TABLE 1.
pH-regulated genes of H. pyloria
| Expression | Class | Gene designation
|
Gene and function | Change (n-fold) at:
|
||||
|---|---|---|---|---|---|---|---|---|
| TIGR | ASTRA | T = 30 | T = 60 | T = 90 | T = 120b | |||
| Induced | Amino acid biosynthesis | HP1282 | JHP1203 | Anthranilate synthase component, trpE | 2.4 | 2.5 | 2.5 | 2.7 |
| HP0106 | JHP0098 | Cystathionine gamma-synthase, metB | 2.3 | 1.8 | 1.8 | 3.5 | ||
| HP1050 | JHP0375 | Homoserine kinase, thrB | 1.9 | 2.3 | 3.0 | 3.1 | ||
| HP0290 | JHP0275 | Diaminopimelate decarboxylase (dap decarboxylase), lysA | 1.2 | 2.4 | 2.9 | 2.9 | ||
| HP0380 | JHP1001 | Glutamate dehydrogenase, gdhA | 2.4 | 1.2 | 1.3 | 2.0 | ||
| Biosynthesis of cofactors, pros- thetic groups, and carriers | HP0306 | JHP0291 | Glutamate-1-semialdehyde 2,1-aminomutase, hemL | 1.9 | 1.9 | 1.6 | 2.6 | |
| HP0755 | JHP0692 | Molybdopterin biosynthesis protein, moeB | 1.7 | 1.6 | 2.2 | 2.2 | ||
| Cell envelope and surface structures | HP1155 | JHP1082 | UDP-n-acetylglucosamine-n-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol n-acetylglucosamine transferase, murG | 3.4 | 1.4 | 1.3 | 1.9 | |
| HP0743 | JHP0680 | Rod shape-determining protein, mreB | 1.6 | 1.9 | 2.4 | 2.5 | ||
| HP0295 | JHP0280 | Flagellin B homolog (HAP3) | 4.2 | 1.4 | 1.9 | 2.0 | ||
| HP1119 | JHP1047 | Flagellar hook-associated protein 1 (HAP1), flgK | 3.9 | 1.7 | 1.3 | 2.1 | ||
| HP1559 | JHP1467 | Flagellar basal-body rod protein (proximal rod protein), flgB | 3.8 | NDc | 2.5 | 2.4 | ||
| HP0115 | JHP0107 | Flagellin, flaB | 3.5 | 1.0 | 1.4 | 1.4 | ||
| HP0870 | JHP0804 | Flagellar hook, flgE | 3.0 | 1.1 | 1.5 | 1.9 | ||
| HP1558 | JHP1466 | Flagellar basal-body rod protein (proximal rod protein), flgC | 2.0 | 1.1 | 1.3 | 1.6 | ||
| HP1031 | JHP0393 | Flagellar motor switch protein, fliM | 1.8 | 2.3 | 1.1 | 2.3 | ||
| HP1122 | JHP1051 | Anti-σ28 factor, flgM | 2.7 | 1.1 | 1.3 | 1.6 | ||
| Cellular processes | HP1332 | JHP1252 | Cochaperone and heat shock protein, cochaperone with DnaK, dnaJ | 4.0 | 4.0 | 3.0 | 3.1 | |
| Central intermediary metabolism | HP0069 | JHP0064 | Urease accessory protein, ureF | 3.0 | 4.0 | 3.4 | 3.5 | |
| HP0071 | JHP0066 | Urease accessory protein, ureI | 2.2 | 4.1 | 6.4 | 5.5 | ||
| HP0068 | JHP0063 | Urease accessory protein, ureG | 1.8 | 2.1 | 1.8 | 3.0 | ||
| HP0067 | JHP0062 | Urease accessory protein, ureH | 1.7 | 2.2 | 1.5 | 3.0 | ||
| HP0073 | JHP0068 | Urease alpha subunit, ureA | 1.7 | 3.8 | 7.2 | 6.9 | ||
| HP0072 | JHP0067 | Urease beta subunit, ureB | 1.2 | 3.4 | 7.1 | 7.2 | ||
| DNA metabolism, restriction and modification | HP1121 | JHP1050 | Cytosine-specific DNA methyltransferase, BSP6IM | 2.2 | 1.3 | 1.2 | 1.6 | |
