The protein quality control machinery regulates its misassembled proteasome subunits

Our study used the baker yeast Saccharomyces cerevisiae as a model system to reveal for the first time how the dysfunctional proteasome, which is associated with age-related pathologies and all the major chronic neurodegenerative disorders, is controlled by the protein quality control machinery.

HFSP Career Development Award holder Shay Ben-Aroya and colleagues
authored on Fri, 26 June 2015

Maintaining proteostasis is crucial for cells given the toxic potential of misfolded proteins and aggregates. In eukaryotes, the ubiquitin proteasome system (UPS), with the help of different chaperones, plays a vital role in protein quality control (PQC) by removing abnormal and toxic proteins generated during a lifetime of environmental damage. Proteins that are not refolded or degraded in the UPS are mobilized to cytoprotective-compartments, which were shown to preclude their delivery by the parental cells to subsequent generations.

Figure. Models: UPS assembly can be naturally impaired by many factors, and thus, there is competition between assembly, degradation and aggregation of proteasome subunits. When the proteasome lids are partially misassembled, as demonstrated in rpn5ΔC mutant (i), the misassembled subunits are targeted to UPS-mediated degradation by the assembled 26S proteasomes which are still available. This degradation can take place in the nucleus, as recently shown for misfolded proteins. The employment of rpn5∆C at the restrictive temperature (ii), shifts the balance to slower assembly, which has a dual effect: it increases the amount of the unassembled subunit, and at the same time decreases its degradation, because there is less proteasomes available. Hence, misassembled proteasome subunits are aggregated in the IPOD, a process that depends mostly on HSP42. Figure source: Peters, L.Z. et al. (2015) The Protein Quality Control Machinery Regulates Its Misassembled Proteasome Subunits. PLOS, DOI: 10.1371/journal.pgen.1005178.

Although ubiquitin-mediated proteasomal degradation of many proteins plays key roles in the PQC system, the proteasome itself can become dysfunctional as a result of transcriptional and translational failures, genomic mutations, or diverse stress conditions, leading to misfolded proteins existing in every compartment of the cell. UPS function can be naturally impaired by many factors, including mutations, errors during transcription and during RNA processing and translation, trapping of a folding intermediate, incorrect incorporation into multimeric complexes or oxidative damage, processes that are accelerated during aging. Dysregulation of this pathway results in intracellular deposits of ubiquitin protein conjugates which can be seen in age-related pathologies and in all the major chronic neurodegenerative disorders such as Alzheimer’s, Parkinson’s and Huntington’s diseases as well as amyotrophic lateral sclerosis (ALS) and others. Still, the regulatory pathways and the identity of the cellular machinery that mediates the sorting sequestration and elimination of misfolded proteasomal subunits remain poorly understood.

In this study, we used a mutated proteasome lid subunit (termed rpn5∆C) in the Saccharomyces cerevisie, as a model system to address this question. We show that the nuclear mislocalization and the cytosolic aggregates formed by this mutant represent a misassembled proteasome lid. With this experimental tool in hand, we were able to demonstrate for the first time, how the dysfunctional proteasome is controlled by the PQC machinery. We found that among the multilayered quality control mechanisms, the UPS-mediated degradation of its own dysfunctional subunits is the favored pathway.  However, in the absence of a functional proteasome, peripheral aggregates that represent misassembled proteasome subunits, accumulate in the cytoprotective compartments, a process mediated by the chaperone Hsp42. We further demonstrate that while the proteasome structure can tolerate the structural defects of the rpn5∆C mutant and assemble into a functional proteasome, the PQC machinery dominates, and the mutated protein is spatially removed by the PQC machinery, leading to proteasome dysfunction. These results highlight the importance of removing potentially cytotoxic protein aggregates, despite the high cost of diverting resources away from producing essential protein products.

Overall, our results demonstrate that proteasome homeostasis is controlled through cellular probing of the quality of proteasome aggregates and the interplay between UPS-mediated degradation of dysfunctional subunits and alternatively, their accumulation in cytoprotective compartments. We believe that the mechanism of proteasome regulation by the PQC in yeast may serve as a paradigm to understand how homeostasis of this essential complex is controlled in higher eukaryotes.


The Protein Quality Control Machinery Regulates Its Misassembled Proteasome Subunits. Lee Zeev Peters, Ofri Karmon, Galit David-Kadoch, Rotem Hazan, Tzenlin Yu, Michael H. Glickman, Shay Ben-Aroya. PLOS, Published: April 28, 2015. DOI: 10.1371/journal.pgen.1005178.

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