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Kaizuka T, Suzuki T, Kishi N, Tamada K, Kilimann MW, Ueyama T, Watanabe M, Shimogori T, Okano H, Dohmae N, Takumi T. Remodeling of the postsynaptic proteome in male mice and marmosets during synapse development. Nat Commun 2024; 15:2496. [PMID: 38548776 PMCID: PMC10979008 DOI: 10.1038/s41467-024-46529-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 02/29/2024] [Indexed: 04/01/2024] Open
Abstract
Postsynaptic proteins play crucial roles in synaptic function and plasticity. During brain development, alterations in synaptic number, shape, and stability occur, known as synapse maturation. However, the postsynaptic protein composition changes during development are not fully understood. Here, we show the trajectory of the postsynaptic proteome in developing male mice and common marmosets. Proteomic analysis of mice at 2, 3, 6, and 12 weeks of age shows that proteins involved in synaptogenesis are differentially expressed during this period. Analysis of published transcriptome datasets shows that the changes in postsynaptic protein composition in the mouse brain after 2 weeks of age correlate with gene expression changes. Proteomic analysis of marmosets at 0, 2, 3, 6, and 24 months of age show that the changes in the marmoset brain can be categorized into two parts: the first 2 months and after that. The changes observed in the first 2 months are similar to those in the mouse brain between 2 and 12 weeks of age. The changes observed in marmoset after 2 months old include differential expression of synaptogenesis-related molecules, which hardly overlap with that in mice. Our results provide a comprehensive proteomic resource that underlies developmental synapse maturation in rodents and primates.
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Affiliation(s)
- Takeshi Kaizuka
- RIKEN Brain Science Institute, Wako, Saitama, 351-0198, Japan
- Department Physiology and Cell Biology, Kobe University School of Medicine, Chuo, Kobe, 650-0117, Japan
| | - Takehiro Suzuki
- Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, Wako, Saitama, 351-0198, Japan
| | - Noriyuki Kishi
- RIKEN Brain Science Institute, Wako, Saitama, 351-0198, Japan
| | - Kota Tamada
- RIKEN Brain Science Institute, Wako, Saitama, 351-0198, Japan
- Department Physiology and Cell Biology, Kobe University School of Medicine, Chuo, Kobe, 650-0117, Japan
| | - Manfred W Kilimann
- Max Planck Institute for Experimental Medicine, Göttingen, 37075, Germany
| | - Takehiko Ueyama
- Laboratory of Molecular Pharmacology, Biosignal Research Center, Kobe University, Nada, Kobe, 657-8501, Japan
| | - Masahiko Watanabe
- Department of Anatomy, Faculty of Medicine, Hokkaido University, Kita, Sapporo, 060-8638, Japan
| | | | - Hideyuki Okano
- RIKEN Brain Science Institute, Wako, Saitama, 351-0198, Japan
- Department of Physiology, Keio University School of Medicine, Shinjuku, Tokyo, 160-8585, Japan
| | - Naoshi Dohmae
- Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, Wako, Saitama, 351-0198, Japan
| | - Toru Takumi
- RIKEN Brain Science Institute, Wako, Saitama, 351-0198, Japan.
- Department Physiology and Cell Biology, Kobe University School of Medicine, Chuo, Kobe, 650-0117, Japan.
- RIKEN Center for Biosystems Dynamics Research, Chuo, Kobe, 650-0047, Japan.
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2
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Kaizuka T, Hirouchi T, Saneyoshi T, Shirafuji T, Collins MO, Grant SGN, Hayashi Y, Takumi T. FAM81A is a postsynaptic protein that regulates the condensation of postsynaptic proteins via liquid-liquid phase separation. PLoS Biol 2024; 22:e3002006. [PMID: 38452102 PMCID: PMC10919877 DOI: 10.1371/journal.pbio.3002006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 01/17/2024] [Indexed: 03/09/2024] Open
Abstract
Proteome analyses of the postsynaptic density (PSD), a proteinaceous specialization beneath the postsynaptic membrane of excitatory synapses, have identified several thousands of proteins. While proteins with predictable functions have been well studied, functionally uncharacterized proteins are mostly overlooked. In this study, we conducted a comprehensive meta-analysis of 35 PSD proteome datasets, encompassing a total of 5,869 proteins. Employing a ranking methodology, we identified 97 proteins that remain inadequately characterized. From this selection, we focused our detailed analysis on the highest-ranked protein, FAM81A. FAM81A interacts with PSD proteins, including PSD-95, SynGAP, and NMDA receptors, and promotes liquid-liquid phase separation of those proteins in cultured cells or in vitro. Down-regulation of FAM81A in cultured neurons causes a decrease in the size of PSD-95 puncta and the frequency of neuronal firing. Our findings suggest that FAM81A plays a crucial role in facilitating the interaction and assembly of proteins within the PSD, and its presence is important for maintaining normal synaptic function. Additionally, our methodology underscores the necessity for further characterization of numerous synaptic proteins that still lack comprehensive understanding.
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Affiliation(s)
- Takeshi Kaizuka
- RIKEN Brain Science Institute, Wako, Saitama, Japan
- Department of Physiology and Cell Biology, Kobe University School of Medicine, Kobe, Chuo, Kobe, Japan
- Centre for Clinical Brain Sciences, Chancellor’s Building, Edinburgh BioQuarter, University of Edinburgh, Edinburgh, United Kingdom
| | - Taisei Hirouchi
- Department of Pharmacology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Takeo Saneyoshi
- Department of Pharmacology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Toshihiko Shirafuji
- Department of Physiology and Cell Biology, Kobe University School of Medicine, Kobe, Chuo, Kobe, Japan
| | - Mark O. Collins
- School of Biosciences, University of Sheffield, Sheffield, United Kingdom
- biOMICS Facility, Mass Spectrometry Centre, University of Sheffield, Sheffield, United Kingdom
| | - Seth G. N. Grant
- Centre for Clinical Brain Sciences, Chancellor’s Building, Edinburgh BioQuarter, University of Edinburgh, Edinburgh, United Kingdom
- Simons Initiative for the Developing Brain (SIDB), Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Yasunori Hayashi
- Department of Pharmacology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Toru Takumi
- RIKEN Brain Science Institute, Wako, Saitama, Japan
- Department of Physiology and Cell Biology, Kobe University School of Medicine, Kobe, Chuo, Kobe, Japan
- RIKEN Center for Biosystems Dynamics Research, Chuo, Kobe, Japan
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3
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Nguyen TTA, Mohanty V, Yan Y, Francis KR, Cologna SM. Comparative Hippocampal Proteome and Phosphoproteome in a Niemann-Pick, Type C1 Mouse Model Reveal Insights into Disease Mechanisms. J Proteome Res 2024; 23:84-94. [PMID: 37999680 DOI: 10.1021/acs.jproteome.3c00375] [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] [Indexed: 11/25/2023]
Abstract
Niemann-Pick disease, type C (NPC) is a neurodegenerative, lysosomal storage disorder in individuals carrying two mutated copies of either the NPC1 or NPC2 gene. Consequently, impaired cholesterol recycling and an array of downstream events occur. Interestingly, in NPC, the hippocampus displays lysosomal lipid storage but does not succumb to progressive neurodegeneration as significantly as other brain regions. Since defining the neurodegeneration mechanisms in this disease is still an active area of research, we use mass spectrometry to analyze the overall proteome and phosphorylation pattern changes in the hippocampal region of a murine model of NPC. Using 3 week old mice representing an early disease time point, we observed changes in the expression of 47 proteins, many of which are consistent with the previous literature. New to this study, changes in members of the SNARE complex, including STX7, VTI1B, and VAMP7, were identified. Furthermore, we identified that phosphorylation of T286 on CaMKIIα and S1303 on NR2B increased in mutant animals, even at the late stage of the disease. These phosphosites are crucial to learning and memory and can trigger neuronal death by altering protein-protein interactions.
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Affiliation(s)
- Thu T A Nguyen
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Varshasnata Mohanty
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Ying Yan
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Kevin R Francis
- Cellular Therapies and Stem Cell Biology Group, Sanford Research, Sioux Falls, South Dakota 57104, United States
- Department of Pediatrics, Sanford School of Medicine, University of South Dakota, Sioux Falls, South Dakota 57105, United States
| | - Stephanie M Cologna
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, United States
- Laboratory of Integrated Neuroscience, University of Illinois Chicago, Chicago, Illinois 60607, United States
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4
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Teo S, Bossio A, Stamatakou E, Pascual-Vargas P, Jones ME, Schuhmacher LN, Salinas PC. S-acylation of the Wnt receptor Frizzled-5 by zDHHC5 controls its cellular localization and synaptogenic activity in the rodent hippocampus. Dev Cell 2023; 58:2063-2079.e9. [PMID: 37557176 DOI: 10.1016/j.devcel.2023.07.012] [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: 09/16/2022] [Revised: 05/05/2023] [Accepted: 07/18/2023] [Indexed: 08/11/2023]
Abstract
Proper localization of receptors for synaptic organizing factors is crucial for synapse formation. Wnt proteins promote synapse assembly through Frizzled (Fz) receptors. In hippocampal neurons, the surface and synaptic localization of Fz5 is regulated by neuronal activity, but the mechanisms involved remain poorly understood. Here, we report that all Fz receptors can be post-translationally modified by S-acylation and that Fz5 is S-acylated on three C-terminal cysteines by zDHHC5. S-acylation is essential for Fz5 localization to the cell surface, axons, and presynaptic sites. Notably, S-acylation-deficient Fz5 is internalized faster, affecting its association with signalosome components at the cell surface. S-acylation-deficient Fz5 also fails to activate canonical and divergent canonical Wnt pathways. Fz5 S-acylation levels are regulated by the pattern of neuronal activity. In vivo studies demonstrate that S-acylation-deficient Fz5 expression fails to induce presynaptic assembly. Our studies show that S-acylation of Frizzled receptors is a mechanism controlling their localization and function.
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Affiliation(s)
- Samuel Teo
- Department of Cell and Developmental Biology, Division of Biosciences, University College London, London WC1E 6BT, UK
| | - Alessandro Bossio
- Department of Cell and Developmental Biology, Division of Biosciences, University College London, London WC1E 6BT, UK
| | - Eleanna Stamatakou
- Department of Cell and Developmental Biology, Division of Biosciences, University College London, London WC1E 6BT, UK
| | - Patricia Pascual-Vargas
- Department of Cell and Developmental Biology, Division of Biosciences, University College London, London WC1E 6BT, UK
| | - Megan E Jones
- Department of Cell and Developmental Biology, Division of Biosciences, University College London, London WC1E 6BT, UK
| | - Laura-Nadine Schuhmacher
- Department of Cell and Developmental Biology, Division of Biosciences, University College London, London WC1E 6BT, UK
| | - Patricia C Salinas
- Department of Cell and Developmental Biology, Division of Biosciences, University College London, London WC1E 6BT, UK.
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5
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Nicoll RA, Schulman H. Synaptic memory and CaMKII. Physiol Rev 2023; 103:2877-2925. [PMID: 37290118 PMCID: PMC10642921 DOI: 10.1152/physrev.00034.2022] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 04/26/2023] [Accepted: 04/30/2023] [Indexed: 06/10/2023] Open
Abstract
Ca2+/calmodulin-dependent protein kinase II (CaMKII) and long-term potentiation (LTP) were discovered within a decade of each other and have been inextricably intertwined ever since. However, like many marriages, it has had its up and downs. Based on the unique biochemical properties of CaMKII, it was proposed as a memory molecule before any physiological linkage was made to LTP. However, as reviewed here, the convincing linkage of CaMKII to synaptic physiology and behavior took many decades. New technologies were critical in this journey, including in vitro brain slices, mouse genetics, single-cell molecular genetics, pharmacological reagents, protein structure, and two-photon microscopy, as were new investigators attracted by the exciting challenge. This review tracks this journey and assesses the state of this marriage 40 years on. The collective literature impels us to propose a relatively simple model for synaptic memory involving the following steps that drive the process: 1) Ca2+ entry through N-methyl-d-aspartate (NMDA) receptors activates CaMKII. 2) CaMKII undergoes autophosphorylation resulting in constitutive, Ca2+-independent activity and exposure of a binding site for the NMDA receptor subunit GluN2B. 3) Active CaMKII translocates to the postsynaptic density (PSD) and binds to the cytoplasmic C-tail of GluN2B. 4) The CaMKII-GluN2B complex initiates a structural rearrangement of the PSD that may involve liquid-liquid phase separation. 5) This rearrangement involves the PSD-95 scaffolding protein, α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptors (AMPARs), and their transmembrane AMPAR-regulatory protein (TARP) auxiliary subunits, resulting in an accumulation of AMPARs in the PSD that underlies synaptic potentiation. 6) The stability of the modified PSD is maintained by the stability of the CaMKII-GluN2B complex. 7) By a process of subunit exchange or interholoenzyme phosphorylation CaMKII maintains synaptic potentiation in the face of CaMKII protein turnover. There are many other important proteins that participate in enlargement of the synaptic spine or modulation of the steps that drive and maintain the potentiation. In this review we critically discuss the data underlying each of the steps. As will become clear, some of these steps are more firmly grounded than others, and we provide suggestions as to how the evidence supporting these steps can be strengthened or, based on the new data, be replaced. Although the journey has been a long one, the prospect of having a detailed cellular and molecular understanding of learning and memory is at hand.
