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CynR DNA-binding transcriptional dual regulator

Synonyms: CynR, CynR-cyanate
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 [3, 4] It negatively regulates its own transcription independently of cyanate [4] CynR belongs to the family of LysR-type transcriptional regulators (LTTRs) [4, 5] 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 [6, 7] In accordance with this, the CynR regulatory domain is sufficient for dimerization, whereas the full-length protein behaves as a higher-order oligomer [8] 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 [9] The promoter regions for the divergently transcribed cynR and cyn operons overlap.
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Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) References
CynR Functional   Apo nd nd nd
CynR-cyanate Functional Allosteric Holo [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IPI] S [1]
Evolutionary Family: LysR
TFBs length: 9
TFBs symmetry: inverted-repeat
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
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 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 Confidence level (C: Confirmed, S: Strong, W: Weak) References
  CynR repressor cynRp Sigma70 -33.0 -52.0 cynR
gccgattgtcATAAGGTAAaagtctcatt
 358738 358746 [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [1], [1], [2]
  CynR repressor cynRp Sigma70 6.0 -14.0 cynR
ttccattggaTTTACTTATaggttgcgaa
 358700 358708 [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [1], [1], [2]
  CynR-cyanate activator cynTp Sigma70 -69.0 -95.0 cynT, cynS, cynX
ttcgcaacctATAAGTAAAtccaatggaa
 358700 358708 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [1], [1], [2]
  CynR-cyanate activator cynTp Sigma70 -31.0 -57.0 cynT, cynS, cynX
aatgagacttTTACCTTATgacaatcggc
 358738 358746 [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [1], [1], [2]


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


Evidence    

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

 [EXP-IPI] Inferred from physical interaction

 [COMP-HINF-SIMILAR-TO-CONSENSUS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [EXP-DAP-SEQ] high throughput DNA Affinity Purification (DAP) Sequencing

 [EXP-IEP-GENE-EXPRESSION-ANALYSIS] 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

 [2] Baumgart LA, Lee JE, Salamov A, Dilworth DJ, Na H, Mingay M, Blow MJ, Zhang Y, Yoshinaga Y, Daum CG, O'Malley RC, 2021, Persistence and plasticity in bacterial gene regulation., Nat Methods, 18(12):1499 10.1038/s41592-021-01312-2

 [3] Sung YC., Fuchs JA., 1988, Characterization of the cyn operon in Escherichia coli K12., J Biol Chem 263(29):14769-75

 [4] Sung YC., Fuchs JA., 1992, The Escherichia coli K-12 cyn operon is positively regulated by a member of the lysR family., J Bacteriol 174(11):3645-50

 [5] Lamblin AF., Fuchs JA., 1993, Expression and purification of the cynR regulatory gene product: CynR is a DNA-binding protein., J Bacteriol 175(24):7990-9

 [6] Muraoka S, Okumura R, Ogawa N, Nonaka T, Miyashita K, Senda T, 2003, Crystal structure of a full-length LysR-type transcriptional regulator, CbnR: unusual combination of two subunit forms and molecular bases for causing and changing DNA bend., J Mol Biol, 328(3):555 10.1016/s0022-2836(03)00312-7

 [7] Maddocks SE, Oyston PCF, 2008, Structure and function of the LysR-type transcriptional regulator (LTTR) family proteins., Microbiology (Reading), 154(Pt 12):3609 10.1099/mic.0.2008/022772-0

 [8] Knapp GS, Hu JC, 2009, The oligomerization of CynR in Escherichia coli., Protein Sci, 18(11):2307 10.1002/pro.241

 [9] Knapp GS, Hu JC, 2010, Specificity of the E. coli LysR-type transcriptional regulators., PLoS One, 5(12):e15189 10.1371/journal.pone.0015189

 [10] Anderson PM., Sung YC., Fuchs JA., 1990, The cyanase operon and cyanate metabolism., FEMS Microbiol Rev 7(3-4):247-52


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