TABLE 5.

pH-regulated oxidative stress response^a

Gene	Function	Log2 pH ratiob			PQ, Sal, or H2O2	Classc
		5/7	8.7/7	8.7/5
acnA	Aconitase A	0.769	−0.143	−0.912	Sal	AH
adhE	Acetaldehyde-coenzyme A dehydrogenase	0.043	−0.380	−0.422	Sal	BL
ahpC	Alkyl hydroperoxide reductase small subunit	1.003	0.436	−0.568	PQ, H2O2	NL
ahpF	Alkyl hydroperoxide reductase large subunit	0.777	−0.222	−0.999	H2O2	AH
aldA	Aldehyde dehydrogenase, NAD linked	0.773	0.764	−0.009	PQ	NL
alx (ygjT)	Membrane protein, alkali induced	−1.317	0.692	2.009	PQ−	AL
artI	Periplasmic arginine binding protein	0.286	0.655	0.369	PQ	BH
aspA	Aspartate ammonia-lyase (aspartase)	−0.592	0.770	1.362	PQ−	BH
carA	Carbamoylphosphate synthase small subunit	0.029	1.059	1.030	PQ−	BH
cfa	Cyclopropane fatty acid synthase	2.075	−0.480	−2.555	Sal	AH
cyaA	Adenylate cyclase	0.691	−0.156	−0.846	Sal	AH
cyoD	Cytochrome o oxidase subunit IV	0.829	−0.192	−1.021	PQ	NL
cysK	Cysteine synthase	1.204	1.351	0.147	PQ, Sal, H2O2	NL
dadX	Alanine racemase	0.683	−0.393	−1.076	PQ	AH
deoA	Thymidine phosphorylase	−1.031	−2.003	−0.972	Sal	BL
deoB	Deoxyribouratase, phosphopentomutase	−0.731	−1.502	−0.771	PQ, Sal	BL
dhaH	Dihydroxyacetone phosphoryl donor	1.547	−0.527	−2.074	Sal	AH
dhaK	Dihydroxyacetone kinase	1.041	−0.379	−1.420	Sal	AH
dnaK	HSP-70-type molecular chaperone	−0.894	−2.249	−1.356	Sal	BL
dps	Stress response DNA-binding protein	1.130	0.105	−1.025	PQ, Sal, H2O2	NL
fliS	Flagellar synthesis; flagellar regulon member	−0.174	−1.947	−1.772	PQ−	BL
fpr	Ferredoxin NADP+ reductase; anaerobic	0.565	0.275	−0.289	PQ, H2O2	NL
gapA	GAPDHd A	0.093	−0.752	−0.844	Sal	BL
gatA	Galactitol-specific enzyme IIA of PTSe	0.929	−0.626	−1.555	PQ, Sal	AH
gatB	Galactitol-specific enzyme IIB of PTS	0.632	−0.895	−1.528	PQ, Sal	AH
gatC	Galactitol-specific enzyme IIC of PTS	0.973	−0.949	−1.922	Sal	AH
gatD	Galactitol-1-phosphate dehydrogenase	1.037	−0.893	−1.930	PQ, Sal	AH
gatZ	Tagatose 6-phosphate aldolase 2	0.774	−0.605	−1.380	Sal	AH
gltA	Citrate synthase	0.288	−0.559	−0.846	PQ, Sal	AH
gltB	Glutamate synthase, large subunit	0.846	−1.425	−2.271	Sal	AH
grxA	Glutaredoxin 1	1.666	−0.106	−1.772	H2O2	AH
gshB	Glutathione synthetase	0.768	−0.081	−0.848	Sal	AH
hdeA	Periplasmic acid chaperone	0.841	−0.326	−1.167	Sal	AH
hdeB	Periplasmic acid chaperone	0.782	−0.622	−1.404	Sal	AH
hisF	Cyclase component of IGP synthase	0.150	0.703	0.553	PQ−	BH
ibpB	Chaperone, HSP20 family	−1.691	−2.618	−0.928	H2O2	BL
katG	Catalase hydrogen peroxidase 1	−0.578	−0.313	0.265	H2O2	AL
