TABLE 1.

Genes coregulated by RpoE and RpoX at 42°C

Gene identificationa	Annotationb	Fold change (ΔrpoE/WT)	Fold change (ΔrpoX/WT)	Promoter region bound by RpoX determined by ChIP-seqc	Virulence-associated gened
N646_4603	Hypothetical protein	−175.96	−1,081.83	Y
N646_4599	Hypothetical protein	−14.42	−263.51
N646_4604	Hemolysin D	−21.50	−119.59	Y	Y
N646_0533	Anti-anti-sigma regulatory factor	−134.98	−108.89		Y
N646_3842	Hypothetical protein	−2.42	−104.79
N646_4684	Hypothetical protein	−4.74	−79.41
N646_4605	Hypothetical protein	−9.17	−55.37
N646_3940	Hypothetical protein	−5.11	−47.04
N646_0523	Putative membrane protein of ExoQ family, involved in exopolysaccharide production	−2.49	−42.23		Y
N646_4610	Hypothetical protein, RpoX	−4.44	−39.73	Y	Y
N646_1050	Hypothetical protein	−3.20	−31.18
N646_4601	Hypothetical protein	−44.33	−29.20	Y
N646_3768	Hypothetical protein	−6.06	−21.91
N646_0526	Putative galactosyltransferase	−5.28	−19.04
N646_4606	ABC transporter outer membrane component	−2.55	−17.99
N646_1186	Sodium-type flagellar protein MotY	−2.35	−16.89		Y
N646_4602	Hypothetical protein	−29.71	−16.78
N646_0512	FMN-dependent NADH-azoreductase	−2.68	−16.44
N646_4598	Hypothetical protein	−6.38	−14.22
N646_4600	Hypothetical protein	−31.74	−11.95	Y
N646_0722	Hypothetical protein	−2.15	−11.33
N646_2916	Hypothetical protein	−20.26	−10.69
N646_2929	Polar flagellar FlgF	−2.52	−10.37		Y
N646_1399	Hypothetical protein	−1.41	−10.16
N646_4608	Hypothetical protein	−3.93	−10.07
N646_1161	Hypothetical protein	−3.12	−9.17
N646_1591	Hypothetical protein	−2.23	−8.63
N646_0708	Putative acetyltransferase	−5.03	−8.55
N646_4609	Hypothetical protein	−4.83	−8.51	Y
N646_3939	Hypothetical protein	−3.08	−7.66
N646_0532	Hypothetical protein	−32.48	−7.18
N646_0389	Hypothetical protein	−4.52	−6.73
N646_0390	Hypothetical protein	−4.98	−6.44
N646_0562	Hypothetical protein	−4.71	−6.43
N646_0384	Putative dioxygenase	−2.40	−6.38
N646_3470	GTP cyclohydrolase II	−2.57	−6.38
N646_0714	Transcriptional regulator, GntR family protein	−2.75	−6.24
N646_4629	Cytochrome c oxidase, subunit II	−2.03	−5.99
N646_1446	50S ribosomal protein L31	−0.46	−5.88
N646_0176	Hypothetical protein	−2.28	−5.39
N646_0385	2-Keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase	−2.42	−4.98
N646_3844	Pirin-related protein	−2.69	−4.98
N646_0013	Hypothetical protein	−111.19	−4.81
N646_4302	Hypothetical protein	−3.03	−4.81
N646_0530	Putative capsular polysaccharide biosynthesis	−4.10	−4.59		Y
N646_2548	Glycerol dehydrogenase	−4.40	−4.31
N646_1338	Flagellar biosynthesis protein FlhF	−5.32	−3.76		Y
N646_1844	Putative fimbrial assembly protein PilM	−2.05	−3.74		Y
N646_0713	Carboxyphosphonoenolpyruvate phosphonomutase	−2.70	−3.71
N646_0456	Hypothetical protein	−2.36	−3.61
N646_4031	Hypothetical protein	−7.04	−3.52
N646_4030	Putative phenylacetate-CoA ligase	−8.34	−3.41
N646_2724	DNA-binding response regulator PhoB	−2.33	−3.26		Y
N646_4032	Oxidoreductase	−6.58	−3.26
