101
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Tong K, Wang Y, Su Z. Phosphotyrosine signalling and the origin of animal multicellularity. Proc Biol Sci 2018; 284:rspb.2017.0681. [PMID: 28768887 DOI: 10.1098/rspb.2017.0681] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 06/26/2017] [Indexed: 12/21/2022] Open
Abstract
The evolution of multicellular animals (i.e. metazoans) from a unicellular ancestor is one of the most important yet least understood evolutionary transitions. Historically, given its indispensable functions in intercellular communication and exclusive presence in metazoans, phosphotyrosine (pTyr) signalling was considered a metazoan-specific evolutionary innovation that might have contributed to the origin of metazoan multicellularity. However, recent studies have led to a new understanding of pTyr signalling evolution and its role in the metazoan origin. Sequence analyses have unravelled a much earlier emergence of pTyr signalling in eukaryotic evolution. Even so, several distinct properties of holozoan pTyr signalling may have paved the way for a hypothesized functional transition of pTyr signalling at the multicellular origin, from environmental sensing to intercellular communication, and for it to evolve as a powerful intercellular signalling system for multicellularity. Biochemical analyses of premetazoan pTyr signalling components have further revealed the premetazoan origin of many key features of metazoan pTyr signalling, and the metazoan establishment of others, including the Csk-mediated negative regulation of the activity of Src, a conserved tyrosine kinase in the Holozoa. Finally, potential future directions are discussed, with a stress on the biological functions of premetazoan pTyr signalling via newly developed gene manipulation tools in non-animal holozoans.
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Affiliation(s)
- Kai Tong
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, People's Republic of China
| | - Yuyu Wang
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, People's Republic of China
| | - Zhixi Su
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, People's Republic of China
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102
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Liu J, Liu B, Chen S, Gong BQ, Chen L, Zhou Q, Xiong F, Wang M, Feng D, Li JF, Wang HB, Wang J. A Tyrosine Phosphorylation Cycle Regulates Fungal Activation of a Plant Receptor Ser/Thr Kinase. Cell Host Microbe 2018; 23:241-253.e6. [DOI: 10.1016/j.chom.2017.12.005] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 08/22/2017] [Accepted: 12/12/2017] [Indexed: 11/24/2022]
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103
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Hillmann F, Forbes G, Novohradská S, Ferling I, Riege K, Groth M, Westermann M, Marz M, Spaller T, Winckler T, Schaap P, Glöckner G. Multiple Roots of Fruiting Body Formation in Amoebozoa. Genome Biol Evol 2018; 10:591-606. [PMID: 29378020 PMCID: PMC5804921 DOI: 10.1093/gbe/evy011] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/11/2018] [Indexed: 02/03/2023] Open
Abstract
Establishment of multicellularity represents a major transition in eukaryote evolution. A subgroup of Amoebozoa, the dictyosteliids, has evolved a relatively simple aggregative multicellular stage resulting in a fruiting body supported by a stalk. Protosteloid amoeba, which are scattered throughout the amoebozoan tree, differ by producing only one or few single stalked spores. Thus, one obvious difference in the developmental cycle of protosteliids and dictyosteliids seems to be the establishment of multicellularity. To separate spore development from multicellular interactions, we compared the genome and transcriptome of a Protostelium species (Protostelium aurantium var. fungivorum) with those of social and solitary members of the Amoebozoa. During fruiting body formation nearly 4,000 genes, corresponding to specific pathways required for differentiation processes, are upregulated. A comparison with genes involved in the development of dictyosteliids revealed conservation of >500 genes, but most of them are also present in Acanthamoeba castellanii for which fruiting bodies have not been documented. Moreover, expression regulation of those genes differs between P. aurantium and Dictyostelium discoideum. Within Amoebozoa differentiation to fruiting bodies is common, but our current genome analysis suggests that protosteliids and dictyosteliids used different routes to achieve this. Most remarkable is both the large repertoire and diversity between species in genes that mediate environmental sensing and signal processing. This likely reflects an immense adaptability of the single cell stage to varying environmental conditions. We surmise that this signaling repertoire provided sufficient building blocks to accommodate the relatively simple demands for cell-cell communication in the early multicellular forms.
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Affiliation(s)
- Falk Hillmann
- Junior Research Group Evolution of Microbial Interaction, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute (HKI), Jena, Germany
| | - Gillian Forbes
- Division of Cell and Developmental Biology, School of Life Sciences, University of Dundee, United Kingdom
| | - Silvia Novohradská
- Junior Research Group Evolution of Microbial Interaction, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute (HKI), Jena, Germany
| | - Iuliia Ferling
- Junior Research Group Evolution of Microbial Interaction, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute (HKI), Jena, Germany
| | - Konstantin Riege
- Bioinformatics/High Throughput Analysis, Friedrich Schiller University Jena, Germany
| | - Marco Groth
- CF DNA-Sequencing, Leibniz Institute on Aging Research, Jena, Germany
| | | | - Manja Marz
- Bioinformatics/High Throughput Analysis, Friedrich Schiller University Jena, Germany
| | - Thomas Spaller
- Pharmaceutical Biology, Institute of Pharmacy, Friedrich Schiller University Jena, Germany
| | - Thomas Winckler
- Pharmaceutical Biology, Institute of Pharmacy, Friedrich Schiller University Jena, Germany
| | - Pauline Schaap
- Division of Cell and Developmental Biology, School of Life Sciences, University of Dundee, United Kingdom
| | - Gernot Glöckner
- Institute of Biochemistry I, Medical Faculty, University of Cologne, Germany
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104
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Live Staining of Drosophila Embryos with RPTP Fusion Proteins to Detect and Characterize Expression of Cell-Surface RPTP Ligands. Methods Mol Biol 2018. [PMID: 27514816 DOI: 10.1007/978-1-4939-3746-2_20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The activity and/or localization of receptor tyrosine kinases and phosphatases are controlled by binding to cell-surface or secreted ligands. Identification of ligands for receptor tyrosine phosphatases (RPTPs) is essential for understanding their in vivo functions during development and disease. Here we describe a novel in vivo method to identify ligands and binding partners for RPTPs by staining live-dissected Drosophila embryos. Live dissected embryos are incubated with RPTP fusion proteins to detect ligand binding in embryos. This method can be streamlined to perform large-scale screens for ligands as well as to search for embryonic phenotypes.
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105
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A shift in the IL-6/STAT3 signalling pathway imbalance towards the SHP2 pathway in severe asthma results in reduced proliferation process. Cell Signal 2017; 43:47-54. [PMID: 29242170 DOI: 10.1016/j.cellsig.2017.12.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 11/16/2017] [Accepted: 12/08/2017] [Indexed: 12/07/2022]
Abstract
BACKGROUND Bronchial fibroblasts are the main structural cells responsible for extracellular matrix production and turnover in lung tissue. They play a key role in airway remodelling in asthma through different cytokines including interleukin (IL-6). OBJECTIVE To decipher IL-6 signalling in bronchial fibroblasts obtained from severe eosinophilic asthmatics compared to mild asthmatics and healthy controls. METHODS Human bronchial fibroblasts were isolated from bronchial biopsies of mild and severe eosinophilic asthmatics and non-atopic healthy controls. IL-6 was assessed by qRT-PCR and ELISA. Phosphorylated STAT3, SHP2 and p38/MAPK were evaluated by Western blot. Chemical inhibitors for SHP2 and p38 were used. Fibroblast proliferation was evaluated by BrdU incorporation test. RESULTS IL-6 release was significantly increased in fibroblasts from mild and severe asthmatics compared to healthy controls. Fibroblasts from severe asthmatics showed a reduced STAT3 activation compared to mild asthmatics and healthy controls. Constitutive activation of phosphatase SHP2 was found to negatively regulate IL-6 induced STAT3 phosphorylation in fibroblasts from severe asthmatics. This effect was accompanied by a decrease in fibroblast proliferation rate due to the activated p38/mitogen-activated protein kinase. SHP2 and p38/MAPK specific inhibitors (PHPS1 and SB212190) significantly induce a restoration of STAT3 phosphorylation, IL-6 target gene expression and cell proliferation. CONCLUSION These data show dysregulated IL-6 signalling in bronchial fibroblasts derived from severe eosinophilic asthmatic subjects involving the protein tyrosine phosphatase SHP2 and p38MAPK. Collectively, our data provides new insights into the mechanisms by which bronchial fibroblasts regulate airway remodelling in severe asthma.
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106
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Naudin C, Chevalier C, Roche S. The role of small adaptor proteins in the control of oncogenic signalingr driven by tyrosine kinases in human cancer. Oncotarget 2017; 7:11033-55. [PMID: 26788993 PMCID: PMC4905456 DOI: 10.18632/oncotarget.6929] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 01/01/2016] [Indexed: 12/15/2022] Open
Abstract
Protein phosphorylation on tyrosine (Tyr) residues has evolved as an important mechanism to coordinate cell communication in multicellular organisms. The importance of this process has been revealed by the discovery of the prominent oncogenic properties of tyrosine kinases (TK) upon deregulation of their physiological activities, often due to protein overexpression and/or somatic mutation. Recent reports suggest that TK oncogenic signaling is also under the control of small adaptor proteins. These cytosolic proteins lack intrinsic catalytic activity and signal by linking two functional members of a catalytic pathway. While most adaptors display positive regulatory functions, a small group of this family exerts negative regulatory functions by targeting several components of the TK signaling cascade. Here, we review how these less studied adaptor proteins negatively control TK activities and how their loss of function induces abnormal TK signaling, promoting tumor formation. We also discuss the therapeutic consequences of this novel regulatory mechanism in human oncology.
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Affiliation(s)
- Cécile Naudin
- CNRS UMR5237, University Montpellier, CRBM, Montpellier, France.,Present address: INSERM U1016, CNRS UMR8104, Institut Cochin, Paris, France
| | - Clément Chevalier
- CNRS UMR5237, University Montpellier, CRBM, Montpellier, France.,Present address: SFR Biosit (UMS CNRS 3480/US INSERM 018), MRic Photonics Platform, University Rennes, Rennes, France
| | - Serge Roche
- CNRS UMR5237, University Montpellier, CRBM, Montpellier, France.,Equipe Labellisée LIGUE 2014, Ligue Contre le Cancer, Paris, France
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107
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Jadwin JA, Curran TG, Lafontaine AT, White FM, Mayer BJ. Src homology 2 domains enhance tyrosine phosphorylation in vivo by protecting binding sites in their target proteins from dephosphorylation. J Biol Chem 2017; 293:623-637. [PMID: 29162725 DOI: 10.1074/jbc.m117.794412] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 11/17/2017] [Indexed: 02/03/2023] Open
Abstract
Phosphotyrosine (pTyr)-dependent signaling is critical for many cellular processes. It is highly dynamic, as signal output depends not only on phosphorylation and dephosphorylation rates but also on the rates of binding and dissociation of effectors containing phosphotyrosine-dependent binding modules such as Src homology 2 (SH2) and phosphotyrosine-binding (PTB) domains. Previous in vitro studies suggested that binding of SH2 and PTB domains can enhance protein phosphorylation by protecting the sites bound by these domains from phosphatase-mediated dephosphorylation. To test whether this occurs in vivo, we used the binding of growth factor receptor bound 2 (GRB2) to phosphorylated epidermal growth factor receptor (EGFR) as a model system. We analyzed the effects of SH2 domain overexpression on protein tyrosine phosphorylation by quantitative Western and far-Western blotting, mass spectrometry, and computational modeling. We found that SH2 overexpression results in a significant, dose-dependent increase in EGFR tyrosine phosphorylation, particularly of sites corresponding to the binding specificity of the overexpressed SH2 domain. Computational models using experimentally determined EGFR phosphorylation and dephosphorylation rates, and pTyr-EGFR and GRB2 concentrations, recapitulated the experimental findings. Surprisingly, both modeling and biochemical analyses suggested that SH2 domain overexpression does not result in a major decrease in the number of unbound phosphorylated SH2 domain-binding sites. Our results suggest that signaling via SH2 domain binding is buffered over a relatively wide range of effector concentrations and that SH2 domain proteins with overlapping binding specificities are unlikely to compete with one another for phosphosites in vivo.
