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RspR DNA-binding transcriptional repressor

Synonyms: RspR
Summary:
YdfH belongs to the GntR transcription factor family [4], for which the consensus sequence is reported to be tnGTnnnACna [5]. Although only one site was determined in a gel shift assay, it is possible that YfdH binds as a complex of flanking regions of the core sequence (-65 to -50) [1]. It was determined by Genomic SELEX screening that a site located upstream of rspAB is the only target of RspR [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
RspR Functional   nd nd nd
Evolutionary Family: GntR
TFBs symmetry: inverted-repeat
Connectivity class: Local Regulator
Gene name: rspR
  Genome position: 1628352-1629038
  Length: 687 bp / 228 aa
Operon name: rspR
TU(s) encoding the TF:
Transcription unit        Promoter
ydfH
ydfHp


Regulon       
Regulated gene(s) rspA, rspB
Multifun term(s) of regulated gene(s)
starvation (2)
Regulated operon(s) rspAB
First gene in the operon(s) rspA
Simple and complex regulons CRP,RspR
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[RspR,-](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
  RspR repressor rspAp nd -35.0 -65.0 rspA, rspB
tttcgatcttTATACTTGTATggtagtagct
 1655201 1655211 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [1], [1], [2], [2], [3]


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

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

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


Reference(s)    

 [1] Sakihama Y., Mizoguchi H., Oshima T., Ogasawara N., 2012, YdfH identified as a repressor of rspA by the use of reduced genome Escherichia coli MGF-01., Biosci Biotechnol Biochem 76(9):1688-93

 [2] Shimada T., Ogasawara H., Kobayashi I., Kobayashi N., Ishihama A., 2021, Single-Target Regulators Constitute the Minority Group of Transcription Factors in Escherichia coli K-12., Front Microbiol 12:697803

 [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] Perez-Rueda E., Collado-Vides J., 2000, The repertoire of DNA-binding transcriptional regulators in Escherichia coli K-12., Nucleic Acids Res 28(8):1838-47

 [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


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