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