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Title: Family of neural wiring receptors in bilaterians defined by phylogenetic, biochemical, and structural evidence

Abstract

The evolution of complex nervous systems was accompanied by the expansion of numerous protein families, including cell-adhesion molecules, surface receptors, and their ligands. These proteins mediate axonal guidance, synapse targeting, and other neuronal wiring-related functions. Recently, 32 interacting cell surface proteins belonging to two newly defined families of the Ig superfamily (IgSF) in fruit flies were discovered to label different subsets of neurons in the brain and ventral nerve cord. They have been shown to be involved in synaptic targeting and morphogenesis, retrograde signaling, and neuronal survival. Here, we show that these proteins, Dprs and DIPs, are members of a widely distributed family of two- and three-Ig domain molecules with neuronal wiring functions, which we refer to as Wirins. Beginning from a single ancestral Wirin gene in the last common ancestor of Bilateria, numerous gene duplications produced the heterophilic Dprs and DIPs in protostomes, along with two other subfamilies that diversified independently across protostome phyla. In deuterostomes, the ancestral Wirin evolved into the IgLON subfamily of neuronal receptors. We show that IgLONs interact with each other and that their complexes can be broken by mutations designed using homology models based on Dpr and DIP structures. The nematode orthologs ZIG-8 andmore » RIG-5 also form heterophilic and homophilic complexes, and crystal structures reveal numerous apparently ancestral features shared with Dpr-DIP complexes. The evolutionary, biochemical, and structural relationships we demonstrate here provide insights into neural development and the rise of the metazoan nervous system.« less

Authors:
 [1];  [1];  [2];  [3];  [3];  [1]; ORCiD logo [1]
  1. Univ. of Chicago, IL (United States)
  2. Univ. of Chicago, IL (United States) ; Jagiellonian Univ., Krakow (Poland)
  3. California Inst. of Technology (CalTech), Pasadena, CA (United States)
Publication Date:
Research Org.:
Argonne National Laboratory (ANL), Argonne, IL (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES); USDOE Office of Science (SC), Biological and Environmental Research (BER); National Institutes of Health (NIH)
OSTI Identifier:
1526067
Grant/Contract Number:  
AC02-76SF00515; AC02-06CH11357
Resource Type:
Accepted Manuscript
Journal Name:
Proceedings of the National Academy of Sciences of the United States of America
Additional Journal Information:
Journal Volume: 116; Journal Issue: 20; Journal ID: ISSN 0027-8424
Publisher:
National Academy of Sciences
Country of Publication:
United States
Language:
ENGLISH
Subject:
59 BASIC BIOLOGICAL SCIENCES; immunoglobulin superfamily; molecular evolution; nervous system; IgLON; Dpr-DIP family