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Affiliation(s)
- Joshua A Jadwin
- From the Raymond and Beverly Sackler Laboratory of Molecular Medicine, Department of Genetics and Genome Sciences, and the Richard D. Berlin Center for Cell Analysis and Modeling, University of Connecticut School of Medicine, Farmington, Connecticut 06030 and
| | - Timothy G Curran
- the Department of Biological Engineering and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Adam T Lafontaine
- From the Raymond and Beverly Sackler Laboratory of Molecular Medicine, Department of Genetics and Genome Sciences, and the Richard D. Berlin Center for Cell Analysis and Modeling, University of Connecticut School of Medicine, Farmington, Connecticut 06030 and
| | - Forest M White
- the Department of Biological Engineering and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Bruce J Mayer
- From the Raymond and Beverly Sackler Laboratory of Molecular Medicine, Department of Genetics and Genome Sciences, and the Richard D. Berlin Center for Cell Analysis and Modeling, University of Connecticut School of Medicine, Farmington, Connecticut 06030 and
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108
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Yao Y, Bian Y, Dong M, Wang Y, Lv J, Chen L, Wang H, Mao J, Dong J, Ye M. SH2 Superbinder Modified Monolithic Capillary Column for the Sensitive Analysis of Protein Tyrosine Phosphorylation. J Proteome Res 2017; 17:243-251. [PMID: 29083189 DOI: 10.1021/acs.jproteome.7b00546] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
In this study, we present a method to specifically capture phosphotyrosine (pTyr) peptides from minute amount of sample for the sensitive analysis of protein tyrosine phosphorylation. We immobilized SH2 superbinder on a monolithic capillary column to construct a microreactor to enrich pTyr peptides. It was found that the synthetic pTyr peptide could be specifically enriched by the microreactor from the peptide mixture prepared by spiking of the synthetic pTyr peptide into the tryptic digests of α-casein and β-casein with molar ratios of 1:1000:1000. The microreactor was further applied to enrich pTyr peptides from pervanadate-treated HeLa cell digests for phosphoproteomics analysis, which resulted in the identification of 796 unique pTyr sites. In contrast, the conventional SH2 superbinder-based method identified 41 pTyr sites for the same sample, only 5.2% of the number achieved by the microreactor. Finally, this microreactor was also applied to analyze the pTyr in Shc1 complex, an immunopurified protein complex, which resulted in the identification of 15 pTyr sites. Together, this technique is best fitted to analyze the pTyr in minute amount of sample and will have broad application in fields where only a limited amount of sample is available.
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Affiliation(s)
- Yating Yao
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS) , Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yangyang Bian
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS) , Dalian 116023, China.,Medical Research Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University , Zhengzhou, Henan 450052, China
| | - Mingming Dong
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS) , Dalian 116023, China.,Dalian Ocean University, Dalian 116023, China
| | - Yan Wang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS) , Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiawen Lv
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS) , Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lianfang Chen
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS) , Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongwei Wang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS) , Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiawei Mao
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS) , Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Dong
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS) , Dalian 116023, China
| | - Mingliang Ye
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS) , Dalian 116023, China
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109
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Abstract
PURPOSE OF REVIEW Reception and transmission of signals across the plasma membrane has been a function generally attributed to transmembrane proteins. In the last 3 years, however, a growing number of reports have further acknowledged important contributions played by membrane lipids in the process of signal transduction. RECENT FINDINGS In particular, the constituency of membrane lipids can regulate how proteins with SH2 domains and molecules like K-Ras expose their catalytic domains to the cytosol and interact with effectors and second messengers. Recent reports have also shown that the degree of saturation of phospholipids can reduce the activation of certain G-protein-coupled receptors, and signaling downstream to Toll-like receptor 4 with consequences to nuclear factor kappa B activation and inflammation. Levels of specific gangliosides in the membrane were reported to activate integrins in a cell-autonomous manner affecting tumor cell migration. Furthermore, high resolution of the association of cholesterol with the smoothened receptor has clarified its participation in sonic hedgehog signaling. These are some of the key advancements that have further propelled our understanding of the broad versatile contributions of membrane lipids in signal transduction. SUMMARY As we gain definitive detail regarding the impact of lipid-protein interactions and their consequences to cell function, the options for therapeutic targeting expand with the possibility of greater specificity.
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Affiliation(s)
- Hannah Sunshine
- Molecular, Cellular and Integrative Physiology Graduate Program, UCLA
| | - M. Luisa Iruela-Arispe
- Departments of Molecular, Cell and Developmental Biology, UCLA, Los Angeles, California 90095
- Molecular Biology Institute, University of California, Los Angeles, California 90095, USA
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110
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Taskinen B, Ferrada E, Fowler DM. Early emergence of negative regulation of the tyrosine kinase Src by the C-terminal Src kinase. J Biol Chem 2017; 292:18518-18529. [PMID: 28939764 DOI: 10.1074/jbc.m117.811174] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 09/19/2017] [Indexed: 02/05/2023] Open
Abstract
Stringent regulation of tyrosine kinase activity is essential for normal cellular function. In humans, the tyrosine kinase Src is inhibited via phosphorylation of its C-terminal tail by another kinase, C-terminal Src kinase (Csk). Although Src and Csk orthologs are present across holozoan organisms, including animals and protists, the Csk-Src negative regulatory mechanism appears to have evolved gradually. For example, in choanoflagellates, Src and Csk are both active, but the negative regulatory mechanism is reportedly absent. In filastereans, a protist clade closely related to choanoflagellates, Src is active, but Csk is apparently inactive. In this study, we use a combination of bioinformatics, in vitro kinase assays, and yeast-based growth assays to characterize holozoan Src and Csk orthologs. We show that, despite appreciable differences in domain architecture, Csk from Corallochytrium limacisporum, a highly diverged holozoan marine protist, is active and can inhibit Src. However, in comparison with other Csk orthologs, Corallochytrium Csk displays broad substrate specificity and inhibits Src in an activity-independent manner. Furthermore, in contrast to previous studies, we show that Csk from the filasterean Capsaspora owczarzaki is active and that the Csk-Src negative regulatory mechanism is present in Csk and Src proteins from C. owczarzaki and the choanoflagellate Monosiga brevicollis Our results suggest that negative regulation of Src by Csk is more ancient than previously thought and that it might be conserved across all holozoan species.
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Affiliation(s)
- Barbara Taskinen
- From the Department of Genome Sciences, University of Washington, Seattle, Washington 98195-5065 and
| | - Evandro Ferrada
- From the Department of Genome Sciences, University of Washington, Seattle, Washington 98195-5065 and
| | - Douglas M Fowler
- From the Department of Genome Sciences, University of Washington, Seattle, Washington 98195-5065 and .,Department of Bioengineering, University of Washington, Seattle, Washington 98195-5065
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111
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Identification and characterization of tyrosine kinases in anole lizard indicate the conserved tyrosine kinase repertoire in vertebrates. Mol Genet Genomics 2017; 292:1405-1418. [PMID: 28819830 DOI: 10.1007/s00438-017-1356-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 08/08/2017] [Indexed: 10/19/2022]
Abstract
The tyrosine kinases (TKs) play principal roles in regulation of multicellular aspects of the organism and are implicated in many cancer types and congenital disorders. The anole lizard has recently been introduced as a model organism for laboratory-based studies of organismal function and field studies of ecology and evolution. However, the TK family of anole lizard has not been systematically identified and characterized yet. In this study, we identified 82 TK-encoding genes in the anole lizard genome and classified them into 28 subfamilies through phylogenetic analysis, with no member from ROS and STYK1 subfamilies identified. Although TK domain sequences and domain organization in each subfamily were conserved, the total number of TKs in different species was much variable. In addition, extensive evolutionary analysis in metazoans indicated that TK repertoire in vertebrates tends to be remarkably stable. Phylogenetic analysis of Eph subfamily indicated that the divergence of EphA and EphB occurred prior to the whole genome duplication (WGD) but after the split of Urochordates and vertebrates. Moreover, the expression pattern analysis of lizard TK genes among 9 different tissues showed that 14 TK genes exhibited tissue-specific expression and 6 TK genes were widely expressed. Comparative analysis of TK expression suggested that the tissue specifically expressed genes showed different expression pattern but the widely expressed genes showed similar pattern between anole lizard and human. These results may provide insights into the evolutionary diversification of animal TK genes and would aid future studies on TK protein regulation of key growth and developmental processes.
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112
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Plattner H. Evolutionary Cell Biology of Proteins from Protists to Humans and Plants. J Eukaryot Microbiol 2017; 65:255-289. [PMID: 28719054 DOI: 10.1111/jeu.12449] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 07/04/2017] [Accepted: 07/07/2017] [Indexed: 01/10/2023]
Abstract
During evolution, the cell as a fine-tuned machine had to undergo permanent adjustments to match changes in its environment, while "closed for repair work" was not possible. Evolution from protists (protozoa and unicellular algae) to multicellular organisms may have occurred in basically two lineages, Unikonta and Bikonta, culminating in mammals and angiosperms (flowering plants), respectively. Unicellular models for unikont evolution are myxamoebae (Dictyostelium) and increasingly also choanoflagellates, whereas for bikonts, ciliates are preferred models. Information accumulating from combined molecular database search and experimental verification allows new insights into evolutionary diversification and maintenance of genes/proteins from protozoa on, eventually with orthologs in bacteria. However, proteins have rarely been followed up systematically for maintenance or change of function or intracellular localization, acquirement of new domains, partial deletion (e.g. of subunits), and refunctionalization, etc. These aspects are discussed in this review, envisaging "evolutionary cell biology." Protozoan heritage is found for most important cellular structures and functions up to humans and flowering plants. Examples discussed include refunctionalization of voltage-dependent Ca2+ channels in cilia and replacement by other types during evolution. Altogether components serving Ca2+ signaling are very flexible throughout evolution, calmodulin being a most conservative example, in contrast to calcineurin whose catalytic subunit is lost in plants, whereas both subunits are maintained up to mammals for complex functions (immune defense and learning). Domain structure of R-type SNAREs differs in mono- and bikonta, as do Ca2+ -dependent protein kinases. Unprecedented selective expansion of the subunit a which connects multimeric base piece and head parts (V0, V1) of H+ -ATPase/pump may well reflect the intriguing vesicle trafficking system in ciliates, specifically in Paramecium. One of the most flexible proteins is centrin when its intracellular localization and function throughout evolution is traced. There are many more examples documenting evolutionary flexibility of translation products depending on requirements and potential for implantation within the actual cellular context at different levels of evolution. From estimates of gene and protein numbers per organism, it appears that much of the basic inventory of protozoan precursors could be transmitted to highest eukaryotic levels, with some losses and also with important additional "inventions."
