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OxyR DNA-binding transcriptional dual regulator

Synonyms: OxyR
Summary:
OxyR, "oxidative stress regulator," is the transcriptional dual regulator for the expression of antioxidant genes in response to oxidative stress, in particular, elevated levels of hydrogen peroxide. The OxyR regulon includes genes involved in peroxide metabolism, redox balance, and peroxide protection by, for example, manganese uptake [22, 25] Moreover, OxyR activates the synthesis of the small, noncoding oxyS RNA. This allows OxyR to regulate as many as 40 additional gene products indirectly by affecting mRNA stability or translation efficiency [37] OxyR acts as a repressor for its own synthesis in both the oxidized and reduced forms [3, 6] Accordingly, point mutations observed in oxyR as a result of adaptive evolution under high iron conditions lead to increased expression levels of OxyR-regulated genes, also termed the OxyR i-modulon []. For more information on i-modulons, see [].
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Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
OxyR Functional   [APPHINH] [1], [2], [3], [4], [5], [6], [7], [8]
Evolutionary Family: LysR
Sensing class: Using internal synthesized signals
Connectivity class: Local Regulator
Gene name: oxyR
  Genome position: 4158490-4159407
  Length: 918 bp / 305 aa
Operon name: oxyR
TU(s) encoding the TF:
Transcription unit        Promoter
oxyR
oxyRp
oxyR
oxyRp2


Regulon       
Regulated gene(s) ahpC, ahpF, ccp, dps, dsbG, elaB, fhuF, flu, fur, gntP, gor, grxA, hcp, hcr, hemH, isrC, katG, metE, metR, mntH, nfsA, oxyR, oxyS, poxB, rimK, sufA, sufB, sufC, sufD, sufE, sufS, trxC, uof, uxuA, uxuB, ybjC, ybjN, ychF, yjjZ, zinT, znuA, znuB, znuC
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
incorporation of metal ions (6)
sulfur metabolism (6)
detoxification (4)
membrane (4)
Transcription related (3)
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Regulated operon(s) ahpCF, ccp, dps, dsbG, elaB, fhuF, fldA-uof-fur, gntP, gor, grxA, hcp-hcr-poxB-ltaE-ybjT, hemH, isrC-flu, katG, metE, metR, mntH, oxyR, oxyS, pth-ychF, sufABCDSE, trxC, uxuAB, ybjC-nfsA-rimK-ybjN, yjjZ, zinT, znuA, znuCB
First gene in the operon(s) ahpC, dps, elaB, fhuF, gntP, gor, grxA, hcp, hemH, isrC, katG, metE, metR, mntH, oxyR, oxyS, sufA, trxC, uof, uxuA, ybjC, ychF, ccp, yjjZ, zinT, znuA, znuC, dsbG
Simple and complex regulons CRP,ExuR,OxyR,UxuR
CRP,OxyR
CRP,OxyR,UxuR
DksA,OxyR,YdcI,ppGpp
FNR,Fur,OxyR
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Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[OxyR,+](24)
[OxyR,-](9)


