Structural Basis for Plexin Activation and Regulation

Summary Class A plexins (PlxnAs) act as semaphorin receptors and control diverse aspects of nervous system development and plasticity, ranging from axon guidance and neuron migration to synaptic organization. PlxnA signaling requires cytoplasmic domain dimerization, but extracellular regulation and activation mechanisms remain unclear. Here we present crystal structures of PlxnA (PlxnA1, PlxnA2, and PlxnA4) full ectodomains. Domains 1–9 form a ring-like conformation from which the C-terminal domain 10 points away. All our PlxnA ectodomain structures show autoinhibitory, intermolecular “head-to-stalk” (domain 1 to domain 4-5) interactions, which are confirmed by biophysical assays, live cell fluorescence microscopy, and cell-based and neuronal growth cone collapse assays. This work reveals a 2-fold role of the PlxnA ectodomains: imposing a pre-signaling autoinhibitory separation for the cytoplasmic domains via intermolecular head-to-stalk interactions and supporting dimerization-based PlxnA activation upon ligand binding. More generally, our data identify a novel molecular mechanism for preventing premature activation of axon guidance receptors.

[1]  Marc Tramier,et al.  Time-domain fluorescence lifetime imaging microscopy: a quantitative method to follow transient protein-protein interactions in living cells. , 2015, Cold Spring Harbor protocols.

[2]  A. Yaron,et al.  Cis interaction between Semaphorin6A and Plexin‐A4 modulates the repulsive response to Sema6A , 2010, The EMBO journal.

[3]  T. Yagi,et al.  Interactions between Plexin-A2, Plexin-A4, and Semaphorin 6A Control Lamina-Restricted Projection of Hippocampal Mossy Fibers , 2007, Neuron.

[4]  Xuewu Zhang,et al.  Class A Plexins Are Organized as Preformed Inactive Dimers on the Cell Surface. , 2015, Biophysical journal.

[5]  D. Marquardt An Algorithm for Least-Squares Estimation of Nonlinear Parameters , 1963 .

[6]  A Leith,et al.  SPIDER and WEB: processing and visualization of images in 3D electron microscopy and related fields. , 1996, Journal of structural biology.

[7]  M van Heel,et al.  A new generation of the IMAGIC image processing system. , 1996, Journal of structural biology.

[8]  Michal Rivlin-Etzion,et al.  On and Off Retinal Circuit Assembly by Divergent Molecular Mechanisms , 2013, Science.

[9]  Philip R. Evans,et al.  An introduction to data reduction: space-group determination, scaling and intensity statistics , 2011, Acta crystallographica. Section D, Biological crystallography.

[10]  Kevin Cowtan,et al.  research papers Acta Crystallographica Section D Biological , 2005 .

[11]  J. Bell,et al.  BirA enzyme: production and application in the study of membrane receptor-ligand interactions by site-specific biotinylation. , 1999, Analytical biochemistry.

[12]  Ewout J. N. Groen,et al.  The intracellular redox protein MICAL-1 regulates the development of hippocampal mossy fibre connections , 2014, Nature Communications.

[13]  J. Takagi,et al.  Structural basis for semaphorin signalling through the plexin receptor , 2010, Nature.

[14]  Roland Contreras,et al.  Structure and function in rhodopsin: High-level expression of rhodopsin with restricted and homogeneous N-glycosylation by a tetracycline-inducible N-acetylglucosaminyltransferase I-negative HEK293S stable mammalian cell line , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[15]  Clemens Vonrhein,et al.  Exploiting structure similarity in refinement: automated NCS and target-structure restraints in BUSTER , 2012, Acta crystallographica. Section D, Biological crystallography.

[16]  K. Tamura,et al.  Metabolic engineering of plant alkaloid biosynthesis. Proc Natl Acad Sci U S A , 2001 .

[17]  G. Bashaw,et al.  Signaling from axon guidance receptors. , 2010, Cold Spring Harbor perspectives in biology.

[18]  Tal Pupko,et al.  Structural Genomics , 2005 .

[19]  P. De Camilli,et al.  Dynamic Interaction of Amphiphysin with N-WASP Regulates Actin Assembly* , 2009, The Journal of Biological Chemistry.

[20]  Y. Goshima,et al.  Identification and characterization of a novel mouse plexin, plexin-A4 , 2003, Mechanisms of Development.

