Table 2.
Abundance differences of Y. pestis proteins profiled in membrane 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) | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 94 | y0032 | lamB | Maltoporin | OM | 331 | 48645 | [4.95 - 5.09] | 0.76 | 1.49 | 0.516 | 0.000 | 1.27 | ||
| 95 | y0543 | hmuR | hemin outer membrane receptor | OM | Fur | 1064 | 76570 | 5.05 | 0.25 | 0.10 | 2.600 | 0.000 | 4.665 | |
| 96 | y0850 | - | putative iron/chelate outer membrane receptor | OM | Fur | 57 | 70302 | [5.5 - 6.0] | 1.54 | 0.22 | 6.978 | 0.000 | 2.430 | |
| 97 | y1355 | - | hypothetical inner membrane protein y1355 | U | 53 | 22715 | 5.59 | 0.32 | 0.57 | 0.560 | 0.000 | 0.820 | ||
| 98 | y1577 | fadL | long-chain fatty acid transport protein (OM receptor) | OM | 1008 | 51392 | [4.77 - 4.87] | 0.37 | 0.81 | 0.460 | 0.000 | 0.370 | ||
| 99 | y1632 | nuoC | NADH dehydrogenase I chain C, D | CY | 654 | 68079 | [5.79 - 5.9] | 0.07 | 0.18 | 0.367 | 0.000 | 0.578 | ||
| 100 | y1682 | ompX | outer membrane protein X | OM | 389 | 18271 | 5.31 | 5.65 | 3.08 | 1.859 | 0.000 | 0.557 | ||
| 101 | y1919 | arnA | bifunctional UDP-glucuronic acid decarboxylase/UDP-4-amino-4-deoxy-L-arabinose formyltransferase | U | 346 | 72392 | [5.86 - 5.92] | 0.76 | 0.20 | 3.748 | 0.000 | > 20 | ||
| 102 | y2404 | psn | pesticin/yersiniabactin outer membrane receptor | OM | Fur | 148 | 67582 | [5.20 - 5.45] | 6.80 | 1.46 | 4.862 | 0.000 | 2.656 | |
| 103 | y2556 | fcuA | ferrichrome receptor, TonB dependent | OM | Fur | 801 | 76097 | [5.64 - 5.94] | 0.20 | 0.18 | 1.070 | 0.710 | 0.860 | |
| 104 | y2633 | ysuR | outer membrane iron/siderophore receptor | OM | Fur | 202 | 73135 | 6.30 | 0.11 | 0.04 | 2.790 | 0.001 | N.D. | |
| 105 | y2735 | ompA | outer membrane porin A, N-t. fragment | OM | 686 | 34018 | [5.52 - 5.75] | 5.05 | 0.70 | 7.245 | 0.000 | 3.390 | ||
| 106 | y2872 | yiuR | putative iron/siderophore outer membrane receptor | OM | Fur | 133 | 67256 | 5.55 | 0.65 | 0.29 | 2.260 | 0.000 | N.D. | |
| 107 | y2966 | ompC | outer membrane porin protein C | OM | 1110 | 43707 | [4.78 - 4.88] | 2.18 | 1.45 | 1.500 | 0.010 | 0.487 | ||
| 108 | y2980 | yfaZ | hypothetical protein y2980 | CM | 96 | 20054 | 5.48 | 0.30 | 0.66 | 0.459 | 0.000 | 0.202 | ||
| 109 | y2983 | phoE | putative outer membrane porin | OM | 65 | 41703 | [4.94 - 5.22] | - | 14.60 | < 0.05 | N.D. | < 0.05 | ||
| 110 | y3674 | - | putative type VI secretion system protein | U | 350 | 63614 | [5.52 - 5.58] | 0.72 | 0.44 | 1.620 | 0.002 | N.D. | ||
a) spot number as denoted in Figure 3; 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; CM: inner membrane; OM: outer membrane; 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 3; 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. Experimental pI values span a pH range because proteins were visualized as spot trains.