Modeling and Analysis of the Eukaryotic Unfolded Protein Response (UPR)

Proteins requiring post-translational modifications such as N-linked glycosylation are processed in the endoplasmic reticulum (ER). A diverse array of cellular stresses can lead to dysfunction of the ER and ultimately to an imbalance between protein-folding capacity and protein-folding load. Cells monitor protein folding by an inbuilt quality control system involving both the ER and the Golgi apparatus. Unfolded or misfolded proteins are tagged for degradation via ER associated degradation (ERAD) or sent back through the folding cycle. Continued accumulation of incorrectly folded proteins can also trigger the Unfolded Protein Response (UPR). In mammalian cells, UPR is a complex signaling program mediated by three ER transmembrane receptors: activating transcription factor 6 (ATF6), inositol requiring kinase 1 (IRE1) and double-stranded RNA-activated protein kinase (PKR)-like endoplasmic reticulum kinase (PERK). UPR performs three functions, adaptation, alarm and apoptosis. During adaptation, the UPR tries to reestablish folding homeostasis by inducing the expression of chaperones that enhance protein folding. Simultaneously, global translation is attenuated to reduce the ER folding load while the degradation rate of unfolded proteins is increased. If these steps fail, the UPR induces a cellular alarm and mitochondrial mediated apoptosis program. UPR malfunctions have been associated with a wide range of disease states including tumor progression, diabetes, as well as immune and inflammatory disorders.

Figure: The calnexin/calreticulin protein folding cycle. Yellow circles denote glucose groups and while blue circles denote mannose groups. After entering the ER lumen, glucosidase I and II remove two glucose groups. The monoglucosylated glycoprotein then interacts with calnexin/calreticulin. These chaperones interact with the thiol-disulphide oxidoreductase ERp57. Cleavage of the last glucose residue by glucosidase II leads to the release of the chaperones. At this time, the protein could have either folded and left the ER or it could have attained an incorrect state. The incorrectly folded proteins are then the substrates of UDP glucose:glycoprotein glucosyltransferase, which puts a glucose residue back to the incorrectly folded protein. This enables the protein to spend some more time in folding in the ER. If the protein fails to fold in a repeated number of cycles, the mannose residue is removed by α-1,2-mannosidase I. This enables the protein to be recognized by ER-degradation-enhancing 1,2-mannosidase-like protein (EDEM). This targets the unfolded proteins for ER-associated degradation (ERAD).