RegulonDB RegulonDB 10.6.3: Regulon Form
   
   


CRP,GalR,GalS,H-NS,HU 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:
GalS Weight Matrix      Tractordb tool
Connectivity class Local Regulator
Sensing Class Sensing external and internal signals
Synonym(s): DNA-binding transcriptional dual regulator GalS, MglD
Gene name(s): galS
Functional conformation(s): GalS-D-galactose , GalS
Coregulator(s): CRP, FlhDC, GalR, GalS, H-NS, HU, NagC
Summary: TF Summary ...[more]
TRANSCRIPTION FACTOR: Info
Name:
GalR Weight Matrix      Tractordb tool
Connectivity class Local Regulator
Sensing Class Sensing external and internal signals
Synonym(s): DNA-binding transcriptional dual regulator GalR
Gene name(s): galR
Functional conformation(s): GalR , GalR-D-galactose
Coregulator(s): CRP, FlhDC, GalR, GalS, H-NS, HU, NagC
Summary: TF Summary ...[more]
TRANSCRIPTION FACTOR: Info
Name:
HU      Tractordb tool
Connectivity class Local Regulator
Sensing Class TFs for DNA-bending
Synonym(s): DNA-binding transcriptional dual regulator HU, HUalpha;beta;
Gene name(s): hupB, hupA
Functional conformation(s): HU
Coregulator(s): AcrR, CRP, GalR, GalS, H-NS, HU, IHF, Lrp, MarA, OmpR, Rob, SoxS, TrpR, TyrR
Summary: TF Summary ...[more]

REGULATION EXERTED BY CRP,GalR,GalS,H-NS,HU Info M3D | Colombos
KNOWN BINDING SITES (The central relative position is relative to the promoter +1)    
CRP activator GalR repressor GalS repressor H-NS repressor HU repressor    
Transcription Factor
Regulated
Binding Sites
Evidence
References
Functional conformation
Function
Promoter
Gene(s)
LeftPos
RigthPos
Central Rel-Pos
Sequence
CRP-cAMP activator galEp1 galM , galK , galT , galE 792112 792133 -41.5 acgattccacTAATTTATTCCATGTCACACTTttcgcatctt [GEA]
[HIBSCS]
[SM]
[1]
[2]
[3]
[4]
[5]
GalS repressor galEp1 galM , galK , galT , galE 792134 792149 -60.5 ctaaattcttGTGTAAACGATTCCACtaatttattc [BPP]
[GEA]
[HIBSCS]
[6]
[5]
[7]
[8]
[9]
H-NS repressor galEp1 galM , galK , galT , galE 792121 792135 -47.0 aaacgattccACTAATTTATTCCATgtcacacttt [BPP] [10]
H-NS repressor galEp1 galM , galK , galT , galE 792110 792124 -36.0 ctaatttattCCATGTCACACTTTTcgcatctttg [BPP] [10]
H-NS repressor galEp1 galM , galK , galT , galE 792092 792106 -18.0 cacttttcgcATCTTTGTTATGCTAtggttatttc [BPP] [10]
H-NS repressor galEp1 galM , galK , galT , galE 792076 792090 -2.0 gttatgctatGGTTATTTCATACCAtaagcctaat [BPP] [10]
HU repressor galEp1 galM , galK , galT , galE 792059 792092 6.5 ttgttatgctATGGTTATTTCATACCATAAGCCTAATGGAGCGAattatgagag [BPP]
[GEA]
[11]
[12]
[13]
[14]
[15]
[16]
[17]
GalR repressor galEp1 galM , galK , galT , galE 792028 792043 46.5 gagagttctgGTTACCGGTGGTAGCGgttacattgg [BPP]
[GEA]
[HIBSCS]
[SM]
[6]
[18]
[13]
[14]
[15]
[2]
[16]
[19]
[5]
[17]
[20]
[7]
[8]
[9]
GalS repressor galEp1 galM , galK , galT , galE 792022 792037 52.5 tctggttaccGGTGGTAGCGGTTACAttggaagtca [BPP]
[GEA]
[HIBSCS]
[6]
[5]
[7]
[8]
[9]
GalR repressor galEp1 galM , galK , galT , galE 792134 792149 -60.5 ctaaattcttGTGTAAACGATTCCACtaatttattc [BPP]
[GEA]
[HIBSCS]
[SM]
[21]
[6]
[18]
[14]
[15]
[2]
[16]
[5]
[17]
[20]
[7]
[8]
[9]

