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Related Concept Videos

Regulation of the Unfolded Protein Response01:31

Regulation of the Unfolded Protein Response

Inositol-requiring kinase one or IRE1 is the most conserved eukaryotic unfolded protein response (UPR) receptor. It is a type I transmembrane protein kinase receptor with a distinctive site-specific RNase activity. As the binding mechanics of the misfolded proteins with the N-terminal domain of IRE-1 are unclear, three binding models — direct, indirect, and allosteric -- are proposed for receptor activation. Nevertheless, it is known that once a misfolded protein associates with IRE1, it...
RNA Interference01:23

RNA Interference

RNA interference (RNAi) is a process in which a small non-coding RNA molecule blocks the post-transcriptional expression of a gene by binding to its messenger RNA (mRNA) and preventing the protein from being translated.
This process occurs naturally in cells, often through the activity of genomically-encoded microRNAs. Researchers can take advantage of this mechanism by introducing synthetic RNAs to deactivate specific genes for research or therapeutic purposes. For example, RNAi could be used...
RNA Interference01:23

RNA Interference

RNA interference (RNAi) is a process in which a small non-coding RNA molecule blocks the post-transcriptional expression of a gene by binding to its messenger RNA (mRNA) and preventing the protein from being translated.
This process occurs naturally in cells, often through the activity of genomically-encoded microRNAs. Researchers can take advantage of this mechanism by introducing synthetic RNAs to deactivate specific genes for research or therapeutic purposes. For example, RNAi could be used...
Experimental RNAi02:15

Experimental RNAi

RNA interference (RNAi) is a cellular mechanism that inhibits gene expression by suppressing its transcription or activating the RNA degradation process. The mechanism was discovered by Andrew Fire and Craig Mello in 1998 in plants. Today, it is observed in almost all eukaryotes, including protozoa, flies, nematodes, insects, parasites, and mammals. This precise cellular mechanism of gene silencing has been developed into a technique that provides an efficient way to identify and determine the...
Ribozymes02:47

Ribozymes

The term ribozyme is used for RNA that can act as an enzyme. Ribozymes are mainly found in selected viruses, bacteria, plant organelles, and lower eukaryotes. Ribozymes were first discovered in 1982 when Tom Cech’s laboratory observed Group I introns acting as enzymes. This was shortly followed by the discovery of another ribozyme, Ribonulcease P, by Sid Altman’s laboratory. Both Cech and Altman received the Nobel Prize in chemistry in 1989 for their work on ribozymes.
Ribozymes can be...
RNA Structure01:23

RNA Structure

Overview
The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA): messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three RNA types consist of a...

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Analysis of RNA Processing Reactions Using Cell Free Systems: 3' End Cleavage of Pre-mRNA Substrates in vitro
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Structural and functional basis for RNA cleavage by Ire1.

Alexei V Korennykh1, Andrei A Korostelev, Pascal F Egea

  • 1Howard Hughes Medical Institute, University Of California, San Francisco, Genentech Hall, 600-16th Street, San Francisco, CA 94158, USA. akorenny@princeton.edu

BMC Biology
|July 7, 2011
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Summary

Researchers elucidated the Ire1 RNase active site mechanism, identifying key residues for RNA cleavage and revealing new substrate specificities, including tRNA. This advances understanding of the unfolded protein response pathway.

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Electrophoretic Mobility Shift Assay (EMSA) for the Study of RNA-Protein Interactions: The IRE/IRP Example
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Last Updated: May 31, 2026

Analysis of RNA Processing Reactions Using Cell Free Systems: 3' End Cleavage of Pre-mRNA Substrates in vitro
09:16

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Electrophoretic Mobility Shift Assay (EMSA) for the Study of RNA-Protein Interactions: The IRE/IRP Example
12:44

Electrophoretic Mobility Shift Assay (EMSA) for the Study of RNA-Protein Interactions: The IRE/IRP Example

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Single-step Purification of Macromolecular Complexes Using RNA Attached to Biotin and a Photo-cleavable Linker
08:12

Single-step Purification of Macromolecular Complexes Using RNA Attached to Biotin and a Photo-cleavable Linker

Published on: January 3, 2019

Area of Science:

  • Molecular Biology
  • Biochemistry
  • Structural Biology

Background:

  • The unfolded protein response (UPR) regulates endoplasmic reticulum (ER) protein folding.
  • Ire1, an ER-resident kinase/endoribonuclease, is central to UPR signaling.
  • Ire1 RNase activity mediates mRNA splicing for UPR target gene regulation.

Purpose of the Study:

  • To experimentally define the active site of Ire1 RNase.
  • To quantitatively assess the role of key active site residues in catalysis.
  • To understand the mechanism of Ire1-mediated RNA cleavage.

Main Methods:

  • X-ray crystallography to determine Ire1 structures.
  • Quantitative enzymological analysis of Ire1 RNase activity.
  • Site-specific RNA cleavage assays.

Main Results:

  • Identified histidine H1061 and tyrosine Y1043 as a catalytic acid-base pair.
  • Determined asparagine N1057 and arginine R1056 coordinate the scissile phosphate.
  • Discovered Ire1 RNase cleaves anticodon stem-loop (ASL) of unmodified tRNAPhe, expanding substrate specificity.

Conclusions:

  • Defined the catalytic center of Ire1 RNase, with each monomer possessing a catalytic apparatus.
  • Proposed a mechanism where two RNase subunits dock the RNA stem-loop.
  • The elucidated mechanism is conserved in metazoan Ire1 and RNase L.