title: Reporter-based growth assay for systematic analysis of protein degradation.
abstract: Protein degradation by the ubiquitin-proteasome system (UPS) is a major regulatory mechanism for protein homeostasis in all eukaryotes. The standard approach to determining intracellular protein degradation relies on biochemical assays for following the kinetics of protein decline. Such methods are often laborious and time consuming and therefore not amenable to experiments aimed at assessing multiple substrates and degradation conditions. As an alternative, cell growth-based assays have been developed, that are, in their conventional format, end-point assays that cannot quantitatively determine relative changes in protein levels. Here we describe a method that faithfully determines changes in protein degradation rates by coupling them to yeast cell-growth kinetics. The method is based on an established selection system where uracil auxotrophy of URA3-deleted yeast cells is rescued by an exogenously expressed reporter protein, comprised of a fusion between the essential URA3 gene and a degradation determinant (degron). The reporter protein is designed so that its synthesis rate is constant whilst its degradation rate is determined by the degron. As cell growth in uracil-deficient medium is proportional to the relative levels of Ura3, growth kinetics are entirely dependent on the reporter protein degradation. This method accurately measures changes in intracellular protein degradation kinetics. It was applied to: (a) Assessing the relative contribution of known ubiquitin-conjugating factors to proteolysis (b) E2 conjugating enzyme structure-function analyses (c) Identification and characterization of novel degrons. Application of the degron-URA3-based system transcends the protein degradation field, as it can also be adapted to monitoring changes of protein levels associated with functions of other cellular pathways.
authors.affiliation: Department of Biological Chemistry, The Hebrew University of Jerusalem.
authors.forename: Itamar
authors.initials: I
authors.lastname: Cohen
authors.affiliation: Department of Biological Chemistry, The Hebrew University of Jerusalem.
authors.forename: Yifat
authors.initials: Y
authors.lastname: Geffen
authors.affiliation: Department of Biological Chemistry, The Hebrew University of Jerusalem.
authors.forename: Guy
authors.initials: G
authors.lastname: Ravid
authors.affiliation: Department of Biological Chemistry, The Hebrew University of Jerusalem; travid@cc.huji.ac.il.
authors.forename: Tommer
authors.initials: T
authors.lastname: Ravid
mesh_terms: D007700:Kinetics; D046988:Proteasome Endopeptidase Complex / Q000737:chemistry / Q000378:metabolism*; D059748:Proteolysis; D011993:Recombinant Fusion Proteins / Q000235:genetics / Q000494:pharmacology; D012441:Saccharomyces cerevisiae / Q000737:chemistry / Q000254:growth & development / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics / Q000378:metabolism / Q000494:pharmacology; D025801:Ubiquitin / Q000737:chemistry / Q000378:metabolism*
chemical_list: D011993:Recombinant Fusion Proteins; D029701:Saccharomyces cerevisiae Proteins; C554167:URA3 protein, S cerevisiae; D025801:Ubiquitin; D046988:Proteasome Endopeptidase Complex