1
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Su Z, Griffin B, Emmons S, Wu Y. Prediction of interactions between cell surface proteins by machine learning. Proteins 2024; 92:567-580. [PMID: 38050713 DOI: 10.1002/prot.26648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 11/15/2023] [Accepted: 11/20/2023] [Indexed: 12/06/2023]
Abstract
Cells detect changes in their external environments or communicate with each other through proteins on their surfaces. These cell surface proteins form a complicated network of interactions in order to fulfill their functions. The interactions between cell surface proteins are highly dynamic and, thus, challenging to detect using traditional experimental techniques. Here, we tackle this challenge using a computational framework. The primary focus of the framework is to develop new tools to identify interactions between domains in the immunoglobulin (Ig) fold, which is the most abundant domain family in cell surface proteins. These interactions could be formed between ligands and receptors from different cells or between proteins on the same cell surface. In practice, we collected all structural data on Ig domain interactions and transformed them into an interface fragment pair library. A high-dimensional profile can then be constructed from the library for a given pair of query protein sequences. Multiple machine learning models were used to read this profile so that the probability of interaction between the query proteins could be predicted. We tested our models on an experimentally derived dataset that contains 564 cell surface proteins in humans. The cross-validation results show that we can achieve higher than 70% accuracy in identifying the PPIs within this dataset. We then applied this method to a group of 46 cell surface proteins in Caenorhabditis elegans. We screened every possible interaction between these proteins. Many interactions recognized by our machine learning classifiers have been experimentally confirmed in the literature. In conclusion, our computational platform serves as a useful tool to help identify potential new interactions between cell surface proteins in addition to current state-of-the-art experimental techniques. The tool is freely accessible for use by the scientific community. Moreover, the general framework of the machine learning classification can also be extended to study the interactions of proteins in other domain superfamilies.
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Affiliation(s)
- Zhaoqian Su
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Brian Griffin
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Scott Emmons
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Yinghao Wu
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, New York, USA
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2
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Correa E, Mialon M, Cizeron M, Bessereau JL, Pinan-Lucarre B, Kratsios P. UNC-30/PITX coordinates neurotransmitter identity with postsynaptic GABA receptor clustering. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.14.580278. [PMID: 38405977 PMCID: PMC10888783 DOI: 10.1101/2024.02.14.580278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Terminal selectors are transcription factors that control neuronal identity by regulating the expression of key effector molecules, such as neurotransmitter (NT) biosynthesis proteins, ion channels and neuropeptides. Whether and how terminal selectors control neuronal connectivity is poorly understood. Here, we report that UNC-30 (PITX2/3), the terminal selector of GABA motor neuron identity in C. elegans , is required for NT receptor clustering, a hallmark of postsynaptic differentiation. Animals lacking unc-30 or madd-4B, the short isoform of the MN-secreted synapse organizer madd-4 ( Punctin/ADAMTSL ), display severe GABA receptor type A (GABA A R) clustering defects in postsynaptic muscle cells. Mechanistically, UNC-30 acts directly to induce and maintain transcription of madd-4B and GABA biosynthesis genes (e.g., unc-25/GAD , unc-47/VGAT ). Hence, UNC-30 controls GABA A R clustering on postsynaptic muscle cells and GABA biosynthesis in presynaptic cells, transcriptionally coordinating two critical processes for GABA neurotransmission. Further, we uncover multiple target genes and a dual role for UNC-30 both as an activator and repressor of gene transcription. Our findings on UNC-30 function may contribute to our molecular understanding of human conditions, such as Axenfeld-Rieger syndrome, caused by PITX2 and PITX3 gene mutations.
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3
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Ajayi T, Thomas A, Nikolic M, Henderson L, Zaheri A, Dwyer DS. Evolutionary conservation of putative suicidality-related risk genes that produce diminished motivation corrected by clozapine, lithium and antidepressants. Front Psychiatry 2024; 15:1341735. [PMID: 38362034 PMCID: PMC10867104 DOI: 10.3389/fpsyt.2024.1341735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 01/17/2024] [Indexed: 02/17/2024] Open
Abstract
Background Genome wide association studies (GWAS) and candidate gene analyses have identified genetic variants and genes that may increase the risk for suicidal thoughts and behaviors (STBs). Important unresolved issues surround these tentative risk variants such as the characteristics of the associated genes and how they might elicit STBs. Methods Putative suicidality-related risk genes (PSRGs) were identified by comprehensive literature search and were characterized with respect to evolutionary conservation, participation in gene interaction networks and associated phenotypes. Evolutionary conservation was established with database searches and BLASTP queries, whereas gene-gene interactions were ascertained with GeneMANIA. We then examined whether mutations in risk-gene counterparts in C. elegans produced a diminished motivation phenotype previously connected to suicide risk factors. Results and conclusions From the analysis, 105 risk-gene candidates were identified and found to be: 1) highly conserved during evolution, 2) enriched for essential genes, 3) involved in significant gene-gene interactions, and 4) associated with psychiatric disorders, metabolic disturbances and asthma/allergy. Evaluation of 17 mutant strains with loss-of-function/deletion mutations in PSRG orthologs revealed that 11 mutants showed significant evidence of diminished motivation that manifested as immobility in a foraging assay. Immobility was corrected in some or all of the mutants with clozapine, lithium and tricyclic antidepressant drugs. In addition, 5-HT2 receptor and muscarinic receptor antagonists restored goal-directed behavior in most or all of the mutants. These studies increase confidence in the validity of the PSRGs and provide initial clues about possible mechanisms that mediate STBs.
