Table 2. Identification of proteins found to be differentially expressed in H. pylori strains from PUD patients (n = 5) compared to NUD patients (n = 5).
| Theoretical | % Vol | |||||||||||||||
| Spot no. | Protein | Cellular function | ORF | Swiss-Prot/NCBI no. | Mw (kDa) | pI | MOWSE score | Peptides matched | Sequence coverage (%) | Average NUD ± S.D | Average DU ± S.D | Variation (DU/NUD) | p value | Variation (GU/DU) | ||
| 1 | CagA, Cytotoxin associated protein A | Induces abnormal proliferation; tight junctions disruption; cytoskeleton rearrangements | HP0547 | gi|307135439 | 131 | 8.9 | 82 | * | 10/16 | 7 | absent | 1.558±0.487 | ↑ | 5.265E-08 | * | ↓ |
| 2 | FlgE, Flagellar hook protein | Component of bacteria flagellum basal body | HP0870 | Q9ZKY0 | 76 | 5.0 | 71 | * | 12/35 | 17 | 0.077±0.036 | 0.136±0.055 | ↑ | 2.099E-02 | * | ↑ |
| 3 | FlaA, Flagellin A | Major component of bacteria flagellum | HP0601 | P0A0S2 | 53 | 6.0 | 121 | * | 14/37 | 14 | 2.130±0.794 | 3.063±0.941 | ↑ | 4.706E-02 | * | ↑ |
| 4 | HspB, Chaperone and heat shock protein | Protein folding/stress response | HP0010 | B6JPA7 | 58 | 5.4 | 93 | * | 18/55 | 26 | 5.021±0.556 | 5.856±0.533 | ↑ | 7.801E-03 | * | - |
| 5 | UreB, Urease beta subunit | Urea metabolism | P14917 | P69996 | 62 | 5.6 | Comparison to 2DE database | 8.815±1.310 | 10.477±1.455 | ↑ | 3.551E-02 | * | ↓ | |||
| 6 | HyuA, Hydantoin utilization protein A | Arginine and proline metabolism | HP0695 | gi|108563105 | 79 | 6.4 | 105 | * | 24/100 | 20 | 0.503±0.128 | 0.204±0.110 | ↓ | 4.079E-04 | * | - |
| 7 | Unknown | — | — | — | — | — | — | 1.094±0.702 | absent | ↓ | 2.706E-04 | * | - | |||
| 8 | RpsA, 30S Ribosomal protein s1 | Translation process | HP0399 | P56008 | 63 | 6.3 | Comparison to 2DE database | 0.126±0.029 | 0.085±0.022 | ↓ | 1.141E-02 | * | - | |||
| 9 | KatA, Catalase | Detoxification | HP0875 | P77872 | 59 | 8.7 | 161 | * | 21/48 | 37 | 4.833±0.962 | 2.669±0.621 | ↓ | 1.292E-04 | * | - |
| 10 | CysS, Cysteinyl-tRNA synthetase | Translation process | HP0886 | B5Z7P5 | 53 | 6.0 | 28 | 4/23 | 8 | 0.152±0.091 | 0.027±0.024 | ↓ | 2.615E-03 | * | - | |
| 11 | AspA, Aspartate ammonia-lyase | Catalyzes the deamination of aspartate originating fumarate | HP0649 | gi|207108618 | 35 | 8.5 | 58 | 5/23 | 10 | 0.396±0.097 | 0.252±0.089 | ↓ | 9.261E-03 | * | - | |
| 12 | Pgk, Phosphoglycerate kinase | Glucose metabolism | HP1345 | gi|261838924 | 44 | 6.3 | 86 | * | 10/33 | 27 | 0.213±0.064 | 0.303±0.069 | ↑ | 2.525E-02 | * | ↑ |
| 13 | HPAG1_1081, Hypothetical protein | Putative function in cell shape | HP1143 | gi|108563506 | 51 | 5.5 | 77 | * | 11/23 | 15 | absent | 0.200±0.072 | ↑ | 3.577E-07 | * | absent |
| 14 | EF-Ts, Elongation factor Ts | Translation process | HP1555 | B6JP47 | 40 | 6.2 | 76 | * | 7/13 | 16 | 0.606±0.101 | 0.613±0.185 | ↔ | 9.206E-01 | normal position | |
| 15 | Putative aldo-keto reductase | Catalyze the reduction of aldehydes and ketones to the corresponding alcohol product | HP1193 | gi|254779741 | 37 | 6.7 | 86 | * | 8/18 | 22 | 0.015±0.040 | 0.147±0.224 | ↑ | 7.418E-03 | * | ↓ |