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Affiliation(s)
- Helmut Plattner
- Department of Biology, University of Konstanz, P. O. Box M625, Konstanz, 78457, Germany
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113
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Seif F, Khoshmirsafa M, Aazami H, Mohsenzadegan M, Sedighi G, Bahar M. The role of JAK-STAT signaling pathway and its regulators in the fate of T helper cells. Cell Commun Signal 2017. [PMID: 28637459 PMCID: PMC5480189 DOI: 10.1186/s12964-017-0177-y] [Citation(s) in RCA: 485] [Impact Index Per Article: 69.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The Janus kinase (JAK)-signal transducer and activator of transcription (STAT) pathway plays critical roles in orchestrating of immune system, especially cytokine receptors and they can modulate the polarization of T helper cells. This pathway is regulated by an array of regulator proteins, including Suppressors of Cytokine Signaling (SOCS), Protein Inhibitors of Activated STATs (PIAS) and Protein Tyrosine Phosphatases (PTPs) determining the initiation, duration and termination of the signaling cascades. Dysregulation of the JAK-STAT pathway in T helper cells may result in various immune disorders. In this review, we represent how the JAK-STAT pathway is generally regulated and then in Th cell subsets in more detail. Finally, we introduce novel targeted strategies as promising therapeutic approaches in the treatment of immune disorders. Studies are ongoing for identifying the other regulators of the JAK-STAT pathway and designing innovative therapeutic strategies. Therefore, further investigation is needed.
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Affiliation(s)
- Farhad Seif
- ENT and Head and Neck Research Center and Department, Hazrat Rasoul Akram Hospital, Iran University of Medical Sciences, Tehran, Iran.,Department of immunology, school of medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Majid Khoshmirsafa
- Department of immunology, school of medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Hossein Aazami
- Department of immunology, school of medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Monireh Mohsenzadegan
- Department of Medical Laboratory Science, Faculty of Allied Medical Sciences, Iran University of Medical Sciences, Tehran, Iran
| | - Gholamreza Sedighi
- Department of immunology, school of medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammadali Bahar
- Department of immunology, school of medicine, Iran University of Medical Sciences, Tehran, Iran.
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114
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Tibaldi E, Pagano MA, Frezzato F, Trimarco V, Facco M, Zagotto G, Ribaudo G, Pavan V, Bordin L, Visentin A, Zonta F, Semenzato G, Brunati AM, Trentin L. Targeted activation of the SHP-1/PP2A signaling axis elicits apoptosis of chronic lymphocytic leukemia cells. Haematologica 2017; 102:1401-1412. [PMID: 28619847 PMCID: PMC5541874 DOI: 10.3324/haematol.2016.155747] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 06/14/2017] [Indexed: 01/07/2023] Open
Abstract
Lyn, a member of the Src family of kinases, is a key factor in the dysregulation of survival and apoptotic pathways of malignant B cells in chronic lymphocytic leukemia. One of the effects of Lyn’s action is spatial and functional segregation of the tyrosine phosphatase SHP-1 into two pools, one beneath the plasma membrane in an active state promoting pro-survival signals, the other in the cytosol in an inhibited conformation and unable to counter the elevated level of cytosolic tyrosine phosphorylation. We herein show that SHP-1 activity can be elicited directly by nintedanib, an agent also known as a triple angiokinase inhibitor, circumventing the phospho-S591-dependent inhibition of the phosphatase, leading to the dephosphorylation of pro-apoptotic players such as procaspase-8 and serine/threonine phosphatase 2A, eventually triggering apoptosis. Furthermore, the activation of PP2A by using MP07-66, a novel FTY720 analog, stimulated SHP-1 activity via dephosphorylation of phospho-S591, which unveiled the existence of a positive feedback signaling loop involving the two phosphatases. In addition to providing further insights into the molecular basis of this disease, our findings indicate that the PP2A/SHP-1 axis may emerge as an attractive, novel target for the development of alternative strategies in the treatment of chronic lymphocytic leukemia.
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Affiliation(s)
- Elena Tibaldi
- Department of Molecular Medicine, University of Padua, Italy
| | - Mario Angelo Pagano
- Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Italy
| | - Federica Frezzato
- Department of Medicine, University of Padua, Italy.,Venetian Institute of Molecular Medicine (VIMM), Centro di Eccellenza per la Ricerca Biomedica, Padua, Italy
| | - Valentina Trimarco
- Department of Medicine, University of Padua, Italy.,Venetian Institute of Molecular Medicine (VIMM), Centro di Eccellenza per la Ricerca Biomedica, Padua, Italy
| | - Monica Facco
- Department of Medicine, University of Padua, Italy.,Venetian Institute of Molecular Medicine (VIMM), Centro di Eccellenza per la Ricerca Biomedica, Padua, Italy
| | - Giuseppe Zagotto
- Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Italy
| | - Giovanni Ribaudo
- Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Italy
| | - Valeria Pavan
- Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Italy
| | - Luciana Bordin
- Department of Molecular Medicine, University of Padua, Italy
| | - Andrea Visentin
- Department of Medicine, University of Padua, Italy.,Venetian Institute of Molecular Medicine (VIMM), Centro di Eccellenza per la Ricerca Biomedica, Padua, Italy
| | - Francesca Zonta
- Department of Biomedical Sciences, University of Padua, Italy
| | - Gianpietro Semenzato
- Department of Medicine, University of Padua, Italy.,Venetian Institute of Molecular Medicine (VIMM), Centro di Eccellenza per la Ricerca Biomedica, Padua, Italy
| | | | - Livio Trentin
- Department of Medicine, University of Padua, Italy.,Venetian Institute of Molecular Medicine (VIMM), Centro di Eccellenza per la Ricerca Biomedica, Padua, Italy
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115
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Hoppmann C, Wong A, Yang B, Li S, Hunter T, Shokat KM, Wang L. Site-specific incorporation of phosphotyrosine using an expanded genetic code. Nat Chem Biol 2017; 13:842-844. [PMID: 28604697 PMCID: PMC5577362 DOI: 10.1038/nchembio.2406] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 03/15/2017] [Indexed: 02/03/2023]
Abstract
Access to phosphoproteins with stoichiometric and site-specific phosphorylation status is key to understanding the role of protein phosphorylation. Here we report an efficient method to generate pure, active phosphotyrosine-containing proteins by genetically encoding a stable phosphotyrosine analog that is convertible to native phosphotyrosine. We demonstrate its general compatibility with proteins of various sizes, phosphotyrosine sites and functions, and reveal a possible role of tyrosine phosphorylation in negative regulation of ubiquitination.
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Affiliation(s)
- Christian Hoppmann
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA
| | - Allison Wong
- Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, California, USA
| | - Bing Yang
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA
| | - Shuwei Li
- Institute for Bioscience and Biotechnology Research, University of Maryland College Park, Rockville, Maryland, USA
| | - Tony Hunter
- The Salk Institute for Biological Studies, Molecular and Cell Biology Laboratory, La Jolla, California, USA
| | - Kevan M Shokat
- Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, California, USA
| | - Lei Wang
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA
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116
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Targeted disruption of TC-PTP in the proliferative compartment augments STAT3 and AKT signaling and skin tumor development. Sci Rep 2017; 7:45077. [PMID: 28322331 PMCID: PMC5359614 DOI: 10.1038/srep45077] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 02/17/2017] [Indexed: 12/30/2022] Open
Abstract
Tyrosine phosphorylation is a vital mechanism that contributes to skin carcinogenesis. It is regulated by the counter-activities of protein tyrosine kinases (PTKs) and protein tyrosine phosphatases (PTPs). Here, we report the critical role of T-cell protein tyrosine phosphatase (TC-PTP), encoded by Ptpn2, in chemically-induced skin carcinogenesis via the negative regulation of STAT3 and AKT signaling. Using epidermal specific TC-PTP knockout (K14Cre.Ptpn2fl/fl) mice, we demonstrate loss of TC-PTP led to a desensitization to tumor initiator 7,12-dimethylbenz[a]anthracene (DMBA)-induced apoptosis both in vivo epidermis and in vitro keratinocytes. TC-PTP deficiency also resulted in a significant increase in epidermal thickness and hyperproliferation following exposure to the tumor promoter, 12-O-tetradecanoylphorbol-13-acetate (TPA). Western blot analysis showed that both phosphorylated STAT3 and phosphorylated AKT expressions were significantly increased in epidermis of TC-PTP-deficient mice compared to control mice following TPA treatment. Inhibition of STAT3 or AKT reversed the effects of TC-PTP deficiency on apoptosis and proliferation. Finally, TC-PTP knockout mice showed a shortened latency of tumorigenesis and significantly increased numbers of tumors during two-stage skin carcinogenesis. Our findings reveal that TC-PTP has potential as a novel target for the prevention of skin cancer through its role in the regulation of STAT3 and AKT signaling.
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117
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Wittouck S, van Noort V. Correlated duplications and losses in the evolution of palmitoylation writer and eraser families. BMC Evol Biol 2017; 17:83. [PMID: 28320309 PMCID: PMC5359973 DOI: 10.1186/s12862-017-0932-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 03/09/2017] [Indexed: 12/27/2022] Open
Abstract
Background Protein post-translational modifications (PTMs) change protein properties. Each PTM type is associated with domain families that apply the modification (writers), remove the modification (erasers) and bind to the modified sites (readers) together called toolkit domains. The evolutionary origin and diversification remains largely understudied, except for tyrosine phosphorylation. Protein palmitoylation entails the addition of a palmitoyl fatty acid to a cysteine residue. This PTM functions as a membrane anchor and is involved in a range of cellular processes. One writer family and two erasers families are known for protein palmitoylation. Results In this work we unravel the evolutionary history of these writer and eraser families. We constructed a high-quality profile hidden Markov model (HMM) of each family, searched for protein family members in fully sequenced genomes and subsequently constructed phylogenetic distributions of the families. We constructed Maximum Likelihood phylogenetic trees and using gene tree rearrangement and tree reconciliation inferred their evolutionary histories in terms of duplication and loss events. We identified lineages where the families expanded or contracted and found that the evolutionary histories of the families are correlated. The results show that the erasers were invented first, before the origin of the eukaryotes. The writers first arose in the eukaryotic ancestor. The writers and erasers show co-expansions in several eukaryotic ancestral lineages. These expansions often seem to be followed by contractions in some or all of the lineages further in evolution. Conclusions A general pattern of correlated evolution appears between writer and eraser domains. These co-evolution patterns could be used in new methods for interaction prediction based on phylogenies. Electronic supplementary material The online version of this article (doi:10.1186/s12862-017-0932-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Stijn Wittouck
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium.,Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| | - Vera van Noort
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium.
