Decoding non-canonical mRNA decay by the endoplasmic-reticulum stress sensor IRE1α.

Area of Science:

• Molecular Biology
• Cellular Biology
• Biochemistry

Background:

• Inositol requiring enzyme 1 (IRE1) is a key sensor of endoplasmic reticulum (ER) stress, central to the unfolded-protein response (UPR).
• IRE1's endoribonuclease activity generates the XBP1s transcription factor and mediates regulated IRE1-dependent decay (RIDD) of cellular mRNAs.
• Mammalian RIDD primarily targets mRNAs with XBP1-like endomotifs, contrasting with less restricted degradation in flies.

Purpose of the Study:

• To investigate the mechanisms of mRNA degradation mediated by IRE1α.
• To identify novel substrates and pathways of IRE1α-mediated RNA decay.
• To elucidate the distinct endoribonuclease modalities of IRE1α.

Main Methods:

• Comparative analysis of nascent and total IRE1α-controlled mRNAs in human cells.
• In vitro assays using IRE1α mutants to assess endonuclease activity.
• Cellular experiments to evaluate the role of IRE1α oligomerization in RNA decay.

Main Results:

• Identified IRE1α-mediated mRNA degradation targets lacking canonical endomotifs, termed RIDDLE (RIDD lacking endomotif).
• Demonstrated two distinct IRE1α endoribonuclease modalities: specific, endomotif-directed cleavage and promiscuous, endomotif-independent processing.
• Showed that an oligomer-deficient IRE1α mutant impairs RIDDLE activity both in vitro and in cells.

Conclusions:

• IRE1α possesses dual endoribonuclease activities, enabling both specific mRNA processing and broader RNA decay.
• The RIDDLE pathway represents a novel mechanism of UPR regulation, distinct from canonical RIDD.
• IRE1α oligomerization is crucial for the endomotif-independent RIDDLE pathway, expanding the understanding of UPR signaling.