TABLE 1.

Log-phase iron-regulated genes of H. pylori

Gene designationaGene function and nameMaximum fold changeb in:
TIGRASTRAExpt 1Expt 2
Repressed genes
    Amino acid biosynthesis
        HP1229JHP1150Aspartokinase, lysC0.40.4
    Cell envelope/Surface structures
        HP0009JHP0007Putative OMP hopZ0.40.4
        HP0351JHP0325Flagellar basal-body M-ring protein, fliF0.30.3
        HP0655JHP0600Putative OMP0.40.4
        HP0858JHP0792ADP-heptose synthase, rfaE0.40.5
        HP0870JHP0804Flagellar hook, flgE0.40.5
        HP0912JHP0848OMP, hopC0.40.5
        #HP1119JHP1047Flagellar hook-associated protein 1 (HAP1), flgK0.30.4
        HP1275JHP1196Phosphomannomutase, algC0.30.4
        HP1450JHP134360-kDa inner membrane protein0.40.5
    Cellular processes
        *HP0103JHP0095Methyl-accepting chemotaxis protein, tlpB0.40.3
        HP0522JHP0471cag PAI protein, cag30.30.4
        HP1126JHP1055Colicin tolerance-like protein, tolB0.20.4
        HP1300JHP1220Preprotein translocase subunit, secY0.30.4
        HP1452JHP1345Thiophene and furan oxidizer, tdhF0.30.5
    DNA metabolism-restriction/modification
        HP0481JHP0433Adenine-specific DNA methyltransferase, MFOKI0.50.5
    Energy metabolism
        HP0509JHP0459Glycolate oxidase subunit, glcD0.40.4
        HP0574JHP0521Galactosidase acetyltransferase, lacA0.50.4
        HP1134JHP1062ATP synthase F1, subunit alpha energy metabolism, atpA0.30.5
    Hypothetical
        HP0248JHP0233Conserved hypothetical protein0.20.3
        HP0270JHP02550.50.4
        HP0466JHP0418Conserved hypothetical protein0.30.4
        HP0554JHP05010.40.5
        HP0659JHP06040.40.4
        HP0783JHP07200.40.5
        #HP0838JHP07760.40.3
        HP0863JHP07970.30.5
        HP1124JHP10530.30.4
        HP1127JHP10560.50.4
        HP1233JHP11540.30.4
    Other categories, adaptations and atypical conditions
        HP1228JHP1149Invasion protein, putative dGTP pyrophosphohydrolase, invA0.30.3
    Purine ribonucleotide biosynthesis
        HP0255JHP0239Adenylosuccinate synthetase, purA0.50.4
    Transcription
        #HP0550JHP0497Transcription termination factor, rho0.20.3
    Translation
        HP0126JHP0116Ribosomal protein L20, rpl200.30.4
        HP0247JHP0232ATP-dependent RNA helicase, DEAD-box family, deaD0.20.4
        #HP0657JHP0602Putative processing protease0.40.4
        HP0658JHP0603Glu-tRNA amidotransferase, subunit b, gatB0.40.3
        HP0886JHP0818Cysteinyl-tRNA synthetase, cysS0.40.5
        HP1298JHP1218Translation initiation factor EF-1, infA0.50.5
        HP1299JHP1219Methionine aminopeptidase, map0.30.5
        HP1304JHP1224Ribosomal protein L6, rpl60.50.5
        HP1305JHP1225Ribosomal protein S8, rps80.50.5
        HP1306JHP1226Ribosomal protein S14, rps140.40.5
        HP1312JHP1232Ribosomal protein L16, rpl160.40.5
        *HP1313JHP1233Ribosomal protein S3, rps30.30.4
        HP1314JHP1234Ribosomal protein L22, rpl220.30.4
        *HP1315JHP1235Ribosomal protein S19, rps190.40.4
        HP1554JHP1445Ribosomal protein S2, rps20.40.4/PICK>
    Transport and binding proteins
        HP0497JHP0449Putative sodium- and chloride-dependent transporter0.30.5
        HP1130JHP1058Biopolymer transport protein, exbB0.30.3
        *HP1400JHP1426Iron(III) dicitrate transport protein, fecA30.30.5
Induced genes
    Amino acid biosynthesis
        HP0134JHP01223-Deoxy-d-arabino-heptulosonate-7-phosphate synthase, aroF3.73.7
     #HP0106JHP0098Cystathionine gamma-synthase, metB2.63.0
     #HP0107JHP0099Cysteine synthetase, cysK2.92.6
        HP0626JHP0570Tetrahydrodipicolinate N-succinyltransferase, dapD3.32.4
        *HP0649JHP0594Aspartate ammonia-lyase, aspA2.12.5
     *#HP0672JHP0615Solute binding signature and mitochondrial signature protein, aspB5.44.1
    Biosynthesis of cofactors, prosthetic     groups, and carriers
        HP0577JHP0524Methylene tetrahydrofolate dehydrogenase, folD2.72.4
        HP0665JHP0610Oxygen-independent coproporphyrinogen III oxidase, hemN2.32.4
        HP0844JHP0782Thiamine biosynthesis protein, thi2.62.2
     *#HP1582JHP1489Pyridoxal phosphate biosynthetic protein J, pdxJ2.44.8
    Cell envelope and surface structures
        HP0601JHP0548Flagellin A, flaA3.12.1
        HP0922JHP0856Toxin-like OMP, putative vacuolating cytotoxin (VacA) paralog3.63.0
        HP1052JHP0373UDP-3-O-acyl-N-acetylglcosamine deacetylase, envA3.22.5
        HP1177JHP1103OMP, omp272.42.2
        HP1192JHP1117Secreted protein involved in flagellar motility2.72.6
