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Dionne U, Percival LJ, Chartier FJM, Landry CR, Bisson N. SRC homology 3 domains: multifaceted binding modules. Trends Biochem Sci 2022; 47:772-784. [PMID: 35562294 DOI: 10.1016/j.tibs.2022.04.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/30/2022] [Accepted: 04/11/2022] [Indexed: 12/15/2022]
Abstract
The assembly of complexes following the detection of extracellular signals is often controlled by signaling proteins comprising multiple peptide binding modules. The SRC homology (SH)3 family represents the archetypical modular protein interaction module, with ~300 annotated SH3 domains in humans that regulate an impressive array of signaling processes. We review recent findings regarding the allosteric contributions of SH3 domains host protein context, their phosphoregulation, and their roles in phase separation that challenge the simple model in which SH3s are considered to be portable domains binding to specific proline-rich peptide motifs.
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Affiliation(s)
- Ugo Dionne
- Centre de recherche sur le cancer et Centre de recherche du CHU de Québec - Université Laval, QC, Canada; Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), QC, Canada
| | - Lily J Percival
- Centre de recherche sur le cancer et Centre de recherche du CHU de Québec - Université Laval, QC, Canada; Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), QC, Canada; School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, The Michael Smith Building, Manchester, UK
| | - François J M Chartier
- Centre de recherche sur le cancer et Centre de recherche du CHU de Québec - Université Laval, QC, Canada; Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), QC, Canada
| | - Christian R Landry
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), QC, Canada; Institute of Integrative and Systems Biology, Université Laval, Quebec, QC, Canada; Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, Quebec, QC, Canada; Department of Biology, Université Laval, Quebec, QC, Canada.
| | - Nicolas Bisson
- Centre de recherche sur le cancer et Centre de recherche du CHU de Québec - Université Laval, QC, Canada; Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), QC, Canada; Department of Molecular Biology, Medical Biochemistry and Pathology, Université Laval, Quebec, QC, Canada.
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2
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Hoffman GE, Ma Y, Montgomery KS, Bendl J, Jaiswal MK, Kozlenkov A, Peters MA, Dracheva S, Fullard JF, Chess A, Devlin B, Sieberts SK, Roussos P. Sex Differences in the Human Brain Transcriptome of Cases With Schizophrenia. Biol Psychiatry 2022; 91:92-101. [PMID: 34154796 PMCID: PMC8463632 DOI: 10.1016/j.biopsych.2021.03.020] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 03/16/2021] [Accepted: 03/18/2021] [Indexed: 01/03/2023]
Abstract
BACKGROUND While schizophrenia differs between males and females in the age of onset, symptomatology, and disease course, the molecular mechanisms underlying these differences remain uncharacterized. METHODS To address questions about the sex-specific effects of schizophrenia, we performed a large-scale transcriptome analysis of RNA sequencing data from 437 controls and 341 cases from two distinct cohorts from the CommonMind Consortium. RESULTS Analysis across the cohorts identified a reproducible gene expression signature of schizophrenia that was highly concordant with previous work. Differential expression across sex was reproducible across cohorts and identified X- and Y-linked genes, as well as those involved in dosage compensation. Intriguingly, the sex expression signature was also enriched for genes involved in neurexin family protein binding and synaptic organization. Differential expression analysis testing a sex-by-diagnosis interaction effect did not identify any genome-wide signature after multiple testing corrections. Gene coexpression network analysis was performed to reduce dimensionality from thousands of genes to dozens of modules and elucidate interactions among genes. We found enrichment of coexpression modules for sex-by-diagnosis differential expression signatures, which were highly reproducible across the two cohorts and involved a number of diverse pathways, including neural nucleus development, neuron projection morphogenesis, and regulation of neural precursor cell proliferation. CONCLUSIONS Overall, our results indicate that the effect size of sex differences in schizophrenia gene expression signatures is small and underscore the challenge of identifying robust sex-by-diagnosis signatures, which will require future analyses in larger cohorts.