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Affiliation(s)
- Roger A Nicoll
- Department of Cellular and Molecular Pharmacology, University of California at San Francisco, San Francisco, California, United States
| | - Howard Schulman
- Department of Neurobiology, Stanford University School of Medicine, Stanford, California, United States
- Panorama Research Institute, Sunnyvale, California, United States
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6
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Ramasamy P, Vandermarliere E, Vranken WF, Martens L. Panoramic Perspective on Human Phosphosites. J Proteome Res 2022; 21:1894-1915. [PMID: 35793420 DOI: 10.1021/acs.jproteome.2c00164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein phosphorylation is the most common reversible post-translational modification of proteins and is key in the regulation of many cellular processes. Due to this importance, phosphorylation is extensively studied, resulting in the availability of a large amount of mass spectrometry-based phospho-proteomics data. Here, we leverage the information in these large-scale phospho-proteomics data sets, as contained in Scop3P, to analyze and characterize proteome-wide protein phosphorylation sites (P-sites). First, we set out to differentiate correctly observed P-sites from false-positive sites using five complementary site properties. We then describe the context of these P-sites in terms of the protein structure, solvent accessibility, structural transitions and disorder, and biophysical properties. We also investigate the relative prevalence of disease-linked mutations on and around P-sites. Moreover, we assess the structural dynamics of P-sites in their phosphorylated and unphosphorylated states. As a result, we show how large-scale reprocessing of available proteomics experiments can enable a more reliable view on proteome-wide P-sites. Furthermore, adding the structural context of proteins around P-sites helps uncover possible conformational switches upon phosphorylation. Moreover, by placing sites in different biophysical contexts, we show the differential preference in protein dynamics at phosphorylated sites when compared to the nonphosphorylated counterparts.
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Affiliation(s)
- Pathmanaban Ramasamy
- VIB-UGent Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium.,Department of Biomolecular Medicine, Faculty of Health Sciences and Medicine, Ghent University, 9000 Ghent, Belgium.,Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, 1050 Brussels, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium.,Centre for Structural Biology, VIB, 1050 Brussels, Belgium
| | | | - Wim F Vranken
- Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, 1050 Brussels, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium.,Centre for Structural Biology, VIB, 1050 Brussels, Belgium
| | - Lennart Martens
- VIB-UGent Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium.,Department of Biomolecular Medicine, Faculty of Health Sciences and Medicine, Ghent University, 9000 Ghent, Belgium
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7
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Fu W, Franchini L, Orlandi C. Comprehensive Spatial Profile of the Orphan G Protein Coupled Receptor GPRC5B Expression in Mouse Brain. Front Neurosci 2022; 16:891544. [PMID: 35812210 PMCID: PMC9259939 DOI: 10.3389/fnins.2022.891544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 06/07/2022] [Indexed: 11/13/2022] Open
Abstract
Orphan G Protein Coupled Receptors (GPCRs) are GPCRs whose endogenous ligands are unknown or still debated. Due to the lack of pharmacological modulators, the physiological function of orphan GPCRs is understudied. However, relevant physiological roles associated with orphan GPCRs have been revealed by analysis of animal models and genome wide association studies illuminating an untapped potential for drug discovery. G Protein Coupled Receptor class C Group 5 Member B (GPRC5B) is among the most expressed GPCRs in the central nervous system. Thus, the expression profiling of GPRC5B is an essential step toward understanding GPRC5B function in health and disease. In this study, we generated new GPRC5B polyclonal antibodies and investigated the expression levels of GPRC5B across different organs and brain regions. We identified high levels of GPRC5B glycosylation both in transfected cells and in mouse brain. Moreover, in situ hybridization imaging analysis indicated that Gprc5b was expressed at the highest level in olfactory bulb, hippocampus, cerebellum, and pons. To dissect expression within various neuronal populations, we conducted a comprehensive spatial profiling of Gprc5b across excitatory and inhibitory neuronal types in medial prefrontal cortex, motor cortex, hippocampal regions, hypothalamus, and cerebellum. Overall, we discovered that GABAergic neurons displayed higher Gprc5b expression levels than glutamatergic neurons in most of the analyzed regions with the important exception of the hippocampal dentate gyrus. Overall, the expression analysis of GPRC5B in mouse brain will guide functional studies ultimately positioning GPRC5B in pathophysiological mechanisms and drug discovery.
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8
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Christensen NR, Pedersen CP, Sereikaite V, Pedersen JN, Vistrup-Parry M, Sørensen AT, Otzen D, Teilum K, Madsen KL, Strømgaard K. Bidirectional protein-protein interactions control liquid-liquid phase separation of PSD-95 and its interaction partners. iScience 2022; 25:103808. [PMID: 35198873 PMCID: PMC8844826 DOI: 10.1016/j.isci.2022.103808] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 09/29/2021] [Accepted: 01/20/2022] [Indexed: 01/08/2023] Open
Abstract
The organization of the postsynaptic density (PSD), a protein-dense semi-membraneless organelle, is mediated by numerous specific protein–protein interactions (PPIs) which constitute a functional postsynapse. The PSD protein 95 (PSD-95) interacts with a manifold of proteins, including the C-terminal of transmembrane AMPA receptor (AMPAR) regulatory proteins (TARPs). Here, we uncover the minimal essential peptide responsible for the Stargazin (TARP-γ2)-mediated liquid–liquid phase separation (LLPS) formation of PSD-95 and other key protein constituents of the PSD. Furthermore, we find that pharmacological inhibitors of PSD-95 can facilitate the formation of LLPS. We found that in some cases LLPS formation is dependent on multivalent interactions, while in other cases short, highly charged peptides are sufficient to promote LLPS in complex systems. This study offers a new perspective on PSD-95 interactions and their role in LLPS formation, while also considering the role of affinity over multivalency in LLPS systems. Charge and valency are important for LLPS formation, both for PSD-95 and the ePSD Peptide inhibitors may be used to induce LLPS formation for PSD-95 and the ePSD
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Affiliation(s)
- Nikolaj Riis Christensen
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark.,Department of Neuroscience, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Christian Parsbæk Pedersen
- Structural Biology and NMR Laboratory & the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
| | - Vita Sereikaite
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Jannik Nedergaard Pedersen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
| | - Maria Vistrup-Parry
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Andreas Toft Sørensen
- Department of Neuroscience, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Daniel Otzen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
| | - Kaare Teilum
- Structural Biology and NMR Laboratory & the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
| | | | - Kristian Strømgaard
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
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9
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Lautz JD, Tsegay KB, Zhu Z, Gniffke EP, Welsh JP, Smith SEP. Synaptic protein interaction networks encode experience by assuming stimulus-specific and brain-region-specific states. Cell Rep 2021; 37:110076. [PMID: 34852231 PMCID: PMC8722361 DOI: 10.1016/j.celrep.2021.110076] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 10/01/2021] [Accepted: 11/09/2021] [Indexed: 11/02/2022] Open
Abstract
A core network of widely expressed proteins within the glutamatergic post-synapse mediates activity-dependent synaptic plasticity throughout the brain, but the specific proteomic composition of synapses differs between brain regions. Here, we address the question, how does proteomic composition affect activity-dependent protein-protein interaction networks (PINs) downstream of synaptic activity? Using quantitative multiplex co-immunoprecipitation, we compare the PIN response of in vivo or ex vivo neurons derived from different brain regions to activation by different agonists or different forms of eyeblink conditioning. We report that PINs discriminate between incoming stimuli using differential kinetics of overlapping and non-overlapping PIN parameters. Further, these "molecular logic rules" differ by brain region. We conclude that although the PIN of the glutamatergic post-synapse is expressed widely throughout the brain, its activity-dependent dynamics show remarkable stimulus-specific and brain-region-specific diversity. This diversity may help explain the challenges in developing molecule-specific drug therapies for neurological disorders.
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Affiliation(s)
- Jonathan D Lautz
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Kaleb B Tsegay
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Zhiyi Zhu
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Edward P Gniffke
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - John P Welsh
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA; Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Stephen E P Smith
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA; Department of Pediatrics, University of Washington, Seattle, WA, USA; Graduate Program in Neuroscience, University of Washington, Seattle, WA, USA.
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10
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Biswas D, Shenoy SV, Chetanya C, Lachén-Montes M, Barpanda A, Athithyan AP, Ghosh S, Ausín K, Zelaya MV, Fernández-Irigoyen J, Manna A, Roy S, Talukdar A, Ball GR, Santamaría E, Srivastava S. Deciphering the Interregional and Interhemisphere Proteome of the Human Brain in the Context of the Human Proteome Project. J Proteome Res 2021; 20:5280-5293. [PMID: 34714085 DOI: 10.1021/acs.jproteome.1c00511] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
This study, which performs an extensive mass spectrometry-based analysis of 19 brain regions from both left and right hemispheres, presents the first draft of the human brain interhemispheric proteome. This high-resolution proteomics data provides comprehensive coverage of 3300 experimentally measured (nonhypothetical) proteins across multiple regions, allowing the characterization of protein-centric interhemispheric differences and synapse biology, and portrays the regional mapping of specific regions for brain disorder biomarkers. In the context of the Human Proteome Project (HPP), the interhemispheric proteome data reveal specific markers like chimerin 2 (CHN2) in the cerebellar vermis, olfactory marker protein (OMP) in the olfactory bulb, and ankyrin repeat domain 63 (ANKRD63) in basal ganglia, in line with regional brain transcriptomes mapped in the Human Protein Atlas (HPA). In addition, an in silico analysis pipeline was used to predict the structure and function of the uncharacterized uPE1 protein ANKRD63, and parallel reaction monitoring (PRM) was applied to validate its region-specific expression. Finally, we have built the Interhemispheric Brain Proteome Map (IBPM) Portal (www.brainprot.org) to stimulate the scientific community's interest in the brain molecular landscape and accelerate and support research in neuroproteomics. Data are available via ProteomeXchange with identifier PXD019936.
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Affiliation(s)
- Deeptarup Biswas
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Sanjyot Vinayak Shenoy
- Department of Mathematics, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Chetanya Chetanya
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Mercedes Lachén-Montes
- Clinical Neuroproteomics Unit, Proteomics Platform, Proteored-ISCIII, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), Navarra Institute for Health Research (IdiSNA), 31008 Pamplona, Spain
| | - Abhilash Barpanda
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | | | - Susmita Ghosh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Karina Ausín
- Clinical Neuroproteomics Unit, Proteomics Platform, Proteored-ISCIII, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), Navarra Institute for Health Research (IdiSNA), 31008 Pamplona, Spain
| | - María Victoria Zelaya
- Clinical Neuroproteomics Unit, Proteomics Platform, Proteored-ISCIII, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), Navarra Institute for Health Research (IdiSNA), 31008 Pamplona, Spain
| | - Joaquín Fernández-Irigoyen
- Clinical Neuroproteomics Unit, Proteomics Platform, Proteored-ISCIII, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), Navarra Institute for Health Research (IdiSNA), 31008 Pamplona, Spain
| | - Akash Manna
- Medicine Department, Medical College Hospital Kolkata, 88 College Street, Kolkata 700072, India
| | - Sudesh Roy
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Arunasu Talukdar
- Medicine Department, Medical College Hospital Kolkata, 88 College Street, Kolkata 700072, India
| | - Graham Roy Ball
- School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, United Kingdom
| | - Enrique Santamaría
- Clinical Neuroproteomics Unit, Proteomics Platform, Proteored-ISCIII, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), Navarra Institute for Health Research (IdiSNA), 31008 Pamplona, Spain
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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11
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Grubisha MJ, Sweet RA, MacDonald ML. Investigating Post-translational Modifications in Neuropsychiatric Disease: The Next Frontier in Human Post-mortem Brain Research. Front Mol Neurosci 2021; 14:689495. [PMID: 34335181 PMCID: PMC8322442 DOI: 10.3389/fnmol.2021.689495] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 06/18/2021] [Indexed: 12/27/2022] Open
Abstract
Gene expression and translation have been extensively studied in human post-mortem brain tissue from subjects with psychiatric disease. Post-translational modifications (PTMs) have received less attention despite their implication by unbiased genetic studies and importance in regulating neuronal and circuit function. Here we review the rationale for studying PTMs in psychiatric disease, recent findings in human post-mortem tissue, the required controls for these types of studies, and highlight the emerging mass spectrometry approaches transforming this research direction.
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Affiliation(s)
- Melanie J. Grubisha
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, United States
| | - Robert A. Sweet
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, United States
| | - Matthew L. MacDonald
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, United States
- Biomedical Mass Spectrometry Center, University of Pittsburgh, Pittsburgh, PA, United States
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12
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Walczyk-Mooradally A, Holborn J, Singh K, Tyler M, Patnaik D, Wesseling H, Brandon NJ, Steen J, Graether SP, Haggarty SJ, Lalonde J. Phosphorylation-dependent control of Activity-regulated cytoskeleton-associated protein (Arc) protein by TNIK. J Neurochem 2021. [PMID: 34077555 DOI: 10.1111/jnc.15077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Activity-regulated cytoskeleton-associated protein (Arc) is an immediate early gene product that support neuroplastic changes important for cognitive function and memory formation. As a protein with homology to the retroviral Gag protein, a particular characteristic of Arc is its capacity to self-assemble into virus-like capsids that can package mRNAs and transfer those transcripts to other cells. Although a lot has been uncovered about the contributions of Arc to neuron biology and behavior, very little is known about how different functions of Arc are coordinately regulated both temporally and spatially in neurons. The answer to this question we hypothesized must involve the occurrence of different protein post-translational modifications acting to confer specificity. In this study, we used mass spectrometry and sequence prediction strategies to map novel Arc phosphorylation sites. Our approach led us to recognize serine 67 (S67) and threonine 278 (T278) as residues that can be modified by TNIK, which is a kinase abundantly expressed in neurons that shares many functional overlaps with Arc and has, along with its interacting proteins such as the NMDA receptor, and been implicated as a risk factor for psychiatric disorders. Furthermore, characterization of each residue using site-directed mutagenesis to create S67 and T278 mutant variants revealed that TNIK action at those amino acids can strongly influence Arc's subcellular distribution and self-assembly as capsids. Together, our findings reveal an unsuspected connection between Arc and TNIK. Better understanding of the interplay between these two proteins in neuronal cells could lead to new insights about apparition and progression of psychiatric disorders. Cover Image for this issue: https://doi.org/10.1111/jnc.15077.