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Affiliation(s)
- Titilade Ajayi
- Department of Pharmacology, Toxicology and Neuroscience, LSU Health Shreveport, Shreveport, LA, United States
| | - Alicia Thomas
- Department of Pharmacology, Toxicology and Neuroscience, LSU Health Shreveport, Shreveport, LA, United States
| | - Marko Nikolic
- Department of Psychiatry and Behavioral Medicine, LSU Health Shreveport, Shreveport, LA, United States
| | - Lauryn Henderson
- Department of Psychiatry and Behavioral Medicine, LSU Health Shreveport, Shreveport, LA, United States
| | - Alexa Zaheri
- Department of Psychiatry and Behavioral Medicine, LSU Health Shreveport, Shreveport, LA, United States
| | - Donard S. Dwyer
- Department of Pharmacology, Toxicology and Neuroscience, LSU Health Shreveport, Shreveport, LA, United States
- Department of Psychiatry and Behavioral Medicine, LSU Health Shreveport, Shreveport, LA, United States
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4
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Zhao J, Gao L, Nurrish S, Kaplan JM. Post-synaptic GABA A receptors potentiate transmission by recruiting CaV2 channels to their inputs. Cell Rep 2023; 42:113161. [PMID: 37742192 PMCID: PMC10873018 DOI: 10.1016/j.celrep.2023.113161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 07/05/2023] [Accepted: 09/07/2023] [Indexed: 09/26/2023] Open
Abstract
We describe a retrograde synaptic signal at the C. elegans GABAergic neuromuscular junction. At this synapse, GABA release is controlled by two voltage-activated calcium channels (UNC-2/CaV2 and EGL-19/CaV1), and muscle responses are mediated by a single GABA receptor (UNC-49/GABAA). Mutations inactivating UNC-49 or those preventing UNC-49 synaptic clustering cause retrograde defects in GABAergic motor neurons, whereby UNC-2/CaV2 levels at active zones, UNC-2 current, and pre-synaptic GABA release are decreased. Inactivating post-synaptic GABAA receptors has no effect on GABA neuron EGL-19/CaV1 levels nor on several other pre-synaptic markers. The effect of GABAA receptors on pre-synaptic strength is not a consequence of decreased GABA transmission and is input selective. Finally, pre-synaptic UNC-2/CaV2 levels are increased when post-synaptic GABAA receptors are increased but are unaffected by increased extra-synaptic receptors. Collectively, these results suggest that clustered post-synaptic GABAA receptors adjust the strength of their inputs by recruiting CaV2 to contacting active zones.
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Affiliation(s)
- Jian Zhao
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Luna Gao
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Stephen Nurrish
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Joshua M Kaplan
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA; Program in Neuroscience, Harvard Medical School, Boston, MA 02115, USA.
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5
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Terada N, Saitoh Y, Saito M, Yamada T, Kamijo A, Yoshizawa T, Sakamoto T. Recent Progress on Genetically Modified Animal Models for Membrane Skeletal Proteins: The 4.1 and MPP Families. Genes (Basel) 2023; 14:1942. [PMID: 37895291 PMCID: PMC10606877 DOI: 10.3390/genes14101942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 10/11/2023] [Accepted: 10/12/2023] [Indexed: 10/29/2023] Open
Abstract
The protein 4.1 and membrane palmitoylated protein (MPP) families were originally found as components in the erythrocyte membrane skeletal protein complex, which helps maintain the stability of erythrocyte membranes by linking intramembranous proteins and meshwork structures composed of actin and spectrin under the membranes. Recently, it has been recognized that cells and tissues ubiquitously use this membrane skeletal system. Various intramembranous proteins, including adhesion molecules, ion channels, and receptors, have been shown to interact with the 4.1 and MPP families, regulating cellular and tissue dynamics by binding to intracellular signal transduction proteins. In this review, we focus on our previous studies regarding genetically modified animal models, especially on 4.1G, MPP6, and MPP2, to describe their functional roles in the peripheral nervous system, the central nervous system, the testis, and bone formation. As the membrane skeletal proteins are located at sites that receive signals from outside the cell and transduce signals inside the cell, it is necessary to elucidate their molecular interrelationships, which may broaden the understanding of cell and tissue functions.
