TABLE 2.

Genes downregulated by acid or upregulated by base (pH 6.0/pH 9.0 ratio is down by fourfold or greater)

Gene	Characteristics	Log2 pH expression ratioa
		6.0/9.0	6.0/7.0	7.0/9.0
rocA	Arginine catabolism	−6.0	−1.4	−4.6
cydA	Cytochrome bd ubiquinol oxidase	−5.9		−5.6
pstS	Phosphate ABC transporter	−5.1		−4.7
cydB	Cytochrome bd ubiquinol oxidase	−4.9		−4.8
yrkO	Unknown	−4.9		−4.7
pstBA	Phosphate ABC transporter	−4.7		−4.5
cydD	ABC transporter	−4.7		−4.5
ctaO	Heme O synthase activity	−4.4	−1.3	−3.1
ldh	l-Lactate dehydrogenase	−4.3	−1.0	−3.3
cydC	ABC transporter	−4.2		−4.0
pstBB	Phosphate ABC transporter	−4.1		−3.8
yhaT	Unknown	−4.1	−0.6	−3.5
yrkN	Unknown	−4.1		−3.9
yrkA	Hemolysin-like homolog	−4.1	−1.5	−2.6
ykuO	Unknown	−4.0	−1.8	−2.3
ykuN	Flavodoxin homolog	−3.9	−1.7	−2.2
rocG	Glutamate dehydrogenase	−3.8	−1.2	−2.6
ykuP	Flavodoxin homolog	−3.8	−1.5	−2.3
fruB	Fructose 1-phosphate kinase	−3.8
yhaS	Unknown	−3.8	−0.9	−2.9
pstA	Phosphate ABC transporter	−3.7		−3.4
yhaU	Na+/H+ antiporter homolog	−3.7	−0.3	−3.4
rocB	Arginine catabolism	−3.6		−3.3
nasD	Assimilatory nitrite reductase	−3.6	−0.6	−3.0
fruA	PTS fructose-specific IIABC component	−3.6		−2.2
pstC	Phosphate ABC transporter	−3.5		−3.1
ywcJ	Nitrite transporter homolog	−3.4	−0.9	−2.5
ycnI	Unknown	−3.4	−1.0	−2.4
ycnK	DeoR transcription regulator homolog	−3.4	−1.2	−2.2
ycnJ	Copper export protein homolog	−3.4	−1.1	−2.2
fruR	Transcriptional repressor of the fructose operon	−3.3	−1.8
ydbN	Unknown	−3.3	−1.5	−1.8
psiE	Predicted phosphate starvation-inducible protein	−3.2		−3.6
dhbC	Isochorismate synthase	−3.1	−1.3	−1.8
fnr	Transcriptional regulator of anaerobic genes	−3.0	−1.2	−1.9
lctP	l-Lactate permease	−3.0	−0.9	−2.2
ysfC	Glycolate oxidase subunit homolog	−3.0	−0.4	−2.6
yrkP	Two-component response regulator (YrkQ) homolog	−2.9		−3.0
ykoM	MarR transcriptional regulator homolog	−2.9	−1.0	−1.9
dhbF	Involved in 2,3-dihydroxybenzoate biosynthesis	−2.9	−0.7	−2.2
yerA	Adenine deaminase homolog	−2.8	−2.3
rapK	Response regulator aspartate phosphatase	−2.8		−2.9
dhbE	2,3-Dihydroxybenzoate-AMP ligase	−2.8	−1.0	−1.8
bglH	Beta-glucosidase	−2.7	−2.1
dhbA	2,3-Dihydro-2,3-dihydroxybenzoate dehydrogenase	−2.7	−1.3	−1.5
bglP	PTS beta-glucoside-specific enzyme IIBCA component	−2.7	−2.0
gltA	Glutamate synthase	−2.6	−1.4	−1.3