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Affiliation(s)
| | - Jennifer Holborn
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Karamjeet Singh
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Marshall Tyler
- Massachusetts General Hospital, Centre for Genomic Medicine, Boston, MA, USA
| | - Debasis Patnaik
- Massachusetts General Hospital, Centre for Genomic Medicine, Boston, MA, USA
| | - Hendrik Wesseling
- Boston Children's Hospital, F.M. Kirby Center for Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Nicholas J Brandon
- Neuroscience, BioPharmaceuticals R&D, AstraZeneca Boston, Waltham, MA, USA
| | - Judith Steen
- Boston Children's Hospital, F.M. Kirby Center for Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Steffen P Graether
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Stephen J Haggarty
- Massachusetts General Hospital, Centre for Genomic Medicine, Boston, MA, USA
| | - Jasmin Lalonde
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
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13
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Walczyk-Mooradally A, Holborn J, Singh K, Tyler M, Patnaik D, Wesseling H, Brandon NJ, Steen J, Graether SP, Haggarty SJ, Lalonde J. Phosphorylation-dependent control of Activity-regulated cytoskeleton-associated protein (Arc) protein by TNIK. J Neurochem 2021; 158:1058-1073. [PMID: 34077555 DOI: 10.1111/jnc.15440] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/24/2021] [Accepted: 05/24/2021] [Indexed: 12/21/2022]
Abstract
Activity-regulated cytoskeleton-associated protein (Arc) is an immediate early gene product that support neuroplastic changes important for cognitive function and memory formation. As a protein with homology to the retroviral Gag protein, a particular characteristic of Arc is its capacity to self-assemble into virus-like capsids that can package mRNAs and transfer those transcripts to other cells. Although a lot has been uncovered about the contributions of Arc to neuron biology and behavior, very little is known about how different functions of Arc are coordinately regulated both temporally and spatially in neurons. The answer to this question we hypothesized must involve the occurrence of different protein post-translational modifications acting to confer specificity. In this study, we used mass spectrometry and sequence prediction strategies to map novel Arc phosphorylation sites. Our approach led us to recognize serine 67 (S67) and threonine 278 (T278) as residues that can be modified by TNIK, which is a kinase abundantly expressed in neurons that shares many functional overlaps with Arc and has, along with its interacting proteins such as the NMDA receptor, and been implicated as a risk factor for psychiatric disorders. Furthermore, characterization of each residue using site-directed mutagenesis to create S67 and T278 mutant variants revealed that TNIK action at those amino acids can strongly influence Arc's subcellular distribution and self-assembly as capsids. Together, our findings reveal an unsuspected connection between Arc and TNIK. Better understanding of the interplay between these two proteins in neuronal cells could lead to new insights about apparition and progression of psychiatric disorders.
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Affiliation(s)
| | - Jennifer Holborn
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Karamjeet Singh
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Marshall Tyler
- Massachusetts General Hospital, Centre for Genomic Medicine, Boston, MA, USA
| | - Debasis Patnaik
- Massachusetts General Hospital, Centre for Genomic Medicine, Boston, MA, USA
| | - Hendrik Wesseling
- Boston Children's Hospital, F.M. Kirby Center for Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Nicholas J Brandon
- Neuroscience, BioPharmaceuticals R&D, AstraZeneca Boston, Waltham, MA, USA
| | - Judith Steen
- Boston Children's Hospital, F.M. Kirby Center for Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Steffen P Graether
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Stephen J Haggarty
- Massachusetts General Hospital, Centre for Genomic Medicine, Boston, MA, USA
| | - Jasmin Lalonde
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
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14
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A unified resource and configurable model of the synapse proteome and its role in disease. Sci Rep 2021; 11:9967. [PMID: 33976238 PMCID: PMC8113277 DOI: 10.1038/s41598-021-88945-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 04/15/2021] [Indexed: 02/03/2023] Open
Abstract
Genes encoding synaptic proteins are highly associated with neuronal disorders many of which show clinical co-morbidity. We integrated 58 published synaptic proteomic datasets that describe over 8000 proteins and combined them with direct protein-protein interactions and functional metadata to build a network resource that reveals the shared and unique protein components that underpin multiple disorders. All the data are provided in a flexible and accessible format to encourage custom use.
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15
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van Gelder CAGH, Altelaar M. Neuroproteomics of the Synapse: Subcellular Quantification of Protein Networks and Signaling Dynamics. Mol Cell Proteomics 2021; 20:100087. [PMID: 33933679 PMCID: PMC8167277 DOI: 10.1016/j.mcpro.2021.100087] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/21/2021] [Accepted: 04/26/2021] [Indexed: 01/21/2023] Open
Abstract
One of the most fascinating features of the brain is its ability to adapt to its surroundings. Synaptic plasticity, the dynamic mechanism of functional and structural alterations in synaptic strength, is essential for brain functioning and underlies a variety of processes such as learning and memory. Although the molecular mechanisms underlying such rapid plasticity are not fully understood, a consensus exists on the important role of proteins. The study of these neuronal proteins using neuroproteomics has increased rapidly in the last decades, and advancements in MS-based proteomics have broadened our understanding of neuroplasticity exponentially. In this review, we discuss the trends in MS-based neuroproteomics for the study of synaptic protein-protein interactions and protein signaling dynamics, with a focus on sample types, different labeling and enrichment approaches, and data analysis and interpretation. We highlight studies from the last 5 years, with a focus on synapse structure, composition, functioning, or signaling and finally discuss some recent developments that could further advance the field of neuroproteomics.
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Affiliation(s)
- Charlotte A G H van Gelder
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands; Netherlands Proteomics Center, Utrecht, The Netherlands
| | - Maarten Altelaar
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands; Netherlands Proteomics Center, Utrecht, The Netherlands.
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16
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Proietti Onori M, van Woerden GM. Role of calcium/calmodulin-dependent kinase 2 in neurodevelopmental disorders. Brain Res Bull 2021; 171:209-220. [PMID: 33774142 DOI: 10.1016/j.brainresbull.2021.03.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 03/17/2021] [Accepted: 03/18/2021] [Indexed: 01/28/2023]
Abstract
Neurodevelopmental disorders are a complex and heterogeneous group of neurological disorders characterized by their early-onset and estimated to affect more than 3% of children worldwide. The rapid advancement of sequencing technologies in the past years allowed the identification of hundreds of variants in several different genes causing neurodevelopmental disorders. Between those, new variants in the Calcium/calmodulin dependent protein kinase II (CAMK2) genes were recently linked to intellectual disability. Despite many years of research on CAMK2, this proves for the first time that this well-known and highly conserved molecule plays an important role in the human brain. In this review, we give an overview of the identified CAMK2 variants, and we speculate on potential mechanisms through which dysfunctions in CAMK2 result in neurodevelopmental disorders. Additionally, we discuss how the identification of CAMK2 variants might result in new exciting discoveries regarding the function of CAMK2 in the human brain.
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Affiliation(s)
- Martina Proietti Onori
- Department of Neuroscience, Erasmus MC, Rotterdam, 3015 GD, the Netherlands; The ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus MC, Rotterdam, 3015 GD, the Netherlands
| | - Geeske M van Woerden
- Department of Neuroscience, Erasmus MC, Rotterdam, 3015 GD, the Netherlands; The ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus MC, Rotterdam, 3015 GD, the Netherlands.
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17
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Farahi N, Lazar T, Wodak SJ, Tompa P, Pancsa R. Integration of Data from Liquid-Liquid Phase Separation Databases Highlights Concentration and Dosage Sensitivity of LLPS Drivers. Int J Mol Sci 2021; 22:ijms22063017. [PMID: 33809541 PMCID: PMC8002189 DOI: 10.3390/ijms22063017] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 03/12/2021] [Accepted: 03/13/2021] [Indexed: 12/13/2022] Open
Abstract
Liquid–liquid phase separation (LLPS) is a molecular process that leads to the formation of membraneless organelles, representing functionally specialized liquid-like cellular condensates formed by proteins and nucleic acids. Integrating the data on LLPS-associated proteins from dedicated databases revealed only modest agreement between them and yielded a high-confidence dataset of 89 human LLPS drivers. Analysis of the supporting evidence for our dataset uncovered a systematic and potentially concerning difference between protein concentrations used in a good fraction of the in vitro LLPS experiments, a key parameter that governs the phase behavior, and the proteomics-derived cellular abundance levels of the corresponding proteins. Closer scrutiny of the underlying experimental data enabled us to offer a sound rationale for this systematic difference, which draws on our current understanding of the cellular organization of the proteome and the LLPS process. In support of this rationale, we find that genes coding for our human LLPS drivers tend to be dosage-sensitive, suggesting that their cellular availability is tightly regulated to preserve their functional role in direct or indirect relation to condensate formation. Our analysis offers guideposts for increasing agreement between in vitro and in vivo studies, probing the roles of proteins in LLPS.
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Affiliation(s)
- Nazanin Farahi
- VIB-VUB Center for Structural Biology, Flemish Institute for Biotechnology, 1050 Brussels, Belgium; (N.F.); (T.L.); (S.J.W.)
- Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
- Department of Biology, Technical University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Tamas Lazar
- VIB-VUB Center for Structural Biology, Flemish Institute for Biotechnology, 1050 Brussels, Belgium; (N.F.); (T.L.); (S.J.W.)
- Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Shoshana J. Wodak
- VIB-VUB Center for Structural Biology, Flemish Institute for Biotechnology, 1050 Brussels, Belgium; (N.F.); (T.L.); (S.J.W.)
- Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Peter Tompa
- VIB-VUB Center for Structural Biology, Flemish Institute for Biotechnology, 1050 Brussels, Belgium; (N.F.); (T.L.); (S.J.W.)
- Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary
- Correspondence: (P.T.); (R.P.)
| | - Rita Pancsa
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary
- Correspondence: (P.T.); (R.P.)
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18
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Xu Y, Song X, Wang D, Wang Y, Li P, Li J. Proteomic insights into synaptic signaling in the brain: the past, present and future. Mol Brain 2021; 14:37. [PMID: 33596935 PMCID: PMC7888154 DOI: 10.1186/s13041-021-00750-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 02/09/2021] [Indexed: 12/29/2022] Open
Abstract
Chemical synapses in the brain connect neurons to form neural circuits, providing the structural and functional bases for neural communication. Disrupted synaptic signaling is closely related to a variety of neurological and psychiatric disorders. In the past two decades, proteomics has blossomed as a versatile tool in biological and biomedical research, rendering a wealth of information toward decoding the molecular machinery of life. There is enormous interest in employing proteomic approaches for the study of synapses, and substantial progress has been made. Here, we review the findings of proteomic studies of chemical synapses in the brain, with special attention paid to the key players in synaptic signaling, i.e., the synaptic protein complexes and their post-translational modifications. Looking toward the future, we discuss the technological advances in proteomics such as data-independent acquisition mass spectrometry (DIA-MS), cross-linking in combination with mass spectrometry (CXMS), and proximity proteomics, along with their potential to untangle the mystery of how the brain functions at the molecular level. Last but not least, we introduce the newly developed synaptomic methods. These methods and their successful applications marked the beginnings of the synaptomics era.
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Affiliation(s)
- Yalan Xu
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Medical College, Qingdao University, Qingdao, 266021, China
| | - Xiuyue Song
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Medical College, Qingdao University, Qingdao, 266021, China
| | - Dong Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Medical College, Qingdao University, Qingdao, 266021, China
| | - Yin Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Medical College, Qingdao University, Qingdao, 266021, China
| | - Peifeng Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Medical College, Qingdao University, Qingdao, 266021, China
| | - Jing Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Medical College, Qingdao University, Qingdao, 266021, China.
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19
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Wilkinson B, Coba MP. Molecular architecture of postsynaptic Interactomes. Cell Signal 2020; 76:109782. [PMID: 32941943 DOI: 10.1016/j.cellsig.2020.109782] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 09/11/2020] [Accepted: 09/12/2020] [Indexed: 01/02/2023]
Abstract
The postsynaptic density (PSD) plays an essential role in the organization of the synaptic signaling machinery. It contains a set of core scaffolding proteins that provide the backbone to PSD protein-protein interaction networks (PINs). These core scaffolding proteins can be seen as three principal layers classified by protein family, with DLG proteins being at the top, SHANKs along the bottom, and DLGAPs connecting the two layers. Early studies utilizing yeast two hybrid enabled the identification of direct protein-protein interactions (PPIs) within the multiple layers of scaffolding proteins. More recently, mass-spectrometry has allowed the characterization of whole interactomes within the PSD. This expansion of knowledge has further solidified the centrality of core scaffolding family members within synaptic PINs and provided context for their role in neuronal development and synaptic function. Here, we discuss the scaffolding machinery of the PSD, their essential functions in the organization of synaptic PINs, along with their relationship to neuronal processes found to be impaired in complex brain disorders.
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Affiliation(s)
- Brent Wilkinson
- Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Marcelo P Coba
- Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; Department of Psychiatry and Behavioral Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA.
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20
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Babenko VN, Galyamina AG, Rogozin IB, Smagin DA, Kudryavtseva NN. Dopamine response gene pathways in dorsal striatum MSNs from a gene expression viewpoint: cAMP-mediated gene networks. BMC Neurosci 2020; 21:12. [PMID: 32216748 PMCID: PMC7099774 DOI: 10.1186/s12868-020-00560-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 03/18/2020] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Medium spiny neurons (MSNs) comprise the main body (95% in mouse) of the dorsal striatum neurons and represent dopaminoceptive GABAergic neurons. The cAMP (cyclic Adenosine MonoPhosphate)-mediated cascade of excitation and inhibition responses observed in MSN intracellular signal transduction is crucial for neuroscience research due to its involvement in the motor and behavioral functions. In particular, all types of addictions are related to MSNs. Shedding the light on the mechanics of the above-mentioned cascade is of primary importance for this research domain. RESULTS A mouse model of chronic social conflicts in daily agonistic interactions was used to analyze dorsal striatum neurons genes implicated in cAMP-mediated phosphorylation activation pathways specific for MSNs. Based on expression correlation analysis, we succeeded in dissecting Drd1- and Drd2-dopaminoceptive neurons (D1 and D2, correspondingly) gene pathways. We also found that D1 neurons genes clustering are split into two oppositely correlated states, passive and active ones, the latter apparently corresponding to D1 firing stage upon protein kinase A (PKA) activation. We observed that under defeat stress in chronic social conflicts the loser mice manifest overall depression of dopamine-mediated MSNs activity resulting in previously reported reduced motor activity, while the aggressive mice with positive fighting experience (aggressive mice) feature an increase in both D1-active phase and D2 MSNs genes expression leading to hyperactive behavior pattern corresponded by us before. Based on the alternative transcript isoforms expression analysis, it was assumed that many genes (Drd1, Adora1, Pde10, Ppp1r1b, Gnal), specifically those in D1 neurons, apparently remain transcriptionally repressed via the reversible mechanism of promoter CpG island silencing, resulting in alternative promoter usage following profound reduction in their expression rate. CONCLUSION Based on the animal stress model dorsal striatum pooled tissue RNA-Seq data restricted to cAMP related genes subset we elucidated MSNs steady states exhaustive projection for the first time. We correspond the existence of D1 active state not explicitly outlined before, and connected with dynamic dopamine neurotransmission cycles. Consequently, we were also able to indicate an oscillated postsynaptic dopamine vs glutamate action pattern in the course of the neurotransmission cycles.
