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. 2003 Oct;71(10):5921–5939. doi: 10.1128/IAI.71.10.5921-5939.2003

TABLE 3.

H. pylori genes up-regulated ≥2-fold with decreasing medium pH with and without urea

Group Avg ratio (exptl pH-Cy5-red/pH 7.4-cy3-green)a
Gene information
pH 7.4
pH 6.2
pH 5.5
pH 4.5
GenBank accession no. Description
5 mM U, (n = 3) 5 mM U (n = 3) No U (n = 4) 5 mM U (n = 4) No U (n = 3) 5 mM U (n = 4) No U (n = 4)
pH homeostasis (8 ORFs) 0.98 1.11 1.19 1.01 0.99 1.02 2.56 HP0070 Urease accessory protein (ureE)
0.95 1.09 1.01 0.98 1.16 1.49 2.35 HP0071 Urease accessory protein (ureI)
0.96 0.99 1.44 0.90 1.88 2.86 7.86 HP0869 Hydrogenase expression/formation protein (hypA)
0.99 1.06 2.38 1.59 3.30 2.14 2.34 HP0900 Hydrogenase expression/formation protein (hypB)
0.96 1.12 1.49 0.97 2.01 1.85 4.76 HP1186 Carbonic anhydrase
0.87 1.06 1.10 1.01 4.05 5.39 17.56 HP0294 Aliphatic amidase (amiE)
0.99 0.96 1.46 1.71 2.20 1.98 2.90 HP0723 l-Asparaginase II (ansB)
0.93 1.08 1.03 1.13 1.69 1.77 6.49 HP1399 Arginase (rocF)
Motility and chemotaxis (12 ORFs) 0.96 1.00 1.70 1.25 1.59 1.52 2.80 HP0019 Chemotaxis protein (cheV)
1.14 1.57 1.50 1.46 1.56 1.52 4.13 HP0082 Methyl-accepting chemotaxis transducer (tlpC)
0.95 0.98 1.42 1.21 2.07 2.01 2.45 HP0115 Flagellin B (flaB)
0.92 1.00 1.43 1.07 1.97 1.58 3.23 HP0325 Flagellar basal-body L-ring protein (flgH)
1.00 1.08 1.19 1.05 1.17 0.99 2.24 HP0393 Chemotaxis protein (cheV)
1.10 1.27 1.79 1.86 1.92 2.06 2.03 HP0601 Flagellin A (flaA)
0.99 0.91 1.27 1.04 2.09 1.97 3.37 HP0751 Polar flagellin (flaG)
1.01 0.97 1.11 1.01 1.21 1.40 2.05 HP0752 Flagellar-hook-associated protein 2 (fliD)
0.99 0.89 1.20 1.29 1.47 1.57 2.31 HP1067 Chemotaxis protein (cheY)
1.02 1.35 3.13 4.36 4.66 6.13 14.12 HP1192 Secreted protein involved in flagellar motility
1.05 0.98 1.02 1.07 1.15 1.01 4.81 HP1557 Flagellar basal-body protein (fliE)
1.07 0.88 0.99 0.91 1.03 1.02 2.13 HP1559 Flagellar basal-body rod protein (flgB)
Pathogenesis (9 ORFs) 1.04 0.93 1.06 1.06 2.01 1.57 2.24 HP0315 Virulence-associated protein D (vapD)
1.06 0.92 1.05 1.03 1.24 1.22 2.47 HP0520 Cag pathogenicity island protein (cag1)
1.06 1.10 1.61 1.29 1.48 1.45 2.22 HP0528 Cag pathogenicity island protein (cag8)
1.01 0.97 1.06 1.01 1.33 1.14 2.06 HP0532 Cag pathogenicity island protein (cag12)
1.03 1.11 1.20 1.01 0.99 1.03 2.35 HP0537 Cag pathogenicity island protein (cag16)
0.94 1.46 1.64 1.42 2.19 2.06 3.44 HP0540 Cag pathogenicity island protein (cag19)
0.93 0.95 1.36 1.12 1.74 1.27 2.45 HP0541 Cag pathogenicity island protein (cag20)
