Grr1-mediated Ubp3 degradation is crucial for HAC1 mRNA translation and unfolded stress response in yeast [RNAseq]

Ribosome ubiquitination induced by ribosome stalling is crucial for quality control pathways targeting mRNA, nascent polypeptides, and non-functional ribosomes. Besides quality control, Not4-mediated monoubiquitination of eS7A is crucial for the efficient translation of HAC1i mRNA in the unfolded protein response (UPR). In this study, we identified a novel E3 ligase, Grr1, an F-box protein component of the SCF ubiquitin ligase complex that is involved in Ubp3 degradation thereby HAC1i mRNA translation. Grr1 degrades Ubp3, a deubiquitinating enzyme of eS7A, under ER stress, thereby increasing eS7A ubiquitination, which facilitates HAC1i translation. Translation of HAC1i mRNA requires Grr1 and eS7 ubiquitination regardless of ER stress. ER stress-specific expression of Hac1 protein is ensured by the multi-step regulation of HAC1u mRNA, including localization on the ER membrane and stress-mediated splicing. Translation of HAC1i mRNA in UPR requires Grr1-mediated eS7 ubiquitination. More importantly, exon 1 of the HAC1i mRNA is crucial for translation activation by eS7 ubiquitination. Collectively, we propose that Grr1 upregulates eS7A monoubiquitination, thereby HAC1i translation and plays a crucial role in UPR. To investigate the transcriptome profile under ER stress conditions, we performed RNA-seq of tunicamycin-treated W303 strains. The dataset includes 4 types of RNA-seq samples in biological replicates (indicated as rep1 and rep2; 8 samples in total). Samples differ by the genotype (wild-type or grr1 deficient), and tunicamycin treatment time (0, 4 hr). We then calculated Translation efficiency (TE) using the read counts from Ribo-seq data shown in another file and the read counts from RNA-seq data. For each genotype (wild-type or grr1 deficient), 0 hr data was compared against data of 4 hr data.