151
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Synaptic nanomodules underlie the organization and plasticity of spine synapses. Nat Neurosci 2018; 21:671-682. [PMID: 29686261 PMCID: PMC5920789 DOI: 10.1038/s41593-018-0138-9] [Citation(s) in RCA: 162] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 02/27/2018] [Indexed: 02/05/2023]
Abstract
Experience results in long-lasting changes in dendritic spine size, yet how the molecular architecture of the synapse responds to plasticity remains poorly understood. Here a combined approach of multicolor stimulated emission depletion microscopy (STED) and confocal imaging in rat and mouse demonstrates that structural plasticity is linked to the addition of unitary synaptic nanomodules to spines. Spine synapses in vivo and in vitro contain discrete and aligned subdiffraction modules of pre- and postsynaptic proteins whose number scales linearly with spine size. Live-cell time-lapse super-resolution imaging reveals that NMDA receptor-dependent increases in spine size are accompanied both by enhanced mobility of pre- and postsynaptic modules that remain aligned with each other and by a coordinated increase in the number of nanomodules. These findings suggest a simplified model for experience-dependent structural plasticity relying on an unexpectedly modular nanomolecular architecture of synaptic proteins.
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152
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Dunn M, Boltaev U, Beskow A, Pampou S, Realubit R, Meira T, Silva JV, Reeb R, Karan C, Jockusch S, Sulzer D, Chang YT, Sames D, Waites CL. Identification of Fluorescent Small Molecule Compounds for Synaptic Labeling by Image-Based, High-Content Screening. ACS Chem Neurosci 2018; 9:673-683. [PMID: 29215865 DOI: 10.1021/acschemneuro.7b00263] [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] [Indexed: 01/14/2023] Open
Abstract
Few tools are available for noninvasive imaging of synapses in the living mammalian brain. Current paradigms require the use of genetically modified mice or viral delivery of genetic material to the brain. To develop an alternative chemical approach, utilizing the recognition of synaptic components by organic small molecules, we designed an imaging-based, high-content screen in cultured cortical neurons to identify molecules based on their colocalization with fluorescently tagged synaptic proteins. We used this approach to screen a library of ∼7000 novel fluorescent dyes, and identified a series of compounds in the xanthone family that exhibited consistent synaptic labeling. Follow-up studies with one of these compounds, CX-G3, demonstrated its ability to label acidic organelles and in particular synaptic vesicles at glutamatergic synapses in cultured neurons and murine brain tissue, indicating the potential of this screening approach to identify promising lead compounds for use as synaptic markers, sensors, and targeting devices.
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Affiliation(s)
- Matthew Dunn
- Department of Chemistry, Columbia University, New York, New York 10027, United States
- Neuro Technology
Center at Columbia University, New York, New York 10027, United States
- Departments of Psychiatry and Neurology, Columbia University Medical Center, New York, New York 10032, United States
| | - Umed Boltaev
- Department of Chemistry, Columbia University, New York, New York 10027, United States
- Neuro Technology
Center at Columbia University, New York, New York 10027, United States
| | - Anne Beskow
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York 10032, United States
| | - Sergey Pampou
- Columbia Genome Center High-throughput Screening Facility, Columbia University Medical Center, New York, New York 10032, United States
| | - Ronald Realubit
- Columbia Genome Center High-throughput Screening Facility, Columbia University Medical Center, New York, New York 10032, United States
| | - Torcato Meira
- Department of Neuroscience, Columbia University Medical Center, New York, New York 10032, United States
- University of Minho, 4710-057 Braga, Portugal
| | - João Vaz Silva
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York 10032, United States
- University of Minho, 4710-057 Braga, Portugal
| | - Rose Reeb
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York 10032, United States
| | - Charles Karan
- Columbia Genome Center High-throughput Screening Facility, Columbia University Medical Center, New York, New York 10032, United States
| | - Steffen Jockusch
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - David Sulzer
- Departments of Psychiatry and Neurology, Columbia University Medical Center, New York, New York 10032, United States
| | - Young Tae Chang
- Department of Chemistry, Pohang University of Science and Technology, Pohang, Gyeongsangbuk-do, Republic of Korea
| | - Dalibor Sames
- Department of Chemistry, Columbia University, New York, New York 10027, United States
- Neuro Technology
Center at Columbia University, New York, New York 10027, United States
| | - Clarissa L. Waites
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York 10032, United States
- Department of Neuroscience, Columbia University Medical Center, New York, New York 10032, United States
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153
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Goodell DJ, Zaegel V, Coultrap SJ, Hell JW, Bayer KU. DAPK1 Mediates LTD by Making CaMKII/GluN2B Binding LTP Specific. Cell Rep 2018; 19:2231-2243. [PMID: 28614711 DOI: 10.1016/j.celrep.2017.05.068] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 05/16/2017] [Accepted: 05/22/2017] [Indexed: 12/22/2022] Open
Abstract
The death-associated protein kinase 1 (DAPK1) is a potent mediator of neuronal cell death. Here, we find that DAPK1 also functions in synaptic plasticity by regulating the Ca2+/calmodulin (CaM)-dependent protein kinase II (CaMKII). CaMKII and T286 autophosphorylation are required for both long-term potentiation (LTP) and depression (LTD), two opposing forms of synaptic plasticity underlying learning, memory, and cognition. T286-autophosphorylation induces CaMKII binding to the NMDA receptor (NMDAR) subunit GluN2B, which mediates CaMKII synaptic accumulation during LTP. We find that the LTP specificity of CaMKII synaptic accumulation is due to its LTD-specific suppression by calcineurin (CaN)-dependent DAPK1 activation, which in turn blocks CaMKII binding to GluN2B. This suppression is enabled by competitive DAPK1 versus CaMKII binding to GluN2B. Negative regulation of DAPK1/GluN2B binding by Ca2+/CaM results in synaptic DAPK1 removal during LTP but retention during LTD. A pharmacogenetic approach showed that suppression of CaMKII/GluN2B binding is a DAPK1 function required for LTD.
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Affiliation(s)
- Dayton J Goodell
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Program in Neuroscience, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Vincent Zaegel
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Steven J Coultrap
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Johannes W Hell
- Department of Pharmacology, School of Medicine, University of California, Davis, Davis, CA 95616, USA
| | - K Ulrich Bayer
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Program in Neuroscience, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
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154
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Lorenz-Guertin JM, Jacob TC. GABA type a receptor trafficking and the architecture of synaptic inhibition. Dev Neurobiol 2018; 78:238-270. [PMID: 28901728 PMCID: PMC6589839 DOI: 10.1002/dneu.22536] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 09/08/2017] [Accepted: 09/08/2017] [Indexed: 12/21/2022]
Abstract
Ubiquitous expression of GABA type A receptors (GABAA R) in the central nervous system establishes their central role in coordinating most aspects of neural function and development. Dysregulation of GABAergic neurotransmission manifests in a number of human health disorders and conditions that in certain cases can be alleviated by drugs targeting these receptors. Precise changes in the quantity or activity of GABAA Rs localized at the cell surface and at GABAergic postsynaptic sites directly impact the strength of inhibition. The molecular mechanisms constituting receptor trafficking to and from these compartments therefore dictate the efficacy of GABAA R function. Here we review the current understanding of how GABAA Rs traffic through biogenesis, plasma membrane transport, and degradation. Emphasis is placed on discussing novel GABAergic synaptic proteins, receptor and scaffolding post-translational modifications, activity-dependent changes in GABAA R confinement, and neuropeptide and neurosteroid mediated changes. We further highlight modern techniques currently advancing the knowledge of GABAA R trafficking and clinically relevant neurodevelopmental diseases connected to GABAergic dysfunction. © 2017 Wiley Periodicals, Inc. Develop Neurobiol 78: 238-270, 2018.
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Affiliation(s)
- Joshua M Lorenz-Guertin
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, 15261
| | - Tija C Jacob
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, 15261
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155
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Schumacher D, Helma J, Schneider AFL, Leonhardt H, Hackenberger CPR. Nanobodies: Chemical Functionalization Strategies and Intracellular Applications. Angew Chem Int Ed Engl 2018; 57:2314-2333. [PMID: 28913971 PMCID: PMC5838514 DOI: 10.1002/anie.201708459] [Citation(s) in RCA: 157] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Indexed: 01/12/2023]
Abstract
Nanobodies can be seen as next-generation tools for the recognition and modulation of antigens that are inaccessible to conventional antibodies. Due to their compact structure and high stability, nanobodies see frequent usage in basic research, and their chemical functionalization opens the way towards promising diagnostic and therapeutic applications. In this Review, central aspects of nanobody functionalization are presented, together with selected applications. While early conjugation strategies relied on the random modification of natural amino acids, more recent studies have focused on the site-specific attachment of functional moieties. Such techniques include chemoenzymatic approaches, expressed protein ligation, and amber suppression in combination with bioorthogonal modification strategies. Recent applications range from sophisticated imaging and mass spectrometry to the delivery of nanobodies into living cells for the visualization and manipulation of intracellular antigens.
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Affiliation(s)
- Dominik Schumacher
- Chemical Biology, Leibniz-Forschungsinstitut für Molekulare, Pharmakologie and Department of ChemistryHumboldt-Universität zu BerlinBerlinGermany
- Department of Biology IILudwig Maximilians Universität München und Center for Integrated Protein Science MunichMartinsriedGermany
| | - Jonas Helma
- Department of Biology IILudwig Maximilians Universität München und Center for Integrated Protein Science MunichMartinsriedGermany
| | - Anselm F. L. Schneider
- Chemical Biology, Leibniz-Forschungsinstitut für Molekulare, Pharmakologie and Department of ChemistryHumboldt-Universität zu BerlinBerlinGermany
| | - Heinrich Leonhardt
- Department of Biology IILudwig Maximilians Universität München und Center for Integrated Protein Science MunichMartinsriedGermany
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156
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Harmansa S, Affolter M. Protein binders and their applications in developmental biology. Development 2018; 145:145/2/dev148874. [PMID: 29374062 DOI: 10.1242/dev.148874] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Developmental biology research would benefit greatly from tools that enable protein function to be regulated, both systematically and in a precise spatial and temporal manner, in vivo In recent years, functionalized protein binders have emerged as versatile tools that can be used to target and manipulate proteins. Such protein binders can be based on various scaffolds, such as nanobodies, designed ankyrin repeat proteins (DARPins) and monobodies, and can be used to block or perturb protein function in living cells. In this Primer, we provide an overview of the protein binders that are currently available and highlight recent progress made in applying protein binder-based tools in developmental and synthetic biology.
