TABLE 4.
Group | Gene | Function | Log2 pH ratioa
|
Classb | ||
---|---|---|---|---|---|---|
5/7 | 8.7/7 | 8.7/5 | ||||
Sugar catabolism and TCA cycle | aceE | Pyruvate dehydrogenase | 1.928 | 0.527 | −1.401 | NL |
aceF | Pyruvate dehydrogenase dihydrolipoamide acetyltransferase | 1.802 | 0.402 | 1.401 | NL | |
aceK | Isocitrate dehydrogenase kinase/phosphatase | 0.667 | 0.038 | −0.629 | AH | |
acnA | Aconitase A, stationary phase induced | 0.769 | −0.143 | −0.912 | AH | |
acnB | Aconitase B; 2-methylaconitate hydratase | 1.036 | −0.041 | −1.077 | NL | |
acrR | Regulator for acrA and acrB | −0.873 | 0.164 | 1.037 | AL | |
dcuR (yjdG) | Fumurate respiration regulator (anaerobic) | −0.220 | 0.055 | 0.275 | AL | |
dcuS (yjdH) | Fumurate respiration regulator (anaerobic) | −0.324 | 0.065 | 0.390 | AL | |
dhaK | Dihydroxyacetone kinase, subunit I | 1.041 | −0.379 | −1.420 | AH | |
dhaL | Dihydroxyacetone kinase, subunit II | 0.742 | −0.385 | −1.127 | AH | |
dld | d-Lactate dehydrogenase | 0.919 | 0.566 | −0.353 | NL | |
eno | Enolase; RNA degradosome | 0.299 | 0.052 | −0.247 | AH | |
fucI | l-Fucose isomerase | −0.693 | −0.173 | 0.520 | AL | |
fucK | l-Fuculose kinase | −1.259 | −0.519 | 0.740 | NH | |
fucR | Positive regulator, fuc operon | −0.046 | 0.495 | 0.541 | BH | |
galF | Putative regulator of galU | NL | ||||
galK | Galactokinase | −0.616 | −0.562 | 0.053 | BL | |
galM | Galactose mutarotase; aldose-1-epimerase | −0.619 | −0.647 | −0.028 | ||
gapA | Glyceraldehyde 3-P dehydrogenase A | 0.093 | −0.752 | −0.844 | BL | |
gatA | Galactitol-specific enzyme IIA of PTSd | 0.929 | −0.626 | −1.555 | AH | |
gatB | Galactitol-specific enzyme IIB of PTS | 0.632 | −0.895 | −1.528 | AH | |
gatC | Galactitol-specific enzyme IIC of PTS | 0.973 | −0.949 | −1.922 | AH | |
gatD | Galactitol-1-phosphate dehydrogenase | 1.037 | −0.893 | −1.930 | AH | |
gatY | d-Tagatose-1,6-bisphosphate aldolase, class II | 0.846 | −0.483 | −1.329 | AH | |
gatZ | Enhances GatY activity | 0.774 | −0.605 | −1.380 | AH | |
glpA | Glycerol-3-phosphate dehydrogenase large subunit (anaerobic) | −0.200 | 0.558 | 0.758 | AL | |
glpB | Glycerol-3-phosphate membrane anchor (anaerobic) | −0.124 | 0.437 | 0.562 | BH | |
glpC | Glycerol-3-phosphate dehydrogenase (anaerobic) small subunit | −0.169 | 0.469 | 0.638 | BH | |
glpX | Fructose 1,6-bisphosphatase | −0.162 | 0.375 | 0.537 | BH | |
gltA | Citrate synthase | 0.288 | −0.559 | −0.846 | AH | |
gnd | Gluconate-6-phosphate dehydrogenase | 0.895 | 0.351 | −0.544 | NL | |
gntT | High-affinity gluconate transport | −0.613 | −0.362 | 0.251 | NH | |
gpsA | Glycerol-3-phosphate dehydrogenase | −0.492 | −0.534 | −0.041 | NH | |
gpmA | Phosphoglycerate mutase I | 0.303 | −0.118 | −0.421 | AH | |
