Cellular & Molecular Engineering Laboratory

Analysis and Modeling of The Unfolded Protein Response in Yeast

Our research program ties both experimental analysis of the interactions within the ER and modeling in order to understand how these interactions effect UPR dynamics. Initial experiments focused on the ER have examining the role of Kar2, the yeast homolog of BiP. In particular, we have tested the effect of Kar2 overexpression on the UPR under various stresses. In vivo experiments have utilized a published UPRE-GFP gene construct for readout of the UPR. Results show that Kar2 overexpression provides some relief to the accumulation of unfolded proteins from both chemical induction of unfolded proteins (DTT, Tunicamycin) and overexpression of secreted proteins. However, the small decrease in UPR seen in cells overexpressing Kar2 is inconsistent with a model where a pool of free Kar2 binding to Ire1p. In such a model a large excess of Kar2 should result in complete inhibition of the UPR under mild stress. Alternative models for Bip-Ire1p interaction are examined in the context of this initial data. These models focus on BiP interactions in other ER processes and the effect of various co-chaperones. A current "work in progress" model of the UPR contains 48 parameters and 106 dynamic states spread across 3 compartments (ER, nucleus, and cytoplasm). Improving the ER portion of the model has been the experimental focus. Further experimentation in testing of the models is considered.

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