RegulonDB RegulonDB 10.8: Operon Form
   

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




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


Transcription unit       
Name: uxaCA
Gene(s): uxaA, uxaC   Genome Browser M3D Gene expression COLOMBOS
Evidence: [PAGTSBP] Products of adjacent genes in the same biological process
Promoter
Name: uxaCp1
+1: 3244843
Distance from start of the gene: 102
Sequence: ggcgcggcctgcagcgagatttaccactttgagagtaatttttttaactacgtttattgaTctaactcacgaaaatatctt
Evidence: [TIM]
Reference(s): [1] Yamamoto K., et al., 2008


Transcription unit          
Name: uxaCA
Gene(s): uxaA, uxaC   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
[IEP] Inferred from expression pattern
Reference(s): [2] Hugouvieux-Cotte-Pattat N., et al., 1982
[3] Mata-Gilsinger M., et al., 1983
[4] Nemoz G., et al., 1976
Promoter
Name: uxaCp
+1: 3244857
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 116
Sequence: gcaaggccagtactggcgcggcctgcagcgagatttaccactttgagagtaatttttttaActacgtttattgatctaact
                       -35                        -10       +1                   
Evidence: [AIPP]
Reference(s): [5] Huerta AM., et al., 2003
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 uxaCp 3244952 3244974 -105.5 atacaactttAAAAGGTGAGAGCCATCACAAATgtgggaatat nd [AIBSCS], [APIORCISFBSCS], [CV(GEA)], [GEA] [7], [8], [9]
[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 uxaCp 3244795 3244812 54.5 cggactctggAAATTGGTGTGATAACTTtgtcagcatc nd [AIBSCS] [8]
proximal ExuR repressor uxaCp 3244850 3244867 -1.5 ctttgagagtAATTTTTTTAACTACGTTtattgatcta nd [AIBSCS] [7], [8]
proximal ExuR repressor uxaCp 3244874 3244891 -25.5 cgcggcctgcAGCGAGATTTACCACTTTgagagtaatt nd [AIBSCS] [8]
remote ExuR repressor uxaCp 3244976 3244993 -127.5 ggcagaaagaTAACTTGTCATACAACTTtaaaaggtga nd [AIBSCS], [CV(GEA)], [GEA] [6], [7]
[FNR,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd FNR1 activator uxaCp nd nd nd nd nd [AIBSCS], [CV(GEA)], [GEA] [10]
Note(s): 1By making use of microarray analysis, Constantinidou et al. Constantinidou C,2006 concluded that FNR activates uxaCA operon expression. They also identified a putative FNR-binding site upstream of the operon, but the sequence was not reported.6By making use of microarray analysis, Constantinidou et al. Constantinidou C,2006 concluded that FNR activates uxaCA operon expression. They also identified a putative FNR-binding site upstream of the operon, but the sequence was not reported.


Evidence    

 [TIM] Transcription initiation mapping

 [AIPP] Automated inference of promoter position

 [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


Reference(s)    

 [1] Yamamoto K., Matsumoto F., Oshima T., Fujita N., Ogasawara N., Ishihama A., 2008, Anaerobic regulation of citrate fermentation by CitAB in Escherichia coli., Biosci Biotechnol Biochem 72(11):3011-4

 [2] Hugouvieux-Cotte-Pattat N., Robert-Baudouy J., 1982, Determination of the transcription direction of the exuT gene in Escherichia coli K-12: divergent transcription of the exuT-uxaCA operons., J Bacteriol 151(1):480-4

 [3] Mata-Gilsinger M., Ritzenthaler P., 1983, Physical mapping of the exuT and uxaC operators by use of exu plasmids and generation of deletion mutants in vitro., J Bacteriol 155(3):973-82

 [4] Nemoz G., Robert-Baudouy J., Stoeber F., 1976, Physiological and genetic regulation of the aldohexuronate transport system in Escherichia coli., J Bacteriol 127(2):706-18

 [5] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78

 [6] Mata-Gilsinger M., Ritzenthaler P., Blanco C., 1983, Characterization of the operator sites of the exu regulon in Escherichia coli K-12 by operator-constitutive mutations and repressor titration., Genetics 105(4):829-42

 [7] 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

 [8] Medina-Rivera A., Abreu-Goodger C., Thomas-Chollier M., Salgado H., Collado-Vides J., van Helden J., 2011, Theoretical and empirical quality assessment of transcription factor-binding motifs., Nucleic Acids Res 39(3):808-24

 [9] 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

 [10] Constantinidou C., Hobman JL., Griffiths L., Patel MD., Penn CW., Cole JA., Overton TW., 2006, A reassessment of the FNR regulon and transcriptomic analysis of the effects of nitrate, nitrite, NarXL, and NarQP as Escherichia coli K12 adapts from aerobic to anaerobic growth., J Biol Chem 281(8):4802-15

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