Prion-based regulation of RNA-modifying enzyme activities

Project Summary/Abstract Prion proteins are notorious in biology for causing deadly, infectious brain diseases. Beyond disease, however, prions completely altered our understanding of heredity, and contrary to their reputation, they are not only disease-causing agents. Instead, they are found across kingdoms of life, and are an epigenetic mechanism that affects a panoply of cellular processes, also producing biologically beneficial traits. In this proposal we focus on prions that regulate RNA, specifically, prionogenic conformations of RNA- modifying enzymes. These highly conserved enzymes catalyze numerous chemical modifications on RNA that are critical for their structure and function. The goal of our research is to understand how prion-like forms of these enzymes may alter their activities on RNA, producing changes to gene expression, and ultimately, leading to long-lasting, heritable growth phenotypes, such as resistance to environmental stress. One recent such example that we have detailed is a prionogenic form of a pseudouridine synthase, which affects cell proliferation, aging, and protein synthesis. This work led us to investigate the capacity for other RNA-modifying enzymes to have prion-like behavior, and we now have several new examples for study. In this proposal, we will investigate whether RNA modifications are changed when the enzymes that make them adopt prion- like conformations, the effects these changes have on gene expression, the role for enzyme catalysis, the structure of the infectious prion protein, and whether the prion- based behavior that we have observed in budding yeast is conserved in human cells. We approach these questions using a combination of genetics, high-throughput sequencing, classical biochemical methods, and fluorescence microscopy. In summary, this work aims to uncover the molecular details of epigenetic, prion-based regulation of RNA that affects cell growth and survival.