Structure and Molecular Mechanism of ER Stress Signaling by the Unfolded Protein Response Signal Activator IRE1

Abstract

The endoplasmic reticulum (ER) is an important site for protein folding and maturation in eukaryotes. The cellular requirement to synthesize proteins within the ER is matched by its folding capacity. However, the physiological demands or aberrations in folding may result in an imbalance which can lead to the accumulation of misfolded protein, also known as "ER stress." The unfolded protein response (UPR) is a cell-signaling system that readjusts ER folding capacity to restore protein homeostasis. The key UPR signal activator, IRE1, responds to stress by propagating the UPR signal from the ER to the cytosol. Here, we discuss the structural and molecular basis of IRE1 stress signaling, with particular focus on novel mechanistic advances. We draw a comparison between the recently proposed allosteric model for UPR induction and the role of Hsp70 during polypeptide import to the mitochondrial matrix.

Keywords: BiP; ER stress; Hsp70; IRE1 inositol-requiring enzyme 1; crystal structures; unfolded protein response (UPR).

Figure 1

Overview of UPR signaling pathway. The UPR instigates a transcriptional and translational response to ER stress. The three UPR activator proteins, IRE1, PERK, and ATF6 give rise to three separate branches of the response, all of which aim to alleviate the burden of misfolded protein and to ensure successful ER protein homeostasis.

Figure 2

Crystal structures of LD. (A) The dimer arrangement of IRE1 LD from both yeast (PDB 2BE1) and human (PDB 2HZ6) proteins, with dimer interface marked by dashed line. (B) PERK LD dimer structure shares similar architecture to IRE1 LD. PERK LD has also been visualized in a tetramer arrangement comprising two sets of dimers (PDB 4YZS and 4YZY), and PERK LD bound to peptide (PDB 5V1D).

Figure 3

A schematic representation of ER stress-sensing mechanisms. (A) Direct association model posits that misfolded proteins bind directly to IRE1 LD, resulting in oligomerization of IRE1 and activation of UPR. (B) In the competition model, IRE1 LD binds to BiP SBD in a chaperone-substrate type interaction. This is the same site that misfolded proteins bind to BiP, leading to a competition for this binding site. BiP interaction to IRE1 is mediated by ERdj4, which ultimately inhibits UPR signaling by facilitating the formation of IRE1 LD monomer. Thus, BiP acts as a repressor of UPR signaling, but is not a direct sensor of ER stress. (C) In the allosteric model, the binding of misfolded proteins and IRE1 LD to BiP occur on different domains; thus, obviating the requirement for competition. Misfolded protein binding induces a conformational change that releases BiP from IRE1, implicating BiP as a direct sensor of ER stress.

Figure 4

Crystal structures of IRE1 cytosolic domain. (A) Schematic depicting the IRE1 cytosolic portion in a face-to-face dimer (PDB 3P23) that enables trans autophosphorylation, and in a back-to-back arrangement (PDB 2RIO), which is suggested to be the RNase active state. The red arrow represents the transition between these two states. (B) A comparison of crystal structures of IRE1 RNase domain when bound to a kinase inhibitor that prevents both kinase and RNase activation (gold, PDB 4YZ9) and when bound to a kinase inhibitor that activates RNase domain (cyan, PDB 4YZC). The small movements within the domain are suggested to enhance splicing activity.