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Schwarz JJ, Grundmann L, Kokot T, Kläsener K, Fotteler S, Medgyesi D, Köhn M, Reth M, Warscheid B. Quantitative proteomics identifies PTP1B as modulator of B cell antigen receptor signaling. Life Sci Alliance 2021; 4:4/11/e202101084. [PMID: 34526379 PMCID: PMC8473724 DOI: 10.26508/lsa.202101084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 08/28/2021] [Accepted: 09/01/2021] [Indexed: 11/24/2022] Open
Abstract
This study analyses the function of the protein tyrosine phosphatase 1B identifying its binding partners and dephosphorylation targets for modulating B cell antigen receptor signaling. B cell antigen receptor (BCR) signaling is initiated by protein kinases and limited by counteracting phosphatases that currently are less well studied in their regulation of BCR signaling. Here, we used the B cell line Ramos to identify and quantify human B cell signaling components. Specifically, a protein tyrosine phosphatase profiling revealed a high expression of the protein tyrosine phosphatase 1B (PTP1B) in Ramos and human naïve B cells. The loss of PTP1B leads to increased B cell activation. Through substrate trapping in combination with quantitative mass spectrometry, we identified 22 putative substrates or interactors of PTP1B. We validated Igα, CD22, PLCγ1/2, CBL, BCAP, and APLP2 as specific substrates of PTP1B in Ramos B cells. The tyrosine kinase BTK and the two adaptor proteins GRB2 and VAV1 were identified as direct binding partners and potential substrates of PTP1B. We showed that PTP1B dephosphorylates the inhibitory receptor protein CD22 at phosphotyrosine 807. We conclude that PTP1B negatively modulates BCR signaling by dephosphorylating distinct phosphotyrosines in B cell-specific receptor proteins and various downstream signaling components.
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Affiliation(s)
- Jennifer J Schwarz
- Biochemistry and Functional Proteomics, Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany.,Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
| | - Lorenz Grundmann
- Biochemistry and Functional Proteomics, Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Thomas Kokot
- Integrative Signalling Research, Institute of Biology III, Faculty of Biology, University of Freiburg, Freiburg, Germany.,Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Kathrin Kläsener
- Department for Molecular Immunology, Institute of Biology III, Faculty of Biology, University of Freiburg, Freiburg, Germany.,Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Sandra Fotteler
- Biochemistry and Functional Proteomics, Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - David Medgyesi
- Department for Molecular Immunology, Institute of Biology III, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Maja Köhn
- Integrative Signalling Research, Institute of Biology III, Faculty of Biology, University of Freiburg, Freiburg, Germany.,Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany.,Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
| | - Michael Reth
- Department for Molecular Immunology, Institute of Biology III, Faculty of Biology, University of Freiburg, Freiburg, Germany.,Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany.,Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
| | - Bettina Warscheid
- Biochemistry and Functional Proteomics, Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany .,Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany.,Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
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Computational Phosphorylation Network Reconstruction: An Update on Methods and Resources. Methods Mol Biol 2021. [PMID: 34270057 DOI: 10.1007/978-1-0716-1625-3_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
Most proteins undergo some form of modification after translation, and phosphorylation is one of the most relevant and ubiquitous post-translational modifications. The succession of protein phosphorylation and dephosphorylation catalyzed by protein kinase and phosphatase, respectively, constitutes a key mechanism of molecular information flow in cellular systems. The protein interactions of kinases, phosphatases, and their regulatory subunits and substrates are the main part of phosphorylation networks. To elucidate the landscape of phosphorylation events has been a central goal pursued by both experimental and computational approaches. Substrate specificity (e.g., sequence, structure) or the phosphoproteome has been utilized in an array of different statistical learning methods to infer phosphorylation networks. In this chapter, different computational phosphorylation network inference-related methods and resources are summarized and discussed.
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Abstract
Phosphatases play key roles in normal physiology and diseases. Studying phosphatases has been both essential and challenging, and the application of conventional genetic and biochemical methods has led to crucial but still limited understanding of their mechanisms, substrates, and exclusive functions within highly intricate networks. With the advances in technologies such as cellular imaging and molecular and chemical biology in terms of sensitive tools and methods, the phosphatase field has thrived in the past years and has set new insights for cell signaling studies and for therapeutic development. In this review, we give an overview of the existing interdisciplinary tools for phosphatases, give examples on how they have been applied to increase our understanding of these enzymes, and suggest how they-and other tools yet barely used in the phosphatase field-might be adapted to address future questions and challenges.
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Affiliation(s)
- Sara Fahs
- European Molecular Biology Laboratory, Genome Biology
Unit, Meyerhofstrasse
1, 69117 Heidelberg, Germany
| | - Pablo Lujan
- European Molecular Biology Laboratory, Genome Biology
Unit, Meyerhofstrasse
1, 69117 Heidelberg, Germany
| | - Maja Köhn
- European Molecular Biology Laboratory, Genome Biology
Unit, Meyerhofstrasse
1, 69117 Heidelberg, Germany
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