RegulonDB RegulonDB 10.6.3: Regulon Form
   
   


ArcA,CRP,DnaA,FNR,MarA,Rob,SoxS regulon in Escherichia coli K-12 genome


TRANSCRIPTION FACTOR: Info
Name:
Rob Weight Matrix      Tractordb tool
Connectivity class Local Regulator
Synonym(s): CbpB, DNA-binding transcriptional dual regulator Rob, RobA, right origin-binding protein
Gene name(s): rob
Functional conformation(s): Rob
Coregulator(s): AcrR, ArcA, CRP, CpxR, Cra, DnaA, EnvR, FNR, Fis, Fur, GadE, H-NS, HU, IHF, Lrp, MarA, MarR, MprA, OmpR, OxyR, PhoP, Rob, SoxR, SoxS
Summary: TF Summary ...[more]
TRANSCRIPTION FACTOR: Info
Name:
FNR Weight Matrix      Tractordb tool
Connectivity class Global Regulator
Sensing Class Using internal synthesized signals
Synonym(s): DNA-binding transcriptional dual regulator FNR, NirA, NirR, OssA, OxrA
Gene name(s): fnr
Functional conformation(s): FNR , FNR-[2Fe-2S]2+ oxidized
Coregulator(s): AcrR, AdiY, ArcA, ArgP, ArgR, CRP, CadC, CaiF, Cbl, CdaR, Cra, CueR, CusR, CysB, DcuR, DksA, DksA-ppGpp, DnaA, DpiA, EvgA, ExuR, FNR, FhlA, Fis, FlhDC, Fur, GadE, GadW, GadX, GcvA, GlpR, H-NS, HdfR, HprR, HyfR, HypT, IHF, LeuO, Lrp, MalT, MarA, MetR, MlrA, ModE, Nac, NagC, NarL, NarP, NfeR, NikR, NorR, NrdR, NsrR, NtrC, OmpR, OxyR, PdhR, PhoB, PhoP, PurR, PuuR, RcsB, Rob, RstA, RutR, SlyA, SoxR, SoxS, TdcA, TdcR, TorR, YeiL, ppGpp
Summary: TF Summary ...[more]
TRANSCRIPTION FACTOR: Info
Name:
CRP Weight Matrix      Tractordb tool
Connectivity class Global Regulator
Sensing Class Using internal synthesized signals
Synonym(s): Cap, Csm, DNA-binding transcriptional dual regulator CRP, GurB
Gene name(s): crp
Functional conformation(s): CRP-cAMP , CRP
Coregulator(s): AcrR, AdiY, AgaR, AraC, ArcA, ArgP, ArgR, AscG, BasR, BtsR, CRP, CaiF, ChbR, ComR, CpxR, Cra, CreB, CsgD, CspA, CsqR, CusR, CytR, DcuR, DeoR, DgoR, DksA-ppGpp, DnaA, DpiA, DsdC, EbgR, EnvY, EvgA, ExuR, FNR, FadR, FeaR, FhlA, Fis, FlhDC, FliZ, FucR, Fur, GadE, GadW, GadX, GalR, GalS, GatR, GcvA, GlaR, GlcC, GlpR, GlrR, GntR, GutM, H-NS, HU, HdfR, HipB, HprR, HyfR, HypT, IHF, IclR, IdnR, LacI, LeuO, LexA, LrhA, Lrp, LsrR, MalI, MalT, MarA, MarR, MatA, McbR, MelR, MetJ, MhpR, Mlc, MlrA, ModE, MprA, MqsA, MurR, Nac, NadR, NagC, NanR, NarL, NarP, NrdR, NsrR, NtrC, OmpR, OxyR, PaaX, PdhR, PhoB, PhoP, PrpR, PurR, PuuR, QseB, RbsR, RcdA, RcsB, RhaR, RhaS, Rob, RstA, SdiA, SlyA, SoxR, SoxS, SrlR, StpA, TdcA, TdcR, TorR, TreR, UhpA, UidR, UlaR, UvrY, UxuR, XylR, YdeO, YiaJ, YjjQ, ZraR, ppGpp
Summary: TF Summary ...[more]
TRANSCRIPTION FACTOR: Info
Name:
SoxS Weight Matrix      Tractordb tool
Connectivity class Local Regulator
Synonym(s): DNA-binding transcriptional dual regulator SoxS, regulation of superoxide response regulon
Gene name(s): soxS
Functional conformation(s): SoxS
Coregulator(s): AcrR, ArcA, BasR, CRP, CpxR, Cra, DnaA, EnvR, FNR, Fis, Fur, H-NS, HU, IHF, Lrp, MarA, MarR, Mlc, MprA, OmpR, OxyR, PhoP, Rob, SoxR, SoxS, Zur
Summary: TF Summary ...[more]
TRANSCRIPTION FACTOR: Info
Name:
ArcA Weight Matrix      Tractordb tool
Connectivity class Global Regulator
Sensing Class External-Two-component systems
Synonym(s): ArcA response regulator, CpxC, DNA-binding transcriptional dual regulator ArcA, Dye, FexA, Msp, Seg, SfrA, dye resistance protein
Gene name(s): arcA
Functional conformation(s): ArcA-Phosphorylated , ArcA
Coregulator(s): AdiY, AppY, ArcA, BetI, CRP, CadC, CaiF, Cra, CusR, CysB, DcuR, DksA-ppGpp, DnaA, DpiA, FNR, FadR, Fis, FlhDC, Fur, GadE, GadW, GadX, GatR, GlcC, GlpR, H-NS, HipB, HprR, HypT, IHF, IclR, IscR, LexA, LldR, Lrp, MarA, McbR, Mlc, ModE, MqsA, NarL, NarP, NsrR, NtrC, OmpR, PdhR, PhoP, PuuR, RcdA, RcsB, RhaS, Rob, RutR, SdiA, SlyA, SoxR, SoxS, TorR, TreR, YdeO, ppGpp
Summary: TF Summary ...[more]
TRANSCRIPTION FACTOR: Info
Name:
MarA Weight Matrix      Tractordb tool
Connectivity class Local Regulator
Synonym(s): CfxB, DNA-binding transcriptional dual regulator MarA, InaR, NfxC, NorB, SoxQ
Gene name(s): marA
Functional conformation(s): MarA
Coregulator(s): AcrR, ArcA, BasR, CRP, CpxR, Cra, DnaA, EnvR, FNR, Fis, FliZ, Fur, GadE, GadW, GadX, H-NS, HU, IHF, Lrp, MarA, MarR, MprA, OmpR, OxyR, PhoP, PurR, PutA, RcsB, Rob, SoxR, SoxS, TorR, YdeO
Summary: TF Summary ...[more]
TRANSCRIPTION FACTOR: Info
Name:
DnaA Weight Matrix      Tractordb tool
Connectivity class Local Regulator
Sensing Class Using internal synthesized signals
Synonym(s): chromosomal replication initiator protein DnaA, chromosomal replication initiator protein/DNA-binding transcriptional dual regulator DnaA
Gene name(s): dnaA
Functional conformation(s): DnaA , DnaA-ATP
Coregulator(s): ArcA, ArgP, CRP, CytR, DnaA, FNR, Fis, H-NS, LexA, MarA, NrdR, PurR, Rob, SoxS, ppGpp
Summary: TF Summary ...[more]