Citation Formats

Cheng, Shouqiang, Park, Yeonwoo, Kurleto, Justyna D., Jeon, Mili, Zinn, Kai, Thornton, Joseph W., and Özkan, Engin. Family of neural wiring receptors in bilaterians defined by phylogenetic, biochemical, and structural evidence. United States: N. p., 2019. Web. doi:10.1073/pnas.1818631116.
Cheng, Shouqiang, Park, Yeonwoo, Kurleto, Justyna D., Jeon, Mili, Zinn, Kai, Thornton, Joseph W., & Özkan, Engin. Family of neural wiring receptors in bilaterians defined by phylogenetic, biochemical, and structural evidence. United States. https://doi.org/10.1073/pnas.1818631116
Cheng, Shouqiang, Park, Yeonwoo, Kurleto, Justyna D., Jeon, Mili, Zinn, Kai, Thornton, Joseph W., and Özkan, Engin. Wed . "Family of neural wiring receptors in bilaterians defined by phylogenetic, biochemical, and structural evidence". United States. https://doi.org/10.1073/pnas.1818631116. https://www.osti.gov/servlets/purl/1526067.
@article{osti_1526067,
title = {Family of neural wiring receptors in bilaterians defined by phylogenetic, biochemical, and structural evidence},
author = {Cheng, Shouqiang and Park, Yeonwoo and Kurleto, Justyna D. and Jeon, Mili and Zinn, Kai and Thornton, Joseph W. and Özkan, Engin},
abstractNote = {The evolution of complex nervous systems was accompanied by the expansion of numerous protein families, including cell-adhesion molecules, surface receptors, and their ligands. These proteins mediate axonal guidance, synapse targeting, and other neuronal wiring-related functions. Recently, 32 interacting cell surface proteins belonging to two newly defined families of the Ig superfamily (IgSF) in fruit flies were discovered to label different subsets of neurons in the brain and ventral nerve cord. They have been shown to be involved in synaptic targeting and morphogenesis, retrograde signaling, and neuronal survival. Here, we show that these proteins, Dprs and DIPs, are members of a widely distributed family of two- and three-Ig domain molecules with neuronal wiring functions, which we refer to as Wirins. Beginning from a single ancestral Wirin gene in the last common ancestor of Bilateria, numerous gene duplications produced the heterophilic Dprs and DIPs in protostomes, along with two other subfamilies that diversified independently across protostome phyla. In deuterostomes, the ancestral Wirin evolved into the IgLON subfamily of neuronal receptors. We show that IgLONs interact with each other and that their complexes can be broken by mutations designed using homology models based on Dpr and DIP structures. The nematode orthologs ZIG-8 and RIG-5 also form heterophilic and homophilic complexes, and crystal structures reveal numerous apparently ancestral features shared with Dpr-DIP complexes. The evolutionary, biochemical, and structural relationships we demonstrate here provide insights into neural development and the rise of the metazoan nervous system.},
doi = {10.1073/pnas.1818631116},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
number = 20,
volume = 116,
place = {United States},
year = {Wed May 01 00:00:00 EDT 2019},
month = {Wed May 01 00:00:00 EDT 2019}
}

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Works referenced in this record:

Shape Complementarity at Protein/Protein Interfaces
journal, December 1993

  • Lawrence, Michael C.; Colman, Peter M.
  • Journal of Molecular Biology, Vol. 234, Issue 4
  • DOI: 10.1006/jmbi.1993.1648

PHENIX: a comprehensive Python-based system for macromolecular structure solution.
text, January 2010

  • Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor
  • Apollo - University of Cambridge Repository
  • DOI: 10.17863/cam.45787

Neuron-Subtype-Specific Expression, Interaction Affinities, and Specificity Determinants of DIP/Dpr Cell Recognition Proteins
journal, December 2018


Neurotrimin Mediates Bifunctional Effects on Neurite Outgrowth via Homophilic and Heterophilic Interactions
journal, November 1998


Biochemical and ultrastructural analyses of iglon cell adhesion molecules, kilon and obcam in the rat brain
journal, March 2003


Identification and Characterization of CEPU-Se—A Secreted Isoform of the IgLON Family Protein, CEPU-1
journal, April 2001

  • Lodge, Anthony P.; McNamee, Christine J.; Howard, Mark R.
  • Molecular and Cellular Neuroscience, Vol. 17, Issue 4
  • DOI: 10.1006/mcne.2001.0964

Basic Local Alignment Search Tool
journal, October 1990


Defective Proboscis Extension Response (DPR), a Member of the Ig Superfamily Required for the Gustatory Response to Salt
journal, May 2002


Synaptic adhesion molecule OBCAM; synaptogenesis and dynamic internalization
journal, August 2007


Combinations of DIPs and Dprs control organization of olfactory receptor neuron terminals in Drosophila
text, January 2018

  • P. C., Volkan,; I., Strunilin,; C. D., Jones,
  • Public Library of Science
  • DOI: 10.17615/n0q8-ma63

Complementary expression and heterophilic interactions between igLON family members neurotrimin and LAMP
journal, April 2002

  • Gil, Orlando D.; Zhang, Li; Chen, Suzanne
  • Journal of Neurobiology, Vol. 51, Issue 3
  • DOI: 10.1002/neu.10050

Ig Superfamily Ligand and Receptor Pairs Expressed in Synaptic Partners in Drosophila
journal, December 2015


Control of Synaptic Connectivity by a Network of Drosophila IgSF Cell Surface Proteins
journal, December 2015


