RegulonDB RegulonDB 10.8: Regulon Form
   
   


AdiY,ArgR,CRP,FNR,Fur,GadE,HdfR,IHF,Lrp,Nac regulon in Escherichia coli K-12 genome


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-[4Fe-4S]2+ reduced , FNR-[2Fe-2S]2+ oxidized , FNR
Coregulator(s): AcrR, AdiY, ArcA, ArgP, ArgR, BtsR, CRP, CadC, CaiF, Cbl, CdaR, Cra, CueR, CusR, CysB, DcuR, DksA, DksA-ppGpp, DnaA, DpiA, EvgA, ExuR, FNR, FhlA, Fis, FlhDC, Fur, GadE, GadE-RcsB, 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 , CRP-cAMP
Coregulator(s): AcrR, AdiY, AgaR, AraC, ArcA, ArgP, ArgR, AscG, BasR, BtsR, CRP, CRP-Sxy, 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, GadE-RcsB, 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, RcsAB, RcsB, RcsB-BglJ, 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:
Nac Weight Matrix      Tractordb tool
Connectivity class Local Regulator
Synonym(s): DNA-binding transcriptional dual regulator Nac
Gene name(s): nac
Functional conformation(s): Nac
Coregulator(s): AdiY, ArgP, ArgR, AsnC, CRP, CytR, FNR, Fur, GadE, HdfR, IHF, Lrp, Nac, NsrR, NtrC, PhoB, PurR, QseB
Summary: TF Summary ...[more]
TRANSCRIPTION FACTOR: Info
Name:
Lrp Weight Matrix      Tractordb tool
Connectivity class Global Regulator
Sensing Class Sensing external and internal signals
Synonym(s): AlsB, DNA-binding transcriptional dual regulator Lrp, Ihb, LivR, Lrs, Lss, LstR, Mbf, OppI, RblA
Gene name(s): lrp
Functional conformation(s): Lrp-leucine , Lrp
Coregulator(s): AcrR, Ada, AdiY, AidB, ArcA, ArgP, ArgR, CRP, CadC, CpxR, Cra, DksA, DksA-ppGpp, EnvY, FNR, Fis, FliZ, Fur, GadE, GadE-RcsB, GadW, GadX, GcvA, GlaR, H-NS, HU, HdfR, IHF, LrhA, Lrp, MarA, Mlc, ModE, Nac, NarL, NhaR, NsrR, OmpR, PhoP, PurR, QseB, RcsB, Rob, SoxS, StpA, TorR, YeiL, YjjQ, ppGpp
Summary: TF Summary ...[more]
TRANSCRIPTION FACTOR: Info
Name:
ArgR Weight Matrix      Tractordb tool
Connectivity class Local Regulator
Sensing Class Sensing external and internal signals
Synonym(s): DNA-binding transcriptional dual regulator ArgR, XerA
Gene name(s): argR
Functional conformation(s): ArgR , ArgR-L-arginine
Coregulator(s): AdiY, ArgR, CRP, DksA-ppGpp, FNR, Fur, GadE, H-NS, HdfR, IHF, Lrp, Nac, NtrC, PhoP, ppGpp
Summary: TF Summary ...[more]
TRANSCRIPTION FACTOR: Info
Name:
GadE Weight Matrix      Tractordb tool
Connectivity class Local Regulator
Synonym(s): DNA-binding transcriptional activator GadE, YhiE, YhiT, acid-responsive regulator of gadA and gadBC
Gene name(s): gadE