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Affiliation(s)
- Gabriel E Hoffman
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York.
| | - Yixuan Ma
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York
| | | | - Jaroslav Bendl
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Manoj Kumar Jaiswal
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York; Mental Illness Research, Education and Clinical Centers, James J. Peters VA Medical Center, Bronx, New York
| | - Alex Kozlenkov
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York; Mental Illness Research, Education and Clinical Centers, James J. Peters VA Medical Center, Bronx, New York
| | | | - Stella Dracheva
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York; Mental Illness Research, Education and Clinical Centers, James J. Peters VA Medical Center, Bronx, New York
| | - John F Fullard
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Andrew Chess
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Bernie Devlin
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | | | - Panos Roussos
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York; Mental Illness Research, Education and Clinical Centers, James J. Peters VA Medical Center, Bronx, New York.
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3
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Alfaidi M, Scott ML, Orr AW. Sinner or Saint?: Nck Adaptor Proteins in Vascular Biology. Front Cell Dev Biol 2021; 9:688388. [PMID: 34124074 PMCID: PMC8187788 DOI: 10.3389/fcell.2021.688388] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 04/28/2021] [Indexed: 12/28/2022] Open
Abstract
The Nck family of modular adaptor proteins, including Nck1 and Nck2, link phosphotyrosine signaling to changes in cytoskeletal dynamics and gene expression that critically modulate cellular phenotype. The Nck SH2 domain interacts with phosphotyrosine at dynamic signaling hubs, such as activated growth factor receptors and sites of cell adhesion. The Nck SH3 domains interact with signaling effectors containing proline-rich regions that mediate their activation by upstream kinases. In vascular biology, Nck1 and Nck2 play redundant roles in vascular development and postnatal angiogenesis. However, recent studies suggest that Nck1 and Nck2 differentially regulate cell phenotype in the adult vasculature. Domain-specific interactions likely mediate these isoform-selective effects, and these isolated domains may serve as therapeutic targets to limit specific protein-protein interactions. In this review, we highlight the function of the Nck adaptor proteins, the known differences in domain-selective interactions, and discuss the role of individual Nck isoforms in vascular remodeling and function.
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Affiliation(s)
- Mabruka Alfaidi
- Department of Pathology and Translational Pathobiology, Louisiana State University Health - Shreveport, Shreveport, LA, United States
| | - Matthew L Scott
- Department of Pathology and Translational Pathobiology, Louisiana State University Health - Shreveport, Shreveport, LA, United States
| | - Anthony Wayne Orr
- Department of Pathology and Translational Pathobiology, Louisiana State University Health - Shreveport, Shreveport, LA, United States.,Department of Cell Biology and Anatomy, LSU Health - Shreveport, Shreveport, LA, United States.,Department of Molecular & Cellular Physiology, LSU Health - Shreveport, Shreveport, LA, United States
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4
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Hallumi E, Shalah R, Lo WL, Corso J, Oz I, Beach D, Wittman S, Isenberg A, Sela M, Urlaub H, Weiss A, Yablonski D. Itk Promotes the Integration of TCR and CD28 Costimulation through Its Direct Substrates SLP-76 and Gads. THE JOURNAL OF IMMUNOLOGY 2021; 206:2322-2337. [PMID: 33931484 DOI: 10.4049/jimmunol.2001053] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 03/15/2021] [Indexed: 11/19/2022]
Abstract
The costimulatory receptor CD28 synergizes with the TCR to promote IL-2 production, cell survival, and proliferation; yet the obligatory interdependence of TCR and CD28 signaling is not well understood. Upon TCR stimulation, Gads, a Grb2-family adaptor, bridges the interaction of two additional adaptors, LAT and SLP-76, to form a TCR-induced effector signaling complex. SLP-76 binds the Tec-family tyrosine kinase, Itk, which phosphorylates SLP-76 Y173 and PLC-γ1 Y783. In this study, we identified TCR-inducible, Itk-mediated phosphorylation of Gads Y45 in a human T cell line and in mouse primary T cells. Y45 is found within the N-terminal SH3 domain of Gads, an evolutionarily conserved domain with no known signaling function. Gads Y45 phosphorylation depended on the interaction of Gads with SLP-76 and on the dimerization-dependent binding of Gads to phospho-LAT. We provide evidence that Itk acts through SLP-76 and Gads to promote the TCR/CD28-induced activation of the RE/AP transcriptional element from the IL-2 promoter. Two Itk-related features of SLP-76, Y173 and a proline-rich Itk SH3 binding motif on SLP-76, were dispensable for activation of NFAT but selectively required for the TCR/CD28-induced increase in cytoplasmic and nuclear c-Rel and consequent RE/AP activation. We provide evidence that unphosphorylated, monomeric Gads mediates an RE/AP-directed inhibitory activity that is mitigated upon Gads dimerization and Y45 phosphorylation. This study illuminates a new, to our knowledge, regulatory module, in which TCR-induced, Itk-mediated phosphorylation sites on SLP-76 and Gads control the transcriptional response to TCR/CD28 costimulation, thus enforcing the obligatory interdependence of the TCR and CD28 signaling pathways.