Two Rounds of Whole Genome Duplication in the Ancestral Vertebrate
journal, September 2005


Combinations of DIPs and Dprs control organization of olfactory receptor neuron terminals in Drosophila
journal, August 2018


Molecular Anatomy of a Trafficking Organelle
journal, November 2006


The IgLON protein Lachesin is required for the blood–brain barrier in Drosophila
journal, May 2006

  • Strigini, Maura; Cantera, Rafael; Morin, Xavier
  • Molecular and Cellular Neuroscience, Vol. 32, Issue 1-2
  • DOI: 10.1016/j.mcn.2006.03.001

Proteomic Analysis of Unbounded Cellular Compartments: Synaptic Clefts
journal, August 2016


RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
journal, January 2014


Cell type– and brain region–resolved mouse brain proteome
journal, November 2015

  • Sharma, Kirti; Schmitt, Sebastian; Bergner, Caroline G.
  • Nature Neuroscience, Vol. 18, Issue 12
  • DOI: 10.1038/nn.4160

Neural immunoglobulin superfamily interaction networks
journal, August 2017


Cavin1 intrinsically disordered domains are essential for fuzzy electrostatic interactions and caveola formation
journal, February 2021


Protein Family Expansions and Biological Complexity
journal, January 2006


Immunoglobulin superfamily cell adhesion molecules: zippers and signals
journal, October 2007


The Drosophila cell adhesion molecule Klingon is required for long-term memory formation and is regulated by Notch
journal, December 2008

  • Matsuno, M.; Horiuchi, J.; Tully, T.
  • Proceedings of the National Academy of Sciences, Vol. 106, Issue 1
  • DOI: 10.1073/pnas.0807665106

IgCAMs redundantly control axon navigation in Caenorhabditis elegans
journal, January 2009

  • Schwarz, Valentin; Pan, Jie; Voltmer-Irsch, Susanne
  • Neural Development, Vol. 4, Issue 1
  • DOI: 10.1186/1749-8104-4-13

PHENIX: a comprehensive Python-based system for macromolecular structure solution
journal, January 2010

  • Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221
  • DOI: 10.1107/S0907444909052925

X-Ray Diffraction data from C. elegans ZIG-8 IG1-RIG-5 IG1 heterodimer, monoclinic form, source of 6ONB structure
dataset, January 2019

  • Cheng, Shouqiang; Kurleto, Justyna D.; Ozkan, Engin
  • SBGrid Data Bank
  • DOI: 10.15785/sbgrid/689

X-Ray Diffraction data from C. elegans ZIG-8 IG1-RIG-5 IG1 heterodimer, tetragonal form, source of 6ON9 structure
dataset, January 2019

  • Cheng, Shouqiang; Kurleto, Justyna D.; Ozkan, Engin
  • SBGrid Data Bank
  • DOI: 10.15785/sbgrid/688

X-Ray Diffraction data from C. elegans RIG-5 IG1 homodimer, source of 6ON6 structure
dataset, January 2019

  • Cheng, Shouqiang; Kurleto, Justyna D.; Ozkan, Engin
  • SBGrid Data Bank
  • DOI: 10.15785/sbgrid/687

Glycosylphosphatidylinositol-Anchored Immunoglobulin Superfamily Cell Adhesion Molecules and Their Role in Neuronal Development and Synapse Regulation
journal, November 2017

  • Tan, Rui P. A.; Leshchyns’ka, Iryna; Sytnyk, Vladimir
  • Frontiers in Molecular Neuroscience, Vol. 10
  • DOI: 10.3389/fnmol.2017.00378

IgLON cell adhesion molecules regulate synaptogenesis in hippocampal neurons
journal, October 2009

  • Hashimoto, Takashi; Maekawa, Shohei; Miyata, Seiji
  • Cell Biochemistry and Function, Vol. 27, Issue 7
  • DOI: 10.1002/cbf.1600

Large-scale screening for novel low-affinity extracellular protein interactions
journal, March 2008

  • Bushell, K. M.; Sollner, C.; Schuster-Boeckler, B.
  • Genome Research, Vol. 18, Issue 4
  • DOI: 10.1101/gr.7187808