Transcription factor regulation    


Transcription factor binding sites (TFBSs) arrangements
      

  Functional conformation Function Promoter Sigma factor Central Rel-Pos Distance to first Gene Genes Sequence LeftPos RightPos Growth Conditions Evidence (Confirmed, Strong, Weak) References
  OxyR activator ahpCp Sigma70 -66.0 -90.0 ahpC, ahpF
tacgaaggttGTAAGGTAAAACTTATCGatttgataat
638847 638863 nd [APIORCISFBSCS], [BPP], [GEA] [9], [10], [11], [12], [13]
  OxyR activator ahpCp Sigma70 -44.0 -68.0 ahpC, ahpF
ttatcgatttGATAATGGAAACGCATTAgccgaatcgg
638869 638885 nd [APIORCISFBSCS], [BPP], [GEA] [9], [10], [11], [12], [13], [14]
  OxyR activator ahpCp2 Sigma70 -76.0 -328.0 ahpC, ahpF
aaagtcgagtAAAAGGCATAACCTATCActgtcatagg
638609 638625 nd [APIORCISFBSCS], [BPP], [GEA] [13]
  OxyR activator ahpCp2 Sigma70 -53.0 -305.0 ahpC, ahpF
tatcactgtcATAGGTAAGAGCTTAGATcaggtgattg
638632 638648 nd [APIORCISFBSCS], [BPP], [CSEUMA], [GEA], [IHBCE], [RSE] [13], [15]
  OxyR activator dpsp Sigma70 -66.0 -105.0 dps
tttgtttttcACGCTTGTTACCACTATTagtgtgatag
849008 849024 nd [APIORCISFBSCS]
  OxyR activator dpsp Sigma70 -44.0 -83.0 dps
actattagtgTGATAGGAACAGCCAGAAtagcggaaca
848986 849002 nd [APIORCISFBSCS]
  OxyR activator dpsp Sigma70 -17.0 -56.0 dps
atagcggaacACATAGCCGGTGCTATACttaatctcgt
848959 848975 nd [CEEUMA], [IHBCE], [RSE] [15]
  OxyR activator dpsp2 Sigma38 -66.0 -105.0 dps
tttgtttttcACGCTTGTTACCACTATTagtgtgatag
849008 849024 nd [APIORCISFBSCS]
  OxyR activator dpsp2 Sigma38 -44.0 -83.0 dps
actattagtgTGATAGGAACAGCCAGAAtagcggaaca
848986 849002 nd [APIORCISFBSCS]
  OxyR activator dpsp2 Sigma38 -17.0 -56.0 dps
atagcggaacACATAGCCGGTGCTATACttaatctcgt
848959 848975 nd [CEEUMA], [IHBCE], [RSE] [15]
  OxyR activator dsbGp nd -77.0 -304.0 dsbG
ccgattcggcTAATGCGTTTCCATTATCaaatcgataa
638869 638885 nd [APIORCISFBSCS], [BPP], [GEA] [13], [14]
  OxyR activator dsbGp nd -55.0 -282.0 dsbG
attatcaaatCGATAAGTTTTACCTTACaaccttcgta
638847 638863 nd [APIORCISFBSCS], [BPP], [GEA] [13]
  OxyR activator elaBp Sigma38 -31.0 -57.0 elaB
cacattgggaTGGCACGCGAGGTAATTCAGGCGTAATCAACAACCCTTGTCTATAGTtagtgacagg
2381061 2381107 nd [APIORCISFBSCS], [BPP], [GEA], [SM] [16]
  OxyR repressor elaBp Sigma38 -31.0 -57.0 elaB
cacattgggaTGGCACGCGAGGTAATTCAGGCGTAATCAACAACCCTTGTCTATAGTtagtgacagg
2381061 2381107 nd [APIORCISFBSCS], [BPP], [GEA], [SM] [16]
  OxyR repressor fhuFp Sigma70 -105.0 -136.0 fhuF
cgtacgttgcAACATGATTTCATCTCTTtcattgataa
4605791 4605807 nd [APIORCISFBSCS], [BPP], [GEA] [13]
  OxyR repressor fhuFp Sigma70 -83.0 -114.0 fhuF
tctctttcatTGATAATGATAACCAATAtcatatgata
4605769 4605785 nd [APIORCISFBSCS], [BPP], [GEA] [13]
  OxyR repressor fhuFp Sigma70 -21.0 -52.0 fhuF
aaatcccttgCTATCGGGTAAACCTATCgctatgatta
4605707 4605723 nd [CEEUMA], [IHBCE], [RSE] [13]
  OxyR repressor fhuFp Sigma70 2.0 -30.0 fhuF
cctatcgctaTGATTAGCAATCATTATCatttagatta
4605685 4605701 nd [APIORCISFBSCS], [BPP], [CEEUMA], [GEA], [IHBCE], [RSE] [13], [15]
  OxyR repressor flup Sigma70 -26.0 -26.0 isrC, flu
actgtctctcTTGTCCGTGCAATAGCTCaataatagaa
2071283 2071299 nd [CEEUMA], [IHBCE], [RSE] [15]
  OxyR repressor flup Sigma70 2.0 2.0 isrC, flu
caataatagaATAAAACGATCAATATCTattttatcga