icdA | Isocitrate dehydrogenase | 1.211 | 0.061 | −1.272 | AH | |
lldD | l-Lactate dehydrogenase | 0.613 | −0.554 | −1.167 | AH | |
lldP | l-Lactate permease; glycolate uptake | 1.527 | 0.219 | −1.307 | NL | |
lpdA | Lipoamide dehydrogenase; E3 component of pyruvate and 2-oxoglutarate dehydrogenase complexes | 1.507 | 0.281 | −1.226 | NL | |
malE | Maltose-binding protein, periplasmic | −3.425 | −2.933 | 0.491 | NH | |
malF | Maltose transport, inner membrane | −1.016 | −0.935 | 0.082 | NH | |
malG | Maltose transport, inner membrane subunit | −1.577 | −1.502 | 0.075 | NH | |
malK | Maltose transport, ATP-binding subunit | −4.790 | −3.748 | 1.041 | NH | |
malM | Periplasmic protein, mal regulon | −4.643 | −3.780 | 0.863 | NH | |
malP | Maltodextrin phosphorylase | −4.000 | −3.373 | 0.627 | NH | |
malQ | Amylomaltase | −3.322 | −2.883 | 0.439 | NH | |
malT | mal positive regulator | −0.103 | 0.617 | 0.720 | BH | |
pdhR | Pyruvate dehydrogenase operon repressor | 0.755 | −0.109 | −0.863 | AH | |
pfkB | 6-Phosphofructokinase-2 | 0.363 | 0.095 | −0.268 | NL | |
pflA | Pyruvate formate lyase I activase | 0.964 | 0.667 | −0.297 | NL | |
pflB | Pyruvate formate lyase I (anaerobic) | 0.812 | 0.578 | −0.234 | NL | |
pgi | Glucose phosphate isomerase | 0.654 | 0.177 | −0.477 | NL | |
pta | Phosphotransacetylase | 1.167 | 0.639 | −0.528 | NL | |
ptsG | Glucose PTS enzyme IIBC | 0.841 | 0.544 | −0.287 | NL | |
ptsH | PTS system histidine phosphocarrier protein Hpr | 0.369 | 0.564 | 0.195 | NL | |
ptsI | PTS system enzyme I | 0.241 | 0.339 | 0.098 | NL | |
ptsO | NPr, N-regulated HPr-like protein | 0.639 | 0.168 | −0.470 | NL | |
rpiA | Ribose-5-phosphate isomerase A | 0.180 | 0.364 | 0.184 | BH | |
srlA | Sorbitol-specific enzyme II of PTS | −1.156 | −1.720 | −0.564 | BL | |
srlB | Sorbitol-specific enzyme III of PTS | −0.908 | −1.140 | −0.232 | BL | |
srlD | Sorbitol-6-phosphate dehydrogenase | −0.660 | −1.334 | −0.674 | BL | |
srlE | srl operon protein | −1.013 | −1.613 | −0.599 | BL | |
srlR | srl regulator | −0.151 | 0.804 | −0.654 | BL | |
sucA | 2-Oxoglutarate dehydrogenase, E1 component | 0.850 | −0.851 | −1.701 | AH | |
sucB | Dihydrolipoamide succinyltransferase component of 2-oxoglutarate dehydrogenase complex (E2) | 0.566 | −1.073 | −1.638 | AH | |
sucC | Succinyl-CoAc synthase beta subunit | 0.494 | −1.019 | −1.513 | AH | |
sucD | Succinyl-CoA synthase alpha subunit | 0.526 | −1.225 | −1.751 | AH | |
tpiA | Triosephosphate isomerase | 0.772 | 0.245 | −0.526 | NL | |
treB | Trehalose-specific PTS enzyme II | −3.156 | 0.739 | 3.895 | AL | |
treC | Trehalose-6-phosphate hydrolase | −2.613 | 0.620 | 3.233 | AL | |
Proton transport and electron transport chain | atpA | ATP synthase subunit alpha, F1 | 0.111 | 0.460 | 0.349 | BH |
