Table 1.
Abundance differences of Y. pestis proteins profiled in periplasmic 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) | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 53 | y0028 | malE | periplasmic maltose-binding protein | PP | 2150 | 43937 | 5.53 | 0.72 | 5.98 | 0.121 | 0.000 | 0.760 | ||
| 54 | y0137 | degQ | serine endoprotease | PP | 1077 | 55588 | 6.43 | 0.39 | 0.11 | 2.41 | 0.0177 | 0.900 | ||
| 55 | y0291 | - | putative tospovirus resistance protein D | U | 486 | 18721 | 5.44 | 2.05 | 0.47 | 4.320 | 0.000 | N.D. | ||
| 56 | y0541 | hmuT | hemin-binding periplasmic protein | PP | Fur | 228 | 27164 | 5.85 | 0.46 | 0.11 | 4.328 | 0.000 | > 20 | |
| 57 | y0542 | hmuS | hemin uptake system component | U | Fur | 989 | 38188 | 5.56 | 0.53 | 0.19 | 2.780 | 0.000 | 2.091 | |
| 58 | y0869 | cybC | cytochrome b(562) | PP | Fur | 626 | 5035 | 5.64 | 0.13 | 0.03 | 4.746 | N.D. | 3.160 | |
| 59 | y0964 | frsA | fermentation/respiration switch protein | U | 586 | 51326 | 5.98 | 0.15 | 0.07 | 2.208 | 0.000 | 1.875 | ||
| 60 | y1128 | bglX | putative beta-glucosidase | PP | 2324 | 81506 | 5.43 | 3.01 | 0.52 | 5.822 | 0.000 | 1.740 | ||
| 61 | y1189 | gltI | solute-binding periplasmic protein of glutamate/aspartate ABC transporter | PP | 2512 | 35927 | 7.20 | 0.41 | 2.91 | 0.141 | 0.005 | N.D. | ||
| 62 | y1223 | nrdE | ribonucleoside-diphosphate reductase 2, alpha subunit | U | Fur | 198 | 79914 | 6.32 | 0.03 | - | > 20 | N.D. | N.D. | |
| 63 | y1222 | nrdF | ribonucleoside-diphosphate reductase 2, beta chain | U | Fur | 561 | 39335 | 5.11 | 0.77 | - | > 20 | N.D. | > 20 | |
| 64 | y1430 | - | putative putative periplasmic iron-binding signal peptide protein | U | 3359 | 41211 | 6.09 | - | 0.57 | < 0.05 | N.D. | < 0.05 | ||
| 65 | y1526 | yfuA | putative solute-binding protein for iron ABC transporter | PP | Fur | 1979 | 39620 | 6.65 | 2.36 | 1.46 | 1.618 | 0.061 | N.D. | |
| 66 | y1607 | hisJ | histidine-binding periplasmic protein of high-affinity histidine transport system | PP | 1494 | 31529 | 5.01 | 0.29 | 0.93 | 0.309 | 0.000 | 0.350 | ||
| 67 | y1744 | - | hypothetical protein y1744 | CY | 324 | 5183 | 5.92 | 0.38 | - | > 20 | N.D. | 4.510 | ||
| 68 | y1897 | yfeA | periplasmic-binding protein for iron and manganese ABC transporter | CM | Fur | 1201 | 31395 | 5.80 | 2.87 | 0.63 | 4.576 | 0.000 | 4.780 | |
| 69 | y1936 | sufC | iron-sulfur cluster assembly protein SufC, ATPase component | ML | Fur | 726 | 28460 | 5.10 | 0.16 | 0.02 | 7.514 | 0.000 | > 20 | |
| 70 | y1937 | sufD | cysteine desulfurase activator complex subunit SufD | U | Fur | 369 | 60476 | 6.76 | 0.06 | - | > 20 | N.D. | N.D. | |
| 71 | y2358 | hmsF | hemin storage system, HmsF protein | U | 542 | 61790 | 5.47 | 0.40 | 0.12 | 3.467 | 0.000 | 1.480 | ||
| 72 | y2368 | - | putative ferrous iron transport protein | U | 532 | 13556 | 5.29 | 1.71 | 1.64 | 1.030 | 0.390 | 2.330 | ||