2071310 2071326 nd [APIORCISFBSCS], [BPP], [GEA], [SM] [17], [18], [19], [20], [21]
  OxyR repressor flup Sigma70 24.0 24.0 isrC, flu
atatctatttTATCGATCGTTTATATCGatcgataagc
2071332 2071348 nd [APIORCISFBSCS], [BPP], [CEEUMA], [GEA], [IHBCE], [RSE], [SM] [15], [17], [18], [19], [20], [21]
  OxyR repressor gntPp Sigma70 -152.0 -190.0 gntP
ccttttggtaAGACATGTCAACCCGAATtctgaaattg
4551478 4551494 nd [APIORCISFBSCS], [GEA] [22]
  OxyR repressor gntPp Sigma70 -130.0 -168.0 gntP
ccgaattctgAAATTGGTTAACCACATCacaagaattt
4551456 4551472 nd [APIORCISFBSCS], [GEA] [22]
  OxyR activator gorp Sigma70 nd nd gor nd nd nd [BPP], [GEA], [IGI] [23]
  OxyR activator gorp2 Sigma38 nd nd gor nd nd nd [BPP], [GEA], [IGI] [23]
  OxyR activator grxAp nd -66.0 -89.0 grxA
tgtttaacagTTATAGCTTTTAGCAATTaatgcaacag
890834 890850 nd [APIORCISFBSCS], [BPP], [CEEUMA], [GEA], [IHBCE], [RSE] [24]
  OxyR activator grxAp nd -44.0 -67.0 grxA
gcaattaatgCAACAGGTTAAACCTACTttcagcgaat
890812 890828 nd [APIORCISFBSCS], [BPP], [GEA] [24]
  OxyR activator grxAp nd 8.0 -16.0 grxA
atcattacagGCATAAATCTATGAGGAGagaaataatg
890761 890777 nd [CCEUMA], [IHBCE], [RSE] [15]
  OxyR activator hcpp nd nd nd hcp, hcr, poxB nd nd nd [BPP], [GEA], [IGI] [4]
  OxyR activator hemHp Sigma70 -55.0 -79.0 hemH
ctattcctttTTCTGATTTGACCTCTCAcagcaattag
497968 497984 nd [BPP], [GEA] [22]
  OxyR activator hemHp Sigma70 -33.0 -57.0 hemH
ctctcacagcAATTAGTTCTTCTTCCTCacttttccgc
497990 498006 nd [BPP], [GEA] [22]
  OxyR activator katGp Sigma70 -66.0 -89.0 katG
ccaacaatatGTAAGATCTCAACTATCGcatccgtgga
4133738 4133754 nd [APIORCISFBSCS], [BPP], [CEEUMA], [GEA], [IHBCE], [RSE] [10], [11], [12], [13], [14], [15]
  OxyR activator katGp Sigma70 -44.0 -67.0 katG
ctatcgcatcCGTGGATTAATTCAATTAtaacttctct
4133760 4133776 nd [APIORCISFBSCS], [BPP], [GEA] [10], [11], [12], [13], [14]
  OxyR activator katGp Sigma70 2.0 -22.0 katG
tgtgtatcgtAACGGTAACACTGTAGAGgggagcacat
4133805 4133821 nd [CEEUMA], [IHBCE], [RSE] [15]
  OxyR activator metEp nd -42.0 -211.0 metE
cttcacttcgGCATGAATAATTTGCGCTtgaggaatat
4012834 4012850 nd [CEEUMA], [IHBCE], [RSE] [15]
  OxyR activator metRp1 nd -5.0 -44.0 metR
ataattggcgGTTACTGTATATTCCTCAagcgcaaatt
4012852 4012868 nd [CEEUMA], [IHBCE], [RSE] [15]
  OxyR activator mntHp Sigma70 -76.0 -104.0 mntH
cttttcgtagTCATAATCCTGGTCTATCagagaaatca
2512802 2512818 nd [APIORCISFBSCS], [CEEUMA], [GEA], [IHBCE], [RSE], [SM] [15], [25], [26]
  OxyR activator mntHp Sigma70 -54.0 -82.0 mntH
tctatcagagAAATCACCACAATCCATTtaaatgaatt
2512780 2512796 nd [AIBSCS], [GEA], [SM] [25], [26]
  OxyR repressor oxyRp Sigma70 -18.0 -51.0 oxyR
tgatagggatAATCGTTCATTGCTATTCtacctatcgc
4158431 4158447 nd [APIORCISFBSCS], [BPP], [GEA] [3], [10], [12]
  OxyR repressor oxyRp Sigma70 5.0 -29.0 oxyR
ctattctaccTATCGCCATGAACTATCGtggcgatgga
4158453 4158469 nd [APIORCISFBSCS], [BPP], [CEEUMA], [GEA], [IHBCE], [RSE] [3], [10], [15]
  OxyR repressor oxyRp2 Sigma38 -18.0 -51.0 oxyR
tgatagggatAATCGTTCATTGCTATTCtacctatcgc
4158431 4158447 nd [APIORCISFBSCS], [BPP], [GEA] [3], [10], [12]
  OxyR repressor oxyRp2 Sigma38 5.0 -29.0 oxyR
ctattctaccTATCGCCATGAACTATCGtggcgatgga
4158453 4158469 nd [APIORCISFBSCS], [BPP], [CEEUMA], [GEA], [IHBCE], [RSE] [3], [10], [15]