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Affiliation(s)
- Stefan Harmansa
- Growth and Development, Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Markus Affolter
- Growth and Development, Biozentrum, University of Basel, 4056 Basel, Switzerland
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157
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Schumacher D, Helma J, Schneider AFL, Leonhardt H, Hackenberger CPR. Nanobodys: Strategien zur chemischen Funktionalisierung und intrazelluläre Anwendungen. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201708459] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Dominik Schumacher
- Chemische Biologie, Leibniz-Forschungsinstitut für Molekulare Pharmakologie; Institut für Chemie; Humboldt-Universität zu Berlin; Berlin Deutschland
- Department Biologie II; Ludwig Maximilians Universität München und Center for Integrated Protein Science Munich; Martinsried Deutschland
| | - Jonas Helma
- Department Biologie II; Ludwig Maximilians Universität München und Center for Integrated Protein Science Munich; Martinsried Deutschland
| | - Anselm F. L. Schneider
- Chemische Biologie, Leibniz-Forschungsinstitut für Molekulare Pharmakologie; Institut für Chemie; Humboldt-Universität zu Berlin; Berlin Deutschland
| | - Heinrich Leonhardt
- Department Biologie II; Ludwig Maximilians Universität München und Center for Integrated Protein Science Munich; Martinsried Deutschland
| | - Christian P. R. Hackenberger
- Chemische Biologie, Leibniz-Forschungsinstitut für Molekulare Pharmakologie; Institut für Chemie; Humboldt-Universität zu Berlin; Berlin Deutschland
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158
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Wang Y, Ji T, Nelson AD, Glanowska K, Murphy GG, Jenkins PM, Parent JM. Critical roles of αII spectrin in brain development and epileptic encephalopathy. J Clin Invest 2018; 128:760-773. [PMID: 29337302 DOI: 10.1172/jci95743] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 11/28/2017] [Indexed: 12/26/2022] Open
Abstract
The nonerythrocytic α-spectrin-1 (SPTAN1) gene encodes the cytoskeletal protein αII spectrin. Mutations in SPTAN1 cause early infantile epileptic encephalopathy type 5 (EIEE5); however, the role of αII spectrin in neurodevelopment and EIEE5 pathogenesis is unknown. Prior work suggests that αII spectrin is absent in the axon initial segment (AIS) and contributes to a diffusion barrier in the distal axon. Here, we have shown that αII spectrin is expressed ubiquitously in rodent and human somatodendritic and axonal domains. CRISPR-mediated deletion of Sptan1 in embryonic rat forebrain by in utero electroporation caused altered dendritic and axonal development, loss of the AIS, and decreased inhibitory innervation. Overexpression of human EIEE5 mutant SPTAN1 in embryonic rat forebrain and mouse hippocampal neurons led to similar developmental defects that were also observed in EIEE5 patient-derived neurons. Additionally, patient-derived neurons displayed aggregation of spectrin complexes. Taken together, these findings implicate αII spectrin in critical aspects of dendritic and axonal development and synaptogenesis, and support a dominant-negative mechanism of SPTAN1 mutations in EIEE5.
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Affiliation(s)
| | | | | | | | - Geoffrey G Murphy
- Molecular and Behavioral Neuroscience Institute.,Department of Molecular and Integrative Physiology, and
| | - Paul M Jenkins
- Department of Pharmacology.,Department of Psychiatry, University of Michigan, Ann Arbor, Michigan, USA
| | - Jack M Parent
- Department of Neurology.,Ann Arbor VA Healthcare System, Ann Arbor, Michigan, USA
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159
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Zhang X, Thayer SA. Monoacylglycerol lipase inhibitor JZL184 prevents HIV-1 gp120-induced synapse loss by altering endocannabinoid signaling. Neuropharmacology 2018; 128:269-281. [PMID: 29061509 PMCID: PMC5752128 DOI: 10.1016/j.neuropharm.2017.10.023] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 10/16/2017] [Accepted: 10/19/2017] [Indexed: 12/22/2022]
Abstract
Monoacylglycerol lipase (MGL) hydrolyzes 2-arachidonoylglycerol to arachidonic acid and glycerol. Inhibition of MGL may attenuate neuroinflammation by enhancing endocannabinoid signaling and decreasing prostaglandin (PG) production. Almost half of HIV infected individuals are afflicted with HIV-associated neurocognitive disorder (HAND), a neuroinflammatory disease in which cognitive decline correlates with synapse loss. HIV infected cells shed the envelope protein gp120 which is a potent neurotoxin that induces synapse loss. Here, we tested whether inhibition of MGL, using the selective inhibitor JZL184, would prevent synapse loss induced by gp120. The number of synapses between rat hippocampal neurons in culture was quantified by imaging clusters of a GFP-tagged antibody-like protein that selectively binds to the postsynaptic scaffolding protein, PSD95. JZL184 completely blocked gp120-induced synapse loss. Inhibition of MGL decreased gp120-induced interleukin-1β (IL-1β) production and subsequent potentiation of NMDA receptor-mediated calcium influx. JZL184-mediated protection of synapses was reversed by a selective cannabinoid type 2 receptor (CB2R) inverse agonist/antagonist. JZL184 also reduced gp120-induced prostaglandin E2 (PGE2) production; PG signaling was required for gp120-induced IL-1β expression and synapse loss. Inhibition of MGL prevented gp120-induced synapse loss by activating CB2R resulting in decreased production of the inflammatory cytokine IL-1β. Because PG signaling was required for gp120-induced synapse loss, JZL184-induced decreases in PGE2 levels may also protect synapses. MGL presents a promising target for preventing synapse loss in neuroinflammatory conditions such as HAND.
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Affiliation(s)
- Xinwen Zhang
- Department of Pharmacology, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Stanley A Thayer
- Department of Pharmacology, University of Minnesota Medical School, Minneapolis, MN, USA.
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160
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Nolan R, Iliopoulou M, Alvarez L, Padilla-Parra S. Detecting protein aggregation and interaction in live cells: A guide to number and brightness. Methods 2017; 140-141:172-177. [PMID: 29221925 DOI: 10.1016/j.ymeth.2017.12.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 12/01/2017] [Accepted: 12/03/2017] [Indexed: 12/31/2022] Open
Abstract
The possibility to detect and quantify protein-protein interactions with good spatial and temporal resolutions in live cells is crucial in biology. Number and brightness is a powerful approach to detect both protein aggregation/desegregation dynamics and stoichiometry in live cells. Importantly, this technique can be applied in commercial set ups: both camera based and laser scanning microscopes. It provides pixel-by-pixel information on protein oligomeric states. If performed with two colours, the technique can retrieve the stoichiometry of the reaction under study. In this review, we discuss the strengths and weaknesses of the technique, stressing which are the correct acquisition parameters for a given microscope, the main challenges in analysis, and the limitations of the technique.
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Affiliation(s)
- Rory Nolan
- Wellcome Centre Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Maro Iliopoulou
- Wellcome Centre Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Luis Alvarez
- Wellcome Centre Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Sergi Padilla-Parra
- Wellcome Centre Human Genetics, University of Oxford, Oxford OX3 7BN, UK; Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford OX3 7BN, UK.
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161
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Optogenetic Tools for Subcellular Applications in Neuroscience. Neuron 2017; 96:572-603. [PMID: 29096074 DOI: 10.1016/j.neuron.2017.09.047] [Citation(s) in RCA: 217] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 03/30/2017] [Accepted: 09/26/2017] [Indexed: 12/21/2022]
Abstract
The ability to study cellular physiology using photosensitive, genetically encoded molecules has profoundly transformed neuroscience. The modern optogenetic toolbox includes fluorescent sensors to visualize signaling events in living cells and optogenetic actuators enabling manipulation of numerous cellular activities. Most optogenetic tools are not targeted to specific subcellular compartments but are localized with limited discrimination throughout the cell. Therefore, optogenetic activation often does not reflect context-dependent effects of highly localized intracellular signaling events. Subcellular targeting is required to achieve more specific optogenetic readouts and photomanipulation. Here we first provide a detailed overview of the available optogenetic tools with a focus on optogenetic actuators. Second, we review established strategies for targeting these tools to specific subcellular compartments. Finally, we discuss useful tools and targeting strategies that are currently missing from the optogenetics repertoire and provide suggestions for novel subcellular optogenetic applications.
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162
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Perturbed Wnt signaling leads to neuronal migration delay, altered interhemispheric connections and impaired social behavior. Nat Commun 2017; 8:1158. [PMID: 29079819 PMCID: PMC5660087 DOI: 10.1038/s41467-017-01046-w] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 08/15/2017] [Indexed: 12/19/2022] Open
Abstract
Perturbed neuronal migration and circuit development have been implicated in the pathogenesis of neurodevelopmental diseases; however, the direct steps linking these developmental errors to behavior alterations remain unknown. Here we demonstrate that Wnt/C-Kit signaling is a key regulator of glia-guided radial migration in rat somatosensory cortex. Transient downregulation of Wnt signaling in migrating, callosal projection neurons results in delayed positioning in layer 2/3. Delayed neurons display reduced neuronal activity with impaired afferent connectivity causing permanent deficit in callosal projections. Animals with these defects exhibit altered somatosensory function with reduced social interactions and repetitive movements. Restoring normal migration by overexpressing the Wnt-downstream effector C-Kit or selective chemogenetic activation of callosal projection neurons during a critical postnatal period prevents abnormal interhemispheric connections as well as behavioral alterations. Our findings identify a link between defective canonical Wnt signaling, delayed neuronal migration, deficient interhemispheric connectivity and abnormal social behavior analogous to autistic characteristics in humans. Functional consequence of transient delay in neuronal migration is unclear. This study shows that Wnt/C-Kit signaling regulates radial migration in rat somatosensory cortex, and that transient delay of L2/3 neuronal migration leads to interhemispheric connectivity alteration and abnormal social behavior.
