Mapping the Landscape of a Eukaryotic Degronome.
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.
Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel.
Yifat
Y
Geffen
Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel; School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel.
Alon
A
Appleboim
Department of Pharmacology, University of Washington, Seattle, WA 98195, USA.
Richard G
RG
Gardner
Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel; School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel. Electronic address: nir@cs.huji.ac.il.
Nir
N
Friedman
Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel; School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel. Electronic address: rsadeh@cs.huji.ac.il.
Ronen
R
Sadeh
Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel. Electronic address: tommer.ravid@mail.huji.ac.il.
Tommer
T
Ravid
D001665:Binding Sites; D002874:Chromosome Mapping; D015966:Gene Expression Regulation, Fungal; D015723:Gene Library; D016681:Genome, Fungal; D057166:High-Throughput Screening Assays; D010766:Phosphorylation; D046988:Proteasome Endopeptidase Complex / Q000378:metabolism*; D011485:Protein Binding; D000072756:Protein Conformation, alpha-Helical; D017510:Protein Folding; D054730:Protein Interaction Domains and Motifs; D059748:Proteolysis; D020543:Proteome / Q000235:genetics / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D025801:Ubiquitin / Q000235:genetics / Q000378:metabolism; D044767:Ubiquitin-Protein Ligases / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism
D020543:Proteome; D029701:Saccharomyces cerevisiae Proteins; C554167:URA3 protein, S cerevisiae; D025801:Ubiquitin; C091362:SSM4 protein, S cerevisiae; D044767:Ubiquitin-Protein Ligases; D046988:Proteasome Endopeptidase Complex