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Affiliation(s)
- Enas Hallumi
- Department of Immunology, Ruth and Bruce Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
| | - Rose Shalah
- Department of Immunology, Ruth and Bruce Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
| | - Wan-Lin Lo
- Rosalind Russell and Ephraim P. Engleman Arthritis Research Center, Division of Rheumatology, Department of Medicine, University of California, San Francisco, San Francisco, CA
| | - Jasmin Corso
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Ilana Oz
- Department of Immunology, Ruth and Bruce Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
| | - Dvora Beach
- Department of Immunology, Ruth and Bruce Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
| | - Samuel Wittman
- Department of Immunology, Ruth and Bruce Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
| | - Amy Isenberg
- Department of Immunology, Ruth and Bruce Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
| | - Meirav Sela
- Department of Immunology, Ruth and Bruce Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.,Bioanalytics Research Group, Institute for Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Arthur Weiss
- Rosalind Russell and Ephraim P. Engleman Arthritis Research Center, Division of Rheumatology, Department of Medicine, University of California, San Francisco, San Francisco, CA.,Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA
| | - Deborah Yablonski
- Department of Immunology, Ruth and Bruce Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
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5
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Solution NMR Structure of the SH3 Domain of Human Caskin1 Validates the Lack of a Typical Peptide Binding Groove and Supports a Role in Lipid Mediator Binding. Cells 2021; 10:cells10010173. [PMID: 33467043 PMCID: PMC7830187 DOI: 10.3390/cells10010173] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 01/10/2021] [Accepted: 01/13/2021] [Indexed: 12/15/2022] Open
Abstract
SH3 domains constitute an important class of protein modules involved in a variety of cellular functions. They participate in protein-protein interactions via their canonical ligand binding interfaces composed of several evolutionarily conserved aromatic residues forming binding grooves for typical (PxxP) and atypical (PxxxPR, RxxK, RKxxY) binding motifs. The calcium/calmodulin-dependent serine protein kinase (CASK)-interacting protein 1, or Caskin1, a multidomain scaffold protein regulating the cortical actin filaments, is enriched in neural synapses in mammals. Based on its known interaction partners and knock-out animal studies, Caskin1 may play various roles in neural function and it is thought to participate in several pathological processes of the brain. Caskin1 has a single, atypical SH3 domain in which key aromatic residues are missing from the canonical binding groove. No protein interacting partner for this SH3 domain has been identified yet. Nevertheless, we have recently demonstrated the specific binding of this SH3 domain to the signaling lipid mediator lysophospatidic acid (LPA) in vitro. Here we report the solution NMR structure of the human Caskin1 SH3 domain and analyze its structural features in comparison with other SH3 domains exemplifying different strategies in target selectivity. The key differences revealed by our structural study show that the canonical binding groove found in typical SH3 domains accommodating proline-rich motifs is missing in Caskin1 SH3, most likely excluding a bona fide protein target for the domain. The LPA binding site is distinct from the altered protein binding groove. We conclude that the SH3 domain of Caskin1 might mediate the association of Caskin1 with membrane surfaces with locally elevated LPA content.
