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Ricard-Blum S, Couchman JR. Conformations, interactions and functions of intrinsically disordered syndecans. Biochem Soc Trans 2023:BST20221085. [PMID: 37334846 DOI: 10.1042/bst20221085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 06/03/2023] [Accepted: 06/07/2023] [Indexed: 06/21/2023]
Abstract
Syndecans are transmembrane heparan sulfate proteoglycans present on most mammalian cell surfaces. They have a long evolutionary history, a single syndecan gene being expressed in bilaterian invertebrates. Syndecans have attracted interest because of their potential roles in development and disease, including vascular diseases, inflammation and various cancers. Recent structural data is providing important insights into their functions, which are complex, involving both intrinsic signaling through cytoplasmic binding partners and co-operative mechanisms where syndecans form a signaling nexus with other receptors such as integrins and tyrosine kinase growth factor receptors. While the cytoplasmic domain of syndecan-4 has a well-defined dimeric structure, the syndecan ectodomains are intrinsically disordered, which is linked to a capacity to interact with multiple partners. However, it remains to fully establish the impact of glycanation and partner proteins on syndecan core protein conformations. Genetic models indicate that a conserved property of syndecans links the cytoskeleton to calcium channels of the transient receptor potential class, compatible with roles as mechanosensors. In turn, syndecans influence actin cytoskeleton organization to impact motility, adhesion and the extracellular matrix environment. Syndecan clustering with other cell surface receptors into signaling microdomains has relevance to tissue differentiation in development, for example in stem cells, but also in disease where syndecan expression can be markedly up-regulated. Since syndecans have potential as diagnostic and prognostic markers as well as possible targets in some forms of cancer, it remains important to unravel structure/function relationships in the four mammalian syndecans.
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Affiliation(s)
- Sylvie Ricard-Blum
- ICBMS, UMR 5246 CNRS, Universite Claude Bernard Lyon 1, F-69622 Villeurbanne, France
| | - John R Couchman
- Biotech Research & Innovation Center, University of Copenhagen, 2200 Copenhagen, Denmark
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2
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Heumüller AW, Jones AN, Mourão A, Klangwart M, Shi C, Wittig I, Fischer A, Muhly-Reinholz M, Buchmann GK, Dieterich C, Potente M, Braun T, Grote P, Jaé N, Sattler M, Dimmeler S. Locus-Conserved Circular RNA cZNF292 Controls Endothelial Cell Flow Responses. Circ Res 2022; 130:67-79. [PMID: 34789007 DOI: 10.1161/circresaha.121.320029] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 11/17/2021] [Indexed: 01/30/2023]
Abstract
BACKGROUND Circular RNAs (circRNAs) are generated by back splicing of mostly mRNAs and are gaining increasing attention as a novel class of regulatory RNAs that control various cellular functions. However, their physiological roles and functional conservation in vivo are rarely addressed, given the inherent challenges of their genetic inactivation. Here, we aimed to identify locus conserved circRNAs in mice and humans, which can be genetically deleted due to retained intronic elements not contained in the mRNA host gene to eventually address functional conservation. METHODS AND RESULTS Combining published endothelial RNA-sequencing data sets with circRNAs of the circATLAS databank, we identified locus-conserved circRNA retaining intronic elements between mice and humans. CRISPR/Cas9 mediated genetic depletion of the top expressed circRNA cZfp292 resulted in an altered endothelial morphology and aberrant flow alignment in the aorta in vivo. Consistently, depletion of cZNF292 in endothelial cells in vitro abolished laminar flow-induced alterations in cell orientation, paxillin localization and focal adhesion organization. Mechanistically, we identified the protein SDOS (syndesmos) to specifically interact with cZNF292 in endothelial cells by RNA-affinity purification and subsequent mass spectrometry analysis. Silencing of SDOS or its protein binding partner Syndecan-4, or mutation of the SDOS-cZNF292 binding site, prevented laminar flow-induced cytoskeletal reorganization thereby recapitulating cZfp292 knockout phenotypes. CONCLUSIONS Together, our data reveal a hitherto unknown role of cZNF292/cZfp292 in endothelial flow responses, which influences endothelial shape.