yrkQ	Two-component sensor histidine kinase (YrkP) homolog	−2.6	0.3	−2.9
ysfD	Glycolate oxidase subunit homolog	−2.6		−2.6
liaI	Putative membrane protein	−2.6	−0.9	−1.8
ycdA	Unknown	−2.6		−2.8
ytkA	Unknown	−2.6	−1.3	−1.3
ywrJ	Unknown	−2.6	−0.5	−2.1
dhbB	Isochorismatase	−2.6	−1.1	−1.5
gltB	Glutamate synthase	−2.6	−1.3	−1.3
yrhP	Efflux protein homolog	−2.6	−0.4	−2.1
yybP	Unknown	−2.5		−2.6
cwlS	Cell wall lytic enzyme associated with cell separation	−2.5	−0.4	−2.1
yxeL	Unknown	−2.5		−2.2
liaH	Phage shock protein A homolog	−2.5	−0.7	−1.8
htpX	Probable protease homolog	−2.5	−1.1	−1.4
yqgY	Unknown	−2.5	−2.0	−0.5
ywoF	Unknown	−2.5	−1.0	−1.4
xkdN	PBSX prophage	−2.4	−2.8
blt	Multidrug-efflux transporter	−2.4	0.4	−2.9
yqaT	Phage-related terminase homolog	−2.4	−0.6	−1.8
bltD	Spermine/spermidine acetyltransferase	−2.4	0.7	−3.1
qcrA	Menaquinol:cytochrome c oxidoreductase	−2.4	−1.5	−0.9
qcrC	Menaquinol:cytochrome c oxidoreductase (bc subunit)	−2.4	−1.5	−0.9
yuiI	Unknown	−2.3	−1.7	−0.6
xkdM	PBSX prophage	−2.3	−2.8
pspA	Phage shock protein A homolog	−2.3	−2.2
spoVG	Required for spore cortex synthesis	−2.3	−0.5	−1.8
ylqB	Unknown	−2.3	−0.9	−1.4
ykoY	Similar to toxic anion resistance protein	−2.3	−0.5	−1.8
rocD	Ornithine aminotransferase	−2.3	1.1	−3.3
yfmQ	Unknown	−2.2	−0.8	−1.4
ybbA	Unknown	−2.2	−1.0	−1.2
bdbA	Thiol-disulfide oxidoreductase	−2.2	−1.2	−0.9
sdpB	Sporulation-delaying protein	−2.2		−2.0
sboA	Subtilisin A	−2.1		−1.9
ctaE	Cytochrome caa3 oxidase	−2.1	−0.8	−1.3
xhlB	Hydrolysis of 5-bromo 4-chloroindolyl phosphate	−2.1	−2.5
xhlA	Involved in cell lysis upon induction of PBSX	−2.1	−2.6
ctaC	Cytochrome caa3 oxidase	−2.1	−1.0	−1.1
fosB	Metallothiol transferase	−2.1	−1.8	−0.3
phrK	Phosphatase (RapK) regulator	−2.1		−2.1
feuB	Iron-uptake system	−2.1	−1.2	−0.9
yxeK	Monooxygenase homolog	−2.1		−1.8
ydjP	Chloroperoxidase homolog	−2.0	−1.9
yxiE	Unknown	−2.0	−1.1	−1.0
yvdS	Molecular chaperone homolog	−2.0	−0.6	−1.5
tcyP	l-Cysteine uptake	−2.0	−0.5	−1.5
feuC	Iron-uptake system	−2.0	−1.2	−0.8
yosU	Unknown	−2.0	−1.4
yydI	ABC transporter homolog	−2.0	−0.7	−1.3
feuA	Iron-uptake system	−2.0	−1.1	−0.9
ykoX	Alkaline phosphatase homolog	−2.0	−1.0	−0.9
xkdF	PBSX prophage	−2.0	−2.5
yuaF	Unknown	−2.0	−1.1	−0.9

^aSignificant values are shown (P ≤ 0.001).