Misfolded proteins are commonly refolded to a functional conformation or degraded by quality control mechanisms. When misfolded proteins evade quality control, they often form aggregates that are sequestered to specific sites in the cell. The proper sequestration of aggregates is thought to prevent potential dysfunction, toxicity and disease that is often associated with the presence of aggregates. However, the cellular mechanisms that underlie the management of newly formed protein aggregates are unclear. To understand the cellular response to protein aggregate formation, I used the aggregation prone prion domain of the Sup35 protein (Sup35NM) in yeast. Previous work observing GFP-tagged Sup35NM (Sup35NM-GFP) through 3D time-lapse microscopy observed consistent two-step behavior of newly formed aggregates. The first step involves the formation of small foci that are highly mobile. These foci can coalesce to form larger mature aggregates. The second step is the sequestration of matured aggregates near the periphery of the cell. In this study I developed novel quantitative techniques to measure aggregate behavior during both steps of formation. Using these techniques, I determined that the mobility and coalescence of protein aggregates, step 1, is dependent on both the actin cytoskeleton and the Myo2p motor protein. However, step 2 is dependent upon actin networks, but not Myo2p. It was unclear whether this behavior was specific to Sup35NM-GFP or part of a general response to protein aggregation; therefore I also quantified the formation of other types of aggregates. Chemically induced stress granules and a human aggregating protein associated with amyotrophic lateral sclerosis, TDP-43, both undergo a two-step formation process that is dependent upon actin. These data suggest that there is a general cellular process in responding to different types of newly formed aggregates. Together, this study provides new insights into the mechanisms used to respond to the formation of protein aggregates, changing the current dogma of the field, and suggests for future consideration
