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Imoto Y, Xue J, Luo L, Raychaudhuri S, Itoh K, Ma Y, Craft GE, Kwan AH, Ogunmowo TH, Ho A, Mackay JP, Ha T, Watanabe S, Robinson PJ. Dynamin 1xA interacts with Endophilin A1 via its spliced long C-terminus for ultrafast endocytosis. EMBO J 2024; 43:3327-3357. [PMID: 38907032 PMCID: PMC11329700 DOI: 10.1038/s44318-024-00145-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 04/26/2024] [Accepted: 05/24/2024] [Indexed: 06/23/2024] Open
Abstract
Dynamin 1 mediates fission of endocytic synaptic vesicles in the brain and has two major splice variants, Dyn1xA and Dyn1xB, which are nearly identical apart from the extended C-terminal region of Dyn1xA. Despite a similar set of binding partners, only Dyn1xA is enriched at endocytic zones and accelerates vesicle fission during ultrafast endocytosis. Here, we report that Dyn1xA achieves this localization by preferentially binding to Endophilin A1 through a newly defined binding site within its long C-terminal tail extension. Endophilin A1 binds this site at higher affinity than the previously reported site, and the affinity is determined by amino acids within the Dyn1xA tail but outside the binding site. This interaction is regulated by the phosphorylation state of two serine residues specific to the Dyn1xA variant. Dyn1xA and Endophilin A1 colocalize in patches near the active zone, and mutations disrupting Endophilin A binding to the long tail cause Dyn1xA mislocalization and stalled endocytic pits on the plasma membrane during ultrafast endocytosis. Together, these data suggest that the specificity for ultrafast endocytosis is defined by the phosphorylation-regulated interaction of Endophilin A1 with the C-terminal extension of Dyn1xA.
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Affiliation(s)
- Yuuta Imoto
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Jing Xue
- Cell Signalling Unit, Children's Medical Research Institute, The University of Sydney, Locked Bag 23, Wentworthville, 2145, NSW, Australia
| | - Lin Luo
- Institute for Molecular Bioscience, Institute for Molecular Bioscience Centre for Inflammation and Disease Research, and Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Sumana Raychaudhuri
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kie Itoh
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Ye Ma
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - George E Craft
- Cell Signalling Unit, Children's Medical Research Institute, The University of Sydney, Locked Bag 23, Wentworthville, 2145, NSW, Australia
| | - Ann H Kwan
- School of Life and Environmental Sciences and Sydney Nano Institute, University of Sydney, Camperdown, NSW, Australia
| | - Tyler H Ogunmowo
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Annie Ho
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Joel P Mackay
- School of Life and Environmental Sciences, University of Sydney, Camperdown, NSW, 2006, Australia
| | - Taekjip Ha
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD, USA
- Howard Hughes Medical Institute, Baltimore, MD, USA
| | - Shigeki Watanabe
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- The Center for Cell Dynamics, Johns Hopkins University, Baltimore, MD, USA.
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University, School of Medicine, Baltimore, MD, USA.
| | - Phillip J Robinson
- Cell Signalling Unit, Children's Medical Research Institute, The University of Sydney, Locked Bag 23, Wentworthville, 2145, NSW, Australia.
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2
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Jiang A, Kudo K, Gormal RS, Ellis S, Guo S, Wallis TP, Longfield SF, Robinson PJ, Johnson ME, Joensuu M, Meunier FA. Dynamin1 long- and short-tail isoforms exploit distinct recruitment and spatial patterns to form endocytic nanoclusters. Nat Commun 2024; 15:4060. [PMID: 38744819 PMCID: PMC11094030 DOI: 10.1038/s41467-024-47677-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Accepted: 04/09/2024] [Indexed: 05/16/2024] Open
Abstract
Endocytosis requires a coordinated framework of molecular interactions that ultimately lead to the fission of nascent endocytic structures. How cytosolic proteins such as dynamin concentrate at discrete sites that are sparsely distributed across the plasma membrane remains poorly understood. Two dynamin-1 major splice variants differ by the length of their C-terminal proline-rich region (short-tail and long-tail). Using sptPALM in PC12 cells, neurons and MEF cells, we demonstrate that short-tail dynamin-1 isoforms ab and bb display an activity-dependent recruitment to the membrane, promptly followed by their concentration into nanoclusters. These nanoclusters are sensitive to both Calcineurin and dynamin GTPase inhibitors, and are larger, denser, and more numerous than that of long-tail isoform aa. Spatiotemporal modelling confirms that dynamin-1 isoforms perform distinct search patterns and undergo dimensional reduction to generate endocytic nanoclusters, with short-tail isoforms more robustly exploiting lateral trapping in the generation of nanoclusters compared to the long-tail isoform.