  OxyR activator oxySp Sigma70 -67.0 -67.0 oxyS
tccatcgccaCGATAGTTCATGGCGATAggtagaatag
4158453 4158469 nd [APIORCISFBSCS], [BPP], [CEEUMA], [GEA], [IHBCE], [RSE] [12], [27]
  OxyR activator oxySp Sigma70 -45.0 -45.0 oxyS
gcgataggtaGAATAGCAATGAACGATTatccctatca
4158431 4158447 nd [APIORCISFBSCS], [BPP], [GEA] [12], [27]
  OxyR activator sufAp Sigma70 -232.0 -264.0 sufA, sufB, sufC, sufD, sufS, sufE
ttctgaacgcTGCACTTTTTTACCTATCtcttaaatag
1764642 1764658 nd [BPP], [CSEUMA], [GEA], [IHBCE], [RSE] [15], [22], [28], [29], [30], [31], [32]
  OxyR activator sufAp Sigma70 -210.0 -242.0 sufA, sufB, sufC, sufD, sufS, sufE
cctatctcttAAATAGTCATTTTCAATAcaactttttc
1764620 1764636 nd [BPP], [GEA], [SM] [22], [28], [29], [30], [31], [32]
  OxyR activator trxCp Sigma70 -57.0 -117.0 trxC
ccaaagcctgCGACTATCATACCTATTGaataaaacag
2718610 2718626 nd [APIORCISFBSCS], [BPP], [CEEUMA], [GEA], [IHBCE], [RSE] [15], [33]
  OxyR activator trxCp Sigma70 -35.0 -95.0 trxC
ctattgaataAAACAGATTGTTGTCTGGaacaatgtcc
2718632 2718648 nd [APIORCISFBSCS], [BPP], [GEA] [33]
  OxyR activator uofp nd -62.0 -166.0 uof, fur
tacgccgtatTAATAGATAATGCCAATCaaaataattg
710883 710899 nd [APIORCISFBSCS], [BPP], [CEEUMA], [GEA], [IHBCE], [RSE] [15], [34]
  OxyR activator uofp nd -40.0 -144.0 uof, fur
ccaatcaaaaTAATTGCTACAAATTTGTaacttttgct
710861 710877 nd [APIORCISFBSCS], [BPP], [GEA] [34]
  OxyR repressor uxuAp Sigma70 -54.0 -172.0 uxuA, uxuB
aaattcttgtGATGTGGTTAACCAATTTcagaattcgg
4551456 4551472 nd [APIORCISFBSCS], [GEA] [22]
  OxyR repressor uxuAp Sigma70 -32.0 -150.0 uxuA, uxuB
caatttcagaATTCGGGTTGACATGTCTtaccaaaagg
4551478 4551494 nd [APIORCISFBSCS], [GEA] [22]
  OxyR repressor ybjCp Sigma70 -72.0 -93.0 ybjC, nfsA, rimK, ybjN
attcgctgaaAGTAGGTTTAACCTGTTGcattaattgc
890812 890828 nd [APIORCISFBSCS], [BPP], [GEA] [22], [24]
  OxyR repressor ybjCp Sigma70 -50.0 -71.0 ybjC, nfsA, rimK, ybjN
ctgttgcattAATTGCTAAAAGCTATAActgttaaaca
890834 890850 nd [APIORCISFBSCS], [BPP], [CEEUMA], [GEA], [IHBCE], [RSE] [15], [22], [24]
  OxyR repressor ychFp Sigma70 9.5 -61.5 ychF
taataggcaaAGTTATTTCCATTTCTGCaatctgttag
1257865 1257881 nd [APIORCISFBSCS], [BPP] [35]
  OxyR repressor ychFp Sigma70 31.5 -39.5 ychF
ttctgcaatcTGTTAGCAATAACAGGTTgattattaag
1257843 1257859 nd [APIORCISFBSCS], [BPP] [35]
  OxyR activator yhjAp Sigma70 -86.0 -159.0 ccp
ctgatctgggTAATAGGCACAGGCTATCttattgatag
3669339 3669355 nd [AIBSCS], [BPP], [CEEUMA], [IHBCE], [RSE] [15], [36]
  OxyR activator yhjAp Sigma70 -64.0 -137.0 ccp
gctatcttatTGATAGTTTATATTCATGtaattgattg
3669317 3669333 nd [APIORCISFBSCS], [BPP] [36]
  OxyR activator yjjZp Sigma70 -62.0 -89.0 yjjZ
taatcatagcGATAGGTTTACCCGATAGcaagggattt
4605707 4605723 nd [APIORCISFBSCS], [BPP], [GEA], [CEEUMA], [IHBCE], [RSE] [13], [15]
  OxyR activator zinTp Sigma70 21.5 -8.5 zinT
tatacattaaCTCTGGAGGAAACTGTTTtggcgattcg
2041358 2041374 nd [CEEUMA], [IHBCE], [RSE] [15]
  OxyR activator znuAp Sigma38 55.5 -23.5 znuA
aatatcacacTTCTCATATTCATTACGAttattggtcg
1942598 1942614 nd [CEEUMA], [IHBCE], [RSE], [CEEUMA], [IHBCE], [RSE] [15]
  OxyR activator znuCp Sigma70 -27.5 -55.5 znuC, znuB
cgaccaataaTCGTAATGAATATGAGAAgtgtgatatt
1942598 1942614 nd [CEEUMA], [IHBCE], [RSE] [15]



