Topographic Mapping of the Synaptic Cleft into Adhesive Nanodomains

Abstract

The cleft is an integral part of synapses, yet its macromolecular organization remains unclear. We show here that the cleft of excitatory synapses exhibits a distinct density profile as measured by cryoelectron tomography (cryo-ET). Aiming for molecular insights, we analyzed the synapse-organizing proteins Synaptic Cell Adhesion Molecule 1 (SynCAM 1) and EphB2. Cryo-ET of SynCAM 1 knockout and overexpressor synapses showed that this immunoglobulin protein shapes the cleft's edge. SynCAM 1 delineates the postsynaptic perimeter as determined by immunoelectron microscopy and super-resolution imaging. In contrast, the EphB2 receptor tyrosine kinase is enriched deeper within the postsynaptic area. Unexpectedly, SynCAM 1 can form ensembles proximal to postsynaptic densities, and synapses containing these ensembles were larger. Postsynaptic SynCAM 1 surface puncta were not static but became enlarged after a long-term depression paradigm. These results support that the synaptic cleft is organized on a nanoscale into sub-compartments marked by distinct trans-synaptic complexes.

Keywords: CADM; EphB2; Nectin-like protein; SynCAM; adhesion; synapse; synaptic cleft.

Figure 1. The excitatory synaptic cleft is structurally organized and SynCAM 1 shapes the edge

(A) Top, side view of a segmented synaptic cleft. Bottom, top view. (B) Top, tomographic slice from a synaptosome at 4 voxels depth (9.2 nm). Bottom, segmented net-like structures closer to the postsynaptic (lower) side are marked in red. The asterisk marks a gold particle for tomogram alignment. Scale bar, 50 nm. (C) Cleft separation into four layers and concentric columns. The outermost column in shown in grey. (D) WT and SynCAM 1 KO cleft tomograms at 4 voxels depth (9.2 nm). Arrowheads mark the less dense central density towards the edge of the KO cleft. Scale bar, 50 nm. (E) Profiles of the outermost WT and KO cleft columns. Lower grayscale values correspond to higher densities. Mean layer values were calculated in each tomogram and averaged per genotype (N=7 WT, 8 KO synapses). (F) SynCAM 1 KO synapses have a higher grayscale value differential and hence lower relative protein density in the outer column compared to the inner columns (N=7 WT, 8 KO synapses). (G) Tomograms of transgenic control and SynCAM 1 overexpressor (OE) clefts at 4 voxel depth (9.2 nm). The central cleft density of the control is barely visible in OE synapses. Scale bar, 50 nm. (H) lat profile of the SynCAM 1 OE cleft. Greyscale values are shown as in (E) (N=5 synapses each). (I) Data in (J) was calculated by subtracting grayscale values of volumes depicted in light gray from those in dark gray. (J) SynCAM 1 OE synapses have higher density in layer 1 relative to layer 2 in the outer cleft column compared to controls (N=5 synapses each). See also Figure S1 and Supplemental Media Files 1 and 2.

Figure 2. Postsynaptic SynCAM 1 marks the perimeter of excitatory synapses and EphB2 is enriched deeper within the postsynaptic area

(A) Immuno-EM of SynCAM 1 in adult hippocampal CA1 area after high pressure freezing. Arrows mark 10 nm gold particles labeling SynCAM 1 at the postsynaptic membrane edge of an asymmetric synapse. (B) majority of synaptic SynCAM 1 localizes to postsynaptic membranes (N=97 micrographs, 3 mice). (C) Measurement of postsynaptic distances for quantification in (D). 0 marks the PSD center and 1 the edge. (D) Postsynaptic membrane SynCAM 1 is enriched at the PSD edge. Particle distances to the PSD center were measured for each synapse and normalized as in (C) (N=97 micrographs, 3 mice). (E) Hippocampal neurons were sequentially immunostained at 14 div to first detect surface SynCAM 1 (blue) and surface EphB2 (green), followed by permeabilization and staining for postsynaptic Homer (red), and confocal imaging. The box marks the synapse enlarged in the insets. Scale bar, 5 μm. (F,G) Hippocampal neurons at 14 div were subjected to sequential immunostaining for (F) surface SynCAM 1 (magenta) and PSD-95 (green) or (G) surface EphB2 (magenta) and Homer (green), and imaged by 2-color STED microscopy. PSD borders based on STED image analysis are shown in center and right panels. Scale bars, 400 nm. (H) Surface SynCAM 1 and EphB2 locations were determined by STED as in (F,G) and distances were measured from the PSD border defined by PSD-95 and Homer images, respectively. SynCAM 1 (red) reached maximum density at the PSD border (green). EphB2 (blue) was prominently located within PSD areas. Densities were normalized to the highest value. SynCAM 1 data from 696 PSD areas in 86 imaging fields; EphB2 data, 111 PSD areas in 10 fields. See also Figure S2.

Figure 3. Distinct 3D distribution of EphB2 and SynCAM 1 and presence of SynCAM 1 ensembles around the cleft

(A,B) Left, hippocampal neurons at 12-14 div were subjected to sequential immunostaining for surface SynCAM 1 (A) or EphB2 (B) (red) and intracellular Homer (green), and imaged by 2-channel 3D STORM. Center and right, enlarged PSD with the calculated border outlined. Scale bar overview, 1 μm; enlarged panels, 400 nm. (C) Surface SynCAM 1 and EphB2 localizations were determined by 3D STORM as in (A,B) and the PSD border was defined by super-resolved Homer localizations. SynCAM 1 localization density (red) reached a maximum around the PSD edge (green) and localizations within Homer hulls were rare. EphB2 (blue) was prominently localized within the area demarcated by the PSD and showed a smaller peak around the edge. SynCAM 1 data from 178 PSDs in 11 imaging fields; EphB2 data, 446 PSDs in 31 fields. (D) Two 3D views of a convex, Homer-defined PSD hull (green; boxed in A) showing adjacent ensembles of SynCAM 1 (red). Scale bars, 200 nm in each axis. (E) Distribution of SynCAM 1 ensemble volumes within 500 nm of the PSD. Gray graph, putative single molecules detected at low thresholds. Red, ensembles detected at a threshold excluding single molecules. (F) PSDs marked by SynCAM 1 ensembles are larger. Cumulative frequency distribution of super-resolved Homer volumes in spines lacking SynCAM 1 ensembles (grey) or containing at least one SynCAM 1 ensemble (red) within 500 nm of the Homer hull. Ensembles were identified as in (E) (N=120 PSDs lacking SynCAM 1 ensembles, 31 PSDs with ensembles from 11 fields of imaging; Mann-Whitney test, p=0.026). See also Figure S3.

Figure 4. Activity-dependent area changes of synaptic SynCAM 1 complexes

(A) Hippocampal neurons at 14 d.i.v. were subjected to chemical LTD. Surface SynCAM 1 was immunolabeled (red), followed by staining for postsynaptic PSD-95 (green) and confocal imaging. Three representative images show control synapses (top) or after chemical LTD treatment (bottom). Scale bar, 0.8 μm. (B) LTD treatment enlarges the area of synaptic SynCAM 1 puncta. The graph shows the cumulative frequency distribution of SynCAM 1 puncta areas located within 0.8 μm of a PSD-95 punctum (Mann-Whitney test, p<0.0001; N=41 neurites each).