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Fis,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, GadE-RcsB, GadW, GadX, GlcC, GlpR, H-NS, HprR, IHF, IscR, LeuO, Lrp, MalT, MarA, MarR, MazE, MazE-MazF, Mlc, MntR, ModE, NanR, NarL, NarP, NrdR, NsrR, NtrC, OmpR, OxyR, PdhR, PepA, PurR, RcsB, RcsB-BglJ, Rob, RstA, RutR, SlyA, SoxS, StpA, TorR, XylR, YdeO, ppGpp
Summary: TF Summary ...[more]

REGULATION EXERTED BY Fis,ppGpp Info M3D | Colombos
KNOWN BINDING SITES (The central relative position is relative to the promoter +1)    
Fis activator ppGpp inhibition    
Transcription Factor
Regulated
Binding Sites
Evidence
References
Functional conformation
Function
Promoter
Gene(s)
LeftPos
RigthPos
Central Rel-Pos
Sequence
Fis activator metTp glnX , glnV , metU , glnW , glnU , leuW , metT 697223 697237 -67.0 cctaaccaaaCAGTCACTTTCGAGCaattttcctt [IHBCE]  
Fis activator tyrTp tpr , tyrV , tyrT 1287787 1287801 -129.0 gtttacggtaATCGAACGATTATTCtttaatcgcc [AIBSCS]
[BPP]
[CV(CHIP-SV/GEA/ROMA)]
[CV(GEA/ROMA)]
[GEA]
[1]
[2]
[3]
[4]
[5]
[6]
[7]
Fis activator tyrTp tpr , tyrV , tyrT 1287756 1287770 -98.0 cgccagcaaaAATAACTGGTTACCTttaatccgtt [AIBSCS]
[BPP]
[CV(CHIP-SV/GEA/ROMA)]
[CV(GEA/ROMA)]
[GEA]
[1]
[2]
[3]
[4]
[5]
[6]
[7]
Fis activator tyrTp tpr , tyrV , tyrT 1287736 1287750 -78.0 tacctttaatCCGTTACGGATGAAAattacgcaac [AIBSCS]
[BCE]
[BPP]
[CV(CHIP-SV/GEA/ROMA)]
[CV(GEA/ROMA)]
[GEA]
[1]
[2]
[3]
[4]
[5]
[6]
[7]
Fis activator thrUp thrU , tyrU , glyT , thrT , tufB 4175251 4175265 -123.0 gcacaatgatGTTGAAAAAGTGTGCtaatctgccc [APIORCISFBSCS]
[BPP]
[CV(CHIP-SV/GEA/ROMA)]
[CV(GEA/ROMA)]
[GEA]
[8]
[9]
[10]
[11]
Fis activator thrUp thrU , tyrU , glyT , thrT , tufB 4175283 4175297 -91.0 ccctccgttcGGCTGTTTCTTCATCgtgtcgcata [APIORCISFBSCS]
[BPP]
[CV(CHIP-SV/GEA/ROMA)]
[CV(GEA/ROMA)]
[GEA]
[8]
[9]
[10]
[11]
Fis activator thrUp thrU , tyrU , glyT , thrT , tufB 4175303 4175317 -71.0 tcatcgtgtcGCATAAAATGTGACCaataaaacaa [APIORCISFBSCS]
[BPP]
[CV(CHIP-SV/GEA/ROMA)]
[CV(GEA/ROMA)]
[GEA]
[IHBCE]
[12]
[8]
[9]
[10]
[11]
Fis activator leuXp leuX 4496304 4496318 -75.0 ctgtatgcaaTGCTGAAAATTTCAGcacttagcga [BCE]  
Fis activator queAp queA 424920 424934 -58.0 aaaattcatcGATTATATTCTATCCaaaagggggt [BPP]
[GEA]
[13]
Fis repressor ppGpp inhibition    
Transcription Factor
Regulated
Binding Sites
Evidence
References
Functional conformation
Function
Promoter
Gene(s)
LeftPos
RigthPos
Central Rel-Pos
Sequence
Fis repressor crpp2 crp 3485854 3485868 -170.0 tcctgacagaGTACGCGTACTAACCaaatcgcgca [APIORCISFBSCS]
[BPP]
[CV(CHIP-SV/GEA/ROMA)]
[CV(GEA/ROMA)]
[GEA]
[14]
Fis repressor crpp2 crp 3485975 3485989 -49.0 atacattgatGTACTGCATGTATGCaaaggacgtc [APIORCISFBSCS]
[BPP]
[CV(CHIP-SV/GEA/ROMA)]
[CV(GEA/ROMA)]
[GEA]
[14]
Fis repressor crpp2 crp 3485993 3486007 -31.0 tgtatgcaaaGGACGTCACATTACCgtgcagtaca [APIORCISFBSCS]
[BPP]
[CV(CHIP-SV/GEA/ROMA)]
[CV(GEA/ROMA)]
[GEA]
[14]
Fis repressor crpp2 crp 3486013 3486027 -11.0 ttaccgtgcaGTACAGTTGATAGCCccttcccagg [APIORCISFBSCS]
[BPP]
[CV(CHIP-SV/GEA/ROMA)]
[CV(GEA/ROMA)]
[GEA]
[14]