1.02 0.92 1.29 1.03 1.48 1.32 3.40 HP0542 Cag pathogenicity island protein (cag21)
1.15 0.98 1.50 1.09 1.82 1.65 2.02 HP0543 Cag pathogenicity island protein (cag22)
Regulatory functions (5 ORFs) 1.07 2.85 1.88 2.58 2.20 2.10 2.41 HP0165 Signal-transducing protein; histidine kinase
1.01 1.36 1.23 1.01 1.06 1.40 4.21 HP0166 Response regulator (ompR-like)
0.93 1.16 1.06 1.30 1.14 1.04 8.61 HP0278 Guanosine pentaphosphate phosphohydrolase (gppA)
0.95 0.98 1.04 1.10 1.28 2.24 4.97 HP1287 Transcriptional regulator (tenA)
1.01 1.53 1.63 1.45 2.09 2.89 2.65 HP1572 Regulatory protein DniR
Cell envelope (8 ORFs) 0.94 0.97 1.84 1.00 2.30 2.18 2.72 HP0025 Outer membrane protein (omp2)
1.00 1.39 1.37 1.60 1.21 3.51 3.61 HP0079 Outer membrane protein (omp3)
1.01 1.23 1.01 1.40 1.86 2.16 3.98 HP0180 Apolipoprotein N-acyltransferase (cute)
0.92 1.19 2.05 1.28 2.07 2.28 5.92 HP0472 Outer membrane protein (omp11)
0.98 1.25 1.54 0.97 1.36 1.80 2.07 HP0567 Membrane protein
0.89 0.96 1.90 1.49 2.60 1.66 4.23 HP0623 UDP-N-acetylmuramate-alanine ligase (murC)
1.07 1.03 1.08 1.06 2.66 1.11 3.97 HP0896 Outer membrane protein (omp19)
0.94 0.95 1.42 1.30 1.53 2.53 3.32 HP1456 Membrane-associated lipoprotein (lpp20)
Energy metabolism (19 ORFs) 0.88 0.93 1.07 0.94 2.07 2.06 2.42 HP0193 Fumarate reductase; cytochrome b subunit (frdC)
0.90 0.99 1.02 1.02 0.97 0.96 2.78 HP0194 Triosephosphate isomerase (tpi)
1.10 0.92 0.91 0.92 1.21 1.22 2.65 HP0277 Ferredoxin
0.98 1.25 1.55 2.10 2.06 2.11 3.09 HP0357 Short-chain alcohol dehydrogenase
0.96 1.05 0.95 0.97 1.01 1.27 2.95 HP0588 Ferrodoxin-like protein
0.96 1.03 1.05 1.13 1.53 1.45 2.59 HP0589 Ferredoxin oxidoreductase; alpha subunit
0.97 0.96 1.06 1.07 1.71 1.52 2.63 HP0590 Ferredoxin oxidoreductase; beta subunit
0.98 0.97 1.17 0.97 1.90 1.27 2.58 HP0591 Ferredoxin oxidoreductase; gamma subunit
0.96 0.90 1.06 1.23 2.22 3.52 6.74 HP0642 NAD(P)H-flavin oxidoreductase
0.85 1.11 1.01 1.05 1.55 1.64 4.84 HP0692 3-Oxoadipate CoA-transferase subunit B (yxjE)
0.93 0.95 1.24 2.10 3.50 2.75 2.49 HP0824 Thioredoxin (frxA)
0.92 0.93 1.14 1.24 1.70 1.45 3.00 HP1099 2-keto-3-deoxy-6-phosphogluconate aldolase (eda)/PICK>
0.95 0.98 1.04 1.47 1.45 1.61 3.11 HP1100 6-phosphogluconate dehydratase
1.10 0.94 1.92 1.70 2.89 3.05 9.17 HP1166 Glucose-6-phosphate isomerase (pgi)
0.95 0.99 1.12 1.05 1.67 1.64 3.60 HP1222 d-Lactate dehydrogenase (dld)
1.05 0.98 1.20 1.25 1.25 1.08 2.38 HP1345 Phosphoglycerate kinase
1.08 1.36 1.61 1.12 1.83 2.23 3.34 HP1386 d-Ribulose-5-phosphate 3 epimerase (rpe)