        HP1456JHP1349Membrane-associated lipoprotein, lpp205.53.5
        HP1469JHP1362OMP, omp312.02.1
        *HP1501JHP1394OMP, omp322.72.9
    Cellular processes
        HP0243JHP0228Neutrophil-activating protein (bacterioferritin), napA4.03.2
        HP0541JHP0489cag PAI protein, cag203.62.1
        HP0547JHP0495cag PAI protein, cag26 (cagA)3.52.5
        HP0875JHP0809Catalase, katA2.62.3
        HP0979JHP0913Cell divison protein, GTPase in circumferential ring formation, ftsZ2.02.3
        *HP1024JHP0400Cochaperone-curved DNA binding protein A, cbpA4.72.2
        HP1069JHP0356Cell division protein, ftsH4.63.0
        HP1431JHP132216S rRNA (adenosine-N6N6)-dimethyltransferase, ksgA2.42.7
        HP1563JHP1471Alkyl hydroperoxide reductase, tsaA2.82.3
    Central intermediary metabolism
        HP0020JHP0018Carboxynorspermidine decarboxylase, nspC2.22.3
        *HP0026JHP0022Citrate synthase, gltA2.32.2
     *#HP0294JHP0279Aliphatic amidase energy metabolism, amiE6.521.4
        HP0589JHP0537Ferredoxin oxidoreductase, alpha subunit, oorA2.22.0
    #HP0642JHP0586NAD(P)H-flavin oxidoreductase2.52.8
        HP0779JHP0716Aconitase B, acnB4.92.4
        *HP0900JHP0837Hydrogenase expression/formation protein, hypB3.24.1
        *HP0943JHP0878d-Amino acid dehydrogenase, dadA3.22.7
        *HP1186JHP1112Carbonic anhydrase2.32.2
        *HP1238JHP1159Aliphatic amidase, amiF2.32.9
        HP1398JHP1428Alanine dehydrogenase, ald3.92.8
        *HP1399JHP1427Arginase energy metabolism, rocF4.02.4
#JHP0585Putative 3-hydroxyacid dehydrogenase2.23.3
    Fatty acid and phospholipid metabolism
        *HP0690JHP0638Acetyl coenzyme A acetyltransferase (thiolase), fadA2.72.3
        *HP0871JHP0805CDP-diglyceride hydrolase, cdh8.26.9
        HP1045Acetyl-CoA synthetase, acoE4.53.6
    Hypothetical
        HP0018JHP00162.53.0
        HP0080JHP00743.53.3
        HP0097JHP00895.12.4
        HP0105JHP0097Conserved hypothetical protein3.22.9
        #HP0204JHP01902.22.0
        HP0305JHP02902.32.3
        *HP0309JHP0294Conserved hypothetical protein5.04.6
        HP0310JHP0295Conserved hypothetical protein6.74.1
        #HP0311JHP02964.62.3
        *HP0318JHP0301Conserved hypothetical protein2.73.9
        HP0367JHP10142.12.5
        *#HP0614JHP05572.12.7
        HP0627JHP05712.32.3
        HP06282.62.5
        HP0641JHP05842.02.3
        *HP0710JHP0649Conserved hypothetical protein3.83.6
        *HP0746JHP06832.42.5
        HP0920JHP0854Conserved hypothetical integral membrane protein3.02.7
        *HP0944JHP0879Conserved hypothetical protein3.03.7
        HP1391JHP14366.82.8
        HP1394JHP1433Conserved hypothetical protein2.12.7
        HP1454JHP13472.82.7
        HP1455JHP13484.13.5
        HP1457JHP13503.93.3
        HP1527JHP14163.42.1
        #HP1588JHP1494Conserved hypothetical protein2.52.1
    Regulatory functions
        HP0224JHP0210Peptide methionine sulfoxide reductase, msrA3.22.6
        HP0714JHP0652RNA polymerase sigma-54 factor, rpoN2.32.1
        *#HP1027JHP0397Ferric uptake regulation protein, fur3.94.1
    Translation
             HP0403JHP0978Phenylalanyl-tRNA synthetase, alpha subunit, pheS2.02.5
             HP0570JHP0517Aminopeptidase a/I, pepA5.04.3
        *HP1012JHP0411Putative zinc protease, pqqE2.52.2
    Transport and binding proteins
        *#HP0686JHP0626Iron(III) dicitrate transport protein, fecAI2.13.3
             HP0715JHP0653ABC transporter, ATP-binding protein5.73.7
        *#HP0807JHP0743Iron(III) dicitrate transport protein, fecA24.14.3
             HP0940JHP0875Amino acid ABC transporter, periplasmic binding protein, yckK2.12.4
        *HP1017JHP0406Amino acid permease, rocE3.22.2
             HP1091JHP0334Alpha-ketoglutarate permease, kgtP2.82.5
             HP1174JHP1101Glucose/galactose transporter, gluP4.02.8
             HP1491JHP1384Phosphate permease3.62.4
    Unknown function
             HP0390JHP0991Adhesin-thiol peroxidase, tagD3.83.3
             HP0569JHP0516GTP binding protein, gtp12.12.6
             HP0625JHP0569Protein E, gcpE3.33.4
        *HP1104JHP1030Cinnamyl-alcohol dehydrogenase, cad3.13.1
  • a *, these genes show differential regulation in both log- and stationary-phase cultures; #, these genes show differential regulation in the iron add-back experiment with the opposite change in expression.

  • b Due to space limitations, the maximum fold change is given for only one of the time points analyzed per experiment.