Characterization of Ubiquitin-mediated Protein Quality Control in the Nucleus
Fredrickson, Eric Kyle
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Due to the importance of proper protein folding, cells have evolved a collection of protein quality control (PQC) mechanisms that maintain overall cellular protein homeostasis. One type of PQC is ubiquitin-proteasome mediated degradation, where misfolded proteins are eliminated from the cell. In the yeast nucleus, San1, a ubiquitinprotein ligase, mediates the degradation of misfolded proteins. The data within this thesis reveals the mechanism by which San1 recognizes misfolded proteins, the abnormal feature San1 recognizes in misfolded proteins and how San1 maintains its stability. First off, San1 directly binds misfolded proteins using N- and C- terminal domains that are largely disordered. This disorder likely allows San1 to adopt different conformations necessary to bind differently shaped misfolded proteins. Additionally, the requirement of molecular chaperones for San1-mediated degradation differs among classes of substrates. Next, the data demonstrates San1 targets exposed hydrophobicity in a diverse collection of misfolded proteins and that recognition can occur with as few as five contiguous hydrophobic residues. Additionally, San1 preferentially targets the hydrophobic residues most likely to lead to protein aggregation (Phe and Ile residues). Further supporting a preference for aggregation prone regions, San1 targets the same hydrophobic regions in misfolded proteins that cause toxicity and aggregation. Lastly, San1 maintains its own stability by lacking Lys residues and highly hydrophobic regions within its disordered N- and C- terminal domains. Addition of either Lys residues or regions of hydrophobicity to these disordered regions led to San1 autodegradation. These features of San1 are highly conserved among fungal homologs, suggesting their importance in maintaining function. Overall, this work elucidates how and why San1 functions as a central regulator of nuclear protein homeostasis.
- Pharmacology