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AllS DNA-binding transcriptional activator

Synonyms: AllS, AllS-allantoin
Summary:
AllS, "allantoin", transcriptional activator participates in controlling genes involved in the utilization of allantoin as a nitrogen source. Although AllS binding does not depend on the presence of allantoin, this compound appears to be necessary for activation, perhaps by interacting with AllS [1] AllS belongs to the LysR family of transcriptional regulators, and like other members of this family, it has a putative helix-turn-helix motif in the N-terminal domain [1] Expression of the allS gene is negligible under aerobic conditions and is increased under anaerobic conditions in the presence of glyoxylate or allantoin. In the absence of its repressor, AllR, allS is expressed under nitrogen-limiting growth conditions, but its induction is independent of the regulators Nac and NtrC, which are active under these conditions [1]


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
AllS Non-Functional   Apo [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IEP-GENE-EXPRESSION-ANALYSIS] S [1]
AllS-allantoin Functional Allosteric Holo [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IEP-GENE-EXPRESSION-ANALYSIS] S [1]
Evolutionary Family: LysR
Sensing class: Sensing external and internal signals
Connectivity class: Local Regulator
Gene name: allS
  Genome position: 531295-532221
  Length: 927 bp / 308 aa
Operon name: allS
TU(s) encoding the TF:
Transcription unit        Promoter
allS
allSp


Regulon       
Regulated gene(s) allC, allD, allE
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
allantoin assimilation (3)
nitrogen metabolism (3)
Regulated operon(s) allDCE
First gene in the operon(s) allD
Simple and complex regulons AllS
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[AllS,+](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
  AllS-allantoin activator allDp Sigma70 -94.0 -142.0 allD, allC, allE
tttaataagcGTTGTTGTTTTAAAAAtcaggttaaa
 546498 546513 [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] W [1], [1], [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-IDA-BINDING-OF-PURIFIED-PROTEINS] Binding of purified proteins

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

 [COMP-HINF-SIMILAR-TO-CONSENSUS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

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

 [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] Binding of cellular extracts


Reference(s)    

 [1] Rintoul MR., Cusa E., Baldoma L., Badia J., Reitzer L., Aguilar J., 2002, Regulation of the Escherichia coli allantoin regulon: coordinated function of the repressor AllR and the activator AllS., J Mol Biol 324(4):599-610

 [2] 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


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