TABLE 2.

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

GeneCharacteristicsLog2 pH expression ratioa
6.0/9.06.0/7.07.0/9.0
rocAArginine catabolism−6.0−1.4−4.6
cydACytochrome bd ubiquinol oxidase−5.9−5.6
pstSPhosphate ABC transporter−5.1−4.7
cydBCytochrome bd ubiquinol oxidase−4.9−4.8
yrkOUnknown−4.9−4.7
pstBAPhosphate ABC transporter−4.7−4.5
cydDABC transporter−4.7−4.5
ctaOHeme O synthase activity−4.4−1.3−3.1
ldhl-Lactate dehydrogenase−4.3−1.0−3.3
cydCABC transporter−4.2−4.0
pstBBPhosphate ABC transporter−4.1−3.8
yhaTUnknown−4.1−0.6−3.5
yrkNUnknown−4.1−3.9
yrkAHemolysin-like homolog−4.1−1.5−2.6
ykuOUnknown−4.0−1.8−2.3
ykuNFlavodoxin homolog−3.9−1.7−2.2
rocGGlutamate dehydrogenase−3.8−1.2−2.6
ykuPFlavodoxin homolog−3.8−1.5−2.3
fruBFructose 1-phosphate kinase−3.8
yhaSUnknown−3.8−0.9−2.9
pstAPhosphate ABC transporter−3.7−3.4
yhaUNa+/H+ antiporter homolog−3.7−0.3−3.4
rocBArginine catabolism−3.6−3.3
nasDAssimilatory nitrite reductase−3.6−0.6−3.0
fruAPTS fructose-specific IIABC component−3.6−2.2
pstCPhosphate ABC transporter−3.5−3.1
ywcJNitrite transporter homolog−3.4−0.9−2.5
ycnIUnknown−3.4−1.0−2.4
ycnKDeoR transcription regulator homolog−3.4−1.2−2.2
ycnJCopper export protein homolog−3.4−1.1−2.2
fruRTranscriptional repressor of the fructose operon−3.3−1.8
ydbNUnknown−3.3−1.5−1.8
psiEPredicted phosphate starvation-inducible protein−3.2−3.6
dhbCIsochorismate synthase−3.1−1.3−1.8
fnrTranscriptional regulator of anaerobic genes−3.0−1.2−1.9
lctPl-Lactate permease−3.0−0.9−2.2
ysfCGlycolate oxidase subunit homolog−3.0−0.4−2.6
yrkPTwo-component response regulator (YrkQ) homolog−2.9−3.0
ykoMMarR transcriptional regulator homolog−2.9−1.0−1.9
dhbFInvolved in 2,3-dihydroxybenzoate biosynthesis−2.9−0.7−2.2
yerAAdenine deaminase homolog−2.8−2.3
rapKResponse regulator aspartate phosphatase−2.8−2.9
dhbE2,3-Dihydroxybenzoate-AMP ligase−2.8−1.0−1.8
bglHBeta-glucosidase−2.7−2.1
dhbA2,3-Dihydro-2,3-dihydroxybenzoate dehydrogenase−2.7−1.3−1.5
bglPPTS beta-glucoside-specific enzyme IIBCA component−2.7−2.0
gltAGlutamate synthase−2.6−1.4−1.3
yrkQTwo-component sensor histidine kinase (YrkP) homolog−2.60.3−2.9
ysfDGlycolate oxidase subunit homolog−2.6−2.6
liaIPutative membrane protein−2.6−0.9−1.8
ycdAUnknown−2.6−2.8
ytkAUnknown−2.6−1.3−1.3
ywrJUnknown−2.6−0.5−2.1
dhbBIsochorismatase−2.6−1.1−1.5
gltBGlutamate synthase−2.6−1.3−1.3
yrhPEfflux protein homolog−2.6−0.4−2.1
yybPUnknown−2.5−2.6
cwlSCell wall lytic enzyme associated with cell separation−2.5−0.4−2.1
yxeLUnknown−2.5−2.2
liaHPhage shock protein A homolog−2.5−0.7−1.8
htpXProbable protease homolog−2.5−1.1−1.4
yqgYUnknown−2.5−2.0−0.5
ywoFUnknown−2.5−1.0−1.4
xkdNPBSX prophage−2.4−2.8
bltMultidrug-efflux transporter−2.40.4−2.9
yqaTPhage-related terminase homolog−2.4−0.6−1.8
bltDSpermine/spermidine acetyltransferase−2.40.7−3.1
qcrAMenaquinol:cytochrome c oxidoreductase−2.4−1.5−0.9
qcrCMenaquinol:cytochrome c oxidoreductase (bc subunit)−2.4−1.5−0.9
yuiIUnknown−2.3−1.7−0.6
xkdMPBSX prophage−2.3−2.8
pspAPhage shock protein A homolog−2.3−2.2
spoVGRequired for spore cortex synthesis−2.3−0.5−1.8
ylqBUnknown−2.3−0.9−1.4
ykoYSimilar to toxic anion resistance protein−2.3−0.5−1.8
rocDOrnithine aminotransferase−2.31.1−3.3
yfmQUnknown−2.2−0.8−1.4
ybbAUnknown−2.2−1.0−1.2
bdbAThiol-disulfide oxidoreductase−2.2−1.2−0.9
sdpBSporulation-delaying protein−2.2−2.0
sboASubtilisin A−2.1−1.9
ctaECytochrome caa3 oxidase−2.1−0.8−1.3
xhlBHydrolysis of 5-bromo 4-chloroindolyl phosphate−2.1−2.5
xhlAInvolved in cell lysis upon induction of PBSX−2.1−2.6
ctaCCytochrome caa3 oxidase−2.1−1.0−1.1
fosBMetallothiol transferase−2.1−1.8−0.3
phrKPhosphatase (RapK) regulator−2.1−2.1
feuBIron-uptake system−2.1−1.2−0.9
yxeKMonooxygenase homolog−2.1−1.8
ydjPChloroperoxidase homolog−2.0−1.9
yxiEUnknown−2.0−1.1−1.0
yvdSMolecular chaperone homolog−2.0−0.6−1.5
tcyPl-Cysteine uptake−2.0−0.5−1.5
feuCIron-uptake system−2.0−1.2−0.8
yosUUnknown−2.0−1.4
yydIABC transporter homolog−2.0−0.7−1.3
feuAIron-uptake system−2.0−1.1−0.9
ykoXAlkaline phosphatase homolog−2.0−1.0−0.9
xkdFPBSX prophage−2.0−2.5
yuaFUnknown−2.0−1.1−0.9
  • a Significant values are shown (P ≤ 0.001).