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Affiliation(s)
- Nobuo Terada
- Health Science Division, Department of Medical Sciences, Shinshu University Graduate School of Medicine, Science and Technology, Matsumoto City, Nagano 390-8621, Japan
| | - Yurika Saitoh
- Health Science Division, Department of Medical Sciences, Shinshu University Graduate School of Medicine, Science and Technology, Matsumoto City, Nagano 390-8621, Japan
- Center for Medical Education, Teikyo University of Science, Adachi-ku, Tokyo 120-0045, Japan
| | - Masaki Saito
- School of Pharma-Science, Teikyo University, Itabashi-ku, Tokyo 173-8605, Japan;
| | - Tomoki Yamada
- Health Science Division, Department of Medical Sciences, Shinshu University Graduate School of Medicine, Science and Technology, Matsumoto City, Nagano 390-8621, Japan
| | - Akio Kamijo
- Health Science Division, Department of Medical Sciences, Shinshu University Graduate School of Medicine, Science and Technology, Matsumoto City, Nagano 390-8621, Japan
- Division of Basic & Clinical Medicine, Nagano College of Nursing, Komagane City, Nagano 399-4117, Japan
| | - Takahiro Yoshizawa
- Division of Animal Research, Research Center for Advanced Science and Technology, Shinshu University, Matsumoto City, Nagano 390-8621, Japan
| | - Takeharu Sakamoto
- Department of Cancer Biology, Institute of Biomedical Science, Kansai Medical University, Hirakata City, Osaka 573-1010, Japan
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6
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Su Z, Griffin B, Emmons S, Wu Y. Prediction of Interactions between Cell Surface Proteins by Machine Learning. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.12.557337. [PMID: 37745607 PMCID: PMC10515853 DOI: 10.1101/2023.09.12.557337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Cells detect changes of external environments or communicate with each other through proteins on their surfaces. These cell surface proteins form a complicated network of interactions in order to fulfill their functions. The interactions between cell surface proteins are highly dynamic and thus challenging to detect using traditional experimental techniques. Here we tackle this challenge by a computational framework. The primary focus of the framework is to develop new tools to identify interactions between domains in immunoglobulin (Ig) fold, which is the most abundant domain family in cell surface proteins. These interactions could be formed between ligands and receptors from different cells, or between proteins on the same cell surface. In practice, we collected all structural data of Ig domain interactions and transformed them into an interface fragment pair library. A high dimensional profile can be then constructed from the library for a given pair of query protein sequences. Multiple machine learning models were used to read this profile, so that the probability of interaction between the query proteins can be predicted. We tested our models to an experimentally derived dataset which contains 564 cell surface proteins in human. The cross-validation results show that we can achieve higher than 70% accuracy in identifying the PPIs within this dataset. We then applied this method to a group of 46 cell surface proteins in C elegans. We screened every possible interaction between these proteins. Many interactions recognized by our machine learning classifiers have been experimentally confirmed in the literatures. In conclusion, our computational platform serves a useful tool to help identifying potential new interactions between cell surface proteins in addition to current state-of-the-art experimental techniques. The tool is freely accessible for use by the scientific community. Moreover, the general framework of the machine learning classification can also be extended to study interactions of proteins in other domain superfamilies.
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Affiliation(s)
- Zhaoqian Su
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY, 10461
| | - Brian Griffin
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY, 10461
| | - Scott Emmons
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY, 10461
| | - Yinghao Wu
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY, 10461
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7
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Cramer TML, Pinan-Lucarre B, Cavaccini A, Damilou A, Tsai YC, Bhat MA, Panzanelli P, Rama N, Mehlen P, Benke D, Karayannis T, Bessereau JL, Tyagarajan SK. Adamtsl3 mediates DCC signaling to selectively promote GABAergic synapse function. Cell Rep 2023; 42:112947. [PMID: 37572323 DOI: 10.1016/j.celrep.2023.112947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 06/23/2023] [Accepted: 07/20/2023] [Indexed: 08/14/2023] Open
Abstract
The molecular code that controls synapse formation and maintenance in vivo has remained quite sparse. Here, we identify that the secreted protein Adamtsl3 functions as critical hippocampal synapse organizer acting through the transmembrane receptor DCC (deleted in colorectal cancer). Traditionally, DCC function has been associated with glutamatergic synaptogenesis and plasticity in response to Netrin-1 signaling. We demonstrate that early post-natal deletion of Adamtsl3 in neurons impairs DCC protein expression, causing reduced density of both glutamatergic and GABAergic synapses. Adult deletion of Adamtsl3 in either GABAergic or glutamatergic neurons does not interfere with DCC-Netrin-1 function at glutamatergic synapses but controls DCC signaling at GABAergic synapses. The Adamtsl3-DCC signaling unit is further essential for activity-dependent adaptations at GABAergic synapses, involving DCC phosphorylation and Src kinase activation. These findings might be particularly relevant for schizophrenia because genetic variants in Adamtsl3 and DCC have been independently linked with schizophrenia in patients.