Functional conformation(s): GadE
Coregulator(s): AdiY, ArcA, ArgR, CRP, CadC, CpxR, Cra, CusR, EvgA, FNR, Fis, FliZ, Fur, GadE, GadE-RcsB, GadW, GadX, H-NS, HdfR, HprR, IHF, Lrp, MarA, MatA, Nac, NsrR, OmpR, PdhR, PhoB, PhoP, PurR, RcsAB, RcsB, Rob, RutR, TorR, YdeO, ppGpp
Summary: TF Summary ...[more]
TRANSCRIPTION FACTOR: Info
Name:
HdfR      Tractordb tool
Connectivity class Local Regulator
Synonym(s): DNA-binding transcriptional dual regulator HdfR, YifA, YifD
Gene name(s): hdfR
Functional conformation(s): HdfR
Coregulator(s): AcrR, AdiY, ArgR, CRP, FNR, FliZ, Fur, GadE, H-NS, HdfR, IHF, LrhA, Lrp, MatA, Nac, OmpR, QseB, RcsAB, YjjQ
Summary: TF Summary ...[more]
TRANSCRIPTION FACTOR: Info
Name:
AdiY      Tractordb tool
Connectivity class Local Regulator
Synonym(s): DNA-binding transcriptional activator AdiY
Gene name(s): adiY
Functional conformation(s): AdiY
Coregulator(s): AdiY, ArcA, ArgR, CRP, FNR, Fis, FliZ, Fur, GadE, GadE-RcsB, GadW, GadX, H-NS, HdfR, IHF, Lrp, Nac, RcsB, TorR, ppGpp
Summary: TF Summary ...[more]
TRANSCRIPTION FACTOR: Info
Name:
IHF Weight Matrix      Tractordb tool
Connectivity class Global Regulator
Sensing Class TFs for DNA-bending
Synonym(s): DNA-binding transcriptional dual regulator IHF
Gene name(s): ihfB, ihfA
Functional conformation(s): IHF
Coregulator(s): AcrR, AdiY, ArcA, ArgR, AtoC, BasR, BtsR, CRP, Cbl, CpxR, Cra, CsgD, CysB, DksA, DksA-ppGpp, EnvY, FNR, FadR, FhlA, Fis, FlhDC, FliZ, Fur, GadE, GlcC, GlpR, GlrR, H-NS, HU, HdfR, HipAB, HipB, IHF, IclR, IscR, LrhA, Lrp, MarA, MatA, MlrA, MntR, ModE, MprA, MqsA, Nac, NagC, NanR, NarL, NarP, NorR, NsrR, NtrC, OmpR, OxyR, PaaX, PdhR, PepA, PhoB, PspF, PurR, QseB, RcdA, RcsAB, Rob, RstA, RtcR, RutR, SlyA, SoxR, SoxS, SutR, TdcA, TdcR, TrpR, TyrR, UlaR, UvrY, YeiL, YiaJ, YjjQ, ppGpp
Summary: TF Summary ...[more]
TRANSCRIPTION FACTOR: Info
Name:
Fur Weight Matrix      Tractordb tool
Connectivity class Local Regulator
Sensing Class External sensing using transported metabolites
Synonym(s): DNA-binding transcriptional dual regulator Fur
Gene name(s): fur
Functional conformation(s): Fur-Mn2+ , Fur , Fur-Fe2+
Coregulator(s): AcrR, AdiY, ArcA, ArgP, ArgR, CRP, CdaR, CpxR, Cra, CusR, EnvY, FNR, Fis, FliZ, Fur, GadE, GadX, H-NS, HdfR, HprR, HypT, IHF, IscR, LrhA, Lrp, MarA, MatA, MetR, MntR, ModE, MqsA, Nac, NagC, NarL, NfeR, NrdR, NsrR, NtrC, OmpR, OxyR, PdhR, PhoB, PurR, QseB, RcnR, RcsAB, Rob, RstA, RutR, SlyA, SoxR, SoxS, YjjQ, Zur, ppGpp
Summary: TF Summary ...[more]

