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PunR DNA-binding transcriptional dual regulator

Synonyms: PunR
Summary:
PunR, formerly named YdhB, regulates a gene involved in the purine transport process in the presence of adenosine [1]. This protein belongs to the LysR family HTH type of transcriptional regulators [1, 2]. It appears to recognize and bind to a palindromic DNA binding motif of 23 bp [1]. The punR gene is located in the genome in an inverted position from its target gene [1]. This arrangement in the genome appears to be conserved in other proteobacteria [1]. A punR knockout mutant reduces cellular growth under nitrogen-limiting conditions [1]. Genome-wide PunR binding sites were determined in vivo by chromatin immunoprecipitation method combined with lambda exonuclease digestion (ChIP-exo) in glucose M9 minimal medium [3]. Read more >


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
PunR Functional   nd nd nd
TFBs symmetry: inverted-repeat
Connectivity class: Local Regulator
Gene name: punR
  Genome position: 1738866-1739798
  Length: 933 bp / 310 aa
Operon name: punR
TU(s) encoding the TF:
Transcription unit        Promoter
ydhB
 


Regulon       
Regulated gene(s)
Regulated operon(s)
First gene in the operon(s)
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)


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



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
  PunR activator punC Gene nd
ccacatagtcTGCCTGCAAAATTTTTGAAACCAGtcatcaaata
1739803 1739826 1739814.0 nd [EXP-IEP-RNA-SEQ], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-GSELEX], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [1]


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


Evidence    


Reference(s)    

 [1] Rodionova IA., Gao Y., Sastry A., Hefner Y., Lim HG., Rodionov DA., Saier MH., Palsson BO., 2021, Identification of a transcription factor, PunR, that regulates the purine and purine nucleoside transporter punC in E. coli., Commun Biol 4(1):991

 [2] Eberhardt S., Richter G., Gimbel W., Werner T., Bacher A., 1996, Cloning, sequencing, mapping and hyperexpression of the ribC gene coding for riboflavin synthase of Escherichia coli., Eur J Biochem 242(3):712-9

 [3] Gao Y., Lim HG., Verkler H., Szubin R., Quach D., Rodionova I., Chen K., Yurkovich JT., Cho BK., Palsson BO., 2021, Unraveling the functions of uncharacterized transcription factors in Escherichia coli using ChIP-exo., Nucleic Acids Res 49(17):9696-9710


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