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6
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Wipa P, Paensuwan P, Ngoenkam J, Woessner NM, Minguet S, Schamel WW, Pongcharoen S. Actin polymerization regulates recruitment of Nck to CD3ε upon T-cell receptor triggering. Immunology 2019; 159:298-308. [PMID: 31674657 DOI: 10.1111/imm.13146] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 10/28/2019] [Accepted: 10/29/2019] [Indexed: 12/15/2022] Open
Abstract
Following T-cell antigen receptor (TCR) engagement, rearrangement of the actin cytoskeleton supports intracellular signal transduction and T-cell activation. The non-catalytic region of the tyrosine kinase (Nck) molecule is an adapter protein implicated in TCR-induced actin polymerization. Further, Nck is recruited to the CD3ε subunit of the TCR upon TCR triggering. Here we examine the role of actin polymerization in the recruitment of Nck to the TCR. To this end, Nck binding to CD3ε was quantified in Jurkat cells using the proximity ligation assay. We show that inhibition of actin polymerization using cytochalasin D delayed the recruitment of Nck1 to the TCR upon TCR triggering. Interestingly, CD3ε phosphorylation was also delayed. These findings suggest that actin polymerization promotes the recruitment of Nck to the TCR, enhancing downstream signaling, such as phosphorylation of CD3ε.
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Affiliation(s)
- Piyamaporn Wipa
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand
| | - Pussadee Paensuwan
- Department of Optometry, Faculty of Allied Health Sciences, Naresuan University, Phitsanulok, Thailand
| | - Jatuporn Ngoenkam
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand
| | - Nadine M Woessner
- Department of Immunology, Faculty of Biology, University of Freiburg, Freiburg, Germany.,Signaling Research Centers BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Susana Minguet
- Department of Immunology, Faculty of Biology, University of Freiburg, Freiburg, Germany.,Signaling Research Centers BIOSS and CIBSS, University of Freiburg, Freiburg, Germany.,Center for Chronic Immunodeficiency CCI, Medical Center Freiburg and Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Wolfgang W Schamel
- Department of Immunology, Faculty of Biology, University of Freiburg, Freiburg, Germany.,Signaling Research Centers BIOSS and CIBSS, University of Freiburg, Freiburg, Germany.,Center for Chronic Immunodeficiency CCI, Medical Center Freiburg and Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Sutatip Pongcharoen
- Division of Immunology, Department of Medicine, Faculty of Medicine, Naresuan University, Phitsanulok, Thailand.,Center of Excellence in Medical Biotechnology, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand.,Research Center for Academic Excellence in Petroleum, Petrochemical, and Advanced Materials, Faculty of Science, Naresuan University, Phitsanulok, Thailand
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7
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Bencsik N, Pusztai S, Borbély S, Fekete A, Dülk M, Kis V, Pesti S, Vas V, Szűcs A, Buday L, Schlett K. Dendritic spine morphology and memory formation depend on postsynaptic Caskin proteins. Sci Rep 2019; 9:16843. [PMID: 31727973 PMCID: PMC6856520 DOI: 10.1038/s41598-019-53317-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 10/30/2019] [Indexed: 12/12/2022] Open
Abstract
CASK-interactive proteins, Caskin1 and Caskin2, are multidomain neuronal scaffold proteins. Recent data from Caskin1 knockout animals indicated only a mild role of Caskin1 in anxiety and pain perception. In this work, we show that deletion of both Caskins leads to severe deficits in novelty recognition and spatial memory. Ultrastructural analyses revealed a reduction in synaptic profiles and dendritic spine areas of CA1 hippocampal pyramidal neurons of double knockout mice. Loss of Caskin proteins impaired LTP induction in hippocampal slices, while miniature EPSCs in dissociated hippocampal cultures appeared to be unaffected. In cultured Caskin knockout hippocampal neurons, overexpressed Caskin1 was enriched in dendritic spine heads and increased the amount of mushroom-shaped dendritic spines. Chemically induced LTP (cLTP) mediated enlargement of spine heads was augmented in the knockout mice and was not influenced by Caskin1. Immunocytochemistry and immunoprecipitation confirmed that Shank2, a master scaffold of the postsynaptic density, and Caskin1 co-localized within the same complex. Phosphorylation of AMPA receptors was specifically altered by Caskin deficiency and was not elevated by cLTP treatment further. Taken together, our results prove a previously unnoticed postsynaptic role of Caskin scaffold proteins and indicate that Caskins influence learning abilities via regulating spine morphology and AMPA receptor localisation.