| Energy metabolism | HP0294 | JHP0279 | Aliphatic amidase energy metabolism, amiF | 4.1 | 2.4 | 11 | 9.5 | |
| HP1238 | JHP1159 | Aliphatic amidase energy metabolism, amiE | 2.4 | 0.8 | 9.0 | 7.5 | ||
| JHP585 | Putative 3-hydroxyacid dehydrogenase | 1.0 | 3.2 | 4.2 | 10.1 | |||
| HP0642 | JHP0586 | NAD(P)H-flavin oxidoreductase | 1.1 | 5.7 | 8.1 | 8.1 | ||
| Fatty acid and phospholipid metabolism and biosynthesis | HP0557 | JHP0504 | Acetyl-coenzyme A carboxylase, accA | 1.4 | 1.4 | 2.3 | 1.7 | |
| Hypothetical gene | HP1233 | JHP1154 | 5.7 | 0.6 | ND | 2.8 | ||
| HP1154 | JHP1081 | 5.1 | 1.1 | 1.4 | 1.9 | |||
| HP0367 | JHP1014 | 4.6 | 1.5 | 2.3 | 2.6 | |||
| HP0119 | 4.5 | 0.9 | 4.1 | 3.7 | ||||
| HP0118 | JHP0110 | 4.3 | 1.7 | 1.7 | 3.2 | |||
| HP1327 | JHP1247 | 3.9 | 1.2 | 1.1 | 1.0 | |||
| HP1187 | JHP1113 | 3.8 | 2.6 | 3.7 | 3.6 | |||
| HP1076 | JHP0349 | 3.6 | 1.8 | 1.5 | 1.6 | |||
| HP0219 | JHP0205 | 2.9 | 3.1 | 3.4 | 3.5 | |||
| HP1173 | JHP1100 | 2.8 | 4.0 | 5.9 | 4.9 | |||
| HP1188 | 2.8 | 0.8 | 1.0 | 1.9 | ||||
| HP1022 | JHP0402 | 2.2 | 2.1 | 2.4 | 2.1 | |||
| HP1440 | JHP1333 | 2.1 | 1.1 | 1.2 | 1.3 | |||
| HP1457 | JHP1350 | 2.0 | 1.4 | 1.2 | 1.6 | |||
| HP0018 | JHP0016 | 1.7 | 2.1 | 1.7 | 2.6 | |||
| HP0554 | JHP0501 | 1.7 | 2.2 | 2.0 | 1.9 | |||
| HP0719 | JHP0657 | 0.8 | 2.0 | 2.3 | 2.8 | |||
| HP0641 | JHP0584 | 1.4 | 1.9 | 5.4 | 5.7 | |||
| HP1331 | JHP1251 | Conserved hypothetical integral membrane protein | 2.7 | 2.5 | 2.6 | 2.6 | ||
| HP0228 | JHP0213 | Conserved hypothetical integral membrane protein | 2.1 | 3.8 | 1.5 | 4.1 | ||
| HP1225 | JHP1146 | Conserved hypothetical integral membrane protein | 2.1 | 1.6 | 1.7 | 2.0 | ||
| HP0318 | JHP0301 | Conserved hypothetical protein | 2.0 | 3.2 | 1.8 | 3.8 | ||
| HP1430 | JHP1323 | Conserved hypothetical ATP-binding protein | 1.8 | ND | 2.5 | 2.2 | ||
| HP1507 | JHP1400 | Conserved hypothetical ATP-binding protein | 1.7 | 1.4 | 1.7 | 4.0 | ||
| HP0759 | JHP0696 | Conserved hypothetical integral membrane protein | 1.5 | 2.3 | 2.7 | 1.8 | ||
| HP1020 | JHP0404 | Conserved hypothetical protein | 1.3 | 3.0 | 3.1 | 2.9 | ||
| Purines, pyrimidines, nucleosides and nucleotides | HP0757 | JHP0694 | β-alanine synthetase homolog | 2.3 | 2.6 | 3.0 | 2.7 | |
| Regulatory functions | HP1021 | JHP0403 | Putative transcriptional regulator | 1.4 | 2.9 | 3.6 | 3.9 | |
| HP0278 | JHP0263 | Guanosine-5′-triphosphate-3′-diphosphate pyrophosphatase, gppA | 0.7 | 1.3 | 1.5 | 3.4 | ||
| Transcription, transcription factors and translation | HP0550 | JHP0497 | Transcription termination factor Rho, rho | 2.6 | 1.6 | 1.0 | 0.7 | |