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Affiliation(s)
- Vladimir N Babenko
- Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.
- Novosibirsk State University, Novosibirsk, Russia.
| | | | - Igor B Rogozin
- National Institutes of Health, Rockville Pike, Bethesda, MD, USA
| | - Dmitry A Smagin
- Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
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21
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Zhu F, Collins MO, Harmse J, Choudhary JS, Grant SGN, Komiyama NH. Cell-type-specific visualisation and biochemical isolation of endogenous synaptic proteins in mice. Eur J Neurosci 2019; 51:793-805. [PMID: 31621109 PMCID: PMC7079123 DOI: 10.1111/ejn.14597] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 09/07/2019] [Accepted: 10/08/2019] [Indexed: 01/01/2023]
Abstract
In recent years, the remarkable molecular complexity of synapses has been revealed, with over 1,000 proteins identified in the synapse proteome. Although it is known that different receptors and other synaptic proteins are present in different types of neurons, the extent of synapse diversity across the brain is largely unknown. This is mainly due to the limitations of current techniques. Here, we report an efficient method for the purification of synaptic protein complexes, fusing a high‐affinity tag to endogenous PSD95 in specific cell types. We also developed a strategy, which enables the visualisation of endogenous PSD95 with fluorescent‐protein tag in Cre‐recombinase‐expressing cells. We demonstrate the feasibility of proteomic analysis of synaptic protein complexes and visualisation of these in specific cell types. We find that the composition of PSD95 complexes purified from specific cell types differs from those extracted from tissues with diverse cellular composition. The results suggest that there might be differential interactions in the PSD95 complexes in different brain regions. We have detected differentially interacting proteins by comparing data sets from the whole hippocampus and the CA3 subfield of the hippocampus. Therefore, these novel conditional PSD95 tagging lines will not only serve as powerful tools for precisely dissecting synapse diversity in specific brain regions and subsets of neuronal cells, but also provide an opportunity to better understand brain region‐ and cell‐type‐specific alterations associated with various psychiatric/neurological diseases. These newly developed conditional gene tagging methods can be applied to many different synaptic proteins and will facilitate research on the molecular complexity of synapses.
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Affiliation(s)
- Fei Zhu
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Mark O Collins
- Department of Biomedical Science, The University of Sheffield, Sheffield, UK
| | - Johan Harmse
- The Wellcome Trust Sanger Institute, Cambridge, UK
| | - Jyoti S Choudhary
- Functional Proteomics Group, Chester Beatty Laboratories, Institute of Cancer Research, London, UK
| | - Seth G N Grant
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK.,The Wellcome Trust Sanger Institute, Cambridge, UK.,Simons Initiative for the Developing Brain (SIDB), University of Edinburgh, Edinburgh, UK
| | - Noboru H Komiyama
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK.,Simons Initiative for the Developing Brain (SIDB), University of Edinburgh, Edinburgh, UK.,The Patrick Wild Centre for Research into Autism, Fragile X Syndrome and Intellectual Disabilities, University of Edinburgh, Edinburgh, UK
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22
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Coba MP. Regulatory mechanisms in postsynaptic phosphorylation networks. Curr Opin Struct Biol 2019; 54:86-94. [PMID: 30807903 PMCID: PMC7018365 DOI: 10.1016/j.sbi.2019.01.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 12/19/2018] [Accepted: 01/06/2019] [Indexed: 12/11/2022]
Abstract
The modulation of the postsynaptic signaling machinery by protein phosphorylation has attracted much interest since it is key for the understanding of the regulation of a variety of synaptic functions. While advances in mass spectrometry have allowed us to begin performing large-scale analysis of protein phosphorylation in components of the PSD, the systematic collection of datasets and their functional significance within the context of regulatory signaling networks is in its infancy. Here, we will focus on the composition of the PSD phosphoproteome describing kinase, phosphatase, and protein domain modules involved in the regulation of phosphorylation signaling. We will discuss the impact of synaptic plasticity mechanisms such as long-term potentiation (LTP) in mammalian kinomes and describe the general rules of signaling organization in the PSD phosphoproteome.
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Affiliation(s)
- Marcelo P Coba
- Zilkha Neurogenetic Institute, Department of Psychiatry and Behavioral Sciences, University of Southern California, Los Angeles, CA, United States.
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23
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Lapek JD, Jiang Z, Wozniak JM, Arutyunova E, Wang SC, Lemieux MJ, Gonzalez DJ, O'Donoghue AJ. Quantitative Multiplex Substrate Profiling of Peptidases by Mass Spectrometry. Mol Cell Proteomics 2019; 18:968-981. [PMID: 30705125 DOI: 10.1074/mcp.tir118.001099] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 12/31/2018] [Indexed: 12/14/2022] Open
Abstract
Proteolysis is an integral component of life and has been implicated in many disease processes. To improve our understanding of peptidase function, it is imperative to develop tools to uncover substrate specificity and cleavage efficiency. Here, we combine the quantitative power of tandem mass tags (TMTs) with an established peptide cleavage assay to yield quantitative Multiplex Substrate Profiling by Mass Spectrometry (qMSP-MS). This assay was validated with papain, a well-characterized cysteine peptidase, to generate cleavage efficiency values for hydrolysis of 275 unique peptide bonds in parallel. To demonstrate the breath of this assay, we show that qMSP-MS can uncover the substrate specificity of minimally characterized intramembrane rhomboid peptidases, as well as define hundreds of proteolytic activities in complex biological samples, including secretions from lung cancer cell lines. Importantly, our qMSP-MS library uses synthetic peptides whose termini are unmodified, allowing us to characterize not only endo- but also exo-peptidase activity. Each cleaved peptide sequence can be ranked by turnover rate, and the amino acid sequence of the best substrates can be used for designing fluorescent reporter substrates. Discovery of peptide substrates that are selectively cleaved by peptidases which are active at the site of disease highlights the potential for qMSP-MS to guide the development of peptidase-activating drugs for cancer and infectious disease.
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Affiliation(s)
- John D Lapek
- From the ‡Department of Pharmacology, University of California San Diego, 9500 Gilman Drive La Jolla, California 92093;; §Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive La Jolla, California 92093;; From the ‡Department of Pharmacology, University of California San Diego, 9500 Gilman Drive La Jolla, California 92093
| | - Zhenze Jiang
- §Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive La Jolla, California 92093;; ¶Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive La Jolla, California 92093;; From the ‡Department of Pharmacology, University of California San Diego, 9500 Gilman Drive La Jolla, California 92093
| | - Jacob M Wozniak
- From the ‡Department of Pharmacology, University of California San Diego, 9500 Gilman Drive La Jolla, California 92093;; §Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive La Jolla, California 92093
| | - Elena Arutyunova
- ‖Department of Biochemistry, Faculty of Medicine and Dentistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
| | - Steven C Wang
- §Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive La Jolla, California 92093;; **Division of Biological Sciences, University of California, San Diego, 9500, Gilman Drive, La Jolla, California 92093
| | - M Joanne Lemieux
- ‖Department of Biochemistry, Faculty of Medicine and Dentistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
| | - David J Gonzalez
- From the ‡Department of Pharmacology, University of California San Diego, 9500 Gilman Drive La Jolla, California 92093;; §Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive La Jolla, California 92093;.
| | - Anthony J O'Donoghue
- §Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive La Jolla, California 92093;.
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24
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McClatchy DB, Yu NK, Martínez-Bartolomé S, Patel R, Pelletier AR, Lavalle-Adam M, Powell SB, Roberto M, Yates JR. Structural Analysis of Hippocampal Kinase Signal Transduction. ACS Chem Neurosci 2018; 9:3072-3085. [PMID: 30053369 DOI: 10.1021/acschemneuro.8b00284] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Kinases are a major clinical target for human diseases. Identifying the proteins that interact with kinases in vivo will provide information on unreported substrates and will potentially lead to more specific methods for therapeutic kinase regulation. Here, endogenous immunoprecipitations of evolutionally distinct kinases (i.e., Akt, ERK2, and CAMK2) from rodent hippocampi were analyzed by mass spectrometry to generate three highly confident kinase protein-protein interaction networks. Proteins of similar function were identified in the networks, suggesting a universal model for kinase signaling complexes. Protein interactions were observed between kinases with reported symbiotic relationships. The kinase networks were significantly enriched in genes associated with specific neurodevelopmental disorders providing novel structural connections between these disease-associated genes. To demonstrate a functional relationship between the kinases and the network, pharmacological manipulation of Akt in hippocampal slices was shown to regulate the activity of potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel(HCN1), which was identified in the Akt network. Overall, the kinase protein-protein interaction networks provide molecular insight of the spatial complexity of in vivo kinase signal transduction which is required to achieve the therapeutic potential of kinase manipulation in the brain.
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Affiliation(s)
- Daniel B. McClatchy
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Nam-Kyung Yu
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States
| | | | - Reesha Patel
- Department of Neuroscience, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Alexander R. Pelletier
- Department of Biochemistry, Microbiology and Immunology and Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Mathieu Lavalle-Adam
- Department of Biochemistry, Microbiology and Immunology and Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Susan B. Powell
- Department of Psychiatry, UCSD, La Jolla, California 92093, United States
| | - Marisa Roberto
- Department of Neuroscience, The Scripps Research Institute, La Jolla, California 92037, United States
| | - John R. Yates
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States
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25
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Shimizu T, Kanai K, Sugawara Y, Uchida C, Uchida T. Prolyl Isomerase Pin1 Directly Regulates Calcium/Calmodulin-Dependent Protein Kinase II Activity in Mouse Brains. Front Pharmacol 2018; 9:1351. [PMID: 30532705 PMCID: PMC6265371 DOI: 10.3389/fphar.2018.01351] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 11/05/2018] [Indexed: 11/28/2022] Open
Abstract
Calcium/calmodulin-dependent protein kinase II (CaMKII) is abundant in the brain and functions as a mediator of calcium signaling. We found that the relative activity of CaMKII was significantly lower in the WT mouse brains than in the Pin1-/- mouse brains. Pin1 binds to phosphorylated CaMKII and weakens its activity. For this reason, the phosphorylation level of tau in the presence of Pin1 is lower than that in the absence of Pin1, and microtubule polymerization is not downregulated by CaMKII when Pin1 is present. These results suggest a novel mechanism of action of Pin1 to prevent neurodegeneration.
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Affiliation(s)
- Taiki Shimizu
- Molecular Enzymology, Department of Molecular Cell Science, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Kenta Kanai
- Molecular Enzymology, Department of Molecular Cell Science, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Yui Sugawara
- Molecular Enzymology, Department of Molecular Cell Science, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Chiyoko Uchida
- Department of Human Development and Culture, Fukushima University, Fukushima, Japan
| | - Takafumi Uchida
- Molecular Enzymology, Department of Molecular Cell Science, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
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26
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G protein subunit phosphorylation as a regulatory mechanism in heterotrimeric G protein signaling in mammals, yeast, and plants. Biochem J 2018; 475:3331-3357. [PMID: 30413679 DOI: 10.1042/bcj20160819] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 09/28/2018] [Accepted: 10/02/2018] [Indexed: 12/15/2022]
Abstract
Heterotrimeric G proteins composed of Gα, Gβ, and Gγ subunits are vital eukaryotic signaling elements that convey information from ligand-regulated G protein-coupled receptors (GPCRs) to cellular effectors. Heterotrimeric G protein-based signaling pathways are fundamental to human health [Biochimica et Biophysica Acta (2007) 1768, 994-1005] and are the target of >30% of pharmaceuticals in clinical use [Biotechnology Advances (2013) 31, 1676-1694; Nature Reviews Drug Discovery (2017) 16, 829-842]. This review focuses on phosphorylation of G protein subunits as a regulatory mechanism in mammals, budding yeast, and plants. This is a re-emerging field, as evidence for phosphoregulation of mammalian G protein subunits from biochemical studies in the early 1990s can now be complemented with contemporary phosphoproteomics and genetic approaches applied to a diversity of model systems. In addition, new evidence implicates a family of plant kinases, the receptor-like kinases, which are monophyletic with the interleukin-1 receptor-associated kinase/Pelle kinases of metazoans, as possible GPCRs that signal via subunit phosphorylation. We describe early and modern observations on G protein subunit phosphorylation and its functional consequences in these three classes of organisms, and suggest future research directions.
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27
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Zhu F, Cizeron M, Qiu Z, Benavides-Piccione R, Kopanitsa MV, Skene NG, Koniaris B, DeFelipe J, Fransén E, Komiyama NH, Grant SGN. Architecture of the Mouse Brain Synaptome. Neuron 2018; 99:781-799.e10. [PMID: 30078578 PMCID: PMC6117470 DOI: 10.1016/j.neuron.2018.07.007] [Citation(s) in RCA: 116] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 06/22/2018] [Accepted: 07/03/2018] [Indexed: 12/11/2022]
Abstract
Synapses are found in vast numbers in the brain and contain complex proteomes. We developed genetic labeling and imaging methods to examine synaptic proteins in individual excitatory synapses across all regions of the mouse brain. Synapse catalogs were generated from the molecular and morphological features of a billion synapses. Each synapse subtype showed a unique anatomical distribution, and each brain region showed a distinct signature of synapse subtypes. Whole-brain synaptome cartography revealed spatial architecture from dendritic to global systems levels and previously unknown anatomical features. Synaptome mapping of circuits showed correspondence between synapse diversity and structural and functional connectomes. Behaviorally relevant patterns of neuronal activity trigger spatiotemporal postsynaptic responses sensitive to the structure of synaptome maps. Areas controlling higher cognitive function contain the greatest synapse diversity, and mutations causing cognitive disorders reorganized synaptome maps. Synaptome technology and resources have wide-ranging application in studies of the normal and diseased brain.
