TABLE 2.

Stationary-phase iron-regulated genes of H. pylori

Gene designationaGene function and nameMaximum fold changeb in:
TIGRASTRAExpt 1Expt 2
Repressed
    Amino acid biosynthesis
        #HP0652JHP0597Phosphoserine phosphatase, serB0.20.2
    Cellular processes, chaperones
         HP0109JHP0101Chaperone and heat shock protein 70, dnaK0.40.5
    Energy metabolism
        #HP0632JHP0575Quinone-reactive Ni/Fe hydrogenase, large subunit, hyaB0.40.4
        #HP0633JHP0576Quinone-reactive Ni/Fe hydrogenase, cytochrome b subunit, hyaC0.50.5
    Hypothetical
        #HP0388JHP0993Conserved hypothetical protein0.30.4
    Transport and binding
        #HP0653JHP0598Nonheme iron-containing ferritin, pfr0.20.1
Induced
    Amino acid biosynthesis
         *HP0649JHP0594Aspartate ammonia-lyase, aspA5.93.5
    *#HP0672JHP0615Solute binding signature and mitochondrial signature protein, aspB5.85.4
    Biosynthesis of cofactors, prosthetic     groups, and carriers
         HP0804JHP0740GTP cyclohydrolase II/3,4-dihydroxy-2-butanone 4-phosphate synthase, ribAB2.42.0
         HP1118JHP1046Gamma-glutamyltranspeptidase, ggt3.32.5
    *#HP1582JHP1489Pyridoxal phosphate biosynthetic protein J, pdxJ8.66.6
        #HP1583JHP1490Pyridoxal phosphate biosynthetic protein A, pdxA6.43.9
    Cell envelope and surface structures
         HP0115JHP0107Flagellin B, flaB4.02.1
         HP0175JHP0161Cell binding factor 2, putative peptidyl-prolyl cis-trans isomerase2.42.7
         *HP1501JHP1394OMP, omp322.02.1
    Cellular processes
         *HP0103JHP0095Methyl-accepting chemotaxis protein, tlpB2.04.9
         HP0887JHP0819Vacuolating cytotoxin, vacA2.62.3
         *HP1024JHP0400Cochaperone-curved DNA binding protein A, cbpA4.63.5
    Central intermediary metabolism
         HP0072JHP0067Urease beta subunit, ureB2.52.1
         HP0073JHP0068Urease alpha subunit, ureA2.72.3
         *HP0900JHP0837Hydrogenase expression/formation protein, hypB2.62.1
         *HP1186JHP1112Carbonic anhydrase3.42.5
    Energy metabolism
         *HP0026JHP0022Citrate synthase, gltA2.62.2
         HP0176JHP0162Fructose-bisphosphate aldolase energy metabolism, fba2.53.0
         HP0277JHP0262Ferredoxin energy metabolism2.93.7
    *#HP0294JHP0279Aliphatic amidase, amiE25.317.0
         HP0691JHP06373-Oxoadipate coenzyme A-transferase subunit A, scoA3.63.7
         HP0692JHP06363-Oxoadipate coenzyme A-transferase subunit B, scoB3.83.3
         *HP0943JHP0878d-Amino acid dehydrogenase, dadA3.82.5
         *HP1238JHP1159Aliphatic amidase, amiF6.34.1
         *HP1399JHP1427Arginase energy metabolism, rocF2.62.1
         HP1538JHP1461Ubiquinol cytochrome c oxidoreductase, cytochrome c1 subunit, petC2.22.1
         HP1539JHP1460Ubiquinol cytochrome c oxidoreductase, cytochrome b subunit, fbcH2.62.6
    Fatty acid and phospholipid metabolism
         HP0416JHP0968Cyclopropane fatty acid synthase, cfa3.93.3
         *HP0690JHP0638Acetyl coenzyme A acetyltransferase (thiolase), fadA3.74.0
         *HP0871JHP0805CDP-diglyceride hydrolase, cdh3.52.2/PICK>
    Hypothetical
        *HP0309JHP0294Conserved hypothetical protein3.32.6
        *HP0318JHP0301Conserved hypothetical protein4.84.9
        HP0595JHP05422.62.0
        *#HP0614JHP05572.92.2
        HP0693JHP0635Conserved hypothetical integral membrane protein, atoE3.22.8
        *HP0710JHP0649Conserved hypothetical protein2.62.1
        HP0719JHP06572.13.5
        HP0721JHP06582.32.8
        *HP0746JHP06832.12.0
        HP0773JHP07102.02.1
        HP0914JHP0850Putative OMP2.12.6
        *HP0944JHP0879Conserved hypothetical protein3.53.0
        HP1173JHP11002.12.2
        HP1182JHP1108Conserved hypothetical protein2.62.5
        HP1507JHP1400Conserved hypothetical ATP binding protein2.62.1
    Other categories, adaptations, and atypical conditions
             HP1496JHP1389General stress protein, putative ribosomal protein L25, ctc2.22.2
    Purines, pyrimidines, nucleosides, and nucleotides
             HP0680JHP0621Ribonucleoside-diphosphate reductase 1 alpha subunit, nrdA2.32.2
    Regulatory functions
        HP0166JHP0152Response regulator, ompR2.42.4
        HP1025JHP0399Putative heat shock protein, putative hspR3.12.5
        *#HP1027JHP0397Ferric uptake regulation protein, fur3.63.0
    Translation
         HP0177JHP0163Translation elongation factor EF-P, efp2.12.5
         *HP1012JHP0411Protease, putative zinc protease, pqqE2.12.5
         HP1019JHP0405Serine protease, htrA2.94.1
         *HP1313JHP1233Ribosomal protein S3, rps32.32.7
         *HP1315JHP1235Ribosomal protein S19, rps192.32.1
    Transport and binding proteins
        HP0140JHP0128l-Lactate permease, lctP2.72.0
        HP0301JHP0286Dipeptide ABC transporter, ATP-binding protein, dppD2.52.1
        *#HP0686JHP0626Iron(III) dicitrate transport protein, fecA16.44.0
        *#HP0807JHP0743Iron(III) dicitrate transport protein, fecA28.23.3
        #HP0876JHP0810Iron-regulated OMP, frpB122.010.8
        HP0942JHP0877d-Alanine glycine permease, dagA2.72.5
        *HP1017JHP0406Amino acid permease, rocE2.42.4
        HP1172JHP1099Glutamine ABC transporter, periplasmic glutamine binding protein, glnH2.63.1
        #HP1339JHP1258Biopolymer transport protein, exbB2.42.5
        *HP1400JHP1426Iron(III) dicitrate transport protein, fecA33.55.5
        #HP1432JHP1321Histidine- and glutamine-rich protein5.42.4
        #HP1561JHP1469Iron(III) ABC transporter, periplasmic iron-binding protein, ceuE13.73.2
        HP1562JHP1470Iron(III) ABC transporter, periplasmic iron-binding protein, ceuE23.62.6
    Unknown function
         *HP1104JHP1030cinnamyl-alcohol dehydrogenase EL13-2, cad3.13.2
  • 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.