RegulonDB RegulonDB 10.6.3: Regulon Form
   
   


CRP,H-NS,LacI regulon in Escherichia coli K-12 genome


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:
LacI      Tractordb tool
Connectivity class Local Regulator
Sensing Class Using internal synthesized signals
Synonym(s): DNA-binding transcriptional repressor LacI, transcriptional repressor of the lac operon
Gene name(s): lacI
Functional conformation(s): LacI , LacI-allolactose
Coregulator(s): CRP, H-NS, LacI
Summary: TF Summary ...[more]

REGULATION EXERTED BY CRP,H-NS,LacI Info M3D | Colombos
KNOWN BINDING SITES (The central relative position is relative to the promoter +1)    
CRP activator H-NS repressor LacI repressor    
Transcription Factor
Regulated
Binding Sites
Evidence
References
Functional conformation
Function
Promoter
Gene(s)
LeftPos
RigthPos
Central Rel-Pos
Sequence
CRP-cAMP activator lacZp1 lacA , lacY , lacZ 366394 366415 -61.5 gcaacgcaatTAATGTGAGTTAGCTCACTCATtaggcacccc [BPP]
[GEA]
[HIBSCS]
[SM]
[1]
[2]
[3]
[4]
[5]
[6]
[7]
[8]
[9]
H-NS repressor lacZp1 lacA , lacY , lacZ 366403 366417 -67.0 gcgcaacgcaATTAATGTGAGTTAGctcactcatt [BPP] [10]
[11]
H-NS repressor lacZp1 lacA , lacY , lacZ 366390 366404 -54.0 aatgtgagttAGCTCACTCATTAGGcaccccaggc [BPP] [10]
[11]
H-NS repressor lacZp1 lacA , lacY , lacZ 366367 366381 -31.0 ggcaccccagGCTTTACACTTTATGcttccggctc [BPP] [10]
[11]
H-NS repressor lacZp1 lacA , lacY , lacZ 366341 366355 -5.0 ttccggctcgTATGTTGTGTGGAATtgtgagcgga [BPP] [10]
[11]
H-NS repressor lacZp1 lacA , lacY , lacZ 366331 366345 6.0 tatgttgtgtGGAATTGTGAGCGGAtaacaatttc [BPP] [10]
[11]
H-NS repressor lacZp1 lacA , lacY , lacZ 366313 366327 24.0 gagcggataaCAATTTCACACAGGAaacagctatg [BPP] [10]
[11]
LacI repressor lacZp1 lacA , lacY , lacZ 365922 365942 412.0 gaatccgacgGGTTGTTACTCGCTCACATTTaatgttgatg [GS]
[HIBSCS]
[SM]
[12]
[13]
[14]
[15]
LacI repressor lacZp1 lacA , lacY , lacZ 366415 366435 -82.0 ctggaaagcgGGCAGTGAGCGCAACGCAATTaatgtgagtt [GS]
[HIBSCS]
[SM]
[12]
[16]
[14]
[15]
LacI repressor lacZp1 lacA , lacY , lacZ 366323 366343 11.0 tgttgtgtggAATTGTGAGCGGATAACAATTtcacacagga [BPP]
[GEA]
[GS]
[HIBSCS]
[SM]
[1]
[12]
[17]
[13]
[14]
[18]
[15]
CRP-cAMP activator lacZp1 lacA , lacY , lacZ 366322 366343 11.5 tgttgtgtggAATTGTGAGCGGATAACAATTTcacacaggaa [BPP]
[HIBSCS]
[19]
[20]
[21]

Evidence: [BPP] Binding of purified proteins
[GEA] Gene expression analysis
[HIBSCS] Human inference based on similarity to consensus sequences
[SM] Site mutation
[GS] genomic SELEX
Reference(s): [1] Belliveau NM., et al., 2018
[2] Czarniecki D., et al., 1997
[3] Liu M., et al., 2004
[4] Liu M., et al., 2003
[5] Meiklejohn AL., et al., 1985
[6] Merkel TJ., et al., 1992
[7] Noel RJ., et al., 1998
[8] Tutar Y., et al., 2006
[9] Xiong XF., et al., 1991
[10] Rimsky S., et al., 1990
[11] Spassky A., et al., 1984
[12] Flashner Y., et al., 1988
[13] Lewis M. 2005
[14] Oehler S., et al., 1990
[15] Shimada T., et al., 2018
[16] Jimenez CR., et al., 2005
[17] Hoare AM., et al., 1978
[18] Rastinejad F., et al., 1993
[19] Hudson JM., et al., 1991
[20] Hudson JM., et al., 1990
[21] Schmitz A. 1981