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Affiliation(s)
- Teresa M L Cramer
- University of Zurich, Institute of Pharmacology and Toxicology, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | | | - Anna Cavaccini
- University of Zurich, Brain Research Institute, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Angeliki Damilou
- University of Zurich, Brain Research Institute, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Yuan-Chen Tsai
- University of Zurich, Institute of Pharmacology and Toxicology, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Musadiq A Bhat
- University of Zurich, Institute of Pharmacology and Toxicology, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Patrizia Panzanelli
- Department of Neuroscience Rita Levi Montalcini, University of Turin, Turin, Italy
| | - Nicolas Rama
- Centre de Recherche en Cancérologie de Lyon, INSERM U1052-CNRS UMR5286, Université de Lyon, Centre Léon Bérard, 69008 Lyon, France
| | - Patrick Mehlen
- Centre de Recherche en Cancérologie de Lyon, INSERM U1052-CNRS UMR5286, Université de Lyon, Centre Léon Bérard, 69008 Lyon, France
| | - Dietmar Benke
- University of Zurich, Institute of Pharmacology and Toxicology, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Theofanis Karayannis
- University of Zurich, Brain Research Institute, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Jean-Louis Bessereau
- University Claude Bernard Lyon 1, CNRS UMR 5284, INSERM U 1314, Melis, 69008 Lyon, France
| | - Shiva K Tyagarajan
- University of Zurich, Institute of Pharmacology and Toxicology, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
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8
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Zang Y, Bashaw GJ. Systematic analysis of the Frazzled receptor interactome establishes previously unreported regulators of axon guidance. Development 2023; 150:dev201636. [PMID: 37526651 PMCID: PMC10445734 DOI: 10.1242/dev.201636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 07/07/2023] [Indexed: 08/02/2023]
Abstract
The Netrin receptor Dcc and its Drosophila homolog Frazzled play crucial roles in diverse developmental process, including axon guidance. In Drosophila, Fra regulates midline axon guidance through a Netrin-dependent and a Netrin-independent pathway. However, what molecules regulate these distinct signaling pathways remain unclear. To identify Fra-interacting proteins, we performed affinity purification mass spectrometry to establish a neuronal-specific Fra interactome. In addition to known interactors of Fra and Dcc, including Netrin and Robo1, our screen identified 85 candidate proteins, the majority of which are conserved in humans. Many of these proteins are expressed in the ventral nerve cord, and gene ontology, pathway analysis and biochemical validation identified several previously unreported pathways, including the receptor tyrosine phosphatase Lar, subunits of the COP9 signalosome and Rho-5, a regulator of the metalloprotease Tace. Finally, genetic analysis demonstrates that these genes regulate axon guidance and may define as yet unknown signaling mechanisms for Fra and its vertebrate homolog Dcc. Thus, the Fra interactome represents a resource to guide future functional studies.
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Affiliation(s)
- Yixin Zang
- Department of Neuroscience, Perelman School of Medicine, University of Pennsylvania, 415 Curie Blvd, Philadelphia, PA, 19104, USA
| | - Greg J. Bashaw
- Department of Neuroscience, Perelman School of Medicine, University of Pennsylvania, 415 Curie Blvd, Philadelphia, PA, 19104, USA
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9
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Hao Y, Liu H, Zeng XT, Wang Y, Zeng WX, Qian KY, Li L, Chi MX, Gao S, Hu Z, Tong XJ. UNC-43/CaMKII-triggered anterograde signals recruit GABA ARs to mediate inhibitory synaptic transmission and plasticity at C. elegans NMJs. Nat Commun 2023; 14:1436. [PMID: 36918518 PMCID: PMC10015018 DOI: 10.1038/s41467-023-37137-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 02/28/2023] [Indexed: 03/16/2023] Open
Abstract
Disturbed inhibitory synaptic transmission has functional impacts on neurodevelopmental and psychiatric disorders. An essential mechanism for modulating inhibitory synaptic transmission is alteration of the postsynaptic abundance of GABAARs, which are stabilized by postsynaptic scaffold proteins and recruited by presynaptic signals. However, how GABAergic neurons trigger signals to transsynaptically recruit GABAARs remains elusive. Here, we show that UNC-43/CaMKII functions at GABAergic neurons to recruit GABAARs and modulate inhibitory synaptic transmission at C. elegans neuromuscular junctions. We demonstrate that UNC-43 promotes presynaptic MADD-4B/Punctin secretion and NRX-1α/Neurexin surface delivery. Together, MADD-4B and NRX-1α recruit postsynaptic NLG-1/Neuroligin and stabilize GABAARs. Further, the excitation of GABAergic neurons potentiates the recruitment of NLG-1-stabilized-GABAARs, which depends on UNC-43, MADD-4B, and NRX-1. These data all support that UNC-43 triggers MADD-4B and NRX-1α, which act as anterograde signals to recruit postsynaptic GABAARs. Thus, our findings elucidate a mechanism for pre- and postsynaptic communication and inhibitory synaptic transmission and plasticity.
