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AidB DNA-binding transcriptional repressor

Synonyms: AidB-isovaleryl-CoA
Summary:
AidB is a multifunctional protein that forms part of E.coli's adaptive response to alkylating agents as defined by the ada regulon. The biological role of AidB is not clear - the purified protein has low levels of isovaleryl-CoA dehydrogenase activity, displays DNA binding activity and can negatively regulate its own expression in vivo. Apo AidB has a high affinity for flavin adenine dinucleotide (FAD), which helps with the assembly of the AidB tetramer [2] AidB was overexpressed, purified, and found to contain a FAD cofactor in stoichiometric quantities [3] The purified protein has a very low level of isovaleryl-CoA dehydrogenase activity and binds double-stranded DNA with a preference for methylated and/or relaxed DNA [3] In in vitro binding experiments AidB shows preferential binding to a DNA region that includes the upstream sequence and -35 box of its own promoter [1].
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Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
AidB-isovaleryl-CoA Functional   [APP], [IEP] [1]
Evolutionary Family: AidB_like
Connectivity class: Local Regulator
Gene name: aidB
  Genome position: 4414275-4415900
  Length: 1626 bp / 541 aa
Operon name: aidB
TU(s) encoding the TF:
Transcription unit        Promoter
aidB
aidBp


Regulon       
Regulated gene(s) aidB
Multifun term(s) of regulated gene(s)
repressor (1)
Regulated operon(s) aidB
First gene in the operon(s) aidB
Simple and complex regulons Ada,AidB,Lrp
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[AidB,-](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 (Confirmed, Strong, Weak) References
  AidB-isovaleryl-CoA repressor aidBp Sigma70, Sigma38 -48.0 -76.0 aidB
ttacattgctGGATAAGAATGTTTTAGCAATCTCTTTctgtcatgaa
4414186 4414212 [BPP], [GEA] [1]


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


Evidence    

 [APP] Assay of partially-purified protein

 [IEP] Inferred from expression pattern

 [BPP] Binding of purified proteins

 [GEA] Gene expression analysis



Reference(s)    

 [1] Rippa V., Amoresano A., Esposito C., Landini P., Volkert M., Duilio A., 2010, Specific DNA binding and regulation of its own expression by the AidB protein in Escherichia coli., J Bacteriol 192(23):6136-42

 [2] Hamill MJ, Jost M, Wong C, Elliott SJ, Drennan CL, 2011, Flavin-induced oligomerization in Escherichia coli adaptive response protein AidB., Biochemistry, 2011 Nov 22

 [3] Rohankhedkar MS, Mulrooney SB, Wedemeyer WJ, Hausinger RP, 2006, The AidB component of the Escherichia coli adaptive response to alkylating agents is a flavin-containing, DNA-binding protein., J Bacteriol, 2006 Jan

 [4] Bowles T, Metz AH, O'Quin J, Wawrzak Z, Eichman BF, 2008, Structure and DNA binding of alkylation response protein AidB., Proc Natl Acad Sci U S A, 2008 Oct 7

 [5] Landini P., Hajec LI., Volkert MR., 1994, Structure and transcriptional regulation of the Escherichia coli adaptive response gene aidB., J Bacteriol 176(21):6583-9

 [6] Volkert MR, Nguyen DC, 1984, Induction of specific Escherichia coli genes by sublethal treatments with alkylating agents., Proc Natl Acad Sci U S A, 1984 Jul

 [7] Volkert MR, Nguyen DC, Beard KC, 1986, Escherichia coli gene induction by alkylation treatment., Genetics, 1986 Jan

 [8] Asad LM, Asad NR, Silva AB, Felzenszwalb I, Leitão AC, 1997, Hydrogen peroxide induces protection against N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) effects in Escherichia coli., Mutat Res, 1997 Mar 12

 [9] Volkert MR, Gately FH, Hajec LI, 1989, Expression of DNA damage-inducible genes of Escherichia coli upon treatment with methylating, ethylating and propylating agents., Mutat Res, 1989 Mar

 [10] Landini P., Volkert MR., 1995, Transcriptional activation of the Escherichia coli adaptive response gene aidB is mediated by binding of methylated Ada protein. Evidence for a new consensus sequence for Ada-binding sites., J Biol Chem 270(14):8285-9

 [11] Landini P., Volkert MR., 1995, RNA polymerase alpha subunit binding site in positively controlled promoters: a new model for RNA polymerase-promoter interaction and transcriptional activation in the Escherichia coli ada and aidB genes., EMBO J 14(17):4329-35

 [12] Landini P., Bown JA., Volkert MR., Busby SJ., 1998, Ada protein-RNA polymerase sigma subunit interaction and alpha subunit-promoter DNA interaction are necessary at different steps in transcription initiation at the Escherichia coli Ada and aidB promoters., J Biol Chem 273(21):13307-12

 [13] Landini P., Busby SJ., 1999, The Escherichia coli Ada protein can interact with two distinct determinants in the sigma70 subunit of RNA polymerase according to promoter architecture: identification of the target of Ada activation at the alkA promoter., J Bacteriol 181(5):1524-9

 [14] Lacour S, Kolb A, Boris Zehnder AJ, Landini P, 2002, Mechanism of specific recognition of the aidB promoter by sigma(S)-RNA polymerase., Biochem Biophys Res Commun, 2002 Apr 12

 [15] Lacour S., Kolb A., Landini P., 2003, Nucleotides from -16 to -12 determine specific promoter recognition by bacterial sigmaS-RNA polymerase., J Biol Chem 278(39):37160-8

 [16] Fram RJ, Marinus MG, Volkert MR, 1988, Gene expression in E. coli after treatment with streptozotocin., Mutat Res, 1988 Mar

 [17] Volkert MR, Hajec LI, Nguyen DC, 1989, Induction of the alkylation-inducible aidB gene of Escherichia coli by anaerobiosis., J Bacteriol, 1989 Feb

 [18] Smirnova GV., Oktyabrsky ON., Moshonkina EV., Zakirova NV., 1994, Induction of the alkylation-inducible aidB gene of Escherichia coli by cytoplasmic acidification and N-ethylmaleimide., Mutat Res 314(1):51-6

 [19] Volkert MR., Hajec LI., Matijasevic Z., Fang FC., Prince R., 1994, Induction of the Escherichia coli aidB gene under oxygen-limiting conditions requires a functional rpoS (katF) gene., J Bacteriol 176(24):7638-45

 [20] Landini P., Hajec LI., Nguyen LH., Burgess RR., Volkert MR., 1996, The leucine-responsive regulatory protein (Lrp) acts as a specific repressor for sigma s-dependent transcription of the Escherichia coli aidB gene., Mol Microbiol 20(5):947-55

 [21] Matijasevic Z., Hajec LI., Volkert MR., 1992, Anaerobic induction of the alkylation-inducible Escherichia coli aidB gene involves genes of the cysteine biosynthetic pathway., J Bacteriol 174(6):2043-6

 [22] Volkert MR., 1988, Adaptive response of Escherichia coli to alkylation damage., Environ Mol Mutagen 11(2):241-55

 [23] Landini P, Volkert MR, 2000, Regulatory responses of the adaptive response to alkylation damage: a simple regulon with complex regulatory features., J Bacteriol, 2000 Dec

 [24] Sedgwick B, Lindahl T, 2002, Recent progress on the Ada response for inducible repair of DNA alkylation damage., Oncogene, 2002 Dec 16

 [25] Janion C, 2006, [Chemically methylated DNA repair in Escherichia coli--the role of alkB protein]., Postepy Biochem, 2006



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