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Affiliation(s)
- Fei Zhu
- Genes to Cognition Program, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK; UCL Institute of Neurology, Queen Square, WC1N 3BG London, UK
| | - Mélissa Cizeron
- Genes to Cognition Program, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK; Institut NeuroMyoGène, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR-5310, INSERM U-1217, 69008 Lyon, France
| | - Zhen Qiu
- Genes to Cognition Program, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Ruth Benavides-Piccione
- Instituto Cajal (CSIC) 28002 Madrid, Centro de Tecnología Biomédica (UPM) 28223 Madrid; CIBERNED, ISCIII, 28031 Madrid, Spain
| | - Maksym V Kopanitsa
- Synome Ltd, Babraham Research Campus, Cambridge CB22 3AT, UK; UK Dementia Research Institute, Imperial College London, London W12 0NN, UK
| | - Nathan G Skene
- Genes to Cognition Program, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK; UCL Institute of Neurology, Queen Square, WC1N 3BG London, UK; Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Babis Koniaris
- Genes to Cognition Program, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Javier DeFelipe
- Instituto Cajal (CSIC) 28002 Madrid, Centro de Tecnología Biomédica (UPM) 28223 Madrid; CIBERNED, ISCIII, 28031 Madrid, Spain
| | - Erik Fransén
- Department of Computational Science and Technology, School of Electrical Engineering and Computer Science, KTH Royal Institute of Technology, 10044 Stockholm, Sweden
| | - Noboru H Komiyama
- Genes to Cognition Program, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Seth G N Grant
- Genes to Cognition Program, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK.
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28
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Roy M, Sorokina O, McLean C, Tapia-González S, DeFelipe J, Armstrong JD, Grant SGN. Regional Diversity in the Postsynaptic Proteome of the Mouse Brain. Proteomes 2018; 6:proteomes6030031. [PMID: 30071621 PMCID: PMC6161190 DOI: 10.3390/proteomes6030031] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 07/26/2018] [Accepted: 07/27/2018] [Indexed: 12/14/2022] Open
Abstract
The proteome of the postsynaptic terminal of excitatory synapses comprises over one thousand proteins in vertebrate species and plays a central role in behavior and brain disease. The brain is organized into anatomically distinct regions and whether the synapse proteome differs across these regions is poorly understood. Postsynaptic proteomes were isolated from seven forebrain and hindbrain regions in mice and their composition determined using proteomic mass spectrometry. Seventy-four percent of proteins showed differential expression and each region displayed a unique compositional signature. These signatures correlated with the anatomical divisions of the brain and their embryological origins. Biochemical pathways controlling plasticity and disease, protein interaction networks and individual proteins involved with cognition all showed differential regional expression. Combining proteomic and connectomic data shows that interconnected regions have specific proteome signatures. Diversity in synapse proteome composition is key feature of mouse and human brain structure.
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Affiliation(s)
- Marcia Roy
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK.
| | - Oksana Sorokina
- School of Informatics, University of Edinburgh, Edinburgh EH8 9AB, UK.
| | - Colin McLean
- School of Informatics, University of Edinburgh, Edinburgh EH8 9AB, UK.
| | - Silvia Tapia-González
- Departamento de Neurobiología Funcional y de Sistemas, Instituto Cajal (CSIC), Ave. Doctor Arce 37, 28002 Madrid and Laboratorio Cajal de Circuitos Corticales, Centro de Tecnología Biomédica (UPM), 28223 Pozuelo de Alarcón, Madrid, Spain.
| | - Javier DeFelipe
- Departamento de Neurobiología Funcional y de Sistemas, Instituto Cajal (CSIC), Ave. Doctor Arce 37, 28002 Madrid and Laboratorio Cajal de Circuitos Corticales, Centro de Tecnología Biomédica (UPM), 28223 Pozuelo de Alarcón, Madrid, Spain.
| | | | - Seth G N Grant
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK.
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29
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Steinberg SF. Post-translational modifications at the ATP-positioning G-loop that regulate protein kinase activity. Pharmacol Res 2018; 135:181-187. [PMID: 30048755 DOI: 10.1016/j.phrs.2018.07.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 07/10/2018] [Accepted: 07/11/2018] [Indexed: 12/27/2022]
Abstract
Protein kinases are a superfamily of enzymes that control a wide range of cellular functions. These enzymes share a highly conserved catalytic core that folds into a similar bilobar three-dimensional structure. One highly conserved region in the protein kinase core is the glycine-rich loop (or G-loop), a highly flexible loop that is characterized by a consensus GxGxxG sequence. The G-loop points toward the catalytic cleft and functions to bind and position ATP for phosphotransfer. Of note, in many protein kinases, the second and third glycine residues in the G-loop triad flank residues that can be targets for phosphorylation (Ser, Thr, or Tyr) or other post-translational modifications (ubiquitination, acetylation, O-GlcNAcylation, oxidation). There is considerable evidence that cyclin-dependent kinases are held inactive through inhibitory phosphorylation of the conserved Thr/Tyr residues in this position of the G-loop and that dephosphorylation by cellular phosphatases is required for CDK activation and progression through the cell cycle. This review summarizes literature that identifies residues in or adjacent to the G-loop in other protein kinases that are targets for functionally important post-translational modifications.
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Affiliation(s)
- Susan F Steinberg
- Department of Pharmacology, College of Physicians and Surgeons, Columbia University, 630 West 168th Street, New York, NY 10032, USA.
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30
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Baltussen LL, Rosianu F, Ultanir SK. Kinases in synaptic development and neurological diseases. Prog Neuropsychopharmacol Biol Psychiatry 2018; 84:343-352. [PMID: 29241837 DOI: 10.1016/j.pnpbp.2017.12.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 12/08/2017] [Accepted: 12/09/2017] [Indexed: 10/18/2022]
Abstract
Neuronal morphogenesis and synapse development is essential for building a functioning nervous system, and defects in these processes are associated with neurological disorders. Our understanding of molecular components and signalling events that contribute to neuronal development and pathogenesis is limited. Genes associated with neurodevelopmental and neurodegenerative diseases provide entry points for elucidating molecular events that contribute to these conditions. Several protein kinases, enzymes that regulate protein function by phosphorylating their substrates, are genetically linked to neurological disorders. Identifying substrates of these kinases is key to discovering their function and providing insight for possible therapies. In this review, we describe how various methods for kinase-substrate identification helped elucidate kinase signalling pathways important for neuronal development and function. We describe recent advances on roles of kinases TAOK2, TNIK and CDKL5 in neuronal development and the converging pathways of LRRK2, PINK1 and GAK in Parkinson's Disease.
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Affiliation(s)
- Lucas L Baltussen
- Kinases and Brain Development Laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Flavia Rosianu
- Kinases and Brain Development Laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Sila K Ultanir
- Kinases and Brain Development Laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom.
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31
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Neumaier F, Alpdogan S, Hescheler J, Schneider T. Protein phosphorylation maintains the normal function of cloned human Ca v2.3 channels. J Gen Physiol 2018; 150:491-510. [PMID: 29453293 PMCID: PMC5839719 DOI: 10.1085/jgp.201711880] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 12/22/2017] [Accepted: 01/24/2018] [Indexed: 11/30/2022] Open
Abstract
Cav2.3 Ca2+ channels are subject to cytosolic regulation, which has been difficult to characterize in native cells. Neumaier et al. demonstrate the role of phosphorylation in the function of these channels and suggest a close relationship between voltage dependence and the phosphorylation state. R-type currents mediated by native and recombinant Cav2.3 voltage-gated Ca2+ channels (VGCCs) exhibit facilitation (run-up) and subsequent decline (run-down) in whole-cell patch-clamp recordings. A better understanding of the two processes could provide insight into constitutive modulation of the channels in intact cells, but low expression levels and the need for pharmacological isolation have prevented investigations in native systems. Here, to circumvent these limitations, we use conventional and perforated-patch-clamp recordings in a recombinant expression system, which allows us to study the effects of cell dialysis in a reproducible manner. We show that the decline of currents carried by human Cav2.3+β3 channel subunits during run-down is related to adenosine triphosphate (ATP) depletion, which reduces the number of functional channels and leads to a progressive shift of voltage-dependent gating to more negative potentials. Both effects can be counteracted by hydrolysable ATP, whose protective action is almost completely prevented by inhibition of serine/threonine but not tyrosine or lipid kinases. Protein kinase inhibition also mimics the effects of run-down in intact cells, reduces the peak current density, and hyperpolarizes the voltage dependence of gating. Together, our findings indicate that ATP promotes phosphorylation of either the channel or an associated protein, whereas dephosphorylation during cell dialysis results in run-down. These data also distinguish the effects of ATP on Cav2.3 channels from those on other VGCCs because neither direct nucleotide binding nor PIP2 synthesis is required for protection from run-down. We conclude that protein phosphorylation is required for Cav2.3 channel function and could directly influence the normal features of current carried by these channels. Curiously, some of our findings also point to a role for leupeptin-sensitive proteases in run-up and possibly ATP protection from run-down. As such, the present study provides a reliable baseline for further studies on Cav2.3 channel regulation by protein kinases, phosphatases, and possibly proteases.
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Affiliation(s)
- Felix Neumaier
- Institute for Neurophysiology, University of Cologne, Cologne, Germany
| | - Serdar Alpdogan
- Institute for Neurophysiology, University of Cologne, Cologne, Germany
| | - Jürgen Hescheler
- Institute for Neurophysiology, University of Cologne, Cologne, Germany
| | - Toni Schneider
- Institute for Neurophysiology, University of Cologne, Cologne, Germany
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32
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Erdem FA, Salzer I, Heo S, Chen WQ, Jung G, Lubec G, Boehm S, Yang JW. Updating In Vivo and In Vitro Phosphorylation and Methylation Sites of Voltage-Gated Kv7.2 Potassium Channels. Proteomics 2018; 17. [PMID: 28834300 DOI: 10.1002/pmic.201700015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 07/26/2017] [Indexed: 02/04/2023]
Abstract
Voltage-gated Kv7.2 potassium channels regulate neuronal excitability. The gating of these channels is tightly controlled by various mediators and neurotransmitters acting via G protein-coupled receptors; the underlying signaling cascades involve phosphatidylinositol-4,5-bisphosphate (PIP2 ), Ca2+ /calmodulin, and phosphorylation. Recent studies found that the PIP2 sensitivity of Kv7.2 channels is affected by two posttranslational modifications, phosphorylation and methylation, harboured within putative PIP2 -binding domains. In this study, we updated phosphorylation and methylation sites in Kv7.2 either heterologously expressed in mammalian cells or as GST-fusion proteins exposed to recombinant protein kinases by using LC-MS/MS. In vitro kinase assays revealed that CDK5, protein kinase C (PKC) alpha, PKA, p38 MAPK, CamKIIα, and GSK3β could mediate phosphorylation. Taken together, we provided a comprehensive map of phosphorylation and methylation in Kv7.2 within protein-protein and protein-lipid interaction domains. This may help to interpret the functional roles of individual PTM sites in Kv7.2 channels. All MS data are available via ProteomeXchange with the identifier PXD005567.
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Affiliation(s)
- Fatma Asli Erdem
- Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Isabella Salzer
- Department of Neurophysiology and Neuropharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Seok Heo
- Department of Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Wei-Qiang Chen
- Department of Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Gangsoo Jung
- Department of Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Gert Lubec
- Neuroproteomics, Paracelsus Medical University of Salzburg, Salzburg, Austria
| | - Stefan Boehm
- Department of Neurophysiology and Neuropharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Jae-Won Yang
- Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
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33
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Zhu J, Zhou Q, Shang Y, Li H, Peng M, Ke X, Weng Z, Zhang R, Huang X, Li SS, Feng G, Lu Y, Zhang M. Synaptic Targeting and Function of SAPAPs Mediated by Phosphorylation-Dependent Binding to PSD-95 MAGUKs. Cell Rep 2017; 21:3781-3793. [DOI: 10.1016/j.celrep.2017.11.107] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 11/13/2017] [Accepted: 11/29/2017] [Indexed: 10/18/2022] Open
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34
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Ji Y, Wei S, Hou J, Zhang C, Xue P, Wang J, Chen X, Guo X, Yang F. Integrated proteomic and N-glycoproteomic analyses of doxorubicin sensitive and resistant ovarian cancer cells reveal glycoprotein alteration in protein abundance and glycosylation. Oncotarget 2017; 8:13413-13427. [PMID: 28077793 PMCID: PMC5355108 DOI: 10.18632/oncotarget.14542] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 12/29/2016] [Indexed: 01/26/2023] Open
Abstract
Ovarian cancer is one of the most common cancer among women in the world, and chemotherapy remains the principal treatment for patients. However, drug resistance is a major obstacle to the effective treatment of ovarian cancers and the underlying mechanism is not clear. An increased understanding of the mechanisms that underline the pathogenesis of drug resistance is therefore needed to develop novel therapeutics and diagnostic. Herein, we report the comparative analysis of the doxorubicin sensitive OVCAR8 cells and its doxorubicin-resistant variant NCI/ADR-RES cells using integrated global proteomics and N-glycoproteomics. A total of 1525 unique N-glycosite-containing peptides from 740 N-glycoproteins were identified and quantified, of which 253 N-glycosite-containing peptides showed significant change in the NCI/ADR-RES cells. Meanwhile, stable isotope labeling by amino acids in cell culture (SILAC) based comparative proteomic analysis of the two ovarian cancer cells led to the quantification of 5509 proteins. As about 50% of the identified N-glycoproteins are low-abundance membrane proteins, only 44% of quantified unique N-glycosite-containing peptides had corresponding protein expression ratios. The comparison and calibration of the N-glycoproteome versus the proteome classified 14 change patterns of N-glycosite-containing peptides, including 8 up-regulated N-glycosite-containing peptides with the increased glycosylation sites occupancy, 35 up-regulated N-glycosite-containing peptides with the unchanged glycosylation sites occupancy, 2 down-regulated N-glycosite-containing peptides with the decreased glycosylation sites occupancy, 46 down-regulated N-glycosite-containing peptides with the unchanged glycosylation sites occupancy. Integrated proteomic and N-glycoproteomic analyses provide new insights, which can help to unravel the relationship of N-glycosylation and multidrug resistance (MDR), understand the mechanism of MDR, and discover the new diagnostic and therapeutic targets.
