Synaptic function crucially depends on uninterrupted synthesis and degradation of synaptic proteins. While much has been learned on synaptic protein synthesis, little is known on the routes by which synaptic proteins are degraded. Here we systematically studied how inhibition of the ubiquitin‐proteasome system (UPS) affects the degradation rates of thousands of neuronal and synaptic proteins. We identified a group of proteins, including several proteins related to glutamate receptor trafficking, whose degradation rates were significantly slowed by UPS inhibition. Unexpectedly, however, degradation rates of most synaptic proteins were not significantly affected. Interestingly, many of the differential effects of UPS inhibition were readily explained by a quantitative framework that considered known metabolic turnover rates for the same proteins. In contrast to the limited effects on protein degradation, UPS inhibition profoundly and preferentially suppressed the synthesis of a large number of synaptic proteins. Our findings point to the importance of the UPS in the degradation of certain synaptic proteins, yet indicate that under basal conditions most synaptic proteins might be degraded through alternative pathways.
Proteasome inhibitors were found to slow the degradation of a number of synaptic proteins, yet degradation rates of most synaptic proteins were not affected. In contrast, proteasomal inhibitors were observed to profoundly and preferentially suppress synaptic protein synthesis.
Multiplexed SILAC (stable isotope labeling with amino acids in cell culture) was used to measure how proteasomal inhibitors affect basal rates of synaptic protein degradation.
Proteasomal inhibitors reduced degradation rates of several (synaptic) proteins, including NEDD4, SAP102/Dlg3, and GluA2.
Degradation rates of most synaptic proteins were not significantly affected, suggesting degradation through alternative pathways.
The synthesis of many synaptic proteins was strongly and preferentially suppressed in the presence of proteasomal inhibitors.
The slow turnover rates of many synaptic proteins and confounding effects on protein synthesis place limitations on the use of proteasomal inhibitors to study synaptic protein catabolism.
The EMBO Journal (2016) 35: 2238–2262
- Received December 1, 2015.
- Revision received August 2, 2016.
- Accepted August 8, 2016.
- © 2016 The Authors