The impact of proteostasis imbalance on proteome solubility
AffiliationBiochemistry and Molecular Biology
Document TypePhD thesis
Access StatusThis item is embargoed and will be available on 2021-04-26.
© 2019 Dr. Xiaojing Sui
A hallmark of neurodegenerative diseases is that certain proteins abnormally aggregate into insoluble deposits. A leading hypothesis is that a breakdown in protein folding quality control mechanisms leads to the accumulation of unfolded or misfolded proteins that are prone to aggregation. The hypothesis of the thesis is that there would be a metastable sub-proteome vulnerable to aggregation when protein quality control is stressed by any mechanism. However, a systematic understanding of the proteins that are affected remains poorly understood. Here extensive quantitative proteomic studies were performed to measure the changes in proteome abundance and proteome solubility (as determined by 100,000 g pelleting for 20 min) arising from different triggers of proteostasis stress that have reported roles in leading to protein misfolding and aggregation. These included three specific inhibitors of key proteostasis hubs (Hsp70, Hsp90 and the proteasome), two exogenous stresses (oxidative stress and ER stress) related to neurodegenerative diseases and aggregation of mutant Huntingtin exon1 protein in a mouse neuroblastoma cell model of Huntington’s disease. Unexpectedly, all stresses led to no detectable change in net proportion of aggregated protein, suggesting that the proteome is robustly buffered against the accumulation of misfolded protein. However, at the individual protein level, there were many changes both upwards and downwards for all stresses. Most changes can be ascribed to a functional remodelling of protein complexes involved in adaptation to stress rather than protein misfolding with stress granule proteins being centrally involved. The comparison of proteome solubility changes across all stresses revealed that different proteostasis stresses yielded highly distinct solubility signatures. Although no common metastable sub-proteome was detected, proteins that were sensitive to stress shared similar physicochemical features. More insoluble proteins were enriched with high molecular weight, low isoelectric point and prion-like domains. By contrast, more soluble proteins were enriched with low molecular weight and low-complexity domains. Indeed, assessment of proteome-wide solubility changes offers richer power into mechanisms than the standard measurement of protein abundance levels. Therefore, it is suggested this methodology can be used more generally alongside standard quantitative proteomic analyses of protein levels to gain deeper insight to molecular function of diverse biological mechanisms.
Keywordsproteostasis; protein aggregation; protein misfolding; Huntington Disease; chaperone; protein misfolding; nuclear pore; stress granule formation
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