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118
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Deng Z, Dong M, Wang Y, Dong J, Li SSC, Zou H, Ye M. Biphasic Affinity Chromatographic Approach for Deep Tyrosine Phosphoproteome Analysis. Anal Chem 2017; 89:2405-2410. [DOI: 10.1021/acs.analchem.6b04288] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Zhenzhen Deng
- Key
Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- Graduate School of Chinese Academy of Sciences, Beijing 1000491, China
| | - Mingming Dong
- Key
Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Yan Wang
- Key
Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- Graduate School of Chinese Academy of Sciences, Beijing 1000491, China
| | - Jing Dong
- Key
Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Shawn S.-C. Li
- Departments
of Biochemistry, Oncology and the Children’s Health Research
Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario N6A 5C1, Canada
| | - Hanfa Zou
- Key
Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Mingliang Ye
- Key
Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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119
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Novel Effects of Lapatinib Revealed in the African Trypanosome by Using Hypothesis-Generating Proteomics and Chemical Biology Strategies. Antimicrob Agents Chemother 2017; 61:AAC.01865-16. [PMID: 27872081 DOI: 10.1128/aac.01865-16] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 11/18/2016] [Indexed: 01/07/2023] Open
Abstract
Human African trypanosomiasis is a neglected tropical disease caused by the protozoan parasite Trypanosoma brucei Lapatinib, a human epidermal growth factor receptor (EGFR) inhibitor, can cure 25% of trypanosome-infected mice, although the parasite lacks EGFR-like tyrosine kinases. Four trypanosome protein kinases associate with lapatinib, suggesting that the drug may be a multitargeted inhibitor of phosphoprotein signaling in the bloodstream trypanosome. Phosphoprotein signaling pathways in T. brucei have diverged significantly from those in humans. As a first step in the evaluation of the polypharmacology of lapatinib in T. brucei, we performed a proteome-wide phosphopeptide analysis before and after drug addition to cells. Lapatinib caused dephosphorylation of Ser/Thr sites on proteins predicted to be involved in scaffolding, gene expression, and intracellular vesicle trafficking. To explore the perturbation of phosphotyrosine (pTyr)-dependent signaling by lapatinib, proteins in lapatinib-susceptible pTyr complexes were identified by affinity chromatography; they included BILBO-1, MORN, and paraflagellar rod (PFR) proteins PFR1 and PFR2. These data led us to hypothesize that lapatinib disrupts PFR functions and/or endocytosis in the trypanosome. In direct chemical biology tests of these speculations, lapatinib-treated trypanosomes (i) lost segments of the PFR inside the flagellum, (ii) were inhibited in the endocytosis of transferrin, and (iii) changed morphology from long and slender to rounded. Thus, our hypothesis-generating phosphoproteomics strategy predicted novel physiological pathways perturbed by lapatinib, which were verified experimentally. General implications of this workflow for identifying signaling pathways perturbed by drug hits discovered in phenotypic screens are discussed.
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120
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An Efficient Semi-supervised Learning Approach to Predict SH2 Domain Mediated Interactions. Methods Mol Biol 2017. [PMID: 28092029 DOI: 10.1007/978-1-4939-6762-9_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Src homology 2 (SH2) domain is an important subclass of modular protein domains that plays an indispensable role in several biological processes in eukaryotes. SH2 domains specifically bind to the phosphotyrosine residue of their binding peptides to facilitate various molecular functions. For determining the subtle binding specificities of SH2 domains, it is very important to understand the intriguing mechanisms by which these domains recognize their target peptides in a complex cellular environment. There are several attempts have been made to predict SH2-peptide interactions using high-throughput data. However, these high-throughput data are often affected by a low signal to noise ratio. Furthermore, the prediction methods have several additional shortcomings, such as linearity problem, high computational complexity, etc. Thus, computational identification of SH2-peptide interactions using high-throughput data remains challenging. Here, we propose a machine learning approach based on an efficient semi-supervised learning technique for the prediction of 51 SH2 domain mediated interactions in the human proteome. In our study, we have successfully employed several strategies to tackle the major problems in computational identification of SH2-peptide interactions.
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121
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Classification and Lineage Tracing of SH2 Domains Throughout Eukaryotes. Methods Mol Biol 2017. [PMID: 28092027 DOI: 10.1007/978-1-4939-6762-9_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Today there exists a rapidly expanding number of sequenced genomes. Cataloging protein interaction domains such as the Src Homology 2 (SH2) domain across these various genomes can be accomplished with ease due to existing algorithms and predictions models. An evolutionary analysis of SH2 domains provides a step towards understanding how SH2 proteins integrated with existing signaling networks to position phosphotyrosine signaling as a crucial driver of robust cellular communication networks in metazoans. However organizing and tracing SH2 domain across organisms and understanding their evolutionary trajectory remains a challenge. This chapter describes several methodologies towards analyzing the evolutionary trajectory of SH2 domains including a global SH2 domain classification system, which facilitates annotation of new SH2 sequences essential for tracing the lineage of SH2 domains throughout eukaryote evolution. This classification utilizes a combination of sequence homology, protein domain architecture and the boundary positions between introns and exons within the SH2 domain or genes encoding these domains. Discrete SH2 families can then be traced across various genomes to provide insight into its origins. Furthermore, additional methods for examining potential mechanisms for divergence of SH2 domains from structural changes to alterations in the protein domain content and genome duplication will be discussed. Therefore a better understanding of SH2 domain evolution may enhance our insight into the emergence of phosphotyrosine signaling and the expansion of protein interaction domains.
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122
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Engelmann BW. High-Throughput Quantification of SH2 Domain-Phosphopeptide Interactions with Cellulose-Peptide Conjugate Microarrays. Methods Mol Biol 2017; 1555:375-394. [PMID: 28092044 DOI: 10.1007/978-1-4939-6762-9_21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The Src Homology 2 (SH2) domain family primarily recognizes phosphorylated tyrosine (pY) containing peptide motifs. The relative affinity preferences among competing SH2 domains for phosphopeptide ligands define "specificity space," and underpins many functional pY mediated interactions within signaling networks. The degree of promiscuity exhibited and the dynamic range of affinities supported by individual domains or phosphopeptides is best resolved by a carefully executed and controlled quantitative high-throughput experiment. Here, I describe the fabrication and application of a cellulose-peptide conjugate microarray (CPCMA) platform to the quantitative analysis of SH2 domain specificity space. Included herein are instructions for optimal experimental design with special attention paid to common sources of systematic error, phosphopeptide SPOT synthesis, microarray fabrication, analyte titrations, data capture, and analysis.
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Affiliation(s)
- Brett W Engelmann
- Department of Human Genetics, The University of Chicago, Chicago, IL, USA.
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123
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Abstract
The Src Homology 2 (SH2) domain is the prototypical protein interaction module that lies at the heart of phosphotyrosine signaling. Since its serendipitous discovery, there has been a tremendous advancement in technologies and an array of techniques available for studying SH2 domains and phosphotyrosine signaling. In this chapter, we provide a glimpse of the history of SH2 domains and describe many of the tools and techniques that have been developed along the way and discuss future directions for SH2 domain studies. We highlight the gist of each chapter in this volume in the context of: the structural biology and phosphotyrosine binding; characterizing SH2 specificity and generating prediction models; systems biology and proteomics; SH2 domains in signal transduction; and SH2 domains in disease, diagnostics, and therapeutics. Many of the individual chapters provide an in-depth approach that will allow scientists to interrogate the function and role of SH2 domains.
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Affiliation(s)
- Bernard A Liu
- Broad Institute of Harvard and MIT, 415 Main St., 5175 JJ, Cambridge, MA, 02142, USA.
| | - Kazuya Machida
- Raymond and Beverly Sackler Laboratory of Genetics and Molecular Medicine, Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, 400 Farmington Ave., Farmington, CT, 06030, USA.
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124
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Everley RA, Huttlin EL, Erickson AR, Beausoleil SA, Gygi SP. Neutral Loss Is a Very Common Occurrence in Phosphotyrosine-Containing Peptides Labeled with Isobaric Tags. J Proteome Res 2016; 16:1069-1076. [PMID: 27978624 DOI: 10.1021/acs.jproteome.6b00487] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
While developing a multiplexed phosphotyrosine peptide quantification assay, an unexpected observation was made: significant neutral loss from phosphotyrosine (pY) containing peptides. Using a 2000-member peptide library, we sought to systematically investigate this observation by comparing unlabeled peptides with the two highest-plex isobaric tags (iTRAQ8 and TMT10) across CID, HCD, and ETD fragmentation using high resolution high mass accuracy Orbitrap instrumentation. We found pY peptide neutral loss behavior was consistent with reduced proton mobility, and does not occur during ETD. The site of protonation at the peptide N-terminus changes from a primary to a tertiary amine as a result of TMT labeling which would increase the gas phase basicity and reduce proton mobility at this site. This change in fragmentation behavior has implications during instrument method development and interpretation of MS/MS spectra, and therefore ensuing follow-up studies. We show how sites not localized to tyrosine by search and site localization algorithms can be confidently reassigned to tyrosine using neutral loss and phosphotyrosine immonium ions. We believe these findings will be of general interest to those studying pY signal transduction using isobaric tags.
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Affiliation(s)
- Robert A Everley
- Department of Cell Biology, Harvard Medical School , Boston, Massachusetts 02115, United States.,Laboratory of Systems Pharmacology, Harvard Medical School , Boston, Massachusetts 02115 United States
| | - Edward L Huttlin
- Department of Cell Biology, Harvard Medical School , Boston, Massachusetts 02115, United States
| | - Alison R Erickson
- Department of Cell Biology, Harvard Medical School , Boston, Massachusetts 02115, United States
| | - Sean A Beausoleil
- Cell Signaling Technology, Inc. , Danvers, Massachusetts 01923, United States
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School , Boston, Massachusetts 02115, United States
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125
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Abstract
Studies in mammals and Drosophila have demonstrated the existence and significance of secreted factors involved in communication between distal organs. In this review, primarily focusing on Drosophila, we examine the known interorgan communication factors and their functions, physiological inducers, and integration in regulating physiology. Moreover, we describe how organ-sensing screens in Drosophila can systematically identify novel conserved interorgan communication factors. Finally, we discuss how interorgan communication enabled and evolved as a result of specialization of organs. Together, we anticipate that future studies will establish a model for metazoan interorgan communication network (ICN) and how it is deregulated in disease.
