RegulonDB RegulonDB 10.6.3: Regulon Form
   
   


DksA,DksA-ppGpp,Fis,H-NS,Lrp,ppGpp 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:
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]

REGULATION EXERTED BY DksA,DksA-ppGpp,Fis,H-NS,Lrp,ppGpp Info M3D | Colombos
KNOWN BINDING SITES (The central relative position is relative to the promoter +1)    
DksA inhibition DksA-ppGpp inhibition Fis activator H-NS repressor Lrp repressor ppGpp inhibition    
Transcription Factor
Regulated
Binding Sites
Evidence
References
Functional conformation
Function
Promoter
Gene(s)
LeftPos
RigthPos
Central Rel-Pos
Sequence
H-NS repressor rrsBp1 rrsB , gltT , rrlB , rrfB 4166334 4166348 -26.0 tttcctcttgTCAGGCCGGAATAACtccctataat [BPP] [1]
H-NS repressor rrsBp1 rrsB , gltT , rrlB , rrfB 4166310 4166324 -50.0 gcgcggtcagAAAATTATTTTAAATttcctcttgt [BPP] [1]
H-NS repressor rrsBp1 rrsB , gltT , rrlB , rrfB 4166277 4166291 -83.0 actggcagttTTAGGCTGATTTGGTtgaatgttgc [BPP] [1]
Fis activator rrsBp1 rrsB , gltT , rrlB , rrfB 4166217 4166231 -143.0 gccaggagctGAACAATTATTGCCCgttttacagc [BPP]
[GEA]
[2]
[3]
[4]
[5]
[6]
[7]
[8]
Fis activator rrsBp1 rrsB , gltT , rrlB , rrfB 4166258 4166272 -102.0 gcttcgaaacGCTCGAAAAACTGGCagttttaggc [BPP]
[GEA]
[2]
[3]
[4]
[5]
[6]
[7]
[8]
Fis activator rrsBp1 rrsB , gltT , rrlB , rrfB 4166289 4166303 -71.0 aggctgatttGGTTGAATGTTGCGCggtcagaaaa [BPP]
[GEA]
[2]
[3]
[4]
[5]
[6]
[7]
[8]
Fis activator rrsCp1 rrsC , gltU , rrlC , rrfC 3941388 3941402 -121.0 tgtgattacgGTTGCAAAAACGGCAaattgcttgt [BPP]
[GEA]
[5]
Fis activator rrsCp1 rrsC , gltU , rrlC , rrfC 3941408 3941422 -101.0 cggcaaattgCTTGTTTTATGGCACattaacgggg [BPP]
[GEA]
[5]
Fis activator rrsCp1 rrsC , gltU , rrlC , rrfC 3941439 3941453 -70.0 ggggcttttgCTGAAAAAATGCGCGgtcagaaaat [BPP]
[GEA]
[5]
Fis activator rrsGp1 rrfG , rrlG , gltW , rrsG 2731553 2731567 -112.0 gctcgtttttGTCTATAAGTTAGACggaaaagact [BPP]
[GEA]
[5]
Fis activator rrsGp1 rrfG , rrlG , gltW , rrsG 2731532 2731546 -91.0 agacggaaaaGACTATATTTAAGATgttttgcctg [BPP]
[GEA]
[5]
Fis activator rrsGp1 rrfG , rrlG , gltW , rrsG 2731512 2731526 -71.0 aagatgttttGCCTGAAAAGTGAGCgaacgataaa [BPP]
[GEA]
[5]
Fis activator rrsHp1 rrsH , ileV , alaV , rrlH , rrfH 223297 223311 -181.0 aagtgctggtGCGTACGGGTAAACCtattacgcct [BPP]
[GEA]
[5]
Fis activator rrsHp1 rrsH , ileV , alaV , rrlH , rrfH 223344 223358 -134.0 gcggcggattGGGTGTTAAATAGCCtggcagacct [BPP]
[GEA]
[5]
Fis activator rrsHp1 rrsH , ileV , alaV , rrlH , rrfH 223387 223401 -91.0 cgataaaaaaGCAGCAAAAACCGGCacaatgatta [BPP]
[GEA]
[5]
Fis activator rrsHp1 rrsH , ileV , alaV , rrlH , rrfH 223407 223421 -71.0 ccggcacaatGATTAAAAGATGAGCggttgaaata [BPP]
[GEA]
[5]
Fis activator rrsDp1 rrfF , thrV , rrfD , rrlD , alaU , ileU , rrsD 3429214 3429228 -174.0 catacttaccTCAGCAATAAATGATttactaatga [BPP]
[GEA]
[5]
Fis activator rrsDp1 rrfF , thrV , rrfD , rrlD , alaU , ileU , rrsD 3429184 3429198 -144.0 aatgactttgGGGGCATTATTGGCCttgtgcaagt [GEA] [5]
Fis activator rrsDp1 rrfF , thrV , rrfD , rrlD , alaU , ileU , rrsD 3429166 3429180 -126.0 attggccttgTGCAAGTCTTTTAGTatgcaaaaaa [BPP]
[GEA]
[5]
Fis activator rrsDp1 rrfF , thrV , rrfD , rrlD , alaU , ileU , rrsD 3429131 3429145 -91.0 gcaccgttttGTGTGCGATTGCAGCaaaaagggtg [BPP]
[GEA]
[5]
Fis activator rrsDp1 rrfF , thrV , rrfD , rrlD , alaU , ileU , rrsD 3429111 3429125 -71.0 gcagcaaaaaGGGTGAAAAAACAACaaacagaaaa [BPP]
[GEA]
[5]
Lrp-leucine repressor rrsBp1 rrsB , gltT , rrlB , rrfB 4166435 4166446 75.0 cggcagagaaAGCAAAAATAAAtgcttgactc [BPP]
[IEP]
[9]
Lrp-leucine repressor rrsBp1 rrsB , gltT , rrlB , rrfB 4166629 4166640 269.0 aattcattacGAAGTTTAATTCtttgagcgtc [BPP]
[IEP]
[9]
Lrp-leucine repressor rrsBp1 rrsB , gltT , rrlB , rrfB 4166308 4166319 -53.0 ttgcgcggtcAGAAAATTATTTtaaatttcct [BPP]
[GEA]
[9]
H-NS repressor rrsCp1 rrsC , gltU , rrlC , rrfC         [GEA] [2]
[10]
Lrp-leucine repressor rrsDp1 rrfF , thrV , rrfD , rrlD , alaU , ileU , rrsD         [GEA] [9]
H-NS repressor rrsGp1 rrfG , rrlG , gltW , rrsG         [GEA]
[TAS]
[2]
[10]
H-NS repressor rrsDp1 rrfF , thrV , rrfD , rrlD , alaU , ileU , rrsD         [GEA] [2]
[10]
Lrp-leucine repressor rrsGp1 rrfG , rrlG , gltW , rrsG         [GEA] [9]
Lrp-leucine repressor rrsHp1 rrsH , ileV , alaV , rrlH , rrfH         [GEA] [9]
H-NS repressor rrsHp1 rrsH , ileV , alaV , rrlH , rrfH         [GEA] [2]
[10]
Lrp-leucine repressor rrsCp1 rrsC , gltU , rrlC , rrfC         [BPP]
[IDA]
[9]

