Document Type


Date of Degree

Summer 2016

Degree Name

PhD (Doctor of Philosophy)

Degree In

Molecular and Cell Biology

First Advisor

Rutkowski, D. Thomas

First Committee Member

Sigmund, Curt D.

Second Committee Member

Moye-Rowley, William S.

Third Committee Member

Dupuy, Adam J.

Fourth Committee Member

Elcock, Adrian H.


The unfolded protein response (UPR) is activated by protein misfolding stress in the endoplasmic reticulum (ER). The UPR is a transcriptional program that aims to maintain ER folding capacity, where imbalances between protein load and processing ability is termed ER stress. Signal transduction of the UPR begins with 3 ER-resident transmembrane sensors: PERK, IRE1 and ATF6. All sensors initiate downstream signaling cascades which culminate in improved protein folding, transcriptional upregulation of genes encoding ER chaperones, and mechanisms to reduce translational and transcriptional ER load, therefore re-establishing ER homeostasis. The signaling cascades of each sensor are distinct but cooperative, and involve a significant amount of crosstalk, feedback and overlap. Indeed, there are many pathological and physiological conditions have an effect on ER protein burden, and therefore on activation of the UPR. Increases in protein load in professional secretory cells, hypoxic conditions in a tumor mass, obesity all induce cause changes in the ER folding environment.

Although we understand how the UPR contributes to relieve ER stress under acute conditions (e.g. pharmacological treatment) much less is understood about the contributions to physiological processes and chronic stress conditions. Our overall goal was to understand how the UPR is activated during physiological settings, the mechanisms it uses to maintain folding capacity under these setting and the specific components responsible for adapting the response to various stresses.

We first decided to understand a chronic stress from a transgenic approach. By creating a knockout mouse, the genetic deletion functions as a stress and we can understand its physiological role. By compounding two genetic deletions in UPR components (ATF6α and p58IPK) we provide evidence for the developmental role these components play. Homozygous deletion ATF6α bears no gross histological phenotype yet causes synthetic lethality when combined with p58IPK deletion. This also reveals that the UPR is able to adapt to genetic impairment of protein folding in vivo.

Next, to better understand these chronic states, we established an experimentally tractable chronic stress treatment in vivo. Our treatment suppressed ATF6α dependent chaperone expression through an mRNA degradative mechanism, which led to long term changes in UPR expression. We determined that chronic conditions can change the sensitivity of the UPR to ER stress, potentially as an adaptive consequence. We also showed that sensitivity to ER stress can be changed during chronic stress.

Finally we simulated the UPR in a computational ordinary differential equation (ODE) model in order to determine how various stresses and component interactions determine the output of the UPR. We built a series of equations to describe the UPR signaling network, entrained it on experimental data and refined it through the use of transgenic knockout cells. Our model was robust enough to recreate experimental measurements of UPR components when tested in parallel with knockout cells. We found that stress sensitivity is dependent on the crosstalk and negative feedback connections of the UPR.

This study has enhanced our understanding of activation of the UPR under non-acute settings. It demonstrates that the UPR is a signaling hub with a broad output range that is capable of handling a variable degree of insults because of the intrinsic properties of the signaling network. This provides a better understanding for the contributions of the UPR to physiological stresses and certain chronic diseases.


Chronic Stress, Computer Modeling, Liver, Mouse Model, Unfolded Protein Response


xiii, 113 pages


Includes bibliographical references (pages 94-109).


Copyright © 2016 Javier Alejandro Gomez Vargas

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Cell Biology Commons