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Affiliation(s)
- Norbert Bencsik
- Department of Physiology and Neurobiology, Eötvös Loránd University, Budapest, Hungary
| | - Szilvia Pusztai
- Department of Physiology and Neurobiology, Eötvös Loránd University, Budapest, Hungary
| | - Sándor Borbély
- Department of Physiology and Neurobiology, Eötvös Loránd University, Budapest, Hungary.,Institute of Cognitive Neuroscience and Psychology, Research Centre of Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Anna Fekete
- Institute of Enzymology, Research Centre of Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Metta Dülk
- Institute of Enzymology, Research Centre of Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Viktor Kis
- Department Anatomy, Cell and Developmental Biology, Eötvös Loránd University, Budapest, Hungary
| | - Szabolcs Pesti
- Department Medical Chemistry, Semmelweis University, Budapest, Hungary
| | - Virág Vas
- Institute of Enzymology, Research Centre of Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Attila Szűcs
- Department of Physiology and Neurobiology, Eötvös Loránd University, Budapest, Hungary
| | - László Buday
- Institute of Enzymology, Research Centre of Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary.,Department Medical Chemistry, Semmelweis University, Budapest, Hungary
| | - Katalin Schlett
- Department of Physiology and Neurobiology, Eötvös Loránd University, Budapest, Hungary.
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8
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Liang LY, Patel O, Janes PW, Murphy JM, Lucet IS. Eph receptor signalling: from catalytic to non-catalytic functions. Oncogene 2019; 38:6567-6584. [PMID: 31406248 DOI: 10.1038/s41388-019-0931-2] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 07/23/2019] [Accepted: 07/24/2019] [Indexed: 12/26/2022]
Abstract
Eph receptors, the largest subfamily of receptor tyrosine kinases, are linked with proliferative disease, such as cancer, as a result of their deregulated expression or mutation. Unlike other tyrosine kinases that have been clinically targeted, the development of therapeutics against Eph receptors remains at a relatively early stage. The major reason is the limited understanding on the Eph receptor regulatory mechanisms at a molecular level. The complexity in understanding Eph signalling in cells arises due to following reasons: (1) Eph receptors comprise 14 members, two of which are pseudokinases, EphA10 and EphB6, with relatively uncharacterised function; (2) activation of Eph receptors results in dimerisation, oligomerisation and formation of clustered signalling centres at the plasma membrane, which can comprise different combinations of Eph receptors, leading to diverse downstream signalling outputs; (3) the non-catalytic functions of Eph receptors have been overlooked. This review provides a structural perspective of the intricate molecular mechanisms that drive Eph receptor signalling, and investigates the contribution of intra- and inter-molecular interactions between Eph receptors intracellular domains and their major binding partners. We focus on the non-catalytic functions of Eph receptors with relevance to cancer, which are further substantiated by exploring the role of the two pseudokinase Eph receptors, EphA10 and EphB6. Throughout this review, we carefully analyse and reconcile the existing/conflicting data in the field, to allow researchers to further the current understanding of Eph receptor signalling.
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Affiliation(s)
- Lung-Yu Liang
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Onisha Patel
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Peter W Janes
- Olivia Newton-John Cancer Research Institute, 145 Studley Road, Heidelberg, VIC, 3084, Australia
| | - James M Murphy
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia. .,Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia.
| | - Isabelle S Lucet
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia. .,Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia.
