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PepA DNA-binding transcriptional repressor

Synonyms: PepA
Summary:
Aminopeptidase A/I is a Peptidase that binds DNA and controls the transcription of the operon involved in the synthesis of carbamoyl phosphate, which is an intermediate related to the pyrimidine nucleotide pathway [1, 2, 3, 4]. This protein also is required for maintenance of plasmid monomers, which is critical for proper plasmid segregation [4, 5, 6, 7, 8]. Aminopeptidase A/I is a part of the site-specific recombination system required to decatenate the plasmids ColE1 and pSC101, maintaining them as monomers [6, 9, 10]. Aminopeptidase A/I is responsible for coordinating DNA strands during recombination, pairing cer sites in ColE1 plasmids and allowing the formation of Holliday junctions [11, 12, 13]. Aminopeptidase A/I, along with ArgR, may be involved in blocking trans-recombination, thus preventing the formation of new catenated plasmids during recombination [14].
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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
PepA Functional   nd nd nd
Evolutionary Family: Aminopeptidase
TFBs length: 27
TFBs symmetry: inverted-repeat
Connectivity class: Local Regulator
Gene name: pepA
  Genome position: 4484440-4485951
  Length: 1512 bp / 503 aa
Operon name: pepA
TU(s) encoding the TF:
Transcription unit        Promoter
pepA
pepAp1
pepA
pepAp2
pepA
pepAp3


Regulon       
Regulated gene(s) carA, carB, pepA
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
arginine (2)
pyrimidine biosynthesis (2)
proteins/peptides/glycopeptides (1)
DNA recombination (1)
Transcription related (1)
Regulated operon(s) carAB, pepA
First gene in the operon(s) carA, pepA
Simple and complex regulons Fis,IHF,PepA,PurR,RutR
PepA
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[PepA,-](2)


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
  PepA repressor carAp1 Sigma70 -173.0 -273.0 carA, carB
aattttgaccATTTGGTCCACTTTTTTCTGCTCGTTTttatttcatg
 29365 29391 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IMP], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [1], [2], [2], [3]
  PepA repressor carAp1 Sigma70 -79.0 -179.0 carA, carB
ttttgtcgctTAATGCCTGTAAAACATGCATGAGCCAcaaaataata
 29459 29485 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [1], [2], [2], [3]
  PepA repressor pepAp1 Sigma70 -43.0 -231.0 pepA
cgtaaaaactCGTCTTTTGCAGGATTTTAGCTTGTTTcatggcttaa
 4486169 4486195 [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [3], [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-IMP] Inferred from mutant phenotype

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


Reference(s)    

 [1] Devroede N., Huysveld N., Charlier D., 2006, Mutational analysis of intervening sequences connecting the binding sites for integration host factor, PepA, PurR, and RNA polymerase in the control region of the Escherichia coli carAB operon, encoding carbamoylphosphate synthase., J Bacteriol 188(9):3236-45

 [2] Devroede N., Thia-Toong TL., Gigot D., Maes D., Charlier D., 2004, Purine and pyrimidine-specific repression of the Escherichia coli carAB operon are functionally and structurally coupled., J Mol Biol 336(1):25-42

 [3] Charlier D., Hassanzadeh G., Kholti A., Gigot D., Pierard A., Glansdorff N., 1995, carP, involved in pyrimidine regulation of the Escherichia coli carbamoylphosphate synthetase operon encodes a sequence-specific DNA-binding protein identical to XerB and PepA, also required for resolution of ColEI multimers., J Mol Biol 250(4):392-406

 [4] Minh PN, Devroede N, Massant J, Maes D, Charlier D, 2009, Insights into the architecture and stoichiometry of Escherichia coli PepA*DNA complexes involved in transcriptional control and site-specific DNA recombination by atomic force microscopy., Nucleic Acids Res, 37(5):1463 10.1093/nar/gkn1078

 [5] Miller CG., Schwartz G., 1978, Peptidase-deficient mutants of Escherichia coli., J Bacteriol 135(2):603-11

 [6] Stirling CJ., Colloms SD., Collins JF., Szatmari G., Sherratt DJ., 1989, xerB, an Escherichia coli gene required for plasmid ColE1 site-specific recombination, is identical to pepA, encoding aminopeptidase A, a protein with substantial similarity to bovine lens leucine aminopeptidase., EMBO J 8(5):1623-7

 [7] Reijns M, Lu Y, Leach S, Colloms SD, 2005, Mutagenesis of PepA suggests a new model for the Xer/cer synaptic complex., Mol Microbiol, 57(4):927 10.1111/j.1365-2958.2005.04716.x

 [8] Paul S, Summers D, 2004, ArgR and PepA, accessory proteins for XerCD-mediated resolution of ColE1 dimers, are also required for stable maintenance of the P1 prophage., Plasmid, 52(1):63 10.1016/j.plasmid.2004.04.003

 [9] Flinn H, Burke M, Stirling CJ, Sherratt DJ, 1989, Use of gene replacement to construct Escherichia coli strains carrying mutations in two genes required for stability of multicopy plasmids., J Bacteriol, 171(4):2241 10.1128/jb.171.4.2241-2243.1989

 [10] Colloms SD, McCulloch R, Grant K, Neilson L, Sherratt DJ, 1996, Xer-mediated site-specific recombination in vitro., EMBO J, 15(5):1172 None

 [11] Gourlay SC., Colloms SD., 2004, Control of Cre recombination by regulatory elements from Xer recombination systems., Mol Microbiol 52(1):53-65

 [12] Guhathakurta A, Summers D, 1995, Involvement of ArgR and PepA in the pairing of ColE1 dimer resolution sites., Microbiology (Reading), 141 ( Pt 5)(None):1163 10.1099/13500872-141-5-1163

 [13] McCulloch R, Coggins LW, Colloms SD, Sherratt DJ, 1994, Xer-mediated site-specific recombination at cer generates Holliday junctions in vivo., EMBO J, 13(8):1844 None

 [14] Guhathakurta A, Viney I, Summers D, 1996, Accessory proteins impose site selectivity during ColE1 dimer resolution., Mol Microbiol, 20(3):613 10.1046/j.1365-2958.1996.5471072.x

 [15] McCulloch R, Burke ME, Sherratt DJ, 1994, Peptidase activity of Escherichia coli aminopeptidase A is not required for its role in Xer site-specific recombination., Mol Microbiol, 12(2):241 10.1111/j.1365-2958.1994.tb01013.x

 [16] Charlier D., Gigot D., Huysveld N., Roovers M., Pierard A., Glansdorff N., 1995, Pyrimidine regulation of the Escherichia coli and Salmonella typhimurium carAB operons: CarP and integration host factor (IHF) modulate the methylation status of a GATC site present in the control region., J Mol Biol 250(4):383-91

 [17] Charlier D, Kholti A, Huysveld N, Gigot D, Maes D, Thia-Toong TL, Glansdorff N, 2000, Mutational analysis of Escherichia coli PepA, a multifunctional DNA-binding aminopeptidase., J Mol Biol, 302(2):411 10.1006/jmbi.2000.4067

 [18] 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

 [19] Sträter N, Sherratt DJ, Colloms SD, 1999, X-ray structure of aminopeptidase A from Escherichia coli and a model for the nucleoprotein complex in Xer site-specific recombination., EMBO J, 18(16):4513 10.1093/emboj/18.16.4513

 [20] Commichau FM, Stülke J, 2008, Trigger enzymes: bifunctional proteins active in metabolism and in controlling gene expression., Mol Microbiol, 67(4):692 10.1111/j.1365-2958.2007.06071.x


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