| 73 | y2394 | ybtS | anthranilate synthase | CY | Fur | 1323 | 50265 | 5.82 | 1.65 | 0.36 | 4.538 | 0.000 | > 20 | |
| 74 | y2401 | ybtU | thiazolinyl-S-HMWP1 reductase of Ybt system | U | Fur | 351 | 48765 | 6.63 | 0.33 | 0.11 | 3.057 | 0.006 | N.D. | |
| 76 | y2403 | ybtE | salicyl-AMP ligase | CY | Fur | 1205 | 58276 | 5.43 | 2.04 | 0.31 | 6.660 | 0.000 | 7.060 | |
| 77 | y2451 | efeO | putative ferrous iron transport protein | U | 998 | 38614 | 4.96 | 1.71 | 0.90 | 1.896 | 0.000 | 1.274 | ||
| 78 | y2638 | ysuG | siderophore biosynthetic protein of the Ysu system | U | Fur | 182 | 77918 | 5.36 | 0.06 | - | > 20 | N.D. | N.D. | |
| 79 | y2662 | mglB | periplasmic D-galactose-binding ABC transport protein | PP | 1440 | 33113 | 5.40 | 0.51 | 1.53 | 0.330 | 0.000 | 0.251 | ||
| 80 | y2828 | pheA | putative chorismate mutase | PP | 630 | 14433 | 5.88 | 0.86 | 0.05 | 19.293 | 0.000 | 2.817 | ||
| 81 | y2842 | - | putative periplasmic binding protein of iron/siderophore ABC transporter | U | 1096 | 51189 | 5.97 | 0.62 | 1.87 | 0.332 | 0.000 | 0.501 | ||
| 82 | y2875 | yiuA | solute-binding periplasmic protein of iron/siderophore ABC transporter | U | Fur | 1690 | 46030 | 6.69 | 0.73 | 0.37 | 1.957 | 0.002 | N.D. | |
| 83 | y3037 | modA | molybdate-binding periplasmic protein of molybdate ABC transporter | PP | 2136 | 27031 | 5.55 | 0.17 | 0.72 | 0.234 | 0.000 | 2.089 | ||
| 84 | y0815 | sodC | periplasmic superoxide dismutase (Cu-Zn) | PP | 695 | 16562 | 7.54 | 0.55 | 0.63 | 0.89 | 0.4490 | N.D. | ||
| 85 | y3165 | ptr | protease III | PP | 1794 | 96878 | 5.60 | 2.71 | 1.86 | 1.454 | 0.001 | 1.032 | ||
| 86 | y3676 | - | putative type VI secretion system protein | CY | 375 | 50035 | 4.81 | 0.29 | - | > 20 | N.D. | N.D. | ||
| 87 | y3772 | lsrB | putative periplasmic autoinducer II-binding protein | U | 917 | 36377 | 6.30 | 0.31 | 1.96 | 0.159 | 0.000 | N.D. | ||
| 88 | y3812 | dsbA | protein disulfide isomerase I | PP | 1587 | 22454 | 5.91 | 2.57 | 1.18 | 2.176 | 0.000 | 0.910 | ||
| 89 | y3825 | dppA | periplasmic dipeptide transport protein of ABC transporter | PP | 1253 | 54903 | 5.52 | 0.68 | 2.46 | 0.277 | 0.000 | 0.696 | ||
| 90 | y3837 | yhjJ | predicted zinc-dependent peptidase | U | 1215 | 62177 | 5.10 | 0.44 | 0.17 | 2.613 | 0.000 | 0.720 | ||
| 91 | y3956 | crp | cAMP-regulatory protein | CY | 220 | 26494 | 7.82 | 0.06 | - | > 20 | N.D. | N.D. | ||
| 92 | y3977 | fkpA | FKBP-type peptidyl-prolyl cis-trans isomerase | PP | 2031 | 33670 | 6.94 | 5.50 | 3.45 | 1.594 | 0.007 | N.D. | ||
| 93 | y4125 | - | putative solute-binding periplasmic protein precursor for ABC transporter | PP | 2766 | 30250 | 6.27 | 6.09 | 3.67 | 1.661 | 0.001 | 2.264 | ||
a) spot number as denoted in Figures 1 and 2; 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; CM: inner membrane; 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 Figures 1-2; 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. exp.pI/Mr = experimental pI and Mr values.