0.99 1.01 1.39 1.07 1.28 2.87 3.07 HP1461 Cytochrome c551 peroxidase
0.99 0.87 0.95 1.51 1.34 1.52 2.56 HP1508 Ferrodoxin-like protein
Fatty acid and phospholipid metabolism (3 ORFs) 1.03 1.02 1.29 0.99 1.81 2.28 7.56 HP0690 Acetyl CoA acetyltransferase (thiolase) (fadA)
0.97 0.89 1.18 1.67 1.21 1.60 4.22 HP0950 Acetyl-CoA carboxylase beta subunit (accD)
0.93 1.05 1.17 0.98 1.42 1.30 2.00 HP1045 Acetyl-CoA synthetase (acoE)
Translation (3 ORFs) 1.03 1.27 1.17 1.01 1.03 1.57 8.30 HP0077 Peptide chain release factor RF-1 (prfA)
1.02 1.58 2.19 2.32 2.12 2.47 5.19 HP0182 Lysyl-tRNA synthetase (lysS)
1.10 1.00 1.45 1.07 1.92 1.94 2.23 HP0972 Glycyl-tRNA synthetase; beta subunit (glyS)
Transporters (11 ORFs) 1.05 0.90 0.94 0.91 0.97 1.12 3.78 HP0299 Dipeptide ABC transporter permease protein (dppB)
0.98 1.00 0.99 0.96 1.05 1.08 3.97 HP0300 Dipeptide ABC transporter permease protein (dppC)
0.86 0.96 0.93 1.01 1.41 1.00 4.04 HP0301 Dipeptide ABC transporter ATP-binding protein (dppD)
0.93 0.94 0.96 1.01 1.09 1.00 2.84 HP0302 Dipeptide ABC transporter ATP-binding protein (dppF)
0.99 0.95 1.04 1.01 1.32 1.10 4.02 HP0613 ABC transporter ATP-binding protein
1.06 1.16 1.56 1.23 1.82 1.67 4.72 HP0715 ABC transporter ATP-binding protein
0.97 0.93 1.04 1.33 2.03 2.20 2.57 HP0876 Iron-regulated outer membrane protein (frpB)
1.20 1.18 2.01 1.28 2.34 2.58 2.51 HP0889 Iron(III) dicitrate ABC transporter permease (fecD)
1.03 1.07 1.13 1.03 1.52 1.44 2.98 HP0942 d-Alanine glycine permease (dagA)
1.07 1.26 1.55 2.39 3.36 4.16 2.64 HP1172 Glutamine ABC transporter; glutamine-binding (glnH)
0.90 1.03 1.03 0.88 0.97 1.04 6.07 HP1174 Glucose/galactose transporter (gluP)
Protein turnover (4 ORFs) 0.91 1.01 1.01 1.61 1.44 1.25 2.79 HP0382 Zinc-metalloprotease (YJR117W)
0.87 1.01 1.16 1.10 1.01 1.06 2.43 HP0570 Aminopeptidase a/i (pepA)
0.92 1.02 1.05 1.02 1.09 1.13 2.37 HP0786 Preprotein translocase subunit (secA)
1.02 1.17 1.15 1.26 1.25 2.33 3.08 HP0793 Polypeptide deformylase (def)
DNA metabolism (16 ORFs) 1.15 1.32 0.97 1.05 1.07 0.98 5.32 HP0259 Exonuclease VII; large subunit (xseA)
1.05 0.94 1.07 1.06 2.24 2.63 3.79 HP0478 Adenine-specific DNA methyltransferase (VSPIM)
0.90 1.01 1.33 1.01 1.93 2.96 2.88 HP0593 Adenine-specific DNA methyltransferase (mod)
1.03 1.25 1.62 2.16 2.15 2.17 2.45 HP0717 DNA polymerase III gamma and tau subunits (dnaX)
0.98 1.40 1.58 2.90 2.10 5.14 3.03 HP1022 Predicted DNA polymeraseI-like 5′-3′ exonuclease
0.99 1.11 1.30 1.41 0.96 1.10 2.82 HP1352 Adenine-specific DNA methyltransferase (HINFIM)
