This vignette from the R package JMDplots version 1.2.19-9 shows chemical metrics for proteins that are differentially expressed in eukaryotic cells exposed to hyperosmotic stress, compared to control conditions. The analysis is described in more detail in a paper (Dick, 2021). Abbreviations:
Differences are calculated as (median value for up-regulated proteins) - (median value for down-regulated proteins). Dashed lines enclose the 50% confidence region for highest probability density.
In the table, values of ΔZC and ΔnH2O are multiplied by 1000, values of ΔMW are multiplied by 100, and negative values are shown in bold. Abbreviations:
| set | reference (description) | ndown | nup | ΔZC | ΔnH2O | ΔnAA | ΔMW |
|---|---|---|---|---|---|---|---|
| a |
DAA+05 (thick ascending limb of Henle’s loop cells in 600 (NaCl added) vs 300 mosmol/kg medium)
|
14 | 24 | -35 | 18 | -106 | -87 |
| b |
MHN+08 (mouse CGR8 embryonic stem cells in 500 (NaCl added) vs 340 mOsM medium)
|
23 | 23 | -15 | 34 | 61 | -162 |
| c |
LTH+11 (Saccharomyces cerevisiae Protein in 0.7 M NaCl vs control medium for 30 min)
|
686 | 203 | 6 | 6 | 6 | -79 |
| d |
LTH+11 (Saccharomyces cerevisiae Protein in 0.7 M NaCl vs control medium for 60 min)
|
554 | 335 | 6 | -16 | 22 | -62 |
| e |
LTH+11 (Saccharomyces cerevisiae Protein in 0.7 M NaCl vs control medium for 90 min)
|
537 | 352 | 5 | -9 | 48 | -62 |
| f |
LTH+11 (Saccharomyces cerevisiae Protein in 0.7 M NaCl vs control medium for 120 min)
|
538 | 351 | 4 | -14 | 36 | -79 |
| g |
LTH+11 (Saccharomyces cerevisiae Protein in 0.7 M NaCl vs control medium for 240 min)
|
564 | 325 | -2 | -10 | 28 | -100 |
| h |
OBBH11 (adipose-derived stem cells in 400 mOsm vs 300 mOsm NaCl)
|
148 | 144 | -4 | 24 | -68 | -1 |
| i |
LFY+12 (cytoplasm of HEK293 cells in 500 (NaCl added) vs 300 mosmol/kg medium for 1 h)
|
19 | 36 | 19 | -42 | 121 | 188 |
| j |
LFY+12 (cytoplasm of HEK293 cells in 500 (NaCl added) vs 300 mosmol/kg medium for 8 h)
|
20 | 34 | -20 | 5 | 16 | -8 |
| k |
LFY+12 (cytoplasm of HEK293 cells in 500 (NaCl added) vs 300 mosmol/kg medium for 2 passages)
|
33 | 66 | -6 | -68 | -47 | 84 |
| l |
LFY+12 (nucleus of HEK293 cells in 500 (NaCl added) vs 300 mosmol/kg medium for 1 h)
|
49 | 80 | -12 | 9 | 138 | -42 |
| m |
LFY+12 (nucleus of HEK293 cells in 500 (NaCl added) vs 300 mosmol/kg medium for 8 h)
|
39 | 64 | -18 | 5 | 138 | -90 |
| n |
LFY+12 (nucleus of HEK293 cells in 500 (NaCl added) vs 300 mosmol/kg medium for 2 passages)
|
22 | 67 | -15 | -36 | -97 | 112 |
| o |
CLG+15 (human conjunctival epithelial cells in 380 or 480 mOsm vs 280 mOsm NaCl)
|
25 | 38 | -4 | 26 | -110 | -37 |
| p |
SCG+15 (Saccharomyces cervisiae in 0.4 M NaCl vs control - nodelay)
|
567 | 266 | -14 | -13 | -14 | -21 |
| q |
SCG+15 (Saccharomyces cervisiae in 0.4 M NaCl vs control - delayed)
|
219 | 67 | 5 | -29 | -55 | -16 |
| r |
YDZ+15 (Yarrowia lipolytica in 4.21 osmol/kg vs 3.17 osmol/kg NaCl)
|
14 | 28 | 16 | -47 | -98 | -12 |
| s |
GAM+16 (human small airway epithelial cells in HTS vs isotonic)
|
211 | 396 | 17 | 5 | 184 | -53 |
| t |
GAM+16 (human small airway epithelial cells in HTS.Cmx vs isotonic.Cmx)
|
303 | 250 | 6 | 4 | 172 | -12 |
| u |
RBP+16 (Paracoccidioides lutzii in 0.1 M KCl vs medium with no added KCl)
|
160 | 141 | 3 | -53 | 0 | 3 |
| v |
JBG+18 (Candida albicans in 1 M NaCl vs medium with no added NaCl)
|
84 | 63 | -2 | -27 | -15 | -125 |