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9
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Katano T, Takao K, Abe M, Yamazaki M, Watanabe M, Miyakawa T, Sakimura K, Ito S. Distribution of Caskin1 protein and phenotypic characterization of its knockout mice using a comprehensive behavioral test battery. Mol Brain 2018; 11:63. [PMID: 30359304 PMCID: PMC6202847 DOI: 10.1186/s13041-018-0407-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 10/14/2018] [Indexed: 01/17/2023] Open
Abstract
Calcium/calmodulin-dependent serine protein kinase (CASK)-interacting protein 1 (Caskin1) is a direct binding partner of the synaptic adaptor protein CASK. Because Caskin1 forms homo-multimers and binds not only CASK but also other neuronal proteins in vitro, it is anticipated to have neural functions; but its exact role in mammals remains unclear. Previously, we showed that the concentration of Caskin1 in the spinal dorsal horn increases under chronic pain. To characterize this protein, we generated Caskin1-knockout (Caskin1-KO) mice and specific anti-Caskin1 antibodies. Biochemical and immunohistochemical analyses demonstrated that Caskin1 was broadly distributed in the whole brain and spinal cord, and that it primarily localized at synapses. To elucidate the neural function of Caskin1 in vivo, we subjected Caskin1-KO mice to comprehensive behavioral analysis. The mutant mice exhibited differences in gait, enhanced nociception, and anxiety-like behavior relative to their wild-type littermates. In addition, the knockouts exhibited strong freezing responses, with or without a cue tone, in contextual and cued-fear conditioning tests as well as low memory retention in the Barnes Maze test. Taken together, these results suggest that Caskin1 contributes to a wide spectrum of behavioral phenotypes, including gait, nociception, memory, and stress response, in broad regions of the central nervous system.
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Affiliation(s)
- Tayo Katano
- Department of Medical Chemistry, Kansai Medical University, Hirakata, 573-1010 Japan
| | - Keizo Takao
- Section of Behavior Patterns, National Institute of Physiological Sciences NINS, Okazaki, Aichi 444-8585 Japan
- Division of Experimental Animal Resource and Development, Life Science Research Center, University of Toyama, Toyama, 930-0194 Japan
| | - Manabu Abe
- Department of Cellular Neurobiology, Brain Research Institute, Niigata University, Niigata, 951-8585 Japan
| | - Maya Yamazaki
- Department of Cellular Neurobiology, Brain Research Institute, Niigata University, Niigata, 951-8585 Japan
- Department of Neurology, University of California, San Francisco, 94158 USA
| | - Masahiko Watanabe
- Department of Anatomy, Hokkaido University School of Medicine, Sapporo, 060-8638 Japan
| | - Tsuyoshi Miyakawa
- Section of Behavior Patterns, National Institute of Physiological Sciences NINS, Okazaki, Aichi 444-8585 Japan
- Division of Systems Medical Science, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Aichi 470-1192 Japan
| | - Kenji Sakimura
- Department of Cellular Neurobiology, Brain Research Institute, Niigata University, Niigata, 951-8585 Japan
| | - Seiji Ito
- Department of Medical Chemistry, Kansai Medical University, Hirakata, 573-1010 Japan
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10
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Denay G, Vachon G, Dumas R, Zubieta C, Parcy F. Plant SAM-Domain Proteins Start to Reveal Their Roles. TRENDS IN PLANT SCIENCE 2017; 22:718-725. [PMID: 28668510 DOI: 10.1016/j.tplants.2017.06.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 06/02/2017] [Accepted: 06/05/2017] [Indexed: 06/07/2023]
Abstract
Proteins often act in complexes assembled via protein-protein interaction domains. The sterile alpha motif (SAM) domain is one of the most prominent interaction domains in animals and is present in proteins of diverse functions. This domain allows head-to-tail closed oligomerisation or polymer formation resulting in homo- and/or heterocomplexes that have been shown to be important for proper protein localisation and function. In plants this domain is also present but has been poorly studied except for recent studies on the LEAFY floral regulator and the tRNA import component (TRIC)1/2 proteins. Here we catalogue SAM domain-containing proteins from arabidopsis (Arabidopsis thaliana), compare plant and other eukaryotic SAM domains, and perform homology modelling to probe plant SAM domain interaction capabilities.
