RegulonDB RegulonDB 10.6.3: Operon Form
   

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




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


Transcription unit          
Name: uxuAB
Gene(s): uxuA, uxuB   Genome Browser M3D Gene expression COLOMBOS
Evidence: [IEP] Inferred from expression pattern
[ITCR] Inferred through co-regulation
Reference(s): [1] Blanco C., et al., 1986
Promoter
Name: uxuAp
+1: 4551518
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 118
Sequence: tgtggttaaccaatttcagaattcgggttgacatgtcttaccaaaaggtagaacttatacGccatctcatccgatgcaacg
                            -35                  -10        +1                   
Note(s): The Pribnow box of the uxuA promoter shows poor homology with the consensus sequence but contains the two most conserved nucleotides: the A in the second position and the T in the last position. The spacer length between this sequence and the -35 region is 17 nucleotides, the optimal distance for promoter efficiency.
Evidence: [HIPP]
[TIM]
Reference(s): [2] Lynch AS., et al., 1996
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 uxuAp 4551365 4551386 -142.5 ggtcaaccatTGTTGCGATGAATGTCACATCCtctgatcaat nd [AIBSCS], [GEA] [4], [5], [6], [7]
proximal CRP-cAMP activator uxuAp 4551450 4551471 -57.5 agagtgaaatTCTTGTGATGTGGTTAACCAATttcagaattc nd [BPP], [HIBSCS] [1], [4]
[ExuR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote ExuR repressor uxuAp 4551350 4551367 -159.5 tatgttatgtAAATTGGTCAACCATTGTtgcgatgaat nd [GEA] [3], [4]
proximal ExuR repressor uxuAp 4551456 4551473 -53.5 aaattcttgtGATGTGGTTAACCAATTTcagaattcgg nd [GEA], [HIBSCS] [3], [4]
[OxyR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal OxyR repressor uxuAp 4551456 4551472 -54.0 aaattcttgtGATGTGGTTAACCAATTtcagaattcg nd [GEA], [HIBSCS] [8]
proximal OxyR repressor uxuAp 4551478 4551494 -32.0 caatttcagaATTCGGGTTGACATGTCttaccaaaag nd [GEA], [HIBSCS] [8]
[UxuR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote UxuR repressor uxuAp 4551350 4551367 -159.5 tatgttatgtAAATTGGTCAACCATTGTtgcgatgaat nd [BPP], [GEA], [HIBSCS], [SM] [4], [5]
proximal UxuR repressor uxuAp 4551456 4551473 -53.5 aaattcttgtGATGTGGTTAACCAATTTcagaattcgg nd [GEA], [HIBSCS] [3], [4], [9], [10]


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Translational
Strand: forward
Evidence: [ICA] Inferred by computational analysis
Reference(s): [11] null null
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -9.7 4551595 4551628 ggttccgcgtCTCTTTGCTGTGGAACCCACTATGTGAAAGAGGaaaaatcatg
  terminator -9.6 4552859 4552894 ggttccttctTCCTTGCCGTCACTCTTTGAAGACGGATTCTGGAGtttacgatga
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    

 [HIPP] Human inference of promoter position

 [TIM] Transcription initiation mapping

 [AIBSCS] Automated inference based on similarity to consensus sequences

 [GEA] Gene expression analysis

 [BPP] Binding of purified proteins

 [HIBSCS] Human inference based on similarity to consensus sequences

 [SM] Site mutation


Reference(s)    

 [1] Blanco C., Ritzenthaler P., Kolb A., 1986, The regulatory region of the uxuAB operon in Escherichia coli K12., Mol Gen Genet 202(1):112-9

 [2] Lynch AS., Lin EC., 1996, Transcriptional control mediated by the ArcA two-component response regulator protein of Escherichia coli: characterization of DNA binding at target promoters., J Bacteriol 178(21):6238-49

 [3] Robert-Baudouy J., Portalier R., Stoeber F., 1981, Regulation of hexuronate system genes in Escherichia coli K-12: multiple regulation of the uxu operon by exuR and uxuR gene products., J Bacteriol 145(1):211-20

 [4] Rodionov DA., Mironov AA., Rakhmaninova AB., Gelfand MS., 2000, Transcriptional regulation of transport and utilization systems for hexuronides, hexuronates and hexonates in gamma purple bacteria., Mol Microbiol 38(4):673-83

 [5] Bates Utz C., Nguyen AB., Smalley DJ., Anderson AB., Conway T., 2004, GntP is the Escherichia coli Fructuronic acid transporter and belongs to the UxuR regulon., J Bacteriol 186(22):7690-6

 [6] Klemm P., Tong S., Nielsen H., Conway T., 1996, The gntP gene of Escherichia coli involved in gluconate uptake., J Bacteriol 178(1):61-7

 [7] Zheng D., Constantinidou C., Hobman JL., Minchin SD., 2004, Identification of the CRP regulon using in vitro and in vivo transcriptional profiling., Nucleic Acids Res 32(19):5874-93

 [8] Zheng M., Wang X., Templeton LJ., Smulski DR., LaRossa RA., Storz G., 2001, DNA microarray-mediated transcriptional profiling of the Escherichia coli response to hydrogen peroxide., J Bacteriol 183(15):4562-70

 [9] Ritzenthaler P., Blanco C., Mata-Gilsinger M., 1985, Genetic analysis of uxuR and exuR genes: evidence for ExuR and UxuR monomer repressors interactions., Mol Gen Genet 199(3):507-11

 [10] Ritzenthaler P., Mata-Gilsinger M., 1982, Use of in vitro gene fusions to study the uxuR regulatory gene in Escherichia coli K-12: direction of transcription and regulation of its expression., J Bacteriol 150(3):1040-7

 [11] null, null, null, null


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