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Affiliation(s)
- Andreas W Heumüller
- Institute of Cardiovascular Regeneration (A.W.H., M.K., A.F., M.M.R., P.G., N.J., S.D.), Goethe University, Frankfurt, Germany
- Faculty for Biological Sciences (A.W.H.), Goethe University, Frankfurt, Germany
| | - Alisha N Jones
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany (A.N.J., A.M., M.S.)
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technical University of Munich, Garching, Germany (A.N.J., A.M., M.S.)
| | - André Mourão
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany (A.N.J., A.M., M.S.)
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technical University of Munich, Garching, Germany (A.N.J., A.M., M.S.)
| | - Marius Klangwart
- Institute of Cardiovascular Regeneration (A.W.H., M.K., A.F., M.M.R., P.G., N.J., S.D.), Goethe University, Frankfurt, Germany
| | - Chenyue Shi
- Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (C.S., M.P., T.B.)
| | - Ilka Wittig
- Functional Proteomics, Institute for Cardiovascular Physiology (I.W.), Goethe University, Frankfurt, Germany
- German Center for Cardiovascular Research (DZHK), Frankfurt, Germany (I.W., M.P., T.B., S.D.)
| | - Ariane Fischer
- Institute of Cardiovascular Regeneration (A.W.H., M.K., A.F., M.M.R., P.G., N.J., S.D.), Goethe University, Frankfurt, Germany
| | - Marion Muhly-Reinholz
- Institute of Cardiovascular Regeneration (A.W.H., M.K., A.F., M.M.R., P.G., N.J., S.D.), Goethe University, Frankfurt, Germany
| | - Giulia K Buchmann
- Institute for Cardiovascular Physiology (G.K.B.), Goethe University, Frankfurt, Germany
| | - Christoph Dieterich
- Institute of Cardiovascular Regeneration (A.W.H., M.K., A.F., M.M.R., P.G., N.J., S.D.), Goethe University, Frankfurt, Germany
- Department of Cardiology, Angiology, and Pneumology, University Hospital Heidelberg, Germany (C.D.)
| | - Michael Potente
- Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (C.S., M.P., T.B.)
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Germany (M.P.)
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany (M.P.)
- German Center for Cardiovascular Research (DZHK), Frankfurt, Germany (I.W., M.P., T.B., S.D.)
- Cardio-Pulmonary Institute (CPI), Frankfurt, Germany (M.P., T.B., S.D.)
| | - Thomas Braun
- Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (C.S., M.P., T.B.)
- German Center for Cardiovascular Research (DZHK), Frankfurt, Germany (I.W., M.P., T.B., S.D.)
- Cardio-Pulmonary Institute (CPI), Frankfurt, Germany (M.P., T.B., S.D.)
| | - Phillip Grote
- Institute of Cardiovascular Regeneration (A.W.H., M.K., A.F., M.M.R., P.G., N.J., S.D.), Goethe University, Frankfurt, Germany
| | - Nicolas Jaé
- Institute of Cardiovascular Regeneration (A.W.H., M.K., A.F., M.M.R., P.G., N.J., S.D.), Goethe University, Frankfurt, Germany
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany (A.N.J., A.M., M.S.)
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technical University of Munich, Garching, Germany (A.N.J., A.M., M.S.)
| | - Stefanie Dimmeler
- Institute of Cardiovascular Regeneration (A.W.H., M.K., A.F., M.M.R., P.G., N.J., S.D.), Goethe University, Frankfurt, Germany
- Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (C.S., M.P., T.B.)
- German Center for Cardiovascular Research (DZHK), Frankfurt, Germany (I.W., M.P., T.B., S.D.)
- Cardio-Pulmonary Institute (CPI), Frankfurt, Germany (M.P., T.B., S.D.)