REGULATION EXERTED BY AdiY,ArgR,CRP,FNR,Fur,GadE,HdfR,IHF,Lrp,Nac Info M3D | Colombos
KNOWN BINDING SITES (The central relative position is relative to the promoter +1)    
AdiY activator ArgR repressor CRP repressor FNR repressor Fur repressor GadE activator HdfR activator IHF activator Lrp activator Nac repressor    
Transcription Factor
Regulated
Binding Sites
Evidence
References
Functional conformation
Function
Promoter
Gene(s)
LeftPos
RigthPos
Central Rel-Pos
Sequence
IHF activator gltBp gltB , gltD , gltF 3354418 3354430 -85.0 ttttaatttcAGTCATTTAATAAagaattttgc [BPP]
[GEA] 		[1]
[2]
IHF activator gltBp gltB , gltD , gltF 3354414 3354426 -89.0 tccattttaaTTTCAGTCATTTAataaagaatt [BPP]
[GEA] 		[1]
[2]
Lrp activator gltBp gltB , gltD , gltF 3354350 3354364 -152.0 cctttatgacAGTCAGGAATTGACTgtttctctaa [APIORCISFBSCS]
[BPP]
[CV(CHIP-SV/SM)]
[SM] 		[3]
[2]
[4]
Lrp activator gltBp gltB , gltD , gltF 3354287 3354301 -215.0 caattaaggcAGTATAAAATGCTGGttttgtcgtc [APIORCISFBSCS]
[BPP]
[CV(CHIP-SV/SM)]
[SM] 		[3]
[2]
[4]
Lrp activator gltBp gltB , gltD , gltF 3354256 3354270 -246.0 aggcaaaaacAGTAGCATGAAACGTcattaccaat [APIORCISFBSCS]
[BPP]
[CV(CHIP-SV/SM)]
[SM] 		[5]
[2]
[4]
CRP-cAMP repressor gltBp gltB , gltD , gltF 3354433 3354454 -65.5 tttaataaagAATTTTGCGCTAAAGCACATTTctgtaccaat [APIORCISFBSCS]
[BPP]
[CV(CHIP-SV/GEA/ROMA)]
[CV(CHIP-SV/SM)]
[CV(GEA/ROMA)]
[CV(GEA/ROMA/SM)]
[GEA]
[SM] 		[2]
Lrp-leucine activator gltBp gltB , gltD , gltF 3354394 3354409 -108.0 ttttagccttAAAGATAAAATCCATTttaatttcag [AIBSCS]
[CV(GEA/ROMA)]
[GEA] 		[6]
ArgR-L-arginine repressor gltBp gltB , gltD , gltF 3354169 3354186 -331.5 aatcaaaattACCGAAATTTCATGCATAatcacataaa [APIORCISFBSCS]
[BPP]
[CV(CHIP-SV/GEA/ROMA)]
[CV(GEA/ROMA)]
[GEA] 		[7]
[2]
ArgR-L-arginine repressor gltBp gltB , gltD , gltF 3354148 3354165 -352.0 gcttttatcaACTGCATAATCAATCAAAattaccgaaa [APIORCISFBSCS]
[BPP]
[CV(CHIP-SV/GEA/ROMA)]
[CV(GEA/ROMA)]
[GEA] 		[7]
[2]
FNR repressor gltBp gltB , gltD , gltF 3354476 3354489 -26.5 agcttgccatTTGACCTGTATCAGctttcccgat [AIBSCS]
[CV(GEA/ROMA)]
[GEA] 		[8]
[9]
HdfR activator gltBp gltB , gltD , gltF         [BPP] [10]
AdiY activator gltBp gltB , gltD , gltF         [BPP] [10]
Nac repressor gltBp gltB , gltD , gltF         [GEA] [11]
GadE activator gltBp gltB , gltD , gltF 3354215 3354234 -284.0 gcttatcttgTGTCAGATTTTTTTATCTCCtgatggattt [BPP]
[CEUMA]
[CV(CHIP-SV/GEA/ROMA)]
[CV(GEA/ROMA)]
[GEA]
[IHBCE]
[RE] 		[12]
[13]
Fur-Fe2+ repressor gltBp gltB , gltD , gltF         [GEA] [9]