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163
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Abudayyeh OO, Gootenberg JS, Essletzbichler P, Han S, Joung J, Belanto JJ, Verdine V, Cox DB, Kellner MJ, Regev A, Lander ES, Voytas DF, Ting AY, Zhang F. RNA targeting with CRISPR-Cas13. Nature 2017; 550:280-284. [PMID: 28976959 PMCID: PMC5706658 DOI: 10.1038/nature24049] [Citation(s) in RCA: 1224] [Impact Index Per Article: 174.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 09/01/2017] [Indexed: 12/12/2022]
Abstract
RNA has important and diverse roles in biology, but molecular tools to manipulate and measure it are limited. For example, RNA interference can efficiently knockdown RNAs, but it is prone to off-target effects, and visualizing RNAs typically relies on the introduction of exogenous tags. Here we demonstrate that the class 2 type VI RNA-guided RNA-targeting CRISPR-Cas effector Cas13a (previously known as C2c2) can be engineered for mammalian cell RNA knockdown and binding. After initial screening of 15 orthologues, we identified Cas13a from Leptotrichia wadei (LwaCas13a) as the most effective in an interference assay in Escherichia coli. LwaCas13a can be heterologously expressed in mammalian and plant cells for targeted knockdown of either reporter or endogenous transcripts with comparable levels of knockdown as RNA interference and improved specificity. Catalytically inactive LwaCas13a maintains targeted RNA binding activity, which we leveraged for programmable tracking of transcripts in live cells. Our results establish CRISPR-Cas13a as a flexible platform for studying RNA in mammalian cells and therapeutic development.
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Affiliation(s)
- Omar O. Abudayyeh
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jonathan S. Gootenberg
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Patrick Essletzbichler
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Shuo Han
- Departments of Genetics, Biology, and Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Julia Joung
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Joseph J. Belanto
- Department of Genetics, Cell Biology &Development and Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Vanessa Verdine
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - David B.T. Cox
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Max J. Kellner
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Eric S. Lander
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Daniel F. Voytas
- Department of Genetics, Cell Biology &Development and Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Alice Y. Ting
- Departments of Genetics, Biology, and Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Feng Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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164
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Yan Q, Zhai L, Zhang B, Dallman JE. Spatial patterning of excitatory and inhibitory neuropil territories during spinal circuit development. J Comp Neurol 2017; 525:1649-1667. [PMID: 27997694 DOI: 10.1002/cne.24152] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Revised: 10/13/2016] [Accepted: 11/14/2016] [Indexed: 01/04/2023]
Abstract
To generate rhythmic motor behaviors, both single neurons and neural circuits require a balance between excitatory inputs that trigger action potentials and inhibitory inputs that promote a stable resting potential (E/I balance). Previous studies have focused on individual neurons and have shown that, over a short spatial scale, excitatory and inhibitory (E/I) synapses tend to form structured territories with inhibitory inputs enriched on cell bodies and proximal dendrites and excitatory inputs on distal dendrites. However, systems-level E/I patterns, at spatial scales larger than single neurons, are largely uncharted. We used immunostaining for PSD-95 and gephyrin postsynaptic scaffolding proteins as proxies for excitatory and inhibitory synapses, respectively, to quantify the numbers and map the distributions of E/I synapses in zebrafish spinal cord at both an embryonic stage and a larval stage. At the embryonic stage, we found that PSD-95 puncta outnumber gephyrin puncta, with the number of gephyrin puncta increasing to match that of PSD-95 puncta at the larval stage. At both stages, PSD-95 puncta are enriched in the most lateral neuropil corresponding to distal dendrites while gephyrin puncta are enriched on neuronal somata and in the medial neuropil. Significantly, similar to synaptic puncta, neuronal processes also exhibit medial-lateral territories at both developmental stages with enrichment of glutamatergic (excitatory) processes laterally and glycinergic (inhibitory) processes medially. This establishment of neuropil excitatory-inhibitory structure largely precedes dendritic arborization of primary motor neurons, suggesting that the structured neuropil could provide a framework for the development of E/I balance at the cellular level. J. Comp. Neurol. 525:1649-1667, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Qing Yan
- Department of Biology, Cox Science Center, University of Miami, 1301 Memorial Drive, Coral Gables, Florida
| | - Lu Zhai
- Department of Biology, Cox Science Center, University of Miami, 1301 Memorial Drive, Coral Gables, Florida
| | - Bo Zhang
- Department of Biology, Cox Science Center, University of Miami, 1301 Memorial Drive, Coral Gables, Florida
| | - Julia E Dallman
- Department of Biology, Cox Science Center, University of Miami, 1301 Memorial Drive, Coral Gables, Florida
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165
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Yasuda R. Biophysics of Biochemical Signaling in Dendritic Spines: Implications in Synaptic Plasticity. Biophys J 2017; 113:2152-2159. [PMID: 28866426 DOI: 10.1016/j.bpj.2017.07.029] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 07/12/2017] [Accepted: 07/20/2017] [Indexed: 11/24/2022] Open
Abstract
Dendritic spines are mushroom-shaped postsynaptic compartments that host biochemical signal cascades important for synaptic plasticity and, ultimately, learning and memory. Signaling events in spines involve a signaling network composed of hundreds of signaling proteins interacting with each other extensively. Synaptic plasticity is typically induced by Ca2+ elevation in spines, which activates a variety of signaling pathways. This leads to changes in the actin cytoskeleton and membrane dynamics, which in turn causes structural and functional changes of the spine. Recent studies have demonstrated that the activities of these proteins have a variety of spatiotemporal patterns, which orchestrate signaling activity in different subcellular compartments at different timescales. The diffusion and the decay kinetics of signaling molecules play important roles in determining the degree of their spatial spreading, and thereby the degree of the spine specificity of the signaling pathway.
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Affiliation(s)
- Ryohei Yasuda
- Max Planck Florida Institute for Neuroscience, Jupiter, Florida.
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166
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Traenkle B, Rothbauer U. Under the Microscope: Single-Domain Antibodies for Live-Cell Imaging and Super-Resolution Microscopy. Front Immunol 2017; 8:1030. [PMID: 28883823 PMCID: PMC5573807 DOI: 10.3389/fimmu.2017.01030] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 08/09/2017] [Indexed: 12/12/2022] Open
Abstract
Single-domain antibodies (sdAbs) have substantially expanded the possibilities of advanced cellular imaging such as live-cell or super-resolution microscopy to visualize cellular antigens and their dynamics. In addition to their unique properties including small size, high stability, and solubility in many environments, sdAbs can be efficiently functionalized according to the needs of the respective imaging approach. Genetically encoded intrabodies fused to fluorescent proteins (chromobodies) have become versatile tools to study dynamics of endogenous proteins in living cells. Additionally, sdAbs conjugated to organic dyes were shown to label cellular structures with high density and minimal fluorophore displacement making them highly attractive probes for super-resolution microscopy. Here, we review recent advances of the chromobody technology to visualize localization and dynamics of cellular targets and the application of chromobody-based cell models for compound screening. Acknowledging the emerging importance of super-resolution microscopy in cell biology, we further discuss advantages and challenges of sdAbs for this technology.
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Affiliation(s)
- Bjoern Traenkle
- Pharmaceutical Biotechnology, Eberhard Karls University Tuebingen, Tuebingen, Germany
| | - Ulrich Rothbauer
- Pharmaceutical Biotechnology, Eberhard Karls University Tuebingen, Tuebingen, Germany.,Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen, Germany
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167
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The Arp2/3 Complex Is Essential for Distinct Stages of Spine Synapse Maturation, Including Synapse Unsilencing. J Neurosci 2017; 36:9696-709. [PMID: 27629719 DOI: 10.1523/jneurosci.0876-16.2016] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 08/02/2016] [Indexed: 12/28/2022] Open
Abstract
UNLABELLED Dendritic filopodia are actin-rich structures that are thought to contribute to early spine synapse formation; however, the actin regulatory proteins important for early synaptogenesis are poorly defined. Using organotypic hippocampal slice cultures and primary neuron hippocampal cultures from Arp2/3 conditional knock-out mice, we analyze the roles of the Arp2/3 complex, an actin regulator that creates branched actin networks, and demonstrate it is essential for distinct stages of both structural and functional maturation of excitatory spine synapses. Our data show that initially the Arp2/3 complex inhibits the formation of dendritic filopodia but that later during development, the Arp2/3 complex drives the morphological maturation from filopodia to typical spine morphology. Furthermore, we demonstrate that although the Arp2/3 complex is not required for key spine maturation steps, such as presynaptic contact and recruitment of MAGUK (membrane-associated guanylate kinase) scaffolding proteins or NMDA receptors, it is necessary for the recruitment of AMPA receptors. This latter process, also known as synapse unsilencing, is a final and essential step in the neurodevelopment of excitatory postsynaptic synaptogenesis, setting the stage for neuronal interconnectivity. These findings provide the first evidence that the Arp2/3 complex is directly involved in functional maturation of dendritic spines during the developmental period of spinogenesis. SIGNIFICANCE STATEMENT Excitatory spine synapse formation (spinogenesis) is a poorly understood yet pivotal period of neurodevelopment that occurs within 2-3 weeks after birth. Neurodevelopmental disorders such as intellectual disability and autism are characterized by abnormal spine structure, which may arise from abnormal excitatory synaptogenesis. The initial stage of spinogenesis is thought to begin with the emergence of actin-rich dendritic filopodia that initiate contact with presynaptic axonal boutons. However, it remains enigmatic how actin cytoskeletal regulation directs dendritic filopodial emergence or their subsequent maturation into dendritic spines during development and on into adulthood. In this study, we provide the first evidence that the Arp2/3 complex, a key actin nucleator, is involved in distinct stages of spine formation and is required for synapse unsilencing.
