Abstract
BackgroundThe endoplasmic reticulum (ER) stress response is widely known to function in eukaryotes to maintain the homeostasis of the ER when unfolded or misfolded proteins are overloaded in the ER. To understand the molecular mechanisms of the ER stress response in rice (Oryza sativa L.), we previously analyzed the expression profile of stably transformed rice in which an ER stress sensor/transducer OsIRE1 was knocked-down, using the combination of preliminary microarray and quantitative RT-PCR. In this study, to obtain more detailed expression profiles of genes involved in the initial stages of the ER stress response in rice, we performed RNA sequencing of wild-type and transgenic rice plants produced by homologous recombination in which endogenous genomic OsIRE1 was replaced by missense alleles defective in ribonuclease activity.ResultsAt least 38,076 transcripts were investigated by RNA sequencing, 380 of which responded to ER stress at a statistically significant level (195 were upregulated and 185 were downregulated). Furthermore, we successfully identified 17 genes from the set of 380 ER stress-responsive genes that were not included in the probe set of the currently available microarray chip in rice. Notably, three of these 17 genes were non-annotated genes, even in the latest version of the Rice Annotation Project Data Base (RAP-DB, version IRGSP-1.0).ConclusionsTherefore, RNA sequencing-mediated expression profiling provided valuable information about the ER stress response in rice plants and led to the discovery of new genes related to ER stress.
Highlights
The endoplasmic reticulum (ER) stress response is widely known to function in eukaryotes to maintain the homeostasis of the ER when unfolded or misfolded proteins are overloaded in the ER
Comprehensive screening of ER stress-responsive genes To obtain detailed information about the expression profiles of genes involved in the ER stress response in root tissues of rice seedlings, especially during the initial stages of the ER stress response, we compared the expression profiles of plants in three pairs of treatment groups: (1) wild type without tunicamycin (TM, an inhibitor of protein glycosylation used as an ER stress-response inducer) treatment vs. wild type with a short period (2 hr) of TM treatment; (2) wild type with DMSO vs. wild type with TM treatment; and (3) wild type with TM treatment vs. K833A with TM treatment
Orthologous genes of newly identified ER stress-responsive genes in Arabidopsis We examined whether orthologous sequences of these 17 transcripts exist in the Arabidopsis genome by searching the Arabidopsis Information Resource (TAIR) database, and we investigated whether any such genes are induced by ER stress in Arabidopsis
Summary
The endoplasmic reticulum (ER) stress response is widely known to function in eukaryotes to maintain the homeostasis of the ER when unfolded or misfolded proteins are overloaded in the ER. The endoplasmic reticulum (ER) is an organelle in which the synthesis of secretory proteins and the folding and assembly of newly synthesized premature proteins occurs. When these functions are perturbed by the accumulation of unfolded or misfolded proteins in the ER, the cells incur ER stress conditions. OsbZIP39 and OsbZIP60 may be regulated in a similar manner to that of ATF6, as truncated recombinant proteins lacking the C-terminal putative transmembrane domain (TMD) induce the ER stress response [6,7]. Counterparts of PERK have not been identified in plants
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