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.
Highlights
Brain function is carried in large by synaptic transmission between neurons
The present study provides a rich resource to interrogate the potential co-assembly and subcellular distribution of synaptic proteins in hippocampus, cortex, and cerebellum
Biological replicates of proteomics analyses were performed on hippocampal microsome (M), pellet 2 (P2), synaptosome (SYN), synaptic membrane (SYM) and postsynaptic density (PSD)
Summary
Generating a synaptic proteome resource for correlation profiling. We isolated biochemical cellular sub-fractions, with emphasis on synaptic compartments, from three brain regions (Fig. 1) followed by labelfree data dependent MS analysis of each fraction similar to previously described spatial/fractionation correlation proteomics[16]. In hippocampus, there is a sizeable amount of extra-synaptic AMPAR, and AMPAR in synaptic cytosol and dendrites, which may form reserve or recycling pools for activity-dependent plastic changes of PSD-trapped AMPARs28 The latter may explain the observed GRIA1 and GRIA2 in the microsome fraction, resulting in a lower correlation to the GRIN2B-DLG4-HOMER1 profile. Compared to the GRIN2B-DLG4-HOMER1 profile, GRIA3 and GRIA4 showed a 0.99 Pearson correlation (median value of these seed proteins) in all three brain regions whereas GRIA1 and GRIA2 showed a lower PSD enrichment in hippocampus reflected by 0.66 and 0.88 correlations, respectively. We selected two PSD proteins for further study, namely ADGRA1 and PLEKHA5, which showed high correlation to the GRIN2B-DLG4-HOMER1 profile and were found in the PSD fraction of all three brain regions. Our large dataset with thousands of proteins covering different synapse sub-fractions from three brain regions allows to interrogate the biochemically-defined spatial distribution of most synaptic proteins in a brain-region specific manner, and may help to generate hypotheses regarding novel protein localizations related to synapse functions
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
