RegulonDB RegulonDB 10.9: Operon Form
   

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




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


Transcription unit          
Name: fixABCX
Gene(s): fixA, fixB, fixC, fixX   Genome Browser M3D Gene expression COLOMBOS
Note(s): On the basis of studies of L-carnitine metabolism and the development of a biosensor, it was determined that crotonobetainyl-CoA is the sought-after coactivator of CaiF in the fixAp promoter 32794733
Evidence: [LTED] Length of transcript experimentally determined
Reference(s): [1] Eichler K., et al., 1995
Promoter
Name: fixAp
+1: 42325
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 78
Sequence: tattgaaagttggatttatctgcgtgtgacattttcaatattggtgattaaagttttattTcaaaattaaagggcgtgata
                          -35                    -10        +1                   
Evidence: [HIPP]
[ICWHO]
[TIM]
Reference(s): [2] Eichler K., et al., 1996
[3] 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-cAMP1 activator fixAp 42188 42209 -126.5 gactttcaatATTGGTGATCCATAAAACAATATtgaaaatttc nd [APIORCISFBSCS], [GEA] [2], [6], [7]
proximal CRP-cAMP2 activator fixAp 42245 42266 -69.5 tgttttcaatATTGGTGAGGAACTTAACAATATtgaaagttgg nd [APIORCISFBSCS], [GEA] [2], [6], [7]
[CaiF,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote CaiF-L-carnitine activator fixAp 42181 42196 -136.5 aacatctgacTTTCAATATTGGTGATCcataaaacaa nd [APIORCISFBSCS], [BPP], [GEA] [6]
remote CaiF-L-carnitine2 activator fixAp 42200 42215 -117.5 tggtgatccaTAAAACAATATTGAAAAtttctttttg nd [APIORCISFBSCS], [BPP], [GEA] [6]
proximal CaiF-L-carnitine activator fixAp 42238 42253 -79.5 tacgccgtgtTTTCAATATTGGTGAGGaacttaacaa nd [APIORCISFBSCS], [BPP], [GEA] [6]
proximal CaiF-L-carnitine4 activator fixAp 42257 42272 -60.5 tggtgaggaaCTTAACAATATTGAAAGttggatttat nd [APIORCISFBSCS], [BPP], [GEA] [6]
[FNR,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote FNR activator fixAp 42121 42134 -197.5 cgttttttcgTTAATTTTGATTAATaatcagtttg nd [AIBSCS], [GEA] [4], [5]
Note(s): 1CaiF and CRP bind cooperatively to the cai-fix intergenic region to activate the fixA promoter.
2CaiF and CRP bind cooperatively to the cai-fix intergenic region to activate the fixA promoter.2CaiF and CRP bind cooperatively to the cai-fix intergenic region to activate the fixA promoter.
4CaiF and CRP bind cooperatively to the cai-fix intergenic region to activate the fixA promoter.3CaiF and CRP bind cooperatively to the cai-fix intergenic region to activate the fixA promoter.
4CaiF and CRP bind cooperatively to the cai-fix intergenic region to activate the fixA promoter.
6CaiF and CRP bind cooperatively to the cai-fix intergenic region to activate the fixA promoter.
7CaiF and CRP bind cooperatively to the cai-fix intergenic region to activate the fixA promoter.


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Translational
Strand: forward
Evidence: [ICA] Inferred by computational analysis
Reference(s): [8] Merino E, et al., 2005
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -19.2 44134 44174 gttgatccacTCTGGCAGGGCTGCATTTTGGCCCTGCCGCTGACAGGGAGctcttatgtc
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

 [ICWHO] Inferred computationally without human oversight

 [TIM] Transcription initiation mapping

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

 [GEA] Gene expression analysis

 [BPP] Binding of purified proteins

 [AIBSCS] Automated inference based on similarity to consensus sequences


Reference(s)    

 [1] Eichler K., Buchet A., Bourgis F., Kleber HP., Mandrand-Berthelot MA., 1995, The fix Escherichia coli region contains four genes related to carnitine metabolism., J Basic Microbiol 35(4):217-27

 [2] Eichler K., Buchet A., Lemke R., Kleber HP., Mandrand-Berthelot MA., 1996, Identification and characterization of the caiF gene encoding a potential transcriptional activator of carnitine metabolism in Escherichia coli., J Bacteriol 178(5):1248-57

 [3] 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

 [4] 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

 [5] Salmon K., Hung SP., Mekjian K., Baldi P., Hatfield GW., Gunsalus RP., 2003, Global gene expression profiling in Escherichia coli K12. The effects of oxygen availability and FNR., J Biol Chem 278(32):29837-55

 [6] Buchet A., Nasser W., Eichler K., Mandrand-Berthelot MA., 1999, Positive co-regulation of the Escherichia coli carnitine pathway cai and fix operons by CRP and the CaiF activator., Mol Microbiol 34(3):562-75

 [7] Buchet A., Eichler K., Mandrand-Berthelot MA., 1998, Regulation of the carnitine pathway in Escherichia coli: investigation of the cai-fix divergent promoter region., J Bacteriol 180(10):2599-608

 [8] Merino E, Yanofsky C., 2005, Transcription attenuation: a highly conserved regulatory strategy used by bacteria., Trends Genet. 2005 May;21(5):260-4.

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