Reference(s)    

 [1] Belliveau NM., Barnes SL., Ireland WT., Jones DL., Sweredoski MJ., Moradian A., Hess S., Kinney JB., Phillips R., 2018, Systematic approach for dissecting the molecular mechanisms of transcriptional regulation in bacteria., Proc Natl Acad Sci U S A 115(21):E4796-E4805

 [2] Czarniecki D., Noel RJ., Reznikoff WS., 1997, The -45 region of the Escherichia coli lac promoter: CAP-dependent and CAP-independent transcription., J Bacteriol 179(2):423-9

 [3] Liu M., Garges S., Adhya S., 2004, lacP1 promoter with an extended -10 motif. Pleiotropic effects of cyclic AMP protein at different steps of transcription initiation., J Biol Chem 279(52):54552-7

 [4] Liu M., Gupte G., Roy S., Bandwar RP., Patel SS., Garges S., 2003, Kinetics of transcription initiation at lacP1. Multiple roles of cyclic AMP receptor protein., J Biol Chem 278(41):39755-61

 [5] Meiklejohn AL., Gralla JD., 1985, Entry of RNA polymerase at the lac promoter., Cell 43(3 Pt 2):769-76

 [6] Merkel TJ., Nelson DM., Brauer CL., Kadner RJ., 1992, Promoter elements required for positive control of transcription of the Escherichia coli uhpT gene., J Bacteriol 174(9):2763-70

 [7] Noel RJ., Reznikoff WS., 1998, CAP, the -45 region, and RNA polymerase: three partners in transcription initiation at lacP1 in Escherichia coli., J Mol Biol 282(3):495-504

 [8] Tutar Y., Harman JG., 2006, Effect of salt bridge on transcription activation of CRP-dependent lactose operon in Escherichia coli., Arch Biochem Biophys 453(2):217-23

 [9] Xiong XF., de la Cruz N., Reznikoff WS., 1991, Downstream deletion analysis of the lac promoter., J Bacteriol 173(15):4570-7

 [10] Rimsky S., Spassky A., 1990, Sequence determinants for H1 binding on Escherichia coli lac and gal promoters., Biochemistry 29(15):3765-71

 [11] Spassky A., Rimsky S., Garreau H., Buc H., 1984, H1a, an E. coli DNA-binding protein which accumulates in stationary phase, strongly compacts DNA in vitro., Nucleic Acids Res 12(13):5321-40

 [12] Flashner Y., Gralla JD., 1988, Dual mechanism of repression at a distance in the lac operon., Proc Natl Acad Sci U S A 85(23):8968-72

 [13] Lewis M., 2005, The lac repressor., C R Biol 328(6):521-48

 [14] Oehler S., Eismann ER., Kramer H., Muller-Hill B., 1990, The three operators of the lac operon cooperate in repression., EMBO J 9(4):973-9

 [15] Shimada T., Ogasawara H., Ishihama A., 2018, Single-target regulators form a minor group of transcription factors in Escherichia coli K-12., Nucleic Acids Res 46(8):3921-3936

 [16] Jimenez CR., Li KW., Smit AB., Janse C., 2005, Auto-inhibitory control of peptidergic molluscan neurons and reproductive senescence., Neurobiol Aging NIL

 [17] Hoare AM., McLeish A., Thompson H., Alexander-Williams J., 1978, Selection of patients for bile diversion surgery: use of bile acid measurement in fasting gastric aspirates., Gut 19(3):163-5

 [18] Rastinejad F., Artz P., Lu P., 1993, Origin of the asymmetrical contact between lac repressor and lac operator DNA., J Mol Biol 233(3):389-99

 [19] Hudson JM., Fried MG., 1991, The binding of cyclic AMP receptor protein to two lactose promoter sites is not cooperative in vitro., J Bacteriol 173(1):59-66

 [20] Hudson JM., Fried MG., 1990, Co-operative interactions between the catabolite gene activator protein and the lac repressor at the lactose promoter., J Mol Biol 214(2):381-96

 [21] Schmitz A., 1981, Cyclic AMP receptor proteins interacts with lactose operator DNA., Nucleic Acids Res 9(2):277-92


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