The spine apparatus is a specialized compartment of the neuronal smooth endoplasmic reticulum (ER) located in a subset of dendritic spines. It consists of stacks of ER cisterns that are interconnected by an unknown dense matrix and are continuous with each other and with the ER of the dendritic shaft. While this organelle was first observed over 60 y ago, its molecular organization remains a mystery. Here, we performed in vivo proximity proteomics to gain some insight into its molecular components. To do so, we used the only known spine apparatus–specific protein, synaptopodin, to target a biotinylating enzyme to this organelle. We validated the specific localization in dendritic spines of a small subset of proteins identified by this approach, and we further showed their colocalization with synaptopodin when expressed in nonneuronal cells. One such protein is Pdlim7, an actin binding protein not previously identified in spines. Pdlim7, which we found to interact with synaptopodin through multiple domains, also colocalizes with synaptopodin on the cisternal organelle, a peculiar stack of ER cisterns resembling the spine apparatus and found at axon initial segments of a subset of neurons. Moreover, Pdlim7 has an expression pattern similar to that of synaptopodin in the brain, highlighting a functional partnership between the two proteins. The components of the spine apparatus identified in this work will help elucidate mechanisms in the biogenesis and maintenance of this enigmatic structure with implications for the function of dendritic spines in physiology and disease.The neuronal endoplasmic reticulum (ER) is an intricate continuous network of membrane tubules and cisterns that runs throughout neuronal processes with region-specific specializations. One such specialization of the smooth ER is the spine apparatus (SA) that is located in a subset of dendritic spines. The SA consists of stacks of flat cisterns that are connected by an unknown dense matrix and are continuous with each other and with the ER of the dendritic shaft (
1–
3) ( and
SI Appendix, Fig. S1A). Morphological changes in the SA have been reported after long-term potentiation (
4) and also, in a variety of human disorders, including several neurodegenerative conditions (
5–
9). While the first observation of the SA by electron microscopy (EM) was reported in 1959 by Gray (
1), our understanding of this organelle remains fairly limited. Its molecular characterization has proven to be challenging due to the difficulty of its biochemical isolation and its absence in organisms suitable for genetic screens.
Open in a separate windowThe localization of synaptopodin (indicated as Synpo in all figures) in cultured hippocampal neurons overlaps with the localization of the SA in dendritic spines of cortical slices. (
A) SA as visualized by transmission EM. (
B and
C) SA and ER reconstructed by a semiautomated algorithm from 3D volumes acquired by FIB-SEM. An SA is shown in
B, while
C shows a portion of a dendritic shaft with spines containing (magenta arrows) and not containing (white arrows) an SA. The plasma membrane (PM) is shown in blue, the ER is in red, and the post-synaptic density (PSD) is in yellow. (
D) Cisternal organelle (CO), as observed in an FIB-SEM optical section, at an axonal initial segment. Note that the stacks of ER cisterns are similar to those characteristics of the SA. (
E) mRFP-synaptopodin coexpressed with cytosolic EGFP as a marker of the entire dendritic volume. Note in the zoomed-in views of the region enclosed by a rectangle (the lower three fields) that synaptopodin is concentrated near the spine neck, where the SA is localized. (
F) Localization by immunofluorescence of endogenous synaptopodin showing strong overlap with a pool of F-actin labeled by phalloidin-Alexa488. Also, in this sample, the magnified views (the lower three fields) show enrichment of synaptopodin, relative to actin, at the spine neck. (
G) mRFP-synaptopodin coexpressed with an ER marker, EGFP-VAPB, showing colocalization of the two proteins. In the zoomed-in views (the lower three fields), red arrows show a spine positive for both the ER marker and synaptopodin, and the blue arrows show a spine with the ER marker but lacking synaptopodin. (
H) Percentage of ER-positive spines that also contain synaptopodin and percentage of synaptopodin-positive spines that contain ER quantified in cultured hippocampal neurons expressing mRFP-synaptopodin and the ER markers EGFP-VAPB or EGFP-Sec61
β. Each data point represents at least 99 spines from a single neuron. (
I) Spine of a synaptopodin KO mouse that lacks the SA but contains the ER. (
J) Quantification of the number of spines where ER was visible in the plane of the section with or without an SA in the brain of wild type (WT) vs. synaptopodin mutant mice (
spines per genotype).The only known protein enriched at the SA and required for its formation is synaptopodin, a protein without transmembrane regions localized in the cytosolic space (
10). Neuronal synaptopodin specifically localizes to dendritic spines and to the axonal initial segment, where another specialization of the ER similar to the SA (stack of flattened cisterns) called the cisternal organelle is present (
11–
14). Lack of synaptopodin in synaptopodin knock-out (KO) mice correlates with the lack of SA and of the cisternal organelle, as well as with a reduction in Hebbian plasticity and spatial memory (
11,
15–
18). A longer isoform of synaptopodin is expressed in the foot processes of podocytes, where it functions as a regulator of the actin cytoskeleton (
19,
20). Synaptopodin binds to and bundles actin (
21) and interacts with several actin binding proteins, such as
α-actinin (
13,
21,
22). While more is known about the interactors of synaptopodin in podocytes, its binding partners at the SA remain unknown.The goal of this work was to gain insight into the molecular composition of the SA. To this aim, we used synaptopodin as a starting point for our analysis. We identified some of its binding partners by an in vivo proximity biotinylation approach and characterized the specific localization of a subset of these proteins in neurons and their interaction with synaptopodin in an exogenous system.
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