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GadE,H-NS,Lrp,NsrR,ppGpp regulon in Escherichia coli K-12 genome


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:
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 , Lrp-leucine
Coregulator(s): AcrR, Ada, AdiY, AidB, ArcA, ArgP, ArgR, CRP, CadC, CpxR, Cra, DksA, DksA-ppGpp, EnvY, FNR, Fis, FliZ, Fur, GadE, GadW, GadX, GcvA, GlaR, H-NS, HU, HdfR, IHF, LrhA, Lrp, MarA, Mlc, ModE, Nac, NarL, NhaR, NsrR, OmpR, PhoP, PurR, RcsB, Rob, SoxS, StpA, TorR, YeiL, YjjQ, 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, GadW, GadX, H-NS, HdfR, HprR, IHF, Lrp, MarA, MatA, Nac, NsrR, OmpR, PdhR, PhoB, PhoP, PurR, RcsB, Rob, RutR, TorR, YdeO, ppGpp
Summary: TF Summary ...[more]
TRANSCRIPTION FACTOR: Info
Name:
NsrR Weight Matrix      Tractordb tool
Connectivity class Local Regulator
Synonym(s): DNA-binding transcriptional repressor NsrR, YjeB
Gene name(s): nsrR
Functional conformation(s): NsrR-nitric oxide , NsrR-[2Fe-2S]2+ oxidized , NsrR
Coregulator(s): ArcA, CRP, CpxR, CsgD, CytR, DksA, DksA-ppGpp, DsdC, FNR, FeaR, FhlA, Fis, FlhDC, Fur, GadE, H-NS, IHF, IscR, Lrp, MatA, MetR, ModE, Nac, NarL, NarP, NorR, NsrR, OxyR, PdhR, PhoB, QseB, SutR, ppGpp
Summary: TF Summary ...[more]

REGULATION EXERTED BY GadE,H-NS,Lrp,NsrR,ppGpp Info M3D | Colombos
KNOWN BINDING SITES (The central relative position is relative to the promoter +1)    
GadE activator H-NS repressor Lrp repressor NsrR repressor ppGpp activation    
Transcription Factor
Regulated
Binding Sites
Evidence
References
Functional conformation
Function
Promoter
Gene(s)
LeftPos
RigthPos
Central Rel-Pos
Sequence
Lrp repressor lrpp lrp 932369 932383 49.0 ataaccatgcATGTAAATACCATGTttaccgtgct [HIBSCS]
[SM]
[1]
[2]
[3]
Lrp repressor lrpp lrp 932265 932279 -56.0 aatatctggcATGTTGTACTAAAAAtcgatgtttt [BCE]
[SM]
[3]
Lrp-leucine repressor lrpp lrp 932328 932343 8.0 aaacattcgaGGAAGAAAAAAAACAGtattcttata [AIBSCS]
[GEA]
[4]
Lrp-leucine repressor lrpp lrp 932351 932368 32.0 cagtattcttATATGCGCATAACCATGCatgtaaatac [AIBSCS]
[GEA]
[4]
NsrR repressor lrpp lrp 932374 932385 52.0 catgcatgtaAATACCATGTTTaccgtgctag [GEA]
[HIBSCS]
[5]
H-NS repressor lrpp lrp         [BPP]
[GEA]
[6]
GadE activator lrpp lrp         [GEA] [7]

Evidence: [HIBSCS] Human inference based on similarity to consensus sequences
[SM] Site mutation
[BCE] Binding of cellular extracts
[AIBSCS] Automated inference based on similarity to consensus sequences
[GEA] Gene expression analysis
[BPP] Binding of purified proteins
Reference(s): [1] Fraenkel YM., et al., 1995
[2] Lin R., et al., 1992
[3] Wang Q., et al., 1994
[4] Lintner RE., et al., 2008
[5] Partridge JD., et al., 2009
[6] Oshima T., et al., 1995
[7] Hommais F., et al., 2004



Reference(s)    

 [1] Fraenkel YM., Mandel Y., Friedberg D., Margalit H., 1995, Identification of common motifs in unaligned DNA sequences: application to Escherichia coli Lrp regulon., Comput Appl Biosci 11(4):379-87

 [2] Lin R., D'Ari R., Newman EB., 1992, Lambda placMu insertions in genes of the leucine regulon: extension of the regulon to genes not regulated by leucine., J Bacteriol 174(6):1948-55

 [3] Wang Q., Wu J., Friedberg D., Plakto J., Calvo JM., 1994, Regulation of the Escherichia coli lrp gene., J Bacteriol 176(7):1831-9

 [4] 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

 [5] Partridge JD., Bodenmiller DM., Humphrys MS., Spiro S., 2009, NsrR targets in the Escherichia coli genome: new insights into DNA sequence requirements for binding and a role for NsrR in the regulation of motility., Mol Microbiol 73(4):680-94

 [6] Oshima T., Ito K., Kabayama H., Nakamura Y., 1995, Regulation of lrp gene expression by H-NS and Lrp proteins in Escherichia coli: dominant negative mutations in lrp., Mol Gen Genet 247(5):521-8

 [7] 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


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