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Affiliation(s)
- Yanlong Ji
- Laboratory of Protein and Peptide Pharmaceuticals and Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shasha Wei
- Laboratory of Protein and Peptide Pharmaceuticals and Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Junjie Hou
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Chengqian Zhang
- Laboratory of Protein and Peptide Pharmaceuticals and Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Peng Xue
- Laboratory of Protein and Peptide Pharmaceuticals and Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jifeng Wang
- Laboratory of Protein and Peptide Pharmaceuticals and Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiulan Chen
- Laboratory of Protein and Peptide Pharmaceuticals and Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaojing Guo
- Laboratory of Protein and Peptide Pharmaceuticals and Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Fuquan Yang
- Laboratory of Protein and Peptide Pharmaceuticals and Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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35
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Baucum AJ. Proteomic Analysis of Postsynaptic Protein Complexes Underlying Neuronal Plasticity. ACS Chem Neurosci 2017; 8:689-701. [PMID: 28211672 DOI: 10.1021/acschemneuro.7b00008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Normal neuronal communication and synaptic plasticity at glutamatergic synapses requires dynamic regulation of postsynaptic molecules. Protein expression and protein post-translational modifications regulate protein interactions that underlie this organization. In this Review, we highlight data obtained over the last 20 years that have used qualitative and quantitative proteomics-based approaches to identify postsynaptic protein complexes. Herein, we describe how these proteomics studies have helped lay the foundation for understanding synaptic physiology and perturbations in synaptic signaling observed in different pathologies. We also describe emerging technologies that can be useful in these analyses. We focus on protein complexes associated with the highly abundant and functionally critical proteins: calcium/calmodulin-dependent protein kinase II, the N-methyl-d-aspartate, and α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid glutamate receptors, and postsynaptic density protein of 95 kDa.
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Affiliation(s)
- Anthony J. Baucum
- Department of Biology, Stark Neurosciences
Research Institute, Indiana University-Purdue University Indianapolis, 723 W. Michigan St., Indianapolis, Indiana 46202, United States
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36
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Shao G, Wang Y, Guan S, Burlingame AL, Lu F, Knox R, Ferriero DM, Jiang X. Proteomic Analysis of Mouse Cortex Postsynaptic Density following Neonatal Brain Hypoxia-Ischemia. Dev Neurosci 2017; 39:66-81. [PMID: 28315865 PMCID: PMC5519436 DOI: 10.1159/000456030] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 01/11/2017] [Indexed: 02/02/2023] Open
Abstract
Proteomics of the synapses and postsynaptic densities (PSDs) have provided a deep understanding of protein composition and signal networks in the adult brain, which underlie neuronal plasticity and neurodegenerative or psychiatric disorders. However, there is a paucity of knowledge about the architecture and organization of PSDs in the immature brain, and how it is modified by brain injury in an early developing stage. Mass spectrometry (MS)-based proteomic analysis was performed on PSDs prepared from cortices of postnatal day 9 naïve mice or pups which had suffered hypoxic-ischemic (HI) brain injury. 512 proteins of different functional groups were identified from PSDs collected 1 h after HI injury, among which 60 have not been reported previously. Seven newly identified proteins involved in neural development were highlighted. HI injury increased the yield of PSDs at early time points upon reperfusion, and multiple proteins were recruited into PSDs following the insult. Quantitative analysis was performed using spectral counting, and proteins whose relative expression was more than 50% up- or downregulated compared to the sham animals 1 h after HI insult were reported. Validation with Western blotting demonstrated changes in expression and phosphorylation of the N-methyl-D-aspartate receptor, activation of a series of postsynaptic protein kinases and dysregulation of scaffold and adaptor proteins in response to neonatal HI insult. This work, along with other recent studies of synaptic protein profiling in the immature brain, builds a foundation for future investigation on the molecular mechanisms underlying developing plasticity. Furthermore, it provides insights into the biochemical changes of PSDs following early brain hypoxia-ischemia, which is helpful for understanding not only the injury mechanisms, but also the process of repair or replenishment of neuronal circuits during recovery from brain damage.
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Affiliation(s)
- Guo Shao
- Inner Mongolia Key Laboratory of Hypoxic Translational Medicine, Baotou Medical College, Baotou, China
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37
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Alexander GM, Huang YZ, Soderblom EJ, He XP, Moseley MA, McNamara JO. Vagal nerve stimulation modifies neuronal activity and the proteome of excitatory synapses of amygdala/piriform cortex. J Neurochem 2017; 140:629-644. [PMID: 27973753 DOI: 10.1111/jnc.13931] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 11/13/2016] [Accepted: 12/09/2016] [Indexed: 12/19/2022]
Abstract
Vagal Nerve Stimulation (VNS) Therapy® is a United States Food and Drug Administration approved neurotherapeutic for medically refractory partial epilepsy and treatment-resistant depression. The molecular mechanisms underlying its beneficial effects are unclear. We hypothesized that one mechanism involves neuronal activity-dependent modifications of central nervous system excitatory synapses. To begin to test this hypothesis, we asked whether VNS modifies the activity of neurons in amygdala and hippocampus. Neuronal recordings from adult, freely moving rats revealed that activity in both amygdala and hippocampus was modified by VNS immediately after its application, and changes were detected following 1 week of stimulation. To investigate whether VNS modifies the proteome of excitatory synapses, we established a label-free, quantitative liquid chromatography-tandem mass spectrometry workflow that enables global analysis of the constituents of the postsynaptic density (PSD) proteome. PSD proteins were biochemically purified from amygdala/piriform cortex of VNS- or dummy-treated rats following 1-week stimulation, and individual PSD protein levels were quantified by liquid chromatography-tandem mass spectrometry analysis. We identified 1899 unique peptides corresponding to 425 proteins in PSD fractions, of which expression levels of 22 proteins were differentially regulated by VNS with changes greater than 150%. Changes in a subset of these proteins, including significantly increased expression of neurexin-1α, cadherin 13 and voltage-dependent calcium channel α2δ1, the primary target of the antiepileptic drug gabapentin, and decreased expression of voltage-dependent calcium channel γ3, were confirmed by western blot analysis of PSD samples. These results demonstrate that VNS modulates excitatory synapses through regulating a subset of the PSD proteome. Our study reveals molecular targets of VNS and point to possible mechanisms underlying its beneficial effects, including activity-dependent formation of excitatory synapses.
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Affiliation(s)
- Georgia M Alexander
- Department of Neurobiology, Duke University Medical Center, Durham, North Carolina, USA
| | - Yang Zhong Huang
- Department of Neurobiology, Duke University Medical Center, Durham, North Carolina, USA
| | - Erik J Soderblom
- Duke Proteomics Core Facility, Duke University Medical Center, Durham, North Carolina, USA
| | - Xiao-Ping He
- Department of Neurobiology, Duke University Medical Center, Durham, North Carolina, USA.,Department of Neurology, Duke University Medical Center, Durham, North Carolina, USA
| | - M Arthur Moseley
- Duke Proteomics Core Facility, Duke University Medical Center, Durham, North Carolina, USA
| | - James O McNamara
- Department of Neurobiology, Duke University Medical Center, Durham, North Carolina, USA.,Department of Neurology, Duke University Medical Center, Durham, North Carolina, USA.,Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina, USA
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38
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Chen J, Zhan L, Lu X, Xiao C, Sun N. The Alteration of ZiBuPiYin Recipe on Proteomic Profiling of Forebrain Postsynaptic Density of db/db Mice with Diabetes-Associated Cognitive Decline. J Alzheimers Dis 2017; 56:471-489. [PMID: 27886008 DOI: 10.3233/jad-160691] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Jing Chen
- Institute (College) of Integrative Medicine, Dalian Medical University, Dalian, Liaoning, China
| | - Libin Zhan
- Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
- The Second Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Xiaoguang Lu
- Department of Emergency Medicine, Zhongshan Hospital, Dalian University, Dalian, Liaoning, China
| | - Chi Xiao
- The Second Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Nijing Sun
- The Second Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
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39
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Tomasetti C, Iasevoli F, Buonaguro EF, De Berardis D, Fornaro M, Fiengo ALC, Martinotti G, Orsolini L, Valchera A, Di Giannantonio M, de Bartolomeis A. Treating the Synapse in Major Psychiatric Disorders: The Role of Postsynaptic Density Network in Dopamine-Glutamate Interplay and Psychopharmacologic Drugs Molecular Actions. Int J Mol Sci 2017; 18:E135. [PMID: 28085108 PMCID: PMC5297768 DOI: 10.3390/ijms18010135] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2016] [Revised: 12/25/2016] [Accepted: 01/08/2017] [Indexed: 12/20/2022] Open
Abstract
Dopamine-glutamate interplay dysfunctions have been suggested as pathophysiological key determinants of major psychotic disorders, above all schizophrenia and mood disorders. For the most part, synaptic interactions between dopamine and glutamate signaling pathways take part in the postsynaptic density, a specialized ultrastructure localized under the membrane of glutamatergic excitatory synapses. Multiple proteins, with the role of adaptors, regulators, effectors, and scaffolds compose the postsynaptic density network. They form structural and functional crossroads where multiple signals, starting at membrane receptors, are received, elaborated, integrated, and routed to appropriate nuclear targets. Moreover, transductional pathways belonging to different receptors may be functionally interconnected through postsynaptic density molecules. Several studies have demonstrated that psychopharmacologic drugs may differentially affect the expression and function of postsynaptic genes and proteins, depending upon the peculiar receptor profile of each compound. Thus, through postsynaptic network modulation, these drugs may induce dopamine-glutamate synaptic remodeling, which is at the basis of their long-term physiologic effects. In this review, we will discuss the role of postsynaptic proteins in dopamine-glutamate signals integration, as well as the peculiar impact of different psychotropic drugs used in clinical practice on postsynaptic remodeling, thereby trying to point out the possible future molecular targets of "synapse-based" psychiatric therapeutic strategies.
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Affiliation(s)
- Carmine Tomasetti
- NHS, Department of Mental Health ASL Teramo, Psychiatric Service of Diagnosis and Treatment, Hospital "Maria SS dello Splendore", 641021 Giulianova, Italy.
- Laboratory of Molecular and Translational Psychiatry, Department of Neuroscience, Reproductive and Odontostomatogical Sciences, University of Naples "Federico II", 80131 Napoli, Italy.
- Polyedra Research Group, 64100 Teramo, Italy.
| | - Felice Iasevoli
- Laboratory of Molecular and Translational Psychiatry, Department of Neuroscience, Reproductive and Odontostomatogical Sciences, University of Naples "Federico II", 80131 Napoli, Italy.
- Polyedra Research Group, 64100 Teramo, Italy.
| | - Elisabetta Filomena Buonaguro
- Laboratory of Molecular and Translational Psychiatry, Department of Neuroscience, Reproductive and Odontostomatogical Sciences, University of Naples "Federico II", 80131 Napoli, Italy.
- Polyedra Research Group, 64100 Teramo, Italy.
| | - Domenico De Berardis
- Polyedra Research Group, 64100 Teramo, Italy.
- NHS, Department of Mental Health ASL Teramo, Psychiatric Service of Diagnosis and Treatment, Hospital "G. Mazzini", 64100 Teramo, Italy.
- Department of Neuroscience and Imaging, University "G. d'Annunzio", 66100 Chieti, Italy.
| | - Michele Fornaro
- Polyedra Research Group, 64100 Teramo, Italy.
- New York State Psychiatric Institute, Columbia University, New York, NY 10027, USA.
| | | | - Giovanni Martinotti
- Polyedra Research Group, 64100 Teramo, Italy.
- Department of Neuroscience and Imaging, University "G. d'Annunzio", 66100 Chieti, Italy.
| | - Laura Orsolini
- Polyedra Research Group, 64100 Teramo, Italy.
- Casa di Cura Villa San Giuseppe, 63100 Ascoli Piceno, Italy.
| | - Alessandro Valchera
- Polyedra Research Group, 64100 Teramo, Italy.
- Casa di Cura Villa San Giuseppe, 63100 Ascoli Piceno, Italy.
| | | | - Andrea de Bartolomeis
- Laboratory of Molecular and Translational Psychiatry, Department of Neuroscience, Reproductive and Odontostomatogical Sciences, University of Naples "Federico II", 80131 Napoli, Italy.
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40
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Phosphorylation of Drebrin and Its Role in Neuritogenesis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1006:49-60. [PMID: 28865014 DOI: 10.1007/978-4-431-56550-5_4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
Neuritogenesis is an early event in neuronal development in which newborn neurons first form growth cones, as a prerequisite for the formation of axons and dendrites. Growth cones emerge from segmented regions of the lamellipodium of embryonic neurons and grow away from the cell body leaving behind a neurite that will eventually polarise into an axon or dendrite. Growth cones also function to navigate precise routes through the embryo to locate an appropriate synaptic partner. Dynamic interactions between two components of the neuronal cytoskeleton, actin filaments and microtubules, are known to be essential for growth cone formation and hence neuritogenesis. The molecular mechanisms that coordinate interactions between actin filaments and dynamic microtubules during neuritogenesis are beginning to be understood. One candidate pathway coupling actin filaments to microtubules consists of the actin filament-binding protein drebrin and the microtubule-binding +TIP protein EB3. This pathway is regulated proximally by cyclin-dependent kinase 5 phosphorylation of drebrin but the upstream elements in the pathway have yet to be identified.