Evidence: [BPP] Binding of purified proteins
[GEA] Gene expression analysis
[APIORCISFBSCS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.
[CV(CHIP-SV/SM)] cross validation(CHIP-SV/SM)
[SM] Site mutation
[CV(CHIP-SV/GEA/ROMA)] cross validation(CHIP-SV/GEA/ROMA)
[CV(GEA/ROMA)] cross validation(GEA/ROMA)
[CV(GEA/ROMA/SM)] cross validation(GEA/ROMA/SM)
[AIBSCS] Automated inference based on similarity to consensus sequences
[CEUMA] ChIP-exo evidence used in manual assertion
[IHBCE] Inferred by a human based on computational evidence
[RE] RNA-seq evidence
Reference(s): [1] Paul L., et al., 2001
[2] Paul L., et al., 2007
[3] Oliver G., et al., 1987
[4] Wiese DE., et al., 1997
[5] Ernsting BR., et al., 1992
[6] Lintner RE., et al., 2008
[7] Cho S., et al., 2015
[8] Constantinidou C., et al., 2006
[9] Kumar R., et al., 2011
[10] Krin E., et al., 2010
[11] Zimmer DP., et al., 2000
[12] Hommais F., et al., 2004
[13] Seo SW., et al., 2015



Reference(s)    

 [1] Paul L., Blumenthal RM., Matthews RG., 2001, Activation from a distance: roles of Lrp and integration host factor in transcriptional activation of gltBDF., J Bacteriol 183(13):3910-8

 [2] Paul L., Mishra PK., Blumenthal RM., Matthews RG., 2007, Integration of regulatory signals through involvement of multiple global regulators: control of the Escherichia coli gltBDF operon by Lrp, IHF, Crp, and ArgR., BMC Microbiol 7:2

 [3] Oliver G., Gosset G., Sanchez-Pescador R., Lozoya E., Ku LM., Flores N., Becerril B., Valle F., Bolivar F., 1987, Determination of the nucleotide sequence for the glutamate synthase structural genes of Escherichia coli K-12., Gene 60(1):1-11

 [4] Wiese DE., Ernsting BR., Blumenthal RM., Matthews RG., 1997, A nucleoprotein activation complex between the leucine-responsive regulatory protein and DNA upstream of the gltBDF operon in Escherichia coli., J Mol Biol 270(2):152-68

 [5] Ernsting BR., Atkinson MR., Ninfa AJ., Matthews RG., 1992, Characterization of the regulon controlled by the leucine-responsive regulatory protein in Escherichia coli., J Bacteriol 174(4):1109-18

 [6] Lintner RE., Mishra PK., Srivastava P., Martinez-Vaz BM., Khodursky AB., Blumenthal RM., 2008, Limited functional conservation of a global regulator among related bacterial genera: Lrp in Escherichia, Proteus and Vibrio., BMC Microbiol 8:60

 [7] Cho S., Cho YB., Kang TJ., Kim SC., Palsson B., Cho BK., 2015, The architecture of ArgR-DNA complexes at the genome-scale in Escherichia coli., Nucleic Acids Res 43(6):3079-88

 [8] 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

 [9] Kumar R., Shimizu K., 2011, Transcriptional regulation of main metabolic pathways of cyoA, cydB, fnr, and fur gene knockout Escherichia coli in C-limited and N-limited aerobic continuous cultures., Microb Cell Fact 10:3

 [10] Krin E., Danchin A., Soutourina O., 2010, Decrypting the H-NS-dependent regulatory cascade of acid stress resistance in Escherichia coli., BMC Microbiol 10:273

 [11] Zimmer DP., Soupene E., Lee HL., Wendisch VF., Khodursky AB., Peter BJ., Bender RA., Kustu S., 2000, Nitrogen regulatory protein C-controlled genes of Escherichia coli: scavenging as a defense against nitrogen limitation., Proc Natl Acad Sci U S A 97(26):14674-9

 [12] Hommais F., Krin E., Coppee JY., Lacroix C., Yeramian E., Danchin A., Bertin P., 2004, GadE (YhiE): a novel activator involved in the response to acid environment in Escherichia coli., Microbiology 150(Pt 1):61-72

 [13] Seo SW., Kim D., O'Brien EJ., Szubin R., Palsson BO., 2015, Decoding genome-wide GadEWX-transcriptional regulatory networks reveals multifaceted cellular responses to acid stress in Escherichia coli., Nat Commun 6:7970

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