Evidence: [GEA] Gene expression analysis
[HIBSCS] Human inference based on similarity to consensus sequences
[SM] Site mutation
[BPP] Binding of purified proteins
Reference(s): [1] Irani M., et al., 1989
[2] Mandal N., et al., 1990
[3] Merkel TJ., et al., 1992
[4] Rostoks N., et al., 2000
[5] Semsey S., et al., 2007
[6] Geanacopoulos M., et al., 1997
[7] Weickert MJ., et al., 1992
[8] Weickert MJ., et al., 1993
[9] Weickert MJ., et al., 1993
[10] Rimsky S., et al., 1990
[11] Aki T., et al., 1997
[12] Geanacopoulos M., et al., 2001
[13] Lewis DE., et al., 1999
[14] Lia G., et al., 2003
[15] Lyubchenko YL., et al., 1997
[16] Perez N., et al., 2000
[17] Semsey S., et al., 2004
[18] Kar S., et al., 2001
[19] Semsey S., et al., 2002
[20] Virnik K., et al., 2003
[21] Choy HE., et al., 1997



Reference(s)    

 [1] Irani M., Musso R., Adhya S., 1989, Cyclic-AMP-dependent switch in initiation of transcription from the two promoters of the Escherichia coli gal operon: identification and assay of 5'-triphosphate ends of mRNA by GTP:RNA guanyltransferase., J Bacteriol 171(3):1623-30

 [2] Mandal N., Su W., Haber R., Adhya S., Echols H., 1990, DNA looping in cellular repression of transcription of the galactose operon., Genes Dev 4(3):410-8

 [3] 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

 [4] Rostoks N., Park S., Choy HE., 2000, Reiterative transcription initiation from galP2 promoter of Escherichia coli., Biochim Biophys Acta 1491(1-3):185-95

 [5] Semsey S., Krishna S., Sneppen K., Adhya S., 2007, Signal integration in the galactose network of Escherichia coli., Mol Microbiol 65(2):465-76

 [6] Geanacopoulos M., Adhya S., 1997, Functional characterization of roles of GalR and GalS as regulators of the gal regulon., J Bacteriol 179(1):228-34

 [7] Weickert MJ., Adhya S., 1992, Isorepressor of the gal regulon in Escherichia coli., J Mol Biol 226(1):69-83

 [8] Weickert MJ., Adhya S., 1993, The galactose regulon of Escherichia coli., Mol Microbiol 10(2):245-51

 [9] Weickert MJ., Adhya S., 1993, Control of transcription of gal repressor and isorepressor genes in Escherichia coli., J Bacteriol 175(1):251-8

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

 [11] Aki T., Adhya S., 1997, Repressor induced site-specific binding of HU for transcriptional regulation., EMBO J 16(12):3666-74

 [12] Geanacopoulos M., Vasmatzis G., Zhurkin VB., Adhya S., 2001, Gal repressosome contains an antiparallel DNA loop., Nat Struct Biol 8(5):432-6

 [13] Lewis DE., Geanacopoulos M., Adhya S., 1999, Role of HU and DNA supercoiling in transcription repression: specialized nucleoprotein repression complex at gal promoters in Escherichia coli., Mol Microbiol 31(2):451-61

 [14] Lia G., Bensimon D., Croquette V., Allemand JF., Dunlap D., Lewis DE., Adhya S., Finzi L., 2003, Supercoiling and denaturation in Gal repressor/heat unstable nucleoid protein (HU)-mediated DNA looping., Proc Natl Acad Sci U S A 100(20):11373-7

 [15] Lyubchenko YL., Shlyakhtenko LS., Aki T., Adhya S., 1997, Atomic force microscopic demonstration of DNA looping by GalR and HU., Nucleic Acids Res 25(4):873-6

 [16] Perez N., Rehault M., Amouyal M., 2000, A functional assay in Escherichia coli to detect non-assisted interaction between galactose repressor dimers., Nucleic Acids Res 28(18):3600-4

 [17] Semsey S., Tolstorukov MY., Virnik K., Zhurkin VB., Adhya S., 2004, DNA trajectory in the Gal repressosome., Genes Dev 18(15):1898-907

 [18] Kar S., Adhya S., 2001, Recruitment of HU by piggyback: a special role of GalR in repressosome assembly., Genes Dev 15(17):2273-81

 [19] Semsey S., Geanacopoulos M., Lewis DE., Adhya S., 2002, Operator-bound GalR dimers close DNA loops by direct interaction: tetramerization and inducer binding., EMBO J 21(16):4349-56

 [20] Virnik K., Lyubchenko YL., Karymov MA., Dahlgren P., Tolstorukov MY., Semsey S., Zhurkin VB., Adhya S., 2003, "Antiparallel" DNA loop in gal repressosome visualized by atomic force microscopy., J Mol Biol 334(1):53-63

 [21] Choy HE., Hanger RR., Aki T., Mahoney M., Murakami K., Ishihama A., Adhya S., 1997, Repression and activation of promoter-bound RNA polymerase activity by Gal repressor., J Mol Biol 272(3):293-300


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