Structures of neurexophilin–neurexin complexes reveal a regulatory mechanism of alternative splicing

Wilson, Steven C.; White, K. Ian; Zhou, Qiangjun; Pfuetzner, Richard A.; Choi, Ucheor B.; Südhof, Thomas C.; Brunger, Axel T.

doi:10.15252/embj.2019101603

Structures of neurexophilin–neurexin complexes reveal a regulatory mechanism of alternative splicing

Journal Article · Mon Sep 30 00:00:00 EDT 2019 · EMBO Journal

DOI:https://doi.org/10.15252/embj.2019101603· OSTI ID:1656574

^[1]; ^[1]; Zhou, Qiangjun ^[1]; Pfuetzner, Richard A. ^[1]; Choi, Ucheor B. ^[1]; ^[2]; ^[2]

Stanford Univ., CA (United States)
Stanford Univ., CA (United States); Stanford Univ., CA (United States). Howard Hughes Medical Inst.

Neurexins are presynaptic, cell-adhesion molecules that specify the functional properties of synapses via interactions with trans-synaptic ligands. Neurexins are extensively alternatively spliced at six canonical sites that regulate multifarious ligand interactions, but the structural mechanisms underlying alternative splicing-dependent neurexin regulation are largely unknown. Here, we determined high-resolution structures of the complex of neurexophilin-1 and the second laminin/neurexin/sex-hormone-binding globulin domain (LNS2) of neurexin-1 and examined how alternative splicing at splice site #2 (SS2) regulates the complex. Our data reveal a unique, extensive, neurexophilin–neurexin binding interface that extends the jelly-roll β-sandwich of LNS2 of neurexin-1 into neurexophilin-1. The SS2A insert of LNS2 augments this interface, increasing the binding affinity of LNS2 for neurexophilin-1. Taken together, our data reveal an unexpected architecture of neurexophilin–neurexin complexes that accounts for the modulation of binding by alternative splicing, which in turn regulates the competition of neurexophilin for neurexin binding with other ligands.

View Accepted Manuscript (DOE)

Research Organization:: SLAC National Accelerator Laboratory (SLAC), Menlo Park, CA (United States)

Sponsoring Organization:: National Institutes of Health (NIH); USDOE Office of Science (SC), Basic Energy Sciences (BES)

Grant/Contract Number:: AC02-06CH11357; AC02-76SF00515

OSTI ID:: 1656574

Alternate ID(s):: OSTI ID: 1601855

Journal Information:: EMBO Journal, Journal Name: EMBO Journal Journal Issue: 22 Vol. 38; ISSN 0261-4189

Publisher:: EMBO PressCopyright Statement

Country of Publication:: United States

Language:: English

References (63)

