Year: 2025
Type: dissertation
Abstract: Protein–protein interactions (PPIs) regulate all cellular processes and are often dysregulated in disease. Mapping transient and condition-specific interactions remains an ongoing challenge. Stress granules (SG) are transiently membraneless organelles that form during cellular stress, but their functions and assembly are not fully understood. Previous proteomic studies identified pre-existing interactions among SG proteins in unstressed cells that may facilitate rapid assembly during stress. To elucidate the dynamic proteomic landscapes of SGs during their formation, our lab utilized proximity-dependent biotinylation (BioID) to sample SG proximal interaction networks during oxidative and hyperosmotic stress. However, traditional mass spectrometry (MS) methods used to analyze BioID data lack the quantitative resolution to capture transient interaction changes. To address these limitations, my thesis presents a data-independent acquisition (DIA) mass spectrometry analysis pipeline tailored for dynamic BioID datasets. This workflow improved data completeness and enhanced the detection of transient interactions. Application to in-house BioID datasets revealed both stressor-nonspecific and -specific PPI changes. Notably, hyperosmotic stress induced SG association of microtubule-associated proteins and large ribosomal subunits—components that are typically absent in canonical SGs—suggesting distinct, stress-specific modes of SG assembly.
Source: TSpace (University of Toronto)
Author: Tsai, Yi-Cheng
Institution: University of Toronto
Language: English
Subfield: Spectroscopy
Field: Chemistry
Domain: Physical Sciences
Open Access status: green
OpenAlex ID: W7132953403