RegulonDB RegulonDB 11.1: 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: [IC-ADJ-GENES-SAME-BIO-PROCESS] 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: [COMP-AINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
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 Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote ArcA-phosphorylated activator caiTp 41981 41995 50.0 tatattaaatGTTAACAAAAATAAAacaaacggga nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [6]
proximal ArcA-phosphorylated activator caiTp 42003 42017 28.0 cgtccacgagGTTAATAATAATTATattaaatgtt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [6]
proximal ArcA-phosphorylated activator caiTp 42121 42135 -91.0 caaactgattATTAATCAAAATTAAcgaaaaaacg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [6]
remote ArcA-phosphorylated activator caiTp 42131 42145 -101.0 cagagcataaCAAACTGATTATTAAtcaaaattaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [6]
[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 activator caiTp 42068 42090 -41.5 acccgaaacaAAAATGTGATACCAATCACAGAAtacagcttat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] S [1], [3], [5], [9]
[CaiF,+] 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 CaiF-L-carnitine activator caiTp 42181 42196 -151.5 tgttttatggATCACCAATATTGAAAgtcagatgtt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [5]
remote CaiF-L-carnitine activator caiTp 42200 42215 -170.5 aaaaagaaatTTTCAATATTGTTTTAtggatcacca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [5]
remote CaiF-L-carnitine activator caiTp 42238 42253 -208.5 tgttaagttcCTCACCAATATTGAAAacacggcgta nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [5]
remote CaiF-L-carnitine activator caiTp 42257 42272 -227.5 taaatccaacTTTCAATATTGTTAAGttcctcacca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [5]
[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 activator caiTp 42072 42085 -41.5 aaacaaaaatGTGATACCAATCACagaatacagc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [7], [8]
proximal FNR activator caiTp 42121 42134 -90.5 aaactgattaTTAATCAAAATTAAcgaaaaaacg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [7], [8]
[H-NS,-] 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 H-NS repressor caiTp nd nd nd nd nd [EXP-IMP] W [1]


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: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
[IC-ADJ-GENES-SAME-BIO-PROCESS] 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: [EXP-IEP]
Reference(s): [10] Zaslaver A., et al., 2006


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

 [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.

 [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] Binding of cellular extracts

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

 [EXP-IMP] Inferred from mutant phenotype

 [EXP-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