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Dan DNA-binding transcriptional activator

Synonyms: Dan-L-tartrate, Dan
Summary:
"DNA-binding protein under anaerobic conditions," Dan [1], formerly TtdR or YgiP, is an LysR-type transcriptional regulator for L-tartrate fermentation. Dan belongs to the same family of growth phase-specific nucleoid proteins as Fis, Dps, HU, IHF, and H-NS [1]. More specifically, Dan belongs to the group II nucleoid proteins, which include Fis, Rob (CbpB), CbpA, and IciA and show irregular distribution within the nucleoid [1]. Dan may have a functional dichotomy, controlling both the structure and function of the nucleoid [1]. In the presence of L- and meso-tartrate, Dan stimulates expression of the divergently transcribed ttdABT operon, encoding L-tartrate dehydratase and the L-tartrate:succinate antiporter [2, 4]. The ttd pathway for L-tartate fermentation and the dcu pathway for general C4-dicarboxylate metabolism interact at the regulatory level [2].
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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
Dan Non-Functional   Apo nd nd nd
Dan-L-tartrate Functional   Holo nd nd nd
Evolutionary Family: LysR
TFBs length: 7
Connectivity class: Local Regulator
Gene name: ttdR
  Genome position: 3205324-3206256
  Length: 933 bp / 310 aa
Operon name: ttdR
TU(s) encoding the TF:
Transcription unit        Promoter
ttdR
ttdRp


Regulon       
Regulated gene(s) ttdA, ttdB, ttdR, ttdT
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
fermentation (2)
Transcription related (1)
activator (1)
repressor (1)
Porters (Uni-, Sym- and Antiporters) (1)
Regulated operon(s) ttdABT, ttdR
First gene in the operon(s) ttdA, ttdR
Simple and complex regulons Dan
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[Dan,+](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 Confidence level (C: Confirmed, S: Strong, W: Weak) References
  Dan-L-tartrate activator ttdAp Sigma70 -163.0 -202.0 ttdA, ttdB, ttdT
attcagcatcGTTAATTatccgcagtt
 3206258 3206264 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [1], [1], [2]
  Dan-L-tartrate activator ttdAp Sigma70 -134.0 -173.0 ttdA, ttdB, ttdT
gataagcgcaGTGTATTtcgcaaaaca
 3206287 3206293 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [1], [1], [2]
  Dan-L-tartrate activator ttdAp Sigma70 -92.0 -131.0 ttdA, ttdB, ttdT
ctggcgcaatATTCATTcttattttcg
 3206329 3206335 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [1], [1], [2], [3]
  Dan-L-tartrate activator ttdAp Sigma70 -74.0 -113.0 ttdA, ttdB, ttdT
ttattttcgcGTTGATTcacgaactgt
 3206347 3206353 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [1], [1], [2], [3]
  Dan-L-tartrate activator ttdAp Sigma70 -59.0 -98.0 ttdA, ttdB, ttdT
ttcacgaactGTTAATTAcatattcacg
 3206362 3206369 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [1], [1], [2], [3]
  Dan-L-tartrate activator ttdRp nd nd nd ttdR
nd
 nd nd [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [2], [2]


Alignment and PSSM for Dan TFBSs    

Aligned TFBS of Dan   
  Sequence
  CATCGTTAATT
  AACTGTTAATT
  TCGCGTTGATT
  CGCAGTGTATT
  CAATATTCATT

Position weight matrix (PWM). Dan matrix-quality result    
A	1	3	1	1	1	0	0	2	5	0	0
C	3	1	2	2	0	0	0	1	0	0	0
G	0	1	1	0	4	0	1	1	0	0	0
T	1	0	1	2	0	5	4	1	0	5	5

Consensus    
;	consensus.strict             	caccGTtaATT
;	consensus.strict.rc          	AATTAACGGTG
;	consensus.IUPAC              	cacyGTtaATT
;	consensus.IUPAC.rc           	AATTAACRGTG
;	consensus.regexp             	cac[ct]GTtaATT
;	consensus.regexp.rc          	AATTAAC[AG]GTG

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    

 [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis

 [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-PURIFIED-PROTEINS] Binding of purified proteins

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


Reference(s)    

 [1] Teramoto J., Yoshimura SH., Takeyasu K., Ishihama A., 2010, A novel nucleoid protein of Escherichia coli induced under anaerobiotic growth conditions., Nucleic Acids Res 38(11):3605-18

 [2] Kim OB., Reimann J., Lukas H., Schumacher U., Grimpo J., Dunnwald P., Unden G., 2009, Regulation of tartrate metabolism by TtdR and relation to the DcuS-DcuR-regulated C4-dicarboxylate metabolism of Escherichia coli., Microbiology 155(Pt 11):3632-40

 [3] 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

 [4] Oshima T., Biville F., 2006, Functional identification of ygiP as a positive regulator of the ttdA-ttdB-ygjE operon., Microbiology 152(Pt 7):2129-35


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