[21]  David S. Booth,et al.  Visualizing proteins and macromolecular complexes by negative stain EM: from grid preparation to image acquisition. , 2011, Journal of visualized experiments : JoVE.

[22]  Marin van Heel,et al.  IMAGIC - A FAST, FLEXIBLE AND FRIENDLY IMAGE-ANALYSIS SOFTWARE SYSTEM , 1981 .

[23]  Collaborative Computational,et al.  The CCP4 suite: programs for protein crystallography. , 1994, Acta crystallographica. Section D, Biological crystallography.

[24]  Nathan A. Baker,et al.  PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations , 2004, Nucleic Acids Res..

[25]  A. Sali,et al.  Modeller: generation and refinement of homology-based protein structure models. , 2003, Methods in enzymology.

[26]  I. Langmuir THE ADSORPTION OF GASES ON PLANE SURFACES OF GLASS, MICA AND PLATINUM. , 1918 .

[27]  Wen Jiang,et al.  EMAN2: an extensible image processing suite for electron microscopy. , 2007, Journal of structural biology.

[28]  Anil Verma,et al.  Lysine Methylation as a Routine Rescue Strategy for Protein Crystallization , 2006, Structure.

[29]  C. H. Bell,et al.  Structural basis of semaphorin–plexin signalling , 2010, Nature.

[30]  Nathan A. Baker,et al.  Electrostatics of nanosystems: Application to microtubules and the ribosome , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[31]  Adrian Whitty,et al.  Understanding cytokine and growth factor receptor activation mechanisms , 2012, Critical reviews in biochemistry and molecular biology.

[32]  E. Jones,et al.  Structural insights into semaphorins and their receptors. , 2013, Seminars in cell & developmental biology.

[33]  Randy J. Read,et al.  Phaser crystallographic software , 2007, Journal of applied crystallography.

[34]  R. Rosenfeld Nature , 2009, Otolaryngology--head and neck surgery : official journal of American Academy of Otolaryngology-Head and Neck Surgery.

[35]  Randy J Read,et al.  Electronic Reprint Biological Crystallography Phenix: Building New Software for Automated Crystallographic Structure Determination Biological Crystallography Phenix: Building New Software for Automated Crystallographic Structure Determination , 2022 .

[36]  K. Henrick,et al.  Inference of macromolecular assemblies from crystalline state. , 2007, Journal of molecular biology.

[37]  A G Leslie,et al.  Biological Crystallography Integration of Macromolecular Diffraction Data , 2022 .

[38]  Ryohei Yasuda,et al.  Imaging spatiotemporal dynamics of neuronal signaling using fluorescence resonance energy transfer and fluorescence lifetime imaging microscopy , 2007, Current Opinion in Neurobiology.

[39]  K. Shen,et al.  Cellular and molecular mechanisms of synaptic specificity. , 2014, Annual review of cell and developmental biology.

[40]  S. Strittmatter,et al.  PlexinA1 Autoinhibition by the Plexin Sema Domain , 2001, Neuron.

[41]  Aymeric Leray,et al.  827Spatio-Temporal Quantification of FRET in Living Cells by Fast Time-Domain FLIM: A Comparative Study of Non-Fitting Methods , 2013, PloS one.

[42]  Fei Long,et al.  Low-resolution refinement tools in REFMAC5 , 2012, Acta crystallographica. Section D, Biological crystallography.

[43]  Xuewu Zhang,et al.  Plexins Are GTPase-Activating Proteins for Rap and Are Activated by Induced Dimerization , 2012, Science Signaling.

[44]  D. Stuart,et al.  Lysosome sorting of β-glucocerebrosidase by LIMP-2 is targeted by the mannose 6-phosphate receptor , 2014, Nature Communications.

[45]  Weixian Lu,et al.  A time- and cost-efficient system for high-level protein production in mammalian cells. , 2006, Acta crystallographica. Section D, Biological crystallography.

[46]  Vladislav V Verkhusha,et al.  Three-chromophore FRET microscopy to analyze multiprotein interactions in living cells , 2004, Nature Methods.

[47]  M. Hausmann,et al.  SPDM: light microscopy with single-molecule resolution at the nanoscale , 2008 .

[48]  P. Schuck,et al.  Size-distribution analysis of macromolecules by sedimentation velocity ultracentrifugation and lamm equation modeling. , 2000, Biophysical journal.

