Transcriptomic response of Arabidopsis thaliana to tunicamycin-induced endoplasmic reticulum stress

Secretory and membrane proteins of eukaryotic cells must be properly folded and assembled in the endoplasmic reticulum (ER) before translocation to their final destination where they function. Perturbation of this process results in accumulation of unfolded proteins in the ER, so-called ER stress. The cells initiate a protective response to maintain cellular homeostasis, which is termed the ER stress response or the unfolded protein response (UPR). In the present study, we performed time-series transcriptome analysis of the ER stress response in Arabidopsis (Arabidopsis thaliana) with the N-linked glycosylation inhibitor tunicamycin, which causes misfolding of proteins in the ER, and therefore, triggers ER stress. A total of 259 genes were identified as tunicamycin-responsive genes, 175 of which were upregulated and 84 were downregulated. Hierarchical clustering and bioinformatic analysis demonstrated that 259 tunicamycin-responsive genes can be assigned to one of the six distinct expression classes and identified a potential novel cis-element, as well as known cis-elements, i.e., ER stress response element and UPR element. We also observed that a considerable number of tunicamycin-inducible genes, including those encoding the ER chaperone BiP and the membrane-bound transcription factor AtbZIP60, are coordinately upregulated at a late pollen development stage in Arabidopsis. This observation suggests that the ER stress response plays an important role in the development and function of pollens.