TABLE 4.

pH 2.5-dependent HP0244 regulon

Functional categoryORFWild-type strain/ΔHP0244 strain ratioaDescription
pH 7.4pH 4.5pH 2.5
Acid acclimationHP0069c , f 1.331.062.47Urease accessory protein (ureF)
HP1399b , f 1.221.472.85Arginase (rocF)
HP0723b 1.771.492.28 l-Asparaginase II (ansB)
Energy metabolismHP11331.481.302.49ATP synthase F1, subunit gamma (atpG)
HP12121.661.633.08ATP synthase F0, subunit c (atpE)
HP0588b , e 1.651.962.92Ferrodoxin-like protein
HP0591b 1.631.742.30Ferredoxin oxidoreductase, gamma subunit
HP1099b 1.691.703.482-Keto-3-deoxy-6-phosphogluconate aldolase (eda)
HP1193b 1.611.433.43Aldo-keto reductase, putative
HP11611.791.792.77Flavodoxin (fldA)
HP1540e 1.681.562.55Ubiquinol cytochrome c oxidoreductase (fbcF)
HP0265e 1.721.342.57Cytochrome c biogenesis protein (ccdA)
HP07791.961.883.80Aconitase B (acnB)
Oxidative stressHP1563f 1.471.883.32Alkyl hydroperoxide reductase (ahpC)
HP0825e , f 1.741.942.82Thioredoxin reductase (trxR)
HP0874b , d 1.331.463.26Catalase (KatA)-associated protein (kapA)
Amino acid biosynthesisHP0380b , c , f 1.611.512.37Glutamate dehydrogenase (gdhA)
HP03301.631.342.31Ketol-acid reductoisomerase (ilvC)
HP10381.691.532.673-Dehydroquinase type II (aroQ)
HP12101.360.932.91Serine acetyltransferase (cysE)
Biosynthesis of cofactorsHP10581.631.172.553-Methyl-2-oxob hydroxymethyltransferase (panB)
HP0306b , c , f 1.341.642.46Glutamate-1-semialdehyde-2,1-aminomutase (hemL)
Cell envelopeHP0025b 1.231.562.56Outer membrane protein (omp2)
HP07061.721.322.49Outer membrane protein (omp15)
HP09121.551.582.26Outer membrane protein (omp20)
HP09131.311.332.05Outer membrane protein (omp21)
HP11571.811.712.46Outer membrane protein (omp26)
HP1564f 1.541.063.43Outer membrane protein
HP07881.851.363.00Predicted outer membrane protein (hofF)
HP11671.431.372.42Predicted outer membrane protein (hofH)
HP0196e 1.431.382.16UDP-3-O-glucosamine N-acyltransferase (lpxD)
HP10521.761.222.51UDP-3-O-acyl N-acetylglucosamine deacetylase (envA)
HP13751.431.342.51UDP-N-acetylglucosamine acyltransferase (lpxA)
HP01601.531.212.36Conserved hypothetical secreted protein
HP00031.731.772.56Octulosonic acid 8-phosphate synthetase (kdsA)
HP04101.501.202.33Neuraminyllactose-binding hemagglutinin (hpaA)
Cellular processesHP09781.291.312.43Cell division protein (ftsA)
HP1069e 1.691.843.50Cell division protein (ftsH)
HP09791.711.242.58Cell divison protein (ftsZ)
HP1067b 1.611.272.29Chemotaxis protein (cheY)
HP0243b , f 1.321.463.73Neutrophil activating protein (napA)
HP0232e 1.731.392.50Secreted protein involved in flagellar motility
HP1192b , d , f 1.611.282.59Secreted protein involved in flagellar motility
HP0485b 1.851.583.26Catalase-like protein
HP10431.471.512.45Response regulator
HP1104b , e , f 1.661.743.20Cinnamyl-alcohol dehydrogenase ELI3-2 (cad)
HP05691.801.793.01GTP-binding protein (gtp1)
HP0480e 1.631.302.39GTP-binding protein, fusA-homolog (yihK)
Purines, pyrimidines, and nucleotidesHP06181.731.632.41Adenylate kinase (adk)
HP00451.431.492.37Nodulation protein (nolK)
HP04091.431.602.40GMP synthase (guaA)
Central intermediate metabolismHP0020b 1.451.672.95Carboxynorspermidine decarboxylase (nspC)
HP06201.511.262.43Inorganic pyrophosphatase (ppa)
Fatty acid and phospholipid metabolismHP02021.401.462.68Beta-ketoacyl-acyl carrier protein synthase III (fabH)
HP05591.531.202.29Acyl carrier protein (acpP)
HP0370e 1.301.372.61Biotin carboxylase (accC)
HP01951.751.342.26Enoyl-(acyl carrier protein) reductase (NADH) (fabI)
HP02151.581.402.25CDP-diglyceride synthetase (cdsA)
Protein fate and translationHP02101.751.772.44Chaperone and heat shock protein C62.5 (htpG)
HP0110b , e 1.430.913.07Cochaperone and heat shock protein (grpE)
HP12021.271.542.44Ribosomal protein L11 (rpl11)
HP10681.711.833.18Ribosomal protein L11 methyltransferase (prmA)
Transport and binding proteinHP10731.431.502.46Copper ion binding protein (copP)
HP1562e 1.601.402.92Iron(III) ABC transporter (ceuE)
HP0302b 1.581.722.61Dipeptide ABC transporter (dppF)
HP11690.840.902.08Glutamine ABC transporter, permease protein (glnP)
HypotheticalHP1037e 1.691.953.06Conserved hypothetical protein
HP09201.801.812.30Conserved hypothetical integral membrane protein
HP01511.581.172.45Conserved hypothetical membrane protein
HP12851.681.152.46Conserved hypothetical secreted protein
HP0318b , c 1.571.622.36Conserved hypothetical protein
HP14591.511.452.88Conserved hypothetical protein
HP0310b 1.871.573.84Conserved hypothetical protein
UnknownHP01130.810.902.71 H. pylori predicted coding region HP0113
HP0218b 1.651.572.74 H. pylori predicted coding region HP0218
HP02311.671.832.54 H. pylori predicted coding region HP0231
HP04231.441.332.61 H. pylori predicted coding region HP0423
HP04861.871.322.31 H. pylori predicted coding region HP0486
HP06051.711.642.37 H. pylori predicted coding region HP0605
HP0719c 1.371.163.04 H. pylori predicted coding region HP0719
HP07731.451.372.23 H. pylori predicted coding region HP0773
HP09531.251.362.53 H. pylori predicted coding region HP0953
HP09961.441.432.61 H. pylori predicted coding region HP0996
HP12471.321.402.49 H. pylori predicted coding region HP1247
HP13341.360.752.57 H. pylori predicted coding region HP1334
HP13581.371.642.48 H. pylori predicted coding region HP1358
  • a Average ratios based on three independent microarray hybridizations with separate RNA preparations for each pH condition.

  • b Acid-responsive gene identified by Wen et al. (50).

  • c Acid-responsive gene identified by Merrell et al. (23).

  • d Acid-responsive gene identified by Bury-Mone et al. (8).

  • e Acid-responsive gene identified by Ang et al. (2).

  • f HP0165 regulon gene identified by Pflock et al. (28).