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[Preprint]. 2023 Sep 24:2023.09.23.559074.
doi: 10.1101/2023.09.23.559074.

Direct ionic stress sensing and mitigation by the transcription factor NFAT5

Affiliations

Direct ionic stress sensing and mitigation by the transcription factor NFAT5

Chandni B Khandwala et al. bioRxiv. .

Abstract

Homeostatic control of intracellular ionic strength is essential for protein, organelle and genome function, yet mechanisms that sense and enable adaptation to ionic stress remain poorly understood in animals. We find that the transcription factor NFAT5 directly senses solution ionic strength using a C-terminal intrinsically disordered region. Both in intact cells and in a purified system, NFAT5 forms dynamic, reversible biomolecular condensates in response to increasing ionic strength. This self-associative property, conserved from insects to mammals, allows NFAT5 to accumulate in the nucleus and activate genes that restore cellular ion content. Mutations that reduce condensation or those that promote aggregation both reduce NFAT5 activity, highlighting the importance of optimally tuned associative interactions. Remarkably, human NFAT5 alone is sufficient to reconstitute a mammalian transcriptional response to ionic or hypertonic stress in yeast. Thus NFAT5 is both the sensor and effector of a cell-autonomous ionic stress response pathway in animal cells.

Keywords: HOG pathway; NFAT5; TonEBP; biomolecular condensates; cell volume regulation; hypertonic stress; intrinsically disordered protein; ion homeostasis; ionic strength; ionic stress; macromolecular crowding; osmolytes; osmotic stress; phase separation; prions; tonicity; transcription.

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Conflict of interest statement

DECLARATION OF INTERESTS The authors declare no competing interests.

