Correlation profiling of brain sub-cellular proteomes reveals co-assembly of synaptic proteins and subcellular distribution

Abstract

Protein correlation profiling might assist in defining co-assembled proteins and subcellular distribution. Here, we quantified the proteomes of five biochemically isolated mouse brain cellular sub-fractions, with emphasis on synaptic compartments, from three brain regions, hippocampus, cortex and cerebellum. We demonstrated the expected co-fractionation of canonical synaptic proteins belonging to the same functional groups. The enrichment profiles also suggested the presence of many novel pre- and post-synaptic proteins. Using super-resolution microscopy on primary neuronal culture we confirmed the postsynaptic localization of PLEKHA5 and ADGRA1. We further detected profound brain region specific differences in the extent of enrichment for some functionally associated proteins. This is exemplified by different AMPA receptor subunits and substantial differences in sub-fraction distribution of their potential interactors, which implicated the differences of AMPA receptor complex compositions. This resource aids the identification of proteins partners and subcellular distribution of synaptic proteins.

Stitching the synapse: Cross-linking mass spectrometry into resolving synaptic protein interactions

“…Protein abundance data were obtained from (12 The depth and sensitivity of the XL-MS approach were interrogated by comparing the abundances of proteins cross-linked over the entire synaptic proteome. Protein abundance data were obtained from our previous study using label-free liquid chromatography-MS (LC-MS) quantification on equivalent preparations (12). The median abundance of the proteins identified by XL-MS was three times higher than the median abundance of the synaptic proteome ( Fig.…”

“…The same package was used to calculate the modularity score of the network. Protein abundances were obtained from our previous proteomic study of synaptosomes and microsomes (12). Protein domain information of all cross-linked proteins in our dataset was retrieved from UniProt (table S1, A and C).…”

“…The number of proteins and median abundance are indicated in each box. Protein abundance data were obtained from(12).…”

Proteomic Analysis of Brain Region and Sex-Specific Synaptic Protein Expression in the Adult Mouse Brain

“…They form the core components of neural circuits and networks, collectively referred to as the brain connectome [3]. Although synapses were originally considered to be simple connection sites between neurons, the identification of synaptic proteins using mass spectrometry has transformed this view within the last decades [4][5][6][7][8][9][10][11]. Synapses are now recognized to be highly sophisticated computational units which are estimated to contain up to several thousands of different proteins [1,10,12].…”

The endosomal protein sorting nexin 4 is a novel synaptic protein

“…Subcellular fractions were obtained from hippocampi from three-month-old C57BL6 mice as previously described 29,30 . Isolated hippocampi were homogenized on a dounce homogenizer (potterS; 12 strokes, 900 rpm) using homogenizer buffer (0.32 M Sucrose, 5 mM HEPES pH 7.4, Protease inhibitor cocktail (Roche)), and spun at 1000xg for 10 minutes at 4 o C to obtain Supernatant 1 (S1).…”