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CynR DNA-binding transcriptional dual regulator

Synonyms: CynR-Cyanate, CynR
Summary:
The transcriptional dual regulator CynR, cyanate regulator, activates the expression of the cyn operon, which is involved in use of cyanate as a sole nitrogen source, in the presence of the inducer cyanate |CITS:[3049588][1592818]|. It negatively regulates its own transcription independently of cyanate |CITS:[1592818]|.
CynR belongs to the family of LysR-type transcriptional regulators (LTTRs) |CITS:[1592818][8253686]|. Members of this family have a conserved structure with an N-terminal DNA-binding helix-turn-helix motif and a C-terminal cofactor-binding domain. They typically form tetramers in solution that can be regarded as dimers of dimers |CITS:[12706716][19047729]|. In accordance with this, the CynR regulatory domain is sufficient for dimerization, whereas the full-length protein behaves as a higher-order oligomer |CITS:[19760662]|. In systematic studies of oligomerization, it was shown that some members of the LysR family, like CynR, interact with other members of the family to form heterodimers, but the physiological significance of this is unknown |CITS:[ 21187915]|.
The promoter regions for the divergently transcribed cynR and cyn operons overlap. CynR binds cooperatively to a 60-bp region that contains two 9-bp repeats separated by 34 bp. The binding region overlaps the -35 region of the promoter for the cyn operon and both the -10 and -35 region of its own promoter |CITS:[8253686][7961413]|. CynR binds to DNA in the presence or absence of cyanate and induces bending of the DNA |CITS:[7961413]|.
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Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
CynR     nd nd
CynR-Cyanate Functional Allosteric Holo [BPP], [IPI] [1]
Evolutionary Family: LysR
Sensing class: External sensing using transported metabolites
Connectivity class: Local Regulator
Gene name: cynR
  Genome position: 357791-358690
  Length: 900 bp / 299 aa
Operon name: cynR
TU(s) encoding the TF:
Transcription unit        Promoter
cynR
cynRp


Regulon       
Regulated gene(s) cynR, cynS, cynT, cynX
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
detoxification (3)
cyanate catabolism (3)
nitrogen metabolism (2)
unassigned reversible reactions (1)
Transcription related (1)
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Regulated operon(s) cynR, cynTSX
First gene in the operon(s) cynR, cynT, cynT
Simple and complex regulons CynR
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[CynR,+](1)
[CynR,-](1)


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
  CynR repressor cynRp Sigma70 -33.0 -52.0 cynR
gccgattgtcATAAGGTAAaagtctcatt
358738 358746 [BPP], [HIBSCS] [1]
  CynR repressor cynRp Sigma70 6.0 -14.0 cynR
ttccattggaTTTACTTATaggttgcgaa
358700 358708 [BPP], [HIBSCS] [1]
  CynR-Cyanate activator cynTp Sigma70 -69.0 -95.0 cynT, cynS, cynX
ttcgcaacctATAAGTAAAtccaatggaa
358700 358708 [BPP], [GEA], [HIBSCS] [1]
  CynR-Cyanate activator cynTp Sigma70 -31.0 -57.0 cynT, cynS, cynX
aatgagacttTTACCTTATgacaatcggc
358738 358746 [BPP], [HIBSCS] [1]


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


Evidence    

 [BPP] Binding of purified proteins

 [IPI] Inferred from physical interaction

 [HIBSCS] Human inference based on similarity to consensus sequences

 [GEA] Gene expression analysis



Reference(s)    

 [1] Lamblin AF., Fuchs JA., 1994, Functional analysis of the Escherichia coli K-12 cyn operon transcriptional regulation., J Bacteriol. 176(21):6613-22



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