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Affiliation(s)
- Grégoire Denay
- LPCV, CEA, CNRS, INRA, Université Grenoble-Alpes, BIG, 38000 Grenoble, France; Institute for Developmental Genetics, Heinrich-Heine-Universität Düsseldorf, Universitätstraße, D-40225 Düsseldorf, Germany
| | - Gilles Vachon
- LPCV, CEA, CNRS, INRA, Université Grenoble-Alpes, BIG, 38000 Grenoble, France
| | - Renaud Dumas
- LPCV, CEA, CNRS, INRA, Université Grenoble-Alpes, BIG, 38000 Grenoble, France
| | - Chloe Zubieta
- LPCV, CEA, CNRS, INRA, Université Grenoble-Alpes, BIG, 38000 Grenoble, France
| | - François Parcy
- LPCV, CEA, CNRS, INRA, Université Grenoble-Alpes, BIG, 38000 Grenoble, France.
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The SH3 domain of Caskin1 binds to lysophosphatidic acid suggesting a direct role for the lipid in intracellular signaling. Cell Signal 2017; 32:66-75. [PMID: 28104445 DOI: 10.1016/j.cellsig.2017.01.019] [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: 10/10/2016] [Revised: 12/15/2016] [Accepted: 01/14/2017] [Indexed: 01/11/2023]
Abstract
Src homology 3 or SH3 domains constitute one of the most common protein domains in signal transduction, generally characterized by their binding to proline-rich sequences on interacting signaling proteins. Caskin1, a scaffold protein regulating cortical actin filaments, enriched in neural synapses in mammals, has an atypical SH3 domain. Key aromatic residues necessary for ligand binding that are present in canonical SH3 domains are missing from Caskin1 SH3. In concordance, proline-rich interacting partner could not be identified yet. Based on previous reports that several SH3 domains are able to bind phospholipids, we sought for lipid interacting partners of the SH3 domain of human Caskin1. We investigated the signaling-born lysophospholipid mediators, such as lysophosphatidic acid (LPA) and sphingosine-1-phosphate (S1P) as potential binding partners for this SH3 domain. These lipid mediators as first messengers activate G protein-coupled receptors. They also exert several G protein-coupled receptor-independent functions but their intracellular target proteins are mostly unknown. Here we provide evidence that the SH3 domain of human Caskin1 selectively binds to LPA in vitro. The binding strength and stoichiometry depend on the association-state of the lipid, with nanomolar affinity to LPA-containing membraneous surfaces. The amino acids involved in the interaction are located in a β-strand structure and are distinct from those corresponding to the canonical proline-rich ligand-binding groove in the SH3 domain of Src kinase. Our results suggest that the SH3 domain of human Caskin1 is a lipid-binding domain rather than a proline-rich motif interacting domain.
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A lack of peptide binding and decreased thermostability suggests that the CASKIN2 scaffolding protein SH3 domain may be vestigial. BMC STRUCTURAL BIOLOGY 2016; 16:14. [PMID: 27619958 PMCID: PMC5020537 DOI: 10.1186/s12900-016-0065-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 09/07/2016] [Indexed: 11/10/2022]
Abstract
Background CASKIN2 is a neuronal signaling scaffolding protein comprised of multiple ankyrin repeats, two SAM domains, and one SH3 domain. The CASKIN2 SH3 domain for an NMR structural determination because its peptide-binding cleft appeared to deviate from the repertoire of aromatic enriched amino acids that typically bind polyproline-rich sequences. Results The structure demonstrated that two non-canonical basic amino acids (K290/R319) in the binding cleft were accommodated well in the SH3 fold. An K290Y/R319W double mutant restoring the typical aromatic amino acids found in the binding cleft resulted in a 20 °C relative increase in the thermal stability. Considering the reduced stability, we speculated that the CASKIN2 SH3 could be a nonfunctional remnant in this scaffolding protein. Conclusions While the NMR structure demonstrates that the CASKIN2 SH3 domain is folded, its cleft has suffered two substitutions that prevent it from binding typical polyproline ligands. This observation led us to additionally survey and describe other SH3 domains in the Protein Data Bank that may have similarly lost their ability to promote protein-protein interactions. Electronic supplementary material The online version of this article (doi:10.1186/s12900-016-0065-5) contains supplementary material, which is available to authorized users.