High-throughput Transcription factor binding sites (TFBSs)
      

  Functional conformation Function Object name Object type Distance to first Gene Sequence LeftPos RightPos Center Position Growth Condition Evidence (Confirmed, Strong, Weak) References
  OxyR activator ahpC gene -324.5
gtcgagtaaaAGGCATAACCTATCACTGTcataggtaag
638611 638630 638620.5 [1] [AIBSCS], [CEEUMA], [RSE], [AIBSCS], [CEEUMA], [RSE] [15]
  OxyR activator ahpC gene -309.5
taacctatcaCTGTCATAGGTAAGAGCTTagatcaggtg
638626 638645 638635.5 [1] [AIBSCS], [CEEUMA], [RSE], [AIBSCS], [CEEUMA], [RSE] [15]
  OxyR activator ahpC gene -302.5
tcactgtcatAGGTAAGAGCTTAGATCAGgtgattgccc
638633 638652 638642.5 [1] [AIBSCS], [CEEUMA], [RSE], [AIBSCS], [CEEUMA], [RSE] [15]
  OxyR activator ahpC gene -86.5
gaaggttgtaAGGTAAAACTTATCGATTTgataatggaa
638849 638868 638858.5 [1] [AIBSCS], [CEEUMA], [RSE], [AIBSCS], [CEEUMA], [RSE] [15]
  OxyR activator ahpF gene 50.5
ggcttaccttGAGAAATTGACCAAGCCTGttgagttaat
639794 639813 639803.5 [1] [AIBSCS], [CEEUMA], [RSE], [AIBSCS], [CEEUMA], [RSE] [15]
  OxyR activator dps gene -86.5
tccgctattcTGGCTGTTCCTATCACACTaatagtggta
848988 849007 848997.5 [1] [AIBSCS], [CEEUMA], [RSE], [AIBSCS], [CEEUMA], [RSE] [15]
  OxyR activator dps gene -101.5
gttcctatcaCACTAATAGTGGTAACAAGcgtgaaaaac
849003 849022 849012.5 [1] [AIBSCS], [CEEUMA], [RSE], [AIBSCS], [CEEUMA], [RSE] [15]
  OxyR activator dps gene -143.5
actaataaagATTCAATGAGTTAGATATAttgataagaa
849045 849064 849054.5 [1] [AIBSCS], [CEEUMA], [RSE], [AIBSCS], [CEEUMA], [RSE] [15]
  OxyR activator dps gene -150.5
aagattcaatGAGTTAGATATATTGATAAgaacaattct
849052 849071 849061.5 [1] [AIBSCS], [CEEUMA], [RSE], [AIBSCS], [CEEUMA], [RSE] [15]
  OxyR activator grxA gene 0.5
ccaaaaataaCGGTTTGCATTATTTCTCTcctcatagat
890743 890762 890752.5 [1] [AIBSCS], [CEEUMA], [RSE], [AIBSCS], [CEEUMA], [RSE] [15]
  OxyR repressor ybjC gene -160.5
ccaaaaataaCGGTTTGCATTATTTCTCTcctcatagat
890743 890762 890752.5 [1] [AIBSCS], [CEEUMA], [RSE], [AIBSCS], [CEEUMA], [RSE] [15]
  OxyR activator grxA gene -70.5
cgctgaaagtAGGTTTAACCTGTTGCATTaattgctaaa
890814 890833 890823.5 [1] [AIBSCS], [CEEUMA], [RSE], [AIBSCS], [CEEUMA], [RSE] [15]
  OxyR repressor ybjC gene -89.5
cgctgaaagtAGGTTTAACCTGTTGCATTaattgctaaa
890814 890833 890823.5 [1] [AIBSCS], [CEEUMA], [RSE], [AIBSCS], [CEEUMA], [RSE] [15]
  OxyR activator grxA gene -85.5
taacctgttgCATTAATTGCTAAAAGCTAtaactgttaa
890829 890848 890838.5 [1] [AIBSCS], [CEEUMA], [RSE], [AIBSCS], [CEEUMA], [RSE] [15]
  OxyR repressor ybjC gene -74.5
taacctgttgCATTAATTGCTAAAAGCTAtaactgttaa
890829 890848 890838.5 [1] [AIBSCS], [CEEUMA], [RSE], [AIBSCS], [CEEUMA], [RSE] [15]
  OxyR activator grxA gene -92.5
ttgcattaatTGCTAAAAGCTATAACTGTtaaacacaat
890836 890855 890845.5 [1] [AIBSCS], [CEEUMA], [RSE], [AIBSCS], [CEEUMA], [RSE] [15]
  OxyR repressor ybjC gene -67.5
ttgcattaatTGCTAAAAGCTATAACTGTtaaacacaat
890836 890855 890845.5 [1] [AIBSCS], [CEEUMA], [RSE], [AIBSCS], [CEEUMA], [RSE] [15]
  OxyR activator grxA gene -98.5
ttaattgctaAAAGCTATAACTGTTAAACAcaatacagtg
890842 890861 890851.5 [1] [AIBSCS], [CEEUMA], [RSE], [AIBSCS], [APIORCISFBSCS], [CEEUMA], [GEA], [RSE] [15]
  OxyR repressor ybjC gene -61.5
ttaattgctaAAAGCTATAACTGTTAAACAcaatacagtg
890842 890861 890851.5 [1] [AIBSCS], [CEEUMA], [RSE], [AIBSCS], [APIORCISFBSCS], [CEEUMA], [GEA], [RSE] [15]
  OxyR activator grxA gene -101.5
ttgctaaaagCTATAACTGTTAAACACAAtacagtgaaa
890845 890864 890854.5 [1] [AIBSCS], [CEEUMA], [RSE], [AIBSCS], [CEEUMA], [RSE] [15]
  OxyR repressor ybjC gene -58.5
ttgctaaaagCTATAACTGTTAAACACAAtacagtgaaa
890845 890864 890854.5 [1] [AIBSCS], [CEEUMA], [RSE], [AIBSCS], [CEEUMA], [RSE] [15]
  OxyR repressor mdtK gene 84.5
atcgcccaaaCTGCGATGGGTTTTGTCGAtaccgtgatg
1743532 1743551 1743541.5 [1] [AIBSCS], [CEEUMA], [RSE], [AIBSCS], [CEEUMA], [RSE] [15]
  OxyR activator sufB gene 24.5
gtccaggtttTGACATCGTCAGTTGCTTCagtattacga
1763975 1763994 1763984.5 [1] [AIBSCS], [CEEUMA], [RSE], [AIBSCS], [CEEUMA], [RSE] [15]
  OxyR activator sufA gene -51.5
aacagcatgtTAGTGATAATGATTATCAGttcaacccag
