A plasma membrane protein proteomic approach to elucidate the role of ubiquitin- dependent endocytosis and lysosomal degradation in cortical neurons

Ubiquitin-dependent receptor endocytosis and subsequent endocytic sorting to the lysosome for degradation plays an essential role in synaptic plasticity by changing the number of membrane receptors at the synaptic sites. However, our knowledge of this pathway on the overall synaptic membrane protein population is still rudimentary. Here, we identify surface synaptic membrane proteins as candidate ubiquitinated targets of the lysosome. We show that the lysosomal inhibition increases surface synaptic membrane protein ubiquitination in neurons. We combine the isolation of biotinylated cell surface membrane proteins, lysosomal perturbation and mass spectroscopy analysis to generate the first large-scale proteomic analysis of the surface synaptic proteome as candidate ubiquitinated targets of the lysosome. After 12 hours treatment, we compared biochemically purified synaptic cell membrane protein fractions between normal and lysosome-perturbed conditions through tandem mass spectrometry. A total of 1600 proteins were identified and quantified, including 539 plasma membrane proteins. Out of these plasma membrane proteins, we found that 105 of them were upregulated, and 207 were downregulated, while 226 did not significantly change in protein level. The proteins with altered pattern include proteins involved in regulating cell adhesion, cellular homeostasis, synaptic transmission, and cellular localization. This suggests that the ubiquitin-dependent lysosomal degradation pathway is important in maintaining synaptic function