TABLE 1.

Differentially expressed genes identified by RNA-seq

Gene expression	Gene no.		Gene name or function	Ratiob
	B8	26695/J99a
Upregulated	HPB8_46	HP1484	Membrane protein	1.53
	HPB8_73	HP1459	rluB, tRNA synthetase	1.54
	HPB8_104	−	Predicted	2.11
	HPB8_111	−	Predicted	1.86
	HPB8_188	HP1426	Predicted	1.62
	HPB8_193	HP1288	Predicted	1.75
	HPB8_243	HP1240	maf, septum formation	1.46
	HPB8_251	−	Predicted	2.22
	HPB8_297	HP1193	tas1, aldoketoreductase	1.49
	HPB8_336	HP1162	Integral membrane protein	1.50
	HPB8_338	HP1160	Predicted	1.85
	HPB8_378	HP1546	Predicted	1.73
	HPB8_386	HP1116	Predicted	1.48
	HPB8_435	HP0385	Predicted	1.53
	HPB8_475	HP1412	Predicted	1.47
	HPB8_476	jhp0955	Predicted	2.35
	HPB8_477	jhp0954	Predicted	1.76
	HPB8_485	HP0441	virB4, ATPase	1.55
	HPB8_528	jhp0936	Predicted	1.64
	HPB8_529	HP0996	Predicted	1.71
	HPB8_530	−	Predicted	1.47
	HPB8_555	jhp1408	Predicted	1.62
	HPB8_562	−	Predicted	1.75
	HPB8_640	HP0008	Predicted	1.60
	HPB8_650	HP0903	ackA, acetate kinase	1.63
	HPB8_883	HP0681	Predicted	1.49
	HPB8_884	HP0682	Predicted	1.61
	HPB8_897	HP0696	acxB	1.65
	HPB8_898	HP0697	acxC	1.60
	HPB8_929	HP0724	dcuA	1.86
	HPB8_930	HP0725	sabA	1.62
	HPB8_976	HP0767	Predicted	1.58
	HPB8_1017	HP0809	fliL	1.49
	HPB8_1088	HP0876	frpB1	1.62
	HPB8_1089	HP0877	ruvC	1.52
	HPB8_1092	HP0882	Predicted	1.53
	HPB8_1124	HP0461	Predicted	1.81
	HPB8_1139	HP1022	Predicted	1.75
	HPB8_1140	HP1022	Predicted	1.47
	HPB8_1154	HP1036	folK	1.60
	HPB8_1176	HP1057	Predicted	1.46
	HPB8_1213	HP1093	Predicted	1.54
	HPB8_1293	HP0269	miaB, tRNA methylation	1.46
	HPB8_1336	HP0229	hopA	1.73
	HPB8_1347	HP0219	Predicted	1.51
	HPB8_1352	HP0213	gidA, division protein	1.49
	HPB8_1408	HP0157	arok	1.51
	HPB8_1430	HP0135	Predicted	1.74
	HPB8_1452	HP0113	Predicted	1.55
	HPB8_1453	HP0112	fucA, fucose metabolism	1.63
	HPB8_1491	−	Predicted	1.62
	HPB8_1514	HP0054	hypAVM, DNA methylase	1.77
	HPB8_1561	HP0427	Predicted	1.85
	HPB8_1562	HP0426	Predicted	1.48
	HPB8_1563	HP0426	Predicted	1.95
	HPB8_1588	HP0036	Predicted	1.55
	HPB8_1600	HP0025	hopD	1.48
	HPB8_1609	HP0016	Predicted	1.55
	HPB8_1610	HP0015	Predicted	1.55
	HPB8_1653	−	Predicted	2.29
	HPB8_1655	HP1564	metQ	1.57
	HPB8_1669	HP1541	mfd, DNA transcription	1.58
	HPB8_1701	HP1399	rocF	1.66
	HPB8_p0001	−	Predicted	1.81
	HPB8_p0002	jhp0828	Predicted	1.74
	HPB8_p0003	−	Predicted	1.47
Downregulated	HPB8_106	HP1435	pspA, signal peptide protease	0.59
	HPB8_159	HP1320	rpsJ	0.60
	HPB8_160	HP1319	rplC	0.56
	HPB8_162	HP1317	rplW	0.67
	HPB8_170	HP1309	rplN	0.68
	HPB8_195	HP1286	Secreted protein	0.53
	HPB8_226	HP1254	bioC, biotin synthesis	0.63
	HPB8_234	HP1246	rpsF	0.68
	HPB8_235	HP1245	ssb, DNA binding protein	0.67
	HPB8_236	HP1244	rpsR	0.65
	HPB8_299	HP1192	Secreted motility protein	0.54
	HPB8_334	HP1163	fixS	0.66
	HPB8_394	HP1100	porA	0.67
	HPB8_439	HP0389	sodB	0.67
	HPB8_743	HP0549	murI, glutamate racemase	0.57
	HPB8_761	HP0565	Predicted	0.46
	HPB8_786	HP0588	oorD, oxoglutarate ferrodoxin oxidoreductase	0.66
	HPB8_800	HP0601	flaA	0.52
	HPB8_829	HP0630	mda66, drug activity modulator	0.37
	HPB8_842	HP0641	Predicted	0.39
	HPB8_843	HP0641	3-Hydroxyacid dehydrogenase	0.39
	HPB8_844	HP0642	frxA, NAD(P)H-flavin oxidoreductase	0.38
	HPB8_921	HP0715	Predicted ABC transporter	0.65
	HPB8_925	HP0719/720	Predicted	0.62
	HPB8_938	HP0731	Predicted	0.67
	HPB8_939	HP0733	Predicted	0.60
	HPB8_958	HP0751	flaG	0.67
	HPB8_1010	HP0802	ribA, riboflavin biosynthesis	0.67
	HPB8_1015	HP0807	fecA2	0.54
	HPB8_1016	HP0808	acpS, ACP synthase	0.67
	HPB8_1020	HP0812	Predicted	0.51
	HPB8_1023	HP0815	motA, flagellar motor	0.66
	HPB8_1061	HP0851	Predicted integral membrane protein	0.59
	HPB8_1108	HP0474	modB, molybdenum transporter	0.65
	HPB8_1111	HP0472	horE	0.56
	HPB8_1122	HP0463	hsdM, restriction enzyme	0.63
	HPB8_1146	HP1028	Predicted	0.64
	HPB8_1238	HP0326	neuA3, CMP-N-acetylneuraminic acid synthetase	0.65
	HPB8_1239	HP0325	flgH, flagellar basal ring	0.64
	HPB8_1247	HP0318	Predicted	0.50
	HPB8_1266	HP0296	rplU	0.68
	HPB8_1271	HP0291	pheA, predicted chorismate mutase	0.65
	HPB8_1307	HP0256	Predicted	0.64
	HPB8_1338	HP0227	hopM/omp5	0.56
	HPB8_1346	HP0220	nifS	0.63
	HPB8_1378	HP0189	Predicted	0.67
	HPB8_1450	HP0115	flaB	0.56
	HPB8_1492	HP0073	ureA	0.67
	HPB8_1493	HP0072	ureB	0.68
	HPB8_1511	HP0057	Predicted	0.41
	HPB8_1525	HP1354	DNA methyltransferase	0.67
	HPB8_1526	HP1355	nadC, NAD synthesis	0.64
	HPB8_1551	HP1382	nucG endonuclease	0.64
	HPB8_1702	HP1400	fecA3	0.39

^aCorresponding 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.

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