RegulonDB RegulonDB 10.8: Regulon Form
   
   


PhoB regulon in Escherichia coli K-12 genome


TRANSCRIPTION FACTOR: Info
Name:
PhoB Weight Matrix      Tractordb tool
Connectivity class Local Regulator
Sensing Class External-Two-component systems
Synonym(s): DNA-binding transcriptional dual regulator PhoB, PhoB response regulator, PhoT
Gene name(s): phoB
Functional conformation(s): PhoB , PhoB-Phosphorylated
Coregulator(s): ArgP, AscG, CRP, CpxR, CusR, EnvY, FNR, Fur, GadE, GadE-RcsB, GadW, GadX, H-NS, HprR, IHF, Nac, NsrR, OmpR, PhoB, PrpR, QseB, RcdA, RstA, RutR
Summary: TF Summary ...[more]

REGULATION EXERTED BY PhoB Info M3D | Colombos
KNOWN BINDING SITES (The central relative position is relative to the promoter +1)    
PhoB activator    
Transcription Factor
Regulated
Binding Sites
Evidence
References
Functional conformation
Function
Promoter
Gene(s)
LeftPos
RigthPos
Central Rel-Pos
Sequence
PhoB-Phosphorylated activator phoAp phoA , psiF 401667 401685 -31.0 ttttcaacagCTGTCATAAAGTTGTCACGgccgagactt [BCE]
[CV(CHIP-SV/GEA/ROMA)]
[CV(CHIP-SV/SM)]
[CV(GEA/ROMA)]
[CV(GEA/ROMA/SM)]
[GEA]
[SM]
[1]
[2]
PhoB-Phosphorylated activator phoBp phoB , phoR 417061 417079 -31.0 tgcgacgagcTTTTCATAAATCTGTCATAaatctgacgc [APIORCISFBSCS]
[BPP]
[CV(CHIP-SV/GEA/ROMA)]
[CV(GEA/ROMA)]
[GEA]
[1]
[2]
[3]
PhoB-Phosphorylated activator ugpBp1 ugpQ , ugpC , ugpE , ugpA , ugpB 3592399 3592417 -30.0 tgtaacaaaaAAGTTATTTTTCTGTAATTcgagcatgtc [APIORCISFBSCS]
[BPP]
[CV(CHIP-SV/GEA/ROMA)]
[CV(GEA/ROMA)]
[GEA]
[4]
[2]
PhoB-Phosphorylated activator phoEp phoE 260261 260281 -113.0 ttttgttgcgCGGGATCAGCAAGCCTAGCGGcagttgttta [BCE]
[CV(CHIP-SV/GEA/ROMA)]
[CV(CHIP-SV/SM)]
[CV(GEA/ROMA)]
[CV(GEA/ROMA/SM)]
[GEA]
[SM]
[2]
[5]
PhoB-Phosphorylated activator phoEp phoE 260237 260255 -88.0 agcggcagttGTTTACGCTTTTATTACAGatttaataaa [BCE]
[CV(CHIP-SV/GEA/ROMA)]
[CV(CHIP-SV/SM)]
[CV(GEA/ROMA)]
[CV(GEA/ROMA/SM)]
[GEA]
[SM]
[2]
[5]
PhoB-Phosphorylated activator phoEp phoE 260181 260199 -32.0 tattattaatCTGTAATATATCTTTAACAatctcaggtt [BCE]
[CV(CHIP-SV/GEA/ROMA)]
[CV(CHIP-SV/SM)]
[CV(GEA/ROMA)]
[CV(GEA/ROMA/SM)]
[GEA]
[SM]
[2]
[5]
PhoB-Phosphorylated activator phoHp1 phoH 1084825 1084843 -31.0 tttttcatcaCTGTCATCACTCTGTCATCtttccagtag [APIORCISFBSCS]
[BPP]
[CV(CHIP-SV/GEA/ROMA)]
[CV(GEA/ROMA)]
[GEA]
[6]
