The Upf proteins that promote nonsense-mediated mRNA decay (NMD) are best known for their role in RNA surveillance, a mechanism that eliminates aberrant transcripts that arise primarily through errors in gene expression. In this research, the principal investigators plan to investigate the role of the Upf proteins in controlling the levels of expression of a substantial subset of protein-coding genes in S. cerevisiae, but for purposes unrelated to RNA surveillance. Recently, the mRNA targets of NMD were identified by a global estimation of RNA decay rates. About one third of the targeted mRNAs produce proteins known to affect either chromosome or cell surface dynamics. Experiments are planned leading to a possible connection between NMD and the environmental stress response (ESR). In ESR, yeast cells adapt to suboptimal environments through global changes in the gene expression program. Like the transcripts affected by NMD, many of the transcripts affected by the ESR code for proteins that influence chromosome and cell surface dynamics. The levels of the transcripts coding for the Upf proteins do not change as part of the ESR. However, NMD might be connected to the ESR through post-translational protein modifications that respond to changes in environmental conditions. Two proteins required for NMD, Upf1p and Upf2p, are phosphoproteins. The principal investigators plan to test the model that the natural mRNA targets of NMD and the ESR are inter-connected through the phosphorylation of Upf proteins and that Upf phosphoproteins may function as ESR sensors. The big unanswered question about NMD is whether the Upf proteins dynamically regulate gene expression in response to the environment.
This project is of general significance to the public because the NMD pathway exists in humans and it has been shown that about one third of all human genetic disorders are caused by mutations that are affected by NMD. In addition, the research contains a plan for integrating research and education by focusing on a group of students who are underserved, under-represented and all but invisible to the academic community - learning disabled (LD) students. Each summer, one LD undergraduate from the UW-Madison campus will be offered a nine week supervised summer research experience in the lab working on experiments in this proposal. The students will be identified through collaboration with the UW McBurney Disability Resource Center. Students will join an existing summer program organized by the UW Center for Biology Education, the "Summer Research Program" (undergraduates from under-represented groups). The summer research experiences will encourage LD students to pursue advanced degrees and professional careers in science. Inclusion of LD students who typically think out of the box and approach problems using alternative learning styles will enhance science and their contributions will benefit society.
NSF MCB 0744017 Outcomes Proteins catalyze and control most of the biochemical reactions in cells. Since proteins function in the context of protein-protein interactions, the amounts of proteins produced are critical to their function and vary according to cell type. The amounts of proteins produced in cells broadly represent the so-called level of gene expression. Genes that code for proteins are transcribed to produce messenger RNA (mRNA), and mRNA is then translated by organelles called ribosomes to produce proteins. Regulation of gene expression from DNA to RNA to protein occurs at many levels, but can be broadly divided into regulation of synthesis and regulation of decay of key molecules in the pathway. In general, proteins levels are a composite of the rates of synthesis and decay. In my laboratory, we study the regulation of the rates of mRNA decay and focus on a specialized pathway called nonsense-mediated mRNA decay (abbreviated NMD). The NMD pathway is directly tied to the ability of ribosomes to translate mRNA, where impairments that prevent translation of mRNA by ribosomes lead to accelerated mRNA decay. We have identified genes that control NMD in yeast, a single-celled model organism. NMD can be thought of as a molecular switch that determines whether translation produces a protein product or alternatively whether the mRNA is broken down and destroyed. NMD regulates the expression of hundreds of endogenous genes at the level of mRNA decay in yeast. We have made progress in understanding the mechanism of NMD in yeast, including how the decay pathway is linked to translation. Our interests are also directed at understanding the biological purpose of the pathway, which we believe may be tied to mechanisms for how yeast cells respond to environmental stress. Our progress is represented in eight published papers that were supported by this grant. The NMD pathway is known to exist in humans. The genes that control NMD in yeast have direct counterparts that have been identified in humans. NMD has an impact on the expression of human genes that carry disease-causing mutations. About one third of the mutations in such genes trigger NMD because they disrupt translation. The result is a decrease in gene expression, which aggravates the severity of clinical outcomes due to the reduced protein levels caused by NMD. By studying yeast as an experimentally tractable organism, we have expanded the base of fundamental information about the molecular biology of NMD. Our work provides the basis for greater knowledge of molecular mechanisms that control gene expression and provides further knowledge that will impact the understanding of genetic disorders in humans. The broader impact of the grant was focused on providing research opportunities for undergraduate students with hidden disabilities. Two female students with documented disabilities were trained. They participated through mentored research working on average about ten hours per week in my laboratory over a period of several years each. Both have now graduated. One of them is enrolled as a medical student at the University of Wisconsin School of Medicine and Public Health, and the other is employed in the biotechnology industry.