Figures

Figure 1.
Figure 1.. Genetic screens to identify positive and negative regu
(A). The expression of three direct NFAT5 target genes was measured by quantitative reverse transcription PCR (RT-qPCR) after 8 hours (hrs) in isotonic media (300 mOsm/L) or after the addition of 200 mOsm/L of NaCl, sorbitol, or urea, raising the total media osmolarity in each case to −500 mOsm/L. (B). Expression of the NFAT5 target gene Akr1b3 in wild-type (WT) IMCD3 cells or a clonal Nfat5−/−cell line after 8 hrs in isotonic or hypertonic media (+200 mOsm/L NaCl). Elimination of NFAT5 in Nfat5−/−cells was confirmed by immunoblotting (right). Data from four additional independent Nfat5−/−clonal cell lines is shown in Figure S1A. (C). GFP fluorescence was measured by flow cytometry in IMCD3-G cells, which stably carry the 8TonE-GFP reporter (left), after 8 hrs in isotonic or hypertonic media (+200 mOsm/L NaCl, Sorbitol or Urea). Each point depicts the median GFP fluorescence from >2000 cells. (D). 8TonE-GFP reporter activity in IMCD3-G cells was measured by flow cytometry at the indicated time points in response to increasing amounts of NaCl added to isotonic media. Total media osmolarity at each concentration of NaCl is shown in red on the secondary x-axis. Each point shows the mean ± Standard Deviation (SD) of three independent median measurements, each from a population of >2000 cells. (E). 8TonE-GFP reporter activity after exposure to hypertonic media (+200 mOsm/L NaCl, 8 hrs) in WT or Nfat5−/−IMCD3 cells. (F). The strategy used for genome-wide loss-of-function screens in mouse IMCD3 and human haploid (HAP1) cells using a stably integrated 8TonE-GFP reporter. Fluorescence activated cell sorting (FACS) was used to collect cells carrying mutations in genes encoding positive or negative regulators of the NFAT5 transcriptional response following exposure to hypertonic stress. The retroviral strategy used for insertional mutagenesis in HAP1 cells is shown in Figure S1H. (G) Volcano plots showing results from the genetic screens outlined in F. For the CRISPR screen (top) in IMCD3 cells, the x-axis shows the enrichment of each gene (calculated as the mean of all four sgRNAs targeting the gene) in the sorted population relative to the unsorted population and the y-axis shows statistical significance as measured by the false discovery rate (FDR)-corrected p-value. For the haploid screen (bottom) in HAP1 cells, the x-axis shows the Intronic Gene-trap Insertion Orientation Bias (IGTIOB) score, which scores the bias towards inactivating insertions in each gene from sorted cells only, and the y-axis shows the FDR- corrected p-value, reflecting the enrichment of gene-trap insertions in sorted over unsorted cells. (H) Venn diagrams representing overlapping positive and negative regulators with FDR-corrected p-values < 0.05 from the independent screens conducted in IMCD3 and HAP1 cells. Statistics: Bars (A,C) or black horizontal lines (B,E) denote mean values calculated from independent measurements shown as points. Statistical significance (A,B,C,E) was determined by a two-way ANOVA test with Sidak’s multiple comparison post-test (n>3 independent experiments). p-values symbol are: **** <0.0001, *** <0.001, **<0.01, and *<0.05. See a<so Figure S1.
Figure 2.
Figure 2.. NFAT5 can be activated by hypertonic stress in Saccharomyces cerevisiae.
(A) Domain structures of mVenus-tagged human full-length and mini-NFAT5 . Mini-NFAT5 was engineered by joining two regions within the C-terminal domain (CTD) of NFAT5 to its DNA Binding Domain (DBD) and a strong heterologous nuclear localization sequence (NLS). (B) The subcellular localization of mVenus-tagged full-length or mini-NFAT5 stably expressed in IMCD3 cells exposed to isotonic or hypertonic (+200 mOsm/L NaCl) media for 30 minutes (min). Fluorescence signal from the mVenus tag fused to NFAT5 is shown alone (top) or merged with a DNA stain for nuclei (DAPI, bottom). Scale bars: 10 im. (C) Expression of an NFAT5 target gene in WT cells, NFAT5 ‘/! cells, or NFAT5 ‘/! IMCD3 cells stably expressing either full-length or mini-NFAT5 (see A) after 8 hrs in isotonic or hypertonic (+200 mOsm/L NaCl) media. (D) Structure of the 8TonE-pC@C1-GFP reporter and galactose-inducible mini-NFAT5 variant genes integrated into wild-type W303 yeast cells (top). Schematic of the experimental workflow used to test reporter activity by flow cytometry in yeast cells following galactose (Gal) induction of the NFAT5 variants and hypertonic stress (bottom). (E) 8TonE-pC@C1-GFP reporter activity in yeast cells expressing the reporter only