Regulation and catalysis of mRNA molecules are important mechanisms for controlling gene expression. The conserved nonsense-mediated mRNA decay (NMD) pathway accelerates the decay of aberrant mRNAs containing premature translational termination codons. Inactivation of the yeast Saccharomyces cerevisiae NMD pathway also affects the accumulation of hundreds of wild-type mRNAs, which suggests that NMD has a second role regulating the expression of a significant number of wild-type genes. Wild-type PPR1 (pyrimidine pathway regulatory 1) mRNA encodes a transcription activator of the uracil metabolic genes and is degraded by the NMD pathway. The long-term goal of this research is to understand how wild-type PPR1 mRNA decay is controlled by the NMD pathway. The Principal Investigator has shown that decay of PPR1 mRNA depends on the same proteins that degrade nonsense mRNAs. Her laboratory also has identified a small region of PPR1 mRNA containing a cis-acting element, called the Upf1p-destabilizing element (UDE), that targets PPR1 mRNA for Upf1p-dependent decay by a novel mechanism. The central hypothesis is that the UDE functions with a downstream sequence element (DSE) to mark an RNA for Upf1p-dependent decay by serving as a trans-acting factor binding site. The UDE trans-acting factor(s) could act directly by interacting with general factors required for NMD to trigger the decay of PPR1 mRNA. Alternatively, the trans-acting factors could act indirectly by causing the ribosomes to shift to a new reading frame causing premature translational termination and then triggering the NMD of PPR1 mRNA. The overall objective of this project is to characterize the structure and function of the PPR1 UDE. This project will advance discovery and understanding of an important gene regulatory mechanism while promoting teaching, training, and learning by undergraduate students, graduate students and a post-doctoral candidate.