[49]  Borries Demeler,et al.  A two-dimensional spectrum analysis for sedimentation velocity experiments of mixtures with heterogeneity in molecular weight and shape , 2010, European Biophysics Journal.

[50]  Marc Tramier,et al.  Quantitative comparison of different fluorescent protein couples for fast FRET-FLIM acquisition. , 2009, Biophysical journal.

[51]  Bart C. Jongbloets,et al.  Semaphorin signalling during development , 2014, Development.

[52]  Julie Wilson,et al.  Benefits of automated crystallization plate tracking, imaging, and analysis. , 2005, Structure.

[53]  Xuewu Zhang,et al.  Structural basis for activation and non-canonical catalysis of the Rap GTPase activating protein domain of plexin , 2013, eLife.

[54]  O. Namy,et al.  Direct Observation of Distinct A/P Hybrid-State tRNAs in Translocating Ribosomes , 2010, Structure.

[55]  D. Higgins,et al.  Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega , 2011, Molecular systems biology.

[56]  J. Pasterkamp,et al.  Getting neural circuits into shape with semaphorins , 2012, Nature Reviews Neuroscience.

[57]  P. Brown,et al.  Characterizing Protein‐Protein Interactions by Sedimentation Velocity Analytical Ultracentrifugation , 2008, Current protocols in immunology.

[58]  A. Leslie,et al.  The integration of macromolecular diffraction data. , 2006, Acta crystallographica. Section D, Biological crystallography.

[59]  Lester G. Carter,et al.  A procedure for setting up high‐throughput nanolitre crystallization experiments. Crystallization workflow for initial screening, automated storage, imaging and optimization , 2005, Acta crystallographica. Section D, Biological crystallography.

[60]  Kevin Cowtan,et al.  Recent developments in classical density modification , 2010, Acta crystallographica. Section D, Biological crystallography.

[61]  Min Lu,et al.  Structure of the Semaphorin-3A Receptor Binding Module , 2003, Neuron.

[62]  Michael J Rust,et al.  Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM) , 2006, Nature Methods.

[63]  C Cremer,et al.  Analysis of Her2/neu membrane protein clusters in different types of breast cancer cells using localization microscopy , 2011, Journal of microscopy.

[64]  N. Pannu,et al.  REFMAC5 for the refinement of macromolecular crystal structures , 2011, Acta crystallographica. Section D, Biological crystallography.

[65]  D. Wilkin,et al.  Neuron , 2001, Brain Research.

[66]  Airlie J. McCoy,et al.  Solving structures of protein complexes by molecular replacement with Phaser , 2006, Acta crystallographica. Section D, Biological crystallography.

[67]  J. Lippincott-Schwartz,et al.  Imaging Intracellular Fluorescent Proteins at Nanometer Resolution , 2006, Science.

[68]  Marc Tramier,et al.  Quantitative FRET analysis by fast acquisition time domain FLIM at high spatial resolution in living cells. , 2008, Biophysical journal.

[69]  K. Garcia,et al.  Structural Basis of Semaphorin-Plexin Recognition and Viral Mimicry from Sema7A and A39R Complexes with PlexinC1 , 2010, Cell.

[70]  R. Klein,et al.  Structurally encoded intraclass differences in EphA clusters drive distinct cell responses , 2013, Nature Structural &Molecular Biology.

[71]  E. Gherardi,et al.  Structure of the Human Receptor Tyrosine Kinase Met in Complex with the Listeria Invasion Protein InlB , 2007, Cell.

[72]  Manfred Kirchgessner,et al.  Accelerating Image Analysis for Localization Microscopy with FPGAs , 2011, 2011 21st International Conference on Field Programmable Logic and Applications.

[73]  Nicole H. Wilson,et al.  Semaphorin 6B acts as a receptor in post-crossing commissural axon guidance , 2014, Development.

[74]  C. Hoogenraad,et al.  Lrig2 Negatively Regulates Ectodomain Shedding of Axon Guidance Receptors by ADAM Proteases. , 2015, Developmental cell.

[75]  M. Z. Cader,et al.  Neuropilins lock secreted semaphorins onto plexins in a ternary signaling complex , 2012, Nature Structural &Molecular Biology.

[76]  A. Kolodkin,et al.  Mechanisms and molecules of neuronal wiring: a primer. , 2011, Cold Spring Harbor perspectives in biology.