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Affiliation(s)
- Yue Hao
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, Beijing, 100190, China
| | - Haowen Liu
- Queensland Brain Institute, Clem Jones Centre for Ageing Dementia Research (CJCADR), The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Xian-Ting Zeng
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Ya Wang
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Wan-Xin Zeng
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, Beijing, 100190, China
| | - Kang-Ying Qian
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, Beijing, 100190, China
| | - Lei Li
- Queensland Brain Institute, Clem Jones Centre for Ageing Dementia Research (CJCADR), The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Ming-Xuan Chi
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Shangbang Gao
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Zhitao Hu
- Queensland Brain Institute, Clem Jones Centre for Ageing Dementia Research (CJCADR), The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Xia-Jing Tong
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
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10
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Mizumoto K, Jin Y, Bessereau JL. Synaptogenesis: unmasking molecular mechanisms using Caenorhabditis elegans. Genetics 2023; 223:iyac176. [PMID: 36630525 PMCID: PMC9910414 DOI: 10.1093/genetics/iyac176] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 10/22/2022] [Indexed: 01/13/2023] Open
Abstract
The nematode Caenorhabditis elegans is a research model organism particularly suited to the mechanistic understanding of synapse genesis in the nervous system. Armed with powerful genetics, knowledge of complete connectomics, and modern genomics, studies using C. elegans have unveiled multiple key regulators in the formation of a functional synapse. Importantly, many signaling networks display remarkable conservation throughout animals, underscoring the contributions of C. elegans research to advance the understanding of our brain. In this chapter, we will review up-to-date information of the contribution of C. elegans to the understanding of chemical synapses, from structure to molecules and to synaptic remodeling.
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Affiliation(s)
- Kota Mizumoto
- Department of Zoology, University of British Columbia, Vancouver V6T 1Z3, Canada
| | - Yishi Jin
- Department of Neurobiology, University of California San Diego, La Jolla, CA 92093, USA
| | - Jean-Louis Bessereau
- Univ Lyon, University Claude Bernard Lyon 1, CNRS UMR 5284, INSERM U 1314, Melis, 69008 Lyon, France
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11
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Li L, Liu H, Qian KY, Nurrish S, Zeng XT, Zeng WX, Wang J, Kaplan JM, Tong XJ, Hu Z. CASK and FARP localize two classes of post-synaptic ACh receptors thereby promoting cholinergic transmission. PLoS Genet 2022; 18:e1010211. [PMID: 36279278 PMCID: PMC9632837 DOI: 10.1371/journal.pgen.1010211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 11/03/2022] [Accepted: 10/10/2022] [Indexed: 11/06/2022] Open
Abstract
Changes in neurotransmitter receptor abundance at post-synaptic elements play a pivotal role in regulating synaptic strength. For this reason, there is significant interest in identifying and characterizing the scaffolds required for receptor localization at different synapses. Here we analyze the role of two C. elegans post-synaptic scaffolding proteins (LIN-2/CASK and FRM-3/FARP) at cholinergic neuromuscular junctions. Constitutive knockouts or muscle specific inactivation of lin-2 and frm-3 dramatically reduced spontaneous and evoked post-synaptic currents. These synaptic defects resulted from the decreased abundance of two classes of post-synaptic ionotropic acetylcholine receptors (ACR-16/CHRNA7 and levamisole-activated AChRs). LIN-2's AChR scaffolding function is mediated by its SH3 and PDZ domains, which interact with AChRs and FRM-3/FARP, respectively. Thus, our findings show that post-synaptic LIN-2/FRM-3 complexes promote cholinergic synaptic transmission by recruiting AChRs to post-synaptic elements.
