Cytoprotective Strategies that Selectively Recognize and Suppress Protein Aggregation in the Cell

Protein misfolding and aggregation are constant threats to cellular homeostasis. The cell must cope with a diverse range of non-native protein conformers and efficiently triage misfolded proteins between pathways for refolding or degradation. In addition, cellular pathways sequester non-native proteins via the microtubule cytoskeleton to distinct subcellular compartments when degradation pathways are saturated. Deficiencies in protein homeostasis occur in a wide variety of human maladies. For example, several disorders including Alzheimer's disease and Huntington's disease are associated with the accumulation of beta-sheet rich, amyloid-like inclusions. Though molecular chaperones are known regulators of amyloid assembly and neurotoxicity, how molecular chaperones selectively bind beta-sheet rich protein conformers and regulate amyloid fibril assembly is largely unknown. Herein, I describe a novel function for the Type I Hsp40 molecular chaperone Ydj1 in regulating aggregation and toxicity of a glutamine/asparagine-rich prion fragment from the yeast protein Rnq1. In the absence of Ydj1, overexpression of this prion fragment was toxic to yeast and resulted in the accumulation of amyloid-like aggregates. Ydj1 binding and suppression of toxicity required its zinc finger-like domain and farnesyl moiety. As a result, Ydj1 utilizes unique chaperone modules to suppress aggregation of an amyloid-like prion and protect cells from the toxic buildup of protein aggregates. Ydj1 also participates in the degradation of misfolded proteins via the ubiquitin-proteasome system. I found that Ydj1 is required to hold polyubiquitinated forms of a misfolded, cytosolic protein in a soluble state. Investigating the degradation of this misfolded protein further, I found that interfering with specific steps in the degradation pathway partitioned this misfolded protein to distinct outcomes including aggregation. Surprisingly, altering the microtubule cytoskeleton drove this misfolded protein to form insoluble aggregates in the cytosol that could not be trafficked to the proteasome. Disrupting microtubule dynamics selectively stabilized some misfolded proteins, while other misfolded proteins are degraded in a microtubule-independent pathway. These observations uncover a novel connection between chaperone-mediated protein quality control and the microtubule cytoskeleton. Furthermore, misfolded proteins are managed in the cytosol by sophisticated quality control networks that utilize adaptable molecular chaperones such as Ydj1 to suppress aberrant protein aggregation.