Cartography of neurexins: More than 1000 isoforms generated by alternative splicing and expressed in distinct subsets of neurons Ullrich, Beate; Ushkaryov, Yuri A.; Südhof, Thomas C. Neuron, Vol. 14, Issue 3 https://doi.org/10.1016/0896-6273(95)90306-2	journal	March 1995
Trans-Synaptic Interaction of GluRδ2 and Neurexin through Cbln1 Mediates Synapse Formation in the Cerebellum Uemura, Takeshi; Lee, Sung-Jin; Yasumura, Misato Cell, Vol. 141, Issue 6 https://doi.org/10.1016/j.cell.2010.04.035	journal	June 2010
Synaptic Neurexin Complexes: A Molecular Code for the Logic of Neural Circuits Südhof, Thomas C. Cell, Vol. 171, Issue 4 https://doi.org/10.1016/j.cell.2017.10.024	journal	November 2017
Molecular Architecture of the Mouse Nervous System Zeisel, Amit; Hochgerner, Hannah; Lönnerberg, Peter Cell, Vol. 174, Issue 4 https://doi.org/10.1016/j.cell.2018.06.021	journal	August 2018
Molecular Diversity and Specializations among the Cells of the Adult Mouse Brain Saunders, Arpiar; Macosko, Evan Z.; Wysoker, Alec Cell, Vol. 174, Issue 4 https://doi.org/10.1016/j.cell.2018.07.028	journal	August 2018
Cbln1 and Cbln4 Are Structurally Similar but Differ in GluD2 Binding Interactions Zhong, Chen; Shen, Jinlong; Zhang, Huibing Cell Reports, Vol. 20, Issue 10 https://doi.org/10.1016/j.celrep.2017.08.031	journal	September 2017
Inference of Macromolecular Assemblies from Crystalline State Krissinel, Evgeny; Henrick, Kim Journal of Molecular Biology, Vol. 372, Issue 3 https://doi.org/10.1016/j.jmb.2007.05.022	journal	September 2007
A Splice Code for trans-Synaptic Cell Adhesion Mediated by Binding of Neuroligin 1 to α- and β-Neurexins Boucard, Antony A.; Chubykin, Alexander A.; Comoletti, Davide Neuron, Vol. 48, Issue 2 https://doi.org/10.1016/j.neuron.2005.08.026	journal	October 2005
A Crystal-Clear Interaction: Relating Neuroligin/Neurexin Complex Structure to Function at the Synapse Levinson, Joshua N.; El-Husseini, Alaa Neuron, Vol. 56, Issue 6 https://doi.org/10.1016/j.neuron.2007.12.003	journal	December 2007
Targeted Combinatorial Alternative Splicing Generates Brain Region-Specific Repertoires of Neurexins Schreiner, Dietmar; Nguyen, Thi-Minh; Russo, Giancarlo Neuron, Vol. 84, Issue 2 https://doi.org/10.1016/j.neuron.2014.09.011	journal	October 2014
Structural Mechanism for Modulation of Synaptic Neuroligin-Neurexin Signaling by MDGA Proteins Elegheert, Jonathan; Cvetkovska, Vedrana; Clayton, Amber J. Neuron, Vol. 96, Issue 1 https://doi.org/10.1016/j.neuron.2017.09.011	journal	September 2017
BacMam system for high-level expression of recombinant soluble and membrane glycoproteins for structural studies Dukkipati, Abhiram; Park, Hyun Ho; Waghray, Deepa Protein Expression and Purification, Vol. 62, Issue 2 https://doi.org/10.1016/j.pep.2008.08.004	journal	December 2008
Regulation of Neurexin 1β Tertiary Structure and Ligand Binding through Alternative Splicing Shen, Kaiser C.; Kuczynska, Dorota A.; Wu, Irene J. Structure, Vol. 16, Issue 3 https://doi.org/10.1016/j.str.2008.01.005	journal	March 2008
The Structure of Neurexin 1α Reveals Features Promoting a Role as Synaptic Organizer Chen, Fang; Venugopal, Vandavasi; Murray, Beverly Structure, Vol. 19, Issue 6 https://doi.org/10.1016/j.str.2011.03.012	journal	June 2011
Unveiled α−Neurexins Take Center Stage Reissner, Carsten; Missler, Markus Structure, Vol. 19, Issue 6 https://doi.org/10.1016/j.str.2011.05.005	journal	June 2011
Conformational Plasticity in the Transsynaptic Neurexin-Cerebellin-Glutamate Receptor Adhesion Complex Cheng, Shouqiang; Seven, Alpay B.; Wang, Jing Structure, Vol. 24, Issue 12 https://doi.org/10.1016/j.str.2016.11.004	journal	December 2016
Gene Selection, Alternative Splicing, and Post-translational Processing Regulate Neuroligin Selectivity for β-Neurexins ^† Comoletti, Davide; Flynn, Robyn E.; Boucard, Antony A. Biochemistry, Vol. 45, Issue 42 https://doi.org/10.1021/bi0614131	journal	October 2006
