RegulonDB RegulonDB 11.1: 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: [IC-ADJ-GENES-SAME-BIO-PROCESS] Products of adjacent genes in the same biological process
Promoter
Name: uxaCp1
+1: 3244843
Distance from start of the gene: 102
Sequence: ggcgcggcctgcagcgagatttaccactttgagagtaatttttttaactacgtttattgaTctaactcacgaaaatatctt
Evidence: [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [1] Yamamoto K., et al., 2008


Transcription unit          
Name: uxaCA
Gene(s): uxaA, uxaC   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
[EXP-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: uxaCp2
+1: 3244857
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 116
Sequence: gcaaggccagtactggcgcggcctgcagcgagatttaccactttgagagtaatttttttaActacgtttattgatctaact
                            -35                        -10  +1                   
Evidence: [COMP-AINF]
[COMP-AINF-POSITIONAL-IDENTIFICATION]
Reference(s): [5] Huerta AM., et al., 2003
TF binding sites (TFBSs)
[CRP,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote CRP-cyclic-AMP activator uxaCp2 3244952 3244974 -105.5 atacaactttAAAAGGTGAGAGCCATCACAAATgtgggaatat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [7], [8], [9]
[ExuR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote ExuR repressor uxaCp2 3244795 3244812 54.5 cggactctggAAATTGGTGTGATAACTTtgtcagcatc nd [COMP-AINF-SIMILAR-TO-CONSENSUS] nd [8]
proximal ExuR repressor uxaCp2 3244850 3244867 -1.5 ctttgagagtAATTTTTTTAACTACGTTtattgatcta nd [COMP-AINF-SIMILAR-TO-CONSENSUS] nd [7], [8]
proximal ExuR repressor uxaCp2 3244874 3244891 -25.5 cgcggcctgcAGCGAGATTTACCACTTTgagagtaatt nd [COMP-AINF-SIMILAR-TO-CONSENSUS] nd [8]
remote ExuR repressor uxaCp2 3244976 3244993 -127.5 ggcagaaagaTAACTTGTCATACAACTTtaaaaggtga nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [6], [7]
[FNR,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd FNR activator uxaCp2 nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [10]


Evidence    

 [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] Transcription initiation mapping

 [COMP-AINF] Inferred computationally without human oversight

 [COMP-AINF-POSITIONAL-IDENTIFICATION] Automated inference of promoter position

 [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis

 [COMP-AINF-SIMILAR-TO-CONSENSUS] Automated inference based on similarity to consensus sequences

 [COMP-HINF-SIMILAR-TO-CONSENSUS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.


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

RegulonDB