Comparison of mRNA localization and regulation during endoplasmic reticulum stress in Drosophila cells

Ire1 is an endoplasmic reticulum (ER) transmembrane protein that senses disturbances in protein folding homeostasis and contributes to a multifaceted response to stress. The nuclease activity of Ire1, in addition to splicing the mRNA encoding the transcription factor Xbp1, mediates mRNA degradation in response to ER stress through a pathway termed regulated Ire1-dependent decay (RIDD). We previously showed that ER targeting of substrates is necessary for RIDD; in this paper, we show that ER localization is also sufficient to induce decay in a normally unaffected mRNA. Using microarrays, we also measured relative mRNA degradation in the presence and absence of ER stress in Drosophila S2 cells, and determined mRNA membrane association using detergent fractionation. The vast majority of mRNAs that were strongly associated with the ER were degraded faster during ER stress in an Ire1-dependent manner, suggesting that RIDD is the default pathway for ER-localized mRNAs during stress. We also show that the mRNA encoding plexin A remains highly polysome associated during stress and escapes degradation by RIDD, and that its 5′ untranslated region can protect a strong RIDD target from degradation. These results suggest that while translation is generally attenuated during ER stress, continued translation of certain messages can protect them from degradation by RIDD.