[2]
PhoB-Phosphorylated activator amnp1 amn 2054989 2055007 -33.0 cgatcttcgcCTTACACTTTTGTTTCACAtttctgtgac [AIBSCS]
[CV(GEA/ROMA)]
[GEA]
[7]
PhoB-Phosphorylated activator ugpBp1 ugpQ , ugpC , ugpE , ugpA , ugpB 3592421 3592439 -52.0 tgacaccttaCTATCTTACAAATGTAACAaaaaagttat [APIORCISFBSCS]
[BPP]
[CV(CHIP-SV/GEA/ROMA)]
[CV(GEA/ROMA)]
[GEA]
[4]
[2]
PhoB-Phosphorylated activator mipAp mipA 1866643 1866663 -146.5 catccataaaTTTTGCATAATTAATGTAAAGaccaggctcg [APIORCISFBSCS]
[BPP]
[CV(CHIP-SV/GEA/ROMA)]
[CV(GEA/ROMA)]
[GEA]
[3]
PhoB-Phosphorylated activator ydfHp ydfH 1628297 1628315 -20.0 gggttattgcTTGTCACAAAAAAGTGGTAgactcatgca [APIORCISFBSCS]
[BPP]
[CV(CHIP-SV/GEA/ROMA)]
[CV(GEA/ROMA)]
[GEA]
[3]
PhoB-Phosphorylated activator yhjCp yhjC         [APIORCISFBSCS]
[BPP]
[CV(CHIP-SV/GEA/ROMA)]
[CV(GEA/ROMA)]
[GEA]
[3]
PhoB-Phosphorylated activator ytfKp ytfK 4439466 4439484 -36.0 ggtaaaaaaaGTTATACGCGGTGGAAACAttgcccggat [APIORCISFBSCS]
[CV(GEA/ROMA)]
[GEA]
[7]
[8]
PhoB-Phosphorylated activator phnCp phnP , phnO , phnN , phnM , phnL , phnK , phnJ , phnI , phnH , phnG , phnF , phnE , phnD , phnC         [APIORCISFBSCS]
[BPP]
[CV(CHIP-SV/GEA/ROMA)]
[CV(GEA/ROMA)]
[GEA]
[9]
[2]
[10]
PhoB-Phosphorylated activator phoQp5 phoQ         [GEA] [2]
PhoB-Phosphorylated activator ytfKp ytfK 4439444 4439462 -58.0 ttctgaataaTTGTAACCTTTAGGTAAAAaaagttatac [APIORCISFBSCS]
[CV(GEA/ROMA)]
[GEA]
[7]
[8]
PhoB-Phosphorylated activator tktBp tktB         [GEA] [2]
PhoB-Phosphorylated activator yegHp yegH         [APIORCISFBSCS]
[BPP]
[CV(CHIP-SV/GEA/ROMA)]
[CV(GEA/ROMA)]
[GEA]
[3]
PhoB-Phosphorylated activator phoUp phoU         [GEA] [2]
PhoB repressor    
Transcription Factor
Regulated
Binding Sites
Evidence
References
Functional conformation
Function
Promoter
Gene(s)
LeftPos
RigthPos
Central Rel-Pos
Sequence
PhoB-Phosphorylated repressor edap3 eda 1932827 1932848 -53.0 ttattcagcgCCTTGCGTGAAAAACTGTCCGGtgccgaacag [APIORCISFBSCS]
[BPP]
[CV(CHIP-SV/GEA/ROMA)]
[CV(GEA/ROMA)]
[GEA]
[11]
PhoB-Phosphorylated repressor sbcDp sbcC , sbcD 417061 417079 -93.0 gcgtcagattTATGACAGATTTATGAAAAgctcgtcgca [APIORCISFBSCS]
[BPP]
[CV(CHIP-SV/GEA/ROMA)]
[CV(GEA/ROMA)]
[GEA]
[1]
[2]
[3]
PhoB-Phosphorylated repressor fruRp8 cra         [GEA] [2]
PhoB-Phosphorylated repressor pitBp pitB         [IMP] [12]