a. Tables II–III of Dihazi et al. (2005). b. Table 1 of Mao et al. (2008). c. d. e. f. g. Dataset S3 of Lee et al. (2011), filtered to include proteins with q-value < 0.05, same direction of change in all 3 replicates for each condition, and median log fold change > 0.2. h. Supplementary Table 1 of Oswald et al. (2011). i. j. k. l. m. n. Supplementary Table S1 of Li et al. (2012) (sheet “All proteins”), filtered to include proteins with q-value < 0.1. o. Table 2 of Chen et al. (2015). p. q. Supplemental Data S1 of Selevsek et al. (2015) (file “ClusterGroup.AllProteins.051814.csv”), filtered to include proteins in clusters 1–4 (differential expression at all time points (1/4) or after > 20 min delay (2/3)). r. Table 1 of Yang et al. (2015). s. t. Supplementary Table 2 of Gamboni et al. (2016), filtered to include proteins with fold change > 2 or < 0.5. u. Supplementary Tables 2 and 3 of Silva Rodrigues et al. (2016). v. Supplementary Tables 1 and 2 of Jacobsen et al. (2018).
Chen L, Li J, Guo T, Ghosh S, Koh SK, Tian D, Zhang L, Jia D, Beuerman RW, Aebersold R, Chan ECY, Zhou L. 2015. Global metabonomic and proteomic analysis of human conjunctival epithelial cells (IOBA-NHC) in response to hyperosmotic stress. Journal of Proteome Research 14:3982–3995. DOI: 10.1021/acs.jproteome.5b00443.
Dihazi H, Asif AR, Agarwal NK, Doncheva Y, Müller GA. 2005. Proteomic analysis of cellular response to osmotic stress in thick ascending limb of Henle’s loop (TALH) cells. Molecular & Cellular Proteomics 4:1445–1458. DOI: 10.1074/mcp.M400184-MCP200.
Gamboni F, Anderson C, Mitra S, Reisz JA, Nemkov T, Dzieciatkowska M, Jones KL, Hansen KC, D’Alessandro A, Banerjee A. 2016. Hypertonic saline primes activation of the p53–p21 signaling axis in human small airway epithelial cells that prevents inflammation induced by pro-inflammatory cytokines. Journal of Proteome Research 15:3813–3826. DOI: 10.1021/acs.jproteome.6b00602.
Jacobsen MD, Beynon RJ, Gethings LA, Claydon AJ, Langridge JI, Vissers JPC, Brown AJP, Hammond DE. 2018. Specificity of the osmotic stress response in Candida albicans highlighted by quantitative proteomics. Scientific Reports 8:14492. DOI: 10.1038/s41598-018-32792-6.
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Mao L, Hartl D, Nolden T, Koppelstätter A, Klose J, Himmelbauer H, Zabel C. 2008. Pronounced alterations of cellular metabolism and structure due to hyper- or hypo-osmosis. Journal of Proteome Research 7:3968–3983. DOI: 10.1021/pr800245x.
Oswald ES, Brown LM, Bulinski JC, Hung CT. 2011. Label-free protein profiling of adipose-derived human stem cells under hyperosmotic treatment. Journal of Proteome Research 10:3050–3059. DOI: 10.1021/pr200030v.
Selevsek N, Chang C-Y, Gillet LC, Navarro P, Bernhardt OM, Reiter L, Cheng L-Y, Vitek O, Aebersold R. 2015. Reproducible and consistent quantification of the Saccharomyces cerevisiae proteome by SWATH-mass spectrometry. Molecular & Cellular Proteomics 14:739–749. DOI: 10.1074/mcp.M113.035550.
Silva Rodrigues LN da, Almeida Brito W de, Parente AFA, Weber SS, Bailão AM, Casaletti L, Borges CL, Almeida Soares CM de. 2016. Osmotic stress adaptation of Paracoccidioides lutzii, Pb01, monitored by proteomics. Fungal Genetics and Biology 95:13–23. DOI: 10.1016/j.fgb.2016.08.001.
Yang L-B, Dai X-M, Zheng Z-Y, Zhu L, Zhan X-B, Lin C-C. 2015. Proteomic analysis of erythritol-producing Yarrowia lipolytica from glycerol in response to osmotic pressure. Journal of Microbiology and Biotechnology 25:1056–1069. DOI: 10.4014/jmb.1412.12026.