atpB | ATP synthase subunit a, F0 | 0.125 | 0.484 | 0.609 | BH | |
atpC | ATP synthase subunit epsilon, F1 | 0.266 | 1.005 | 0.739 | BH | |
atpD | ATP synthase subunit beta, F1 | 0.542 | 1.172 | 0.630 | BH | |
atpE | ATP synthase subunit c, F0 | 0.182 | 0.503 | 0.321 | BH | |
atpF | ATP synthase subunit b, F0 | −0.055 | 0.321 | 0.377 | BH | |
atpG | ATP synthase subunit gamma, F1 | 0.372 | 0.632 | 0.260 | BH | |
atpH | ATP synthase subunit delta, F1 | −0.172 | 0.186 | 0.358 | AL | |
atpI | ATP synthase subunit, F1F0-type proton-ATPase | 0.017 | 0.499 | 0.482 | BH | |
cydA | Cytochrome d (bd-I) terminal oxidase subunit I (microaerobic) | −0.268 | 0.872 | 1.140 | BH | |
cydB | Cytochrome d (bd-I) terminal oxidase subunit II (microaerobic) | −0.097 | 0.777 | 0.874 | BH | |
cydC | Cysteine exporter to periplasm required for Cyd assembly | 0.135 | 0.490 | 0.355 | BH | |
cydD | Cysteine exporter to periplasm required for cytochrome assembly | 0.232 | 0.574 | 0.342 | BH | |
cyoA | Cytochrome o oxidase subunit II | 1.160 | 0.217 | −0.943 | NL | |
cyoB | Cytochrome o oxidase subunit I | 0.812 | −0.204 | −1.016 | NL | |
cyoC | Cytochrome o oxidase subunit III | 1.026 | 0.019 | −1.007 | NL | |
cyoD | Cytochrome o oxidase subunit IV | 0.829 | −0.192 | −1.021 | NL | |
cyoE | Cytochrome o oxidase subunit protoheme IX farnesyltransferase | 1.094 | 0.225 | −0.869 | NL | |
fdoG | Formate dehydrogenase-O, major selenopeptide subunit | 0.353 | −0.138 | −0.491 | AH | |
fdoH | Formate dehydrogenase-O Fe-S subunit | 0.003 | −0.414 | −0.416 | BL | |
frdA | Fumarate reductase flavoprotein subunit | −0.305 | 0.046 | 0.351 | AL | |
frdC | Fumarate reductase membrane anchor polypeptide | −0.378 | −0.008 | 0.370 | AL | |
fumA | Fumarase A | 0.595 | −0.647 | −1.242 | AH | |
nfsA (mdaA) | Nitroreductase A | 0.561 | −0.419 | −0.980 | AH | |
mdaB | Probable nitroreductase or quinone reductase | 0.444 | −0.223 | −0.667 | AH | |
napC | Cytochrome electron source for NapAB, membrane bound | −0.797 | −0.382 | 0.416 | NH | |
ndh | Respiratory NADH dehydrogenase II; NADH:ubiquinone oxidoreductase II | 0.789 | 0.161 | −0.628 | NL | |
nuoC | NADH:ubiquinone oxidoreductase subunit C | 0.440 | −0.084 | −0.524 | AH | |
nuoG | NADH:ubiquinone oxidoreductase subunit G; NADH dehydrogenase I | 0.525 | 0.103 | −0.442 | NL | |
nuoH | NADH:ubiquinone oxidoreductase subunit H; NADH dehydrogenase I | 0.564 | 0.185 | −0.379 | NL | |
nuoI | NADH:ubiquinone oxidoreductase subunit I; NADH dehydrogenase I | 0.792 | 0.310 | −0.481 | NL | |
nuoJ | NADH:ubiquinone oxidoreductase subunit J; NADH dehydrogenase I | 0.468 | 0.234 | −0.234 | NL | |
nuoK | NADH:ubiquinone oxidoreductase subunit K; NADH dehydrogenase I | 0.766 | 0.460 | −0.306 | NL | |