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Affiliation(s)
- Ilia A Droujinine
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115; ,
| | - Norbert Perrimon
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115; ,
- Howard Hughes Medical Institute, Boston, Massachusetts 02115
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126
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127
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Tyrosine phosphorylation stimulates activity of human RAD51 recombinase through altered nucleoprotein filament dynamics. Proc Natl Acad Sci U S A 2016; 113:E6045-E6054. [PMID: 27671650 DOI: 10.1073/pnas.1604807113] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The DNA strand exchange protein RAD51 facilitates the central step in homologous recombination, a process fundamentally important for accurate repair of damaged chromosomes, restart of collapsed replication forks, and telomere maintenance. The active form of RAD51 is a nucleoprotein filament that assembles on single-stranded DNA (ssDNA) at the sites of DNA damage. The c-Abl tyrosine kinase and its oncogenic counterpart BCR-ABL fusion kinase phosphorylate human RAD51 on tyrosine residues 54 and 315. We combined biochemical reconstitutions of the DNA strand exchange reactions with total internal reflection fluorescence microscopy to determine how the two phosphorylation events affect the biochemical activities of human RAD51 and properties of the RAD51 nucleoprotein filament. By mimicking RAD51 tyrosine phosphorylation with a nonnatural amino acid, p-carboxymethyl-l-phenylalanine (pCMF), we demonstrated that Y54 phosphorylation enhances the RAD51 recombinase activity by at least two different mechanisms, modifies the RAD51 nucleoprotein filament formation, and allows RAD51 to compete efficiently with ssDNA binding protein RPA. In contrast, Y315 phosphorylation has little effect on the RAD51 activities. Based on our work and previous cellular studies, we propose a mechanism underlying RAD51 activation by c-Abl/BCR-ABL kinases.
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128
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Gordley RM, Bugaj LJ, Lim WA. Modular engineering of cellular signaling proteins and networks. Curr Opin Struct Biol 2016; 39:106-114. [PMID: 27423114 DOI: 10.1016/j.sbi.2016.06.012] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 05/16/2016] [Accepted: 06/15/2016] [Indexed: 12/31/2022]
Abstract
Living cells respond to their environment using networks of signaling molecules that act as sensors, information processors, and actuators. These signaling systems are highly modular at both the molecular and network scales, and much evidence suggests that evolution has harnessed this modularity to rewire and generate new physiological behaviors. Conversely, we are now finding that, following nature's example, signaling modules can be recombined to form synthetic tools for monitoring, interrogating, and controlling the behavior of cells. Here we highlight recent progress in the modular design of synthetic receptors, optogenetic switches, and phospho-regulated proteins and circuits, and discuss the expanding role of combinatorial design in the engineering of cellular signaling proteins and networks.
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Affiliation(s)
- Russell M Gordley
- Howard Hughes Medical Institute, United States; Department of Cellular & Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, 94158, United States
| | - Lukasz J Bugaj
- Department of Cellular & Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, 94158, United States
| | - Wendell A Lim
- Howard Hughes Medical Institute, United States; Department of Cellular & Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, 94158, United States.
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129
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Rensing SA. (Why) Does Evolution Favour Embryogenesis? TRENDS IN PLANT SCIENCE 2016; 21:562-573. [PMID: 26987708 DOI: 10.1016/j.tplants.2016.02.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 02/14/2016] [Accepted: 02/19/2016] [Indexed: 05/05/2023]
Abstract
Complex multicellular organisms typically possess life cycles in which zygotes (formed by gamete fusion) and meiosis occur. Canonical animal embryogenesis describes development from zygote to birth. It involves polarisation of the egg/zygote, asymmetric cell divisions, establishment of axes, symmetry breaking, formation of organs, and parental nutrition (at least in early stages). Similar developmental patterns have independently evolved in other eukaryotic lineages, including land plants and brown algae. The question arises whether embryo-like structures and associated developmental processes recurrently emerge because they are local optima of the evolutionary landscape. To understand which evolutionary principles govern complex multicellularity, we need to analyse why and how similar processes evolve convergently - von Baer's and Haeckel's phylotypic stage revisited in other phyla.
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Affiliation(s)
- Stefan A Rensing
- Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch-Str. 8, D-35043 Marburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany.
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130
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Sheng R, Jung DJ, Silkov A, Kim H, Singaram I, Wang ZG, Xin Y, Kim E, Park MJ, Thiagarajan-Rosenkranz P, Smrt S, Honig B, Baek K, Ryu S, Lorieau J, Kim YM, Cho W. Lipids Regulate Lck Protein Activity through Their Interactions with the Lck Src Homology 2 Domain. J Biol Chem 2016; 291:17639-50. [PMID: 27334919 DOI: 10.1074/jbc.m116.720284] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Indexed: 11/06/2022] Open
Abstract
Lymphocyte-specific protein-tyrosine kinase (Lck) plays an essential role in T cell receptor (TCR) signaling and T cell development, but its activation mechanism is not fully understood. To explore the possibility that plasma membrane (PM) lipids control TCR signaling activities of Lck, we measured the membrane binding properties of its regulatory Src homology 2 (SH2) and Src homology 3 domains. The Lck SH2 domain binds anionic PM lipids with high affinity but with low specificity. Electrostatic potential calculation, NMR analysis, and mutational studies identified the lipid-binding site of the Lck SH2 domain that includes surface-exposed basic, aromatic, and hydrophobic residues but not the phospho-Tyr binding pocket. Mutation of lipid binding residues greatly reduced the interaction of Lck with the ζ chain in the activated TCR signaling complex and its overall TCR signaling activities. These results suggest that PM lipids, including phosphatidylinositol 4,5-bisphosphate and phosphatidylinositol 3,4,5-trisphosphate, modulate interaction of Lck with its binding partners in the TCR signaling complex and its TCR signaling activities in a spatiotemporally specific manner via its SH2 domain.
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Affiliation(s)
- Ren Sheng
- From the Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607
| | - Da-Jung Jung
- the Division of Integrative Biosciences and Biotechnology and
| | - Antonina Silkov
- the Department of Biochemistry and Molecular Biophysics, Howard Hughes Medical Institute, Columbia University, New York, New York 11032, and
| | - Hyunjin Kim
- From the Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607
| | - Indira Singaram
- From the Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607
| | - Zhi-Gang Wang
- From the Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607
| | - Yao Xin
- From the Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607
| | - Eui Kim
- the Division of Integrative Biosciences and Biotechnology and
| | - Mi-Jeong Park
- the Division of Integrative Biosciences and Biotechnology and
| | | | - Sean Smrt
- From the Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607
| | - Barry Honig
- the Department of Biochemistry and Molecular Biophysics, Howard Hughes Medical Institute, Columbia University, New York, New York 11032, and
| | - Kwanghee Baek
- the Department of Genetic Engineering, Kyung Hee University, Yongin 446-701, Korea
| | - Sungho Ryu
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 790-784, Korea
| | - Justin Lorieau
- From the Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607
| | - You-Me Kim
- the Division of Integrative Biosciences and Biotechnology and Department of Life Sciences, Pohang University of Science and Technology, Pohang 790-784, Korea,
| | - Wonhwa Cho
- From the Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, the Department of Genetic Engineering, Kyung Hee University, Yongin 446-701, Korea
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131
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SH2 Domains Serve as Lipid-Binding Modules for pTyr-Signaling Proteins. Mol Cell 2016; 62:7-20. [PMID: 27052731 DOI: 10.1016/j.molcel.2016.01.027] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 12/21/2015] [Accepted: 01/26/2016] [Indexed: 01/26/2023]
Abstract
The Src-homology 2 (SH2) domain is a protein interaction domain that directs myriad phosphotyrosine (pY)-signaling pathways. Genome-wide screening of human SH2 domains reveals that ∼90% of SH2 domains bind plasma membrane lipids and many have high phosphoinositide specificity. They bind lipids using surface cationic patches separate from pY-binding pockets, thus binding lipids and the pY motif independently. The patches form grooves for specific lipid headgroup recognition or flat surfaces for non-specific membrane binding and both types of interaction are important for cellular function and regulation of SH2 domain-containing proteins. Cellular studies with ZAP70 showed that multiple lipids bind its C-terminal SH2 domain in a spatiotemporally specific manner and thereby exert exquisite spatiotemporal control over its protein binding and signaling activities in T cells. Collectively, this study reveals how lipids control SH2 domain-mediated cellular protein-protein interaction networks and suggest a new strategy for therapeutic modulation of pY-signaling pathways.
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132
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Hydrophobic Core Variations Provide a Structural Framework for Tyrosine Kinase Evolution and Functional Specialization. PLoS Genet 2016; 12:e1005885. [PMID: 26925779 PMCID: PMC4771162 DOI: 10.1371/journal.pgen.1005885] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2015] [Accepted: 01/30/2016] [Indexed: 02/07/2023] Open
Abstract
Protein tyrosine kinases (PTKs) are a group of closely related enzymes that have evolutionarily diverged from serine/threonine kinases (STKs) to regulate pathways associated with multi-cellularity. Evolutionary divergence of PTKs from STKs has occurred through accumulation of mutations in the active site as well as in the commonly conserved hydrophobic core. While the functional significance of active site variations is well understood, relatively little is known about how hydrophobic core variations contribute to PTK evolutionary divergence. Here, using a combination of statistical sequence comparisons, molecular dynamics simulations, mutational analysis and in vitro thermostability and kinase assays, we investigate the structural and functional significance of key PTK-specific variations in the kinase core. We find that the nature of residues and interactions in the hydrophobic core of PTKs is strikingly different from other protein kinases, and PTK-specific variations in the core contribute to functional divergence by altering the stability and dynamics of the kinase domain. In particular, a functionally critical STK-conserved histidine that stabilizes the regulatory spine in STKs is selectively mutated to an alanine, serine or glutamate in PTKs, and this loss-of-function mutation is accommodated, in part, through compensatory PTK-specific interactions in the core. In particular, a PTK-conserved phenylalanine in the I-helix appears to structurally and functionally compensate for the loss of STK-histidine by interacting with the regulatory spine, which has far-reaching effects on enzyme activity, inhibitor sensing, and stability. We propose that hydrophobic core variations provide a selective advantage during PTK evolution by increasing the conformational flexibility, and therefore the allosteric potential of the kinase domain. Our studies also suggest that Tyrosine Kinase Like kinases such as RAF are intermediates in PTK evolutionary divergence inasmuch as they share features of both PTKs and STKs in the core. Finally, our studies provide an evolutionary framework for identifying and characterizing disease and drug resistance mutations in the kinase core. Proteins evolve new functions through accumulation of mutations in the primary sequence. Understanding how naturally occurring mutations shape protein function can provide insights into how non-natural mutations contribute to disease. Here, we identify sequence variants associated with the functional specialization of tyrosine kinases, a large and medically important class of proteins associated with the evolution of complex multicellular functions and diseases such as cancer. We find that mutations distal from the active site contribute to functional specialization by altering the stability, activity and dynamics of the kinase core. Our findings have implications for understanding the evolution of allosteric regulation in tyrosine kinases, and in predicting the structural and functional impact of disease and drug resistance mutations in the kinase core.