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Affiliation(s)
- Anmin Jiang
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Kye Kudo
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Rachel S Gormal
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Sevannah Ellis
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Sikao Guo
- Department of Biophysics, Johns Hopkins University, 3400 N Charles St, Baltimore, MD, 21218, USA
| | - Tristan P Wallis
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Shanley F Longfield
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Phillip J Robinson
- Cell Signalling Unit, Children's Medical Research Institute, The University of Sydney, Sydney, NSW, 2145, Australia
| | - Margaret E Johnson
- Department of Biophysics, Johns Hopkins University, 3400 N Charles St, Baltimore, MD, 21218, USA
| | - Merja Joensuu
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia.
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, 4072, Australia.
| | - Frédéric A Meunier
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia.
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia.
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3
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Imoto Y, Xue J, Luo L, Raychaudhuri S, Itoh K, Ma Y, Craft GE, Kwan AH, Mackay JP, Ha T, Watanabe S, Robinson PJ. Dynamin 1xA interacts with Endophilin A1 via its spliced long C-terminus for ultrafast endocytosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.21.558797. [PMID: 37790502 PMCID: PMC10542163 DOI: 10.1101/2023.09.21.558797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Dynamin 1 (Dyn1) has two major splice variants, xA and xB, with unique C-terminal extensions of 20 and 7 amino acids, respectively. Of these, only Dyn1xA is enriched at endocytic zones and accelerates vesicle fission during ultrafast endocytosis. Here, we report that the long tail variant, Dyn1xA, achieves this localization by preferentially binding to Endophilin A through a newly defined Class II binding site overlapping with its extension, at a site spanning the splice boundary. Endophilin binds this site at higher affinity than the previously reported site, and this affinity is determined by amino acids outside the binding sites acting as long distance elements within the xA tail. Their interaction is regulated by the phosphorylation state of two serine residues specific to the xA variant. Dyn1xA and Endophilin colocalize in patches near the active zone of synapses. Mutations selectively disrupting Endophilin binding to the long extension cause Dyn1xA mislocalization along axons. In these mutants, endocytic pits are stalled on the plasma membrane during ultrafast endocytosis. These data suggest that the specificity for ultrafast endocytosis is defined by the phospho-regulated interaction of Endophilin A through a newly identified site of Dyn1xA's long tail.
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Affiliation(s)
- Yuuta Imoto
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore MD, USA
| | - Jing Xue
- Cell Signalling Unit, Children’s Medical Research Institute, The University of Sydney, Locked Bag 23, Wentworthville 2145, NSW, Australia
| | - Lin Luo
- Institute for Molecular Bioscience, Institute for Molecular Bioscience Centre for Inflammation and Disease Research, and Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Sumana Raychaudhuri
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore MD, USA
| | - Kie Itoh
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore MD, USA
| | - Ye Ma
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - George E. Craft
- Cell Signalling Unit, Children’s Medical Research Institute, The University of Sydney, Locked Bag 23, Wentworthville 2145, NSW, Australia
| | - Ann H. Kwan
- School of Life and Environmental Sciences and Sydney Nano Institute, University of Sydney, New South Wales, Australia
| | - Joel P. Mackay
- School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia
| | - Taekjip Ha
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD, USA
- Howard Hughes Medical Institute, Baltimore, MD, USA
| | - Shigeki Watanabe
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore MD, USA
- The Center for Cell Dynamics, Johns Hopkins University, Baltimore, MD, USA
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University, School of Medicine, Baltimore MD, USA
| | - Phillip J. Robinson
- Cell Signalling Unit, Children’s Medical Research Institute, The University of Sydney, Locked Bag 23, Wentworthville 2145, NSW, Australia
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Wu X, Qiu H, Zhang M. Interactions between Membraneless Condensates and Membranous Organelles at the Presynapse: A Phase Separation View of Synaptic Vesicle Cycle. J Mol Biol 2023; 435:167629. [PMID: 35595170 DOI: 10.1016/j.jmb.2022.167629] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/03/2022] [Accepted: 05/04/2022] [Indexed: 02/04/2023]
Abstract
Action potential-induced neurotransmitter release in presynaptic boutons involves coordinated actions of a large list of proteins that are associated directly or indirectly with membrane structures including synaptic vesicles and plasma membranes. These proteins are often highly abundant in different synaptic bouton sub-compartments, and they rarely act alone. Instead, these proteins interact with each other forming intricate and distinct molecular complexes. Many of these complexes form condensed clusters on membrane surfaces. This review summarizes findings in recent years showing that many of presynaptic protein complex assemblies are formed via phase separation. These protein condensates extensively interact with lipid membranes via distinct modes, forming various mesoscale structures by different mode of organizations between membraneless condensates and membranous organelles. We discuss that such mesoscale interactions could have deep implications on mobilization, exocytosis, and retrieval of synaptic vesicles.
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Affiliation(s)
- Xiandeng Wu
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Hua Qiu
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Mingjie Zhang
- Greater Bay Biomedical Innocenter, Shenzhen Bay Laboratory, Shenzhen 518036, China; School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China.