or the reporter in addition to mRuby3, mRuby3-DBD, or mRuby3-mini-NFAT5 (2 independent clones) in response to increasing amounts of NaCl added to complete synthetic media (CSM). (F) 8TonE-pC@C1-GFP reporter activity in yeast cells expressing mini-NFAT5 in response to increasing concentrations of NaCl, sorbitol, or urea. (G) Two separate sets of mutations introduced in the DBD in NLS-mRuby3-mini-NFAT5 to abrogate DNA- binding (DB) or dimerization (DIM). Abundances of the proteins encoded by these mini-NFAT5 variant constructs were compared by immunoblotting (bottom). (H) 8TonE-pC@C1-GFP reporter activity in yeast cells expressing the indicated variants of mini-NFAT5 exposed to increasing amounts of NaCl for 4 hrs. Two independent clones of the DNA-binding (DB) and dimerization (DIM) mutants (see G) were tested. (I) Sequence of the WT tonicity enhancer (TonE) binding site, compared to a mutant version known to abrogate its interaction with NFAT5 . Graph on the right shows activity of the WT or mutant 8TonE-pC@C1-GFP reporter in yeast cells expressing the indicated variants of mini-NFAT5 in response to increasing concentrations of NaCl. (J) The HOG (high-osmolarity glycerol) pathway in S. cerevisiae. Coloured X’s denote three different genes or gene sets that were deleted to disrupt the pathway at various levels: HOG1, PBS2, or the combined triple deletion of SSK2, SSK22 and SHO1. (K) 8TonE-pC@C1-GFP reporter activity in WT, hog1 V, pbs2V, or ssk2V ssk22V sho1V cells (also expressing mini-NFAT5 ) in response to increasing amounts of NaCl (left) or sorbitol (right). Statistics: Each point (E,F,H,I,K) shows the mean ± SD of >3 independent median measurements, each from a population of >5000 cells. Solid horizontal lines (C) denote mean values calculated from three independent measurements shown as points. Statistical significance (C) was determined by a two-way ANOVA test with Sidak’s multiple comparison post-test (n>3 independent experiments). P-value symbols are: **** p- value<0.0001 and * p-value<0.05. See a<so Figure S2.
Figure 3.
Figure 3.. NFAT5 is activated by ionic stress.
(A) Temporal sequence of cellular changes triggered by hypertonic stress. Hypertonic stress causes rapid cell shrinkage. The resulting increase in macromolecular crowding activates the regulatory volume increase (RVI) pathway: WNK1 initiates a kinase cascade that increases net influx of ions, leading to cell volume recovery within min, but at the cost of elevated intracellular ionic strength. If hypertonic stress persists, NFAT5 activation (over a slower timescale) allows the replacement of these excess ions with osmolytes, allowing restoration of the normal intracellular ion content. (B) Mechanism by which ammonium acetate (NH)OAc) crosses the plasma membrane and permeates cells. (C) Confocal images of IMCD3 cells treated with NaCl or NH)OAc (+200 mOsm/L added to isotonic media) and stained with DAPI to show nuclei (top) and CellMask to show the plasma membranes (bottom). Cells were imaged in the xz plane to show changes in cell height at 10 and 60 min after stress initiation. Scale bar: 2 im. (D) The height of IMCD3 cells (n>28 per condition) was measured using confocal images of the type shown in C at various time points after addition of NaCl or NH)OAc (+200 mOsm/L) to isotonic media. (E) Volume of single IMCD3 cells (n>26 cells per condition) was measured using high-speed confocal imaging to capture z-stacks 10 min after the addition of 200 mOsm/L of urea, sorbitol, NaCl, or NH)OAc to isotonic media. (F) Cartoon showing the genetically-encoded Fluorescence Resonance Energy Transfer (FRET) sensor used to detect changes in intracellular ionic strength (left). Charged molecules like ions screen the attraction between the positively and negatively charged helices, reducing the FRET signal. Graph (right) shows the change in the mean mCitrine/mCerulean3 fluorescence ratio, along with an error envelope showing the SEM, from 20 individual IMCD3 cells after the addition of 200 mOsm/L NH)OAc to isotonic media. (G) Distribution of GFP fluorescence in WnkT1‘ IMCD3 cells stably expressing GFP-WNK1 30 min after the addition of NH)OAc, NaCl, or sorbitol (+400 mOsm/L each) to isotonic media. (H) Immunoblotting was used to measure the abundance of phosphorylated SPAK and total SPAK in IMCD3 cells 30 min after the addition of NH)OAc, NaCl, or sorbitol (+400 mOsm/L each) to isotonic media. (I) Nuclear mVenus-NFAT5 fluorescence (n>145 IMCD3 cells per condition) at the indicated time points after the addition of NaCl or NH)OAc (+200 mOsm/L) to isotonic media. Representative