IRE1-dependent transcriptional change under a canonical endoplasmic-reticulum stressing stimulus and upon diauxic shift in Saccharomyces cerevisiae cells
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PROVIDER: PRJEB27382 | ENA |
REPOSITORIES: ENA
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Project description:Ire1 is an endoplasmic reticulum (ER)-located transmembrane protein that triggers the unfolded protein response. I recently noticed that Ire1 is activated not only in response to ER accumulation of unfolded proteins but also alongside diauxic shift in yeast Saccharomyces cerevisiae cells. I thus asked how different the Ire1-target genes upon two distinct scenes, a canonical ER -stressing stimuli and diauxic shift. Thus NGS transcriptome analysis was performed by using IRE1+ and ire1-delta mutant yeast cells under these conditions.
2019-03-01 | E-MTAB-6923 | biostudies-arrayexpress
Project description:To determine where Tup1 binds to chromatin during log phase, diauxic shift and stationary phase, we performed ChIP-seq.
2022-08-17 | GSE210932 | GEO
Project description:The yeast Hsp31 mini-family proteins (Hsp31, Hsp32, Hsp33, Hsp34) belong to the highly conserved DJ-1 superfamily. The human DJ-1 protein is associated with cancer and neurodegenerative disorders, such as Parkinson’s disease. However, the precise function of human and yeast DJ-1 proteins is unclear. Here we show that the yeast DJ-1 homologs have a role in diauxic-shift, characterized by metabolic reprogramming due to glucose limitation. We find that the Hsp31 genes are strongly induced in diauxic-shift and in stationary phase (SP), and that deletion of these genes reduces chronological lifespan, impairs transcriptional reprogramming at diauxic-shift, and impairs the acquisition of several typical characteristics of SP, including autophagy induction. In addition, under carbon starvation, the HSP31 family gene deletion strains display impaired autophagy, disrupted TORC1 localization to P-bodies, and caused abnormal TORC1-mediated Atg13 phosphorylation. Repression of TORC1 by rapamycin in the gene deletion strains completely reversed their sensitivity to heat shock. Altogether, our data indicate that Hsp31 mini-family is required for diauxic-shift reprogramming and cell survival in SP, and plays a role upstream of TORC1. The enhanced understanding of the cellular function of these genes sheds light into the biological role of other members of the superfamily, including DJ-1, which is an attractive target for therapeutic intervention in cancer and in Parkinson’s disease. hsp31∆, hsp32∆, hsp33∆ are compared with its parental strain BY4741. We used One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling from Agilent.
2014-03-25 | GSE56124 | GEO
Project description:The yeast Hsp31 mini-family proteins (Hsp31, Hsp32, Hsp33, Hsp34) belong to the highly conserved DJ-1 superfamily. The human DJ-1 protein is associated with cancer and neurodegenerative disorders, such as Parkinson’s disease. However, the precise function of human and yeast DJ-1 proteins is unclear. Here we show that the yeast DJ-1 homologs have a role in diauxic-shift, characterized by metabolic reprogramming due to glucose limitation. We find that the Hsp31 genes are strongly induced in diauxic-shift and in stationary phase (SP), and that deletion of these genes reduces chronological lifespan, impairs transcriptional reprogramming at diauxic-shift, and impairs the acquisition of several typical characteristics of SP, including autophagy induction. In addition, under carbon starvation, the HSP31 family gene deletion strains display impaired autophagy, disrupted TORC1 localization to P-bodies, and caused abnormal TORC1-mediated Atg13 phosphorylation. Repression of TORC1 by rapamycin in the gene deletion strains completely reversed their sensitivity to heat shock. Altogether, our data indicate that Hsp31 mini-family is required for diauxic-shift reprogramming and cell survival in SP, and plays a role upstream of TORC1. The enhanced understanding of the cellular function of these genes sheds light into the biological role of other members of the superfamily, including DJ-1, which is an attractive target for therapeutic intervention in cancer and in Parkinson’s disease. hsp31∆, hsp32∆, hsp33∆ are compared with its parental strain BY4741. We used One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling from Agilent. Cultures were grown in synthetic complete media until reached diauxic shift. At this time cultures were collected.