Precision mapping of the human O-GalNAc glycoproteome through SimpleCell technology Steentoft, Catharina; Vakhrushev, Sergey Y.; Joshi, Hiren J. The EMBO Journal, Vol. 32, Issue 10 https://doi.org/10.1038/emboj.2013.79	journal	April 2013
Seq-ing the cortex one neuron at a time Chen, Hsu-Hsin; Arlotta, Paola Nature Neuroscience, Vol. 19, Issue 2 https://doi.org/10.1038/nn.4230	journal	January 2016
Single-cell RNAseq reveals cell adhesion molecule profiles in electrophysiologically defined neurons Földy, Csaba; Darmanis, Spyros; Aoto, Jason Proceedings of the National Academy of Sciences, Vol. 113, Issue 35 https://doi.org/10.1073/pnas.1610155113	journal	August 2016
Dystroglycan Binding to α-Neurexin Competes with Neurexophilin-1 and Neuroligin in the Brain Reissner, Carsten; Stahn, Johanna; Breuer, Dorothee Journal of Biological Chemistry, Vol. 289, Issue 40 https://doi.org/10.1074/jbc.m114.595413	journal	August 2014
A stoichiometric complex of neurexins and dystroglycan in brain Sugita, Shuzo; Saito, Fumiaki; Tang, Jiong The Journal of Cell Biology, Vol. 154, Issue 2 https://doi.org/10.1083/jcb.200105003	journal	July 2001
Deciphering key features in protein structures with the new ENDscript server Robert, Xavier; Gouet, Patrice Nucleic Acids Research, Vol. 42, Issue W1 https://doi.org/10.1093/nar/gku316	journal	April 2014
Dali server update Holm, Liisa; Laakso, Laura M. Nucleic Acids Research, Vol. 44, Issue W1 https://doi.org/10.1093/nar/gkw357	journal	April 2016
A time- and cost-efficient system for high-level protein production in mammalian cells Aricescu, A. Radu; Lu, Weixian; Jones, E. Yvonne Acta Crystallographica Section D Biological Crystallography, Vol. 62, Issue 10 https://doi.org/10.1107/s0907444906029799	journal	September 2006
ATSAS 2.8 : a comprehensive data analysis suite for small-angle scattering from macromolecular solutions Franke, D.; Petoukhov, M. V.; Konarev, P. V. Journal of Applied Crystallography, Vol. 50, Issue 4 https://doi.org/10.1107/s1600576717007786	journal	June 2017
Structural Basis for Variant-Specific Neuroligin-Binding by α-Neurexin Tanaka, Hiroki; Nogi, Terukazu; Yasui, Norihisa PLoS ONE, Vol. 6, Issue 4 https://doi.org/10.1371/journal.pone.0019411	journal	April 2011
Structure and Evolution of Neurexophilin Petrenko, Alexander G.; Ullrich, Beate; Missler, Markus The Journal of Neuroscience, Vol. 16, Issue 14 https://doi.org/10.1523/jneurosci.16-14-04360.1996	journal	July 1996
Neurexophilins Form a Conserved Family of Neuropeptide-Like Glycoproteins Missler, Markus; Südhof, Thomas C. The Journal of Neuroscience, Vol. 18, Issue 10 https://doi.org/10.1523/jneurosci.18-10-03630.1998	journal	May 1998
Neuronal Dystroglycan Is Necessary for Formation and Maintenance of Functional CCK-Positive Basket Cell Terminals on Pyramidal Cells Früh, Simon; Romanos, Jennifer; Panzanelli, Patrizia The Journal of Neuroscience, Vol. 36, Issue 40 https://doi.org/10.1523/jneurosci.1823-16.2016	journal	October 2016
Regulated Dynamic Trafficking of Neurexins Inside and Outside of Synaptic Terminals Neupert, Christian; Schneider, Romy; Klatt, Oliver The Journal of Neuroscience, Vol. 35, Issue 40 https://doi.org/10.1523/jneurosci.4041-14.2015	journal	October 2015
Cerebellins are differentially expressed in selective subsets of neurons throughout the brain: SEIGNEUR and SÜDHOF Seigneur, Erica; Südhof, Thomas C. Journal of Comparative Neurology, Vol. 525, Issue 15 https://doi.org/10.1002/cne.24278	journal	July 2017
[20] Processing of X-ray diffraction data collected in oscillation mode Otwinowski, Zbyszek; Minor, Wladek Macromolecular Crystallography Part A, 307-326 https://doi.org/10.1016/S0076-6879(97)76066-X	book	January 1997