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Imoto Y, Raychaudhuri S, Ma Y, Fenske P, Sandoval E, Itoh K, Blumrich EM, Matsubayashi HT, Mamer L, Zarebidaki F, Söhl-Kielczynski B, Trimbuch T, Nayak S, Iwasa JH, Liu J, Wu B, Ha T, Inoue T, Jorgensen EM, Cousin MA, Rosenmund C, Watanabe S. Dynamin is primed at endocytic sites for ultrafast endocytosis. Neuron 2022; 110:2815-2835.e13. [PMID: 35809574 PMCID: PMC9464723 DOI: 10.1016/j.neuron.2022.06.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 03/24/2022] [Accepted: 06/09/2022] [Indexed: 02/06/2023]
Abstract
Dynamin mediates fission of vesicles from the plasma membrane during endocytosis. Typically, dynamin is recruited from the cytosol to endocytic sites, requiring seconds to tens of seconds. However, ultrafast endocytosis in neurons internalizes vesicles as quickly as 50 ms during synaptic vesicle recycling. Here, we demonstrate that Dynamin 1 is pre-recruited to endocytic sites for ultrafast endocytosis. Specifically, Dynamin 1xA, a splice variant of Dynamin 1, interacts with Syndapin 1 to form molecular condensates on the plasma membrane. Single-particle tracking of Dynamin 1xA molecules confirms the liquid-like property of condensates in vivo. When Dynamin 1xA is mutated to disrupt its interaction with Syndapin 1, the condensates do not form, and consequently, ultrafast endocytosis slows down by 100-fold. Mechanistically, Syndapin 1 acts as an adaptor by binding the plasma membrane and stores Dynamin 1xA at endocytic sites. This cache bypasses the recruitment step and accelerates endocytosis at synapses.
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Affiliation(s)
- Yuuta Imoto
- Department of Cell Biology, Johns Hopkins University, Baltimore, MD 21205, USA.
| | - Sumana Raychaudhuri
- Department of Cell Biology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Ye Ma
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Pascal Fenske
- Institute of Neurophysiology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Eduardo Sandoval
- Department of Cell Biology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Kie Itoh
- Department of Cell Biology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Eva-Maria Blumrich
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, Scotland EH8 9XD, UK; The Muir Maxwell Epilepsy Centre, University of Edinburgh, Edinburgh, Scotland EH8 9XD, UK; Simons Initiatives for the Developing Brain, University of Edinburgh, Edinburgh, Scotland EH8 9XD, UK
| | - Hideaki T Matsubayashi
- Department of Cell Biology, Johns Hopkins University, Baltimore, MD 21205, USA; The Center for Cell Dynamics, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Lauren Mamer
- Institute of Neurophysiology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Fereshteh Zarebidaki
- Institute of Neurophysiology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | | | - Thorsten Trimbuch
- Institute of Neurophysiology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Shraddha Nayak
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84112-0840, USA
| | - Janet H Iwasa
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84112-0840, USA
| | - Jian Liu
- Department of Cell Biology, Johns Hopkins University, Baltimore, MD 21205, USA; Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, Scotland EH8 9XD, UK
| | - Bin Wu
- The Center for Cell Dynamics, Johns Hopkins University, Baltimore, MD 21205, USA; Solomon H. Snyder Department of Neuroscience, Johns Hopkins University, Baltimore, MD 21205, USA; Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Taekjip Ha
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA; Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD 21205, USA; Howard Hughes Medical Institute, Baltimore, MD 21205, USA
| | - Takanari Inoue
- Department of Cell Biology, Johns Hopkins University, Baltimore, MD 21205, USA; The Center for Cell Dynamics, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Erik M Jorgensen
- HHMI, Department of Biology, University of Utah, Salt Lake City, UT 84112-0840, USA
| | - Michael A Cousin
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, Scotland EH8 9XD, UK; The Muir Maxwell Epilepsy Centre, University of Edinburgh, Edinburgh, Scotland EH8 9XD, UK; Simons Initiatives for the Developing Brain, University of Edinburgh, Edinburgh, Scotland EH8 9XD, UK
| | - Christian Rosenmund
- Institute of Neurophysiology, Charité Universitätsmedizin Berlin, Berlin, Germany.
| | - Shigeki Watanabe
- Department of Cell Biology, Johns Hopkins University, Baltimore, MD 21205, USA; The Center for Cell Dynamics, Johns Hopkins University, Baltimore, MD 21205, USA; Solomon H. Snyder Department of Neuroscience, Johns Hopkins University, Baltimore, MD 21205, USA.
