Endoplasmic Reticulum Membrane Homeostasis and the Unfolded Protein Response

Abstract

The endoplasmic reticulum (ER) is the key organelle for membrane biogenesis. Most lipids are synthesized in the ER, and most membrane proteins are first inserted into the ER membrane before they are transported to their target organelle. The composition and properties of the ER membrane must be carefully controlled to provide a suitable environment for the insertion and folding of membrane proteins. The unfolded protein response (UPR) is a powerful signaling pathway that balances protein and lipid production in the ER. Here, we summarize our current knowledge of how aberrant compositions of the ER membrane, referred to as lipid bilayer stress, trigger the UPR.

Figure 1

Lipid composition of the endoplasmic reticulum (ER) from Saccharomyces cerevisiae and HeLa cells. The lipid class composition (A), the unsaturation of phosphatidylcholine (PC) species (B), and total acyl chain length of PC species as the sum of Catoms in both fatty acyl chains (C) are given as relative abundance (in mol%). (This figure is based on data in Reinhard et al. 2022 and Sokoya et al. 2022 for the yeast and mammalian ER, respectively.)

Figure 2

The three branches of the unfolded protein response (UPR) in mammalian cells. The UPR in mammalian cells has three branches, relying on the stress sensors IRE1, PERK, and ATF6. Each branch regulates the expression of specific UPR target genes by activating branch-specific transcription factors. IRE1 interacts with the endoplasmic reticulum (ER) chaperone BiP and forms monomers and dimers in resting cells. ER stress stabilizes IRE1 dimers and higher oligomers, thereby activating the cytosolic kinase “K” and RNase “R” domains. The activated RNase domain removes an intron from XBP1 mRNA and initiates unconventional splicing that yields spliced XBP1 mRNA (XBP1S). Translation of the matured mRNA yields the XBP1 transcription factor. Like IRE1, PERK is activated by oligomerization. Dimerization and the formation of higher order oligomers activate the cytosolic kinase domain. Phosphorylation of the eukaryotic initiation factor 2α (eIF2α) decreases global transcription via the integrated stress response, but selectively promotes the production of the transcription factor ATF4. ATF6 is a membrane-tethered basic leucine-zipper transcription factor. During ER stress, a specific disulfide-linked ATF6 dimer of the redox-sensitive protein is transported to the Golgi complex, where it is proteolytically cleaved bysite-1 and site-2 proteases (S1P, S2P), releasing the soluble p50 transcription factor (ATF6p50). The ER chaperone BiP (blue) interacts with all three UPR transducers in the unstressed ER.

Figure 3. Sensing proteotoxic stress by IRE1.

(A) Crystal structures of the lumenal domains of yeast (green) and mammalian (blue) IRE1, as determined by Credle et al. (2005) and Zhou et al. (2006), respectively. Cartoon models (left) and surface models (right) are depicted. The interfaces for dimerization (dashed line) and oligomerization (arrowheads) are indicated in the cartoons. (B) Oligomerization of IRE1α can shape the endoplasmic reticulum (ER) into constricted tubes. The ER–luminal domains of dimeric IRE1α serves as a proteinaceous zipper that juxtaposes two ER membranes. (C) Segmented tomograms showing normal ER (bright orange) and constricted ER membranes that colocalize with IRE1. Scale bar, 100 nm. (Tomogram is adapted, with permission, from Tran et al. 2021.) (D) Three models of proteotoxic stress sensing by IRE1, as explained in the text. The ER chaperone BiP and accumulated unfolded proteins are depicted in blue and red, respectively.

Figure 4. Sensing of lipid bilayer stress.

(A) A diverse set of lipid metabolic perturbations triggers the unfolded protein response (UPR) by a membrane-based mechanism. Inositol depletion, increased abundances of tightly-packing, saturated lipids, increased levels of cholesterol and reduced PC-to-PE ratios cause lipid bilayer stress. (B) ScIRE1 (green) uses a hydrophobic mismatch-based mechanism for sensing ER membrane compressibility. With its short transmembrane helix and an adjacent amphipathic helix, ScIRE1 induces a local membrane thinning and establishes an ellipsoid membrane footprint (orange and red color). Increased membrane thickness and reduced compressibility provide a driving force for ScIRE1 oligomerization. Upon dimerization, the total area of the membrane distortion is minimized, and large parts of the membrane footprints coalesce where the transmembrane helices “meet.” Compared to unrelated, single-pass membrane proteins (blue), ScIRE1 gains more free energy upon dimerization because a much larger distorted membrane region coalesces. The cytosolic side of the ER membrane is labeled C, the luminal side L.