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168
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Noma K, Goncharov A, Ellisman MH, Jin Y. Microtubule-dependent ribosome localization in C. elegans neurons. eLife 2017; 6:26376. [PMID: 28767038 PMCID: PMC5577916 DOI: 10.7554/elife.26376] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 08/01/2017] [Indexed: 01/23/2023] Open
Abstract
Subcellular localization of ribosomes defines the location and capacity for protein synthesis. Methods for in vivo visualizing ribosomes in multicellular organisms are desirable in mechanistic investigations of the cell biology of ribosome dynamics. Here, we developed an approach using split GFP for tissue-specific visualization of ribosomes in Caenorhabditis elegans. Labeled ribosomes are detected as fluorescent puncta in the axons and synaptic terminals of specific neuron types, correlating with ribosome distribution at the ultrastructural level. We found that axonal ribosomes change localization during neuronal development and after axonal injury. By examining mutants affecting axonal trafficking and performing a forward genetic screen, we showed that the microtubule cytoskeleton and the JIP3 protein UNC-16 exert distinct effects on localization of axonal and somatic ribosomes. Our data demonstrate the utility of tissue-specific visualization of ribosomes in vivo, and provide insight into the mechanisms of active regulation of ribosome localization in neurons.
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Affiliation(s)
- Kentaro Noma
- Division of Biological Sciences, Neurobiology Section, University of California, San Diego, San Diego, United States.,Howard Hughes Medical Institute, University of California, San Diego, San Diego, United States
| | - Alexandr Goncharov
- Division of Biological Sciences, Neurobiology Section, University of California, San Diego, San Diego, United States.,Howard Hughes Medical Institute, University of California, San Diego, San Diego, United States
| | - Mark H Ellisman
- National Center for Research in Biological Systems, Department of Neurosciences, School of Medicine, University of California, San Diego, San Diego, United States
| | - Yishi Jin
- Division of Biological Sciences, Neurobiology Section, University of California, San Diego, San Diego, United States.,Howard Hughes Medical Institute, University of California, San Diego, San Diego, United States
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169
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Bauer KE, Kiebler MA, Segura I. Visualizing RNA granule transport and translation in living neurons. Methods 2017. [DOI: 10.1016/j.ymeth.2017.06.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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170
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Perrin L, Roudeau S, Carmona A, Domart F, Petersen JD, Bohic S, Yang Y, Cloetens P, Ortega R. Zinc and Copper Effects on Stability of Tubulin and Actin Networks in Dendrites and Spines of Hippocampal Neurons. ACS Chem Neurosci 2017; 8:1490-1499. [PMID: 28323401 DOI: 10.1021/acschemneuro.6b00452] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Zinc and copper ions can modulate the activity of glutamate receptors. However, labile zinc and copper ions likely represent only the tip of the iceberg and other neuronal functions are suspected for these metals in their bound state. We performed synchrotron X-ray fluorescence imaging with 30 nm resolution to image total biometals in dendrites and spines from hippocampal neurons. We found that zinc is distributed all along the dendrites while copper is mainly pinpointed within the spines. In spines, zinc content is higher within the spine head while copper is higher within the spine neck. Such specific distributions suggested metal interactions with cytoskeleton proteins. Zinc supplementation induced the increase of β-tubulin content in dendrites. Copper supplementation impaired the β-tubulin and F-actin networks. Copper chelation resulted in the decrease of F-actin content in dendrites, drastically reducing the number of F-actin protrusions. These results indicate that zinc is involved in microtubule stability whereas copper is essential for actin-dependent stability of dendritic spines, although copper excess can impair the dendritic cytoskeleton.
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Affiliation(s)
- Laura Perrin
- University of Bordeaux, CENBG,
UMR 5797, F-33170 Gradignan, France
- CNRS, IN2P3, CENBG, UMR 5797, F-33170 Gradignan, France
| | - Stéphane Roudeau
- University of Bordeaux, CENBG,
UMR 5797, F-33170 Gradignan, France
- CNRS, IN2P3, CENBG, UMR 5797, F-33170 Gradignan, France
| | - Asuncion Carmona
- University of Bordeaux, CENBG,
UMR 5797, F-33170 Gradignan, France
- CNRS, IN2P3, CENBG, UMR 5797, F-33170 Gradignan, France
| | - Florelle Domart
- University of Bordeaux, CENBG,
UMR 5797, F-33170 Gradignan, France
- CNRS, IN2P3, CENBG, UMR 5797, F-33170 Gradignan, France
- University of Bordeaux, Interdisciplinary Institute for Neuroscience,
UMR 5297, 33000 Bordeaux, France
- CNRS, Interdisciplinary Institute for Neuroscience,
UMR 5297, 33000 Bordeaux, France
| | - Jennifer D. Petersen
- University of Bordeaux, Interdisciplinary Institute for Neuroscience,
UMR 5297, 33000 Bordeaux, France
- CNRS, Interdisciplinary Institute for Neuroscience,
UMR 5297, 33000 Bordeaux, France
- Bordeaux Imaging Center, UMS 3420 CNRS, US4 INSERM,
University of Bordeaux, 33000 Bordeaux, France
| | - Sylvain Bohic
- ESRF, The European Synchrotron, 38000 Grenoble, France
- Inserm U1216, 38000 Grenoble, France
- Grenoble Institut
des Neurosciences, GIN University of Grenoble Alpes, 38000 Grenoble, France
| | - Yang Yang
- ESRF, The European Synchrotron, 38000 Grenoble, France
| | | | - Richard Ortega
- University of Bordeaux, CENBG,
UMR 5797, F-33170 Gradignan, France
- CNRS, IN2P3, CENBG, UMR 5797, F-33170 Gradignan, France
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171
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Ni Q, Mehta S, Zhang J. Live-cell imaging of cell signaling using genetically encoded fluorescent reporters. FEBS J 2017; 285:203-219. [PMID: 28613457 DOI: 10.1111/febs.14134] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 05/19/2017] [Accepted: 06/09/2017] [Indexed: 12/31/2022]
Abstract
Synergistic advances in fluorescent protein engineering and live-cell imaging techniques in recent years have fueled the concurrent development and application of genetically encoded fluorescent reporters that are tailored for tracking signaling dynamics in living systems over multiple length and time scales. These biosensors are uniquely suited for this challenging task, owing to their specificity, sensitivity, and versatility, as well as to the noninvasive and nondestructive nature of fluorescence and the power of genetic encoding. Over the past 10 years, a growing number of fluorescent reporters have been developed for tracking a wide range of biological signals in living cells and animals, including second messenger and metabolite dynamics, enzyme activation and activity, and cell cycle progression and neuronal activity. Many of these biosensors are gaining wide use and are proving to be indispensable for unraveling the complex biological functions of individual signaling molecules in their native environment, the living cell, shedding new light on the structural and molecular underpinnings of cell signaling. In this review, we highlight recent advances in protein engineering that are likely to help expand and improve the design and application of these valuable tools. We then turn our focus to specific examples of live-cell imaging using genetically encoded fluorescent reporters as an important platform for advancing our understanding of G protein-coupled receptor signaling and neuronal activity.
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Affiliation(s)
- Qiang Ni
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA
| | - Sohum Mehta
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA
| | - Jin Zhang
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA.,Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA
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172
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Visual Deprivation During the Critical Period Enhances Layer 2/3 GABAergic Inhibition in Mouse V1. J Neurosci 2017; 36:5914-9. [PMID: 27251614 DOI: 10.1523/jneurosci.0051-16.2016] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 04/23/2016] [Indexed: 11/21/2022] Open
Abstract
UNLABELLED The role of GABAergic signaling in establishing a critical period for experience in visual cortex is well understood. However, the effects of early experience on GABAergic synapses themselves are less clear. Here, we show that monocular deprivation (MD) during the adolescent critical period produces marked enhancement of GABAergic signaling in layer 2/3 of mouse monocular visual cortex. This enhancement coincides with a weakening of glutamatergic inputs, resulting in a significant reduction in the ratio of excitation to inhibition. The potentiation of GABAergic transmission arises from both an increased number of inhibitory synapses and an enhancement of presynaptic GABA release from parvalbumin- and somatostatin-expressing interneurons. Our results suggest that augmented GABAergic inhibition contributes to the experience-dependent regulation of visual function. SIGNIFICANCE STATEMENT Visual experience shapes the synaptic organization of cortical circuits in the mouse brain. Here, we show that monocular visual deprivation enhances GABAergic synaptic inhibition in primary visual cortex. This enhancement is mediated by an increase in both the number of postsynaptic GABAergic synapses and the probability of presynaptic GABA release. Our results suggest a contributing mechanism to altered visual responses after deprivation.
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173
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Chambers AR, Rumpel S. A stable brain from unstable components: Emerging concepts and implications for neural computation. Neuroscience 2017; 357:172-184. [PMID: 28602920 DOI: 10.1016/j.neuroscience.2017.06.005] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 06/02/2017] [Accepted: 06/05/2017] [Indexed: 11/28/2022]
Abstract
Neuroscientists have often described the adult brain in similar terms to an electronic circuit board- dependent on fixed, precise connectivity. However, with the advent of technologies allowing chronic measurements of neural structure and function, the emerging picture is that neural networks undergo significant remodeling over multiple timescales, even in the absence of experimenter-induced learning or sensory perturbation. Here, we attempt to reconcile the parallel observations that critical brain functions are stably maintained, while synapse- and single-cell properties appear to be reformatted regularly throughout adult life. In this review, we discuss experimental evidence at multiple levels ranging from synapses to neuronal ensembles, suggesting that many parameters are maintained in a dynamic equilibrium. We highlight emerging hypotheses that could explain how stable brain functions may be generated from dynamic elements. Furthermore, we discuss the impact of dynamic circuit elements on neural computations, and how they could provide living neural circuits with computational abilities a fixed structure cannot offer. Taken together, recent evidence indicates that continuous dynamics are a fundamental property of neural circuits compatible with macroscopically stable behaviors. In addition, they may be a unique advantage imparting robustness and flexibility throughout life.
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Affiliation(s)
- Anna R Chambers
- Focus Program Translational Neuroscience (FTN), Johannes Gutenberg University, Mainz, Germany; Institute of Physiology, Johannes Gutenberg University, Mainz, Germany
| | - Simon Rumpel
- Focus Program Translational Neuroscience (FTN), Johannes Gutenberg University, Mainz, Germany; Institute of Physiology, Johannes Gutenberg University, Mainz, Germany.