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The temporal profile of activity-dependent presynaptic phospho-signalling reveals long-lasting patterns of poststimulus regulation. PLoS Biol 2019; 17:e3000170. [PMID: 30822303 PMCID: PMC6415872 DOI: 10.1371/journal.pbio.3000170] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 03/13/2019] [Indexed: 12/23/2022] Open
Abstract
Depolarization of presynaptic terminals stimulates calcium influx, which evokes neurotransmitter release and activates phosphorylation-based signalling. Here, we present the first global temporal profile of presynaptic activity-dependent phospho-signalling, which includes two KCl stimulation levels and analysis of the poststimulus period. We profiled 1,917 regulated phosphopeptides and bioinformatically identified six temporal patterns of co-regulated proteins. The presynaptic proteins with large changes in phospho-status were again prominently regulated in the analysis of 7,070 activity-dependent phosphopeptides from KCl-stimulated cultured hippocampal neurons. Active zone scaffold proteins showed a high level of activity-dependent phospho-regulation that far exceeded the response from postsynaptic density scaffold proteins. Accordingly, bassoon was identified as the major target of neuronal phospho-signalling. We developed a probabilistic computational method, KinSwing, which matched protein kinase substrate motifs to regulated phosphorylation sites to reveal underlying protein kinase activity. This approach allowed us to link protein kinases to profiles of co-regulated presynaptic protein networks. Ca2+- and calmodulin-dependent protein kinase IIα (CaMKIIα) responded rapidly, scaled with stimulus strength, and had long-lasting activity. Mitogen-activated protein kinase (MAPK)/extracellular signal–regulated kinase (ERK) was the main protein kinase predicted to control a distinct and significant pattern of poststimulus up-regulation of phosphorylation. This work provides a unique resource of activity-dependent phosphorylation sites of synaptosomes and neurons, the vast majority of which have not been investigated with regard to their functional impact. This resource will enable detailed characterization of the phospho-regulated mechanisms impacting the plasticity of neurotransmitter release. Analysis of activity-dependent phosphorylation-based signalling in synaptosomes revealed six patterns of long-lasting presynaptic regulation from 1,917 phosphopeptides. The authors identified patterns most likely to be regulated by CamKII and MAPK/ERK and showed the active zone scaffold protein bassoon to be a major signalling target. Neurobiological processes are altered by linking neuronal activity to regulated changes in protein phosphorylation levels that influence protein function. Although some of the major targets of activity-dependent phospho-signalling have been identified, a large number of substrates remain unknown. Here, we have screened systematically for these substrates and extended the list from hundreds to thousands of phosphorylation sites, thereby providing a new depth of understanding. We monitored phospho-signalling for 15 min after the stimulation, which to our knowledge had not been attempted at a large scale. We focused on presynaptic protein substrates of phospho-signalling by isolating the presynaptic terminal. We also stimulated hippocampal neurons but did not monitor the poststimulus. Although the phospho-signalling is immensely complex, the findings could be simplified through data exploration. We identified distinct patterns of presynaptic phospho-regulation across the time course that may constitute co-regulated protein networks. In addition, we found a subset of proteins that had many more phosphorylation sites than the average and high-magnitude responses, implying major signalling or functional roles for these proteins. We also determined the likely protein kinases with the strongest responses to the stimulus at different times using KinSwing, a computational tool that we developed. This resource reveals a new depth of activity-dependent phospho-signalling and identifies major signalling targets, major protein kinases, and co-regulated phosphoprotein networks.
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7
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Abstract
Clathrin-mediated endocytosis (CME) is the major endocytic pathway in mammalian cells. It is responsible for the uptake of transmembrane receptors and transporters, for remodeling plasma membrane composition in response to environmental changes, and for regulating cell surface signaling. CME occurs via the assembly and maturation of clathrin-coated pits that concentrate cargo as they invaginate and pinch off to form clathrin-coated vesicles. In addition to the major coat proteins, clathrin triskelia and adaptor protein complexes, CME requires a myriad of endocytic accessory proteins and phosphatidylinositol lipids. CME is regulated at multiple steps-initiation, cargo selection, maturation, and fission-and is monitored by an endocytic checkpoint that induces disassembly of defective pits. Regulation occurs via posttranslational modifications, allosteric conformational changes, and isoform and splice-variant differences among components of the CME machinery, including the GTPase dynamin. This review summarizes recent findings on the regulation of CME and the evolution of this complex process.
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Affiliation(s)
- Marcel Mettlen
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA; , , , ,
| | - Ping-Hung Chen
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA; , , , ,
| | - Saipraveen Srinivasan
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA; , , , ,
| | - Gaudenz Danuser
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA; , , , , .,Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, Texas 75235, USA
| | - Sandra L Schmid
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA; , , , ,
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Krishnan S, Collett M, Robinson PJ. SH3 Domains Differentially Stimulate Distinct Dynamin I Assembly Modes and G Domain Activity. PLoS One 2015; 10:e0144609. [PMID: 26659814 PMCID: PMC4687643 DOI: 10.1371/journal.pone.0144609] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 11/20/2015] [Indexed: 11/19/2022] Open
Abstract
Dynamin I is a highly regulated GTPase enzyme enriched in nerve terminals which mediates vesicle fission during synaptic vesicle endocytosis. One regulatory mechanism involves its interactions with proteins containing Src homology 3 (SH3) domains. At least 30 SH3 domain-containing proteins bind dynamin at its proline-rich domain (PRD). Those that stimulate dynamin activity act by promoting its oligomerisation. We undertook a systematic parallel screening of 13 glutathione-S-transferase (GST)-tagged endocytosis-related SH3 domains on dynamin binding, GTPase activity and oligomerisation. No correlation was found between dynamin binding and their potency to stimulate GTPase activity. There was limited correlation between the extent of their ability to stimulate dynamin activity and the level of oligomerisation, indicating an as yet uncharacterised allosteric coupling of the PRD and G domain. We examined the two variants, dynamin Iab and Ibb, which differ in the alternately splice middle domain α2 helix. They responded differently to the panel of SH3s, with the extent of stimulation between the splice variants varying greatly between the SH3s. This study reveals that SH3 binding can act as a heterotropic allosteric regulator of the G domain via the middle domain α2 helix, suggesting an involvement of this helix in communicating the PRD-mediated allostery. This indicates that SH3 binding both stabilises multiple conformations of the tetrameric building block of dynamin, and promotes assembly of dynamin-SH3 complexes with distinct rates of GTP hydrolysis.
