This vignette from the R package JMDplots version 1.2.19-9 shows chemical metrics for proteins that are differentially expressed in halophiles under hyperosmotic or hypoosmotic conditions. The analysis is described in more detail in a paper (Dick et al., 2020). Abbreviations:
Differences are calculated as (median value for up-regulated proteins) - (median value for down-regulated proteins). Circles and squares represent hyperosmotic and hypoosmotic experiments, respectively.
In the table, values of ΔZC, ΔnH2O, and ΔGRAVY are multiplied by 1000, values of ΔpI and ΔMW are multiplied by 100, and negative values are shown in bold. Abbreviations:
| set | reference (description) | ndown | nup | ΔZC | ΔnH2O | ΔpI | ΔGRAVY | ΔnAA | ΔMW |
|---|---|---|---|---|---|---|---|---|---|
| a |
LRB+09 (Halobacterium salinarium 2.6 M / 4.3 M NaCl)
|
105 | 62 | -8 | -45 | -8 | 64 | 82 | -77 |
| b |
LRB+09 (Halobacterium salinarium 5.1 M / 4.3 M NaCl)
|
74 | 64 | 2 | -12 | 0 | 21 | 102 | -90 |
| c |
ZLZ+16 (Nocardiopsis xinjiangensis 6% / 10% NaCl)
|
146 | 131 | -10 | -6 | 19 | 97 | 58 | 50 |
| d |
ZLZ+16 (Nocardiopsis xinjiangensis 17.5% / 10% NaCl)
|
57 | 82 | -13 | 9 | 60 | 202 | 194 | -115 |
| e |
LLYL17 (Tetragenococcus halophilus 0 M / 1 M NaCl)
|
47 | 131 | -59 | -15 | 65 | 149 | -24 | 217 |
| f |
LLYL17 (Tetragenococcus halophilus 3.5 M / 1 M NaCl)
|
92 | 39 | 36 | -13 | -92 | -44 | 54 | -135 |
| g |
JSP+19 (Haloferax volcanii 10.8% / 15% NaCl)
|
278 | 109 | -2 | 29 | -5 | -43 | -82 | 87 |
| h |
JSP+19 (Haloferax volcanii 19.2% / 15% NaCl)
|
337 | 159 | -5 | 2 | -9 | 39 | 121 | -26 |
a. b. Tables 1 and 2 of Leuko et al. (2009). c. d. Table S-1 of Zhang et al. (2016). Values of reporter intensities at each condition (6%, 10%, and 17.5% NaCl) were quantile normalized (R function preprocessCore::normalize.quantiles); normalized values were used to compute intensity ratios (6% / 10% NaCl and 17.5% / 10% NaCl). Only proteins with expression ratios > 1.3 in either direction (Zhang et al., 2016), p-values < 0.05, and at least 2 peptides were included. e. f. Tables S2 and S3 of Lin et al. (2017). g. h. Supporting Table 1C of Jevtić et al. (2019). Only proteins with at least 2-fold expression difference and marked as significant were included.
Jevtić Ž, Stoll B, Pfeiffer F, Sharma K, Urlaub H, Marchfelder A, Lenz C. 2019. The response of Haloferax volcanii to salt and temperature stress: A proteome study by label-free mass spectrometry. Proteomics 19:1800491. DOI: 10.1002/pmic.201800491.
Leuko S, Raftery MJ, Burns BP, Walter MR, Neilan BA. 2009. Global protein-level responses of Halobacterium salinarum NRC-1 to prolonged changes in external sodium chloride concentrations. Journal of Proteome Research 8:2218–2225. DOI: 10.1021/pr800663c.
Lin J, Liang H, Yan J, Luo L. 2017. The molecular mechanism and post-transcriptional regulation characteristic of Tetragenococcus halophilus acclimation to osmotic stress revealed by quantitative proteomics. Journal of Proteomics 168:1–14. DOI: 10.1016/j.jprot.2017.08.014.
Zhang Y, Li Y, Zhang Y, Wang Z, Zhao M, Su N, Zhang T, Chen L, Wei W, Luo J, Zhou Y, Xu Y, Xu P, Li W, Tao Y. 2016. Quantitative proteomics reveals membrane protein-mediated hypersaline sensitivity and adaptation in halophilic Nocardiopsis xinjiangensis. Journal of Proteome Research 15:68–85. DOI: 10.1021/acs.jproteome.5b00526.