Hidden proteome of synaptic vesicles in the mammalian brain

Abstract

Current proteomic studies clarified canonical synaptic proteins that are common to many types of synapses. However, proteins of diversified functions in a subset of synapses are largely hidden because of their low abundance or structural similarities to abundant proteins. To overcome this limitation, we have developed an “ultra-definition” (UD) subcellular proteomic workflow. Using purified synaptic vesicle (SV) fraction from rat brain, we identified 1,466 proteins, three times more than reported previously. This refined proteome includes all canonical SV proteins, as well as numerous proteins of low abundance, many of which were hitherto undetected. Comparison of UD quantifications between SV and synaptosomal fractions has enabled us to distinguish SV-resident proteins from potential SV-visitor proteins. We found 134 SV residents, of which 86 are present in an average copy number per SV of less than one, including vesicular transporters of nonubiquitous neurotransmitters in the brain. We provide a fully annotated resource of all categorized SV-resident and potential SV-visitor proteins, which can be utilized to drive novel functional studies, as we characterized here Aak1 as a regulator of synaptic transmission. Moreover, proteins in the SV fraction are associated with more than 200 distinct brain diseases. Remarkably, a majority of these proteins was found in the low-abundance proteome range, highlighting its pathological significance. Our deep SV proteome will provide a fundamental resource for a variety of future investigations on the function of synapses in health and disease.

Deep parallel characterization of AAV tropism and AAV-mediated transcriptional changes via single-cell RNA sequencing

“…Meanwhile, the growth arrest genes, Gadd45g and Gadd45b (Vairapandi et al, 2002), are upregulated. Genes involved in synaptic vesicle cycling, such as Unc13c (Palfreyman and Jorgensen, 2017) and Slc32a1 (Taoufiq et al, 2020), are also downregulated at 3 DPI. Some genes remain upregulated throughout the study, such as Npas4, responsible for regulating excitatory-inhibitory balance (Spiegel et al, 2014).…”

A unified resource and configurable model of the synapse proteome and its role in disease

“…1 D,F). For instance, the latest study by Taoufiq et al 47 brought in over 400 new genes to our presynaptic list.…”

Localization, proteomics, and metabolite profiling reveal a putative vesicular transporter for UDP-glucose

“…In addition to our study, a subset of SLC35 family members was also reported by SV proteomics. SLC35G2 was recently reported in SV proteomics using an improved workflow (Taoufiq et al, 2020). Interestingly, SLC35D3 was not simultaneously identified, potentially due to a few reasons: (1) the proteome may vary across different species at different ages (SD rats at 4-6 weeks vs C57BL6 mice at 6-8 weeks); (2) SLC35D3 has an even lower protein abundance compared with SLC35G2 (Fig 2G ), which is more challenging for detection;…”