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41
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Ramadan N, Ghazale H, El-Sayyad M, El-Haress M, Kobeissy FH. Neuroproteomics Studies: Challenges and Updates. Methods Mol Biol 2017; 1598:3-19. [PMID: 28508355 DOI: 10.1007/978-1-4939-6952-4_1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The Human Genome Project in 2003 has resulted in the complete sequence of ~99% of the human genome paving the road for the Human Proteome Project (HPP) assessing the full characterization of the translated protein map of the 20,300 protein-coding genes. Consequently, the emerging of the proteomics field has successfully been adopted as the method of choice for the proteome characterization. Proteomics is a term that is used to encompass multidisciplinary approaches combining different technologies that aim to study the entire spectrum of protein changes at a specific physiological condition. Proteomics research has shown excellent outcomes in different fields, among which is neuroscience; however, the complexity of the nervous systems necessitated the genesis of a new subdiscipline of proteomics termed as "neuroproteomics." Neuroproteomics studies involve assessing the quantitative and qualitative aspects of nervous system components encompassing global dynamic events underlying various brain-related disorders ranging from neuropsychiatric disorders, degenerative disorders, mental illness, and most importantly brain-specific neurotrauma-related injuries. In this introductory chapter, we will provide a brief historical perspective on the field of neuroproteomics. In doing so, we will highlight on the recent applications of neuroproteomics in the areas of neurotrauma, an area that has benefitted from neuroproteomics in terms of biomarker research, spatiotemporal injury mechanism, and its use to translate its findings from experimental settings to human translational applications. Importantly, this chapter will include some recommendation to the general studies in the area of neuroproteomics and the need to move from this field from being a descriptive, hypothesis-free approach to being an independent mature scientific discipline.
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Affiliation(s)
- Naify Ramadan
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Hussein Ghazale
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | | | - Mohamad El-Haress
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
- Faculty of Medicine, Beirut Arab University, Beirut, Lebanon
| | - Firas H Kobeissy
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon.
- Department of Psychiatry, Center for Neuroproteomics and Biomarkers Research, University of Florida, Gainesville, FL, USA.
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42
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Zeng M, Shang Y, Araki Y, Guo T, Huganir RL, Zhang M. Phase Transition in Postsynaptic Densities Underlies Formation of Synaptic Complexes and Synaptic Plasticity. Cell 2016; 166:1163-1175.e12. [PMID: 27565345 DOI: 10.1016/j.cell.2016.07.008] [Citation(s) in RCA: 363] [Impact Index Per Article: 45.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 05/15/2016] [Accepted: 07/07/2016] [Indexed: 11/17/2022]
Abstract
Postsynaptic densities (PSDs) are membrane semi-enclosed, submicron protein-enriched cellular compartments beneath postsynaptic membranes, which constantly exchange their components with bulk aqueous cytoplasm in synaptic spines. Formation and activity-dependent modulation of PSDs is considered as one of the most basic molecular events governing synaptic plasticity in the nervous system. In this study, we discover that SynGAP, one of the most abundant PSD proteins and a Ras/Rap GTPase activator, forms a homo-trimer and binds to multiple copies of PSD-95. Binding of SynGAP to PSD-95 induces phase separation of the complex, forming highly concentrated liquid-like droplets reminiscent of the PSD. The multivalent nature of the SynGAP/PSD-95 complex is critical for the phase separation to occur and for proper activity-dependent SynGAP dispersions from the PSD. In addition to revealing a dynamic anchoring mechanism of SynGAP at the PSD, our results also suggest a model for phase-transition-mediated formation of PSD.
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Affiliation(s)
- Menglong Zeng
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Yuan Shang
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Yoichi Araki
- Department of Neuroscience and Kavli Neuroscience Discovery Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Tingfeng Guo
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Richard L Huganir
- Department of Neuroscience and Kavli Neuroscience Discovery Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Mingjie Zhang
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China; Center of Systems Biology and Human Health, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China.
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43
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Salzer I, Erdem FA, Chen WQ, Heo S, Koenig X, Schicker KW, Kubista H, Lubec G, Boehm S, Yang JW. Phosphorylation regulates the sensitivity of voltage-gated Kv7.2 channels towards phosphatidylinositol-4,5-bisphosphate. J Physiol 2016; 595:759-776. [PMID: 27621207 PMCID: PMC5215842 DOI: 10.1113/jp273274] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 08/30/2016] [Indexed: 12/22/2022] Open
Abstract
Key points Phosphatidylinositol‐4,5‐bisphosphate (PIP2) is a key regulator of many membrane proteins, including voltage‐gated Kv7.2 channels. In this study, we identified the residues in five phosphorylation sites and their corresponding protein kinases, the former being clustered within one of four putative PIP2‐binding domains in Kv7.2. Dephosphorylation of these residues reduced the sensitivity of Kv7.2 channels towards PIP2. Dephosphorylation of Kv7.2 affected channel inhibition via M1 muscarinic receptors, but not via bradykinin receptors. Our data indicated that phosphorylation of the Kv7.2 channel was necessary to maintain its low affinity for PIP2, thereby ensuring the tight regulation of the channel via G protein‐coupled receptors.
Abstract The function of numerous ion channels is tightly controlled by G protein‐coupled receptors (GPCRs). The underlying signalling mechanisms may involve phosphorylation of channel proteins and participation of phosphatidylinositol‐4,5‐bisphosphate (PIP2). Although the roles of both mechanisms have been investigated extensively, thus far only little has been reported on their interaction in channel modulation. GPCRs govern Kv7 channels, the latter playing a major role in the regulation of neuronal excitability by determining the levels of PIP2 and through phosphorylation. Using liquid chromatography‐coupled mass spectrometry for Kv7.2 immunoprecipitates of rat brain membranes and transfected cells, we mapped a cluster of five phosphorylation sites in one of the PIP2‐binding domains. To evaluate the effect of phosphorylation on PIP2‐mediated Kv7.2 channel regulation, a quintuple alanine mutant of these serines (S427/S436/S438/S446/S455; A5 mutant) was generated to mimic the dephosphorylated state. Currents passing through these mutated channels were less sensitive towards PIP2 depletion via the voltage‐sensitive phosphatase Dr‐VSP than were wild‐type channels. In vitro phosphorylation assays with the purified C‐terminus of Kv7.2 revealed that CDK5, p38 MAPK, CaMKIIα and PKA were able to phosphorylate the five serines. Inhibition of these protein kinases reduced the sensitivity of wild‐type but not mutant Kv7.2 channels towards PIP2 depletion via Dr‐VSP. In superior cervical ganglion neurons, the protein kinase inhibitors attenuated Kv7 current regulation via M1 receptors, but left unaltered the control by B2 receptors. Our results revealed that the phosphorylation status of serines located within a putative PIP2‐binding domain determined the phospholipid sensitivity of Kv7.2 channels and supported GPCR‐mediated channel regulation. Phosphatidylinositol‐4,5‐bisphosphate (PIP2) is a key regulator of many membrane proteins, including voltage‐gated Kv7.2 channels. In this study, we identified the residues in five phosphorylation sites and their corresponding protein kinases, the former being clustered within one of four putative PIP2‐binding domains in Kv7.2. Dephosphorylation of these residues reduced the sensitivity of Kv7.2 channels towards PIP2. Dephosphorylation of Kv7.2 affected channel inhibition via M1 muscarinic receptors, but not via bradykinin receptors. Our data indicated that phosphorylation of the Kv7.2 channel was necessary to maintain its low affinity for PIP2, thereby ensuring the tight regulation of the channel via G protein‐coupled receptors.
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Affiliation(s)
- Isabella Salzer
- Department of Neurophysiology and Neuropharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, 1090, Vienna, Austria
| | - Fatma Asli Erdem
- Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, 1090, Vienna, Austria
| | - Wei-Qiang Chen
- Department of Pediatrics, Medical University of Vienna, 1090, Vienna, Austria
| | - Seok Heo
- Department of Pediatrics, Medical University of Vienna, 1090, Vienna, Austria
| | - Xaver Koenig
- Department of Neurophysiology and Neuropharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, 1090, Vienna, Austria
| | - Klaus W Schicker
- Department of Neurophysiology and Neuropharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, 1090, Vienna, Austria
| | - Helmut Kubista
- Department of Neurophysiology and Neuropharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, 1090, Vienna, Austria
| | - Gert Lubec
- Department of Pharmaceutical Chemistry, University of Vienna, 1090, Vienna, Austria
| | - Stefan Boehm
- Department of Neurophysiology and Neuropharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, 1090, Vienna, Austria
| | - Jae-Won Yang
- Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, 1090, Vienna, Austria
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44
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Patrizio A, Specht CG. Counting numbers of synaptic proteins: absolute quantification and single molecule imaging techniques. NEUROPHOTONICS 2016; 3:041805. [PMID: 27335891 PMCID: PMC4891561 DOI: 10.1117/1.nph.3.4.041805] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 05/02/2016] [Indexed: 06/06/2023]
Abstract
The ability to count molecules is essential to elucidating cellular mechanisms, as these often depend on the absolute numbers and concentrations of molecules within specific compartments. Such is the case at chemical synapses, where the transmission of information from presynaptic to postsynaptic terminals requires complex interactions between small sets of molecules. Be it the subunit stoichiometry specifying neurotransmitter receptor properties, the copy numbers of scaffold proteins setting the limit of receptor accumulation at synapses, or protein packing densities shaping the molecular organization and plasticity of the postsynaptic density, all of these depend on exact quantities of components. A variety of proteomic, electrophysiological, and quantitative imaging techniques have yielded insights into the molecular composition of synaptic complexes. In this review, we compare the different quantitative approaches and consider the potential of single molecule imaging techniques for the quantification of synaptic components. We also discuss specific neurobiological data to contextualize the obtained numbers and to explain how they aid our understanding of synaptic structure and function.
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Affiliation(s)
- Angela Patrizio
- Institute of Biology, Biologie Cellulaire de la Synapse, Inserm U1024, CNRS 8197, École Normale Supérieure (ENS), 46 rue d’Ulm, Paris 75005, France
| | - Christian G. Specht
- Institute of Biology, Biologie Cellulaire de la Synapse, Inserm U1024, CNRS 8197, École Normale Supérieure (ENS), 46 rue d’Ulm, Paris 75005, France
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45
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Vogt J, Yang JW, Mobascher A, Cheng J, Li Y, Liu X, Baumgart J, Thalman C, Kirischuk S, Unichenko P, Horta G, Radyushkin K, Stroh A, Richers S, Sahragard N, Distler U, Tenzer S, Qiao L, Lieb K, Tüscher O, Binder H, Ferreiros N, Tegeder I, Morris AJ, Gropa S, Nürnberg P, Toliat MR, Winterer G, Luhmann HJ, Huai J, Nitsch R. Molecular cause and functional impact of altered synaptic lipid signaling due to a prg-1 gene SNP. EMBO Mol Med 2016; 8:25-38. [PMID: 26671989 PMCID: PMC4718157 DOI: 10.15252/emmm.201505677] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Loss of plasticity‐related gene 1 (PRG‐1), which regulates synaptic phospholipid signaling, leads to hyperexcitability via increased glutamate release altering excitation/inhibition (E/I) balance in cortical networks. A recently reported SNP in prg‐1 (R345T/mutPRG‐1) affects ~5 million European and US citizens in a monoallelic variant. Our studies show that this mutation leads to a loss‐of‐PRG‐1 function at the synapse due to its inability to control lysophosphatidic acid (LPA) levels via a cellular uptake mechanism which appears to depend on proper glycosylation altered by this SNP. PRG‐1+/− mice, which are animal correlates of human PRG‐1+/mut carriers, showed an altered cortical network function and stress‐related behavioral changes indicating altered resilience against psychiatric disorders. These could be reversed by modulation of phospholipid signaling via pharmacological inhibition of the LPA‐synthesizing molecule autotaxin. In line, EEG recordings in a human population‐based cohort revealed an E/I balance shift in monoallelic mutPRG‐1 carriers and an impaired sensory gating, which is regarded as an endophenotype of stress‐related mental disorders. Intervention into bioactive lipid signaling is thus a promising strategy to interfere with glutamate‐dependent symptoms in psychiatric diseases.