Nectin family of cell-adhesion molecules: structural and molecular aspects of function and specificity
journal, October 2014


The Secreted Immunoglobulin Domain Proteins ZIG-5 and ZIG-8 Cooperate with L1CAM/SAX-7 to Maintain Nervous System Integrity
journal, July 2012


An Extracellular Interactome of Immunoglobulin and LRR Proteins Reveals Receptor-Ligand Networks
journal, July 2013


Crystal Structure of the ZIG-8-RIG-5 IG1-IG1 heterodimer, tetragonal form
text, January 2019


Crystal Structure of the ZIG-8-RIG-5 IG1-IG1 heterodimer, monoclinic form
text, January 2019


Crystal Structure of the RIG-5 IG1 homodimer
text, January 2019


Lachesin: an immunoglobulin superfamily protein whose expression correlates with neurogenesis in grasshopper embryos
journal, June 1993

  • Karlstrom, R. O.; Wilder, L. P.; Bastiani, M. J.
  • Development, Vol. 118, Issue 2
  • DOI: 10.1242/dev.118.2.509

Basic local alignment search tool
journal, October 1990

  • Altschul, Stephen F.; Gish, Warren; Miller, Webb
  • Journal of Molecular Biology, Vol. 215, Issue 3, p. 403-410
  • DOI: 10.1016/S0022-2836(05)80360-2

X-Ray Diffraction data from C. elegans RIG-5 IG1 homodimer, source of 6ON6 structure
dataset, January 2019

  • Cheng, Shouqiang; Kurleto, Justyna D.; Ozkan, Engin
  • SBGrid Data Bank
  • DOI: 10.15785/sbgrid/687

X-Ray Diffraction data from C. elegans ZIG-8 IG1-RIG-5 IG1 heterodimer, tetragonal form, source of 6ON9 structure
dataset, January 2019

  • Cheng, Shouqiang; Kurleto, Justyna D.; Ozkan, Engin
  • SBGrid Data Bank
  • DOI: 10.15785/sbgrid/688

X-Ray Diffraction data from C. elegans ZIG-8 IG1-RIG-5 IG1 heterodimer, monoclinic form, source of 6ONB structure
dataset, January 2019

  • Cheng, Shouqiang; Kurleto, Justyna D.; Ozkan, Engin
  • SBGrid Data Bank
  • DOI: 10.15785/sbgrid/689

Control of Synaptic Connectivity by a Network of Drosophila IgSF Cell Surface Proteins
journal, December 2015


The IgLON protein Lachesin is required for the blood–brain barrier in Drosophila
journal, May 2006

  • Strigini, Maura; Cantera, Rafael; Morin, Xavier
  • Molecular and Cellular Neuroscience, Vol. 32, Issue 1-2
  • DOI: 10.1016/j.mcn.2006.03.001

Large-scale screening for novel low-affinity extracellular protein interactions
journal, March 2008

  • Bushell, K. M.; Sollner, C.; Schuster-Boeckler, B.
  • Genome Research, Vol. 18, Issue 4
  • DOI: 10.1101/gr.7187808

Lachesin: an immunoglobulin superfamily protein whose expression correlates with neurogenesis in grasshopper embryos
journal, June 1993

  • Karlstrom, R. O.; Wilder, L. P.; Bastiani, M. J.
  • Development, Vol. 118, Issue 2
  • DOI: 10.1242/dev.118.2.509

Two Rounds of Whole Genome Duplication in the Ancestral Vertebrate
journal, September 2005


Works referencing / citing this record:

Interactions between Dpr11 and DIP-γ control selection of amacrine neurons in Drosophila color vision circuits
journal, November 2019

  • Menon, Kaushiki P.; Kulkarni, Vivek; Takemura, Shin-ya
  • eLife, Vol. 8
  • DOI: 10.7554/elife.48935

Interactions between Dpr11 and DIP-γ control selection of amacrine neurons in Drosophila color vision circuits
journal, November 2019

  • Menon, Kaushiki P.; Kulkarni, Vivek; Takemura, Shin-ya
  • eLife, Vol. 8
  • DOI: 10.7554/elife.48935