nuoL | NADH:ubiquinone oxidoreductase subunit L; NADH dehydrogenase I | 0.311 | 0.078 | −0.233 | NL | |
nuoN | NADH:ubiquinone oxidoreductase subunit N; NADH dehydrogenase I | 0.126 | −0.210 | −0.336 | AH | |
sdhA | Succinate dehydrogenase flavoprotein subunit | 1.438 | −0.018 | −1.458 | AH | |
sdhB | Succinate dehydrogenase iron-sulfur protein | 1.833 | 0.329 | −1.505 | AH | |
sdhC | Succinate dehydrogenase membrane anchor subunit, cytochrome b556 | 2.728 | 0.890 | −1.838 | NL | |
sdhD | Succinate dehydrogenase hydrophobic subunit | 2.349 | 0.595 | −1.754 | NL | |
Amino acid catabolism and transport | artI | Arginine periplasmic binding protein | 0.286 | 0.655 | 0.369 | BH |
artM | Arginine periplasmic binding protein | −0.115 | 0.293 | 0.407 | BH | |
cadA | Lysine decarboxylase, degradative | 1.024 | 0.137 | −0.887 | AH | |
cysK | O-Acetylserine sulfhydrylase A (cysteine synthase) | 1.204 | 1.351 | 0.147 | NL | |
dadA | d-Amino acid dehydrogenase | 1.273 | −0.229 | −1.501 | AH | |
dadX | d-Amino acid dehydrogenase | 0.683 | −0.393 | −1.076 | AH | |
dppC | Dipeptide permease system | −0.346 | −0.032 | 0.315 | AL | |
gdhA | Glutamate dehydrogenase | −0.080 | −0.496 | −0.416 | BL | |
hisC | Histidinol-phosphate aminotransferase | 0.253 | 0.984 | 0.731 | BH | |
hisF | Imidazole glycerol phosphate synthase (cyclase) | 0.150 | 0.703 | 0.553 | BH | |
hisH | Amidotransferase of imidazole glycerol phosphate synthase | 0.034 | 0.393 | 0.359 | BH | |
hisI | PR-ATP pyrophosphatase and PR-AMP cyclohydrolase | 0.234 | 0.641 | 0.407 | BH | |
hisJ | Histidine-binding protein | −0.149 | 0.400 | 0.549 | BH | |
lysC | Aspartokinase III | 1.464 | −0.226 | −1.690 | AH | |
lysP | Lysine permease | 2.662 | 0.963 | −1.698 | NL | |
lysU | Lysine-tRNA ligase | 0.544 | −0.077 | −0.621 | AH | |
potD | Putrescine-ornithine transporter | 0.053 | 0.509 | 0.456 | BH | |
sdaA | l-Serine deaminase, degradative | −0.409 | 0.638 | 1.048 | BH | |
sdaB | l-Serine deaminase | −1.111 | −0.434 | 0.678 | AL | |
sdaC | H+/serine symporter; regulator of serine deaminase | −1.205 | −0.410 | 0.794 | AL | |
tnaA | Tryptophan deaminase, degradative; also deaminases serine and cysteine | −3.805 | 0.223 | 4.028 | AL | |
tnaB | Tryptophan transporter | −1.840 | 1.153 | 2.993 | AL | |
tnaC | tnaA leader peptide | −5.026 | 0.490 | 5.517 | AL | |
tdcB | Threonine dehydratase, degradative | −0.849 | −0.296 | 0.553 | NH | |
ydfG | l-allo-Threonine, l-serine, d-serine dehydrogenase | 0.407 | 0.287 | −0.120 | NL |
Values in boldface are significant (α = 0.001).
NL, Neutral Low; AH, Acid High; AL, Acid Low; BH, Base High; BL, Base Low; NH, Neutral High.
CoA, coenzyme A.
PTS, phosphotransferase.