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DicA DNA-binding transcriptional repressor

Synonyms: DicA
Summary:
The transcription factor DicA, "Division control," is a temperature-sensitive repressor that controls the transcription of genes involved in the cell division process [1, 4, 5, 6] and activation of its own expression [2]. Nevertheless, the signal to which DicA responds is still unknown. The family to which DicA belongs has not been established; it is a protein of 15 kDa with a hypothetical DNA-binding domain in the N-terminal domain [4]. DicA is homologous in structure and function to RovA (Yersinia) and SlyA (Salmonella), both of which are activators for pathogenicity-related genes [2].


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
DicA Functional   nd nd nd
Evolutionary Family: HTH_3
TFBs symmetry: inverted-repeat
Connectivity class: Local Regulator
Gene name: dicA
  Genome position: 1647934-1648341
  Length: 408 bp / 135 aa
Operon name: dicA
TU(s) encoding the TF:
Transcription unit        Promoter
dicA
 


Regulon       
Regulated gene(s) dicB, dicC, insD7, intQ, ydfD, ydfE, ydfW, ydfX
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
prophage genes and phage related functions (7)
cell cycle physiology (1)
Regulated operon(s) dicB-ydfDE-insD7-intQ, dicC-ydfXW
First gene in the operon(s) dicB, dicC
Simple and complex regulons DicA
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[DicA,-](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
  DicA repressor dicBp Sigma70 nd nd dicB, ydfD, ydfE, insD7, intQ
nd
 nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [1], [1]
  DicA repressor dicCp Sigma70 2.5 -24.5 dicC, ydfX, ydfW
taacatctatCTTGTTAGTTATGACTAACAAtaaaggtgtt
 1647865 1647885 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [2], [2], [3]



High-throughput Transcription factor binding sites (TFBSs)
      

  Functional conformation Function Object name Object type Distance to first Gene Sequence LeftPos RightPos Center Position Growth Condition Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) References
  DicA activator dicA Transcription-Unit nd
aacacctttaTTGTTAGTCATAACTAACAAGatagatgtta
1647865 1647885 1647874.5 nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [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-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis

 [COMP-HINF] Inferred by a human based on computational evidence

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

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


Reference(s)    

 [1] Bejar S., Bouche JP., 1985, A new dispensable genetic locus of the terminus region involved in control of cell division in Escherichia coli., Mol Gen Genet 201(2):146-50

 [2] Yun SH., Ji SC., Jeon HJ., Wang X., Kim SW., Bak G., Lee Y., Lim HM., 2012, The CnuK9E H-NS complex antagonizes DNA binding of DicA and leads to temperature-dependent filamentous growth in E. coli., PLoS One 7(9):e45236

 [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] Béjar S, Cam K, Bouché JP, 1986, Control of cell division in Escherichia coli. DNA sequence of dicA and of a second gene complementing mutation dicA1, dicC., Nucleic Acids Res, 14(17):6821 10.1093/nar/14.17.6821

 [5] Cam K., Bejar S., Gil D., Bouche JP., 1988, Identification and sequence of gene dicB: translation of the division inhibitor from an in-phase internal start., Nucleic Acids Res 16(14A):6327-38

 [6] Labie C, Bouché F, Bouché JP, 1989, Isolation and mapping of Escherichia coli mutations conferring resistance to division inhibition protein DicB., J Bacteriol, 171(8):4315 10.1128/jb.171.8.4315-4319.1989


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