RegulonDB RegulonDB 11.2: Operon Form
   

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




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


Transcription unit          
Name: citCDEFXG
Gene(s): citG, citX, citF, citE, citD, citC   Genome Browser M3D Gene expression COLOMBOS
Note(s): Transcription of the citCDEFXG operon is dependent on CitB when E. coli is grown in the presence of citrate and the absence of nitrate and oxygen Scheu PD,2012. Yamamoto et al. in 2008 showed that CitB (DpiA), in the presence of citrate, activates the transcription of three promoters, citCp2, citCp1, and citAp (dpiBp), in the intergenic region located between the citC and citA genes (dpiB) Yamamoto K,2008. But they have not shown the mechanism of action of CitB in the activation of the divergent operons.
Evidence: [COMP-AINF] Inferred computationally without human oversight
[IC-ADJ-GENES-SAME-BIO-PROCESS] Products of adjacent genes in the same biological process
Promoter
Name: citCp1
+1: 651952
Distance from start of the gene: 96
Sequence: ccgaaatactccttaggatgtatagcgaaaggagaaaaagatatacctcgatcaccccctTtctcccaagtgaaaataaaa
Evidence: [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [1] Yamamoto K., et al., 2008
TF binding sites (TFBSs)
[ArcA,-] 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 ArcA-phosphorylated repressor citCp1 651884 651894 64.5 attcgttgcaAATCGATAACAacatgcacct nd [COMP-AINF-SIMILAR-TO-CONSENSUS] nd [3]
[DpiA,+] 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 DpiA-phosphorylated activator citCp1 652049 652072 -108.0 ttaaaaaactTAAAATCATTAAATAAATAAAAAAccactaactc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-GSELEX], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [1], [2], [3]
remote DpiA-phosphorylated activator citCp1 652076 652099 -135.0 ctgcgagtcaTTTCGTAATTACATTAATTAAAAAacttaaaatc nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-GSELEX], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [1], [2], [3]
remote DpiA-phosphorylated activator citCp1 652118 652141 -177.0 cgtggcaaatTTTATTCATTAAATCAATTAAATCacttaaacct nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-GSELEX], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [1], [2], [3]


Transcription unit          
Name: citCDEFXG
Gene(s): citG, citX, citF, citE, citD, citC   Genome Browser M3D Gene expression COLOMBOS
Note(s): Transcription of the citCDEFXG operon is dependent on CitB when E. coli is grown in the presence of citrate and the absence of nitrate and oxygen Scheu PD,2012. Yamamoto et al. in 2008 showed that CitB (DpiA), in the presence of citrate, activates the transcription of three promoters, citCp2, citCp1, and citAp (dpiBp), in the intergenic region located between the citC and citA genes (dpiB) Yamamoto K,2008. But they have not shown the mechanism of action of CitB in the activation of the divergent operons.
Evidence: [IC-ADJ-GENES-SAME-BIO-PROCESS] Products of adjacent genes in the same biological process
Promoter
Name: citCp2
+1: 652039
Distance from start of the gene: 183
Sequence: tttcgtaattacattaattaaaaaacttaaaatcattaaataaataaaaaaccactaactCtatgtgaaataaatcaaaat
Evidence: [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [1] Yamamoto K., et al., 2008
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
proximal CRP-cyclic-AMP repressor citCp2 652018 652039 11.5 accactaactCTATGTGAAATAAATCAAAATTtcacgccgaa nd [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [3]
[DpiA,+] 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
proximal DpiA-phosphorylated activator citCp2 652049 652072 -21.0 ttaaaaaactTAAAATCATTAAATAAATAAAAAAccactaactc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-GSELEX], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [1], [2], [3]
proximal DpiA-phosphorylated activator citCp2 652076 652099 -48.0 ctgcgagtcaTTTCGTAATTACATTAATTAAAAAacttaaaatc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-GSELEX], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [1], [2], [3]
proximal DpiA-phosphorylated activator citCp2 652118 652141 -90.0 cgtggcaaatTTTATTCATTAAATCAATTAAATCacttaaacct nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-GSELEX], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [1], [2], [3]
[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
proximal FNR repressor citCp2 652022 652035 11.5 ctaactctatGTGAAATAAATCAAaatttcacgc nd [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [3]
[NarL,-] 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 NarL-phosphorylated repressor citCp2 652000 652007 37.0 tcacgccgaaATACTCCTtaggatgtat nd [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [3]


Evidence    

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

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

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

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

 [EXP-DAP-SEQ] high throughput DNA Affinity Purification (DAP) Sequencing

 [EXP-GSELEX] high throughput Genomic SELEX-chip evidence

 [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] Binding of purified proteins


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] Ingmer H., Miller CA., Cohen SN., 1998, Destabilized inheritance of pSC101 and other Escherichia coli plasmids by DpiA, a novel two-component system regulator., Mol Microbiol 29(1):49-59

 [3] Scheu PD., Witan J., Rauschmeier M., Graf S., Liao YF., Ebert-Jung A., Basche T., Erker W., Unden G., 2012, CitA/CitB two-component system regulating citrate fermentation in Escherichia coli and its relation to the DcuS/DcuR system in vivo., J Bacteriol 194(3):636-45

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