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133
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Mijakovic I, Grangeasse C, Turgay K. Exploring the diversity of protein modifications: special bacterial phosphorylation systems. FEMS Microbiol Rev 2016; 40:398-417. [PMID: 26926353 DOI: 10.1093/femsre/fuw003] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 02/02/2016] [Indexed: 12/31/2022] Open
Abstract
Protein modifications not only affect protein homeostasis but can also establish new cellular protein functions and are important components of complex cellular signal sensing and transduction networks. Among these post-translational modifications, protein phosphorylation represents the one that has been most thoroughly investigated. Unlike in eukarya, a large diversity of enzyme families has been shown to phosphorylate and dephosphorylate proteins on various amino acids with different chemical properties in bacteria. In this review, after a brief overview of the known bacterial phosphorylation systems, we focus on more recently discovered and less widely known kinases and phosphatases. Namely, we describe in detail tyrosine- and arginine-phosphorylation together with some examples of unusual serine-phosphorylation systems and discuss their potential role and function in bacterial physiology, and regulatory networks. Investigating these unusual bacterial kinase and phosphatases is not only important to understand their role in bacterial physiology but will help to generally understand the full potential and evolution of protein phosphorylation for signal transduction, protein modification and homeostasis in all cellular life.
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Affiliation(s)
- Ivan Mijakovic
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg 41296, Sweden Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2970 Hørsholm, Denmark
| | - Christophe Grangeasse
- Unité Microbiologie Moléculaire et Biochimie Structurale, UMR 5086-CNRS/ Université Lyon 1, Lyon 69367, France
| | - Kürşad Turgay
- Institut für Mikrobiologie, Leibniz Universität Hannover, D-30419 Hannover, Germany
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134
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Bah A, Forman-Kay JD. Modulation of Intrinsically Disordered Protein Function by Post-translational Modifications. J Biol Chem 2016; 291:6696-705. [PMID: 26851279 DOI: 10.1074/jbc.r115.695056] [Citation(s) in RCA: 358] [Impact Index Per Article: 44.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Post-translational modifications (PTMs) produce significant changes in the structural properties of intrinsically disordered proteins (IDPs) by affecting their energy landscapes. PTMs can induce a range of effects, from local stabilization or destabilization of transient secondary structure to global disorder-to-order transitions, potentially driving complete state changes between intrinsically disordered and folded states or dispersed monomeric and phase-separated states. Here, we discuss diverse biological processes that are dependent on PTM regulation of IDPs. We also present recent tools for generating homogenously modified IDPs for studies of PTM-mediated IDP regulatory mechanisms.
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Affiliation(s)
- Alaji Bah
- From the Program in Molecular Structure & Function, The Hospital for Sick Children, Toronto, Ontario M5G 0A4 and the Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Julie D Forman-Kay
- From the Program in Molecular Structure & Function, The Hospital for Sick Children, Toronto, Ontario M5G 0A4 and the Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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135
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Stites EC, Aziz M, Creamer MS, Von Hoff DD, Posner RG, Hlavacek WS. Use of mechanistic models to integrate and analyze multiple proteomic datasets. Biophys J 2016; 108:1819-1829. [PMID: 25863072 DOI: 10.1016/j.bpj.2015.02.030] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Revised: 02/18/2015] [Accepted: 02/24/2015] [Indexed: 11/30/2022] Open
Abstract
Proteins in cell signaling networks tend to interact promiscuously through low-affinity interactions. Consequently, evaluating the physiological importance of mapped interactions can be difficult. Attempts to do so have tended to focus on single, measurable physicochemical factors, such as affinity or abundance. For example, interaction importance has been assessed on the basis of the relative affinities of binding partners for a protein of interest, such as a receptor. However, multiple factors can be expected to simultaneously influence the recruitment of proteins to a receptor (and the potential of these proteins to contribute to receptor signaling), including affinity, abundance, and competition, which is a network property. Here, we demonstrate that measurements of protein copy numbers and binding affinities can be integrated within the framework of a mechanistic, computational model that accounts for mass action and competition. We use cell line-specific models to rank the relative importance of protein-protein interactions in the epidermal growth factor receptor (EGFR) signaling network for 11 different cell lines. Each model accounts for experimentally characterized interactions of six autophosphorylation sites in EGFR with proteins containing a Src homology 2 and/or phosphotyrosine-binding domain. We measure importance as the predicted maximal extent of recruitment of a protein to EGFR following ligand-stimulated activation of EGFR signaling. We find that interactions ranked highly by this metric include experimentally detected interactions. Proteins with high importance rank in multiple cell lines include proteins with recognized, well-characterized roles in EGFR signaling, such as GRB2 and SHC1, as well as a protein with a less well-defined role, YES1. Our results reveal potential cell line-specific differences in recruitment.
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Affiliation(s)
- Edward C Stites
- Clinical Translational Research Division, Translational Genomics Research Institute, Phoenix, Arizona; Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, Missouri.
| | - Meraj Aziz
- Clinical Translational Research Division, Translational Genomics Research Institute, Phoenix, Arizona
| | - Matthew S Creamer
- Clinical Translational Research Division, Translational Genomics Research Institute, Phoenix, Arizona; Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut
| | - Daniel D Von Hoff
- Clinical Translational Research Division, Translational Genomics Research Institute, Phoenix, Arizona
| | - Richard G Posner
- Clinical Translational Research Division, Translational Genomics Research Institute, Phoenix, Arizona; Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona.
| | - William S Hlavacek
- Clinical Translational Research Division, Translational Genomics Research Institute, Phoenix, Arizona; Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico.
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136
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Yuan J, Zhang F, Niu R. Multiple regulation pathways and pivotal biological functions of STAT3 in cancer. Sci Rep 2015; 5:17663. [PMID: 26631279 PMCID: PMC4668392 DOI: 10.1038/srep17663] [Citation(s) in RCA: 170] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 11/03/2015] [Indexed: 02/07/2023] Open
Abstract
STAT3 is both a transcription activator and an oncogene that is tightly regulated under normal physiological conditions. However, abundant evidence indicates that STAT3 is persistently activated in several cancers, with a crucial position in tumor onset and progression. In addition to its traditional role in cancer cell proliferation, invasion, and migration, STAT3 also promotes cancer through altering gene expression via epigenetic modification, inducing epithelial–mesenchymal transition (EMT) phenotypes in cancer cells, regulating the tumor microenvironment, and promoting cancer stem cells (CSCs) self-renewal and differentiation. STAT3 is regulated not only by the canonical cytokines and growth factors, but also by the G-protein-coupled receptors, cadherin engagement, Toll-like receptors (TLRs), and microRNA (miRNA). Despite the presence of diverse regulators and pivotal biological functions in cancer, no effective therapeutic inventions are available for inhibiting STAT3 and acquiring potent antitumor effects in the clinic. An improved understanding of the complex roles of STAT3 in cancer is required to achieve optimal therapeutic effects.
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Affiliation(s)
- Jie Yuan
- Public Laboratory, Key Laboratory of Breast Cancer Prevention and Therapy, Ministry of Education, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin Medical University, Huan-Hu-Xi Road, Ti-Yuan-Bei, He Xi District, Tianjin, 300060, People's Republic of China
| | - Fei Zhang
- Public Laboratory, Key Laboratory of Breast Cancer Prevention and Therapy, Ministry of Education, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin Medical University, Huan-Hu-Xi Road, Ti-Yuan-Bei, He Xi District, Tianjin, 300060, People's Republic of China
| | - Ruifang Niu
- Public Laboratory, Key Laboratory of Breast Cancer Prevention and Therapy, Ministry of Education, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin Medical University, Huan-Hu-Xi Road, Ti-Yuan-Bei, He Xi District, Tianjin, 300060, People's Republic of China
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137
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Schaap P, Barrantes I, Minx P, Sasaki N, Anderson RW, Bénard M, Biggar KK, Buchler NE, Bundschuh R, Chen X, Fronick C, Fulton L, Golderer G, Jahn N, Knoop V, Landweber LF, Maric C, Miller D, Noegel AA, Peace R, Pierron G, Sasaki T, Schallenberg-Rüdinger M, Schleicher M, Singh R, Spaller T, Storey KB, Suzuki T, Tomlinson C, Tyson JJ, Warren WC, Werner ER, Werner-Felmayer G, Wilson RK, Winckler T, Gott JM, Glöckner G, Marwan W. The Physarum polycephalum Genome Reveals Extensive Use of Prokaryotic Two-Component and Metazoan-Type Tyrosine Kinase Signaling. Genome Biol Evol 2015; 8:109-25. [PMID: 26615215 PMCID: PMC4758236 DOI: 10.1093/gbe/evv237] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/23/2015] [Indexed: 12/13/2022] Open
Abstract
Physarum polycephalum is a well-studied microbial eukaryote with unique experimental attributes relative to other experimental model organisms. It has a sophisticated life cycle with several distinct stages including amoebal, flagellated, and plasmodial cells. It is unusual in switching between open and closed mitosis according to specific life-cycle stages. Here we present the analysis of the genome of this enigmatic and important model organism and compare it with closely related species. The genome is littered with simple and complex repeats and the coding regions are frequently interrupted by introns with a mean size of 100 bases. Complemented with extensive transcriptome data, we define approximately 31,000 gene loci, providing unexpected insights into early eukaryote evolution. We describe extensive use of histidine kinase-based two-component systems and tyrosine kinase signaling, the presence of bacterial and plant type photoreceptors (phytochromes, cryptochrome, and phototropin) and of plant-type pentatricopeptide repeat proteins, as well as metabolic pathways, and a cell cycle control system typically found in more complex eukaryotes. Our analysis characterizes P. polycephalum as a prototypical eukaryote with features attributed to the last common ancestor of Amorphea, that is, the Amoebozoa and Opisthokonts. Specifically, the presence of tyrosine kinases in Acanthamoeba and Physarum as representatives of two distantly related subdivisions of Amoebozoa argues against the later emergence of tyrosine kinase signaling in the opisthokont lineage and also against the acquisition by horizontal gene transfer.