N646_2270	Hypothetical protein	−3.55	−3.16
N646_3227	CsuA	−22.07	−3.06		Y
N646_4508	Enoyl-CoA hydratase	−2.04	−2.99
N646_0645	Amino acid ABC transporter, periplasmic amino-acid-binding protein	−2.64	−2.89
N646_4675	Hypothetical protein	−2.06	−2.71
N646_2932	Flagellar P-ring protein FlgI	−3.54	−2.67		Y
N646_0301	Hypothetical protein	−5.28	−2.67
N646_4059	Hypothetical protein	−2.10	−2.66
N646_2799	Small protein A	−2.16	−2.60
N646_2936	Flagellin	−2.28	−2.57		Y
N646_3225	CsuC	−15.77	−2.49		Y
N646_4417	Hypothetical protein	−10.82	−2.40
N646_3072	Hypothetical protein	−2.52	−2.36
N646_4028	Hypothetical protein	−14.67	−2.36
N646_0455	Hypothetical protein	−2.10	−2.27
N646_0799	Hypothetical protein	−3.72	−2.27
N646_0531	Periplasmic protein involved in polysaccharide export	−16.16	−2.27		Y
N646_0807	Hypothetical protein	−2.45	−2.24
N646_3224	CsuD	−5.06	−2.22		Y
N646_4029	Putative high-affinity branched-chain-amino-acid transport ATP-binding protein	−11.73	−2.21
N646_0145	Tryptophanyl-tRNA synthetase	−2.99	−2.19
N646_3223	CsuE	−2.97	−2.17		Y
N646_0685	Hypothetical protein	−3.58	−2.04
N646_4419	Hypothetical protein	−2.18	−2.03
N646_0561	Formate dehydrogenase accessory protein	−3.67	−2.00
N646_0626	Hypothetical protein	5.81	2.05
N646_2558	Hypothetical protein	2.20	2.05
N646_0313	Imidazolonepropionase	2.47	2.07
N646_2232	Hypothetical protein	3.12	2.10
N646_3280	Pyruvate formate-lyase	2.88	2.10
N646_1747	Aspartate carbamoyltransferase regulatory subunit	2.64	2.15
N646_3214	Hypothetical protein	3.47	2.15
N646_0304	Outer membrane protein	2.02	2.19
N646_0641	Hypothetical protein	3.82	2.28
N646_3434	Putative ribosomal protein N-acetyltransferase	2.58	2.39
N646_2428	UTP-glucose-1-phosphate uridylyltransferase	2.36	2.47
N646_4424	Hypothetical protein	2.15	2.47
N646_4184	Hypothetical protein	2.06	2.56
N646_3925	Putative acriflavine resistance protein	2.99	2.62
N646_3664	Thermolabile hemolysin	2.75	2.65		Y
N646_4456	Putative KHG/KDPG aldolase	2.44	2.81
N646_3202	Putative ABC transporter membrane-spanning permease	2.03	2.96
N646_3782	Hypothetical protein	3.47	4.15
N646_3806	Alcohol dehydrogenase, zinc-binding domain protein	3.66	4.21
N646_3556	Putative hydrolase	3.26	5.04
N646_2057	Hypothetical protein	2.95	5.26
N646_4487	Arginine ABC transporter, periplasmic arginine-binding protein	11.25	5.30
N646_3755	Putative muconate cycloisomerase I	2.24	6.51
N646_3685	Hypothetical protein	5.67	7.51
N646_3856	Hypothetical protein	3.03	7.62
N646_3885	Glyceraldehyde-3-phosphate dehydrogenase	2.77	7.82
N646_4611	Hypothetical protein	1.02	−1.27	Y
N646_1623	50S ribosomal protein L19	1.09	2.37	Y
N646_1624	tRNA (guanine-N1)-methyltransferase	1.03	2.67	Y

^aAll the genes with differential expression with a P value of <0.001.

^bFMN, flavin mononucleotide.

^cY indicates that the promoter region of the gene was also bound by RpoX, as identified by ChIP-seq analysis.

^dY indicates that the gene was annotated as a virulence-associated genes.