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Affiliation(s)
- Lei Li
- Queensland Brain Institute, Clem Jones Centre for Ageing Dementia Research (CJCADR), The University of Queensland, Brisbane, Australia
| | - Haowen Liu
- Queensland Brain Institute, Clem Jones Centre for Ageing Dementia Research (CJCADR), The University of Queensland, Brisbane, Australia
| | - Kang-Ying Qian
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Stephen Nurrish
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Neurobiology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Xian-Ting Zeng
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Wan-Xin Zeng
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Jiafan Wang
- Queensland Brain Institute, Clem Jones Centre for Ageing Dementia Research (CJCADR), The University of Queensland, Brisbane, Australia
| | - Joshua M. Kaplan
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Neurobiology, Harvard Medical School, Boston, Massachusetts, United States of America
- Program in Neuroscience, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Xia-Jing Tong
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Zhitao Hu
- Queensland Brain Institute, Clem Jones Centre for Ageing Dementia Research (CJCADR), The University of Queensland, Brisbane, Australia
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12
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Identification, molecular characterization, and in silico structural analysis of larval salivary glands Netrin-A as a potent biomarker from Lucilia sericata (Diptera: Calliphoridae). Genetica 2022; 150:379-394. [PMID: 36136258 DOI: 10.1007/s10709-022-00164-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 07/29/2022] [Indexed: 11/04/2022]
Abstract
The greenbottle blowfly Lucilia sericata (L. sericata) is increasingly used in larval therapy of chronic wounds. Netrins as bifunctional proteins are in the superfamily of Laminins secreted from larval salivary glands. The Netrin protein has a significant instructive role in axon guidance, causing neuronal outgrowth, angiogenesis, and cell migration. It seems to be crucial in wound healing and acts as a potential biomarker in diagnosing some clinical diseases. This survey aimed to identify molecular features and analyze in silico structural configuration of Netrin-A in L. sericata larvae. The larvae were reared under standard maggotarium conditions. The nucleic acid sequence of L. sericata Netrin-A (LSN-A) was then identified using rapid amplification of circular DNA ends (RACE) and rapid amplification of genomic ends (RAGE). Parts of the Netrin-A gene, including the middle, 3'-, and 5'-ends, were identified, TA cloned in pTG19 plasmid, and transferred into DH5ɑ Escherichia coli. Each part was sequenced and assembled using SeqMan software. This gene structure was further subjected to in silico analysis. The DNA of LSN-A was identified to be 2407 bp, while its mRNA sequence was recognized as 2115 bp by Oligo0.7 software. It translated the Netrin-A protein with 704 amino acid residues. Its estimated molecular weight was 78.6 kDa. Sequencing of this fragment and its BLAST analysis revealed laminin-based high (95%) similarity with the mRNA sequence of Lucilia cuprina Netrin-A. The 3-D structure of Netrin-A drawn by SWISS-MODEL exhibited its partial resemblance to the reference molecule Netrin-1 of Homo sapiens. This study supports the molecular and structural analyses of LSN-A protein, which could lead to wound treatment. Ultimately, it can be an effective candidate to ameliorate injury. Our next attempt is to produce LSN-A recombinant protein for use in biomedical sciences.
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Godini R, Fallahi H, Pocock R. The regulatory landscape of neurite development in Caenorhabditis elegans. Front Mol Neurosci 2022; 15:974208. [PMID: 36090252 PMCID: PMC9453034 DOI: 10.3389/fnmol.2022.974208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 07/26/2022] [Indexed: 11/18/2022] Open
Abstract
Neuronal communication requires precise connectivity of neurite projections (axons and dendrites). Developing neurites express cell-surface receptors that interpret extracellular cues to enable correct guidance toward, and connection with, target cells. Spatiotemporal regulation of neurite guidance molecule expression by transcription factors (TFs) is critical for nervous system development and function. Here, we review how neurite development is regulated by TFs in the Caenorhabditis elegans nervous system. By collecting publicly available transcriptome and ChIP-sequencing data, we reveal gene expression dynamics during neurite development, providing insight into transcriptional mechanisms governing construction of the nervous system architecture.
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Affiliation(s)
- Rasoul Godini
- Development and Stem Cells Program, Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, VIC, Australia
- *Correspondence: Rasoul Godini,
| | - Hossein Fallahi
- Department of Biology, School of Sciences, Razi University, Kermanshah, Iran
| | - Roger Pocock
- Development and Stem Cells Program, Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, VIC, Australia
- Roger Pocock,
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González-Calvo I, Cizeron M, Bessereau JL, Selimi F. Synapse Formation and Function Across Species: Ancient Roles for CCP, CUB, and TSP-1 Structural Domains. Front Neurosci 2022; 16:866444. [PMID: 35546877 PMCID: PMC9083331 DOI: 10.3389/fnins.2022.866444] [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: 01/31/2022] [Accepted: 03/28/2022] [Indexed: 11/17/2022] Open
Abstract
The appearance of synapses was a crucial step in the creation of the variety of nervous systems that are found in the animal kingdom. With increased complexity of the organisms came a greater number of synaptic proteins. In this review we describe synaptic proteins that contain the structural domains CUB, CCP, or TSP-1. These domains are found in invertebrates and vertebrates, and CUB and CCP domains were initially described in proteins belonging to the complement system of innate immunity. Interestingly, they are found in synapses of the nematode C. elegans, which does not have a complement system, suggesting an ancient function. Comparison of the roles of CUB-, CCP-, and TSP-1 containing synaptic proteins in various species shows that in more complex nervous systems, these structural domains are combined with other domains and that there is partial conservation of their function. These three domains are thus basic building blocks of the synaptic architecture. Further studies of structural domains characteristic of synaptic proteins in invertebrates such as C. elegans and comparison of their role in mammals will help identify other conserved synaptic molecular building blocks. Furthermore, this type of functional comparison across species will also identify structural domains added during evolution in correlation with increased complexity, shedding light on mechanisms underlying cognition and brain diseases.
