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DgoR DNA-binding transcriptional repressor

Synonyms: DgoR, DgoR-D-galactonate
Summary:
DgoR belongs to the FadR subfamily within the GntR family of transcriptional regulators, and its DNA-binding operator sequence is [5'-TTGTA(G/C)TACA(A/T)-3'] [4, 5]. The signature of GntR family regulators that also bind inverted repeats is [5'-(N)yGT(N)xAC(N)y-3'] [6]. As with the the other members of the family, the oligomeric form of DgoR is a dimer [1]. There are three IRs (inverted repeats) in the regulation regions of the dgo genes. DgoR binds the IR1 and IR2 sites in the cis-acting element for repressing the dgoRKADT operon, and IR1 is essential for DgoR activity. The D7, L34, T40, R42, R46, and S51 amino acid residues are important for DgoR to bind its cis-acting element. On the other hand, the IR3 site is not critical for the interaction of DgoR with its cis-acting element [4]. The DgoR binding sites overlap with the promoter, repressing the transcription of the dgoRKADT operon by occluding the binding of RNA polymerase [4, 7]. Based on a bioinformatics study, DgoR exists together with its binding sites in 13 genomes of different bacterial species, with the majority of members belonging to the family Enterobacteriaceae [6]. Production of the enzymes involved in D-galactonate degradation are induced by growth on galactonate [8].
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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
DgoR Functional   nd nd nd
DgoR-D-galactonate Non-Functional   Holo nd nd nd
TFBs symmetry: inverted-repeat
Connectivity class: Local Regulator
Gene name: dgoR
  Genome position: 3874471-3875160
  Length: 690 bp / 229 aa
Operon name: dgoRKADT
TU(s) encoding the TF:
Transcription unit        Promoter
dgoRKADT
dgoRp


Regulon       
Regulated gene(s) dgoA, dgoD, dgoK, dgoR, dgoT
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
carbon compounds (4)
Transcription related (1)
repressor (1)
operon (1)
Porters (Uni-, Sym- and Antiporters) (1)
Regulated operon(s) dgoRKADT
First gene in the operon(s) dgoR
Simple and complex regulons CRP,DgoR
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[DgoR,-](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
  DgoR repressor dgoRp Sigma70 -110.0 -135.0 dgoR, dgoK, dgoA, dgoD, dgoT
tgtgatctaaATTGTAGTACAAcaatataagt
 3875290 3875301 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-PATTERN-DISCOVERY], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [1], [1], [2], [2], [3], [3], [4], [4]
  DgoR repressor dgoRp Sigma70 -88.5 -113.5 dgoR, dgoK, dgoA, dgoD, dgoT
acaatataagTTTGTACTACATTacacgcacgg
 3875268 3875280 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-PATTERN-DISCOVERY], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [1], [1], [2], [2], [3], [3], [4], [4]


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


Evidence    

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

 [COMP-AINF-PATTERN-DISCOVERY] Automated inference based on sequence pattern discovery

 [COMP-AINF-SIMILAR-TO-CONSENSUS] Automated inference based on similarity to consensus sequences

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

 [EXP-IMP-SITE-MUTATION] Site mutation


Reference(s)    

 [1] Arya G., Pal M., Sharma M., Singh B., Singh S., Agrawal V., Chaba R., 2021, Molecular insights into effector binding by DgoR, a GntR/FadR family transcriptional repressor of D-galactonate metabolism in Escherichia coli., Mol Microbiol 115(4):591-609

 [2] Belliveau NM., Barnes SL., Ireland WT., Jones DL., Sweredoski MJ., Moradian A., Hess S., Kinney JB., Phillips R., 2018, Systematic approach for dissecting the molecular mechanisms of transcriptional regulation in bacteria., Proc Natl Acad Sci U S A 115(21):E4796-E4805

 [3] Lin Z., Sun Y., Liu Y., Tong S., Shang Z., Cai Y., Lin W., 2020, Structural and Functional Analyses of the Transcription Repressor DgoR From Escherichia coli Reveal a Divalent Metal-Containing D-Galactonate Binding Pocket., Front Microbiol 11:590330

 [4] Singh B., Arya G., Kundu N., Sangwan A., Nongthombam S., Chaba R., 2019, Molecular and Functional Insights into the Regulation of d-Galactonate Metabolism by the Transcriptional Regulator DgoR in Escherichia coli., J Bacteriol 201(4)

 [5] Rigali S., Derouaux A., Giannotta F., Dusart J., 2002, Subdivision of the helix-turn-helix GntR family of bacterial regulators in the FadR, HutC, MocR, and YtrA subfamilies., J Biol Chem 277(15):12507-15

 [6] Suvorova IA., Korostelev YD., Gelfand MS., 2015, GntR Family of Bacterial Transcription Factors and Their DNA Binding Motifs: Structure, Positioning and Co-Evolution., PLoS One 10(7):e0132618

 [7] Rojo F, 1999, Repression of transcription initiation in bacteria., J Bacteriol, 181(10):2987 10.1128/JB.181.10.2987-2991.1999

 [8] Deacon J, Cooper RA, 1977, D-Galactonate utilisation by enteric bacteria. The catabolic pathway in Escherichia coli., FEBS Lett, 77(2):201 10.1016/0014-5793(77)80234-2

 [9] Cooper RA, 1978, The utilisation of D-galactonate and D-2-oxo-3-deoxygalactonate by Escherichia coli K-12. Biochemical and genetical studies., Arch Microbiol, 118(2):199 10.1007/BF00415730


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