Functions of the ubiquitin-proteasome system in Saccharomyces cerevisiae : cotranslational protein degradation and regulation of the UBR1 pathway

Abstract

The ubiquitin-proteasome system is the major pathway for protein degradation in the cytoplasm of eukaryotic cells. This pathway serves two main functions: protein quality control - removing damaged or misfolded proteins, and concentration control - regulating levels of the protein components of biochemical switches and oscillators. Misfolded proteins expose hydrophobic patches that act as degradation signals recognized by the ubiquitin-proteasome system. Nascent proteins being synthesized by the ribosome expose similar patches that might also serve as degradation signals. I show here that nascent polypeptides carrying a strong degradation signal of the Ub-proteasome system experience a kinetic competition between degradation and biogenesis. These results suggest that there may be a proofreading pathway for protein folding that recognizes and degrades proteins that fail to fold correctly. Levels of regulatory proteins must be adjusted in response to many different signals, both environmental and cell-intrinsic. I show here that the activity of a specific ubiquitin-protein ligase (E3), Ubr1, is allosterically regulated. UbrI regulates dipeptide uptake in saccharomyces cerevisiae by controlling the degradation of Cup9, a homeodomain-containing repressor of the dipeptide transporter Ptr2. UbrI is allosterically activated by dipeptides bearing destabilizing residues according to the N-end rule. The import of these dipeptides stimulates Ubri, increasing Cup9 degradation, thereby de-repressing ptr2 expression. Thus, the expression of the machinery required for dipeptide uptake is coupled to the availability of dipeptides. I also outline a novel pathway governing Ubrl activity. Free amino acids induce Ptr2 expression via a signal transduction cascade containing Ssy1, a putative transmembrane amino acid receptor, and Ptr3, a novel downstream signaling component. One of the targets of this signal transduction pathway is Ubr1. Ubrl is activated in the presence of amino acids, accelerating Cup9 degradation, thus inducing Ptr2.