images are shown in Figure S3A. These cells stably express full-length mVenus-NFAT5 (see Figure 2B). (J) 8TonE-GFP reporter activity in IMCD3-G cells was measured by flow cytometry at the indicated time points in response to increasing amounts of NH)OAc added to isotonic media. Each point shows the mean ± SD of three individual median measurements, each from a population of >2000 cells. (K) 8TonE-pC@C1-GFP reporter activity in yeast cells expressing mini-NFAT5 (Figure 2D) was measured by flow cytometry in response to increasing amounts of NH)OAc added to media (CSM). Each point shows the mean ± SD of six individual median measurements, each from a population of >5000 cells. (L) The diameter of yeast cells (n>98 per condition) was measured by microscopy 5 min after the addition of 1200 mOsm/L NaCl or NH4OAc to CSM. Statistics: Circles in (D,E,I,L) denote measurements from single cells and the black horizontal line marks the median of the population. The statistical significance of differences in comparison to the isotonic condition was determined by a Kruskal-Wallis test with Dunn’s multiple comparison test. P-value symbols are: **** p- value<0.0001, *** p-value<0.001, ** p-value<0.01, and * p-value<0.05. In (D), columns without symbols have p-values that are not significant. See a<so Figure S3.
Figure 4.
Figure 4.. NFAT5 forms drop
(A) Domain structure (top), predicted disorder tendency (middle) and predicted prion-like regions (bottom) of human NFAT5 , all drawn on the same linear scale. NFAT5 has a predicted prion-like domain (PLD) and a structured DNA binding domain (DBD) embedded within intrinsically disordered regions (IDRs)., (B) Snapshots from live cell imaging of 293T cells transiently transfected with GFP-NFAT5 and subjected to hypertonic stress. Isotonic media was replaced with hypertonic media (+100 mOsm/L NaCl) at t=15 seconds and images were collected for 25 min. (C) Live cell time course to test the reversibility of GFP-NFAT5 condensates in 293T cells. Cells were cycled from isotonic to hypertonic (+100 mOsm/L NaCl) and back to isotonic media according to the protocol shown on the bottom left. Mean (±SEM) number of droplets in 15 individual cells is shown on the graph (bottom right). Representative of three independent experiments. (D) Snapshots from a fluorescence recovery after photobleaching (FRAP) time course of a GFP-NFAT5 condensate in 293T subjected to hypertonic stress (+100 mOsm/L NaCl, 30 min). A corresponding recovery curve is shown on the right (mean ± SEM, n=9). (E,F) Subcellular distribution of full-length GFP-NFAT5 (E) or mVenus-mini-NFAT5 (F) stably expressed from a single locus in Nfat5−/−IMCD3 cells (see methods) after the addition of NaCl, NH)OAc, sorbitol or urea (+200 mOsm/L each, 30 min) to isotonic media. The middle row of each panel shows NFAT5 distribution relative to nuclei. Line scans show fluorescence intensity traces along the trajectories of the yellow line in the images. (G) Live cell time course images of NH)OAc treated IMCD3 cells carrying NFAT5 tagged at its endogenous genomic locus with mNeonGreen (mNG) at the N-terminus in IMCD3 cells subjected to NH)OAc (see Figures S5C, S5D and S5E for characterization of this cell line). Line scans correspond to fluorescence intensity traces along the trajectories of the yellow lines shown in the images. (H) Maximum intensity projections of a live cell, super-resolution image (Structured Illumination Microscopy) of an IMCD3 nucleus carrying the endogenously tagged mNG-NFAT5 . Cells were subjected to ionic stress (+200 mOsm/L NH)OAc) for 30 min prior to imaging. (I) Number of nuclear puncta in IMCD3 cells (n~34 cells per condition) carrying endogenously-tagged mNG-NFAT5 after the addition of NaCl or NH)OAc (+200 mOsm/L, 30 min). Black horizontal line shows the median of each population and statistical significance of differences relative to the isotonic condition was determined using a Kruskal-Wallis test with Dunn’s multiple comparison post-test (n>3 independent experiments). P-value symbol: **** p-value<0.0001. (J) FRAP recovery images and corresponding recovery curve (n=13; mean ± SEM) of endogenous mNG-NFAT5 puncta in IMCD3 cells subjected to ionic stress (+200 mOsm/L NH)OAc). Scale bars for panels (B,C,E,F,G,H): 10 im; panels (D,J): 1 im. See a<so Figure S4 and S5.
Figure 5.
Figure 5.. The C-terminal intrinsically disordered region of NFAT5 can sense solution ionic strength.
