RegulonDB RegulonDB 10.6.3: Regulon Form
   
   


ArgP,CRP,DnaA,Fis,H-NS,NrdR regulon in Escherichia coli K-12 genome


TRANSCRIPTION FACTOR: Info
Name:
Fis Weight Matrix      Tractordb tool
Connectivity class Global Regulator
Sensing Class TFs for DNA-bending
Synonym(s): DNA-binding transcriptional dual regulator Fis, Nbp, site-specific DNA inversion stimulation factor
Gene name(s): fis
Functional conformation(s): Fis
Coregulator(s): AcrR, AdiY, AppY, ArcA, ArgP, BasR, CRP, CpxR, Cra, CreB, CspA, CusR, CytR, DeoR, DksA, DksA-ppGpp, DnaA, FNR, FadR, Fis, FlhDC, FliZ, Fur, GadE, GadW, GadX, GlcC, GlpR, H-NS, HprR, IHF, IscR, LeuO, Lrp, MalT, MarA, MarR, MazE, Mlc, MntR, ModE, NanR, NarL, NarP, NrdR, NsrR, NtrC, OmpR, OxyR, PdhR, PepA, PurR, RcsB, Rob, RstA, RutR, SlyA, SoxS, StpA, TorR, XylR, YdeO, ppGpp
Summary: TF Summary ...[more]
TRANSCRIPTION FACTOR: Info
Name:
ArgP Weight Matrix      Tractordb tool
Connectivity class Local Regulator
Sensing Class Using internal synthesized signals
Synonym(s): DNA-binding transcriptional dual regulator ArgP, IciA
Gene name(s): argP
Functional conformation(s): ArgP-lysine , ArgP , ArgP-arginine
Coregulator(s): ArgP, CRP, DnaA, FNR, Fis, Fur, H-NS, Lrp, LysR, Nac, NrdR, PhoB, 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:
H-NS      Tractordb tool
Connectivity class Global Regulator
Sensing Class TFs for DNA-bending
Synonym(s): BglY, Cur, DNA-binding protein HLP-II (HU, BH2, HD, NS), DNA-binding transcriptional dual regulator H-NS, Drc, DrdX, Drs, FimG, Hns, HnsA, Irk, MsyA, OsmZ, PilG, TopS, TopX, VirR
Gene name(s): hns
Functional conformation(s): H-NS
Coregulator(s): AcrR, AdiY, ArcA, ArgP, ArgR, BasR, CRP, CadC, CaiF, CdaR, CpxR, Cra, CsgD, CspA, CysB, DksA, DksA-ppGpp, DnaA, DpiA, EvgA, FNR, Fis, FlhDC, FliZ, Fur, GadE, GadW, GadX, GalR, GalS, GlaR, GutM, H-NS, HU, HdfR, HypT, IHF, LacI, LeuO, LrhA, Lrp, MarA, MatA, McbR, MlrA, MntR, MqsA, NagC, NanR, NarL, NarP, NhaR, NrdR, NsrR, OmpR, OxyR, PhoB, PhoP, QseB, RcdA, RcsB, Rob, RstA, RutR, SdiA, SlyA, SoxS, SrlR, StpA, SutR, TorR, UvrY, YdeO, YjjQ, ppGpp
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]
TRANSCRIPTION FACTOR: Info
Name:
NrdR Weight Matrix      Tractordb tool
Connectivity class Local Regulator
Synonym(s): NrdR transcriptional repressor, YbaD
Gene name(s): nrdR
Functional conformation(s): NrdR-Zn2+ , NrdR-dATP , NrdR-ATP
Coregulator(s): ArgP, CRP, DnaA, FNR, Fis, Fur, H-NS, IscR, NrdR
Summary: TF Summary ...[more]