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Han KA, Jeon S, Um JW, Ko J. Emergent Synapse Organizers: LAR-RPTPs and Their Companions. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2016; 324:39-65. [PMID: 27017006 DOI: 10.1016/bs.ircmb.2016.01.002] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Leukocyte common antigen-related receptor tyrosine phosphatases (LAR-RPTPs) have emerged as key players that organize various aspects of neuronal development, including axon guidance, neurite extension, and synapse formation and function. Recent research has highlighted the roles of LAR-RPTPs at neuronal synapses in mediating distinct synaptic adhesion pathways through interactions with a host of extracellular ligands and in governing a variety of intracellular signaling cascades through binding to various scaffolds and signaling proteins. In this chapter, we review and update current research progress on the extracellular ligands of LAR-RPTPs, regulation of their extracellular interactions by alternative splicing and heparan sulfates, and their intracellular signaling machineries. In particular, we review structural insights on complexes of LAR-RPTPs with their various ligands. These studies lend support to general molecular mechanisms underlying LAR-RPTP-mediated synaptic adhesion and signaling pathways.
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Affiliation(s)
- K A Han
- Department of Physiology and BK21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, South Korea
| | - S Jeon
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea
| | - J W Um
- Department of Physiology and BK21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, South Korea
| | - J Ko
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea.
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Aquea G, Bresky G, Lancellotti D, Madariaga JA, Zaffiri V, Urzua U, Haberle S, Bernal G. Increased expression of P2RY2, CD248 and EphB1 in gastric cancers from Chilean patients. Asian Pac J Cancer Prev 2014; 15:1931-6. [PMID: 24716914 DOI: 10.7314/apjcp.2014.15.5.1931] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Gastric cancer (GC) ranks as one of the major causes of mortality due to cancer worldwide. In Chile, it is currently the leading cause of cancer death. Identification of novel molecular markers that may help to improve disease diagnosis at early stages is imperative. MATERIALS AND METHODS Using whole-genome DNA microarrays we determined differential mRNA levels in fresh human GC samples compared to adjacent healthy mucosa from the same patients. Genes significantly overexpressed in GC were validated by RT-PCR in a group of 14 GC cases. RESULTS The genes CD248, NSD1, RAB17, ABCG8, Ephb1 and P2RY2 were detected as the top overexpressed in GC biopsies. P2RY2, Ephb1 and CD248 showed the best sensitivity for GC detection with values of 92.9%, 85.7% and 64.3% (p<0.05), respectively. Specificity was 85.7%, 71.4% and 71.4% (p<0.05), for each respectively.
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Affiliation(s)
- Gisela Aquea
- Departamento de Ciencias Biomedicas, Facultad de Medicina, Universidad Catolica del Norte, Coquimbo, Chile E-mail :
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Anjum R, Ayoubian H, Schmitz F. Differential synaptic distribution of the scaffold proteins Cask and Caskin1 in the bovine retina. Mol Cell Neurosci 2014; 62:19-29. [DOI: 10.1016/j.mcn.2014.08.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 07/24/2014] [Accepted: 08/10/2014] [Indexed: 11/26/2022] Open
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LAR-RPTPs: synaptic adhesion molecules that shape synapse development. Trends Cell Biol 2013; 23:465-75. [DOI: 10.1016/j.tcb.2013.07.004] [Citation(s) in RCA: 131] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Revised: 07/07/2013] [Accepted: 07/08/2013] [Indexed: 12/21/2022]
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