REGULATION EXERTED BY ArcA,CRP,DnaA,FNR,MarA,Rob,SoxS Info M3D | Colombos
KNOWN BINDING SITES (The central relative position is relative to the promoter +1)    
ArcA repressor CRP activator DnaA repressor FNR repressor MarA activator Rob activator SoxS activator    
Transcription Factor
Regulated
Binding Sites
Evidence
References
Functional conformation
Function
Promoter
Gene(s)
LeftPos
RigthPos
Central Rel-Pos
Sequence
CRP-cAMP activator aldAp aldA 1488120 1488141 -59.5 ttacacttgtTTTTATGAAGCCCTTCACAGAAttgtcctttc [BCE]
[GEA]
[1]
ArcA-Phosphorylated repressor aldAp aldA 1488046 1488060 -137.0 aaattgcccgTTTGTGAACCACTTGtttgcaaacg [BPP]
[HIBSCS]
[2]
ArcA-Phosphorylated repressor aldAp aldA 1488195 1488209 13.0 aacaatgtatTCACCGAAAACAAACatataaatca [AIBSCS]
[BPP]
[SM]
[3]
[2]
ArcA-Phosphorylated repressor aldAp aldA 1488184 1488198 2.0 tgatgttaatTAACAATGTATTCACcgaaaacaaa [AIBSCS]
[BPP]
[3]
[2]
DnaA-ATP repressor aldAp aldA 1488178 1488186 -7.5 gatgattgatGTTAATTAAcaatgtattc [BPP]
[GEA]
[4]
ArcA-Phosphorylated repressor aldAp aldA 1488178 1488192 -5.0 gatgattgatGTTAATTAACAATGTattcaccgaa [BPP]
[HIBSCS]
[SM]
[3]
[2]
ArcA-Phosphorylated repressor aldAp aldA 1488026 1488040 -157.0 aaagtcgctcGTTACGTTAAAAATTgcccgtttgt [BPP]
[HIBSCS]
[2]
FNR repressor aldAp aldA 1488173 1488186 -10.5 tctctgatgaTTGATGTTAATTAAcaatgtattc [AIBSCS]
[GEA]
[5]
SoxS activator aldAp aldA 1488019 1488038 -161.0 gcgatggaaaGTCGCTCGTTACGTTAAAAAttgcccgttt [AIBSCS]
[GEA]
[6]
Rob activator aldAp aldA 1488019 1488038 -161.0 gcgatggaaaGTCGCTCGTTACGTTAAAAAttgcccgttt [AIBSCS]
[GEA]
[6]
MarA activator aldAp aldA 1488019 1488038 -161.0 gcgatggaaaGTCGCTCGTTACGTTAAAAAttgcccgttt [AIBSCS]
[GEA]
[6]

