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AllR DNA-binding transcriptional repressor

Synonyms: AllR-allantoin, AllR-glyoxylate, AllR
Summary:
AllR (for "allantoin repressor") regulates several genes involved in the anaerobic utilization of allantoin as a nitrogen source [1, 4] At very low concentrations of glyoxylate, AllR represses transcription from allAp, allSp, and gclp. A highly conserved region featuring an almost perfect palindromic sequence has been identified in gclp and in the intergenic region between the divergent promoters allAp and allSp. It has been proven that AllR binds to this region, and it has been proposed that it may interfere with RNA polymerase by steric hindrance or contact inhibition, thus repressing transcription. In the presence of glyoxylate (the coeffector molecule of this regulator), DNA binding by AllR is inhibited and transcription of the allantoin regulon is derepressed [1, 5] AllR belongs to the IclR family. Members of this family of regulators feature a conserved domain architecture, with a DNA-binding motif in the N-terminal domain and a ligand-binding motif in the C-terminal domain. This regulator adopts a tetrameric conformation [1, 5] The allR gene is expressed under both aerobic and anaerobic conditions, and it is autoregulated [5] 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
AllR Functional   Apo [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IEP-GENE-EXPRESSION-ANALYSIS] S [1]
AllR-allantoin Functional   Holo nd nd nd
AllR-glyoxylate Non-Functional Allosteric Holo [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IEP-GENE-EXPRESSION-ANALYSIS] S [1]
Evolutionary Family: IclR
TFBs length: 17
TFBs symmetry: inverted-repeat
Sensing class: External sensing using transported metabolites
Connectivity class: Local Regulator
Gene name: allR
  Genome position: 533011-533826
  Length: 816 bp / 271 aa
Operon name: allR
TU(s) encoding the TF:
Transcription unit        Promoter
allR
allRp


Regulon       
Regulated gene(s) allA, allB, allS, gcl, glxK, glxR, hyi, ybbW, ybbY
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
glyoxylate degradation (3)
allantoin assimilation (2)
nitrogen metabolism (2)
glycolate metabolism (2)
carbon compounds (2)
Read more >
Regulated operon(s) allA, allS, gcl-hyi-glxR-ybbW-allB-ybbY-glxK
First gene in the operon(s) allA, allS, gcl
Simple and complex regulons AllR
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[AllR,-](3)


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
  AllR-allantoin repressor allAp nd -53.0 -114.0 allA
aaatctagttTTGGAAAAATATTCCAActtttgtatt
 532329 532345 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [1], [1], [2], [2], [3]
  AllR-allantoin repressor allSp nd -37.0 -116.0 allS
aatacaaaagTTGGAATATTTTTCCAAaactagattt
 532329 532345 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [1], [1], [2], [2], [3]
  AllR-allantoin repressor gclp Sigma70 -20.0 -29.0 gcl, hyi, glxR, ybbW, allB, ybbY, glxK
aatttgaaagTTGGAAAAATTTTCCAAtaaatagagg
 533879 533895 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [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-IDA-BINDING-OF-PURIFIED-PROTEINS] Binding of purified proteins

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

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

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

 [EXP-IMP-SITE-MUTATION] Site mutation


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] Hasegawa A., Ogasawara H., Kori A., Teramoto J., Ishihama A., 2008, The transcription regulator AllR senses both allantoin and glyoxylate and controls a set of genes for degradation and reutilization of purines., Microbiology 154(Pt 11):3366-78

 [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] Cusa E., Obradors N., Baldoma L., Badia J., Aguilar J., 1999, Genetic analysis of a chromosomal region containing genes required for assimilation of allantoin nitrogen and linked glyoxylate metabolism in Escherichia coli., J Bacteriol 181(24):7479-84

 [5] Walker JR, Altamentova S, Ezersky A, Lorca G, Skarina T, Kudritska M, Ball LJ, Bochkarev A, Savchenko A, 2006, Structural and biochemical study of effector molecule recognition by the E.coli glyoxylate and allantoin utilization regulatory protein AllR., J Mol Biol, 358(3):810 10.1016/j.jmb.2006.02.034


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