2014-03-25 | E-GEOD-56124 | biostudies-arrayexpress
Project description:To investigate the effect of Tup1, Xbp1, Isw2, and Sds3 on transcription we generated knockout strains and measured their transcript abundance compared to wild type during diauxic shift and stationary phase.
2022-08-17 | GSE210930 | GEO
Project description:Gcr1, the most important transcription factor for glycolytic genes in Saccharomyces cerevisiae, was recently revealed to have two isoforms, Gcr1(U) and Gcr1(S), produced from unspliced and spliced transcripts, respectively. We generated strains expressing only Gcr1(U) or Gcr1(S) form using the CRISPR/Cas9 system, and added a TAP tag protein to the Gcr1(U) and Gcr1(S), using HIS3MX6 marker system. We conducted ChIP-seq for both strains during the glycolytic phase or after the diauxic shift.
2020-07-07 | GSE153841 | GEO
Project description:Gcr1, the most important transcription factor for glycolytic genes in Saccharomyces cerevisiae, was recently revealed to have two isoforms, Gcr1(U) and Gcr1(S), produced from unspliced and spliced transcripts, respectively. We generated strains expressing only Gcr1(U) or Gcr1(S) form using the CRISPR/Cas9 system, and performed RNA-seq for the two strains. Since Gcr1 works as a glycolytic gene transcription factor, we extracted whole RNA at the exponential phase (6 hrs after incubation) and the diauxic shift (12 hrs after incubation).
2020-07-07 | GSE153842 | GEO
Project description:The unfolded protein response (UPR) continually monitors the protein folding capacity of the endoplasmic reticulum (ER). In S. pombe, Ire1, an ER membrane-resident kinase/endoribonuclease, utilizes a mechanism of selective degradation of ER-targeted mRNAs (RIDD) to maintain ER homeostasis. Here, we used a genetic screen to identify factors critical to the Ire1-mediated UPR response in S. pombe and found several proteins, Dom34, Hbs1 and SkiX, previously implicated in ribosome rescue and the no-go-decay (NGD) pathway. Ribosome profiling in ER-stressed cells lacking these factors revealed that Ire1-mediated cleavage on ER-associated mRNAs results in ribosome stalling on the cleaved transcript and, ultimately in full mRNA degradation. The process engages mechanisms of precise, iterated cleavage of the mRNAs and ribosome rescue. This clear signature allowed us to discover hundreds of novel mRNA targets of Ire1. Our results reveal that the UPR in S. pombe executes RIDD in an intricate interplay between Ire1, translation, and the NGD surveillance pathway, and establish a critical role for NGD in maintaining ER homeostasis.
2017-09-14 | GSE98934 | GEO
Project description:Protein phosphorylation has long been recognized as an essential regulator of protein activity, structure, complex formation, and sub-cellular localization among other cellular mechanisms. However, interpretation of the changes in protein phosphorylation is difficult. To address this difficulty, we measured protein and phosphorylation site changes across 11 points of a time course and developed a method for categorizing phosphorylation site behavior relative to protein level changes using the diauxic shift in yeast as a model and TMT11 sample multiplexing. We classified quantified proteins into behavioral categories that reflected differences in kinase activity, protein complex structure, and growth and metabolic pathway regulation across different phases of the diauxic shift. These data also provide a valuable resource for the study of fermentative versus respiratory growth and set a new benchmark for temporal quantitative proteomics and phosphoproteomics for Diauxic Shift in Saccharomyces cerevisiae.
2021-03-04 | PXD022741 | Pride
Project description:Tup1 binding during log phase, diauxic shift, and stationary phase.
| PRJNA868336 | ENA