A chemical-genetic screen for identifying substrates of the ER kinase PERK

Cells constantly encounter changing environments that challenge the ability to adapt and survive. Signal transduction networks enable cells to appropriately sense and respond to these changes, and are often mediated through the activity of protein kinases. Protein kinases are a class of enzyme responsible for regulating a broad spectrum of cellular functions by transferring phosphate groups from ATP to substrate proteins, thereby altering substrate activity and function. PERK is a resident kinase of the endoplasmic reticulum, and is responsible for sensing perturbations in the protein folding capacity of the ER. When the influx of unfolded, nascent proteins exceeds the folding capacity of the ER, PERK initiates a cascade of signaling events that enable cell adaptation and ER stress resolution. These signaling pathways are not only essential for the survival of normal cells undergoing ER stress, but are also co-opted by tumor cells in order to survive the oxygen and nutrient-restricted conditions of the tumor microenvironment. Not surprisingly, PERK signaling is known to influence a variety of pro-tumorigenic processes. Therefore, from a purely biological standpoint as well as from a clinical perspective, it is important to understand this critical cell adaptive pathway in greater detail through identifying its interacting partners and thereby elucidating additional downstream signaling branches. Prior to the work described herein, only three direct PERK substrates had been identified. Using chemical-genetic screening techniques, we have generated a significant list of putative PERK substrates, several of which have been confirmed as PERK substrates in vitro. These preliminary results suggest new connections between known UPR pathways, as well as entirely novel signaling branches downstream of PERK. This work will provide a solid foundation for launching future PERK-related discovery studies. This dissertation is available at ScholarlyCommons: http://repository.upenn. edu/edissertations/1354 Degree Type Dissertation Degree Name Doctor of Philosophy (PhD) Graduate Group Cell & Molecular Biology First Advisor Alan Diehl Subject Categories Biology | Cell Biology | Molecular Biology This dissertation is available at ScholarlyCommons: http://repository.upenn. edu/edissertations/1354 A CHEMICAL-GENETIC SCREEN FOR IDENTIFYING SUBSTRATES OF THE ER KINASE PERK Nancy L. Maas A DISSERTATION in Cell and Molecular Biology Presented to the Faculties of the University of Pennsylvania in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy 2014 Supervisor of Dissertation _________________ J. Alan Diehl, Ph.D., Professor of Cancer Biology Graduate Group Chairperson _________________ Daniel S. Kessler, Ph.D., Associate Professor of Cell and Developmental Biology Dissertation Committee Roger A. Greenberg, M.D., Ph.D., Assistant Professor of Cancer Biology M. Celeste Simon, Ph.D., Professor of Cell and Developmental Biology F. Bradley Johnson, M.D., Ph.D., Assistant Professor of Pathology and Laboratory Medicine Eric S. Witze, Ph.D., Assistant Professor of Cancer Biology