| 16 | HELPY_0944, Hypothetical protein | Motility | HP0958 | gi|254779556 | 30 | 5.6 | 99 | * | 13/46 | 41 | 0.231±0.080 | 0.165±0.026 | ↓ | 8.453E-02 | - | |
| 17 | HP_1588, UPF0174 protein | Unknown | HP1588 | O26107 | 29 | 5.5 | 85 | * | 8/17 | 15 | 0.322±0.123 | 0.563±0.373 | ↑ | 2.293E-03 | * | ↓ |
| 18 | HP_1588, UPF0174 protein | Unknown | HP1588 | O26107 | 29 | 5.5 | 90 | * | 10/30 | 28 | 0.853±0.192 | 0.399±0.167 | ↓ | 5.076E-04 | * | - |
| 19 | ScoA, Succinyl-CoA-transferase subunit A | Citric acid cycle | HP0691 | P56006 | 26 | 5.8 | 41 | 3/7 | 11 | 0.199±0.051 | 0.052±0.053 | ↓ | 3.739E-05 | * | - | |
| 20 | UreA, Urease subunit alpha | Urea metabolism | HP0073 | Q9ZMZ4 | 27 | 8.5 | 145 | * | 12/26 | 43 | 0.798±0.078 | 1.082±0.214 | ↑ | 3.314E-03 | * | ↓ |
| 21 | ScoB, Succinyl-CoA-transferase subunit B | Citric acid cycle | HP0692 | gi|208434607 | 22 | 5.4 | 104 | * | 10/33 | 33 | 0.242±0.066 | 0.149±0.061 | ↓ | 1.070E-02 | * | - |
| 22 | AroQ, 3-dehydroquinate dehydratase | Aromatic aminoacid biosynthesis | HP1038 | B6JKY5 | 19 | 5.1 | 77 | * | 8/36 | 35 | 0.520±0.108 | 0.622±0.077 | ↑ | 5.503E-02 | ↑ | |
| 23 | Pfr, Ferritin | Iron storage protein | HP0653 | Q9ZLI1 | 19 | 5.4 | 40 | 4/23 | 23 | 0.728±0.295 | 1.185±0.193 | ↑ | 4.285E-03 | * | - | |
| 24 | Porγ, Pyruvate flavodoxin oxidoreductase, gamma subunit | Decarboxylation of pyruvate in acetyl-CoA | HP1108 | gi|15645722 | 21 | 8.5 | 88 | * | 10/33 | 36 | 0.313±0.086 | 0.141±0.033 | ↓ | 1.133E-04 | * | - |
| 25 | FldA, Flavodoxin | Electron transport process | HP1161 | O25776 | 17 | 4.5 | 73 | * | 5/14 | 42 | 0.657±0.277 | 1.259±0.430 | ↑ | 6.800E-03 | * | - |
| 26 | NapA, Neutrophil activating protein A | Protects DNA from oxidative damage; activates neutrophils, mast cells and monocytes | HP0243 | gi|7188724 | 17 | 5.7 | 103 | * | 16/100 | 79 | 1.350±0.567 | 1.933±0.360 | ↑ | 2.996E-02 | * | - |
| 27 | HPG27_1480 | Putative function in cell shape | HP1542 | gi|208435422 | 11 | 5.6 | 48 | 3/13 | 35 | 0.065±0.016 | 0.088±0.007 | ↑ | 4.953E-03 | * | - | |
“Comparison to 2DE databases” indicates spots for which identification was done by finding the corresponding spot on the standard H. pylori 2DE gel from the database [14]. All of the others were identified by PMF analysis. For each spot the average of the % Vol ± S.D. is indicated. In the Variation (DU/NUD) column: ↑, proteins for which the average of the % Vol of spots on DU 2DE maps was higher than that on NUD 2DE maps; ↓, proteins for which the average of the % Vol of spots on DU 2DE maps was lower than that on NUD 2DE maps; ↔, proteins that were shifted right in the DU 2DE-maps regarding their position on the NUD 2DE-maps. In the Variation (GU/NUD) column: ↑, proteins for which the average of the % Vol of spots on GU 2-DE maps was higher than that on the DU 2DE maps; ↓, proteins for which the average of the % Vol of spots on GU 2DE maps was lower than that on DU 2DE maps; = , proteins showing the same pattern of expression observed for the H. pylori strains associated with DU. Asterisks indicate statistical significant results (p<0.05). 1Indicates the identified ORF in the 26695 reference strain.