(A, B) Distribution (A) of GFP-CTD (C-terminal domain of NFAT5 , a.a. 544–1531) or GFP-PLD (prion-like domain of NFAT5 , a.a. 999–1454) in 293T cells 30 min after the addition of NaCl, NH)OAc or sorbitol (+100 mOsm/L each) to isotonic media (see Figure 2A for the position of the CTD and PLD in full-length NFAT5 ). Images of the type shown in (A) were used to measure the number of puncta per cell (n>25 cells, with black horizontal line showing the median and each point showing the number of puncta in one cell). (C) Domain structure of WT and chimeric GFP-tagged WNK1 constructs. The WNK1 1–494 fragment contains a fully intact kinase domain and a C-terminal (a.a. 495–2382) IDR that senses macromolecular crowding. In the chimeras, the IDR of WNK1 is replaced with the CTD or the PLD of NFAT5 . (D) Distribution of full-length and chimeric GFP-tagged WNK1 constructs (shown in C) in 293T cells 30 min after the addition of the indicated concentrations of NaCl or NH)OAc to isotonic media. The graphs (right) show the number of puncta in cells treated with NaCl or NH)OAc (200 mOsm/L, 30 min) (n>20 cells with black horizontal line showing the median and each point showing the number of puncta in one cell). (E) Design of synthetic transcription factors through fusion of the DNA binding domain (DBD, a.a. 1–147) of the S. cerevisiae GAL4 protein to either the NFAT5 CTD, PLD or N-terminal domain (NTD, Figure 2A) (left). Each of the GAL4 fusions were tested for their abilities to activate a firefly luciferase reporter gene in response to NaCl (+200 mOsm/L) or NH)OAc (+100 mOsm/L). Solid horizontal lines denote mean values calculated from >3 independent measurements shown as points. (F) Fluorescence microscopy was used to assess droplet formation in vitro by purified (Figure S6A) GFP-CTD (70 iM, top row) and GFP-PLD (90 iM, bottom row) in buffer containing 5% dextran and the indicated concentrations of NaCl. (G) Reversibility of GFP-CTD condensates assessed by a centrifugation and resuspension assay. Condensates (which cause turbidity, top panel) triggered by the addition of NaCl to a solution of 70 iM GFP-CTD can be sedimented (middle panel). This condensate pellet readily dissolves to a clear solution in a low ionic strength buffer (bottom panel). All solutions contain 5% dextran. (H) Phase diagrams for purified GFP-CTD (top) and GFP-PLD (bottom). Blue shading denotes conditions where the GFP fluorescence was exclusively in droplets while the unshaded area encompasses conditions where GFP fluorescence remained diffuse (see F for examples of each). The boundary between the shaded and unshaded areas of the graph is taken as the phase boundary; crossing this boundary leads to the abrupt drop of diffuse fluorescence and emergence of droplets. Images were obtained across three replicates per condition. (I,J) Full-bleach (I) and half-bleach (J) FRAP recovery images and corresponding recovery curves (n=10; mean ± SEM) of GFP-CTD condensates assembled in buffer with 5% dextran, 200 mOsm/L NaCl and 70 iM protein. Scale bars for panels (A,D): 10 im; panels (F,I,J): 5 im. Statistics: Statistical significance of the differences in comparison to the isotonic condition was determined in (B,D) with a Kruskal-Wallis test and Dunn’s multiple comparison test and in (E) with a two-way ANOVA test and Sidak’s multiple comparison test (n>3 independent experiments). P-value symbols are: **** p-value<0.0001 and *** p-value<0.001. See a<so Figure S6.
Figure 6.
Figure 6.. NFAT5 activity corre
(A) Distribution of nuclear GFP-NFAT5 stably expressed in Nfat5−/−IMCD3 cells exposed to hypertonic stress (+200 mOsm/L NaCl added to isotonic media) in the presence or absence of 1% 1,6-hexanediol (1,6-HD) (left). The percentage of cells with nuclear puncta was calculated from >100 cells per point shown; the bar shows the mean of 6–7 independent measurements (right). (B) Expression of the NFAT5 target gene Akr1b3 in response to a 6 hr treatment of 0, 0.5, or 1% 1,6-HD in isotonic or hypertonic (+200 mOsm/L NaCl) media. Bars denotes the mean of 4 independent experiments shown as points. (C) Domain structure of NFAT5 with the positions of all glutamine residues marked with vertical blue lines (top). Amino acid composition in NFAT5 or its isolated CTD and PLD fragments compared to the composition in the human proteome (bottom). (D,E) Subcellular distribution (D) of full-length GFP-NFAT5 or the GFP-NFAT5 _QA mutant (all 109 glutamine residues in the PLD mutated to alanine) stably expressed from a single locus in Nfat5−/−IMCD3 cells after the addition of NaCl (+200 mOsm/L, 30 min) to isotonic media. Fluorescence signal from NFAT5 is shown alone (top) and merged with DAPI signal to show nuclei (bottom). Images of the type shown