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Affiliation(s)
- Pauline Schaap
- School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Israel Barrantes
- Magdeburg Centre for Systems Biology and Institute for Biology, University of Magdeburg, Magdeburg, Germany
| | - Pat Minx
- The Genome Institute, Washington University School of Medicine, St Louis
| | - Narie Sasaki
- Department of Biological Sciences, Graduate School of Science, Nagoya University, Furocho, Chikusaku, Nagoya, Aichi, Japan
| | - Roger W Anderson
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, United Kingdom
| | - Marianne Bénard
- UPMC Univ Paris 06, Institut de Biologie Paris-Seine (IBPS), CNRS UMR-7622, Paris, France
| | - Kyle K Biggar
- Biochemistry Department, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Nicolas E Buchler
- Department of Biology and Center for Genomic and Computational Biology, Duke University, Durham Department of Physics, Duke University, Durham
| | - Ralf Bundschuh
- Department of Physics and Center for RNA Biology, The Ohio State University, Columbus Department of Chemistry & Biochemistry, The Ohio State University, Columbus Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus
| | - Xiao Chen
- Department of Ecology & Evolutionary Biology, Princeton University, Princeton
| | - Catrina Fronick
- The Genome Institute, Washington University School of Medicine, St Louis
| | - Lucinda Fulton
- The Genome Institute, Washington University School of Medicine, St Louis
| | - Georg Golderer
- Biological Chemistry, Biocenter, Innsbruck Medical University, Innsbruck, Austria
| | - Niels Jahn
- Genome Analysis, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany
| | - Volker Knoop
- IZMB - Institut für Zelluläre und Molekulare Botanik, Universität Bonn, Bonn, Germany
| | - Laura F Landweber
- Department of Ecology & Evolutionary Biology, Princeton University, Princeton
| | - Chrystelle Maric
- Institut Jacques Monod, CNRS UMR7592, Université Paris Diderot Paris7, Paris, France
| | - Dennis Miller
- The University of Texas at Dallas, Biological Sciences, Richardson
| | - Angelika A Noegel
- Institute for Biochemistry I, Medical Faculty, University of Cologne, Cologne, Germany
| | - Rob Peace
- Carleton University, Ottawa, Ontario, Canada
| | - Gérard Pierron
- Institut Jacques Monod, CNRS UMR7592, Université Paris Diderot Paris7, Paris, France
| | - Taeko Sasaki
- Department of Biological Sciences, Graduate School of Science, Nagoya University, Furocho, Chikusaku, Nagoya, Aichi, Japan
| | | | - Michael Schleicher
- Institute for Anatomy III / Cell Biology, BioMedCenter, Ludwig-Maximilians-Universität, Planegg-Martinsried, Germany
| | - Reema Singh
- School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Thomas Spaller
- Institut für Pharmazie, Friedrich-Schiller-Universität Jena, Jena, Germany
| | | | - Takamasa Suzuki
- Department of Biological Sciences, Graduate School of Science and JST ERATO Higashiyama Live-holonics Project, Nagoya University, Furocho, Chikusaku, Nagoya, Aichi, Japan
| | - Chad Tomlinson
- The Genome Institute, Washington University School of Medicine, St Louis
| | - John J Tyson
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg
| | - Wesley C Warren
- The Genome Institute, Washington University School of Medicine, St Louis
| | - Ernst R Werner
- Biological Chemistry, Biocenter, Innsbruck Medical University, Innsbruck, Austria
| | | | - Richard K Wilson
- The Genome Institute, Washington University School of Medicine, St Louis
| | - Thomas Winckler
- Institut für Pharmazie, Friedrich-Schiller-Universität Jena, Jena, Germany
| | - Jonatha M Gott
- Center for RNA Molecular Biology, Case Western Reserve University, School of Medicine, Cleveland
| | - Gernot Glöckner
- Institute for Biochemistry I, Medical Faculty, University of Cologne, Cologne, Germany Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
| | - Wolfgang Marwan
- Magdeburg Centre for Systems Biology and Institute for Biology, University of Magdeburg, Magdeburg, Germany
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138
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McSkimming DI, Dastgheib S, Talevich E, Narayanan A, Katiyar S, Taylor SS, Kochut K, Kannan N. ProKinO: a unified resource for mining the cancer kinome. Hum Mutat 2015; 36:175-86. [PMID: 25382819 PMCID: PMC4342772 DOI: 10.1002/humu.22726] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Accepted: 10/21/2014] [Indexed: 12/31/2022]
Abstract
Protein kinases represent a large and diverse family of evolutionarily related proteins that are abnormally regulated in human cancers. Although genome sequencing studies have revealed thousands of variants in protein kinases, translating "big" genomic data into biological knowledge remains a challenge. Here, we describe an ontological framework for integrating and conceptualizing diverse forms of information related to kinase activation and regulatory mechanisms in a machine readable, human understandable form. We demonstrate the utility of this framework in analyzing the cancer kinome, and in generating testable hypotheses for experimental studies. Through the iterative process of aggregate ontology querying, hypothesis generation and experimental validation, we identify a novel mutational hotspot in the αC-β4 loop of the kinase domain and demonstrate the functional impact of the identified variants in epidermal growth factor receptor (EGFR) constitutive activity and inhibitor sensitivity. We provide a unified resource for the kinase and cancer community, ProKinO, housed at http://vulcan.cs.uga.edu/prokino.
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139
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Creixell P, Palmeri A, Miller CJ, Lou HJ, Santini CC, Nielsen M, Turk BE, Linding R. Unmasking determinants of specificity in the human kinome. Cell 2015; 163:187-201. [PMID: 26388442 PMCID: PMC4644237 DOI: 10.1016/j.cell.2015.08.057] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2014] [Revised: 04/09/2015] [Accepted: 08/12/2015] [Indexed: 01/01/2023]
Abstract
Protein kinases control cellular responses to environmental cues by swift and accurate signal processing. Breakdowns in this high-fidelity capability are a driving force in cancer and other diseases. Thus, our limited understanding of which amino acids in the kinase domain encode substrate specificity, the so-called determinants of specificity (DoS), constitutes a major obstacle in cancer signaling. Here, we systematically discover several DoS and experimentally validate three of them, named the αC1, αC3, and APE-7 residues. We demonstrate that DoS form sparse networks of non-conserved residues spanning distant regions. Our results reveal a likely role for inter-residue allostery in specificity and an evolutionary decoupling of kinase activity and specificity, which appear loaded on independent groups of residues. Finally, we uncover similar properties driving SH2 domain specificity and demonstrate how the identification of DoS can be utilized to elucidate a greater understanding of the role of signaling networks in cancer (Creixell et al., 2015 [this issue of Cell]). Residues driving specificity in the kinase and SH2 domains are globally identified Three new such residues, termed αC1, αC3, and APE-7, are experimentally validated Specificity and catalytic activity appear to be encoded in distinct sets of residues The global identification of determinants allows the modeling of rewiring mutations
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Affiliation(s)
- Pau Creixell
- Department of Systems Biology, Technical University of Denmark, 2800 Lyngby, Denmark.
| | - Antonio Palmeri
- Centre for Molecular Bioinformatics, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Chad J Miller
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Hua Jane Lou
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Cristina C Santini
- Department of Systems Biology, Technical University of Denmark, 2800 Lyngby, Denmark; Biotech Research & Innovation Centre (BRIC), University of Copenhagen (UCPH), 2200 Copenhagen, Denmark
| | - Morten Nielsen
- Department of Systems Biology, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Benjamin E Turk
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Rune Linding
- Department of Systems Biology, Technical University of Denmark, 2800 Lyngby, Denmark; Biotech Research & Innovation Centre (BRIC), University of Copenhagen (UCPH), 2200 Copenhagen, Denmark.
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140
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Nephrocyte-neurocyte interaction and cellular metabolic analysis on membrane-integrated microfluidic device. Sci China Chem 2015. [DOI: 10.1007/s11426-015-5453-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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141
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Peng M, Aye TT, Snel B, van Breukelen B, Scholten A, Heck AJR. Spatial Organization in Protein Kinase A Signaling Emerged at the Base of Animal Evolution. J Proteome Res 2015; 14:2976-87. [DOI: 10.1021/acs.jproteome.5b00370] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Mao Peng
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Netherlands Proteomics Centre, Padualaan
8, 3584 CH Utrecht, The Netherlands
- Department
of Toxicogenomics, Maastricht University, 6200 MD Maastricht, The Netherlands
| | - Thin Thin Aye
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Netherlands Proteomics Centre, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Berend Snel
- Theoretical
Biology and Bioinformatics, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Bas van Breukelen
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Netherlands Proteomics Centre, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Arjen Scholten
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Netherlands Proteomics Centre, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Albert J. R. Heck
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Netherlands Proteomics Centre, Padualaan
8, 3584 CH Utrecht, The Netherlands
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142
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Constitutive Activity in an Ancestral Form of Abl Tyrosine Kinase. PLoS One 2015; 10:e0131062. [PMID: 26090675 PMCID: PMC4474922 DOI: 10.1371/journal.pone.0131062] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 05/28/2015] [Indexed: 11/19/2022] Open
Abstract
The c-abl proto-oncogene encodes a nonreceptor tyrosine kinase that is found in all metazoans, and is ubiquitously expressed in mammalian tissues. The Abl tyrosine kinase plays important roles in the regulation of mammalian cell physiology. Abl-like kinases have been identified in the genomes of unicellular choanoflagellates, the closest relatives to the Metazoa, and in related unicellular organisms. Here, we have carried out the first characterization of a premetazoan Abl kinase, MbAbl2, from the choanoflagellate Monosiga brevicollis. The enzyme possesses SH3, SH2, and kinase domains in a similar arrangement to its mammalian counterparts, and is an active tyrosine kinase. MbAbl2 lacks the N-terminal myristoylation and cap sequences that are critical regulators of mammalian Abl kinase activity, and we show that MbAbl2 is constitutively active. When expressed in mammalian cells, MbAbl2 strongly phosphorylates cellular proteins on tyrosine, and transforms cells much more potently than mammalian Abl kinase. Thus, MbAbl2 appears to lack the autoinhibitory mechanism that tightly constrains the activity of mammalian Abl kinases, suggesting that this regulatory apparatus arose more recently in metazoan evolution.
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143
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Macho AP, Lozano-Durán R, Zipfel C. Importance of tyrosine phosphorylation in receptor kinase complexes. TRENDS IN PLANT SCIENCE 2015; 20:269-272. [PMID: 25795237 DOI: 10.1016/j.tplants.2015.02.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Revised: 02/17/2015] [Accepted: 02/25/2015] [Indexed: 05/09/2023]
Abstract
Tyrosine phosphorylation is an important post-translational modification that is known to regulate receptor kinase (RK)-mediated signaling in animals. Plant RKs are annotated as serine/threonine kinases, but recent work has revealed that tyrosine phosphorylation is also crucial for the activation of RK-mediated signaling in plants. These initial observations have paved the way for subsequent detailed studies on the mechanism of activation of plant RKs and the biological relevance of tyrosine phosphorylation for plant growth and immunity. In this Opinion article we review recent reports on the contribution of RK tyrosine phosphorylation in plant growth and immunity; we propose that tyrosine phosphorylation plays a major regulatory role in the initiation and transduction of RK-mediated signaling in plants.
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Affiliation(s)
- Alberto P Macho
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK.
| | - Rosa Lozano-Durán
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Cyril Zipfel
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK.