REGULATION EXERTED BY ArgP,CRP,DnaA,Fis,H-NS,NrdR Info M3D | Colombos
KNOWN BINDING SITES (The central relative position is relative to the promoter +1)    
ArgP activator CRP activator DnaA dual Fis activator H-NS repressor NrdR repressor    
Transcription Factor
Regulated
Binding Sites
Evidence
References
Functional conformation
Function
Promoter
Gene(s)
LeftPos
RigthPos
Central Rel-Pos
Sequence
CRP-cAMP activator nrdAp nrdA , nrdB , yfaE 2344608 2344629 -136.5 gaaatcgccgAACAGTTATTTTTAACAAATTTttctcttccc [AIBSCS]
[GEA]
[1]
DnaA-ATP activator nrdAp nrdA , nrdB , yfaE 2344703 2344711 -48.0 ccttcctgagTTATCCACAaagttatgca [BPP]
[HIBSCS]
[SM]
[2]
[3]
DnaA-ATP activator nrdAp nrdA , nrdB , yfaE 2344714 2344722 -36.5 tatccacaaaGTTATGCACttgcaagagg [BPP]
[HIBSCS]
[SM]
[2]
[3]
Fis activator nrdAp nrdA , nrdB , yfaE 2344425 2344439 -323.0 aacaataaccGAATAGAAAACAACCatttcgccat [BPP]
[HIBSCS]
[2]
[4]
Fis activator nrdAp nrdA , nrdB , yfaE 2344479 2344493 -269.0 cttatatattGACCACAACTGATACatcagattat [BPP]
[HIBSCS]
[2]
[4]
Fis activator nrdAp nrdA , nrdB , yfaE 2344549 2344563 -199.0 ttagcaaaaaGATTAATAAGCCATCtatatcaatt [BPP]
[HIBSCS]
[2]
[4]
Fis activator nrdAp nrdA , nrdB , yfaE 2344620 2344634 -128.0 cagttattttTAACAAATTTTTCTCttcccattga [HIBSCS] [4]
Fis activator nrdAp nrdA , nrdB , yfaE 2344592 2344606 -156.0 ctattatgccGTTCAAGAAATCGCCgaacagttat [BPP]
[GEA]
[HIBSCS]
[SM]
[2]
ArgP activator nrdAp nrdA , nrdB , yfaE 2344527 2344546 -218.5 cttagatcaaTTTTTGCAATCATTAGCAAAaagattaata [BPP]
[GEA]
[IC]
[3]
[5]
ArgP activator nrdAp nrdA , nrdB , yfaE 2344555 2344574 -190.5 aaaagattaaTAAGCCATCTATATCAATTTatctaaccta [BPP]
[GEA]
[IC]
[3]
[5]
ArgP activator nrdAp nrdA , nrdB , yfaE 2344582 2344601 -163.5 tttatctaacCTATTATGCCGTTCAAGAAAtcgccgaaca [BPP]
[GEA]
[IC]
[3]
[5]
NrdR-Zn2+ repressor nrdAp nrdA , nrdB , yfaE 2344740 2344755 -7.5 agggtcatttTCACACTATCTTGCAGtgaatcccaa [BPP]
[GEA]
[HIBSCS]
[SM]
[6]
NrdR-Zn2+ repressor nrdAp nrdA , nrdB , yfaE 2344772 2344787 25.5 ccaaacatacCCCCTATATATAGTGTtctaagcagc [BPP]
[GEA]
[HIBSCS]
[SM]
[6]
DnaA-ATP repressor nrdAp nrdA , nrdB , yfaE 2344737 2344745 -14.0 aagagggtcaTTTTCACACtatcttgcag [HIBSCS] [7]
ArgP activator nrdAp nrdA , nrdB , yfaE 2344501 2344520 -244.5 tacatcagatTATGTGATGACTCGTGCTTAgatcaatttt [BPP]
[GEA]
[IC]
[3]
[5]
ArgP activator nrdAp nrdA , nrdB , yfaE 2344464 2344483 -281.5 aatctcttacATTCGCTTATATATTGACCAcaactgatac [BPP]
[GEA]
[IC]
[3]
[5]
ArgP activator nrdAp nrdA , nrdB , yfaE 2344411 2344430 -334.5 atggcttagcATTTAACAATAACCGAATAGaaaacaacca [BPP]
[GEA]
[IC]
[5]
[8]
H-NS repressor nrdAp nrdA , nrdB , yfaE 2344309 2344323 -439.0 gtgcgtcataATTCAAGTTAATAACcttcagggat [BPP]
[GEA]
[SM]
[9]
H-NS repressor nrdAp nrdA , nrdB , yfaE 2344333 2344347 -415.0 ccttcagggaTATCAGTTATATTTAaactaaatta [BPP]
[GEA]
[HIBSCS]
[SM]
[9]

Evidence: [AIBSCS] Automated inference based on similarity to consensus sequences
[GEA] Gene expression analysis
[BPP] Binding of purified proteins
[HIBSCS] Human inference based on similarity to consensus sequences
[SM] Site mutation
[IC] Inferred by curator
Reference(s): [1] Zheng D., et al., 2004
[2] Augustin LB., et al., 1994
[3] Han JS., et al., 1998
[4] Hengen PN., et al., 1997
[5] Marbaniang CN., et al., 2011
[6] Torrents E., et al., 2007
[7] Olliver A., et al., 2010
[8] Ohtsubo T., et al., 1998
[9] Cendra Mdel M., et al., 2013



Reference(s)    

 [1] Zheng D., Constantinidou C., Hobman JL., Minchin SD., 2004, Identification of the CRP regulon using in vitro and in vivo transcriptional profiling., Nucleic Acids Res 32(19):5874-93

 [2] Augustin LB., Jacobson BA., Fuchs JA., 1994, Escherichia coli Fis and DnaA proteins bind specifically to the nrd promoter region and affect expression of an nrd-lac fusion., J Bacteriol 176(2):378-87

 [3] Han JS., Kwon HS., Yim JB., Hwang DS., 1998, Effect of IciA protein on the expression of the nrd gene encoding ribonucleoside diphosphate reductase in E. coli., Mol Gen Genet 259(6):610-4

 [4] Hengen PN., Bartram SL., Stewart LE., Schneider TD., 1997, Information analysis of Fis binding sites., Nucleic Acids Res 25(24):4994-5002

 [5] Marbaniang CN., Gowrishankar J., 2011, Role of ArgP (IciA) in Lysine-Mediated Repression in Escherichia coli., J Bacteriol 193(21):5985-96

 [6] Torrents E., Grinberg I., Gorovitz-Harris B., Lundstrom H., Borovok I., Aharonowitz Y., Sjoberg BM., Cohen G., 2007, NrdR controls differential expression of the Escherichia coli ribonucleotide reductase genes., J Bacteriol 189(14):5012-21

 [7] Olliver A., Saggioro C., Herrick J., Sclavi B., 2010, DnaA-ATP acts as a molecular switch to control levels of ribonucleotide reductase expression in Escherichia coli., Mol Microbiol 76(6):1555-71

 [8] Ohtsubo T., Matsuda O., Iba K., Terashima I., Sekiguchi M., Nakabeppu Y., 1998, Molecular cloning of AtMMH, an Arabidopsis thaliana ortholog of the Escherichia coli mutM gene, and analysis of functional domains of its product., Mol Gen Genet 259(6):577-90

 [9] Cendra Mdel M., Juarez A., Madrid C., Torrents E., 2013, H-NS is a novel transcriptional modulator of the ribonucleotide reductase genes in Escherichia coli., J Bacteriol 195(18):4255-63


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