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174
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Lin L, Lo LHY, Lyu Q, Lai KO. Determination of dendritic spine morphology by the striatin scaffold protein STRN4 through interaction with the phosphatase PP2A. J Biol Chem 2017; 292:9451-9464. [PMID: 28442576 DOI: 10.1074/jbc.m116.772442] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 04/15/2017] [Indexed: 11/06/2022] Open
Abstract
Dendritic spines are heterogeneous and exist with various morphologies. Altered spine morphology might underlie the cognitive deficits in neurodevelopmental disorders such as autism, but how different subtypes of dendritic spines are selectively maintained along development is still poorly understood. Spine maturation requires spontaneous activity of N-methyl-d-aspartate (NMDA) receptor and local dendritic protein synthesis. STRN4 (also called zinedin) belongs to the striatin family of scaffold proteins, and some of the potential striatin-interacting proteins are encoded by autism risk genes. Although previous studies have demonstrated their localization in dendritic spines, the function of various striatin family members in the neuron remains unknown. Here, we demonstrate that Strn4 mRNA is present in neuronal dendrites, and the local expression of STRN4 protein depends on NMDA receptor activation. Notably, STRN4 is preferentially expressed in mushroom spines, and STRN4 specifically maintains mushroom spines but not thin spines and filopodia through interaction with the phosphatase PP2A. Our findings have therefore unraveled the local expression of STRN4 as a novel mechanism for the control of dendritic spine morphology.
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Affiliation(s)
| | | | | | - Kwok-On Lai
- From the School of Biomedical Sciences and .,State Key Laboratory of Brain and Cognitive Sciences, University of Hong Kong, Hong Kong, China
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175
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Sha F, Salzman G, Gupta A, Koide S. Monobodies and other synthetic binding proteins for expanding protein science. Protein Sci 2017; 26:910-924. [PMID: 28249355 PMCID: PMC5405424 DOI: 10.1002/pro.3148] [Citation(s) in RCA: 113] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 02/20/2017] [Accepted: 02/21/2017] [Indexed: 01/20/2023]
Abstract
Synthetic binding proteins are constructed using nonantibody molecular scaffolds. Over the last two decades, in‐depth structural and functional analyses of synthetic binding proteins have improved combinatorial library designs and selection strategies, which have resulted in potent platforms that consistently generate binding proteins to diverse targets with affinity and specificity that rival those of antibodies. Favorable attributes of synthetic binding proteins, such as small size, freedom from disulfide bond formation and ease of making fusion proteins, have enabled their unique applications in protein science, cell biology and beyond. Here, we review recent studies that illustrate how synthetic binding proteins are powerful probes that can directly link structure and function, often leading to new mechanistic insights. We propose that synthetic proteins will become powerful standard tools in diverse areas of protein science, biotechnology and medicine.
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Affiliation(s)
- Fern Sha
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois, 60637
| | - Gabriel Salzman
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois, 60637
| | - Ankit Gupta
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois, 60637.,Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY, 10016
| | - Shohei Koide
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois, 60637.,Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY, 10016.,Department of Biochemistry and Molecular Pharmacology New York University School of Medicine, New York, NY, 10016
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176
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Uezu A, Kanak DJ, Bradshaw TWA, Soderblom EJ, Catavero CM, Burette AC, Weinberg RJ, Soderling SH. Identification of an elaborate complex mediating postsynaptic inhibition. Science 2017; 353:1123-9. [PMID: 27609886 DOI: 10.1126/science.aag0821] [Citation(s) in RCA: 223] [Impact Index Per Article: 31.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 07/25/2016] [Indexed: 12/13/2022]
Abstract
Inhibitory synapses dampen neuronal activity through postsynaptic hyperpolarization. The composition of the inhibitory postsynapse and the mechanistic basis of its regulation, however, remain poorly understood. We used an in vivo chemico-genetic proximity-labeling approach to discover inhibitory postsynaptic proteins. Quantitative mass spectrometry not only recapitulated known inhibitory postsynaptic proteins but also revealed a large network of new proteins, many of which are either implicated in neurodevelopmental disorders or are of unknown function. Clustered regularly interspaced short palindromic repeats (CRISPR) depletion of one of these previously uncharacterized proteins, InSyn1, led to decreased postsynaptic inhibitory sites, reduced the frequency of miniature inhibitory currents, and increased excitability in the hippocampus. Our findings uncover a rich and functionally diverse assemblage of previously unknown proteins that regulate postsynaptic inhibition and might contribute to developmental brain disorders.
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Affiliation(s)
- Akiyoshi Uezu
- The Department of Cell Biology, Duke University Medical School, Durham, NC 27703, USA
| | - Daniel J Kanak
- The Department of Cell Biology, Duke University Medical School, Durham, NC 27703, USA
| | - Tyler W A Bradshaw
- The Department of Cell Biology, Duke University Medical School, Durham, NC 27703, USA
| | - Erik J Soderblom
- The Department of Cell Biology, Duke University Medical School, Durham, NC 27703, USA. Duke Proteomics and Metabolomics Shared Resource and Duke Center for Genomic and Computational Biology, Duke University Medical School, Durham, NC 27703, USA
| | - Christina M Catavero
- The Department of Cell Biology, Duke University Medical School, Durham, NC 27703, USA
| | - Alain C Burette
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, NC 27599, USA. Neuroscience Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Richard J Weinberg
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, NC 27599, USA. Neuroscience Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Scott H Soderling
- The Department of Cell Biology, Duke University Medical School, Durham, NC 27703, USA. The Department of Neurobiology, Duke University Medical School, Durham, NC 27703, USA.
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177
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Walker AS, Neves G, Grillo F, Jackson RE, Rigby M, O'Donnell C, Lowe AS, Vizcay-Barrena G, Fleck RA, Burrone J. Distance-dependent gradient in NMDAR-driven spine calcium signals along tapering dendrites. Proc Natl Acad Sci U S A 2017; 114:E1986-E1995. [PMID: 28209776 PMCID: PMC5347575 DOI: 10.1073/pnas.1607462114] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Neurons receive a multitude of synaptic inputs along their dendritic arbor, but how this highly heterogeneous population of synaptic compartments is spatially organized remains unclear. By measuring N-methyl-d-aspartic acid receptor (NMDAR)-driven calcium responses in single spines, we provide a spatial map of synaptic calcium signals along dendritic arbors of hippocampal neurons and relate this to measures of synapse structure. We find that quantal NMDAR calcium signals increase in amplitude as they approach a thinning dendritic tip end. Based on a compartmental model of spine calcium dynamics, we propose that this biased distribution in calcium signals is governed by a gradual, distance-dependent decline in spine size, which we visualized using serial block-face scanning electron microscopy. Our data describe a cell-autonomous feature of principal neurons, where tapering dendrites show an inverse distribution of spine size and NMDAR-driven calcium signals along dendritic trees, with important implications for synaptic plasticity rules and spine function.
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Affiliation(s)
- Alison S Walker
- Centre for Developmental Neurobiology, Kings College London, London SE1 1UL, United Kingdom
| | - Guilherme Neves
- Centre for Developmental Neurobiology, Kings College London, London SE1 1UL, United Kingdom
| | - Federico Grillo
- Centre for Developmental Neurobiology, Kings College London, London SE1 1UL, United Kingdom
| | - Rachel E Jackson
- Centre for Developmental Neurobiology, Kings College London, London SE1 1UL, United Kingdom
| | - Mark Rigby
- Centre for Developmental Neurobiology, Kings College London, London SE1 1UL, United Kingdom
| | - Cian O'Donnell
- Department of Computer Science, University of Bristol, Bristol BS8 1UB, United Kingdom
| | - Andrew S Lowe
- Centre for Developmental Neurobiology, Kings College London, London SE1 1UL, United Kingdom
| | - Gema Vizcay-Barrena
- Centre for Ultrastructural Imaging, Kings College London, London SE1 1UL, United Kingdom
| | - Roland A Fleck
- Centre for Ultrastructural Imaging, Kings College London, London SE1 1UL, United Kingdom
| | - Juan Burrone
- Centre for Developmental Neurobiology, Kings College London, London SE1 1UL, United Kingdom;
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178
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Sinnen BL, Bowen AB, Forte JS, Hiester BG, Crosby KC, Gibson ES, Dell'Acqua ML, Kennedy MJ. Optogenetic Control of Synaptic Composition and Function. Neuron 2017; 93:646-660.e5. [PMID: 28132827 DOI: 10.1016/j.neuron.2016.12.037] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 10/22/2016] [Accepted: 12/22/2016] [Indexed: 10/20/2022]
Abstract
The molecular composition of the postsynaptic membrane is sculpted by synaptic activity. During synaptic plasticity at excitatory synapses, numerous structural, signaling, and receptor molecules concentrate at the postsynaptic density (PSD) to regulate synaptic strength. We developed an approach that uses light to tune the abundance of specific molecules in the PSD. We used this approach to investigate the relationship between the number of AMPA-type glutamate receptors in the PSD and synaptic strength. Surprisingly, adding more AMPA receptors to excitatory contacts had little effect on synaptic strength. Instead, we observed increased excitatory input through the apparent addition of new functional sites. Our data support a model where adding AMPA receptors is sufficient to activate synapses that had few receptors to begin with, but that additional remodeling events are required to strengthen established synapses. More broadly, this approach introduces the precise spatiotemporal control of optogenetics to the molecular control of synaptic function.
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Affiliation(s)
- Brooke L Sinnen
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Aaron B Bowen
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Jeffrey S Forte
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Brian G Hiester
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Kevin C Crosby
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Emily S Gibson
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Mark L Dell'Acqua
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Matthew J Kennedy
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA.