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Affiliation(s)
- Inés González-Calvo
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, PSL Research University, Paris, France
| | - Mélissa Cizeron
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR-5284, INSERM U-1314, MeLiS, Institut NeuroMyoGène, Lyon, France
| | - Jean-Louis Bessereau
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR-5284, INSERM U-1314, MeLiS, Institut NeuroMyoGène, Lyon, France
| | - Fekrije Selimi
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, PSL Research University, Paris, France
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Zhou X, Vachon C, Cizeron M, Romatif O, Bülow HE, Jospin M, Bessereau JL. The HSPG syndecan is a core organizer of cholinergic synapses. J Cell Biol 2021; 220:212450. [PMID: 34213535 PMCID: PMC8258370 DOI: 10.1083/jcb.202011144] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 04/13/2021] [Accepted: 05/26/2021] [Indexed: 12/15/2022] Open
Abstract
The extracellular matrix has emerged as an active component of chemical synapses regulating synaptic formation, maintenance, and homeostasis. The heparan sulfate proteoglycan (HSPG) syndecans are known to regulate cellular and axonal migration in the brain. They are also enriched at synapses, but their synaptic functions remain more elusive. Here, we show that SDN-1, the sole orthologue of syndecan in C. elegans, is absolutely required for the synaptic clustering of homomeric α7-like acetylcholine receptors (AChRs) and regulates the synaptic content of heteromeric AChRs. SDN-1 is concentrated at neuromuscular junctions (NMJs) by the neurally secreted synaptic organizer Ce-Punctin/MADD-4, which also activates the transmembrane netrin receptor DCC. Those cooperatively recruit the FARP and CASK orthologues that localize α7-like-AChRs at cholinergic NMJs through physical interactions. Therefore, SDN-1 stands at the core of the cholinergic synapse organization by bridging the extracellular synaptic determinants to the intracellular synaptic scaffold that controls the postsynaptic receptor content.
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Affiliation(s)
- Xin Zhou
- Université de Lyon, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique Unite Mixte de Recherche 5310, Institut National de la Santé et de la Recherche Médicale U1217, Institut NeuroMyoGène, Lyon, France
| | - Camille Vachon
- Université de Lyon, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique Unite Mixte de Recherche 5310, Institut National de la Santé et de la Recherche Médicale U1217, Institut NeuroMyoGène, Lyon, France
| | - Mélissa Cizeron
- Université de Lyon, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique Unite Mixte de Recherche 5310, Institut National de la Santé et de la Recherche Médicale U1217, Institut NeuroMyoGène, Lyon, France
| | - Océane Romatif
- Université de Lyon, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique Unite Mixte de Recherche 5310, Institut National de la Santé et de la Recherche Médicale U1217, Institut NeuroMyoGène, Lyon, France
| | - Hannes E Bülow
- Department of Genetics and Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY
| | - Maëlle Jospin
- Université de Lyon, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique Unite Mixte de Recherche 5310, Institut National de la Santé et de la Recherche Médicale U1217, Institut NeuroMyoGène, Lyon, France
| | - Jean-Louis Bessereau
- Université de Lyon, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique Unite Mixte de Recherche 5310, Institut National de la Santé et de la Recherche Médicale U1217, Institut NeuroMyoGène, Lyon, France
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Cizeron M, Granger L, Bülow HE, Bessereau JL. Specific heparan sulfate modifications stabilize the synaptic organizer MADD-4/Punctin at C. elegans neuromuscular junctions. Genetics 2021; 218:6275221. [PMID: 33983408 DOI: 10.1093/genetics/iyab073] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 04/16/2021] [Indexed: 01/01/2023] Open
Abstract
Heparan sulfate proteoglycans contribute to the structural organization of various neurochemical synapses. Depending on the system, their role involves either the core protein or the glycosaminoglycan chains. These linear sugar chains are extensively modified by heparan sulfate modification enzymes, resulting in highly diverse molecules. Specific modifications of glycosaminoglycan chains may thus contribute to a sugar code involved in synapse specificity. Caenorhabditis elegans is particularly useful to address this question because of the low level of genomic redundancy of these enzymes, as opposed to mammals. Here, we systematically mutated the genes encoding heparan sulfate modification enzymes in C. elegans and analyzed their impact on excitatory and inhibitory neuromuscular junctions. Using single chain antibodies that recognize different heparan sulfate modification patterns, we show in vivo that these two heparan sulfate epitopes are carried by the SDN-1 core protein, the unique C. elegans syndecan orthologue, at neuromuscular junctions. Intriguingly, these antibodies differentially bind to excitatory and inhibitory synapses, implying unique heparan sulfate modification patterns at different neuromuscular junctions. Moreover, while most enzymes are individually dispensable for proper organization of neuromuscular junctions, we show that 3-O-sulfation of SDN-1 is required to maintain wild-type levels of the extracellular matrix protein MADD-4/Punctin, a central synaptic organizer that defines the identity of excitatory and inhibitory synaptic domains at the plasma membrane of muscle cells.