1764428 1764447 1764437.5 [1] [AIBSCS], [CEEUMA], [RSE], [AIBSCS], [CEEUMA], [RSE] [15]
  OxyR repressor flu gene -230.5
tgcaatagctCAATAATAGAATAAAACGAtcaatatcta
2071299 2071318 2071308.5 [1] [AIBSCS], [CEEUMA], [RSE], [AIBSCS], [CEEUMA], [RSE] [15]
  OxyR repressor flu gene -223.5
gctcaataatAGAATAAAACGATCAATATctattttatc
2071306 2071325 2071315.5 [1] [AIBSCS], [CEEUMA], [RSE], [AIBSCS], [CEEUMA], [RSE] [15]
  OxyR repressor flu gene -204.5
cgatcaatatCTATTTTATCGATCGTTTAtatcgatcga
2071325 2071344 2071334.5 [1] [AIBSCS], [CEEUMA], [RSE], [AIBSCS], [CEEUMA], [RSE] [15]
  OxyR repressor flu gene -198.5
atatctatttTATCGATCGTTTATATCGAtcgataagct
2071331 2071350 2071340.5 [1] [AIBSCS], [CEEUMA], [RSE], [AIBSCS], [CEEUMA], [RSE] [15]
  OxyR repressor flu gene -191.5
ttttatcgatCGTTTATATCGATCGATAAgctaataata
2071338 2071357 2071347.5 [1] [AIBSCS], [CEEUMA], [RSE], [AIBSCS], [CEEUMA], [RSE] [15]
  OxyR activator mntH gene 90.5
ttaccgggatCGATATAACCAATCGCCGCaatgaacgca
2512606 2512625 2512615.5 [1] [AIBSCS], [CEEUMA], [RSE], [AIBSCS], [CEEUMA], [RSE] [15]
  OxyR activator mntH gene -85.5
tcatttaaatGGATTGTGGTGATTTCTCTgatagaccag
2512782 2512801 2512791.5 [1] [AIBSCS], [CEEUMA], [RSE], [AIBSCS], [CEEUMA], [RSE] [15]
  OxyR activator mntH gene -107.5
tttctctgatAGACCAGGATTATGACTACgaaaagattg
2512804 2512823 2512813.5 [1] [AIBSCS], [CEEUMA], [RSE], [AIBSCS], [CEEUMA], [RSE] [15]
  OxyR activator trxC gene -122.5
ttcgtaccaaAGCCTGCGACTATCATACCtattgaataa
2718603 2718622 2718612.5 [1] [AIBSCS], [CEEUMA], [RSE], [AIBSCS], [CEEUMA], [RSE] [15]
  OxyR activator trxC gene -113.5
aagcctgcgaCTATCATACCTATTGAATAaaacagattg
2718612 2718631 2718621.5 [1] [AIBSCS], [CEEUMA], [RSE], [AIBSCS], [CEEUMA], [RSE] [15]
  OxyR repressor ribB gene -324.5
tctggtttatGACTTACCCTTATCGCACTacaatggcac
3184781 3184800 3184790.5 [1] [AIBSCS], [CEEUMA], [RSE], [AIBSCS], [CEEUMA], [RSE] [15]
  OxyR repressor yidD gene -336.5
gaccgtttctAAGTAATAAAGCTAACCCCtgagtggtta
3884470 3884489 3884479.5 [1] [AIBSCS], [CEEUMA], [RSE], [AIBSCS], [CEEUMA], [RSE] [15]
  OxyR activator metE gene -237.5
aggtgttttaCTTCGATCATGAAAGTCCTtcacttcggc
4012806 4012825 4012815.5 [1] [AIBSCS], [CEEUMA], [RSE], [AIBSCS], [CEEUMA], [RSE] [15]
  OxyR activator metR gene 0.5
aggtgttttaCTTCGATCATGAAAGTCCTtcacttcggc
4012806 4012825 4012815.5 [1] [AIBSCS], [CEEUMA], [RSE], [AIBSCS], [CEEUMA], [RSE] [15]
  OxyR activator oxyR gene -63.5
cagtcagaatGCTTGATAGGGATAATCGTtcattgctat
4158417 4158436 4158426.5 [1] [AIBSCS], [CEEUMA], [RSE], [AIBSCS], [CEEUMA], [RSE] [15]
  OxyR activator oxyR gene -54.5
tgcttgatagGGATAATCGTTCATTGCTAttctacctat
4158426 4158445 4158435.5 [1] [AIBSCS], [CEEUMA], [RSE], [AIBSCS], [CEEUMA], [RSE] [15]
  OxyR activator oxyR gene -25.5
ttctacctatCGCCATGAACTATCGTGGCgatggaggat
4158455 4158474 4158464.5 [1] [AIBSCS], [CEEUMA], [RSE], [AIBSCS], [CEEUMA], [RSE] [15]
  OxyR repressor rdcA gene -75.5
ttatttcttgCAGTAATTATAAAAGCCGAaaacagaact
4327050 4327069 4327059.5 [1] [AIBSCS], [CEEUMA], [RSE], [AIBSCS], [CEEUMA], [RSE] [15]
  OxyR repressor fimB gene -269.5
catgatatatAGATAAGATTAGTTGCATTaatgatgagg
4540678 4540697 4540687.5 [1] [AIBSCS], [CEEUMA], [RSE], [AIBSCS], [CEEUMA], [RSE] [15]
  OxyR activator yjjZ gene -370.5
catcggttggTTGCGATAGATATGATCGGaatagaccgc
4605424 4605443 4605433.5 [1] [AIBSCS], [CEEUMA], [RSE], [AIBSCS], [CEEUMA], [RSE] [15]
  OxyR activator yjjZ gene -92.5
ttgctaatcaTAGCGATAGGTTTACCCGAtagcaaggga
4605702 4605721 4605711.5 [1] [AIBSCS], [CEEUMA], [RSE], [AIBSCS], [CEEUMA], [RSE] [15]
  OxyR activator yjjZ gene -29.5
aattatcataTGATATTGGTTATCATTATcaatgaaaga
4605765 4605784 4605774.5 [1] [AIBSCS], [CEEUMA], [RSE], [AIBSCS], [CEEUMA], [RSE] [15]
  OxyR activator yjjZ gene -23.5
catatgatatTGGTTATCATTATCAATGAaagagatgaa
4605771 4605790 4605780.5 [1] [AIBSCS], [CEEUMA], [RSE], [AIBSCS], [CEEUMA], [RSE] [15]
  OxyR activator yjjZ gene -8.5
atcattatcaATGAAAGAGATGAAATCATgttgcaacgt
4605786 4605805 4605795.5 [1] [AIBSCS], [CEEUMA], [RSE], [AIBSCS], [CEEUMA], [RSE] [15]
Other High-throughput regulatory interactions with weak evidence


