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AlpA DNA-binding transcriptional repressor

Synonyms: AlpA
Summary:
AlpA is a transcriptional regulator of intA expression [2]. It is part of the CP4-57 cryptic prophage that is similar to bacteriophage P4 [3]. AlpA is also involved in the negative regulation of cell persister resuscitation [1] alpA was first identified as a multicopy suppressor of lon mutants that leads to the expression of an alternative Lon protease activity named Alp [2, 4]. AlpA expression leads to increased synthesis of IntA, which results in excision of the CP4-57 cryptic prophage. The excision inactivates the gene upstream of intA, ssrA, encoding |FRAME: SSRA-RNA| [3]. Expression of alpA increases 6.5-fold upon deletion of tqsA; alpA expression may thus be involved in biofilm formation [5]. CP4-57: "cryptic P4-like prophage at min 57" [3] AlpA: "alternative Lon protease" [4] 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
AlpA Functional   nd nd nd
Evolutionary Family: AlpA
TFBs symmetry: inverted-repeat
Connectivity class: Local Regulator
Gene name: alpA
  Genome position: 2758644-2758856
  Length: 213 bp / 70 aa
Operon name: alpA
TU(s) encoding the TF:
Transcription unit        Promoter
alpA
 


Regulon       
Regulated gene(s) phoB, phoR
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
phosphorous metabolism (2)
two component regulatory systems (external signal) (2)
Transcription related (1)
activator (1)
repressor (1)
Read more >
Regulated operon(s) phoBR
First gene in the operon(s) phoB
Simple and complex regulons AlpA,PhoB
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[AlpA,-](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
  AlpA repressor phoBp Sigma70 nd nd phoB, phoR
nd
 nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [1]



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
  AlpA activator intA Transcription-Unit nd
nd
nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [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-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis


Reference(s)    

 [1] Song S., Kim JS., Yamasaki R., Oh S., Benedik MJ., Wood TK., 2021, Escherichia coli cryptic prophages sense nutrients to influence persister cell resuscitation., Environ Microbiol 23(11):7245-7254

 [2] Trempy JE., Kirby JE., Gottesman S., 1994, Alp suppression of Lon: dependence on the slpA gene., J Bacteriol 176(7):2061-7

 [3] Kirby JE., Trempy JE., Gottesman S., 1994, Excision of a P4-like cryptic prophage leads to Alp protease expression in Escherichia coli., J Bacteriol 176(7):2068-81

 [4] Trempy JE., Gottesman S., 1989, Alp, a suppressor of lon protease mutants in Escherichia coli., J Bacteriol 171(6):3348-53

 [5] Herzberg M., Kaye IK., Peti W., Wood TK., 2006, YdgG (TqsA) controls biofilm formation in Escherichia coli K-12 through autoinducer 2 transport., J Bacteriol 188(2):587-98


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