Co-translational mRNA surveillance by the ER stress sensor, IRE1.

IRE1, a membrane protein in the endoplasmic reticulum (ER) monitors the protein folding status of the ER and corrects the buildup of misfolded proteins. This process termed the unfolded protein response is responsible for the maintenance of protein homeostasis in all eukaryotic cells. IRE1 issues corrective action by two main pathways; by upregulation of chaperones through cleavage and expression of XBP1, a transcription factor and by reducing the burden of ER-targeted proteins by cleaving mRNAs. How IRE1 senses mRNAs in close proximity for cleavage is currently unknown. Recent work from our lab suggests that IRE1 interacts with the co-translational machinery directly possibly sensing mRNAs on the ribosome but molecular details of this interaction are lacking. Here we present the composition of ribosomes that engage with IRE1 in mammalian cells using single-particle cryoEM. Under steady conditions, IRE1 interacts with translating ribosomes surveilling the mRNA for the presence of a consensus endomotif. However, under ER stress IRE1 engages with predominantly stalled ribosomes. IRE1 binds the mRNA entry channel engaged with ribosomal proteins. Finally, through next-generation sequencing we identified a core set of ER-targeted mRNAs that are recognized by IRE1. Our results reveal the mechanistic details of IRE1 interacting with the co-translational machinery.