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144
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Fan G, Aleem S, Yang M, Miller WT, Tonks NK. Protein-tyrosine Phosphatase and Kinase Specificity in Regulation of SRC and Breast Tumor Kinase. J Biol Chem 2015; 290:15934-47. [PMID: 25897081 DOI: 10.1074/jbc.m115.651703] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Indexed: 11/06/2022] Open
Abstract
Despite significant evidence to the contrary, the view that phosphatases are "nonspecific" still pervades the field. Systems biology approaches to defining how signal transduction pathways are integrated at the level of whole organisms also often downplay the contribution of phosphatases, defining them as "erasers" that serve merely to restore the system to its basal state. Here, we present a study that counteracts the idea of "nonspecific phosphatases." We have characterized two structurally similar and functionally related kinases, BRK and SRC, which are regulated by combinations of activating autophosphorylation and inhibitory C-terminal sites of tyrosine phosphorylation. We demonstrated specificity at the level of the kinases in that SRMS phosphorylated the C terminus of BRK, but not SRC; in contrast, CSK is the kinase responsible for C-terminal phosphorylation of SRC, but not BRK. For the phosphatases, we observed that RNAi-mediated suppression of PTP1B resulted in opposing effects on the activity of BRK and SRC and have defined the mechanisms underlying this specificity. PTP1B inhibited BRK by directly dephosphorylating the Tyr-342 autophosphorylation site. In contrast, PTP1B potentiated SRC activity, but not by dephosphorylating SRC itself directly; instead, PTP1B regulated the interaction between CBP/PAG and CSK. SRC associated with, and phosphorylated, the transmembrane protein CBP/PAG at Tyr-317, resulting in CSK recruitment. We identified PAG as a substrate of PTP1B, and dephosphorylation abolished recruitment of the inhibitory kinase CSK. Overall, these findings illustrate how the combinatorial effects of PTKs and PTPs may be integrated to regulate signaling, with both classes of enzymes displaying exquisite specificity.
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Affiliation(s)
- Gaofeng Fan
- From the Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724-2208 and
| | - Saadat Aleem
- the Department of Physiology and Biophysics, Stony Brook University, Stony Brook, New York 11794-8661
| | - Ming Yang
- From the Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724-2208 and
| | - W Todd Miller
- the Department of Physiology and Biophysics, Stony Brook University, Stony Brook, New York 11794-8661
| | - Nicholas K Tonks
- From the Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724-2208 and
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145
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Delaney C, Frank S, Huang RS. Pharmacogenomics of EGFR-targeted therapies in non-small cell lung cancer: EGFR and beyond. CHINESE JOURNAL OF CANCER 2015; 34:149-60. [PMID: 25962919 PMCID: PMC4593375 DOI: 10.1186/s40880-015-0007-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Accepted: 12/22/2014] [Indexed: 02/08/2023]
Abstract
Commonly observed aberrations in epidermal growth factor receptor (EGFR) signaling have led to the development of EGFR-targeted therapies for various cancers, including non–small cell lung cancer (NSCLC). EGFR mutations and overexpression have further been shown to modulate sensitivity to these EGFR-targeted therapies in NSCLC and several other types of cancers. However, it is clear that mutations and/or genetic variations in EGFR alone cannot explain all of the variability in the responses of patients with NSCLC to EGFR-targeted therapies. For instance, in addition to EGFR genotype, genetic variations in other members of the signaling pathway downstream of EGFR or variations in parallel receptor tyrosine kinase (RTK) pathways are now recognized to have a significant impact on the efficacy of certain EGFR-targeted therapies. In this review, we highlight the mutations and genetic variations in such genes downstream of EGFR and in parallel RTK pathways. Specifically, the directional effects of these pharmacogenetic factors are discussed with a focus on two commonly prescribed EGFR inhibitors: cetuximab and erlotinib. The results of this comprehensive review can be used to optimize the treatment of NSCLC with EGFR inhibitors. Furthermore, they may provide the rationale for the design of subsequent combination therapies that involve the inhibition of EGFR.
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Affiliation(s)
- Christopher Delaney
- Biological Sciences Division, University of Chicago, Chicago, IL, 60637, USA.
| | - Samuel Frank
- Biological Sciences Division, University of Chicago, Chicago, IL, 60637, USA.
| | - R Stephanie Huang
- Department of Medicine, University of Chicago, 900 E 57th street, KCBD room 7148, Chicago, IL, 60637, USA. .,The Affiliated Hospital, School of Medicine, Ningbo University, Ningbo, Zhejiang, 315211, P. R. China.
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146
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Grossmann A, Benlasfer N, Birth P, Hegele A, Wachsmuth F, Apelt L, Stelzl U. Phospho-tyrosine dependent protein-protein interaction network. Mol Syst Biol 2015; 11:794. [PMID: 25814554 PMCID: PMC4380928 DOI: 10.15252/msb.20145968] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Post-translational protein modifications, such as tyrosine phosphorylation, regulate protein–protein interactions (PPIs) critical for signal processing and cellular phenotypes. We extended an established yeast two-hybrid system employing human protein kinases for the analyses of phospho-tyrosine (pY)-dependent PPIs in a direct experimental, large-scale approach. We identified 292 mostly novel pY-dependent PPIs which showed high specificity with respect to kinases and interacting proteins and validated a large fraction in co-immunoprecipitation experiments from mammalian cells. About one-sixth of the interactions are mediated by known linear sequence binding motifs while the majority of pY-PPIs are mediated by other linear epitopes or governed by alternative recognition modes. Network analysis revealed that pY-mediated recognition events are tied to a highly connected protein module dedicated to signaling and cell growth pathways related to cancer. Using binding assays, protein complementation and phenotypic readouts to characterize the pY-dependent interactions of TSPAN2 (tetraspanin 2) and GRB2 or PIK3R3 (p55γ), we exemplarily provide evidence that the two pY-dependent PPIs dictate cellular cancer phenotypes.
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Affiliation(s)
- Arndt Grossmann
- Otto-Warburg Laboratory, Max-Planck Institute for Molecular Genetics (MPIMG), Berlin, Germany
| | - Nouhad Benlasfer
- Otto-Warburg Laboratory, Max-Planck Institute for Molecular Genetics (MPIMG), Berlin, Germany
| | - Petra Birth
- Otto-Warburg Laboratory, Max-Planck Institute for Molecular Genetics (MPIMG), Berlin, Germany
| | - Anna Hegele
- Otto-Warburg Laboratory, Max-Planck Institute for Molecular Genetics (MPIMG), Berlin, Germany
| | - Franziska Wachsmuth
- Otto-Warburg Laboratory, Max-Planck Institute for Molecular Genetics (MPIMG), Berlin, Germany
| | - Luise Apelt
- Otto-Warburg Laboratory, Max-Planck Institute for Molecular Genetics (MPIMG), Berlin, Germany
| | - Ulrich Stelzl
- Otto-Warburg Laboratory, Max-Planck Institute for Molecular Genetics (MPIMG), Berlin, Germany
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147
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Selvan N, Mariappa D, van den Toorn HWP, Heck AJR, Ferenbach AT, van Aalten DMF. The Early Metazoan Trichoplax adhaerens Possesses a Functional O-GlcNAc System. J Biol Chem 2015; 290:11969-82. [PMID: 25778404 PMCID: PMC4424335 DOI: 10.1074/jbc.m114.628750] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Indexed: 01/09/2023] Open
Abstract
Protein O-GlcNAcylation is a reversible post-translational signaling modification of nucleocytoplasmic proteins that is essential for embryonic development in bilateria. In a search for a reductionist model to study O-GlcNAc signaling, we discovered the presence of functional O-GlcNAc transferase (OGT), O-GlcNAcase (OGA), and nucleocytoplasmic protein O-GlcNAcylation in the most basal extant animal, the placozoan Trichoplax adhaerens. We show via enzymatic characterization of Trichoplax OGT/OGA and genetic rescue experiments in Drosophila melanogaster that these proteins possess activities/functions similar to their bilaterian counterparts. The acquisition of O-GlcNAc signaling by metazoa may have facilitated the rapid and complex signaling mechanisms required for the evolution of multicellular organisms.
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Affiliation(s)
| | - Daniel Mariappa
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, United Kingdom and
| | - Henk W P van den Toorn
- the Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Albert J R Heck
- the Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | | | - Daan M F van Aalten
- From the Division of Molecular Microbiology and MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, United Kingdom and
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148
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Cai B, Cai JP, Luo YL, Chen C, Zhang S. The Specific Roles of JAK/STAT Signaling Pathway in Sepsis. Inflammation 2015; 38:1599-608. [DOI: 10.1007/s10753-015-0135-z] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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149
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Robertson J, Jacquemet G, Byron A, Jones MC, Warwood S, Selley JN, Knight D, Humphries JD, Humphries MJ. Defining the phospho-adhesome through the phosphoproteomic analysis of integrin signalling. Nat Commun 2015; 6:6265. [PMID: 25677187 PMCID: PMC4338609 DOI: 10.1038/ncomms7265] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 01/09/2015] [Indexed: 01/09/2023] Open
Abstract
Cell–extracellular matrix (ECM) adhesion is a fundamental requirement for multicellular existence due to roles in positioning, proliferation and differentiation. Phosphorylation plays a major role in adhesion signalling; however, a full understanding of the phosphorylation events that occur at sites of adhesion is lacking. Here we report a proteomic and phosphoproteomic analysis of adhesion complexes isolated from cells spread on fibronectin. We identify 1,174 proteins, 499 of which are phosphorylated (1,109 phosphorylation sites), including both well-characterized and novel adhesion-regulated phosphorylation events. Immunoblotting suggests that two classes of phosphorylated residues are found at adhesion sites—those induced by adhesion and those constitutively phosphorylated but recruited in response to adhesion. Kinase prediction analysis identifies novel kinases with putative roles in adhesion signalling including CDK1, inhibition of which reduces adhesion complex formation. This phospho-adhesome data set constitutes a valuable resource to improve our understanding of the signalling mechanisms through which cell–ECM interactions control cell behaviour. Protein phosphorylation is known to play an important role in cell adhesion signalling. Robertson et al. present a proteomic resource mapping the phosphorylation states of proteins isolated from adhesion complexes and, taking advantage of this data set, show that the cell cycle kinase CDK1 may influence cell adhesion.
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Affiliation(s)
- Joseph Robertson
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
| | - Guillaume Jacquemet
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
| | - Adam Byron
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
| | - Matthew C Jones
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
| | - Stacey Warwood
- Biological Mass Spectrometry Core Facility, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
| | - Julian N Selley
- Biological Mass Spectrometry Core Facility, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
| | - David Knight
- Biological Mass Spectrometry Core Facility, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
| | - Jonathan D Humphries
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
| | - Martin J Humphries
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
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150
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Kovacs E, Zorn JA, Huang Y, Barros T, Kuriyan J. A structural perspective on the regulation of the epidermal growth factor receptor. Annu Rev Biochem 2015; 84:739-64. [PMID: 25621509 DOI: 10.1146/annurev-biochem-060614-034402] [Citation(s) in RCA: 226] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The epidermal growth factor receptor (EGFR) is a receptor tyrosine kinase that plays a critical role in the pathogenesis of many cancers. The structure of intact forms of this receptor has yet to be determined, but intense investigations of fragments of the receptor have provided a detailed view of its activation mechanism, which we review here. Ligand binding converts the receptor to a dimeric form, in which contacts are restricted to the receptor itself, allowing heterodimerization of the four EGFR family members without direct ligand involvement. Activation of the receptor depends on the formation of an asymmetric dimer of kinase domains, in which one kinase domain allosterically activates the other. Coupling between the extracellular and intracellular domains may involve a switch between alternative crossings of the transmembrane helices, which form dimeric structures. We also discuss how receptor regulation is compromised by oncogenic mutations and the structural basis for negative cooperativity in ligand binding.
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