in (D) were used in (E) to measure nuclear NFAT5 fluorescence (left) and number of NFAT5 nuclear puncta (right) per cell (n>30 cells, with black horizontal line showing the median and each point showing the measurement in one cell). (F) Expression of the NFAT5 target gene Akr1b3 following the addition of NaCl to isotonic media (red arrowhead) for 8 hrs. (G) Domain structure of NFAT5 with the positions of all histidine residues marked by vertical blue lines. Red shading highlights the seven histidines within the PLD targeted for mutagenesis. Cross-species sequence conservation of a subset of these histidines is shown (top). (H) In vitro droplet formation propensity of purified (Figure S6A) GFP-CTD (70 iM, top row), GFP-CTD_HK (70 iM) and GFP-CTD_HF (70 iM) at the indicated NaCl concentrations. The seven histidines in the NFAT5 PLD highlighted in (G) were mutated to lysines or phenylalanines in GFP-CTD_HK and GFP-CTD_HF, respectively. Magnified insets show droplet shape (uniformly spherical for GFP-CTD and GFP-CTD_HK and both irregular and polymorphic for GFP-CTD_HF) (I) Phase diagrams for purified GFP-CTD_HK (left) and GFP-CTD_HF (right) (see Figure 5H for description). Shaded areas mark conditions where GFP-CTD_HK (green shading, left) or GFP-CTD_HF (gray shading, right) form droplets or aggregates, respectively. The blue trace indicates the position of the boundary between diffuse and droplet phases of WT GFP-CTD (from Figure 5H). Images were obtained across 3 biological replicates per condition. (J,K) Subcellular distribution (J) of full-length GFP-NFAT5 or the corresponding HK and HF mutants (see G) stably expressed from a single locus in Nfat5−/−IMCD3 cells after the addition of NaCl (+200 mOsm/L, 30 min) to isotonic media. Fluorescence signal from NFAT5 is shown alone (top) and merged with DAPI to mark nuclei (bottom). (K) Images of the type shown in (J) were used to measure the nuclear NFAT5 fluorescence (left) and number of NFAT5 nuclear puncta (right) per cell (n>30 cells, with black horizontal line showing the median and each point showing the measurement in one cell). Red arrowheads mark the isotonic condition. (L) Expression of the NFAT5 target gene Akr1b3 8 hrs after the addition of NaCl to isotonic media (red arrowheads). Bars denote the mean of 3 measurements, each shown as points. Representative of 4 independent experiments. In panels (F,K,L) red arrowheads indicate the isotonic (300 mOsm/L) condition. Scale bars for panels (D,J): 10 im; panel (H): 5 im. Statistics: For (A,B,F,L), statistical significance was determined by a two-way ANOVA test, Sidak’s multiple comparison. For (E,K) statistical significance was determined by a Kruskal-Wallis test, Dunn’s multiple comparison. P-value symbols are: **** p-value<0.0001 and *** p-value<0.001. See a<so Figure S7.
Figure 7.
Figure 7.. A mode< for hypertonic and ionic stress adaptation.
(A) Fluorescence microscopy (left) was used to measure the propensity of GFP, GFP-CTD, GFP-CTD_HK and GFP-CTD_HF (all green) to co-condense with the IDR of MED1 (mCherry-MED1iDR, red). All reactions contained 5% Dextran and the indicated concentrations of NaCl. Enrichment ratio (right) of GFP, GFP-CTD, or GFP-CTD mutants in MED1idr complex droplets (n>50 droplets). Solid horizontal lines denote the median from the individual measurements shown as points. Statistical significance was determined by a Kruskal-Wallis test, Dunn’s multiple comparison. P-value symbol is: **** p-value<0.0001. (B) Dual IDR-mediated responses to hypertonic and ionic stress in animal cells. The IDRs in WNK1 and NFAT5 each sense different chemical properties of the intracellular environment that are relevant to cell adaptation at short and long timescales. At short time points (min), increase in macromolecular crowding caused by water loss and cell shrinkage is sensed by the WNK1 IDR, triggering a kinase cascade that promotes net ion influx and rapid cell volume recovery (RVI). However, the rapid recovery of cell volume and intracellular water content comes at the cost of increased intracellular ionic strength, which is incompatible with cell survival over longer time scales (hours). The NFAT5 IDR senses this ionic stress and triggers a transcriptional response that allows replacement of these ions with osmolytes that are non-perturbing to macromolecules and organelles even at high concentrations. We speculate that NFAT5 has evolved to sense and facilitate adaptation to diverse ionic stressors (even those, like NH)OAc, that do not cause hypertonic stress).

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