The role of pseudouridine synthases in autophagy

Oakland University received a $562,320 Project Grant from the National Institute of General Medical Sciences (NIGMS) under the Biomedical Research and Research Training program (CFDA 93.859), effective September 1, 2025 through August 31, 2028. This award supports fundamental biomedical research investigating the role of pseudouridine synthases in autophagy—a critical cellular degradation and recycling pathway essential for cell survival under stress conditions. The research addresses a significant gap in understanding the molecular mechanisms that regulate autophagy, which involves more than 40 autophagy-related genes conserved from yeast to humans.

The project delivers scientific research aimed at elucidating how pseudouridine synthases regulate autophagy, with implications for understanding cellular responses to environmental stress and disease pathogenesis. This basic research contributes to NIGMS's mission of advancing understanding of biological processes and establishing foundational knowledge for disease diagnosis, treatment, and prevention. Aberrant autophagy is associated with diverse human pathologies including neurodegeneration, cancer, and metabolic disorders; therefore, clarifying autophagy regulation mechanisms advances the scientific foundation necessary for developing therapeutic interventions and synthetic cellular applications in biomedical contexts.

Abstract

The balance between cell death and survival is a critical factor for maintaining human health. Cells must rapidly adapt to stress conditions within their environment to survive. Cytoprotective measures require the cell to process stimuli, and often, alter gene expression within regulatory circuits. The ability to design and build synthetic cells for innovative biomedical applications requires a complete understanding of how critical cellular pathways are regulated. However, a comprehensive model for how a single cell functions has remained elusive. This GAP in knowledge is a major barrier to developing synthetic cells for biomedical purposes. Thus, there is an urgent need to elucidate molecular mechanisms required for cell survival. Macroautophagy/autophagy is an essential mechanism that preserves cell health under homeostatic conditions and supports survival under stress. Autophagy is a dynamic pathway of cellular degradation and recycling that is conserved from yeast to humans. Basal autophagy is low, but is markedly upregulated during stressful conditions. At present, >40 autophagy- related (ATG) genes have been identified in yeast; many of these genes are conserved in humans. This complexity requires the cell to maintain precise control over autophagy at multiple regulatory levels. Despite this need for strict regulation, much remains unknown about how autophagy is fine-tuned in the cell. In humans, perturbation of autophagy can have deleterious effects on cell health and survival, contributing to disease pathogenesis. In fact, aberrant autophagy is associated with diverse human pathologies such as neurodegeneration, cancer, and lysosomal storage and metabolic disorders. The rationale for this project is that there is a GAP in our understanding of the molecular mechanisms driving responses necessary for cell survival under stress conditions. Our objective is to determine the role(s) of pseudouridine synthases (PUS7 and PUS4) in nonselective and selective autophagy. PUS enzymes catalyze the RNA-independent isomerization of uridine to pseudouridine (ψ). Our hypothesis has been developed based on preliminary data that was generated using the budding yeast model system. The yeast system provides numerous advantages, including the ability to perform biochemical and molecular genetic experiments quickly and easily, and in ways that are suitable to actively engage undergraduate students in authentic biomedical research. Since autophagy is highly conserved from yeast to humans, we expect that our findings from this project can be applied to furthering our understanding of cell survival in humans. This project will increase the participation of undergraduates in a rewarding biomedical research experience at oakland university, which is in the detroit metro area. This project is innovative because IT provides insight into the mechanistic role(s) of PUS7 and PUS4 in cell responses to stress and uses innovative approaches to do so. The proposed work is significant because IT advances our knowledge of the physiological roles of PUS enzymes in cells and how cells dynamically respond to environmental stress. This project will generate fundamental knowledge required for understanding cell survival mechanisms under stress conditions.