Table 2. Genes involved in the oxidative stress response that are differentially expressed under Na⁺ depleted conditions.

		Parent ATCC 33277−/+Na+			rprY mutant −/+Na+
Locusa	Common name	Fold expb	P valc	Repeats	Fold exp	P val	Repeats
PG0034	Thioredoxin	2.95	0.0004	12	3.25	0.0001	12
PG0046	Phosphatidate cytidylyltransferase	2.21	0.0028	12	2.25	0.0001	12
PG0047	Cell division protein FtsH, putative	2.04	0.0026	12	2.12	0.0016	12
PG0095	DNA mismatch repair protein MutS	0.65	0.0806	8	1.91	0.0041	8
PG0209	Formate-nitrite transporter	3.71	0.0004	12	3.39	0.0241	11
PG0258	ABC transporter, ATP-binding protein	1.78	0.0028	12	3.94	0.0000	12
PG0275	Thioredoxin family protein	1.71	0.0049	12	4.09	0.0000	12
PG0432	NOL1-NOP2-sun family protein	2.82	0.0517	12	3.58	0.0001	12
PG0433	Tetrapyrrole methylase family protein	2.88	0.0165	12	7.43	0.0001	8
PG0618	Alkyl hydroperoxide reductase, C subunit	1.17	0.1644	12	1.85	0.0119	12
PG0889	Peptidase, M24 family	2.35	0.0004	12	2.94	0.0002	12
PG0890	Alkaline phosphatase, putative	2.37	0.0002	12	3.46	0.0000	12
PG1043	Ferrous iron transport protein B	0.96	0.7002	7	2.01	0.0501	9
PG1044	Iron dependent repressor, putative	1.50	0.2211	12	3.27	0.0067	8
PG1088	Acetyltransferase, GNAT family	2.14	0.0001	12	0.94	0.5204	12
PG1089	DNA-binding response regulator RprY	1.58	0.0001	12	2.05d	0.0000	12
PG1124	ATP:cob(I)alamin adenosyltransferase, putative	1.12	0.4240	12	2.02	0.0000	12
PG1134	Thioredoxin reductase	1.27	0.0248	12	1.93	0.0075	12
PG1190	Glycerate dehydrogenase	1.56	0.1968	12	4.20	0.0000	10
PG1286	Ferritin	2.03	0.0005	12	4.00	0.0000	12
PG1321	Formate–tetrahydrofolate ligase	4.79	0.0001	12	6.78	0.0000	12
PG1545	Superoxide dismutase, Fe-Mn	1.96	0.0069	12	4.44	0.0001	12
PG1640	DNA-damage-inducible protein F	1.60	0.0011	12	2.16	0.0001	10
PG1642	Cation-transporting ATPase, authentic frameshift	1.88	0.0000	12	3.50	0.0000	12
PG1729	Thiol peroxidase	3.03	0.0000	12	3.68	0.0000	12
PG1841	Conserved hypothetical protein	3.20	0.0006	12	4.02	0.0005	12
PG1868	Membrane protein, putative	1.50	0.4660	10	3.83	0.0013	12
PG2008	TonB-dependent receptor, putative	1.03	0.8227	5	3.11	0.0620	8
PG2213	Nitrite reductase-related protein	1.54	0.0004	12	2.26	0.0005	12

^aLoci numbers are those from the annotation of the genome of strain W83 and the microarrays.

^bFold expression.

^c P values were calculated using LIMMA.

^dThe microarray PCR amplicon for rprY is upstream from the erythromycin resistance cassette that was used to generate the rprY mutation, thus an expression signal was still detectable.