Evidence: [IHBCE] Inferred by a human based on computational evidence
[AIBSCS] Automated inference based on similarity to consensus sequences
[BPP] Binding of purified proteins
[CV(CHIP-SV/GEA/ROMA)] cross validation(CHIP-SV/GEA/ROMA)
[CV(GEA/ROMA)] cross validation(GEA/ROMA)
[GEA] Gene expression analysis
[BCE] Binding of cellular extracts
[APIORCISFBSCS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.
Reference(s): [1] Auner H., et al., 2003
[2] Lazarus LR., et al., 1993
[3] Li S., et al., 1997
[4] Muskhelishvili G., et al., 1997
[5] Muskhelishvili G., et al., 1995
[6] Pemberton IK., et al., 2002
[7] Travers A., et al., 2001
[8] Hengen PN., et al., 1997
[9] Nilsson L., et al., 1990
[10] Verbeek H., et al., 1990
[11] van Delft JH., et al., 1987
[12] Bosch L., et al., 1990
[13] Slany RK., et al., 1992
[14] Gonzalez-Gil G., et al., 1998



Reference(s)    

 [1] Auner H., Buckle M., Deufel A., Kutateladze T., Lazarus L., Mavathur R., Muskhelishvili G., Pemberton I., Schneider R., Travers A., 2003, Mechanism of transcriptional activation by FIS: role of core promoter structure and DNA topology., J Mol Biol 331(2):331-44

 [2] Lazarus LR., Travers AA., 1993, The Escherichia coli FIS protein is not required for the activation of tyrT transcription on entry into exponential growth., EMBO J 12(6):2483-94

 [3] Li S., Waters R., 1997, Induction and repair of cyclobutane pyrimidine dimers in the Escherichia coli tRNA gene tyrT: Fis protein affects dimer induction in the control region and suppresses preferential repair in the coding region of the transcribed strand, except in a short region near the transcription start site., J Mol Biol 271(1):31-46

 [4] Muskhelishvili G., Buckle M., Heumann H., Kahmann R., Travers AA., 1997, FIS activates sequential steps during transcription initiation at a stable RNA promoter., EMBO J 16(12):3655-65

 [5] Muskhelishvili G., Travers AA., Heumann H., Kahmann R., 1995, FIS and RNA polymerase holoenzyme form a specific nucleoprotein complex at a stable RNA promoter., EMBO J 14(7):1446-52

 [6] Pemberton IK., Muskhelishvili G., Travers AA., Buckle M., 2002, FIS modulates the kinetics of successive interactions of RNA polymerase with the core and upstream regions of the tyrT promoter., J Mol Biol 318(3):651-63

 [7] Travers A., Schneider R., Muskhelishvili G., 2001, DNA supercoiling and transcription in Escherichia coli: The FIS connection., Biochimie 83(2):213-7

 [8] Hengen PN., Bartram SL., Stewart LE., Schneider TD., 1997, Information analysis of Fis binding sites., Nucleic Acids Res 25(24):4994-5002

 [9] Nilsson L., Vanet A., Vijgenboom E., Bosch L., 1990, The role of FIS in trans activation of stable RNA operons of E. coli., EMBO J 9(3):727-34

 [10] Verbeek H., Nilsson L., Baliko G., Bosch L., 1990, Potential binding sites of the trans-activator FIS are present upstream of all rRNA operons and of many but not all tRNA operons., Biochim Biophys Acta 1050(1-3):302-6

 [11] van Delft JH., Marinon B., Schmidt DS., Bosch L., 1987, Transcription of the tRNA-tufB operon of Escherichia coli: activation, termination and antitermination., Nucleic Acids Res 15(22):9515-30

 [12] Bosch L., Nilsson L., Vijgenboom E., Verbeek H., 1990, FIS-dependent trans-activation of tRNA and rRNA operons of Escherichia coli., Biochim Biophys Acta 1050(1-3):293-301

 [13] Slany RK., Kersten H., 1992, The promoter of the tgt/sec operon in Escherichia coli is preceded by an upstream activation sequence that contains a high affinity FIS binding site., Nucleic Acids Res 20(16):4193-8

 [14] Gonzalez-Gil G., Kahmann R., Muskhelishvili G., 1998, Regulation of crp transcription by oscillation between distinct nucleoprotein complexes., EMBO J 17(10):2877-85


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