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Transient intracellular acidification regulates the core transcriptional heat shock response

Citation

Triandafillou, Catherine; Katanski, Christopher; Dinner, Aaron R.; Drummond, D. Allan (2020), Transient intracellular acidification regulates the core transcriptional heat shock response, Dryad, Dataset, https://doi.org/10.5061/dryad.zgmsbcc6v

Abstract

Heat shock induces a conserved transcriptional program regulated by heat shock factor 1 (Hsf1) in eukaryotic cells. Activation of this heat-shock response is triggered by heat-induced misfolding of newly synthesized polypeptides, and so has been thought to depend on ongoing protein synthesis. Here, using the budding yeast Saccharomyces cerevisiae, we report the discovery that Hsf1 can be robustly activated when protein synthesis is inhibited, so long as cells undergo cytosolic acidification. Heat shock has long been known to cause transient intracellular acidification which, for reasons which have remained unclear, is associated with increased stress resistance in eukaryotes. We demonstrate that acidification is required for heat shock response induction in translationally inhibited cells, and specifically affects Hsf1 activation. Physiological heat-triggered acidification also increases population fitness and promotes cell cycle reentry following heat shock. Our results uncover a previously unknown adaptive dimension of the well-studied eukaryotic heat shock response. 

Methods

Raw data: Flow cytometry .fcs files (contained in zipped directories starting with 'Triandafillou') are raw flow cytometry data; the experiment names contain the metadata. The script 'process-raw-data.R' processes raw flow cytometry data (internally normalizes fluorescent readings and performs calibration curve analysis to calculate intracellular pH where appropriate) and combines experiments into tidy datasets.

Processed data: Processed data are .tsv and .csv files and include processed flow datasets (generated by 'process-raw-data.R'). Raw qPCR data, and raw protein translation data (generated by liquid scintillation counting (LSC) of samples from radiolabeled amino acid incorporation experiments) are also included.

Zipped directory 2017-11-18_pH-TSP-bio1.zip contains SDS-PAGE gel and Western Blot data; protocol, raw images, quantification, and processed images and summaries are all included.

Usage Notes

analysis-scripts.zip contains R markdown notebooks that generate figures from the raw LSC and qPCR data.

Funding

National Institute of Biomedical Imaging And Bioengineering of the National Institutes of Health (NIH), Award: T32EB009412

National Science Foundation Graduate Research Fellowship, Award: DGE-1144082

National Institutes of Health, Award: R01 GM109455

National Institutes of Health, Award: R01 GM126547

US Army Research Office, Award: W911NF-14-1-0411

National Institutes of Health, Award: R01GM127406