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Affiliation(s)
- Sai Krishnan
- Cell Signalling Unit, Children’s Medical Research Institute, The University of Sydney, Westmead, New South Wales, Australia
| | - Michael Collett
- Cell Signalling Unit, Children’s Medical Research Institute, The University of Sydney, Westmead, New South Wales, Australia
| | - Phillip J. Robinson
- Cell Signalling Unit, Children’s Medical Research Institute, The University of Sydney, Westmead, New South Wales, Australia
- * E-mail:
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9
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Melo-Braga MN, Meyer M, Zeng X, Larsen MR. Characterization of human neural differentiation from pluripotent stem cells using proteomics/PTMomics-Current state-of-the-art and challenges. Proteomics 2015; 15:656-74. [DOI: 10.1002/pmic.201400388] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Revised: 11/11/2014] [Accepted: 11/19/2014] [Indexed: 01/18/2023]
Affiliation(s)
- Marcella Nunes Melo-Braga
- Department of Biochemistry and Molecular Biology; University of Southern Denmark; Odense Denmark
- Center for Clinical Proteomics; University of Southern Denmark; Odense Denmark
| | - Morten Meyer
- Department of Neurobiology Research; Institute of Molecular Medicine; University of Southern Denmark; Odense Denmark
| | | | - Martin Røssel Larsen
- Department of Biochemistry and Molecular Biology; University of Southern Denmark; Odense Denmark
- Center for Clinical Proteomics; University of Southern Denmark; Odense Denmark
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10
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The ∼ 16 kDa C-terminal sequence of clathrin assembly protein AP180 is essential for efficient clathrin binding. PLoS One 2014; 9:e110557. [PMID: 25329427 PMCID: PMC4203807 DOI: 10.1371/journal.pone.0110557] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2014] [Accepted: 09/22/2014] [Indexed: 11/19/2022] Open
Abstract
Brain-specific AP180 is present in clathrin coats at equal concentration to the adapter complex, AP2, and assembles clathrin faster than any other protein in vitro. Both AP180 and its ubiquitously expressed homolog clathrin assembly lymphoid myeloid leukemia protein (CALM) control vesicle size and shape in clathrin mediated endocytosis. The clathrin assembly role of AP180 is mediated by a long disordered C-terminal assembly domain. Within this assembly domain, a central acidic clathrin and adapter binding (CLAP) sub-domain contains all of the known short binding motifs for clathrin and AP2. The role of the remaining ∼ 16 kDa C-terminal sequence has not been clear. We show that this sequence has a separate function in ensuring efficient binding of clathrin, based on in vitro binding and ex vivo transferrin uptake assays. Sequence alignment suggests the C-terminal sub-domain is conserved in CALM.
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11
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Chen X, Shi SP, Suo SB, Xu HD, Qiu JD. Proteomic analysis and prediction of human phosphorylation sites in subcellular level reveal subcellular specificity. Bioinformatics 2014; 31:194-200. [DOI: 10.1093/bioinformatics/btu598] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
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12
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Engholm-Keller K, Larsen MR. Technologies and challenges in large-scale phosphoproteomics. Proteomics 2013; 13:910-31. [PMID: 23404676 DOI: 10.1002/pmic.201200484] [Citation(s) in RCA: 130] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Revised: 01/18/2013] [Accepted: 01/31/2013] [Indexed: 12/23/2022]
Abstract
Phosphorylation, the reversible addition of a phosphate group to amino acid side chains of proteins, is a fundamental regulator of protein activity, stability, and molecular interactions. Most cellular processes, such as inter- and intracellular signaling, protein synthesis, degradation, and apoptosis, rely on phosphorylation. This PTM is thus involved in many diseases, rendering localization and assessment of extent of phosphorylation of major scientific interest. MS-based phosphoproteomics, which aims at describing all phosphorylation sites in a specific type of cell, tissue, or organism, has become the main technique for discovery and characterization of phosphoproteins in a nonhypothesis driven fashion. In this review, we describe methods for state-of-the-art MS-based analysis of protein phosphorylation as well as the strategies employed in large-scale phosphoproteomic experiments with focus on the various challenges and limitations this field currently faces.
