The accumulation of ubiquitinated proteinaceous inclusions represents a complex process, reflecting the disequilibrium between aggregate formation and aggregate clearance. Although decreasing aggregate formation or augmenting aggregate clearance will ultimately lead to diminished aggregate-burden, in terms of disease pathogenesis, the different approaches can have distinct outcomes. Using a novel cell based assay that can distinguish newly formed versus preformed inclusions, we demonstrate that two proteins previously implicated in the autophagic clearance of expanded polyglutamine inclusions, HspB7 and Alfy, actually affect very distinct cellular processes to affect aggregate-burden. Using this cell-based assay we also establish that constitutive expression of the aggregation prone protein can measurably slow the elimination of protein aggregates, since not all aggregates appear to be available for degradation. This new assay can therefore not only determine at what step a modifier may impact aggregate burden, but also can be used to provide new insight into how protein aggregates are targeted for degradation
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