Structures of Neuroligin-1 and the Neuroligin-1/Neurexin-1β Complex Reveal Specific Protein-Protein and Protein-Ca2+ Interactions Araç, Demet; Boucard, Antony A.; Özkan, Engin Neuron, Vol. 56, Issue 6 https://doi.org/10.1016/j.neuron.2007.12.002	journal	December 2007
Structural Mechanism for Modulation of Synaptic Neuroligin-Neurexin Signaling by MDGA Proteins Elegheert, Jonathan; Cvetkovska, Vedrana; Clayton, Amber J. Neuron, Vol. 95, Issue 4 https://doi.org/10.1016/j.neuron.2017.07.040	journal	August 2017
Structural Mechanism for Modulation of Synaptic Neuroligin-Neurexin Signaling by MDGA Proteins Elegheert, Jonathan; Cvetkovska, Vedrana; Clayton, Amber J. Neuron, Vol. 109, Issue 1 https://doi.org/10.1016/j.neuron.2020.12.006	journal	January 2021
Development of the Twin-Strep-tag® and its application for purification of recombinant proteins from cell culture supernatants Schmidt, Thomas G. M.; Batz, Lilia; Bonet, Lidia Protein Expression and Purification, Vol. 92, Issue 1 https://doi.org/10.1016/j.pep.2013.08.021	journal	November 2013
The Crystal Structure of the α-Neurexin-1 Extracellular Region Reveals a Hinge Point for Mediating Synaptic Adhesion and Function Miller, Meghan T.; Mileni, Mauro; Comoletti, Davide Structure, Vol. 19, Issue 6 https://doi.org/10.1016/j.str.2011.03.011	journal	June 2011
Adult mouse cortical cell taxonomy revealed by single cell transcriptomics Tasic, Bosiljka; Menon, Vilas; Nguyen, Thuc Nghi Nature Neuroscience, Vol. 19, Issue 2 https://doi.org/10.1038/nn.4216	journal	January 2016
Screening and large-scale expression of membrane proteins in mammalian cells for structural studies Goehring, April; Lee, Chia-Hsueh; Wang, Kevin H. Nature Protocols, Vol. 9, Issue 11 https://doi.org/10.1038/nprot.2014.173	journal	October 2014
PARP1 exhibits enhanced association and catalytic efficiency with γH2A.X-nucleosome Sharma, Deepti; De Falco, Louis; Padavattan, Sivaraman Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-13641-0	journal	December 2019
Cryo-EM structure of the respiratory syncytial virus RNA polymerase Cao, Dongdong; Gao, Yunrong; Roesler, Claire Nature Communications, Vol. 11, Issue 1 https://doi.org/10.1038/s41467-019-14246-3	journal	January 2020
Cavin1 intrinsically disordered domains are essential for fuzzy electrostatic interactions and caveola formation Tillu, Vikas A.; Rae, James; Gao, Ya Nature Communications, Vol. 12, Issue 1 https://doi.org/10.1038/s41467-021-21035-4	journal	February 2021
Putative cell type discovery from single-cell gene expression data Miao, Zhichao; Moreno, Pablo; Huang, Ni Nature Methods, Vol. 17, Issue 6 https://doi.org/10.1038/s41592-020-0825-9	journal	May 2020
Modulation of synaptic function through the α-neurexin–specific ligand neurexophilin-1 Born, Gesche; Breuer, Dorothee; Wang, Shaopeng Proceedings of the National Academy of Sciences, Vol. 111, Issue 13 https://doi.org/10.1073/pnas.1312112111	journal	March 2014
Cartography of neurexin alternative splicing mapped by single-molecule long-read mRNA sequencing Treutlein, Barbara; Gokce, Ozgun; Quake, Stephen R. Proceedings of the National Academy of Sciences, Vol. 111, Issue 13 https://doi.org/10.1073/pnas.1403244111	journal	March 2014
Carbonic anhydrase-related protein CA10 is an evolutionarily conserved pan-neurexin ligand Sterky, Fredrik H.; Trotter, Justin H.; Lee, Sung-Jin Proceedings of the National Academy of Sciences, Vol. 114, Issue 7 https://doi.org/10.1073/pnas.1621321114	journal	February 2017
Neurexophilin Binding to α-Neurexins: A SINGLE LNS DOMAIN FUNCTIONS AS AN INDEPENDENTLY FOLDING LIGAND-BINDING UNIT Missler, Markus; Hammer, Robert E.; Südhof, Thomas C. Journal of Biological Chemistry, Vol. 273, Issue 52 https://doi.org/10.1074/jbc.273.52.34716	journal	December 1998
Dystroglycan Binding to α-Neurexin Competes with Neurexophilin-1 and Neuroligin in the Brain Reissner, Carsten; Stahn, Johanna; Breuer, Dorothee Journal of Biological Chemistry, Vol. 289, Issue 40 https://doi.org/10.1074/jbc.M114.595413	journal	August 2014
