DNA-binding protein under anaerobic conditions, Dan , 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 . 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 . Dan may have a functional dichotomy, controlling both the structure and function of the nucleoid .
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 [1, 3].
The ttd pathway for L-tartate fermentation and the dcu pathway for general C4-dicarboxylate metabolism interact at the regulatory level .
Expression of ttdR (dan gene) is positively autoregulated in response to L-tartrate [1, 3] and activated by the two-component system DcuSR in the presence of L-tartrate, meso-tartrate, D-malate or fumarate . ttdR (dan gene) is repressed by FNR and the nitrate and nitrite two-component systems NarXL and NarPQ .Read more >
In an electrophoretic mobility shift assay it was shown that Dan binds to the ttdA-ttdR intergenic region .
Based on genomic SELEX analysis, of a total of 688 Dan-binding sites, 504 were located within intergenic noncoding regions and 184 were within coding regions .
Dan is a DNA-binding protein with recognition preference for the GTTNATT sequence. This motif suggests a role for Dan in resistance to a metal, as with Dps against iron . Dan contains two sets of Cys-Cys pairs: one consisting of Cys170 and Cys193, and other of Cys288 and Cys296 .
Dan is highly expressed in cells grown under hypoxic or anaerobic conditions, and it plays a role in local folding of DNA .
|Connectivity class:||Local Regulator|
|Length:||933 bp / 310 aa|
|TU(s) encoding the TF:||
|Regulated gene(s)||ttdA, ttdB, ttdR, ttdT|
|Multifun term(s) of regulated gene(s)||
MultiFun Term (List of genes associated to the multifun term)
Transcription related (1)
Porters (Uni-, Sym- and Antiporters) (1)
|Regulated operon(s)||ttdABT, ttdR|
|First gene in the operon(s)||ttdA, ttdR|
|Simple and complex regulons|
|Simple and complex regulatory phrases||
Regulatory phrase (List of promoters regulated by the phrase)
|Functional conformation||Function||Promoter||Sigma factor||Central Rel-Pos||Distance to first Gene||Genes||Sequence||LeftPos||RightPos||Evidence (Confirmed, Strong, Weak)||References|
|Dan-L-tartrate||activator||ttdAp||Sigma70||-163.0||-202.0||ttdA, ttdB, ttdT||
|3206258||3206264||[BPP], [GEA], [HIBSCS]||, |
|Dan-L-tartrate||activator||ttdAp||Sigma70||-134.0||-173.0||ttdA, ttdB, ttdT||
|3206287||3206293||[BPP], [GEA], [HIBSCS]||, |
|Dan-L-tartrate||activator||ttdAp||Sigma70||-92.0||-131.0||ttdA, ttdB, ttdT||
|3206329||3206335||[BPP], [GEA], [HIBSCS]||, |
|Dan-L-tartrate||activator||ttdAp||Sigma70||-74.0||-113.0||ttdA, ttdB, ttdT||
|3206347||3206353||[BPP], [GEA], [HIBSCS]||, |
|Dan-L-tartrate||activator||ttdAp||Sigma70||-59.0||-98.0||ttdA, ttdB, ttdT||
|3206362||3206368||[BPP], [GEA], [HIBSCS]||, |
|Alignment and PSSM for Dan TFBSs|
|Aligned TFBS of Dan|
|Position weight matrix (PWM).|
A 1 0 0 2 5 0 0 C 0 0 0 1 0 0 0 G 4 0 1 1 0 0 0 T 0 5 4 1 0 5 5
|Evolutionary conservation of regulatory elements|
 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