RegulonDB RegulonDB 10.9: Operon Form
   

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




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


Transcription unit          
Name: caiTABCDE
Gene(s): caiE, caiD, caiC, caiB, caiA, caiT   Genome Browser M3D Gene expression COLOMBOS
Note(s): The transcript of caiE is increased after σE induction, as observed in high-throughput analysis of gene expression Lacoux C,2020.
Evidence: [PAGTSBP] Products of adjacent genes in the same biological process
Reference(s): [1] Eichler K., et al., 1994
[2] Eichler K., et al., 1996
Promoter
Name: caiTp
+1: 42037
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 106
Sequence: cgaaacaaaaatgtgataccaatcacagaatacagcttattgaatacccattatgagttaGccattaacgcgtccacgagg
                      -35                        -10        +1                   
Evidence: [ICWHO]
[TIM]
Reference(s): [3] Buchet A., et al., 1998
[4] Huerta AM., et al., 2003
TF binding sites (TFBSs)
[ArcA,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote ArcA-phosphorylated activator caiTp 41981 41995 50.0 ttatattaaaTGTTAACAAAAATAAAacaaacggga nd [AIBSCS], [GEA] [6]
proximal ArcA-phosphorylated activator caiTp 42003 42017 28.0 gcgtccacgaGGTTAATAATAATTATattaaatgtt nd [AIBSCS], [GEA] [6]
proximal ArcA-phosphorylated activator caiTp 42121 42135 -91.0 acaaactgatTATTAATCAAAATTAAcgaaaaaacg nd [AIBSCS], [GEA] [6]
remote ArcA-phosphorylated activator caiTp 42131 42145 -101.0 acagagcataACAAACTGATTATTAAtcaaaattaa nd [AIBSCS], [GEA] [6]
[CRP,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal CRP-cAMP activator caiTp 42068 42090 -41.5 acccgaaacaAAAATGTGATACCAATCACAGAAtacagcttat nd [AIBSCS], [APIORCISFBSCS], [BCE], [GEA] [1], [3], [5], [9]
[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 caiTp 42181 42196 -151.5 ttgttttatgGATCACCAATATTGAAAgtcagatgtt nd [APIORCISFBSCS], [BPP], [GEA] [5]
remote CaiF-L-carnitine activator caiTp 42200 42215 -170.5 caaaaagaaaTTTTCAATATTGTTTTAtggatcacca nd [APIORCISFBSCS], [BPP], [GEA] [5]
remote CaiF-L-carnitine activator caiTp 42238 42253 -208.5 ttgttaagttCCTCACCAATATTGAAAacacggcgta nd [APIORCISFBSCS], [BPP], [GEA] [5]
remote CaiF-L-carnitine activator caiTp 42257 42272 -227.5 ataaatccaaCTTTCAATATTGTTAAGttcctcacca nd [APIORCISFBSCS], [BPP], [GEA] [5]
[FNR,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal FNR1 activator caiTp 42072 42085 -41.5 gaaacaaaaaTGTGATACCAATCACagaatacagc nd [AIBSCS], [GEA] [7], [8]
proximal FNR activator caiTp 42121 42134 -90.5 caaactgattATTAATCAAAATTAAcgaaaaaacg nd [AIBSCS], [GEA] [7], [8]
[H-NS,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd H-NS repressor caiTp nd nd nd nd nd [BPP], [GEA], [IGI] [1]
Note(s): 1By making use of microarray analyses, it was concluded that FNR activates cai operon expression under anaerobiosis Salmon K,2003. Constantinidou C,2006.
9By making use of microarray analyses, it was concluded that FNR activates cai operon expression under anaerobiosis Salmon K,2003. Constantinidou C,2006.


Transcription unit       
Name: caiCDE
Gene(s): caiE, caiD, caiC   Genome Browser M3D Gene expression COLOMBOS
Note(s): The transcript of caiE is increased after σE induction, as observed in high-throughput analysis of gene expression Lacoux C,2020.
Evidence: [BTEI] Boundaries of transcription experimentally identified
[PAGTSBP] Products of adjacent genes in the same biological process
Reference(s): [10] Zaslaver A., et al., 2006
Promoter
Name: caiCp
+1: Unknown
Note(s): Zaslaver et al. demonstrated in 2006, by means of a library of fluorescent transcription fusions, that this promoter can be transcribed in vitro Zaslaver A,2006. Based on this, a putative promoter was suggested, but the +1 site of the transcription initiation has not been determined, although there exists promoter activity.
Evidence: [IEP]
Reference(s): [10] Zaslaver A., et al., 2006


Evidence    

 [ICWHO] Inferred computationally without human oversight

 [TIM] Transcription initiation mapping

 [AIBSCS] Automated inference based on similarity to consensus sequences

 [GEA] Gene expression analysis

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

 [BCE] Binding of cellular extracts

 [BPP] Binding of purified proteins

 [IGI] Inferred from genetic interaction

 [IEP] Inferred from expression pattern


Reference(s)    

 [1] Eichler K., Bourgis F., Buchet A., Kleber HP., Mandrand-Berthelot MA., 1994, Molecular characterization of the cai operon necessary for carnitine metabolism in Escherichia coli., Mol Microbiol 13(5):775-86

 [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] 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

 [4] 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

 [5] 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

 [6] Liu X., De Wulf P., 2004, Probing the ArcA-P modulon of Escherichia coli by whole genome transcriptional analysis and sequence recognition profiling., J Biol Chem 279(13):12588-97

 [7] 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

 [8] 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

 [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] Zaslaver A., Bren A., Ronen M., Itzkovitz S., Kikoin I., Shavit S., Liebermeister W., Surette MG., Alon U., 2006, A comprehensive library of fluorescent transcriptional reporters for Escherichia coli., Nat Methods 3(8):623-8

 [11] Beisel CL., Updegrove TB., Janson BJ., Storz G., 2012, Multiple factors dictate target selection by Hfq-binding small RNAs., EMBO J 31(8):1961-74

RegulonDB