lamB	Maltose high-affinity uptake	−4.881	−3.735	1.146	PQ	NH
lldP	l-Lactate permease	1.527	0.219	−1.307	Sal	NL
lysU	Lysyl tRNA synthetase, inducible	0.544	−0.077	−0.621	Sal	AH
malE	Maltose-binding protein, periplasmic	−3.425	−2.933	0.491	PQ	NH
malK	Maltose transport complex, ATP-binding subunit	−4.790	−3.748	1.041	PQ	NH
manX	PTS family, mannose-specific enzyme IIA component	0.000	0.517	0.517	Sal	AL
map	Methionine aminopeptidase	0.510	0.056	−0.454	PQ	AH
marA	Multiple antibiotic resistance	1.321	−0.516	−1.836	PQ, Sal	AH
marB	Regulator for mar	0.894	−0.172	−1.066	Sal	AH
marR	Repressor of mar	0.352	−0.437	−0.789	Sal	AH
mdaB	Drug activity modulator	0.444	−0.223	−0.667	Sal	AH
murF	d-Alanyl:d-alanine adding to cell wall	0.216	−0.170	−0.386	PQ	AH
nfnB	Nitrofurantoin resistance; nitroreductase	0.818	−0.204	−1.022	PQ, Sal	AH
nuoI	NADH dehydrogenase I subunit	0.792	0.310	−0.481	PQ	NL
nuoK	NADH dehydrogenase I subunit	0.766	0.460	−0.306	PQ	NL
ompF	Outer membrane porin	−2.834	−0.892	1.942	PQ−	AL
ompT	Outer membrane protease VII	−0.815	−1.204	−0.389	Sal−	BL
pdhR	Repressor of pdh	0.755	−0.109	−0.863	PQ	AH
pepN	Aminopeptidase N	0.671	0.118	−0.553	Sal	NL
pflB	Pyruvate formate lyase I (anaerobic)	0.812	0.578	−0.234	Sal	NL
pgi	Glucose phosphate isomerase	0.654	0.177	−0.477	PQ	NL
ptsG	PTS family IIC, glucose specific	0.841	0.554	−0.287	PQ	NL
putA	Proline dehydrogenase	−1.062	−0.353	0.708	Sal	AL
pyrB	Aspartate transcarbamylase	0.133	0.608	0.475	PQ−, Sal−	BH
sdhB	Succinate dehydrogenase	1.833	0.329	−1.505	PQ	AH
tnaA	Tryptophanase	−3.805	0.223	4.028	H2O2	AL
treB	Tre-specific PTS enzyme II	−3.156	0.739	3.895	Sal−	AL
yahA	Putative repressor	−0.667	0.422	1.089	PQ−	AL
yaiA	Function unknown	1.154	0.416	−0.738	H2O2	NL
ybjC	Function unknown	0.463	−0.447	−0.910	PQ, Sal	AH
ycfR	Function unknown	0.537	−0.819	−1.356	H2O2	AH
yfiA	Stabilizes ribosome against dissociation	−1.782	0.581	2.364	PQ−, Sal, H2O2	AL
yggJ	Function unknown	0.576	−0.178	−0.755	Sal	AH
yqjD	Function unknown	−0.347	0.378	0.725	Sal	AL
yncE	Function unknown	−0.476	0.331	0.808	PQ, Sal	AL

^aOxidative response is based on data in references 54 and 84. Induction was by H₂O₂, paraquat (PQ), or sodium salicylate (Sal). Repression is indicated by minus sign (Sal−, PQ−).

^bValues in boldface indicate significance (α = 0.001).

^cAH, Acid High; AL, Acid Low; BH, Base High; BL, Base Low; NH, Neutral High; NL, Neutral Low.

^dGAPDH, glyceraldehyde-3-phosphate dehydrogenase.

^ePTS, phosphotransferase.