TABLE 1

Differentially expressed genes identified by RNA-seq

Gene expressionGene no.Gene name or functionRatiob
B826695/J99a
UpregulatedHPB8_46HP1484Membrane protein1.53
HPB8_73HP1459rluB, tRNA synthetase1.54
HPB8_104Predicted2.11
HPB8_111Predicted1.86
HPB8_188HP1426Predicted1.62
HPB8_193HP1288Predicted1.75
HPB8_243HP1240maf, septum formation1.46
HPB8_251Predicted2.22
HPB8_297HP1193tas1, aldoketoreductase1.49
HPB8_336HP1162Integral membrane protein1.50
HPB8_338HP1160Predicted1.85
HPB8_378HP1546Predicted1.73
HPB8_386HP1116Predicted1.48
HPB8_435HP0385Predicted1.53
HPB8_475HP1412Predicted1.47
HPB8_476jhp0955Predicted2.35
HPB8_477jhp0954Predicted1.76
HPB8_485HP0441virB4, ATPase1.55
HPB8_528jhp0936Predicted1.64
HPB8_529HP0996Predicted1.71
HPB8_530Predicted1.47
HPB8_555jhp1408Predicted1.62
HPB8_562Predicted1.75
HPB8_640HP0008Predicted1.60
HPB8_650HP0903ackA, acetate kinase1.63
HPB8_883HP0681Predicted1.49
HPB8_884HP0682Predicted1.61
HPB8_897HP0696acxB1.65
HPB8_898HP0697acxC1.60
HPB8_929HP0724dcuA1.86
HPB8_930HP0725sabA1.62
HPB8_976HP0767Predicted1.58
HPB8_1017HP0809fliL1.49
HPB8_1088HP0876frpB11.62
HPB8_1089HP0877ruvC1.52
HPB8_1092HP0882Predicted1.53
HPB8_1124HP0461Predicted1.81
HPB8_1139HP1022Predicted1.75
HPB8_1140HP1022Predicted1.47
HPB8_1154HP1036folK1.60
HPB8_1176HP1057Predicted1.46
HPB8_1213HP1093Predicted1.54
HPB8_1293HP0269miaB, tRNA methylation1.46
HPB8_1336HP0229hopA1.73
HPB8_1347HP0219Predicted1.51
HPB8_1352HP0213gidA, division protein1.49
HPB8_1408HP0157arok1.51
HPB8_1430HP0135Predicted1.74
HPB8_1452HP0113Predicted1.55
HPB8_1453HP0112fucA, fucose metabolism1.63
HPB8_1491Predicted1.62
HPB8_1514HP0054hypAVM, DNA methylase1.77
HPB8_1561HP0427Predicted1.85
HPB8_1562HP0426Predicted1.48
HPB8_1563HP0426Predicted1.95
HPB8_1588HP0036Predicted1.55
HPB8_1600HP0025hopD1.48
HPB8_1609HP0016Predicted1.55
HPB8_1610HP0015Predicted1.55
HPB8_1653Predicted2.29
HPB8_1655HP1564metQ1.57
HPB8_1669HP1541mfd, DNA transcription1.58
HPB8_1701HP1399rocF1.66
HPB8_p0001Predicted1.81
HPB8_p0002jhp0828Predicted1.74
HPB8_p0003Predicted1.47
DownregulatedHPB8_106HP1435pspA, signal peptide protease0.59
HPB8_159HP1320rpsJ0.60
HPB8_160HP1319rplC0.56
HPB8_162HP1317rplW0.67
HPB8_170HP1309rplN0.68
HPB8_195HP1286Secreted protein0.53
HPB8_226HP1254bioC, biotin synthesis0.63
HPB8_234HP1246rpsF0.68
HPB8_235HP1245ssb, DNA binding protein0.67
HPB8_236HP1244rpsR0.65
HPB8_299HP1192Secreted motility protein0.54
HPB8_334HP1163fixS0.66
HPB8_394HP1100porA0.67
HPB8_439HP0389sodB0.67
HPB8_743HP0549murI, glutamate racemase0.57
HPB8_761HP0565Predicted0.46
HPB8_786HP0588oorD, oxoglutarate ferrodoxin oxidoreductase0.66
HPB8_800HP0601flaA0.52
HPB8_829HP0630mda66, drug activity modulator0.37
HPB8_842HP0641Predicted0.39
HPB8_843HP06413-Hydroxyacid dehydrogenase0.39
HPB8_844HP0642frxA, NAD(P)H-flavin oxidoreductase0.38
HPB8_921HP0715Predicted ABC transporter0.65
HPB8_925HP0719/720Predicted0.62
HPB8_938HP0731Predicted0.67
HPB8_939HP0733Predicted0.60
HPB8_958HP0751flaG0.67
HPB8_1010HP0802ribA, riboflavin biosynthesis0.67
HPB8_1015HP0807fecA20.54
HPB8_1016HP0808acpS, ACP synthase0.67
HPB8_1020HP0812Predicted0.51
HPB8_1023HP0815motA, flagellar motor0.66
HPB8_1061HP0851Predicted integral membrane protein0.59
HPB8_1108HP0474modB, molybdenum transporter0.65
HPB8_1111HP0472horE0.56
HPB8_1122HP0463hsdM, restriction enzyme0.63
HPB8_1146HP1028Predicted0.64
HPB8_1238HP0326neuA3, CMP-N-acetylneuraminic acid synthetase0.65
HPB8_1239HP0325flgH, flagellar basal ring0.64
HPB8_1247HP0318Predicted0.50
HPB8_1266HP0296rplU0.68
HPB8_1271HP0291pheA, predicted chorismate mutase0.65
HPB8_1307HP0256Predicted0.64
HPB8_1338HP0227hopM/omp50.56
HPB8_1346HP0220nifS0.63
HPB8_1378HP0189Predicted0.67
HPB8_1450HP0115flaB0.56
HPB8_1492HP0073ureA0.67
HPB8_1493HP0072ureB0.68
HPB8_1511HP0057Predicted0.41
HPB8_1525HP1354DNA methyltransferase0.67
HPB8_1526HP1355nadC, NAD synthesis0.64
HPB8_1551HP1382nucG endonuclease0.64
HPB8_1702HP1400fecA30.39
  • a Corresponding genes in the H. pylori 26695 and J99 genomes are shown (63, 64). The gene name for H. pylori J99 is listed if the gene is absent in H. pylori 26695. A minus indicates the absence of the corresponding gene in H. pylori 26695 and J99.

  • b Ratios of transcript abundance (high-salt versus routine conditions) were calculated as described in Materials and Methods.