Growth Condition    

 [1] 

C: Escherichia coli str. K-12 substr. MG1655| wild type| M9 minimal medium| paraquat 0.25 mM; glucose 0.2%| mid exponential phase
E: Escherichia coli str. K-12 substr. MG1655| oxyR knockout mutant| M9 minimal medium| paraquat 0.25 mM; glucose 0.2%| mid exponential phase



Alignment and PSSM for OxyR TFBSs    

Aligned TFBS of OxyR   
  Sequence
  AAAGGCATAACCTATCACTG
  ATCGGGTAAACCTATCGCTA
  GTAGGTTTAACCTGTTGCAT
  ATTGCTAAAAGCTATAACTG
  ATTGGCATTATCTATTAATA
  ATTGGTTATCATTATCAATG
  TAAGCTCTTACCTATGACAG
  TAAGGTAAAACTTATCGATT
  TAAGATCTCAACTATCGCAT
  ATCGATATAAACGATCGATA
  ATCGCCATGAACTATCGTGG
  ATAGAATAAAACGATCAATA
  ATGAATATAAACTATCAATA
  ATAGCCTGTGCCTATTACCC
  TCTGATTTGACCTCTCACAG
  TCTGGCTGTTCCTATCACAC
  ATTGAAAATGACTATTTAAG
  ATGTGGTTAACCAATTTCAG
  ATAGCAATGAACGATTATCC
  GCTTGTTACCACTATTAGTG
  ATTAGCAATCATTATCATTT
  ATAGACCAGGATTATGACTA
  ATGCGTTTCCATTATCAAAT
  TTCGGCATGAATAATTTGCG
  CACTTTTTTACCTATCTCTT
  GACTATCATACCTATTGAAT
  CATGATTTCATCTCTTTCAT
  ATGGATTGTGGTGATTTCTC
  TTCGGGTTGACATGTCTTAC
  GTGGATTAATTCAATTATAA
  TTAGCAATAACAGGTTGATT
  CAGGCATAAATCTATGAGGA
  TCTGGAGGAAACTGTTTTGG
  GGAAGAAGAACTAATTGCTG
  AATCGTAATGAATATGAGAA
  TGAGGAATATACAGTAACCG
  GTTCCAGACAACAATCTGTT
  CAAAGTTATTTCCATTTCTG
  TAACGGTAACACTGTAGAGG
  CAAATTTGTAGCAATTATTT
  TATAGCACCGGCTATGTGTT
  TCTTGTCCGTGCAATAGCTC

Position weight matrix (PWM). OxyR matrix-quality result   
A	18	13	15	6	11	9	16	16	16	26	18	3	8	34	0	4	20	11	13	9
C	5	5	7	4	8	9	5	2	6	5	14	31	1	2	0	16	0	18	4	6
G	6	2	6	27	21	4	2	6	7	6	5	0	5	6	0	5	11	6	4	15
T	13	22	14	5	2	20	19	18	13	5	5	8	28	0	42	17	11	7	21	12

Consensus   
;	consensus.strict             	ataGgtttaacCtATcactg
;	consensus.strict.rc          	CAGTGATAGGTTAAACCTAT
;	consensus.IUPAC              	wwwGgywwwamCtATyrcwg
;	consensus.IUPAC.rc           	CWGYRATAGKTWWWRCCWWW
;	consensus.regexp             	[at][at][at]Gg[ct][at][at][at]a[ac]CtAT[ct][ag]c[at]g
;	consensus.regexp.rc          	C[AT]G[CT][AG]ATAG[GT]T[AT][AT][AT][AG]CC[AT][AT][AT]

PWM logo   


 


Evolutionary conservation of regulatory elements    
     Note: Evolutionary conservation of regulatory interactions and promoters is limited to gammaproteobacteria.
TF-target gene evolutionary conservation
Promoter-target gene evolutionary conservation




Reference(s)    

 [1] Blattner FR., Burland V., Plunkett G., Sofia HJ., Daniels DL., 1993, Analysis of the Escherichia coli genome. IV. DNA sequence of the region from 89.2 to 92.8 minutes., Nucleic Acids Res 21(23):5408-17

 [2] Bolker M., Kahmann R., 1989, The Escherichia coli regulatory protein OxyR discriminates between methylated and unmethylated states of the phage Mu mom promoter., EMBO J 8(8):2403-10

 [3] Christman MF., Storz G., Ames BN., 1989, OxyR, a positive regulator of hydrogen peroxide-inducible genes in Escherichia coli and Salmonella typhimurium, is homologous to a family of bacterial regulatory proteins., Proc Natl Acad Sci U S A 86(10):3484-8

 [4] Seth D., Hausladen A., Wang YJ., Stamler JS., 2012, Endogenous protein S-Nitrosylation in E. coli: regulation by OxyR., Science 336(6080):470-3

 [5] Tao K., Fujita N., Ishihama A., 1993, Involvement of the RNA polymerase alpha subunit C-terminal region in co-operative interaction and transcriptional activation with OxyR protein., Mol Microbiol 7(6):859-64

 [6] Tao K., Makino K., Yonei S., Nakata A., Shinagawa H., 1991, Purification and characterization of the Escherichia coli OxyR protein, the positive regulator for a hydrogen peroxide-inducible regulon., J Biochem 109(2):262-6

 [7] Tao K., Makino K., Yonei S., Nakata A., Shinagawa H., 1989, Molecular cloning and nucleotide sequencing of oxyR, the positive regulatory gene of a regulon for an adaptive response to oxidative stress in Escherichia coli: homologies between OxyR protein and a family of bacterial activator proteins., Mol Gen Genet 218(3):371-6

 [8] Warne SR., Varley JM., Boulnois GJ., Norton MG., 1990, Identification and characterization of a gene that controls colony morphology and auto-aggregation in Escherichia coli K12., J Gen Microbiol 136(3):455-62

 [9] Campos E., Montella C., Garces F., Baldoma L., Aguilar J., Badia J., 2007, Aerobic L-ascorbate metabolism and associated oxidative stress in Escherichia coli., Microbiology 153(Pt 10):3399-408

 [10] Tartaglia LA., Gimeno CJ., Storz G., Ames BN., 1992, Multidegenerate DNA recognition by the OxyR transcriptional regulator., J Biol Chem 267(3):2038-45

 [11] Tartaglia LA., Storz G., Ames BN., 1989, Identification and molecular analysis of oxyR-regulated promoters important for the bacterial adaptation to oxidative stress., J Mol Biol 210(4):709-19

 [12] Toledano MB., Kullik I., Trinh F., Baird PT., Schneider TD., Storz G., 1994, Redox-dependent shift of OxyR-DNA contacts along an extended DNA-binding site: a mechanism for differential promoter selection., Cell 78(5):897-909

 [13] Zheng M., Wang X., Doan B., Lewis KA., Schneider TD., Storz G., 2001, Computation-directed identification of OxyR DNA binding sites in Escherichia coli., J Bacteriol 183(15):4571-9

