Method uncovers synaptic vesicles’ hidden proteome

Synaptic vesicles are tiny, membrane-enclosed compartments that package and release messenger compounds, such as neurotransmitters, in neurons. Researchers have identified common proteins associated with synaptic vesicles, but they think many low-abundance proteins found in subsets of vesicles remain hidden. An improved inventory of such proteins could be useful for understanding brain diseases.

To dig up such hidden proteins, Zacharie Taoufiq and Tomoyuki Takahashi of the Okinawa Institute of Science and Technology Graduate University, Reinhard Jahn of the Max Planck Institute for Biophysical Chemistry, and coworkers have developed a method for revealing the proteome of subcellular compartments (Proc. Natl. Acad. Sci. U.S.A. 2020, DOI: 10.1073/pnas.2011870117). The approach involves digesting proteins with two enzymes that target different cleavage sites, followed by separating the peptides with two chromatographic methods before mass spectrometric detection.

Using the method with synaptic vesicles purified from rat brains, the researchers identified 1,466 proteins, more than three times as many proteins as had been previously identified. They were able to identify multiple transporters that had been predicted but not seen in synaptic vesicles, including ones with unknown functions.

By comparing levels of proteins found in synaptic vesicles with those found in a nearby part of the neuron, the team categorized proteins found in vesicles as either “resident” or transiently present “visitor” proteins. Even those categorized as residents could be present at extremely low levels—many at less than one copy per vesicle on average. This suggests that synaptic vesicles may each be more specialized in what they transport than previously thought.