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179
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Cristino L, Imperatore R, Di Marzo V. Techniques for the Cellular and Subcellular Localization of Endocannabinoid Receptors and Enzymes in the Mammalian Brain. Methods Enzymol 2017; 593:61-98. [DOI: 10.1016/bs.mie.2017.05.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
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180
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Maric HM, Hausrat TJ, Neubert F, Dalby NO, Doose S, Sauer M, Kneussel M, Strømgaard K. Gephyrin-binding peptides visualize postsynaptic sites and modulate neurotransmission. Nat Chem Biol 2016; 13:153-160. [DOI: 10.1038/nchembio.2246] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2016] [Accepted: 09/15/2016] [Indexed: 11/09/2022]
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181
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Cetin M, Evenson WE, Gross GG, Jalali-Yazdi F, Krieger D, Arnold D, Takahashi TT, Roberts RW. RasIns: Genetically Encoded Intrabodies of Activated Ras Proteins. J Mol Biol 2016; 429:562-573. [PMID: 27865780 DOI: 10.1016/j.jmb.2016.11.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 11/11/2016] [Accepted: 11/12/2016] [Indexed: 01/11/2023]
Abstract
K- and H-Ras are the most commonly mutated genes in human tumors and are critical for conferring and maintaining the oncogenic phenotype in tumors with poor prognoses. Here, we design genetically encoded antibody-like ligands (intrabodies) that recognize active, GTP-bound K- and H-Ras. These ligands, which use the 10th domain of human fibronectin as their scaffold, are stable inside the cells and when fused with a fluorescent protein label, the constitutively active G12V mutant H-Ras. Primary selection of ligands against Ras with mRNA display resulted in an intrabody (termed RasIn1) that binds with a KD of 2.1μM to H-Ras(G12V) (GTP), excellent state selectivity, and remarkable specificity for K- and H-Ras. RasIn1 recognizes residues in the Switch I region of Ras, similar to Raf-RBD, and competes with Raf-RBD for binding. An affinity maturation selection based on RasIn1 resulted in RasIn2, which binds with a KD of 120nM and also retains excellent state selectivity. Both of these intrabodies colocalize with H-Ras, K-Ras, and G12V mutants inside the cells, providing new potential tools to monitor and modulate Ras-mediated signaling. Finally, RasIn1 and Rasin2 both display selectivity for the G12V mutants as compared with wild-type Ras providing a potential route for mutant selective recognition of Ras.
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Affiliation(s)
- Mehmet Cetin
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - William E Evenson
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Garrett G Gross
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Farzad Jalali-Yazdi
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, CA 90089, USA
| | - Daniel Krieger
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Don Arnold
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Terry T Takahashi
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Richard W Roberts
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA; Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA; Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, CA 90089, USA; USC Norris Comprehensive Cancer Center, Los Angeles, CA 90089, USA.
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182
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Wefelmeyer W, Puhl CJ, Burrone J. Homeostatic Plasticity of Subcellular Neuronal Structures: From Inputs to Outputs. Trends Neurosci 2016; 39:656-667. [PMID: 27637565 PMCID: PMC5236059 DOI: 10.1016/j.tins.2016.08.004] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 08/18/2016] [Accepted: 08/19/2016] [Indexed: 01/02/2023]
Abstract
Neurons in the brain are highly plastic, allowing an organism to learn and adapt to its environment. However, this ongoing plasticity is also inherently unstable, potentially leading to aberrant levels of circuit activity. Homeostatic forms of plasticity are thought to provide a means of controlling neuronal activity by avoiding extremes and allowing network stability. Recent work has shown that many of these homeostatic modifications change the structure of subcellular neuronal compartments, ranging from changes to synaptic inputs at both excitatory and inhibitory compartments to modulation of neuronal output through changes at the axon initial segment (AIS) and presynaptic terminals. Here we review these different forms of structural plasticity in neurons and the effects they may have on network function.
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Affiliation(s)
- Winnie Wefelmeyer
- Centre for Developmental Neurobiology, King's College London, New Hunt's House, Guy's Hospital Campus, London, SE1 1UL, UK.
| | - Christopher J Puhl
- Centre for Developmental Neurobiology, King's College London, New Hunt's House, Guy's Hospital Campus, London, SE1 1UL, UK
| | - Juan Burrone
- Centre for Developmental Neurobiology, King's College London, New Hunt's House, Guy's Hospital Campus, London, SE1 1UL, UK.
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183
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Mele M, Leal G, Duarte CB. Role of GABAAR trafficking in the plasticity of inhibitory synapses. J Neurochem 2016; 139:997-1018. [DOI: 10.1111/jnc.13742] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 07/12/2016] [Accepted: 07/13/2016] [Indexed: 12/22/2022]
Affiliation(s)
- Miranda Mele
- Center for Neuroscience and Cell Biology; University of Coimbra; Coimbra Portugal
| | - Graciano Leal
- Center for Neuroscience and Cell Biology; University of Coimbra; Coimbra Portugal
| | - Carlos B. Duarte
- Center for Neuroscience and Cell Biology; University of Coimbra; Coimbra Portugal
- Department of Life Sciences; University of Coimbra; Coimbra Portugal
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184
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Pratt SE, Speltz EB, Mochrie SGJ, Regan L. Designed Proteins as Novel Imaging Reagents in Living Escherichia coli. Chembiochem 2016; 17:1652-7. [PMID: 27304706 DOI: 10.1002/cbic.201600252] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Indexed: 11/06/2022]
Abstract
Fluorescence imaging is a powerful tool to study protein function in living cells. Here, we introduce a novel imaging strategy that is fully genetically encodable, does not require the use of exogenous substrates, and adds a minimally disruptive tag to the protein of interest (POI). Our method was based on a set of designed tetratricopeptide repeat affinity proteins (TRAPs) that specifically and reversibly interact with a short, extended peptide tag. We co-expressed the TRAPs fused to fluorescent proteins (FPs) and the peptide tags fused to the POIs. We illustrated the method using the Escherichia coli protein FtsZ and showed that our system could track distinct FtsZ structures under both low and high expression conditions in live cells. We anticipate that our imaging strategy will be a useful tool for imaging the subcellular localization of many proteins, especially those recalcitrant to imaging by direct tagging with FPs.
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Affiliation(s)
- Susan E Pratt
- Department of Physics, Yale University, 217 Prospect Street, New Haven, CT, 06511, USA.,Integrated Graduate Program in Physical and Engineering Biology, Yale University, 266 Whitney Avenue, New Haven, CT, 06511, USA
| | - Elizabeth B Speltz
- Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT, 06511, USA
| | - Simon G J Mochrie
- Department of Physics, Yale University, 217 Prospect Street, New Haven, CT, 06511, USA. .,Integrated Graduate Program in Physical and Engineering Biology, Yale University, 266 Whitney Avenue, New Haven, CT, 06511, USA. .,Department of Applied Physics, Yale University, 15 Prospect Street, New Haven, CT, 06511, USA.
| | - Lynne Regan
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, 266 Whitney Avenue, New Haven, CT, 06511, USA. .,Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT, 06511, USA. .,Department of Chemistry, Yale University, 225 Prospect Street, New Haven, CT, 06511, USA.
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185
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SRGAP2 and Its Human-Specific Paralog Co-Regulate the Development of Excitatory and Inhibitory Synapses. Neuron 2016; 91:356-69. [PMID: 27373832 DOI: 10.1016/j.neuron.2016.06.013] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 04/12/2016] [Accepted: 05/25/2016] [Indexed: 10/21/2022]
Abstract
The proper function of neural circuits requires spatially and temporally balanced development of excitatory and inhibitory synapses. However, the molecular mechanisms coordinating excitatory and inhibitory synaptogenesis remain unknown. Here we demonstrate that SRGAP2A and its human-specific paralog SRGAP2C co-regulate the development of excitatory and inhibitory synapses in cortical pyramidal neurons in vivo. SRGAP2A promotes synaptic maturation, and ultimately the synaptic accumulation of AMPA and GABAA receptors, by interacting with key components of both excitatory and inhibitory postsynaptic scaffolds, Homer and Gephyrin. Furthermore, SRGAP2A limits the density of both types of synapses via its Rac1-GAP activity. SRGAP2C inhibits all identified functions of SRGAP2A, protracting the maturation and increasing the density of excitatory and inhibitory synapses. Our results uncover a molecular mechanism coordinating critical features of synaptic development and suggest that human-specific duplication of SRGAP2 might have contributed to the emergence of unique traits of human neurons while preserving the excitation/inhibition balance.
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186
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Marvin JS, Looger LL. Falling apart. eLife 2016; 5. [PMID: 27345573 PMCID: PMC4922843 DOI: 10.7554/elife.18203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 06/22/2016] [Indexed: 11/13/2022] Open
Abstract
Destabilized nanobodies can be used to deliver fluorescent proteins and enzymes to specific targets inside cells.
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Affiliation(s)
- Jonathan S Marvin
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Loren L Looger
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
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187
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An E3-ligase-based method for ablating inhibitory synapses. Nat Methods 2016; 13:673-8. [PMID: 27271196 PMCID: PMC5312699 DOI: 10.1038/nmeth.3894] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 05/09/2016] [Indexed: 01/08/2023]
Abstract
Although neuronal activity can be modulated using a variety of techniques, there are currently few methods for controlling neuronal connectivity. We introduce a tool (GFE3) that mediates the fast, specific and reversible elimination of inhibitory synaptic inputs onto genetically determined neurons. GFE3 is a fusion between an E3 ligase, which mediates the ubiquitination and rapid degradation of proteins, and a recombinant, antibody-like protein (FingR) that binds to gephyrin. Expression of GFE3 leads to a strong and specific reduction of gephyrin in culture or in vivo and to a substantial decrease in phasic inhibition onto cells that express GFE3. By temporarily expressing GFE3 we showed that inhibitory synapses regrow following ablation. Thus, we have created a simple, reversible method for modulating inhibitory synaptic input onto genetically determined cells.