 [14] Storz G., Tartaglia LA., Ames BN., 1990, Transcriptional regulator of oxidative stress-inducible genes: direct activation by oxidation., Science 248(4952):189-94

 [15] Seo SW., Kim D., Szubin R., Palsson BO., 2015, Genome-wide Reconstruction of OxyR and SoxRS Transcriptional Regulatory Networks under Oxidative Stress in Escherichia coli K-12 MG1655., Cell Rep 12(8):1289-99

 [16] Guo Y., Li Y., Zhan W., Wood TK., Wang X., 2019, Resistance to oxidative stress by inner membrane protein ElaB is regulated by OxyR and RpoS., Microb Biotechnol 12(2):392-404

 [17] Haagmans W., van der Woude M., 2000, Phase variation of Ag43 in Escherichia coli: Dam-dependent methylation abrogates OxyR binding and OxyR-mediated repression of transcription., Mol Microbiol 35(4):877-87

 [18] Henderson IR., Owen P., 1999, The major phase-variable outer membrane protein of Escherichia coli structurally resembles the immunoglobulin A1 protease class of exported protein and is regulated by a novel mechanism involving Dam and oxyR., J Bacteriol 181(7):2132-41

 [19] Waldron DE., Owen P., Dorman CJ., 2002, Competitive interaction of the OxyR DNA-binding protein and the Dam methylase at the antigen 43 gene regulatory region in Escherichia coli., Mol Microbiol 44(2):509-20

 [20] Wallecha A., Correnti J., Munster V., van der Woude M., 2003, Phase variation of Ag43 is independent of the oxidation state of OxyR., J Bacteriol 185(7):2203-9

 [21] Wallecha A., Munster V., Correnti J., Chan T., van der Woude M., 2002, Dam- and OxyR-dependent phase variation of agn43: essential elements and evidence for a new role of DNA methylation., J Bacteriol 184(12):3338-47

 [22] Zheng M., Wang X., Templeton LJ., Smulski DR., LaRossa RA., Storz G., 2001, DNA microarray-mediated transcriptional profiling of the Escherichia coli response to hydrogen peroxide., J Bacteriol 183(15):4562-70

 [23] Becker-Hapak M., Eisenstark A., 1995, Role of rpoS in the regulation of glutathione oxidoreductase (gor) in Escherichia coli., FEMS Microbiol Lett 134(1):39-44

 [24] Tao K., 1997, oxyR-dependent induction of Escherichia coli grx gene expression by peroxide stress., J Bacteriol 179(18):5967-70

 [25] Anjem A., Varghese S., Imlay JA., 2009, Manganese import is a key element of the OxyR response to hydrogen peroxide in Escherichia coli., Mol Microbiol 72(4):844-58

 [26] Kehres DG., Janakiraman A., Slauch JM., Maguire ME., 2002, Regulation of Salmonella enterica serovar Typhimurium mntH transcription by H(2)O(2), Fe(2+), and Mn(2+)., J Bacteriol 184(12):3151-8

 [27] Kullik I., Toledano MB., Tartaglia LA., Storz G., 1995, Mutational analysis of the redox-sensitive transcriptional regulator OxyR: regions important for oxidation and transcriptional activation., J Bacteriol 177(5):1275-84

 [28] Engl C., Jovanovic G., Brackston RD., Kotta-Loizou I., Buck M., 2020, The route to transcription initiation determines the mode of transcriptional bursting in E. coli., Nat Commun 11(1):2422

 [29] Jang S., Imlay JA., 2010, Hydrogen peroxide inactivates the Escherichia coli Isc iron-sulphur assembly system, and OxyR induces the Suf system to compensate., Mol Microbiol 78(6):1448-67

 [30] Lee JH., Yeo WS., Roe JH., 2004, Induction of the sufA operon encoding Fe-S assembly proteins by superoxide generators and hydrogen peroxide: involvement of OxyR, IHF and an unidentified oxidant-responsive factor., Mol Microbiol 51(6):1745-55

 [31] Outten FW., Djaman O., Storz G., 2004, A suf operon requirement for Fe-S cluster assembly during iron starvation in Escherichia coli., Mol Microbiol 52(3):861-72

 [32] Yeo WS., Lee JH., Lee KC., Roe JH., 2006, IscR acts as an activator in response to oxidative stress for the suf operon encoding Fe-S assembly proteins., Mol Microbiol 61(1):206-18

 [33] Ritz D., Patel H., Doan B., Zheng M., Aslund F., Storz G., Beckwith J., 2000, Thioredoxin 2 is involved in the oxidative stress response in Escherichia coli., J Biol Chem 275(4):2505-12

 [34] Zheng M., Doan B., Schneider TD., Storz G., 1999, OxyR and SoxRS regulation of fur., J Bacteriol 181(15):4639-43

 [35] Wenk M., Ba Q., Erichsen V., Macinnes K., Wiese H., Warscheid B., Koch HG., 2012, A Universally Conserved ATPase Regulates the Oxidative Stress Response in Escherichia coli., J Biol Chem 287(52):43585-98

 [36] Partridge JD., Poole RK., Green J., 2007, The Escherichia coli yhjA gene, encoding a predicted cytochrome c peroxidase, is regulated by FNR and OxyR., Microbiology 153(Pt 5):1499-509

 [37] Altuvia S., Weinstein-Fischer D., Zhang A., Postow L., Storz G., 1997, A small, stable RNA induced by oxidative stress: role as a pleiotropic regulator and antimutator., Cell 90(1):43-53

 [38] Gonzalez-Flecha B., Demple B., 1997, Transcriptional regulation of the Escherichia coli oxyR gene as a function of cell growth., J Bacteriol 179(19):6181-6



RegulonDB