The ubiquitin-proteasome system (UPS) for protein degradation has been under intensive study, and yet, we have only partial understanding of mechanisms by which proteins are selected to be targeted for proteolysis. One of the obstacles in studying these recognition pathways is the limited repertoire of known degradation signals (degrons). To better understand what determines the susceptibility of intracellular proteins to degradation by the UPS, we developed an unbiased method for large-scale identification of eukaryotic degrons. Using a reporter-based high-throughput competition assay, followed by deep sequencing, we measured a degradation potency index for thousands of native polypeptides in a single experiment. We further used this method to identify protein quality control (PQC)-specific and compartment-specific degrons. Our method provides an unprecedented insight into the yeast degronome, and it can readily be modified to study protein degradation signals and pathways in other organisms and in various settings.
Bibliographical noteFunding Information:
We thank Prof. R. Kulka for the useful advises during the screen setup and for the pOC9 plasmid. We also thank Mr. Omri Alfassy for his important contribution in setting the initial yeast growth assay. This research was supported by the bi-national USA-Israel Scientific Foundation Grant 2011253 (T.R. and R.G.G.) and by ISF I-CORE (N.F.) and ERC Grant 340712 (N.F.)
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