Bioinformatic pipeline to identify candidate mRNA transcripts targeted by the putative Regulated Ire1-Dependent Decay pathway of Dictyostelium discoideum .
Jun 2026· microPublication Biology· Vol 2026· 0 citations· 15 references
Medicine
TL;DR
A bioinformatic pipeline is developed that identified 21 mRNA transcripts of D. discoideum that contain a consensus Ire1 cut site found within a secondary mRNA hairpin loop structure and have the potential to be cut by IreA.
Abstract
Inositol-requiring protein 1 (Ire1) is a eukaryotic stress sensor that counteracts the buildup of unfolded proteins in the endoplasmic reticulum (ER) by activating the Unfolded Protein Response (UPR) via a specific ribonuclease (RNase) activity. The amoeba Dictyostelium discoideum relies on an ire1 ortholog, ireA , to survive ER stress, but the mRNA transcripts targeted by the IreA ribonuclease remain unknown. In this work, we developed a bioinformatic pipeline that identified 21 mRNA transcripts of D. discoideum that contain a consensus Ire1 cut site found within a secondary mRNA hairpin loop structure and have the potential to be cut by IreA.
Inositol-requiring enzyme 1α (IRE1α) is a canonical signaling factor in the unfolded protein response (UPR). In addition to this essential role (which prevents the accumulation of misfolded proteins in the endoplasmic reticulum), the endoribonuclease activity of IRE1α targets multiple mRNAs for degradation through a pr...
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The unfolded protein response (UPR) is a cellular mechanism that maintains protein homeostasis (proteostasis) under conditions of endoplasmic reticulum (ER) stress. The dual kinase/RNase Ire1 is a conserved regulator of the UPR, mediating the unconventional cytosolic splicing of HAC1 mRNA in yeast and XBP1 mRNA in huma...
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Post-transcriptional gene silencing (PTGS) is a conserved RNA-based defense mechanism that protects plants against viruses and other invasive nucleic acids (Tan et al. 2020). During PTGS, double-stranded RNAs (dsRNAs) are processed by DICER LIKE 4 (DCL4) and DCL2 into 21-and 22-nucleotide small interfering RNAs (siRNAs...
The unfolded protein response (UPR) controls cellular homeostasis and virus infections. It is canonically initiated by dissociation of ER chaperone BiP/GRP78 from lumenal domains of transmembrane sensor proteins, including the central UPR sensor inositol-requiring enzyme 1 alpha (IRE1a). This results in IRE1a activatio...
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