The unfolded protein response (UPR) is a large-scale, coordinated response to correct misfolded proteins in eukaryotes. The diverse set of actions a cell coordinates in parallel (approx. 380 genes in yeast) to alleviate the various problems that can occur in protein synthesis, folding, glycosylation, and translocation of membrane-bound and secreted proteins has a large impact on therapeutic protein production and aggregated protein-related disease. The proposed work will map the biological information flow through the many genes involved in the response to achieve an understanding of the UPR and identify targets for altering the response. A biological interaction network of the UPR will be constructed from available biological interaction data for yeast. Transcriptional, proteomic, metabolomic, and metabolic flux data will be collected for recombinant yeast producing preinsulin and TNFa with modulated UPR induction. UPR- associated changes in biological molecule levels detected from the X-omics data will be superimposed onto the interaction network, revealing the flow of biological information in the UPR. This combination of information from biological interaction networks and X-omics-scale data will lead to a better understanding of secreted protein production. In particular, metabolite measurements can indicate possible limitations in glycosylation pathways, amino acid supply, energetics, redox balance, or lipid synthesis. Transcript and protein levels may reveal pathways that benefit or detract from high level secretion of protein. From this information, important biological molecules and interactions can be targeted to improve protein production and, in humans, identify targets to prevent/treat aggregated-protein related disease. The findings of the proposed work will be very helpful in understanding the molecules and their interconnections involved in stress response. This strategy represents a multifaceted approach to understanding a complex biological response and is consistent with the NIH Building Blocks, Biological Pathways, and Networks roadmap initiative. Yeast is an attractive commercial producer of therapeutic proteins, but can be limited by low product yields or poor quality that could be improved by this work. A thorough understanding of the UPR could have consequences for prevention and treatment of disease known to be related to aggregated protein, such as Alzheimer's, Type 2 diabetes, and apoptosis-resistant, uncontrolled protein production in certain cancers.
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