SummaryHelicobacter pylori, the causative agent of gastritis, ulcer and stomach carcinoma, infects approximately half of the worlds population. After sequencing the complete genome of two strains, 26695 and J99, we have approached the demanding task of investigating the functional part of the genetic information containing macromolecules, the proteome. The proteins of three strains of H. pylori, 26695 and J99, and a prominent strain used in animal models SS1, were separated by a high-resolution two-dimensional electrophoresis technique with a resolution power of 5000 protein spots. Up to 1800 protein species were separated from H. pylori which had been cultivated for 5 days on agar plates. Using matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) peptide mass fingerprinting we have identified 152 proteins, including nine known virulence factors and 28 antigens. The three strains investigated had only a few protein spots in common. We observe that proteins with an amino acid exchange resulting in a net change of only one charge are shifted in the two-dimensional electrophoresis (2-DE) pattern. The expression of 27 predicted conserved hypothetical open reading frames (ORFs) and six unknown ORFs were confirmed. The growth conditions of the bacteria were shown to have an effect on the presence of certain proteins. A preliminary immunoblotting study using human sera revealed that this approach is ideal for identifying proteins of diagnostic or therapeutic value.

Table S1. Baseline features of the inflammatory satus in the gastric mucosa of 248 H. pylori-infected women patients with functional dyspepsia stratified by IL1B -31C/T genotypes. GenotypesP C allele dominance P T allele dominance P CC CT TT CC+CT TT CC CT+TT Corpus Chronic inflammation 0.639 0.377 0.508 Absent / Mild 42 (73.7) 74 (71.2) 58 (66.7) 116 (72.0) 58 (66.7) 42 (73.7) 132 (69.1) Moderate / Severe 15 (26.3) 30 (28.8) 29 (33.3) 45 (28.0) 29 (33.3) 15 (26.3) 59 (30.9) Inflammatory activity 0.201 0.126 0.143 Absent / Mild 50 (87.7) 85 (81.7) 66 (75.9) 135 (83.9) 66 (75.9) 50 (87.7) 151 (79.1) Moderate / Severe 7 (12.3) 19 (18.3) 21 (24.1) 26 (16.1) 21 (24.1) 7 (12.3) 40 (20.9) Incisura Chronic inflammation 0.988 0.885 0.999 Absent / Mild 20 (35.1) 37 (35.6) 30 (34.5) 57 (35.4) 30 (34.5) 20 (35.1) 67 (35.1) Moderate / Severe 37 (64.9) 67 (64.4) 57 (65.5) 104 (64.6) 57 (65.5) 37 (64.9) 124 (64.9) Inflammatory activity* 0.201 0.227 0.467 Absent / Mild 37 (64.9) 78 (75.0) 55 (64.0) 115 (71.4) 55 (64.0) 37 (64.9) 133 (70.0) Moderate / Severe 20 (35.1) 26 (25.0) 31 (36.0) 46 (28.6) 31 (36.0) 20 (35.1) 57 (30.0) Antrum Chronic inflammation 0.036 0.015 0.881 Absent / Mild 17 (29.8) 38 (36.5) 17 (19.5) 55 (34.2) 17 (19.5) 17 (29.8) 55 (28.8) Moderate / Severe 40 (70.2) 66 (63.5) 70 (80.5) 106 (65.8) 70 (80.5) 40 (70.2) 136 (71.2) Inflammatory activity 0.119 0.075 0.809 Absent / Mild 33 (57.9) 69 (66.3) 45 (51.7) 102 (63.4) 45 (51.7) 33 (57.9) 114 (59.7) Moderate / Severe 24 (42.1) 35 (33.7) 42 (48.3) 59 (36.6) 42 (48.3) 24 (42.1) 77 (40.3) * N = 247, data missing for one patient.