany
| | - Dörte Becher
- From the ‡Institute for Microbiology, University of Greifswald, Germany
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Junker S, Maaβ S, Otto A, Michalik S, Morgenroth F, Gerth U, Hecker M, Becher D. Spectral Library Based Analysis of Arginine Phosphorylations in Staphylococcus aureus. MOLECULAR & CELLULAR PROTEOMICS : MCP 2017. [PMID: 29183913 DOI: 10.1074/mcp.ra117.000378.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Reversible protein phosphorylation is one of the major mechanisms in the regulation of protein expression and protein activity, controlling physiological functions of the important human pathogen Staphylococcus aureus Phosphorylations at serine, threonine and tyrosine are known to influence for example protein activity in central metabolic pathways and the more energy-rich phosphorylations at histidine, aspartate or cysteine can be found as part of two component system sensor domains or mediating bacterial virulence. In addition to these well-known phosphorylations, the phosphorylation at arginine residues plays an essential role. Hence, the deletion mutant S. aureus COL ΔptpB (protein tyrosine phosphatase B) was studied because the protein PtpB is assumed to be an arginine phosphatase. A gel-free approach was applied to analyze the changes in the phosphoproteome of the deletion mutant ΔptpB and the wild type in growing cells, thereby focusing on the occurrence of phosphorylation on arginine residues. In order to enhance the reliability of identified phosphorylation sites at arginine residues, a subset of arginine phosphorylated peptides was chemically synthesized. Combined spectral libraries based on phosphoenriched samples, synthetic arginine phosphorylated peptides and classical proteome samples provide a sophisticated tool for the analysis of arginine phosphorylations. This way, 212 proteins phosphorylated on serine, threonine, tyrosine or arginine residues were identified within the mutant ΔptpB and 102 in wild type samples. Among them, 207 arginine phosphosites were identified exclusively within the mutant ΔptpB, widely distributed along the whole bacterial metabolism. This identification of putative targets of PtpB allows further investigation of the physiological relevance of arginine phosphorylations and provides the basis for reliable quantification of arginine phosphorylations in bacteria.
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Affiliation(s)
- Sabryna Junker
- From the ‡Institute for Microbiology, University of Greifswald, Germany
| | - Sandra Maaβ
- From the ‡Institute for Microbiology, University of Greifswald, Germany
| | - Andreas Otto
- From the ‡Institute for Microbiology, University of Greifswald, Germany
| | - Stephan Michalik
- From the ‡Institute for Microbiology, University of Greifswald, Germany
| | | | - Ulf Gerth
- From the ‡Institute for Microbiology, University of Greifswald, Germany
| | - Michael Hecker
- From the ‡Institute for Microbiology, University of Greifswald, Germany
| | - Dörte Becher
- From the ‡Institute for Microbiology, University of Greifswald, Germany
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