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188
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Tang JC, Drokhlyansky E, Etemad B, Rudolph S, Guo B, Wang S, Ellis EG, Li JZ, Cepko CL. Detection and manipulation of live antigen-expressing cells using conditionally stable nanobodies. eLife 2016; 5. [PMID: 27205882 PMCID: PMC4922844 DOI: 10.7554/elife.15312] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 05/19/2016] [Indexed: 12/18/2022] Open
Abstract
The ability to detect and/or manipulate specific cell populations based upon the presence of intracellular protein epitopes would enable many types of studies and applications. Protein binders such as nanobodies (Nbs) can target untagged proteins (antigens) in the intracellular environment. However, genetically expressed protein binders are stable regardless of antigen expression, complicating their use for applications that require cell-specificity. Here, we created a conditional system in which the stability of an Nb depends upon an antigen of interest. We identified Nb framework mutations that can be used to rapidly create destabilized Nbs. Fusion of destabilized Nbs to various proteins enabled applications in living cells, such as optogenetic control of neural activity in specific cell types in the mouse brain, and detection of HIV-infected human cells by flow cytometry. These approaches are generalizable to other protein binders, and enable the rapid generation of single-polypeptide sensors and effectors active in cells expressing specific intracellular epitopes. DOI:http://dx.doi.org/10.7554/eLife.15312.001 Biologists often wish to study the role of a particular cell type within an organism, but such studies are often not possible due to the lack of reagents that allow one to gain control of the cell type of interest. One method that can be used to detect and manipulate the cells that express specific proteins uses molecules called antibodies. An antibody can strongly bind to a specific part of a protein, and a diversity of antibodies that bind to different proteins can be isolated by animal immunization, or by using molecular or cell-based methods. Antibodies from camelid species (which include camels and llamas) are increasingly being used to detect and manipulate proteins in living cells. The variable region of these antibodies – also known as the nanobody – recognises the proteins that the antibody binds to, and often just this fragment of the antibody is used in protein detection experiments. However, nanobodies are stable even in cells that do not contain their target proteins, which makes it difficult to use nanobodies to study just a specific cell type within an organism. Tang, Drokhlyansky et al. have now developed a way of engineering the sequence of a nanobody so that it is broken down in living cells unless it is bound to its protein target inside the cell. Any protein that is tethered to the engineered nanobody is also broken down. For example, some tethered proteins with useful biological activities are fluorescent proteins and enzymes that can modify DNA. When one of these engineered nanobodies binds to a protein target of interest, the activity of the nanobody-tethered protein can be turned on in just those cells that produce the targeted protein. Thus, this strategy of engineering allows “conditionally stable” tools to be generated. A core set of sequence alterations can be used to modify different nanobodies that target different proteins. Tang, Drokhlyansky et al. have demonstrated the uses of several of the resulting conditionally stable nanobodies. In one application, the nanobodies were used to target specific cell types in the mouse brain in a way that allowed the activity of these cells to be controlled by light. Another application of the technique enables live human cells that have been infected with HIV to be detected and isolated. The conditionally stable nanobody tools can be used to detect and manipulate cells that express any protein for which a camelid antibody exists. Tang, Drokhlyansky et al. therefore hope that biologists who work in a wide range of fields will find the tools useful for studying many different types of organisms and biological processes. DOI:http://dx.doi.org/10.7554/eLife.15312.002
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Affiliation(s)
- Jonathan Cy Tang
- Department of Genetics, Howard Hughes Medical Institute, Harvard Medical School, Boston, United States.,Department of Ophthalmology, Howard Hughes Medical Institute, Harvard Medical School, Boston, United States
| | - Eugene Drokhlyansky
- Department of Genetics, Howard Hughes Medical Institute, Harvard Medical School, Boston, United States.,Department of Ophthalmology, Howard Hughes Medical Institute, Harvard Medical School, Boston, United States
| | - Behzad Etemad
- Brigham and Women's Hospital, Harvard Medical School, Boston, United States
| | - Stephanie Rudolph
- Department of Neurobiology, Harvard Medical School, Boston, United States
| | - Binggege Guo
- Department of Genetics, Howard Hughes Medical Institute, Harvard Medical School, Boston, United States.,Department of Ophthalmology, Howard Hughes Medical Institute, Harvard Medical School, Boston, United States
| | - Sui Wang
- Department of Genetics, Howard Hughes Medical Institute, Harvard Medical School, Boston, United States.,Department of Ophthalmology, Howard Hughes Medical Institute, Harvard Medical School, Boston, United States
| | - Emily G Ellis
- Department of Neurobiology, Harvard Medical School, Boston, United States
| | - Jonathan Z Li
- Brigham and Women's Hospital, Harvard Medical School, Boston, United States
| | - Constance L Cepko
- Department of Genetics, Howard Hughes Medical Institute, Harvard Medical School, Boston, United States.,Department of Ophthalmology, Howard Hughes Medical Institute, Harvard Medical School, Boston, United States
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189
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Mikuni T, Nishiyama J, Sun Y, Kamasawa N, Yasuda R. High-Throughput, High-Resolution Mapping of Protein Localization in Mammalian Brain by In Vivo Genome Editing. Cell 2016; 165:1803-1817. [PMID: 27180908 DOI: 10.1016/j.cell.2016.04.044] [Citation(s) in RCA: 150] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 03/14/2016] [Accepted: 04/13/2016] [Indexed: 12/25/2022]
Abstract
A scalable and high-throughput method to identify precise subcellular localization of endogenous proteins is essential for integrative understanding of a cell at the molecular level. Here, we developed a simple and generalizable technique to image endogenous proteins with high specificity, resolution, and contrast in single cells in mammalian brain tissue. The technique, single-cell labeling of endogenous proteins by clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9-mediated homology-directed repair (SLENDR), uses in vivo genome editing to insert a sequence encoding an epitope tag or a fluorescent protein to a gene of interest by CRISPR-Cas9-mediated homology-directed repair (HDR). Single-cell, HDR-mediated genome editing was achieved by delivering the editing machinery to dividing neuronal progenitors through in utero electroporation. We demonstrate that SLENDR allows rapid determination of the localization and dynamics of many endogenous proteins in various cell types, regions, and ages in the brain. Thus, SLENDR provides a high-throughput platform to map the subcellular localization of endogenous proteins with the resolution of micro- to nanometers in the brain.
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Affiliation(s)
- Takayasu Mikuni
- Neuronal Signal Transduction Group, Max Planck Florida Institute for Neuroscience, Jupiter, FL 33458, USA
| | - Jun Nishiyama
- Neuronal Signal Transduction Group, Max Planck Florida Institute for Neuroscience, Jupiter, FL 33458, USA.
| | - Ye Sun
- Neuronal Signal Transduction Group, Max Planck Florida Institute for Neuroscience, Jupiter, FL 33458, USA; Integrative Program in Biology and Neuroscience, Florida Atlantic University, Jupiter, FL 33458, USA
| | - Naomi Kamasawa
- Electron Microscopy Core Facility, Max Planck Florida Institute for Neuroscience, Jupiter, FL 33458, USA
| | - Ryohei Yasuda
- Neuronal Signal Transduction Group, Max Planck Florida Institute for Neuroscience, Jupiter, FL 33458, USA.
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190
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Feng S, Arnold DB. Techniques for studying protein trafficking and molecular motors in neurons. Cytoskeleton (Hoboken) 2016; 73:508-15. [PMID: 26800506 DOI: 10.1002/cm.21274] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Revised: 01/13/2016] [Accepted: 01/19/2016] [Indexed: 01/29/2023]
Abstract
This review focused on techniques that facilitated the visualization of protein trafficking. In the mid-1990s the cloning of GFP allowed fluorescently tagged proteins to be expressed in cells and then visualized in real time. This advance allowed a glimpse, for the first time, of the complex system within cells for distributing proteins. It quickly became apparent, however, that time-lapse sequences of exogenously expressed GFP-labeled proteins can be difficult to interpret. Reasons for this include the relatively low signal that comes from moving proteins and high background rates from stationary proteins and other sources, as well as the difficulty of identifying the origins and destinations of specific vesicular carriers. In this review a range of techniques that have overcome these issues to varying degrees was reviewed and the insights into protein trafficking that they have enabled were discussed. Concentration will be on neurons, as they are highly polarized and, thus, their trafficking systems tend to be accessible for study. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Shanxi Feng
- Department of Biological Sciences, Program in Neuroscience, University of Southern California, Los Angeles, California
| | - Don B Arnold
- Department of Biological Sciences, Program in Neuroscience, University of Southern California, Los Angeles, California.
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191
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Transgenic FingRs for Live Mapping of Synaptic Dynamics in Genetically-Defined Neurons. Sci Rep 2016; 6:18734. [PMID: 26728131 PMCID: PMC4700522 DOI: 10.1038/srep18734] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 11/25/2015] [Indexed: 12/03/2022] Open
Abstract
Tools for genetically-determined visualization of synaptic circuits and interactions are necessary to build connectomics of the vertebrate brain and to screen synaptic properties in neurological disease models. Here we develop a transgenic FingR (fibronectin intrabodies generated by mRNA display) technology for monitoring synapses in live zebrafish. We demonstrate FingR labeling of defined excitatory and inhibitory synapses, and show FingR applicability for dissecting synapse dynamics in normal and disease states. Using our system we show that chronic hypoxia, associated with neurological defects in preterm birth, affects dopaminergic neuron synapse number depending on the developmental timing of hypoxia.
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192
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Bieli D, Alborelli I, Harmansa S, Matsuda S, Caussinus E, Affolter M. Development and Application of Functionalized Protein Binders in Multicellular Organisms. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2016; 325:181-213. [DOI: 10.1016/bs.ircmb.2016.02.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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193
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Lin WC, Tsai MC, Davenport CM, Smith CM, Veit J, Wilson NM, Adesnik H, Kramer RH. A Comprehensive Optogenetic Pharmacology Toolkit for In Vivo Control of GABA(A) Receptors and Synaptic Inhibition. Neuron 2015; 88:879-891. [PMID: 26606997 DOI: 10.1016/j.neuron.2015.10.026] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 08/21/2015] [Accepted: 10/01/2015] [Indexed: 01/27/2023]
Abstract
Exogenously expressed opsins are valuable tools for optogenetic control of neurons in circuits. A deeper understanding of neural function can be gained by bringing control to endogenous neurotransmitter receptors that mediate synaptic transmission. Here we introduce a comprehensive optogenetic toolkit for controlling GABA(A) receptor-mediated inhibition in the brain. We developed a series of photoswitch ligands and the complementary genetically modified GABA(A) receptor subunits. By conjugating the two components, we generated light-sensitive versions of the entire GABA(A) receptor family. We validated these light-sensitive receptors for applications across a broad range of spatial scales, from subcellular receptor mapping to in vivo photo-control of visual responses in the cerebral cortex. Finally, we generated a knockin mouse in which the "photoswitch-ready" version of a GABA(A) receptor subunit genomically replaces its wild-type counterpart, ensuring normal receptor expression. This optogenetic pharmacology toolkit allows scalable interrogation of endogenous GABA(A) receptor function with high spatial, temporal, and biochemical precision.