| HP1203 | JHP1126 | Transcription termination factor NusG, nusG | 1.8 | 2.0 | 2.2 | 2.0 | ||
| HP0123 | JHP0113 | Threonyl-tRNA synthetase, thrS | 2.0 | 1.8 | 2.1 | 2.0 | ||
| HP1019 | JHP0405 | Serine protease, htrA | 2.5 | 3.4 | 4.2 | 3.9 | ||
| Transport and binding proteins | HP1171 | JHP1098 | Glutamine ABC transporter, ATP-binding protein, glnQ | 1.1 | 1.9 | 2.3 | 2.1 | |
| HP1172 | JHP1099 | Glutamine ABC transporter, periplasmic glutamine-binding protein, glnH | 1.0 | 1.8 | 2.0 | 3.6 | ||
| HP0471 | JHP0423 | Glutathione-regulated potassium efflux system, kefB | 2.1 | 1.4 | 1.2 | 1.2 | ||
| HP1339 | JHP1258 | Biopolymer transport protein, exbB | 3.0 | 1.9 | 1.8 | 2.0 | ||
| HP1340 | JHP1259 | Biopolymer transport protein, exbD | 2.3 | 1.4 | 0.9 | 2.1 | ||
| HP0876 | JHP0810 | Iron-regulated OMP, frpB | 1.4 | 3.3 | 1.9 | 1.2 | ||
| HP0715 | JHP0653 | ABC transporter, ATP-binding protein | 2.2 | 1.0 | 1.2 | 1.4 | ||
| HP1432 | JHP1321 | Putative histidine and glutamine-rich metal-binding protein | 2.0 | 2.4 | 2.8 | 3.1 | ||
| HP1465 | JHP1358 | ABC transporter, ATP-binding protein, HI1087 | 1.7 | 1.3 | 1.3 | 2.6 | ||
| Repressed | Amino acid biosynthesis | HP1038 | JHP0386 | 3-Dehydroquinase type II, aroD | 0.6 | 0.4 | 0.6 | 0.5 |
| HP0695 | JHP0633 | Hydantoin utilization protein A, hyuA | 1.0 | 0.3 | 0.4 | 0.4 | ||
| Cell envelope | HP0722 | JHP0659 | Putative OMP, hopO | 0.7 | 0.1 | 0.1 | 0.1 | |
| HP0638 | JHP0581 | OMP, omp13 (hopH) | 0.7 | 0.7 | 0.4 | 0.4 | ||
| HP0913 | JHP0849 | OMP, hopB | 0.7 | 0.5 | 0.4 | 0.4 | ||
| HP0317 | OMP, omp9 (hopU) | 0.7 | 0.4 | 0.5 | 0.4 | |||
| HP0725 | JHP0662 | Putative OMP, hopP | 0.7 | 0.7 | 0.7 | 0.4 | ||
| HP1177 | JHP1103 | OMP, omp27 (hopQ) | 0.6 | 0.1 | 0.1 | 0.1 | ||
| HP0009 | JHP0007 | OMP, hopZ | 0.6 | 0.8 | 0.4 | 0.3 | ||
| HP1469 | JHP1362 | OMP, omp31 (horJ) | 0.6 | 0.5 | 0.3 | 0.3 | ||
| HP0229 | JHP0214 | OMP, hopA | 0.5 | 0.2 | 0.2 | 0.2 | ||
| HP1501 | JHP1394 | OMP, omp32 (horK) | 0.5 | 0.1 | 0.1 | 0.1 | ||
| HP0912 | JHP0848 | OMP, hopC | 0.4 | 0.3 | 0.3 | 0.2 | ||
| HP1167 | JHP1094 | Conserved putative OMP, hofH | 0.5 | ND | 0.2 | 0.3 | ||
| Cellular processes | HP0010 | JHP0008 | Chaperone and heat shock protein, 60-kDa chaperone, groEL | 0.7 | 0.4 | 0.4 | 0.2 | |
| HP0109 | JHP0101 | Chaperone and heat shock protein, 70, 70-kDa chaperone, dnaK | 0.6 | 0.4 | 0.4 | 0.2 | ||
| HP0110 | JHP0102 | Cochaperone and heat shock protein, 24-kDa chaperone, grpE | 0.5 | 0.4 | 0.4 | 0.2 | ||
| HP0887 | JHP0819 | Vacuolating cytotoxin, vacA | 0.8 | 0.3 | 0.3 | 0.2 | ||
| HP0547 | JHP0495 | Cag pathogenicity island protein, cag26 (cagA) | 0.8 | 0.3 | 0.4 | 0.4 | ||
| Central intermediary metabolism | HP1186 | JHP1112 | Carbonic anhydrase | 1.2 | 0.5 | 0.7 | 0.3 | |
