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Table 3 Abundance differences of Y. pestis proteins profiled in cytoplasmic fractions of iron-rich vs. iron-starved cells

From: Proteomic analysis of iron acquisition, metabolic and regulatory responses of Yersinia pestis to iron starvation

Spot No a) Gene locus
b)
gene name
c)
Protein description c) Subc. Loc.
d)
Fur/RyhB e) Mascot Score
f)
exp Mr (Da) exp pI 26°C, Vs (-Fe) g) 26°C, Vs (+Fe) h) 26-ratio -Fe/+Fe i) 26°C P-value j) 37-ratio -Fe/+Fe k)
1 y0015 aceB malate synthase A CY Fur 688 63974 5.86 0.06 1.73 0.036 0.000 0.421
2 y0016 aceA isocitrate lyase CY   741 54571 5.47 0.38 4.19 0.090 0.000 0.408
3 y0047 glpK glycerol kinase CY   828 60235 6.01 0.07 0.33 0.198 0.000 0.570
4 y0320 oxyR DNA-binding transcriptional regulator OxyR CY   510 36649 5.82 0.49 0.40 1.237 0.004 0.791
5 y0548 metF2 putative methylenetetrahydrofolate reductase U   321 31848 5.73 1.77 1.06 1.677 0.000 0.543
6 y0617 frdA fumarate reductase, anaerobic, flavoprotein subunit PP   437 80764 5.77 - 0.23 < 0.05 N.D. 0.339
7 y0668 mdh malate dehydrogenase ML   2170 34545 5.55 1.03 1.80 0.576 0.001 1.253
8 y0771 acnB aconitate hydrase B CY RyhB 1408 95757 5.13 0.22 0.98 0.220 0.000 0.229
9 y0801 erpA iron-sulfur cluster insertion protein ErpA U   76 10730 4.41 1.41 0.57 2.492 0.008 1.260
10 y0818 cysJ sulfite reductase subunit alpha U   340 72332 4.97 - 0.20 < 0.05 N.D. < 0.05
11 y0854 fumA fumarase A CY RyhB 255 68184 6.02 - 0.50 < 0.05 N.D. < 0.05
12 y0870 katY catalase; hydroperoxidase HPI(I) U   768 78569 6.32 0.11 0.48 0.231 0.000 0.081
13 y0888 luxS predicted S-ribosylhomocysteinase CY   670 19733 5.46 0.79 0.30 2.617 0.000 2.164
14 y0988 ahpC putative peroxidase CY   898 24298 5.75 5.02 6.10 0.823 0.202 1.376
15 y1069 ymt murine toxin U   7052 67771 5.64 13.61 9.61 1.415 0.143 1.359
16 y1069 ymt murine toxin, C-t. fragment U   245 33893 5.30 0.89 0.19 4.634 0.000 N.D.
17 y1069 ymt murine toxin, N-t. fragment U   164 39074 6.11 0.84 0.17 4.860 0.000 N.D.
18 y1208 fur ferric uptake regulator CY   95 13425 6.16 0.11 0.17 0.651 0.055 N.D.
19 y1282 yfiD formate acetyltransferase, glycyl radical cofactor GrcA CY   521 13866 4.75 1.27 2.27 0.560 0.000 0.456
20 y1334 iscS selenocysteine lyase/cysteine desulfurase U   408 51519 5.96 - - N.D. N.D. 0.59
21 y1339 hscA chaperone protein HscA CY   384 49149 5.53 - - N.D. N.D. 0.48
22 y1342 pepB aminopeptidase B U   855 52355 5.69 0.12 0.75 0.153 0.000 0.681
23 y1452 ypeA predicted acyltransferase CY   188 12771 4.83 0.39 0.14 2.844 0.000 3.300
24 y1677 dps DNA starvation/stationary phase protection protein U   724 14844 5.94 0.27 0.80 0.337 0.000 0.808
25 y1791 pepT putative peptidase T CY   310 51106 5.89 - 0.18 < 0.05 N.D. N.D.