0.99 0.97 1.78 1.37 2.29 1.83 4.93 HP1402 Type I restriction enzyme R protein (hsdR)
1.01 0.99 2.07 1.79 2.01 1.95 3.23 HP1403 Type I restriction enzyme M protein (hsdM)
1.04 0.87 1.48 1.46 2.08 2.23 10.09 HP0669 Remnant of type I restriction-modification peptide
0.92 0.93 1.11 0.97 1.04 1.09 2.55 HP1470 DNA polymerase I (polA)
1.12 1.10 1.08 1.51 1.51 2.23 6.19 HP0437 IS605 transposase (tnpA)
1.02 0.94 1.09 1.57 1.57 2.40 3.81 HP0988 IS605 transposase (tnpA)
1.07 1.12 1.07 1.40 1.25 2.11 2.51 HP0998 IS605 transposase (tnpA)
1.03 1.01 1.14 1.65 1.79 1.66 4.14 HP1008 IS200 insertion sequence from SARA17
0.95 1.10 1.14 0.90 1.80 1.48 4.18 HP1095 IS605 transposase (tnpB)
1.14 1.35 1.20 1.68 1.73 1.96 4.07 HP1096 Is605 transposase (tnpA)
Biosynthesis (13 ORFs) 0.97 1.19 1.67 1.06 1.26 1.11 2.38 HP0183 Serine hydroxymethyltransferase (glyA)
0.96 1.05 2.04 1.63 2.39 2.92 6.00 HP0380 Glutamate dehydrogenase (gdhA)
0.95 0.98 1.39 0.90 1.70 1.41 2.68 HP0649 Aspartate ammonia-lyase (aspA)
0.96 0.81 1.45 1.01 1.90 2.02 3.64 HP0695 Hydantoin utilization protein A (hyuA)
0.93 1.13 0.98 1.05 1.52 1.79 2.09 HP1050 Homoserine kinase (thrB)
0.96 1.05 1.17 1.01 1.20 1.13 2.57 HP1468 Branched-chain amino-acid aminotransferase (ilvE)
0.88 1.43 2.52 1.96 2.08 3.35 2.28 HP0306 Glutamate-1-semialdehyde 2,1-aminomutase (hemL)
0.93 1.59 2.28 2.35 1.91 5.93 3.21 HP0376 Ferrochelatase (hemH)
1.03 0.96 1.38 1.36 1.60 2.86 2.96 HP0844 Thiamine biosynthesis protein (thi)
1.10 0.94 1.17 1.48 2.16 2.15 3.66 HP0845 Thiamin phosphate pyrophosphorylase (thiM)
1.04 1.09 1.20 1.05 1.16 1.02 2.84 HP1582 Pyridoxal phosphate biosynthetic protein J (pdxJ)
0.87 1.01 1.23 0.95 1.05 1.02 3.22 HP1583 Pyridoxal phosphate biosynthetic protein A (pdxA)
0.94 1.43 1.90 2.47 2.14 1.67 2.32 HP0854 GMP reductase (guaC)
General stress response (9 ORFs) 1.03 1.18 1.10 1.04 1.35 1.24 2.39 HP0243 Neutrophil-activating protein (napA) (bacterioferritin)
0.93 1.03 1.07 0.97 1.43 1.55 3.75 HP0875 Catalase
0.99 1.04 1.07 0.93 1.52 1.67 2.32 HP0020 Carboxynorspermidine decarboxylase (nspC)
0.99 1.22 2.03 1.80 1.64 1.65 2.08 HP0047 Hydrogenase expression/formation protein (hypE)
1.10 0.99 2.10 1.62 1.91 2.38 2.88 HP0899 Hydrogenase expression/formation protein (hypC)
1.01 1.02 0.87 1.09 1.70 1.84 2.09 HP0485 Catalase-like protein
0.91 0.97 1.45 1.67 1.44 2.21 3.38 HP1104 Cinnamyl-alcohol dehydrogenase ELI3-2 (cad)
1.04 1.01 1.10 0.93 1.26 1.09 2.79 HP1193 Aldo-keto reductase; putative
0.91 1.12 1.03 1.07 1.10 1.17 2.10 HP0595 Predicted DsbB-like protein
a

U, urea.