Evidence: [BPP] Binding of purified proteins
[GEA] Gene expression analysis
[IEP] Inferred from expression pattern
[TAS] Traceable author statement
[IDA] Inferred from direct assay
Reference(s): [1] Tippner D., et al., 1994
[2] Afflerbach H., et al., 1998
[3] Appleman JA., et al., 1998
[4] Bartlett MS., et al., 2000
[5] Hirvonen CA., et al., 2001
[6] Liebig B., et al., 1995
[7] Ross W., et al., 1990
[8] Zhang X., et al., 1996
[9] Pul U., et al., 2005
[10] Gralla JD. 2005



Reference(s)    

 [1] Tippner D., Afflerbach H., Bradaczek C., Wagner R., 1994, Evidence for a regulatory function of the histone-like Escherichia coli protein H-NS in ribosomal RNA synthesis., Mol Microbiol 11(3):589-604

 [2] Afflerbach H., Schroder O., Wagner R., 1998, Effects of the Escherichia coli DNA-binding protein H-NS on rRNA synthesis in vivo., Mol Microbiol 28(3):641-53

 [3] Appleman JA., Ross W., Salomon J., Gourse RL., 1998, Activation of Escherichia coli rRNA transcription by FIS during a growth cycle., J Bacteriol 180(6):1525-32

 [4] Bartlett MS., Gaal T., Ross W., Gourse RL., 2000, Regulation of rRNA transcription is remarkably robust: FIS compensates for altered nucleoside triphosphate sensing by mutant RNA polymerases at Escherichia coli rrn P1 promoters., J Bacteriol 182(7):1969-77

 [5] Hirvonen CA., Ross W., Wozniak CE., Marasco E., Anthony JR., Aiyar SE., Newburn VH., Gourse RL., 2001, Contributions of UP elements and the transcription factor FIS to expression from the seven rrn P1 promoters in Escherichia coli., J Bacteriol 183(21):6305-14

 [6] Liebig B., Wagner R., 1995, Effects of different growth conditions on the in vivo activity of the tandem Escherichia coli ribosomal RNA promoters P1 and P2., Mol Gen Genet 249(3):328-35

 [7] Ross W., Thompson JF., Newlands JT., Gourse RL., 1990, E.coli Fis protein activates ribosomal RNA transcription in vitro and in vivo., EMBO J 9(11):3733-42

 [8] Zhang X., Bremer H., 1996, Effects of Fis on ribosome synthesis and activity and on rRNA promoter activities in Escherichia coli., J Mol Biol 259(1):27-40

 [9] Pul U., Wurm R., Lux B., Meltzer M., Menzel A., Wagner R., 2005, LRP and H-NS--cooperative partners for transcription regulation at Escherichia coli rRNA promoters., Mol Microbiol 58(3):864-76

 [10] Gralla JD., 2005, Escherichia coli ribosomal RNA transcription: regulatory roles for ppGpp, NTPs, architectural proteins and a polymerase-binding protein., Mol Microbiol 55(4):973-7


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