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Affiliation(s)
- Wan-Chen Lin
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Ming-Chi Tsai
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Christopher M Davenport
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Caleb M Smith
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Julia Veit
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Neil M Wilson
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Hillel Adesnik
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Richard H Kramer
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA 94720, USA.
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194
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Studying neuronal microtubule organization and microtubule-associated proteins using single molecule localization microscopy. Methods Cell Biol 2015; 131:127-49. [PMID: 26794511 DOI: 10.1016/bs.mcb.2015.06.017] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The formation and maintenance of highly polarized neurons critically depends on the proper organization of the microtubule (MT) cytoskeleton. In axons, MTs are uniformly oriented with their plus-end pointing outward whereas in mature dendrites MTs have mixed orientations. MT organization and dynamics can be regulated by MT-associated proteins (MAPs). Plus-end tracking proteins are specialized MAPs that decorate plus-ends of growing MTs and regulate neuronal polarity, neurite extension, and dendritic spine morphology. Conventional fluorescence microscopy enables observation of specific cellular components through molecule-specific labeling but provides limited resolution (∼250 nm). Therefore, electron microscopy has until now provided most of our knowledge about the precise MT organization in neurons. In the past decade, super-resolution fluorescence microscopy techniques have emerged that circumvent the diffraction limit of light and enable high-resolution reconstruction of the MT network combined with selective protein labeling. However, preserving MT ultrastructure, MAP binding, high labeling density, and antibody specificity after fixation protocols is still quite challenging. In this chapter, we provide an optimized protocol for two-color direct stochastic optical reconstruction microscopy imaging of neuronal MTs together with their growing plus-ends to probe MT architecture and polarity.
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195
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Barcomb K, Goodell DJ, Arnold DB, Bayer KU. Live imaging of endogenous Ca²⁺/calmodulin-dependent protein kinase II in neurons reveals that ischemia-related aggregation does not require kinase activity. J Neurochem 2015. [PMID: 26212614 DOI: 10.1111/jnc.13263] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The Ca(2+) /calmodulin-dependent protein kinase II (CaMKII) forms 12meric holoenzymes. These holoenzymes cluster into larger aggregates within neurons under ischemic conditions and in vitro when ischemic conditions are mimicked. This aggregation is thought to be mediated by interaction between the regulatory domain of one kinase subunit with the T-site of another kinase subunit in a different holoenzyme, an interaction that requires stimulation by Ca(2+) /CaM and nucleotide for its induction. This model makes several predictions that were verified here: Aggregation in vitro was reduced by the CaMKII inhibitors tatCN21 and tatCN19o (which block the T-site) as well as by KN93 (which is CaM-competitive). Notably, these and previously tested manipulations that block CaMKII activation all reduced aggregation, suggesting an alternative mechanism that instead requires kinase activity. However, experiments with the nucleotide-competitive broad-spectrum kinase inhibitors staurosporin and H7 showed that this is not the case. In vitro, staurosporine and H7 enabled CaMKII aggregation even in the absence of nucleotide. Within rat hippocampal neurons, an intra-body enabled live monitoring of endogenous CaMKII aggregation. This aggregation was blocked by tatCN21, but not by staurosporine, even though both effectively inhibit CaMKII activity. These results support the mechanistic model for CaMKII aggregation and show that kinase activity is not required. CaMKII aggregation is prevented by inhibiting kinase activity with mutations (red italics; shown previously) or inhibitors (red bold; shown here), indicating requirement of kinase activity. However, we show here that nucleotide-competitive inhibitors (green) allow CaMKII aggregation (including endogenous CaMKII within neurons), demonstrating that kinase activity is not required and supporting the current mechanistic model for CaMKII aggregation.
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Affiliation(s)
- Kelsey Barcomb
- Department of Pharmacology, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, Colorado, USA
| | - Dayton J Goodell
- Department of Pharmacology, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, Colorado, USA
| | - Don B Arnold
- Department of Biology, University of Southern California, Los Angeles, California, USA
| | - K Ulrich Bayer
- Department of Pharmacology, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, Colorado, USA
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196
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Helma J, Cardoso MC, Muyldermans S, Leonhardt H. Nanobodies and recombinant binders in cell biology. J Cell Biol 2015; 209:633-44. [PMID: 26056137 PMCID: PMC4460151 DOI: 10.1083/jcb.201409074] [Citation(s) in RCA: 158] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Antibodies are key reagents to investigate cellular processes. The development of recombinant antibodies and binders derived from natural protein scaffolds has expanded traditional applications, such as immunofluorescence, binding arrays, and immunoprecipitation. In addition, their small size and high stability in ectopic environments have enabled their use in all areas of cell research, including structural biology, advanced microscopy, and intracellular expression. Understanding these novel reagents as genetic modules that can be integrated into cellular pathways opens up a broad experimental spectrum to monitor and manipulate cellular processes.
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Affiliation(s)
- Jonas Helma
- Department of Biology II, Ludwig Maximilians University Munich and Center for Integrated Protein Science Munich, 82152 Planegg-Martinsried, Germany
| | - M Cristina Cardoso
- Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany
| | - Serge Muyldermans
- Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Heinrich Leonhardt
- Department of Biology II, Ludwig Maximilians University Munich and Center for Integrated Protein Science Munich, 82152 Planegg-Martinsried, Germany
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197
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Abstract
To create a presynaptic terminal, molecular signaling events must be orchestrated across a number of subcellular compartments. In the soma, presynaptic proteins need to be synthesized, packaged together, and attached to microtubule motors for shipment through the axon. Within the axon, transport of presynaptic packages is regulated to ensure that developing synapses receive an adequate supply of components. At individual axonal sites, extracellular interactions must be translated into intracellular signals that can incorporate mobile transport vesicles into the nascent presynaptic terminal. Even once the initial recruitment process is complete, the components and subsequent functionality of presynaptic terminals need to constantly be remodeled. Perhaps most remarkably, all of these processes need to be coordinated in space and time. In this review, we discuss how these dynamic cellular processes occur in neurons of the central nervous system in order to generate presynaptic terminals in the brain.
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Affiliation(s)
- Luke A D Bury
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Shasta L Sabo
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH, USA Department of Neuroscience, Case Western Reserve University School of Medicine, Cleveland, OH, USA
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198
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Specific GFP-binding artificial proteins (αRep): a new tool for in vitro to live cell applications. Biosci Rep 2015; 35:BSR20150080. [PMID: 26182430 PMCID: PMC4613692 DOI: 10.1042/bsr20150080] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 04/23/2015] [Indexed: 02/08/2023] Open
Abstract
Artificial proteins, named αRep, binding tightly and specifically to EGFP are described. The structures of αRep–EGFP complexes explain how αRep recognize their cognate partner. Specific αRep can be used for biochemical or live cells experiments. A family of artificial proteins, named αRep, based on a natural family of helical repeat was previously designed. αRep members are efficiently expressed, folded and extremely stable proteins. A large αRep library was constructed creating proteins with a randomized interaction surface. In the present study, we show that the αRep library is an efficient source of tailor-made specific proteins with direct applications in biochemistry and cell biology. From this library, we selected by phage display αRep binders with nanomolar dissociation constants against the GFP. The structures of two independent αRep binders in complex with the GFP target were solved by X-ray crystallography revealing two totally different binding modes. The affinity of the selected αReps for GFP proved sufficient for practically useful applications such as pull-down experiments. αReps are disulfide free proteins and are efficiently and functionally expressed in eukaryotic cells: GFP-specific αReps are clearly sequestrated by their cognate target protein addressed to various cell compartments. These results suggest that αRep proteins with tailor-made specificity can be selected and used in living cells to track, modulate or interfere with intracellular processes.
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199
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Choii G, Ko J. Gephyrin: a central GABAergic synapse organizer. Exp Mol Med 2015; 47:e158. [PMID: 25882190 DOI: 10.1038/emm.2015.5] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2014] [Accepted: 12/18/2014] [Indexed: 01/22/2023] Open
Abstract
Gephyrin is a central element that anchors, clusters and stabilizes glycine and γ-aminobutyric acid type A receptors at inhibitory synapses of the mammalian brain. It self-assembles into a hexagonal lattice and interacts with various inhibitory synaptic proteins. Intriguingly, the clustering of gephyrin, which is regulated by multiple posttranslational modifications, is critical for inhibitory synapse formation and function. In this review, we summarize the basic properties of gephyrin and describe recent findings regarding its roles in inhibitory synapse formation, function and plasticity. We will also discuss the implications for the pathophysiology of brain disorders and raise the remaining open questions in this field.
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Affiliation(s)
- Gayoung Choii
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea
| | - Jaewon Ko
- 1] Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea [2] Department of Psychiatry, Yonsei University College of Medicine, Seoul, Korea
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200
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Live imaging of endogenous PSD-95 using ENABLED: a conditional strategy to fluorescently label endogenous proteins. J Neurosci 2015; 34:16698-712. [PMID: 25505322 DOI: 10.1523/jneurosci.3888-14.2014] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Stoichiometric labeling of endogenous synaptic proteins for high-contrast live-cell imaging in brain tissue remains challenging. Here, we describe a conditional mouse genetic strategy termed endogenous labeling via exon duplication (ENABLED), which can be used to fluorescently label endogenous proteins with near ideal properties in all neurons, a sparse subset of neurons, or specific neuronal subtypes. We used this method to label the postsynaptic density protein PSD-95 with mVenus without overexpression side effects. We demonstrated that mVenus-tagged PSD-95 is functionally equivalent to wild-type PSD-95 and that PSD-95 is present in nearly all dendritic spines in CA1 neurons. Within spines, while PSD-95 exhibited low mobility under basal conditions, its levels could be regulated by chronic changes in neuronal activity. Notably, labeled PSD-95 also allowed us to visualize and unambiguously examine otherwise-unidentifiable excitatory shaft synapses in aspiny neurons, such as parvalbumin-positive interneurons and dopaminergic neurons. Our results demonstrate that the ENABLED strategy provides a valuable new approach to study the dynamics of endogenous synaptic proteins in vivo.
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