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Table 2 Core pH-dependent genes (both aerobic and oxygen-limited)1

From: Oxygen limitation modulates pH regulation of catabolism and hydrogenases, multidrug transporters, and envelope composition in Escherichia coli K-12

Acid up-regulated Base up-regulated
acnA gatZ rcsF acfD katG tsx
apaG gcd rob acrA lamB ubiB
argO gdhA rpoE acrR maa uxuA
aspC gloA rseA alx malE yahA
azoR gnd skp artQ malF yahA
b1052 groS sodB atpA malG yajC
cadA grxB srlA atpC malK ybjK
cdd hdeA srlB atpF malM yccA
cfa hdeB srlD atpH malP yceI
clpB hsdR srlE b1172 malQ ycfS
crcB hybG srlR b3913 malT yciC
cyaA idi tas bdm mdoD ydcV
dadA kdsA tehB borD mltD ydeH
dapB kefB tpiA cpxA mppA yebE
deoA lysA uspD cpxP mutL yeeI
deoB lysC wrbA cpxR nmpC ygaH
deoC lysU yagU cvpA nrdD ygaZ
deoD mazG yafE dedA nrdG yghG
dhaK mcrB ybaK dnaX ompF yghJ
dhaL mdaB ybhB dsbA ompT ygiB
dhaM mdtI ybjN fadL osmB ygiC
dpiA mdtJ ycfP folP pheA yjdM
dps menB ychH ftnB pitA yjfO
edd menF ydhM fucR pntA yjhC
fbp metK ydiH gcvT potD yjhR
fimA metN ydiZ glk ppiA ymgD
fimI mrp yeaQ glpF pppA ynfD
flgB murI yeiA glpX proV  
flgC nadC yfiD gpmM purA  
flgD narG ygdQ hemY purH  
flgE narH yggE hflK purM  
flgF nemA ygiN hflX rdoA  
flgG nhaB ygiS hisB recA  
fliA npr yhbJ hisC rnk  
fliK nupG yheL hisD sdaA  
fliL pan E yheN hisF sdaC  
fre pdxH yheO hisG sdiA  
galP pdxK yhhX hisH slt  
gapC pdxY yieE hisI spy  
gatA pfkB yieF hisJ_ sulA  
gatB pgi yieP htpX tatA  
gatC pps yiiS ilvG tgt  
gatD rbsA yjjU ilvN tnaB  
gatR rbsC ykgA insH treB  
gatY rbsD yqhD ivbL treC  
Acid up-regulated (anaerobic)
Base up-regulated (aerobic)
Base up-regulated (anaerobic)
Acid up-regulated (aerobic)
cydA nhaA ybjH aceE hslJ rfbC
cydB pyrB ydcH aceF icd rfe
dsdX rbsB yehU aceK lgt ribA
fdhF tdcA ygeW add lpxD rplI
glgS tdcB yhaN argZ lysP sdhA
hupA tdcC yjeJ aspA mltC sdhB
lsrK tdcD yjgB b0725 nfsA sdhC
manX torR yjiY cyoA ndk sdhD
manY udp yodD cyoB nuoA sucA
manZ uspF yohK cyoC nuoB sucB
narI ybaT yqjD cyoD nuoC sucC
    dnaJ nuoE sucD
    dnaK nuoF thrC
    fdoG nuoG tpx
    fdoH nuoH wbbI
    fimG nuoI yeaC
    galF nuoK yebK
    gltA nuoL yeiU
    gpmA oppC yfdI
    groL oppD yffB
    guaB oppF yihG
    hha purU ylaC
    hsdS rcsA yqeG
  1. 1Genes were selected as "core pH-dependent" based on their significant differences in expression between acid and base growth conditions, both under oxygen limitation (this report) and under aeration [2].