TABLE 5.

Changes in transcript levels in the ΔrpoE mutant strain and its wild-type strain after treatment with 250 μM Cu(II)^a

Change	Gene	Description	Comparison (Q value)
			+Cu/−Cu		ΔrpoE/WT
			WT	ΔrpoE	−Cu	+Cu
Down regulation in Cu ± rpoE comparison	ompC	Outer membrane protein 1b (Ib; c)	1.56	1.28	0.04	0.03
	rpoE	Sigma-E factor; heat shock and oxidative stress	1.31	1.30	0.05	0.05
	rseA	Sigma-E factor, negative regulatory protein	1.56	0.98	0.66	0.41
	ompA	Outer membrane protein 3a (II*;G;d)	1.28	1.54	0.42	0.50
Up regulation in Cu ± rpoE comparison	pspA	Phage shock protein, inner membrane protein	1.10	1.15	2.75	2.89
	pspB	Phage shock protein	1.67	1.66	2.82	2.80
	sohA	Putative protease; htrA suppressor protein	0.88	1.02	1.84	2.14
	yjbE	ORF, hypothetical protein	1.04	1.04	2.88	2.88
	pspC	Phage shock protein: activates psp expression	1.47	1.31	2.48	2.20
	pspD	Phage shock protein	1.06	0.99	2.20	2.04
Upregulation in WT upon copper stress (WT ± Cu)b	ylcC	cusF, periplasmic copper-binding protein	396.85	350.18	0.94	0.83
	ylcB	cusC, OMF of the Cus system	102.98	54.55	1.35	0.72
	ybdE	cusA, RND of the Cus system	15.30	11.90	1.07	0.83
	ylcA	cusR, response regulator of cus 2,3-dihydro-2,3- dihydroxybenzoate	10.59	8.39	1.01	0.80
	entA	Dehydrogenase, enterobactin biosynthesis	7.60	5.62	1.13	0.83
	ybdB	ORF, hypothetical protein	6.37	4.98	1.07	0.83
	soxS	Regulation of superoxide response regulon	6.24	5.62	0.93	0.84
	fepA	Outer membrane receptor for ferric enterobactin and colicins B and D	5.51	3.62	1.19	0.78
	ylcD	cusB, MFP of the Cus system	5.47	4.42	0.96	0.78
Down regulation in WT upon copper stress (WT ± Cu)c	yiaO	Putative solute-binding transport protein	0.14	0.14	0.94	0.93
	b2875	Putative synthase	0.15	0.14	0.86	0.83
	ydeD	ORF, hypothetical protein	0.15	0.15	0.94	0.92

^aThe genes are listed by increasing or decreasing quotients of their message concentrations (Q values) in the Cu ± rpoE and WT ± Cu 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.

^bNine top-ranking genes (of 61) are shown.

^cThree top-ranking genes (of 229) are shown.