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PaaX DNA-binding transcriptional repressor

Synonyms: PaaX
The phenylacetic acid regulator [4], PaaX, is a transcriptional repressor that participates in controlling transcriptional regulation of genes involved in the catabolism of an aromatic compound, phenylacetic acid (PA) [1]. When PaaX is overexpressed, it causes elevated levels of mutations in the genome; therefore, it is a candidate to regulate DNA replication, recombination, or repair [5].
PaaX contains a helix-turn-helix motif for DNA binding that is similar to the motif found in the N terminal of members of the GntR family of transcriptional regulators [4]. Members of this family share similar N-terminal DNA-binding domains but are classified into four subfamilies according to their divergence in their C-terminal domains, which are involved in effector binding and oligomerization [6].
Homology with PaaX has been found in other bacteria, such as Pseudomonas putida, Bacillus halodurans, and Arthrobacter sp., among others [1].
The majority of work concerning PaaX has been done in E.
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Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
PaaX     nd nd
Evolutionary Family: PaaX
Sensing class: Using internal synthesized signals
Connectivity class: Local Regulator
Gene name: paaX
  Genome position: 1463539-1464489
  Length: 951 bp / 316 aa
Operon name: paaXY
TU(s) encoding the TF:
Transcription unit        Promoter

Regulated gene(s) paaA, paaB, paaC, paaD, paaE, paaF, paaG, paaH, paaI, paaJ, paaK, paaX, paaY, paaZ
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
carbon compounds (13)
metabolism (1)
Transcription related (1)
repressor (1)
Regulated operon(s) paaABCDEFGHIJK, paaXY, paaZ
First gene in the operon(s) paaA, paaX, paaZ
Simple and complex regulons CRP,IHF,PaaX
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)

Transcription factor binding sites (TFBSs) arrangements       

  Functional conformation Function Promoter Sigma factor Central Rel-Pos Distance to first Gene Genes Sequence LeftPos RightPos Evidence (Confirmed, Strong, Weak) References
  PaaX repressor paaAp Sigma70 30.0 -33.0 paaA, paaB, paaC, paaD, paaE, paaF, paaG, paaH, paaI, paaJ, paaK
1453875 1453913 [BCE], [GEA], [HIBSCS], [SM] [1], [2]
  PaaX repressor paaXp Sigma70 10.5 -20.5 paaX, paaY
1463500 1463537 [BPP], [HIBSCS] [3]
  PaaX repressor paaZp nd -6.5 -34.5 paaZ
1453657 1453696 [BCE], [GEA], [HIBSCS], [SM] [1], [2]

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


 [BCE] Binding of cellular extracts

 [GEA] Gene expression analysis

 [HIBSCS] Human inference based on similarity to consensus sequences

 [SM] Site mutation

 [BPP] Binding of purified proteins


 [1] Ferrandez A., Garcia JL., Diaz E., 2000, Transcriptional regulation of the divergent paa catabolic operons for phenylacetic acid degradation in Escherichia coli., J Biol Chem. 275(16):12214-22

 [2] Kim HS., Kang TS., Hyun JS., Kang HS., 2004, Regulation of penicillin G acylase gene expression in Escherichia coli by repressor PaaX and the cAMP-cAMP receptor protein complex., J Biol Chem. 279(32):33253-62

 [3] Fernandez C., Diaz E., Garcia JL., 2014, Insights on the regulation of the phenylacetate degradation pathway from Escherichia coli., Environ Microbiol Rep. 6(3):239-50

 [4] Ferrandez A., Minambres B., Garcia B., Olivera ER., Luengo JM., Garcia JL., Diaz E., 1998, Catabolism of phenylacetic acid in Escherichia coli. Characterization of a new aerobic hybrid pathway., J Biol Chem. 273(40):25974-86

 [5] Yang H., Wolff E., Kim M., Diep A., Miller JH., 2004, Identification of mutator genes and mutational pathways in Escherichia coli using a multicopy cloning approach., Mol Microbiol. 53(1):283-95

 [6] 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

 [7] del Peso-Santos T., Bartolome-Martin D., Fernandez C., Alonso S., Garcia JL., Diaz E., Shingler V., Perera J., 2006, Coregulation by phenylacetyl-coenzyme A-responsive PaaX integrates control of the upper and lower pathways for catabolism of styrene by Pseudomonas sp. strain Y2., J Bacteriol. 188(13):4812-21

 [8] Rojas-Altuve A., Carrasco-Lopez C., Hernandez-Rocamora VM., Sanz JM., Hermoso JA., 2011, Crystallization and preliminary X-ray diffraction studies of the transcriptional repressor PaaX, the main regulator of the phenylacetic acid degradation pathway in Escherichia coli W., Acta Crystallogr Sect F Struct Biol Cryst Commun. 67(Pt 10):1278-80