26 y1802 icdA isocitrate dehydrogenase, specific for NADP+ CY   459 53760 5.46 0.92 1.80 0.511 0.002 1.238
27 y1934 sufA iron-sulfur cluster assembly scaffold protein SufA U Fur 156 13330 4.48 0.13 - > 20 N.D. 2.170
28 y1935 sufB cysteine desulfurase activator complex subunit SufB U Fur 330 70431 4.69 0.25 0.06 4.022 0.000 3.836
29 y1938 sufS selenocysteine lyase U Fur 369 46479 5.55 0.65 0.15 4.294 0.000 2.420
30 y1944 pykF pyruvate kinase I CY   525 62400 5.93 0.38 1.23 0.309 0.525 1.265
31 y1951 sodB superoxide dismutase, iron U RyhB 285 21541 5.75 0.16 0.94 0.172 0.000 >20
32 y1968 gst glutathionine S-transferase CY   1326 25438 6.25 3.15 2.14 1.471 0.054 1.247
33 y1990 tpx thiol peroxidase U   479 18655 5.13 3.02 3.06 0.986 0.816 1.198
34 y2063 acnA aconitate hydratase A CY RyhB 565 97825 6.08 - 0.22 < 0.05 N.D. < 0.05
35 y2255 yebC hypothetical protein y2255 U   219 39957 4.74 0.11 0.40 0.285 0.000 0.777
36 y2524 ftnA ferritin iron storage complex protein CY RyhB 223 14143 4.99 2.67 1.61 1.656 0.000 1.275
37 y2790 pflB formate acetyltransferase 1 CY   804 80979 5.49 0.63 1.38 0.454 0.000 0.980
38 y2802 trxB thioredoxin reductase ML   702 37892 5.21 0.96 0.99 0.967 0.446 1.037
39 y2821 poxB pyruvate oxidase CY   448 67362 5.91 1.89 0.33 5.722 0.000 3.710
40 y2981 katE catalase; hydroperoxidase HPII(III) CY RyhB 481 66313 6.09 0.04 1.20 0.032 0.000 0.113
41 y3064 sucD succinyl-CoA synthetase, alpha subunit CY   597 33015 6.04 0.33 0.91 0.363 0.000 0.472
42 y3067 sucA 2-oxoglutarate dehydrogenase (decarboxylase component) CY   1153 102739 5.98 - 0.43 < 0.05 N.D. 0.277
43 y3069 sdhA succinate dehydrogenase, flavoprotein subunit ML RyhB 965 75497 5.56 0.05 0.21 0.248 0.000 0.207
44 y3142 fldA3 predicted flavodoxin CY   267 11842 4.37 0.93 0.39 2.395 0.003 1.502
45 y3499 yqhD NADP-dependent dehydrogenase CY   369 46727 5.76 0.35 1.922 0.179 0.001 1.404
46 y3600 uxaC D-glucuronate/D-galacturonate isomerase U   842 56072 5.75 0.09 - > 20 N.D. 2.383
47 y3673 hcp1 hemolysin-coregulated protein U   508 14459 5.16 8.35 4.38 1.908 0.001 N.D.
48 y3675 - putative type VI secretion protein CY   392 25923 4.62 0.43 0.16 2.735 0.001 N.D.
49 y3802 bipA putative GTP-binding factor CY   435 82945 5.27 - - N.D. N.D. 4.096
50 y3966 tauD taurine dioxygenase U   228 40946 6.12 0.50 0.16 3.129 0.001 N.D.
51 y3988 bfr bacterioferritin, iron storage and detoxification protein CY RyhB 143 17087 4.92 0.22 0.29 0.779 0.006 0.927
52 y4080 sodA superoxide dismutase, manganese U   597 25405 5.86 4.11 5.10 0.805 0.074 0.877
75 y2402 ybtT yersiniabactin thioesterase U Fur 123 34389 5.88 0.10 - > 20 N.D. 12.08
111 y3066 sucB 2-oxoglutarate dehydrogenase (dihydrolipoyltranssuccinase E2 component) CY   789 58844 5.38 0.29 0.76 0.38 0.0468 0.38
  1. a) spot number as denoted in Figure 4; b) protein accession number and locus tag as listed in Y. pestis KIM genome database (NCBI); c) gene name and protein description from the KIM database or a conserved E. coli K12 ortholog http://www.ecocyc.org, if >65 pct. sequence identity; d) subcellular localization based on PSORTb data: CY, cytoplasm; ML: multiple localizations; PP, periplasm; U: unknown; e) proven or putative regulation by Fur or a Fur-dependent small RNA (e.g. RyhB); f) highest Mascot score for a protein from LC-MS/MS or MALDI data; g) Vs (-Fe): average spot volume (n ≥ 3) in 2D gels for iron-depleted growth conditions at 26°C as shown in Figure 4; h) Vs (+Fe): average spot volume (n ≥ 3) in 2D gels for iron-supplemented growth conditions at 26°C; i) spot volume ratio (-Fe/+Fe) at 26°C, N.D.: not determined; -: no spot detected; j) two-tailed t-test p-value for spot abundance change at 26°C, 0.000 stands for < 0.001; k) average spot volume ratio (-Fe/+Fe) at 37°C; additional data for the statistical spot analysis at 37°C are part of Additional Table 1.