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Affiliation(s)
- Kasper Engholm-Keller
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
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13
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Mallozzi C, D'Amore C, Camerini S, Macchia G, Crescenzi M, Petrucci TC, Di Stasi AMM. Phosphorylation and nitration of tyrosine residues affect functional properties of Synaptophysin and Dynamin I, two proteins involved in exo-endocytosis of synaptic vesicles. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2013; 1833:110-21. [DOI: 10.1016/j.bbamcr.2012.10.022] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Revised: 10/08/2012] [Accepted: 10/21/2012] [Indexed: 12/14/2022]
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14
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Xie W, Adayev T, Zhu H, Wegiel J, Wieraszko A, Hwang YW. Activity-Dependent Phosphorylation of Dynamin 1 at Serine 857. Biochemistry 2012; 51:6786-96. [DOI: 10.1021/bi2017798] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Wen Xie
- Department of Biology, College of Staten Island, City University of New York, Staten Island, New York 10314,
United States
| | | | | | | | - Andrzej Wieraszko
- Department of Biology, College of Staten Island, City University of New York, Staten Island, New York 10314,
United States
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15
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The Rhodadyns, a New Class of Small Molecule Inhibitors of Dynamin GTPase Activity. ACS Med Chem Lett 2012; 3:352-6. [PMID: 24900478 DOI: 10.1021/ml200284s] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2011] [Accepted: 03/26/2012] [Indexed: 02/04/2023] Open
Abstract
Six focused rhodanine-based libraries, 60 compounds in total, were synthesized and evaluated as potential dynamin I GTPase inhibitors. Twenty-six were more potent than the lead compound with 13 returning IC50 values ≤10 μM, making the Rhodadyn series among the most active dynamin inhibitors reported. Two analogues were highly effective at blocking receptor-mediated endocytosis: C10 and D10 with IC50(RME) = 7.0 ± 2.2 and 5.9 ± 1.0 μM, respectively. These compounds are equipotent with the best reported in-cell dynamin inhibitors.
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16
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Evans C, Noirel J, Ow SY, Salim M, Pereira-Medrano AG, Couto N, Pandhal J, Smith D, Pham TK, Karunakaran E, Zou X, Biggs CA, Wright PC. An insight into iTRAQ: where do we stand now? Anal Bioanal Chem 2012; 404:1011-27. [PMID: 22451173 DOI: 10.1007/s00216-012-5918-6] [Citation(s) in RCA: 223] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2012] [Revised: 02/28/2012] [Accepted: 02/29/2012] [Indexed: 01/09/2023]
Abstract
The iTRAQ (isobaric tags for relative and absolute quantification) technique is widely employed in proteomic workflows requiring relative quantification. Here, we review the iTRAQ literature; in particular, we focus on iTRAQ usage in relation to other commonly used quantitative techniques e.g. stable isotope labelling in culture (SILAC), label-free methods and selected reaction monitoring (SRM). As a result, we identify several issues arising with respect to iTRAQ. Perhaps frustratingly, iTRAQ's attractiveness has been undermined by a number of technical and analytical limitations: it may not be truly quantitative, as the changes in abundance reported will generally be underestimated. We discuss weaknesses and strengths of iTRAQ as a methodology for relative quantification in the light of this and other technical issues. We focus on technical developments targeted at iTRAQ accuracy and precision, use of 4-plex over 8-plex reagents and application of iTRAQ to post-translational modification (PTM) workflows. We also discuss iTRAQ in relation to label-free approaches, to which iTRAQ is losing ground.
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Affiliation(s)
- Caroline Evans
- The ChELSI Institute, Chemical and Biological Engineering, The University of Sheffield, Sheffield, UK
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17
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Xue J, Graham ME, Novelle AE, Sue N, Gray N, McNiven MA, Smillie KJ, Cousin MA, Robinson PJ. Calcineurin selectively docks with the dynamin Ixb splice variant to regulate activity-dependent bulk endocytosis. J Biol Chem 2011; 286:30295-30303. [PMID: 21730063 DOI: 10.1074/jbc.m111.273110] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Depolarization of nerve terminals stimulates rapid dephosphorylation of two isoforms of dynamin I (dynI), mediated by the calcium-dependent phosphatase calcineurin (CaN). Dephosphorylation at the major phosphorylation sites Ser-774/778 promotes a dynI-syndapin I interaction for a specific mode of synaptic vesicle endocytosis called activity-dependent bulk endocytosis (ADBE). DynI has two main splice variants at its extreme C terminus, long or short (dynIxa and dynIxb) varying only by 20 (xa) or 7 (xb) residues. Recombinant GST fusion proteins of dynIxa and dynIxb proline-rich domains (PRDs) were used to pull down interacting proteins from rat brain nerve terminals. Both bound equally to syndapin, but dynIxb PRD exclusively bound to the catalytic subunit of CaNA, which recruited CaNB. Binding of CaN was increased in the presence of calcium and was accompanied by further recruitment of calmodulin. Point mutations showed that the entire C terminus of dynIxb is a CaN docking site related to a conserved CaN docking motif (PXIXI(T/S)). This sequence is unique to dynIxb among all other dynamin variants or genes. Peptide mimetics of the dynIxb tail blocked CaN binding in vitro and selectively inhibited depolarization-evoked dynI dephosphorylation in nerve terminals but not of other dephosphins. Therefore, docking to dynIxb is required for the regulation of both dynI splice variants, yet it does not regulate the phosphorylation cycle of other dephosphins. The peptide blocked ADBE, but not clathrin-mediated endocytosis of synaptic vesicles. Our results indicate that Ca(2+) influx regulates assembly of a fully active CaN-calmodulin complex selectively on the tail of dynIxb and that the complex is recruited to sites of ADBE in nerve terminals.
