The unfolded protein response and endoplasmic reticulum protein targeting machineries converge on the stress sensor IRE1

Elife. 2018 Dec 24:7:e43036. doi: 10.7554/eLife.43036.

Abstract

The protein folding capacity of the endoplasmic reticulum (ER) is tightly regulated by a network of signaling pathways, known as the unfolded protein response (UPR). UPR sensors monitor the ER folding status to adjust ER folding capacity according to need. To understand how the UPR sensor IRE1 maintains ER homeostasis, we identified zero-length crosslinks of RNA to IRE1 with single nucleotide precision in vivo. We found that IRE1 specifically crosslinks to a subset of ER-targeted mRNAs, SRP RNA, ribosomal and transfer RNAs. Crosslink sites cluster in a discrete region of the ribosome surface spanning from the A-site to the polypeptide exit tunnel. Moreover, IRE1 binds to purified 80S ribosomes with high affinity, indicating association with ER-bound ribosomes. Our results suggest that the ER protein translocation and targeting machineries work together with the UPR to tune the ER's protein folding load.

Keywords: IRE1; RNA-protein interactome; cell biology; co-translational protein targeting; endoplasmic reticulum; human; ribosome; unfolded protein response.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Endoplasmic Reticulum / metabolism*
  • Endoribonucleases / metabolism*
  • HEK293 Cells
  • Humans
  • Protein Binding
  • Protein Folding
  • Protein Serine-Threonine Kinases / metabolism*
  • Protein Transport
  • RNA / metabolism
  • Ribosomes / metabolism
  • Unfolded Protein Response*

Substances

  • RNA
  • ERN1 protein, human
  • Protein Serine-Threonine Kinases
  • Endoribonucleases