| DNA metabolism, DNA replication, recombination, and repair | HP1460 | JHP1353 | DNA polymerase III alpha subunit, dnaE | 0.6 | 0.3 | 0.4 | 0.5 | |
| Energy metabolism | HP0056 | JHP0048 | Δ-1-pyrroline-5-carboxylate dehydrogenase, putA | 0.8 | 0.4 | 0.5 | 0.5 | |
| HP0723 | JHP0661 | l-asparaginase II energy metabolism, ansB | 0.5 | 0.8 | 0.4 | 0.5 | ||
| HP1458 | JHP1351 | Thioredoxin | 0.8 | 0.4 | 0.3 | 0.4 | ||
| HP1101 | JHP1027 | Glucose-6-phosphate dehydrogenase, g6pD | 0.5 | 0.6 | 0.8 | 0.5 | ||
| Fatty acid and phospholipid metabolism | HP0871 | JHP0805 | CDP-diglyceride hydrolase, cdh | 0.6 | 0.4 | 0.5 | 0.4 | |
| HP1045 | Acetyl-coenzyme synthetase, acoE | 0.7 | 0.3 | 0.4 | 0.4 | |||
| Hypothetical gene | HP1002 | 1.4 | 0.9 | 0.4 | 0.5 | |||
| HP0637 | JHP0580 | 0.7 | 0.7 | 0.4 | 0.4 | |||
| HP0097 | JHP0089 | 0.6 | 0.4 | 0.4 | 0.3 | |||
| HP1527 | JHP1416 | 0.6 | 0.5 | 0.6 | 0.4 | |||
| HP1322 | JHP1242 | 0.6 | 0.5 | 0.5 | 0.5 | |||
| HP0111 | JHP0103 | 0.4 | 0.5 | 0.5 | 0.2 | |||
| HP1175 | JHP1102 | Conserved hypothetical integral membrane protein | 0.8 | 0.7 | 0.8 | 0.3 | ||
| HP0310 | JHP0295 | Conserved hypothetical protein | 0.7 | 0.6 | 0.6 | 0.4 | ||
| HP1285 | JHP1205 | Conserved hypothetical secreted protein | 0.6 | 0.4 | 0.4 | 0.5 | ||
| Purines, pyrimidines, nucleosides, and nucleotides | HP1178 | JHP1104 | Purine-nucleoside phosphorylase, deoD | 0.7 | 0.5 | 0.3 | 0.4 | |
| Translation | HP0382 | JHP0999 | Putative zinc-metalloprotease, yjr117w | 0.5 | 0.7 | 0.8 | 0.4 | |
| Transport and binding proteins | HP1561 | JHP1469 | Iron (III) ABC transporter, periplasmic iron-binding protein, ceuE1 | 0.7 | 0.6 | 0.3 | 0.3 | |
| HP1562 | JHP1470 | Iron (III) ABC transporter, periplasmic iron-binding protein, ceuE2 | 0.7 | 0.3 | 0.3 | 0.3 | ||
| HP1180 | JHP1106 | Pyrimidine nucleoside transport protein, nupC | 0.4 | 0.2 | 0.3 | 0.4 | ||
| HP0653 | JHP0598 | Nonheme iron-containing ferritin, pfr | 0.8 | 0.5 | 0.2 | 0.2 | ||
| HP0916 | Iron-regulated OMP, frpB2 | 0.7 | 0.3 | 0.4 | 0.3 | |||
| HP1512 | JHP1405 | Iron-regulated OMP, frpB4 | 0.5 | 0.3 | 0.3 | 0.1 | ||
| Unknown function | HP0485 | JHP0437 | Catalase-like protein | 1.1 | 0.4 | 0.5 | 0.5 | |
| HP1193 | Aldo-ketoreductase, putative | 0.7 | 0.4 | 0.6 | 0.4 | |||
a
Data presented are relative changes (n-fold) from the zero-time-point starting culture. Changes (n-fold) for a single experiment are given. Data for the biological replicate experiment are available as supplementary information at http://falkow.stanford.edu/whatwedo/supplementarydata/ and show a similar pattern of expression for each gene.
b
Time is measured in minutes.
c
ND, no data.