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Affiliation(s)
- Jing Xue
- Cell Signalling Unit, Children's Medical Research Institute, University of Sydney, Locked Bag 23, Wentworthville 2145, New South Wales, Australia
| | - Mark E Graham
- Cell Signalling Unit, Children's Medical Research Institute, University of Sydney, Locked Bag 23, Wentworthville 2145, New South Wales, Australia
| | - Aimee E Novelle
- Cell Signalling Unit, Children's Medical Research Institute, University of Sydney, Locked Bag 23, Wentworthville 2145, New South Wales, Australia
| | - Nancy Sue
- Cell Signalling Unit, Children's Medical Research Institute, University of Sydney, Locked Bag 23, Wentworthville 2145, New South Wales, Australia
| | - Noah Gray
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota 55905
| | - Mark A McNiven
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota 55905
| | - Karen J Smillie
- Membrane Biology Group, Centre for Integrative Physiology, University of Edinburgh, George Square, Edinburgh EH8 9XD, United Kingdom
| | - Michael A Cousin
- Membrane Biology Group, Centre for Integrative Physiology, University of Edinburgh, George Square, Edinburgh EH8 9XD, United Kingdom
| | - Phillip J Robinson
- Cell Signalling Unit, Children's Medical Research Institute, University of Sydney, Locked Bag 23, Wentworthville 2145, New South Wales, Australia.
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18
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Kim J, Kim JS, Kim HE, Jeon YJ, Kim DW, Soh Y, Seo KS, Lee HK, Choi NJ, Chung HM, Lee DS, Chae JI. Proteomic analysis of phosphotyrosyl proteins in human embryonic stem cell-derived neural stem cells. Neurosci Lett 2011; 499:158-63. [PMID: 21640791 DOI: 10.1016/j.neulet.2011.05.039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2011] [Revised: 05/04/2011] [Accepted: 05/17/2011] [Indexed: 01/07/2023]
Abstract
Phosphorylation can reveal essential cell functions, such as cell differentiation, signal transduction, metabolic maintenance and cell division. The aim of this study was to investigate phosphorylated protein expression changes during neuronal lineage differentiation from hESCs. To measure the phosphorylated protein expression change during neuronal differentiation, we performed a comparative phosphoproteome analysis using 2-DE after MALDI-TOF MS and an MS/MS protein identification method, making a comparison between neural lineage differentiating cells and normal embryoid bodies (EBs) differentiated from human embryonic stem cells (hESCs) and profiling constituent phosphorylated proteins. Of 36 differentially expressed protein spots, 12 spots were shown to be up-regulated in differentiating neural cells. Specifically, the 7 up-regulated proteins of the 12 have potential roles in neuronal differentiation or neuronal damage recovery, including ACTB, heterogeneous nuclear ribonucleoprotein A2B1 (hnRNP A2B1), heterogeneous nuclear ribonucleoprotein L (hnRNP L), SET, chaperonin-containing TCP-1, vimentin and voltage-dependent anion channel protein 1 (VDAC1). These proteins are discussed further below.
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Affiliation(s)
- Jumi Kim
- CHA Bio & Diostech Co., Ltd., 606-16 Yeoksam 1 dong, Gangnam gu, Seoul 135-907, Republic of Korea
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Graham ME, Thaysen-Andersen M, Bache N, Craft GE, Larsen MR, Packer NH, Robinson PJ. A novel post-translational modification in nerve terminals: O-linked N-acetylglucosamine phosphorylation. J Proteome Res 2011; 10:2725-33. [PMID: 21500857 DOI: 10.1021/pr1011153] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein phosphorylation and glycosylation are the most common post-translational modifications observed in biology, frequently on the same protein. Assembly protein AP180 is a synapse-specific phosphoprotein and O-linked beta-N-acetylglucosamine (O-GlcNAc) modified glycoprotein. AP180 is involved in the assembly of clathrin coated vesicles in synaptic vesicle endocytosis. Unlike other types of O-glycosylation, O-GlcNAc is nucleocytoplasmic and reversible. It was thought to be a terminal modification, that is, the O-GlcNAc was not found to be additionally modified in any way. We now show that AP180 purified from rat brain contains a phosphorylated O-GlcNAc (O-GlcNAc-P) within a highly conserved sequence. O-GlcNAc or O-GlcNAc-P, but not phosphorylation alone, was found at Thr-310. Analysis of synthetic GlcNAc-6-P produced identical fragmentation products to GlcNAc-P from AP180. Direct O-linkage of GlcNAc-P to a Thr residue was confirmed by electron transfer dissociation MS. A second AP180 tryptic peptide was also glycosyl phosphorylated, but the site of modification was not assigned. Sequence similarities suggest there may be a common motif within AP180 involving glycosyl phosphorylation and dual flanking phosphorylation sites within 4 amino acid residues. This novel type of protein glycosyl phosphorylation adds a new signaling mechanism to the regulation of neurotransmission and more complexity to the study of O-GlcNAc modification.
