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CaiF DNA-binding transcriptional activator

Synonyms: CaiF, CaiF-L-carnitine
Summary:
Under anaerobiosis and in the presence of "carnitine," CaiF activates the transcription of genes involved in carnitine metabolism [2]. This protein recognizes and binds to two 11-bp inverted repeat half-sites separated by 13 bp in the intergenic region of two operons located divergently in the genome (caiTABCDE and fixABCX). CaiF possibly binds as a dimer, with each monomer of the complex recognizing one half of the site. A genome-wide computerized scan demonstrated that there are no more sites in the genome for CaiF [1]. A complex composed of two CRP dimers and two CaiF dimers needs to be bound in order for the RNA polymerase to bind to the promoter. CRP, which makes contact with the RNA polymerase, seems to be the main protein of the complex. CaiF was suggested to counteract the repression effect of HNS. It has been proposed that CRP and CaiF bind to opposite DNA strands [1]. Carnitine and crotonobetaine, the putative inducers of carnitine metabolism, seem to be of no help in CaiF binding [1].
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Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
CaiF Non-Functional   Apo nd nd
CaiF-L-carnitine Functional   Holo nd nd
Evolutionary Family: CaiF
Sensing class: External sensing using transported metabolites
Connectivity class: Local Regulator
Gene name: caiF
  Genome position: 34300-34695
  Length: 396 bp / 131 aa
Operon name: caiF
TU(s) encoding the TF:
Transcription unit        Promoter
caiF
caiFp


Regulon       
Regulated gene(s) caiA, caiB, caiC, caiD, caiE, caiT, fixA, fixB, fixC, fixX
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
carnitine metabolism (6)
amines (2)
energy production/transport (2)
electron acceptors (1)
carbon compounds (1)
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Regulated operon(s) caiTABCDE, fixABCX
First gene in the operon(s) caiT, fixA
Simple and complex regulons ArcA,CRP,CaiF,FNR,H-NS
CRP,CaiF,FNR
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[CaiF,+](2)


Transcription factor regulation    


Transcription factor binding sites (TFBSs) arrangements
      

  Functional conformation Function Promoter Sigma factor Central Rel-Pos Distance to first Gene Genes Sequence
LeftPos RightPos Evidence (Confirmed, Strong, Weak) References
  CaiF-L-carnitine activator caiTp Sigma70 -227.5 -333.5 caiT, caiA, caiB, caiC, caiD, caiE
taaatccaacTTTCAATATTGTTAAGttcctcacca
42257 42272 [APIORCISFBSCS], [BPP], [GEA] [1]
  CaiF-L-carnitine activator caiTp Sigma70 -208.5 -314.5 caiT, caiA, caiB, caiC, caiD, caiE
tgttaagttcCTCACCAATATTGAAAacacggcgta
42238 42253 [APIORCISFBSCS], [BPP], [GEA] [1]
  CaiF-L-carnitine activator caiTp Sigma70 -170.5 -276.5 caiT, caiA, caiB, caiC, caiD, caiE
aaaaagaaatTTTCAATATTGTTTTAtggatcacca
42200 42215 [APIORCISFBSCS], [BPP], [GEA] [1]
  CaiF-L-carnitine activator caiTp Sigma70 -151.5 -257.5 caiT, caiA, caiB, caiC, caiD, caiE
tgttttatggATCACCAATATTGAAAgtcagatgtt
42181 42196 [APIORCISFBSCS], [BPP], [GEA] [1]
  CaiF-L-carnitine activator fixAp Sigma70 -136.5 -214.5 fixA, fixB, fixC, fixX
aacatctgacTTTCAATATTGGTGATccataaaaca
42181 42196 [APIORCISFBSCS], [BPP], [GEA] [1]
  CaiF-L-carnitine activator fixAp Sigma70 -117.5 -195.5 fixA, fixB, fixC, fixX
tggtgatccaTAAAACAATATTGAAAatttcttttt
42200 42215 [APIORCISFBSCS], [BPP], [GEA] [1]
  CaiF-L-carnitine activator fixAp Sigma70 -79.5 -157.5 fixA, fixB, fixC, fixX
tacgccgtgtTTTCAATATTGGTGAGgaacttaaca
42238 42253 [APIORCISFBSCS], [BPP], [GEA] [1]
  CaiF-L-carnitine activator fixAp Sigma70 -60.5 -138.5 fixA, fixB, fixC, fixX
tggtgaggaaCTTAACAATATTGAAAgttggattta
42257 42272 [APIORCISFBSCS], [BPP], [GEA] [1]


Alignment and PSSM for CaiF TFBSs    

Aligned TFBS of CaiF   
  Sequence
  CACCAATATTGAAAGTCAG
  TAACAATATTGAAAGTTGG
  CACCAATATTGAAAACACG
  AAACAATATTGAAAATTTC

Position weight matrix (PWM). CaiF matrix-quality result   
A	1	4	2	0	4	4	0	4	0	0	0	4	4	4	2	0	1	1	0
C	2	0	2	4	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1
G	0	0	0	0	0	0	0	0	0	0	4	0	0	0	2	0	0	1	3
T	1	0	0	0	0	0	4	0	4	4	0	0	0	0	0	3	2	1	0

Consensus   
;	consensus.strict             	cAcCAATATTGAAAgttgG
;	consensus.strict.rc          	CCAACTTTCAATATTGGTG
;	consensus.IUPAC              	cAmCAATATTGAAAryysS
;	consensus.IUPAC.rc           	SSRRYTTTCAATATTGKTG
;	consensus.regexp             	cA[ac]CAATATTGAAA[ag][ct][ct][cg][CG]
;	consensus.regexp.rc          	[CG][CG][AG][AG][CT]TTTCAATATTG[GT]TG

PWM logo   


 


Evolutionary conservation of regulatory elements    
     Note: Evolutionary conservation of regulatory interactions and promoters is limited to gammaproteobacteria.
TF-target gene evolutionary conservation
Promoter-target gene evolutionary conservation


Evidence    

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

 [BPP] Binding of purified proteins

 [GEA] Gene expression analysis



Reference(s)    

 [1] 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

 [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



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