UCSF

The endoplasmic reticulum (ER) is the compartment in eukaryotic cells in which secreted and membrane-spanning proteins are folded, modified and assembled. These proteins are the means by which cells sense and respond to their environment and neighboring cells. Thus it is vital that these proteins fold into their appropriate structures so they can function properly. When cells are exposed to various environmental stresses, mutations or differentiation cues, the ER protein folding machinery can become overwhelmed, a condition known as ER stress. During ER stress unfolded and misfolded proteins accumulate in the ER, eliciting an intracellular signaling pathway called the unfolded protein response (UPR) that functions as a feedback loop to restore homeostasis to protein folding in the ER.

The UPR is an ancient pathway found in all organisms with an ER. The most conserved component of the UPR is Ire1, an ER-resident transmembrane protein that contains a domain in the ER lumen that senses unfolded proteins and effector kinase and RNase domains in the cytosol that initiate the response. In most organisms misfolded proteins in the ER activate Ire1 to initiate a nonconventional mRNA splicing reaction. Splicing results in the production of a transcription factor that induces UPR target genes to increase the folding capacity of the ER and thereby relieve the stress.

In the work compiled in this thesis, we find that maintaining homeostasis in the ER requires not only that Ire1 activates specifically, but also that Ire1 deactivates efficiently. Activation and deactivation of the UPR are regulated at the level of Ire1 oligomerization on both sides of the ER membrane. Binding to unfolded proteins drives oligomerization while de-oligomerization is aided by binding to the chaperone protein BiP in the lumen of the ER (Chapter 2) and Ire1's kinase activity in the cytoplasm (Chapter 3). Unmitigated UPR signaling imposes a fitness cost on cells (Chapter 4) underscoring the need for such deactivation mechanisms. Similar deactivation mechanisms may play underappreciated roles in controlling activity in many signaling pathways and stress responses.