Evidence: [BCE] Binding of cellular extracts
[CV(CHIP-SV/GEA/ROMA)] cross validation(CHIP-SV/GEA/ROMA)
[CV(CHIP-SV/SM)] cross validation(CHIP-SV/SM)
[CV(GEA/ROMA)] cross validation(GEA/ROMA)
[CV(GEA/ROMA/SM)] cross validation(GEA/ROMA/SM)
[GEA] Gene expression analysis
[SM] Site mutation
[APIORCISFBSCS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.
[BPP] Binding of purified proteins
[AIBSCS] Automated inference based on similarity to consensus sequences
[IMP] Inferred from mutant phenotype
Reference(s): [1] Makino K., et al., 1986
[2] Marzan LW., et al., 2013
[3] Yang C., et al., 2012
[4] Kasahara M., et al., 1991
[5] Tommassen J., et al., 1987
[6] Kim SK., et al., 1993
[7] Baek JH., et al., 2006
[8] Yoshida Y., et al., 2011
[9] Makino K., et al., 1991
[10] Wanner BL., et al., 1990
[11] Murray EL., et al., 2005
[12] Harris RM., et al., 2001



Reference(s)    

 [1] Makino K., Shinagawa H., Amemura M., Nakata A., 1986, Nucleotide sequence of the phoB gene, the positive regulatory gene for the phosphate regulon of Escherichia coli K-12., J Mol Biol 190(1):37-44

 [2] Marzan LW., Hasan CM., Shimizu K., 2013, Effect of acidic condition on the metabolic regulation of Escherichia coli and its phoB mutant., Arch Microbiol 195(3):161-71

 [3] Yang C., Huang TW., Wen SY., Chang CY., Tsai SF., Wu WF., Chang CH., 2012, Genome-wide PhoB binding and gene expression profiles reveal the hierarchical gene regulatory network of phosphate starvation in Escherichia coli., PLoS One 7(10):e47314

 [4] Kasahara M., Makino K., Amemura M., Nakata A., Shinagawa H., 1991, Dual regulation of the ugp operon by phosphate and carbon starvation at two interspaced promoters., J Bacteriol 173(2):549-58

 [5] Tommassen J., Koster M., Overduin P., 1987, Molecular analysis of the promoter region of the Escherichia coli K-12 phoE gene. Identification of an element, upstream from the promoter, required for efficient expression of phoE protein., J Mol Biol 198(4):633-41

 [6] Kim SK., Makino K., Amemura M., Shinagawa H., Nakata A., 1993, Molecular analysis of the phoH gene, belonging to the phosphate regulon in Escherichia coli., J Bacteriol 175(5):1316-24

 [7] Baek JH., Lee SY., 2006, Novel gene members in the Pho regulon of Escherichia coli., FEMS Microbiol Lett 264(1):104-9

 [8] Yoshida Y., Sugiyama S., Oyamada T., Yokoyama K., Kim SK., Makino K., 2011, Identification of PhoB binding sites of the yibD and ytfK promoter regions in Escherichia coli., J Microbiol 49(2):285-9

 [9] Makino K., Kim SK., Shinagawa H., Amemura M., Nakata A., 1991, Molecular analysis of the cryptic and functional phn operons for phosphonate use in Escherichia coli K-12., J Bacteriol 173(8):2665-72

 [10] Wanner BL., Boline JA., 1990, Mapping and molecular cloning of the phn (psiD) locus for phosphonate utilization in Escherichia coli., J Bacteriol 172(3):1186-96

 [11] Murray EL., Conway T., 2005, Multiple regulators control expression of the Entner-Doudoroff aldolase (Eda) of Escherichia coli., J Bacteriol 187(3):991-1000

 [12] Harris RM., Webb DC., Howitt SM., Cox GB., 2001, Characterization of PitA and PitB from Escherichia coli., J Bacteriol 183(17):5008-14


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