RegulonDB RegulonDB 10.8: Operon Form
   

xylFGHR operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: xylFGHR
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit          
Name: xylFGHR
Gene(s): xylF, xylG, xylH, xylR   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
[ITC] Inferred through co-regulation
Reference(s): [1] Song S., et al., 1997
[2] Sumiya M., et al., 1995
Promoter
Name: xylFp
+1: 3731069
Distance from start of the gene: 62
Sequence: cgtaatcgaaagataaaaatctgtaattgttttcccctgtttagttgctaaaaattggttAcgtttatcgcggtgattgtt
Note(s): xylF is negatively regulated during entry into stationary phase. The effect by RpoS is likely indirect and might be mediated by an intermediate regulator that itself is directly regulated by RpoS Xu J,1995
Evidence: [TIM]
Reference(s): [1] Song S., et al., 1997
TF binding sites (TFBSs)
[CRP,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote CRP-cAMP activator xylFp 3730878 3730900 -180.5 gataattcacAAGTGTGCGCTCGCTCGCAAAATaaaatggaat nd [AIBSCS], [APIORCISFBSCS], [CV(GEA)], [GEA] [1], [3], [4]
[Fis,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal Fis repressor xylFp 3730978 3730997 -82.0 aagtaagatcTCGGTCATAAATCAAGAAATaaaccaaaaa nd [AIBSCS], [CV(GEA)], [GEA] [5]
proximal Fis repressor xylFp 3730985 3731004 -75.0 atctcggtcaTAAATCAAGAAATAAACCAAaaatcgtaat nd [AIBSCS], [CV(GEA)], [GEA] [5]
proximal Fis3 repressor xylFp 3731081 3731100 22.0 gtttatcgcgGTGATTGTTACTTATTAAAActgtcctcta nd [AIBSCS], [CV(GEA)], [GEA] [5], [6]
[XylR,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal XylR-xylose activator xylFp 3730999 3731016 -61.5 tcaagaaataAACCAAAAATCGTAATCGaaagataaaa nd [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA] [1], [3]
proximal XylR-xylose activator xylFp 3731020 3731037 -40.5 gtaatcgaaaGATAAAAATCTGTAATTGttttcccctg nd [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA] [1], [3]
Note(s): 3Fis and RpoS inhibit xylF expression in an rpoS fis double mutant strain. The rpoS effects could be indirect Xu J,1995.6Fis and RpoS inhibit xylF expression in an rpoS fis double mutant strain. The rpoS effects could be indirect Xu J,1995.


Transcription unit          
Name: xylR
Gene(s): xylR   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [1] Song S., et al., 1997
[2] Sumiya M., et al., 1995
Promoter
Name: xylRp
+1: 3734906
Distance from start of the gene: 73
Sequence: gtgcgattctgttgctggcagtatggatggactccgcaaccaaacgccgttcttgattttGataaaaattttctcaaagcc
Evidence: [TIM]
Reference(s): [1] Song S., et al., 1997
TF binding sites (TFBSs)
[ArcA,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd ArcA-Phosphorylated1 activator xylRp nd nd nd nd nd [AIBSCS], [CV(GEA)], [GEA] [7]
Note(s): 1ArcA activates xylR gene expression under anaerobiosis. A putative ArcA-binding site 112 bp upstream of this gene was identified, but the sequence of it was not shown Salmon KA,2005.1ArcA activates xylR gene expression under anaerobiosis. A putative ArcA-binding site 112 bp upstream of this gene was identified, but the sequence of it was not shown Salmon KA,2005.


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: forward
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -17.9 3734918 3734955 aaaaattttcTCAAAGCCGGTTACGTATTACCGGTTTTGAGTTTTTGcatgattcag
  anti-terminator -4.7 3734893 3734933 accaaacgccGTTCTTGATTTTGATAAAAATTTTCTCAAAGCCGGTTACGtattaccggt
Notes: "The provided "Sequence" is that of the RNA strand, i.e. U's are shown instead of T's and regulators on the reverse strand will appear as the reverse complement of the sequence delimited by LeftPos-RigtPos"


Evidence    

 [TIM] Transcription initiation mapping

 [AIBSCS] Automated inference based on similarity to consensus sequences

 [APIORCISFBSCS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [CV(GEA)] cross validation(GEA)

 [GEA] Gene expression analysis

 [BPP] Binding of purified proteins


Reference(s)    

 [1] Song S., Park C., 1997, Organization and regulation of the D-xylose operons in Escherichia coli K-12: XylR acts as a transcriptional activator., J Bacteriol 179(22):7025-32

 [2] Sumiya M., Davis EO., Packman LC., McDonald TP., Henderson PJ., 1995, Molecular genetics of a receptor protein for D-xylose, encoded by the gene xylF, in Escherichia coli., Receptors Channels 3(2):117-28

 [3] Laikova ON., Mironov AA., Gelfand MS., 2001, Computational analysis of the transcriptional regulation of pentose utilization systems in the gamma subdivision of Proteobacteria., FEMS Microbiol Lett 205(2):315-22

 [4] Tsai MJ., Wang JR., Yang CD., Kao KC., Huang WL., Huang HY., Tseng CP., Huang HD., Ho SY., 2018, PredCRP: predicting and analysing the regulatory roles of CRP from its binding sites in Escherichia coli., Sci Rep 8(1):951

 [5] Bradley MD., Beach MB., de Koning AP., Pratt TS., Osuna R., 2007, Effects of Fis on Escherichia coli gene expression during different growth stages., Microbiology 153(Pt 9):2922-40

 [6] Xu J., Johnson RC., 1995, Identification of genes negatively regulated by Fis: Fis and RpoS comodulate growth-phase-dependent gene expression in Escherichia coli., J Bacteriol 177(4):938-47

 [7] Salmon KA., Hung SP., Steffen NR., Krupp R., Baldi P., Hatfield GW., Gunsalus RP., 2005, Global gene expression profiling in Escherichia coli K12: effects of oxygen availability and ArcA., J Biol Chem 280(15):15084-96

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