Crystal Structure of the Second LNS/LG Domain from Neurexin 1α: Ca ²⁺ BINDING AND THE EFFECTS OF ALTERNATIVE SPLICING Sheckler, Lauren R.; Henry, Lisa; Sugita, Shuzo Journal of Biological Chemistry, Vol. 281, Issue 32 https://doi.org/10.1074/jbc.M603464200	journal	June 2006
A time- and cost-efficient system for high-level protein production in mammalian cells Aricescu, A. Radu; Lu, Weixian; Jones, E. Yvonne Acta Crystallographica Section D Biological Crystallography, Vol. 62, Issue 10 https://doi.org/10.1107/S0907444906029799	journal	September 2006
PHENIX: a comprehensive Python-based system for macromolecular structure solution Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221 https://doi.org/10.1107/S0907444909052925	journal	January 2010
Features and development of Coot Emsley, P.; Lohkamp, B.; Scott, W. G. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4 https://doi.org/10.1107/S0907444910007493	journal	March 2010
ATSAS 2.8 : a comprehensive data analysis suite for small-angle scattering from macromolecular solutions Franke, D.; Petoukhov, M. V.; Konarev, P. V. Journal of Applied Crystallography, Vol. 50, Issue 4 https://doi.org/10.1107/S1600576717007786	journal	June 2017
Cbln family proteins promote synapse formation by regulating distinct neurexin signaling pathways in various brain regions: Synapse formation by Cbln family proteins and neurexins Matsuda, Keiko; Yuzaki, Michisuke European Journal of Neuroscience, Vol. 33, Issue 8 https://doi.org/10.1111/j.1460-9568.2011.07638.x	journal	March 2011
Structural basis for integration of GluD receptors within synaptic organizer complexes Elegheert, Jonathan; Kakegawa, Wataru; Clay, Jordan E. Science, Vol. 353, Issue 6296 https://doi.org/10.1126/science.aae0104	journal	July 2016
Structure and Evolution of Neurexophilin Petrenko, Alexander G.; Ullrich, Beate; Missler, Markus The Journal of Neuroscience, Vol. 16, Issue 14 https://doi.org/10.1523/JNEUROSCI.16-14-04360.1996	journal	July 1996
Neurexophilins Form a Conserved Family of Neuropeptide-Like Glycoproteins Missler, Markus; Südhof, Thomas C. The Journal of Neuroscience, Vol. 18, Issue 10 https://doi.org/10.1523/JNEUROSCI.18-10-03630.1998	journal	May 1998
Neuronal Dystroglycan Is Necessary for Formation and Maintenance of Functional CCK-Positive Basket Cell Terminals on Pyramidal Cells Früh, Simon; Romanos, Jennifer; Panzanelli, Patrizia The Journal of Neuroscience, Vol. 36, Issue 40 https://doi.org/10.1523/JNEUROSCI.1823-16.2016	journal	October 2016
Regulated Dynamic Trafficking of Neurexins Inside and Outside of Synaptic Terminals Neupert, Christian; Schneider, Romy; Klatt, Oliver The Journal of Neuroscience, Vol. 35, Issue 40 https://doi.org/10.1523/JNEUROSCI.4041-14.2015	journal	October 2015
PHENIX: a comprehensive Python-based system for macromolecular structure solution. Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.45787	text	January 2010
Neuronal Dystroglycan Is Necessary for Formation and Maintenance of Functional CCK-Positive Basket Cell Terminals on Pyramidal Cells Früh, Simon; Romanos, Jennifer; Panzanelli, Patrizia Society for Neuroscience https://doi.org/10.5167/uzh-126680	text	January 2016
Single-cell RNAseq reveals cell adhesion molecule profiles in electrophysiologically defined neurons Földy, Csaba; Darmanis, Spyros; Aoto, Jason National Academy of Sciences https://doi.org/10.5167/uzh-134167	text	January 2016

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59 BASIC BIOLOGICAL SCIENCES
alternative splicing
neurexin
neurexophilin
synapse
synaptic cell-adhesion molecules

Structures of neurexophilin–neurexin complexes reveal a regulatory mechanism of alternative splicing

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