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Affiliation(s)
- Johannes Vogt
- Institute for Microscopic Anatomy and Neurobiology, University Medical Center, Johannes Gutenberg-University, Mainz, Germany
| | - Jenq-Wei Yang
- Institute for Physiology and Pathophysiology, University Medical Center, Johannes Gutenberg-University, Mainz, Germany
| | - Arian Mobascher
- Department of Psychiatry and Psychotherapy, University Medical Center, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Jin Cheng
- Institute for Microscopic Anatomy and Neurobiology, University Medical Center, Johannes Gutenberg-University, Mainz, Germany
| | - Yunbo Li
- Institute for Microscopic Anatomy and Neurobiology, University Medical Center, Johannes Gutenberg-University, Mainz, Germany
| | - Xingfeng Liu
- Institute for Microscopic Anatomy and Neurobiology, University Medical Center, Johannes Gutenberg-University, Mainz, Germany
| | - Jan Baumgart
- Institute for Microscopic Anatomy and Neurobiology, University Medical Center, Johannes Gutenberg-University, Mainz, Germany
| | - Carine Thalman
- Institute for Microscopic Anatomy and Neurobiology, University Medical Center, Johannes Gutenberg-University, Mainz, Germany
| | - Sergei Kirischuk
- Institute for Physiology and Pathophysiology, University Medical Center, Johannes Gutenberg-University, Mainz, Germany
| | - Petr Unichenko
- Institute for Physiology and Pathophysiology, University Medical Center, Johannes Gutenberg-University, Mainz, Germany
| | - Guilherme Horta
- Institute for Microscopic Anatomy and Neurobiology, University Medical Center, Johannes Gutenberg-University, Mainz, Germany
| | - Konstantin Radyushkin
- Focus Program Translational Neuroscience (FTN), University Medical Center, Johannes Gutenberg-University, Mainz, Germany
| | - Albrecht Stroh
- Institute for Microscopic Anatomy and Neurobiology, University Medical Center, Johannes Gutenberg-University, Mainz, Germany
| | - Sebastian Richers
- Institute for Microscopic Anatomy and Neurobiology, University Medical Center, Johannes Gutenberg-University, Mainz, Germany
| | - Nassim Sahragard
- Institute for Microscopic Anatomy and Neurobiology, University Medical Center, Johannes Gutenberg-University, Mainz, Germany
| | - Ute Distler
- Focus Program Translational Neuroscience (FTN), University Medical Center, Johannes Gutenberg-University, Mainz, Germany Institute for Immunology, University Medical Center, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Stefan Tenzer
- Institute for Immunology, University Medical Center, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Lianyong Qiao
- Institute for Microscopic Anatomy and Neurobiology, University Medical Center, Johannes Gutenberg-University, Mainz, Germany
| | - Klaus Lieb
- Department of Psychiatry and Psychotherapy, University Medical Center, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Oliver Tüscher
- Department of Psychiatry and Psychotherapy, University Medical Center, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Harald Binder
- Institute of Medical Biostatistics, Epidemiology and Informatics, University Medical Center, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Nerea Ferreiros
- Institute of Clinical Pharmacology Goethe-University Hospital, Frankfurt am Main, Germany
| | - Irmgard Tegeder
- Institute of Clinical Pharmacology Goethe-University Hospital, Frankfurt am Main, Germany
| | - Andrew J Morris
- Division of Cardiovascular Medicine, Gill Heart Institute, University of Kentucky, Lexington, KY, USA
| | - Sergiu Gropa
- Department of Neurology, University Medical Center, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Peter Nürnberg
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
| | - Mohammad R Toliat
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
| | - Georg Winterer
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
| | - Heiko J Luhmann
- Institute for Physiology and Pathophysiology, University Medical Center, Johannes Gutenberg-University, Mainz, Germany
| | - Jisen Huai
- Institute for Microscopic Anatomy and Neurobiology, University Medical Center, Johannes Gutenberg-University, Mainz, Germany
| | - Robert Nitsch
- Institute for Microscopic Anatomy and Neurobiology, University Medical Center, Johannes Gutenberg-University, Mainz, Germany
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46
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Uys JD, McGuier NS, Gass JT, Griffin WC, Ball LE, Mulholland PJ. Chronic intermittent ethanol exposure and withdrawal leads to adaptations in nucleus accumbens core postsynaptic density proteome and dendritic spines. Addict Biol 2016; 21:560-74. [PMID: 25787124 DOI: 10.1111/adb.12238] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Alcohol use disorder is a chronic relapsing brain disease characterized by the loss of ability to control alcohol (ethanol) intake despite knowledge of detrimental health or personal consequences. Clinical and pre-clinical models provide strong evidence for chronic ethanol-associated alterations in glutamatergic signaling and impaired synaptic plasticity in the nucleus accumbens (NAc). However, the neural mechanisms that contribute to aberrant glutamatergic signaling in ethanol-dependent individuals in this critical brain structure remain unknown. Using an unbiased proteomic approach, we investigated the effects of chronic intermittent ethanol (CIE) exposure on neuroadaptations in postsynaptic density (PSD)-enriched proteins in the NAc of ethanol-dependent mice. Compared with controls, CIE exposure significantly changed expression levels of 50 proteins in the PSD-enriched fraction. Systems biology and functional annotation analyses demonstrated that the dysregulated proteins are expressed at tetrapartite synapses and critically regulate cellular morphology. To confirm this latter finding, the density and morphology of dendritic spines were examined in the NAc core of ethanol-dependent mice. We found that CIE exposure and withdrawal differentially altered dendrite diameter and dendritic spine density and morphology. Through the use of quantitative proteomics and functional annotation, these series of experiments demonstrate that ethanol dependence produces neuroadaptations in proteins that modify dendritic spine morphology. In addition, these studies identified novel PSD-related proteins that contribute to the neurobiological mechanisms of ethanol dependence that drive maladaptive structural plasticity of NAc neurons.
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Affiliation(s)
- Joachim D. Uys
- Department of Cell and Molecular Pharmacology; Medical University of South Carolina; Charleston SC USA
| | - Natalie S. McGuier
- Department of Neuroscience; Medical University of South Carolina; Charleston SC USA
| | - Justin T. Gass
- Department of Neuroscience; Medical University of South Carolina; Charleston SC USA
| | - William C. Griffin
- Department of Psychiatry and Behavioral Sciences; Medical University of South Carolina; Charleston SC USA
| | - Lauren E. Ball
- Department of Cell and Molecular Pharmacology; Medical University of South Carolina; Charleston SC USA
| | - Patrick J. Mulholland
- Department of Neuroscience; Medical University of South Carolina; Charleston SC USA
- Department of Psychiatry and Behavioral Sciences; Medical University of South Carolina; Charleston SC USA
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47
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Kohansal-Nodehi M, Chua JJ, Urlaub H, Jahn R, Czernik D. Analysis of protein phosphorylation in nerve terminal reveals extensive changes in active zone proteins upon exocytosis. eLife 2016; 5. [PMID: 27115346 PMCID: PMC4894758 DOI: 10.7554/elife.14530] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 04/25/2016] [Indexed: 12/31/2022] Open
Abstract
Neurotransmitter release is mediated by the fast, calcium-triggered fusion of synaptic vesicles with the presynaptic plasma membrane, followed by endocytosis and recycling of the membrane of synaptic vesicles. While many of the proteins governing these processes are known, their regulation is only beginning to be understood. Here we have applied quantitative phosphoproteomics to identify changes in phosphorylation status of presynaptic proteins in resting and stimulated nerve terminals isolated from the brains of Wistar rats. Using rigorous quantification, we identified 252 phosphosites that are either up- or downregulated upon triggering calcium-dependent exocytosis. Particularly pronounced were regulated changes of phosphosites within protein constituents of the presynaptic active zone, including bassoon, piccolo, and RIM1. Additionally, we have mapped kinases and phosphatases that are activated upon stimulation. Overall, our study provides a snapshot of phosphorylation changes associated with presynaptic activity and provides a foundation for further functional analysis of key phosphosites involved in presynaptic plasticity. DOI:http://dx.doi.org/10.7554/eLife.14530.001 The human nervous system contains more than a hundred billion neurons that are connected with each other via junctions called synapses. When an electrical impulse travelling along a neuron arrives at a synapse, it triggers bubble-like packages called synaptic vesicles within the neuron to merge with the neuron’s surface membrane. The contents of these vesicles – chemical messengers called neurotransmitters – are then released into the synapse and carry the signal to the next neuron. Complex molecular machines made from many different proteins control the release of neurotransmitters. Quite a few of these proteins are regulated by the addition of phosphate groups at specific sites. However, not all of the proteins involved in the release of neurotransmitters have been studied in detail and it is largely unclear how most of them are regulated. Now, Kohansal-Nodehi et al. have used techniques involving mass spectrometry to find out which proteins have phosphate groups added or removed in neurons that are releasing neurotransmitters. The experiments used pinched-off synapses isolated from rat brains. These structures, referred to as “synaptosomes”, lend themselves to this kind of study because they can be induced to continuously release neurotransmitters for several minutes. Kohansal-Nodehi et al. identified over 250 specific sites on proteins in the synaptosomes where phosphate groups are attached, including many on the key proteins known to operate in neurotransmitter release. Moreover, some proteins were modified at multiple sites, especially the proteins that form a scaffold to capture synaptic vesicles close to the membrane and prepare them for release. The data also revealed important clues about the enzymes that either attach or remove the phosphate groups. Together, these findings provide new insights into the regulatory networks that control many proteins at the same time. The next challenge is to sort out which of these modifications change the interactions between the proteins that control neurotransmitter release, and to understand how these changes influence the trafficking of synaptic vesicles. DOI:http://dx.doi.org/10.7554/eLife.14530.002
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Affiliation(s)
| | - John Je Chua
- Interactomics and Intracellular Trafficking laboratory, National University of Singapore, Singapore, Singapore.,Department of Physiology, National University of Singapore, Singapore, Singapore.,Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Neurobiology/Ageing Programme, National University of Singapore, Singapore, Singapore
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.,Bioanalytics Group, University Medical Center Göttingen, Göttingen, Germany
| | - Reinhard Jahn
- Department of Neurobiology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Dominika Czernik
- Department of Neurobiology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
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48
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Sweet RA, MacDonald ML, Kirkwood CM, Ding Y, Schempf T, Jones-Laughner J, Kofler J, Ikonomovic MD, Lopez OL, Garver ME, Fitz NF, Koldamova R, Yates NA. Apolipoprotein E*4 (APOE*4) Genotype Is Associated with Altered Levels of Glutamate Signaling Proteins and Synaptic Coexpression Networks in the Prefrontal Cortex in Mild to Moderate Alzheimer Disease. Mol Cell Proteomics 2016; 15:2252-62. [PMID: 27103636 DOI: 10.1074/mcp.m115.056580] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Indexed: 01/26/2023] Open
Abstract
It has been hypothesized that Alzheimer disease (AD) is primarily a disorder of the synapse. However, assessment of the synaptic proteome in AD subjects has been limited to a small number of proteins and often included subjects with end-stage pathology. Protein from prefrontal cortex gray matter of 59 AD subjects with mild to moderate dementia and 12 normal elderly subjects was assayed using targeted mass spectrometry to quantify 191 synaptically expressed proteins. The profile of synaptic protein expression clustered AD subjects into two groups. One of these was characterized by reduced expression of glutamate receptor proteins, significantly increased synaptic protein network coexpression, and associated withApolipoprotein E*4 (APOE*4) carrier status. The second group, by contrast, showed few differences from control subjects. A subset of AD subjects had altered prefrontal cortex synaptic proteostasis for glutamate receptors and their signaling partners. Efforts to therapeutically target glutamate receptors in AD may have outcomes dependent on APOE*4 genotype.
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Affiliation(s)
- Robert A Sweet
- From the Departments of ‡Psychiatry, **Neurology, and ‡‡VISN 4 Mental Illness Research, Education and Clinical Center (MIRECC) and
| | | | | | | | | | | | | | - Milos D Ikonomovic
- **Neurology, and §§Geriatric Research, Education and Clinical Center (GRECC), VA Pittsburgh Healthcare System, Pittsburgh, PA
| | - Oscar L Lopez
- From the Departments of ‡Psychiatry, **Neurology, and
| | | | - Nicholas F Fitz
- ¶¶Environmental & Occupational Health, University of Pittsburgh, Pittsburgh, PA
| | - Radosveta Koldamova
- ¶¶Environmental & Occupational Health, University of Pittsburgh, Pittsburgh, PA
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49
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Xiao Q, Miao B, Bi J, Wang Z, Li Y. Prioritizing functional phosphorylation sites based on multiple feature integration. Sci Rep 2016; 6:24735. [PMID: 27090940 PMCID: PMC4835696 DOI: 10.1038/srep24735] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 04/04/2016] [Indexed: 12/15/2022] Open
Abstract
Protein phosphorylation is an important type of post-translational modification that is involved in a variety of biological activities. Most phosphorylation events occur on serine, threonine and tyrosine residues in eukaryotes. In recent years, many phosphorylation sites have been identified as a result of advances in mass-spectrometric techniques. However, a large percentage of phosphorylation sites may be non-functional. Systematically prioritizing functional sites from a large number of phosphorylation sites will be increasingly important for the study of their biological roles. This study focused on exploring the intrinsic features of functional phosphorylation sites to predict whether a phosphosite is likely to be functional. We found significant differences in the distribution of evolutionary conservation, kinase association, disorder score, and secondary structure between known functional and background phosphorylation datasets. We built four different types of classifiers based on the most representative features and found that their performances were similar. We also prioritized 213,837 human phosphorylation sites from a variety of phosphorylation databases, which will be helpful for subsequent functional studies. All predicted results are available for query and download on our website (Predict Functional Phosphosites, PFP, http://pfp.biosino.org/).
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Affiliation(s)
- Qingyu Xiao
- Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, P. R. China.,University of Chinese Academy of Sciences, Beijing, P. R. China
| | - Benpeng Miao
- Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, P. R. China.,University of Chinese Academy of Sciences, Beijing, P. R. China
| | - Jie Bi
- University of Chinese Academy of Sciences, Beijing, P. R. China.,Key Lab of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, P. R. China
| | - Zhen Wang
- Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, P. R. China
| | - Yixue Li
- Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, P. R. China.,Shanghai Center for Bioinformation Technology, Shanghai Industrial Technology Institute, Shanghai, P. R. China
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50
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Dieterich DC, Kreutz MR. Proteomics of the Synapse--A Quantitative Approach to Neuronal Plasticity. Mol Cell Proteomics 2016; 15:368-81. [PMID: 26307175 PMCID: PMC4739661 DOI: 10.1074/mcp.r115.051482] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 07/29/2015] [Indexed: 11/06/2022] Open
Abstract
The advances in mass spectrometry based proteomics in the past 15 years have contributed to a deeper appreciation of protein networks and the composition of functional synaptic protein complexes. However, research on protein dynamics underlying core mechanisms of synaptic plasticity in brain lag far behind. In this review, we provide a synopsis on proteomic research addressing various aspects of synaptic function. We discuss the major topics in the study of protein dynamics of the chemical synapse and the limitations of current methodology. We highlight recent developments and the future importance of multidimensional proteomics and metabolic labeling. Finally, emphasis is given on the conceptual framework of modern proteomics and its current shortcomings in the quest to gain a deeper understanding of synaptic plasticity.
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Affiliation(s)
- Daniela C Dieterich
- From the ‡Institute for Pharmacology and Toxicology, Otto-von-Guericke University Magdeburg, Germany; Research Group Neuralomics, Leibniz Institute for Neurobiology Magdeburg, Germany; ¶Center for Behavioral Brain Sciences (CBBS), Magdeburg, Germany.
| | - Michael R Kreutz
- §RG Neuroplasticity, Leibniz Institute for Neurobiology, Magdeburg, Germany; ¶Center for Behavioral Brain Sciences (CBBS), Magdeburg, Germany.
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