Proteomic Analysis of Unbounded Cellular Compartments: Synaptic Clefts

Cell. 2016 Aug 25;166(5):1295-1307.e21. doi: 10.1016/j.cell.2016.07.041.


Cellular compartments that cannot be biochemically isolated are challenging to characterize. Here we demonstrate the proteomic characterization of the synaptic clefts that exist at both excitatory and inhibitory synapses. Normal brain function relies on the careful balance of these opposing neural connections, and understanding how this balance is achieved relies on knowledge of their protein compositions. Using a spatially restricted enzymatic tagging strategy, we mapped the proteomes of two of the most common excitatory and inhibitory synaptic clefts in living neurons. These proteomes reveal dozens of synaptic candidates and assign numerous known synaptic proteins to a specific cleft type. The molecular differentiation of each cleft allowed us to identify Mdga2 as a potential specificity factor influencing Neuroligin-2's recruitment of presynaptic neurotransmitters at inhibitory synapses.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Antigens, CD / metabolism
  • Cell Adhesion Molecules, Neuronal / metabolism*
  • GABAergic Neurons / metabolism*
  • Glutamic Acid / metabolism
  • HEK293 Cells
  • Humans
  • Immunoglobulins / metabolism*
  • Membrane Glycoproteins / metabolism*
  • Mice
  • Nerve Tissue Proteins / metabolism*
  • Neural Cell Adhesion Molecules / metabolism
  • Peroxidase / genetics
  • Peroxidase / metabolism
  • Proteome / metabolism*
  • Proteomics
  • Rats
  • Receptors, GABA / metabolism
  • Recombinant Fusion Proteins / genetics
  • Recombinant Fusion Proteins / metabolism
  • Synaptic Membranes / metabolism*
  • Thalamus / metabolism


  • Antigens, CD
  • Cell Adhesion Molecules, Neuronal
  • Immunoglobulins
  • MDGA1 protein, rat
  • MDGA2 protein, rat
  • Membrane Glycoproteins
  • Nerve Tissue Proteins
  • Neural Cell Adhesion Molecules
  • Proteome
  • Receptors, GABA
  • Recombinant Fusion Proteins
  • neuroligin 2
  • Glutamic Acid
  • Peroxidase
  • antigens, CD200