Defects in IRE1 enhance cell death and fail to degrade mRNAs encoding secretory pathway proteins in the Arabidopsis unfolded protein response

Abstract

The unfolded protein response (UPR) is a cellular response highly conserved in eukaryotes to obviate accumulation of misfolded proteins in the endoplasmic reticulum (ER). Inositol-requiring enzyme 1 (IRE1) catalyzes the cytoplasmic splicing of mRNA encoding bZIP transcription factors to activate the UPR signaling pathway. Arabidopsis IRE1 was recently shown to be involved in the cytoplasmic splicing of bZIP60 mRNA. In the present study, we demonstrated that an Arabidopsis mutant with defects in two IRE1 paralogs showed enhanced cell death upon ER stress compared with a mutant with defects in bZIP60 and wild type, suggesting an alternative function of IRE1 in the UPR. Analysis of our previous microarray data and subsequent quantitative PCR indicated degradation of mRNAs encoding secretory pathway proteins by tunicamycin, DTT, and heat in an IRE1-dependent manner. The degradation of mRNAs localized to the ER during the UPR was considered analogous to a molecular mechanism referred to as the regulated IRE1-dependent decay of mRNAs reported in metazoans. Another microarray analysis conducted in the condition repressing transcription with actinomycin D and a subsequent Gene Set Enrichment Analysis revealed the regulated IRE1-dependent decay of mRNAs-mediated degradation of a significant portion of mRNAs encoding the secretory pathway proteins. In the mutant with defects in IRE1, genes involved in the cytosolic protein response such as heat shock factor A2 were upregulated by tunicamycin, indicating the connection between the UPR and the cytosolic protein response.heat stress | protein folding | bioinformatics T he unfolded protein response (UPR) or the endoplasmic reticulum (ER) stress response is a cellular response that is highly conserved in eukaryotes to obviate accumulation of misfolded proteins and to alleviate protein overload in the ER (1-3). Inositol-requiring enzyme 1 (IRE1), which is the primary transducer of the UPR in various organisms, catalyzes the unconventional or cytoplasmic splicing of mRNAs encoding bZIP transcription factors to up-regulate the UPR-related genes, such as genes for the ER-resident molecular chaperones, through its ribonuclease domain. The cytoplasmic splicing by IRE1 activates the bZIP transcription factors HAC1, XBP1, and bZIP60 in yeast, animals, and plants, respectively, by producing active proteins. Although the fundamental mechanism of the cytoplasmic splicing by IRE1 appears to be highly conserved, the mechanism of transcription factor activation is diverse among organisms (4).In addition to the cytoplasmic splicing of mRNAs for transcription factors, other functions of metazoan IRE1 have been reported. One such function is the degradation of mRNAencoding proteins in the secretory pathway referred to as regulated IRE1-dependent decay (RIDD) (5-7). RIDD is considered to contribute to reducing the amount of proteins entering the ER in the UPR. The metazoan UPR has an alternative mechanism to reduce the amount of protein entering the ER, and this mechanism is regulated by PKR-li...

Protein kinase and ribonuclease domains of IRE1 confer stress tolerance, vegetative growth, and reproductive development in Arabidopsis

“…Mishiba et al (12) recently reported that RIDD is required for the ER stress tolerance in Arabidopsis. They showed that the mRNAs for a set of secreted proteins were degraded in response to ER stress.…”

“…Mishiba et al (12) recently showed that IRE1 is also involved in RIDD, a process by which mRNAs encoding secreted proteins on membrane-bound ribosomes are degraded in response to stress. In addition, they identified several RIDD target mRNAs in Arabidopsis.…”

“…Up to this time, the analysis of single mutants in the pathway had not revealed functions for the UPR in plant growth and stress tolerance, although an ire1a ire1b double mutant was found to show a modest short root phenotype and increased sensitivity to ER stress agents (12). The lack of distinctive phenotypes led us to question whether the UPR really plays an important role in plant growth or stress tolerance.…”

Effect of overexpression of kinase- or RNase-deficient OsIRE1 on the endoplasmic reticulum stress response in transgenic rice plants

“…3,12,13 In view of these findings, OsIRE1 may play other important roles in addition to OsbZIP50 mRNA splicing and its function may be species specific.…”

Inositol-requiring enzyme 1 affects meristematic division in roots under moderate salt stress in Arabidopsis

“…In addition, IRE1A and IRE1B function in RIDD (Mishiba et al 2013) as in other organisms. A broad range of mRNAs encoding secretory and membrane proteins are destabilized through RIDD in Arabidopsis.…”