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Botuyan MV, Cui G, Drané P, Oliveira C, Detappe A, Brault ME, Parnandi N, Chaubey S, Thompson JR, Bragantini B, Zhao D, Chapman JR, Chowdhury D, Mer G. Mechanism of 53BP1 activity regulation by RNA-binding TIRR and a designer protein. Nat Struct Mol Biol 2018; 25:591-600. [PMID: 29967538 PMCID: PMC6045459 DOI: 10.1038/s41594-018-0083-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 06/04/2018] [Indexed: 12/25/2022]
Abstract
Dynamic protein interaction networks such as DNA double-strand break (DSB) signaling are modulated by post-translational modifications. The DNA repair factor 53BP1 is a rare example of a protein whose post-translational modification-binding function can be switched on and off. 53BP1 is recruited to DSBs by recognizing histone lysine methylation within chromatin, an activity directly inhibited by the 53BP1-binding protein TIRR. X-ray crystal structures of TIRR and a designer protein bound to 53BP1 now reveal a unique regulatory mechanism in which an intricate binding area centered on an essential TIRR arginine residue blocks the methylated-chromatin-binding surface of 53BP1. A 53BP1 separation-of-function mutation that abolishes TIRR-mediated regulation in cells renders 53BP1 hyperactive in response to DSBs, highlighting the key inhibitory function of TIRR. This 53BP1 inhibition is relieved by TIRR-interacting RNA molecules, providing proof-of-principle of RNA-triggered 53BP1 recruitment to DSBs.
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Affiliation(s)
| | - Gaofeng Cui
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Pascal Drané
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Catarina Oliveira
- Genome Integrity Laboratory, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Alexandre Detappe
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Marie Eve Brault
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nishita Parnandi
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Shweta Chaubey
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - James R Thompson
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Benoît Bragantini
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Debiao Zhao
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - J Ross Chapman
- Genome Integrity Laboratory, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Dipanjan Chowdhury
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
| | - Georges Mer
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA.
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Drané P, Brault ME, Cui G, Meghani K, Chaubey S, Detappe A, Parnandi N, He Y, Zheng XF, Botuyan MV, Kalousi A, Yewdell WT, Münch C, Harper JW, Chaudhuri J, Soutoglou E, Mer G, Chowdhury D. TIRR regulates 53BP1 by masking its histone methyl-lysine binding function. Nature 2017; 543:211-216. [PMID: 28241136 PMCID: PMC5441565 DOI: 10.1038/nature21358] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 01/03/2017] [Indexed: 01/13/2023]
Abstract
P53-binding protein 1 (53BP1) is a multi-functional double-strand break repair protein that is essential for class switch recombination in B lymphocytes and for sensitizing BRCA1-deficient tumours to poly-ADP-ribose polymerase-1 (PARP) inhibitors. Central to all 53BP1 activities is its recruitment to double-strand breaks via the interaction of the tandem Tudor domain with dimethylated lysine 20 of histone H4 (H4K20me2). Here we identify an uncharacterized protein, Tudor interacting repair regulator (TIRR), that directly binds the tandem Tudor domain and masks its H4K20me2 binding motif. Upon DNA damage, the protein kinase ataxia-telangiectasia mutated (ATM) phosphorylates 53BP1 and recruits RAP1-interacting factor 1 (RIF1) to dissociate the 53BP1-TIRR complex. However, overexpression of TIRR impedes 53BP1 function by blocking its localization to double-strand breaks. Depletion of TIRR destabilizes 53BP1 in the nuclear-soluble fraction and alters the double-strand break-induced protein complex centring 53BP1. These findings identify TIRR as a new factor that influences double-strand break repair using a unique mechanism of masking the histone methyl-lysine binding function of 53BP1.
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Affiliation(s)
- Pascal Drané
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, 02115
| | - Marie-Eve Brault
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, 02115
| | - Gaofeng Cui
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905
| | - Khyati Meghani
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, 02115
| | - Shweta Chaubey
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, 02115
| | - Alexandre Detappe
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, 02115
| | - Nishita Parnandi
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, 02115
| | - Yizhou He
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, 02115
| | - Xiao-Feng Zheng
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, 02115
| | | | - Alkmini Kalousi
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France
| | - William T Yewdell
- Immunology Program, Memorial Sloan-Kettering Cancer Center, Gerstner Sloan-Kettering Graduate School, New York, NY 10065; and Immunology and Microbial Pathogenesis Program, Weill-Cornell Medical School, New York, NY 10065
| | - Christian Münch
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - J Wade Harper
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Jayanta Chaudhuri
- Immunology Program, Memorial Sloan-Kettering Cancer Center, Gerstner Sloan-Kettering Graduate School, New York, NY 10065; and Immunology and Microbial Pathogenesis Program, Weill-Cornell Medical School, New York, NY 10065
| | - Evi Soutoglou
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France
| | - Georges Mer
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905
| | - Dipanjan Chowdhury
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, 02115
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
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