Structural Biochemistry/Proteins/Unfolded Protein Response

Unfolded Protein Response (UPR) is a response to cellular stress that is related to the endoplasmic reticulum (ER) in mammalian species, but has also been found in yeast and worms.

When ER conditions are disrupted (such as alterations of redox state, calcium levels, failure to posttranslationally modify secretory proteins, etc.) or the chaperone proteins that assist protein folding is overcapacity (both are considered ER stress), the cell launches signals that try to deal with these changes and make a favorable folding environment. When the UPR is not sufficient to deal with this stress, apoptotic cell death happens.

Introduction
The ER lumen's environment is made so that it favors the production of secretory and membrane proteins and a good amount of these proteins are rapidly degraded which is probably due to improper protein folding. This would pose a problem for the cell due to a possibility of misfolded protein buildup. This would be even more of a problem if the changes in this environment would occur. These changes will deter the overall ability to make properly folded proteins and more improper proteins will build.

UPR monitors and responds to changes in the ER protein folding environment. It monitors the protein-folding capacity of the ER and sends signals of cell responses to help maintain the folding capacity to prevent a buildup of unwanted protein products. For mammals, this response is the transient inhibition of protein synthesis to hinder the production of new proteins, followed by transcriptional induction of chaperone genes to initiate protein folding and induction of the activation of the ER-associated degradation system. If this process fails, then the UPR tells the cell to go to a destructive pathway. The UPR has three main signaling systems: (IRE1), PERK, and ATF6.

IRE1 Pathway
IRE1 is a type I transmembraned protein that contained serine/threonine kinase activity as a stress sensor. Once activated, the enodribonuclease activity in the carboxyl terminus of IRE1 catalyzes splicing of the HAC1 (which is responsible for inducing the expression of ER stress response genes) mRNA.

In yeast organisms, the IRE1 contains nuclear localization sequences in the carboxyl terminus, which can interact with components of nuclear pore complex and target IRE1 to the inner nuclear membrane. The result is that the COOH-terminal domain is now facing the inside of the nucleus and can now have access to nuclear mRNA. HAC1 then moves into the nucleus and binds to a promotor element to induce the expression of genes required for various reactions.

In mammals, the IRE1 pathway is like that of yeast, except that two IRE1 genes have been cloned. Alpha and Beta -IRE1. It does not contain nuclear localization sequences like in yeast IRE1. IRE1 has also shown to mediate cleavage of additional mRNAs targeted to the endoplasmic reticulum as well as cleavage of the 28S ribosomal subunit. This leads to the beliefe that IRE1 has a role in translation attenuation by degrading these mRNA transcripts and/or the ribosomal subunits.

PERK Pathway
When undergoing ER stress, the first response is transient global translation attenuation and this is mediated by PERK. PERK is a type I ER-resident transmembrane protein that detects stress though its lumenal domain. It also binds to chaperone protein Grp78, but when unfolded proteins start to build up during ER stress, this protein Grp78 starts to dissociate and PERK then autophosphorylates and dimerize. Once activated, PERK phosphorylates serine-51 of eukaryotic initiation factor 2α (eIF2α). eIF2α is unable start translation when phosphorylated, and this leads to inhibition of global protein synthesis. In reverse, phosphorylated eIF2α initiates translation of ATF4 mRNA. ATF4 upregulates ER stress genes. Translational recovery is mediated by the stress-induced phophatase growth arrest and DNA damage-inducible gene.

ATF6 Pathway
ATF6 exist in to isoforms (alpha and beta ATF6). These have fairly balanced tissue distributions. ATF6 pathway activation involves a mechanism called regulated intramembrane proteolysis (RIP). In RIP, the protein translocates from the ER to the Golgi for proteolytic processing. The stress-sensing mechanism of ATF6 dissociates the Grp78 from its lumenal domain (This is similar to the processes of IRE1 and PERK pathways). Frp78 signals to two Golgi localization signals to allow ATF6 to enter the COPII vesicles to translocate the Golgi compartment. Disulfide bonds in ATF6 lumenal domain are also believed to keep ATF6 inactive. During ER stress disulfide bonds are reduced and an increase ability of ATF6 to exit arises.

Apoptosis
The three UPR pathways do not only contribute to fixing of improperly folded proteins, it also as can contribute to a cell's apoptosis if the UPR fails to restore folding capacity.