A functional protein quality control machinery is crucial to maintaining cellular and organismal physiology. Perturbation in the protein homeostasis network can lead to the formation of misfolded and aggregated proteins that are a hallmark of protein conformational disorders and aging. Protein aggregation is counteracted by the action of chaperones that can resolubilize aggregated proteins. An alternative protein clearance strategy is the elimination by proteolysis employing the ubiquitin-proteasome system (UPS) or autophagy. Little is known how these three protein aggregate clearance strategies are regulated and coordinated in an organismal level with the progression of aging or upon expression of disease-associated proteins. In this study, I aimed to unravel the crosstalk between the different clearance options. To address this, I investigated how autophagy and UPS respond to the expression of disease-associated proteins and during aging when the chaperone capacity is compromised in C. elegans and HEK293 cells. Here, I demonstrate that wild-type animals display a reduced autophagic flux with the progression of aging whereas the UPS activity is altered in a tissue-specific manner (reduced activity in the neuronal cells and increased activity in the muscle cells). A knockdown of chaperones that constitute the HSP110/70/J disaggregation complex leads to an activation of autophagy that probably serves as a compensatory mechanism to rebalance proteostasis. Notably, the compensatory effect of autophagy in response to a depletion of chaperones is diminished with the progression of aging in C. elegans. Interestingly, the proteasomal activity and 20S levels are reduced in response to chaperone depletion, in particular upon knockdown of hsp-110/hspa4. Moreover, the capacity of the clearance machinery was analyzed in neurodegenerative disease models. The expression of aggregation-prone and disease-associated Aβ and polyglutamine (Q40) proteins leads to an impairment of both proteolytic pathways. Notably, the expression of Aβ perturbs the proteasome system also in a distal tissue demonstrating a trans-tissue communication. Lastly, in order to better understand how amyloid aggregates affect the cellular environment, correlative light and electron microscopy studies were performed in C. elegans. The Q40 aggregates display an amyloid structure and are not enclosed by any membrane. The lack of a surrounding membrane exposes the aggregate to all cellular components, which allows it to sequester numerous cellular components. The results obtained in this thesis, further elucidate the tight coordination between the different nodes of the proteostasis network with the progression of aging and disease on a cellular and organismal level.
