Abstract
In recent years, the remarkable molecular complexity of synapses has been revealed, with over 1,000 proteins identified in the synapse proteome. Although it is known that different receptors and other synaptic proteins are present in different types of neurons, the extent of synapse diversity across the brain is largely unknown. This is mainly due to the limitations of current techniques. Here, we report an efficient method for the purification of synaptic protein complexes, fusing a high‐affinity tag to endogenous PSD95 in specific cell types. We also developed a strategy, which enables the visualisation of endogenous PSD95 with fluorescent‐protein tag in Cre‐recombinase‐expressing cells. We demonstrate the feasibility of proteomic analysis of synaptic protein complexes and visualisation of these in specific cell types. We find that the composition of PSD95 complexes purified from specific cell types differs from those extracted from tissues with diverse cellular composition. The results suggest that there might be differential interactions in the PSD95 complexes in different brain regions. We have detected differentially interacting proteins by comparing data sets from the whole hippocampus and the CA3 subfield of the hippocampus. Therefore, these novel conditional PSD95 tagging lines will not only serve as powerful tools for precisely dissecting synapse diversity in specific brain regions and subsets of neuronal cells, but also provide an opportunity to better understand brain region‐ and cell‐type‐specific alterations associated with various psychiatric/neurological diseases. These newly developed conditional gene tagging methods can be applied to many different synaptic proteins and will facilitate research on the molecular complexity of synapses.
Highlights
Information processing in the mammalian brain depends on synapse proteins
We still have insufficient knowledge on precisely how individual synapses differ in their molecular composition and how these different types of synapses are distributed with regard to neuronal cell type and brain region
We have previously reported the generation of a constitutive PSD95‐tandem affinity purification (TAP) tag knock‐in mouse line (Fernandez et al, 2009), in which PSD95 was in‐frame fused with the small peptide TAP tag, for highly efficient synaptic protein purifications
Summary
Information processing in the mammalian brain depends on synapse proteins. Over the past two decades, proteomic studies have revealed remarkable synapse complexity and diversity. It has been reported that many synaptic proteins, including different subtypes of receptors, isoforms of scaffolding proteins and adhesion molecules, are differentially expressed in various brain regions (Bayes et al, 2012, 2011; Collins et al, 2006; Emes et al, 2008; Frank et al, 2016; Frank, Zhu, Komiyama, & Grant, 2017; Husi, Ward, Choudhary, Blackstock, & Grant, 2000; Komiyama et al, 2002; Lein et al, 2007; Micheva, Busse, Weiler, O'Rourke, & Smith, 2010; Roy et al, 2018) Despite this recent progress, we still have insufficient knowledge on precisely how individual synapses differ in their molecular composition and how these different types of synapses are distributed with regard to neuronal cell type and brain region. These populations differed in synaptic features such as synaptic density, size and punctate morphology, and in molecular composition of PSD95 complexes as revealed by proteomic analysis
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