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Affiliation(s)
- Mark E Graham
- Cell Signalling Unit, Children's Medical Research Institute, The University of Sydney, Westmead, Australia.
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20
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Kozlov SV, Graham ME, Jakob B, Tobias F, Kijas AW, Tanuji M, Chen P, Robinson PJ, Taucher-Scholz G, Suzuki K, So S, Chen D, Lavin MF. Autophosphorylation and ATM activation: additional sites add to the complexity. J Biol Chem 2011; 286:9107-19. [PMID: 21149446 PMCID: PMC3059052 DOI: 10.1074/jbc.m110.204065] [Citation(s) in RCA: 152] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2010] [Indexed: 12/18/2022] Open
Abstract
The recognition and signaling of DNA double strand breaks involves the participation of multiple proteins, including the protein kinase ATM (mutated in ataxia-telangiectasia). ATM kinase is activated in the vicinity of the break and is recruited to the break site by the Mre11-Rad50-Nbs1 complex, where it is fully activated. In human cells, the activation process involves autophosphorylation on three sites (Ser(367), Ser(1893), and Ser(1981)) and acetylation on Lys(3016). We now describe the identification of a new ATM phosphorylation site, Thr(P)(1885) and an additional autophosphorylation site, Ser(P)(2996), that is highly DNA damage-inducible. We also confirm that human and murine ATM share five identical phosphorylation sites. We targeted the ATM phosphorylation sites, Ser(367) and Ser(2996), for further study by generating phosphospecific antibodies against these sites and demonstrated that phosphorylation of both was rapidly induced by radiation. These phosphorylations were abolished by a specific inhibitor of ATM and were dependent on ATM and the Mre11-Rad50-Nbs1 complex. As found for Ser(P)(1981), ATM phosphorylated at Ser(367) and Ser(2996) localized to sites of DNA damage induced by radiation, but ATM recruitment was not dependent on phosphorylation at these sites. Phosphorylation at Ser(367) and Ser(2996) was functionally important because mutant forms of ATM were defective in correcting the S phase checkpoint defect and restoring radioresistance in ataxia-telangiectasia cells. These data provide further support for the importance of autophosphorylation in the activation and function of ATM in vivo.
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Affiliation(s)
- Sergei V. Kozlov
- From Radiation Biology and Oncology, Queensland Institute of Medical Research, Brisbane, Queensland 4029, Australia
| | - Mark E. Graham
- the Children's Medical Research Institute, University of Sydney, Westmead, New South Wales 2145, Australia
| | - Burkhard Jakob
- GSI Helmholtzzentrum für Schwerionenforschung GmbH, Biophysik, Planckstrasse 1, D-64291 Darmstadt, Germany
| | - Frank Tobias
- GSI Helmholtzzentrum für Schwerionenforschung GmbH, Biophysik, Planckstrasse 1, D-64291 Darmstadt, Germany
| | - Amanda W. Kijas
- From Radiation Biology and Oncology, Queensland Institute of Medical Research, Brisbane, Queensland 4029, Australia
| | - Marcel Tanuji
- From Radiation Biology and Oncology, Queensland Institute of Medical Research, Brisbane, Queensland 4029, Australia
| | - Philip Chen
- From Radiation Biology and Oncology, Queensland Institute of Medical Research, Brisbane, Queensland 4029, Australia
| | - Phillip J. Robinson
- the Children's Medical Research Institute, University of Sydney, Westmead, New South Wales 2145, Australia
| | - Gisela Taucher-Scholz
- GSI Helmholtzzentrum für Schwerionenforschung GmbH, Biophysik, Planckstrasse 1, D-64291 Darmstadt, Germany
| | - Keiji Suzuki
- the Department of Molecular Medicine, Nagasaki University Graduate School of Biomedical Sciences, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan
| | - Sairai So
- the University of Texas Southwestern Medical Center, Dallas, Texas 75390, and
| | - David Chen
- the University of Texas Southwestern Medical Center, Dallas, Texas 75390, and
| | - Martin F. Lavin
- From Radiation Biology and Oncology, Queensland Institute of Medical Research, Brisbane, Queensland 4029, Australia
- the University of Queensland Centre for Clinical Research, Brisbane, Queensland 4029, Australia
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