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Affiliation(s)
- Mélissa Cizeron
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U 1217, Institut NeuroMyoGène, 69008 Lyon, France
| | - Laure Granger
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U 1217, Institut NeuroMyoGène, 69008 Lyon, France
| | - Hannes E Bülow
- Department of Genetics & Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, United States
| | - Jean-Louis Bessereau
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U 1217, Institut NeuroMyoGène, 69008 Lyon, France
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Platsaki S, Zhou X, Pinan-Lucarré B, Delauzun V, Tu H, Mansuelle P, Fourquet P, Bourne Y, Bessereau JL, Marchot P. The Ig-like domain of Punctin/MADD-4 is the primary determinant for interaction with the ectodomain of neuroligin NLG-1. J Biol Chem 2020; 295:16267-16279. [PMID: 32928959 DOI: 10.1074/jbc.ra120.014591] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 09/02/2020] [Indexed: 02/01/2023] Open
Abstract
Punctin/MADD-4, a member of the ADAMTSL extracellular matrix protein family, was identified as an anterograde synaptic organizer in the nematode Caenorhabditis elegans. At GABAergic neuromuscular junctions, the short isoform MADD-4B binds the ectodomain of neuroligin NLG-1, itself a postsynaptic organizer of inhibitory synapses. To identify the molecular bases of their partnership, we generated recombinant forms of the two proteins and carried out a comprehensive biochemical and biophysical study of their interaction, complemented by an in vivo localization study. We show that spontaneous proteolysis of MADD-4B first generates a shorter N-MADD-4B form, which comprises four thrombospondin (TSP) domains and one Ig-like domain and binds NLG-1. A second processing event eliminates the C-terminal Ig-like domain along with the ability of N-MADD-4B to bind NLG-1. These data identify the Ig-like domain as the primary determinant for N-MADD-4B interaction with NLG-1 in vitro We further demonstrate in vivo that this Ig-like domain is essential, albeit not sufficient per se, for efficient recruitment of GABAA receptors at GABAergic synapses in C. elegans The interaction of N-MADD-4B with NLG-1 is also disrupted by heparin, used as a surrogate for the extracellular matrix component, heparan sulfate. High-affinity binding of heparin/heparan sulfate to the Ig-like domain may proceed from surface charge complementarity, as suggested by homology three-dimensional modeling. These data point to N-MADD-4B processing and cell-surface proteoglycan binding as two possible mechanisms to regulate the interaction between MADD-4B and NLG-1 at GABAergic synapses.
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Affiliation(s)
- Semeli Platsaki
- CNRS/Aix-Marseille Univ, Laboratory "Architecture et Fonction des Macromolécules Biologiques" (AFMB), Marseille, France
| | - Xin Zhou
- Univ Lyon/Univ Claude Bernard Lyon 1/CNRS/INSERM, Institut NeuroMyoGène (INMG), Lyon, France
| | - Bérangère Pinan-Lucarré
- Univ Lyon/Univ Claude Bernard Lyon 1/CNRS/INSERM, Institut NeuroMyoGène (INMG), Lyon, France
| | - Vincent Delauzun
- CNRS/Aix-Marseille Univ, Laboratory "Architecture et Fonction des Macromolécules Biologiques" (AFMB), Marseille, France
| | - Haijun Tu
- Univ Lyon/Univ Claude Bernard Lyon 1/CNRS/INSERM, Institut NeuroMyoGène (INMG), Lyon, France
| | - Pascal Mansuelle
- CNRS/Aix-Marseille Univ, Institut de Microbiologie de la Méditerranée (IMM), Marseille Proteomics (MaP), Marseille, France
| | - Patrick Fourquet
- Aix-Marseille Univ/INSERM/CNRS, Institut Paoli-Calmettes, Centre de Recherche en Cancérologie de Marseille (CRCM), Marseille Proteomics (MaP), Marseille, France
| | - Yves Bourne
- CNRS/Aix-Marseille Univ, Laboratory "Architecture et Fonction des Macromolécules Biologiques" (AFMB), Marseille, France
| | - Jean-Louis Bessereau
- Univ Lyon/Univ Claude Bernard Lyon 1/CNRS/INSERM, Institut NeuroMyoGène (INMG), Lyon, France
| | - Pascale Marchot
- CNRS/Aix-Marseille Univ, Laboratory "Architecture et Fonction des Macromolécules Biologiques" (AFMB), Marseille, France.
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