Evidence: [BCE] Binding of cellular extracts
[GEA] Gene expression analysis
[BPP] Binding of purified proteins
[HIBSCS] Human inference based on similarity to consensus sequences
[AIBSCS] Automated inference based on similarity to consensus sequences
[SM] Site mutation
Reference(s): [1] Limon A., et al., 1997
[2] Pellicer MT., et al., 1999
[3] Liu X., et al., 2004
[4] Ozaki T., et al., 2001
[5] Constantinidou C., et al., 2006
[6] Martin RG., et al., 2002



Reference(s)    

 [1] Limon A., Hidalgo E., Aguilar J., 1997, The aldA gene of Escherichia coli is under the control of at least three transcriptional regulators., Microbiology 143 ( Pt 6):2085-95

 [2] Pellicer MT., Lynch AS., De Wulf P., Boyd D., Aguilar J., Lin EC., 1999, A mutational study of the ArcA-P binding sequences in the aldA promoter of Escherichia coli., Mol Gen Genet 261(1):170-6

 [3] Liu X., De Wulf P., 2004, Probing the ArcA-P modulon of Escherichia coli by whole genome transcriptional analysis and sequence recognition profiling., J Biol Chem 279(13):12588-97

 [4] Ozaki T., Kumaki Y., Kitagawa R., Ogawa T., 2001, Anomalous DnaA protein binding to the regulatory region of the Escherichia coli aldA gene., Microbiology 147(Pt 1):153-9

 [5] Constantinidou C., Hobman JL., Griffiths L., Patel MD., Penn CW., Cole JA., Overton TW., 2006, A reassessment of the FNR regulon and transcriptomic analysis of the effects of nitrate, nitrite, NarXL, and NarQP as Escherichia coli K12 adapts from aerobic to anaerobic growth., J Biol Chem 281(8):4802-15

 [6] Martin RG., Rosner JL., 2002, Genomics of the marA/soxS/rob regulon of Escherichia coli: identification of directly activated promoters by application of molecular genetics and informatics to microarray data., Mol Microbiol 44(6):1611-24


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