UBC Theses and Dissertations

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UBC Theses and Dissertations

Salmonella Typhimurium based genome-wide CRISPR/Cas9 knockout screen to study p16 degradation Dawo, Sebastian


The state of a cell and cell function is ultimately characterized by the expression of specific proteins. The equilibrium of a “healthy” amount of protein is maintained by the balance between newly generated proteins via translation and the degradation. Proteins half-life in eukaryotic cells can span from minutes to several days and are tightly controlled by the selective degradation of proteins via the ubiquitin-proteasome system. Finding specific genes that are involved in the degradation of a protein of interest harbours many applications for translational medicine, but also enables a better understanding of basic cellular biology. To enable such screens, we have established a FACS-based genome-wide CRISPR/Cas9 knockout screening platform, based on protein delivery via the type three secretion system (T3SS) of an avirulent strain of Salmonella typhimurium. We discovered that the delivered proteins are dynamically degraded following transfer, therefore this protein delivery system offers a suitable and unique approach to study protein degradation. As a proof of concept, we studied the poorly understood degradation of the key tumor suppressor protein p16, which additionally is lysine-free, contradicting a longstanding concept that canonical ubiquitin is conjugated to a lysine residue. The screen yielded several promising candidate genes including genes of the Torsin family, the Sec62/63 complex, and COPS6. Validation of the candidate genes uncovered THAP1 as a potential general regulator of protein degradation. We anticipate this method will offer novel mechanistic insights into the degradation of intracellularly delivered proteins and might uncover new pathways of protein homeostasis.

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