TABLE 2.

Selection of genes whose average mRNA ratio was altered ≥2-fold (P value, ≤0.05) under iron excess or under iron limitation in at least two independent experiments^a

Category and NCgl gene no.	Description of product and gene designation	mRNA ratio
		Fe excess	Fe limitation
Genes presumably involved in iron acquisition, storage, or metabolism
NCgl0377	Put. secreted heme transport associated protein, C-term. TMH	16.82	5.00
NCgl0378	Heme ABC transporter, secreted lipoprotein, hmuT	3.54	2.64*
NCgl0379	Heme ABC transporter, permease, hmuU	9.33	3.98
NCgl0381	Put. secreted heme transport associated protein, C-term. TMH	17.66	5.99
NCgl0382	Put. secreted heme transport associated protein, C-term. TMH	13.99	6.51*
NCgl0482	Put. siderophore ABC transporter, ATPase	5.72	1.73
NCgl0483	Put. siderophore ABC transporter, permease, FecCD family	6.43	1.55*
NCgl0635	Put. soluble, cytoplasmic siderophore-interacting protein	6.53	1.70
NCgl0636	Put. siderophore ABC transporter, ATPase	6.78	1.62
NCgl0637	Put. siderophore ABC transporter, permease, FecCD family	5.70	1.74
NCgl0638	Put. siderophore ABC transporter, permease, FecCD family	2.35	1.42
NCgl0639	Put. siderophore ABC transporter, secreted lipoprotein	7.85	1.72
NCgl0773	Put. soluble, cytoplasmic siderophore-interacting protein	11.63	2.38
NCgl0774	Put. siderophore ABC transporter, secreted lipoprotein	8.43	2.51
NCgl0776	Put. siderophore ABC transporter, secreted lipoprotein	4.16	1.17*
NCgl0779	Put. siderophore ABC transporter, ATPase	4.21	1.27*
NCgl1200	Put. soluble, cytoplasmic siderophore-interacting protein	4.76	2.42*
NCgl1209	Put. siderophore ABC transporter, secreted lipoprotein	3.31	1.94*
NCgl1502	Fe-S cluster assembly protein, sufD	0.47	0.43
NCgl1503	Fe-S cluster assembly protein, sufB	0.48	0.43
NCgl1959	Put. secreted siderophore binding lipoprotein	8.48	3.26
NCgl2146	Heme oxygenase, hmuO	4.02	3.17
NCgl2439	Ferritin, ftn	1.07*	2.54
NCgl2897	Starvation-inducible DNA-binding protein, dps	1.28**	6.39**
NCgl2969	Transporter of major facilitator superfamily	4.35	1.43
NCgl2970	Put. secreted siderophore binding lipoprotein	4.94	1.37
Genes known to be regulated by RipA
NCgl0251	Catalase, katA	0.27	3.06
NCgl0359	Succinate dehydrogenase, sdhC	0.16	0.46*
NCgl0360	Succinate dehydrogenase, sdhA	0.08	0.28*
NCgl0361	Succinate dehydrogenase, sdhB	0.18	0.46
NCgl1141	Nitrate reductase, β subunit, narH	0.21	0.24*
NCgl1142	Nitrate reductase, α subunit, narG	0.10	0.41
NCgl1143	Nitrate/nitrite transporter, narK	0.34	0.60*
NCgl1262	3-Isopropylmalate dehydratase, large subunit, leuC	0.28	0.50*
NCgl1263	3-Isopropylmalate dehydratase small subunit, leuD	0.28	0.59*
NCgl1482	Aconitase, acn	0.29	0.63*
NCgl2319	Catechol 1,2-dioxygenase, catA	0.05	0.14
NCgl2657	Phosphotransacetylase, pta	0.26	1.10*
Genes encoding transcriptional regulators
NCgl0358	Transcriptional regulator, ramB	0.39	0.67*
NCgl0430	Transcriptional regulator, ArsR family	6.68	7.39
NCgl0943	Transcriptional regulator, AraC family, ripA	12.16	4.13
Further genes with a >10-fold increased mRNA level in the ΔdtxR mutant
NCgl0122	Hypothetical protein	31.33	21.49*
NCgl0123	Hypothetical protein	20.93	10.76
NCgl1618	Hypothetical protein	5.88	17.48
NCgl1635	Hypothetical protein	24.00	20.55
NCgl1646	Secretory serine protease	33.09	11.92
NCgl1651	Hypothetical exported protein	13.72	11.53
NCgl1677	Hypothetical protein	7.47	14.78
NCgl1678	Hypothetical protein	23.04	10.11
NCgl1679	Hypothetical protein	16.00	9.27*
NCgl1680	Hypothetical protein	14.99	9.97
NCgl1682	Hypothetical protein	10.40	8.04
NCgl1685	Hypothetical protein	12.54	9.10
NCgl2450	Put. 2-methylcitrate dehydratase	10.10	11.52

^aThe mRNA ratios (ΔdtxR mutant/wild type) represent average values obtained from four (iron excess) or three (iron limitation) DNA microarray experiments performed with RNA isolated from four or three independent cultures in CGXII minimal medium containing either 100 μM FeSO₄ or 1 μM FeSO₄. Ratios labeled with a single asterisk could be analyzed in only a single experiment; for the ratios labeled with two asterisks, the P value was above 0.05. A list of all genes showing twofold-altered mRNA levels in the ΔdtxR mutant is provided in Table S2 in the supplemental material. Put., putative; TMH, transmembrane helix.