TABLE 7.

Changes in transcript levels in the ΔrpoE mutant strain and its wild-type strain after treatment with 100 μM Zn(II)^a

Change	Gene	Description	Comparison (Q values)
			+Zn/−Zn		ΔrpoE/WT
			WT	ΔrpoE	−Zn	+Zn
Down regulation in Zn ± rpoE comparisonb	rpoE	RNA polymerase, sigma-E factor	4.52	1.88	0.05	0.02
	ompC	Outer membrane protein 1b (Ib;c)	1.05	1.59	0.04	0.06
	htrA	Periplasmic serine protease HtrA = DegP	11.41	2.20	0.83	0.16
	rseA	Sigma-E factor, negative regulatory protein	5.08	1.23	0.66	0.16
	ychH	ORF, hypothetical protein	5.02	0.36	3.63	0.26
Upregulation in Zn ± rpoE comparisonc	pspA	Phage shock protein, inner membrane protein	1.76	2.11	2.75	3.29
	ompX	Outer membrane protein X	0.57	1.32	1.31	3.04
	ycfS	ORF, hypothetical protein	1.39	2.96	1.40	2.98
	pspB	Phage shock protein	2.81	2.95	2.82	2.96
	pspC	Phage shock protein: activating function	1.89	2.16	2.48	2.83
Upregulation in WT upon zinc stress (WT ± Zn)d	yjaI	zraP	326.78	75.94	1.18	0.63
	htrA	Periplasmic serine protease HtrA	11.41	2.20	0.83	0.16
	entA	2,3-Dihydro-2,3-dihydroxybenzoate dehydrogenase, enterobactin biosynthesis	10.12	4.96	1.13	0.55
	ybdB	ORF, hypothetical protein	7.02	3.80	1.07	0.58
	entB	2,3-Dihydro-2,3-dihydroxybenzoate synthetase, enterobactin biosynthesis	6.67	2.92	1.27	0.55
	nrdE	Ribonucleoside-diphosphate reductase 2, alpha subunit, enterobactin biosynthesis	5.53	3.64	1.04	0.69
	fhuE	Outer membrane receptor for ferric siderophore uptake	5.48	3.24	1.24	0.73
Down regulation in WT upon zinc stress (WT ± Zn)e	ompF	Outer membrane protein 1a (Ia;b;F)	0.10	0.17	0.62	1.05
	rpsU	30S ribosomal subunit protein S21	0.19	0.79	0.38	1.58
	ymbA	ORF hypothetical protein	0.20	0.27	0.70	0.92

^aThe genes are listed by increasing or decreasing quotients of their message concentrations (Q values) in the Zn ± rpoE and WT ± Zn comparisons. All comparisons result from one data set. The Q values used for the ranking are identified by boldfacing. The full data set is available in the supplementary material.

^bTop-ranked 5 of 17 genes.

^cTop-ranked 5 of 16 genes.

^dTop-ranked 8 of 256 genes.

^eTop-ranked 6 of 115 genes.