TABLE 6.

Changes in transcript levels in the ΔrpoE mutant strain and its wild-type strain after treatment with 25 μM Cd(II)^a

Change	Gene	Description	Comparison (Q values)
			+Cd/−Cd		ΔrpoE/WT
			WT	ΔrpoE	−Cd	+Cd
Down regulation in Cd ± rpoE comparisonb	ompC	Outer membrane protein 1b (Ib;c)	0.90	0.96	0.04	0.04
	rpoE	RNA polymerase, sigma-E factor	0.76	0.75	0.05	0.05
	ompA	Outer membrane protein 3a (II*;G;d)	1.68	1.41	0.42	0.35
	katG	Catalase; hydroperoxidase HPI(I)	4.19	1.56	1.02	0.38
	grxA	Glutaredoxin 1	4.90	2.30	0.86	0.40
Upregulation in Cd ± rpoE comparison	yjbE	ORF, hypothetical protein	0.79	1.13	2.88	4.13
	pspA	phage shock protein, inner membrane protein	1.07	1.30	2.75	3.33
	pspB	phage shock protein	1.68	1.79	2.82	3.01
	pspC	phage shock protein: activates phage shock protein expression	1.56	1.54	2.48	2.44
	b1481	ORF, hypothetical protein	1.38	1.68	1.92	2.33
Upregulation in WT upon cadmium stress (WT ± Cd)c	ycfR	ORF, hypothetical protein	25.19	5.97	1.89	0.45
	b1973	zinT(yodA), zinc binding outer membrane protein	21.87	23.41	1.06	1.14
	yebL	znuA	12.73	13.74	0.93	1.01
	Ftn	ftnA, cytoplasmic ferritin (iron storage protein)	11.84	9.13	0.98	0.75
	zntA	Zinc-transporting ATPase	7.66	8.58	0.99	1.11
	cysH	3′-Phosphoadenosine 5′-phosphosulfate reductase	5.07	4.03	0.78	0.62
Downregulation in WT upon cadmium stress (WT ± Cd)d	yhdV	ORF, hypothetical protein	0.11	0.12	0.95	0.97
	ydeD	ORF, hypothetical protein	0.12	0.13	0.94	0.99
	fliP	Flagellar biosynthesis	0.12	0.13	0.90	0.95

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

^cTop-ranked 6 of 133 genes.

^dTop-ranked 3 of 302 genes.