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BirA DNA-binding transcriptional repressor

Synonyms: BirA, BirA-biotinyl-5'-adenylate
Summary:
BirA is a bifunctional protein that exhibits biotin ligase activity and also acts as the DNA binding transcriptional repressor of the biotin operon [6]. The effector of BirA transcriptional repression activity, biotinyl-5'-adenylate (bio-5'-AMP), is also a substrate in the BirA-mediated biotinylation of the biotin carboxyl carrier protein monomer (apoBCCP), and this relationship results in repression of the biotin operon when the abundance of apoBCCP (and therefore the cellular demand for biotin) is reduced [7]. BirA is observed to be predominantly monomeric in solution [6, 8, 9], with some minor multimeric species observed [6]. BirA binds as a dimer to its 40 bp DNA site, the biotin operator [4]. An additional, low-affinity BirA DNA binding site has been identified [10].
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Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
BirA Non-Functional   Apo nd nd
BirA-biotinyl-5'-adenylate Functional Allosteric Holo [HIFS], [IPI], [SM] [1], [2]
Evolutionary Family: BirA
Sensing class: Using internal synthesized signals
Connectivity class: Local Regulator
Gene name: birA
  Genome position: 4173082-4174047
  Length: 966 bp / 321 aa
Operon name: murB-birA
TU(s) encoding the TF:
Transcription unit        Promoter
 
 


Regulon       
Regulated gene(s) bioA, bioB, bioC, bioD, bioF
Multifun term(s) of regulated gene(s)
biotin (5)
Regulated operon(s) bioA, bioBFCD
First gene in the operon(s) bioA, bioB
Simple and complex regulons BirA
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[BirA,-](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 (Confirmed, Strong, Weak) References
  BirA-biotinyl-5'-adenylate repressor bioAp Sigma70 11.5 -24.5 bioA
aattcggtgtAGACTTGTAAACCTAAATCTTTTCAATTTGGTTTACAAGTCgattatgaca
809262 809302 [SM] [3], [4], [5]
  BirA-biotinyl-5'-adenylate repressor bioBp Sigma70 -20.5 -62.5 bioB, bioF, bioC, bioD
tgtcataatcGACTTGTAAACCAAATTGAAAAGATTTAGGTTTACAAGTCTacaccgaatt
809262 809302 [SM] [3], [4], [5]


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


Evidence    

 [HIFS] Human inference of function from sequence

 [IPI] Inferred from physical interaction

 [SM] Site mutation



Reference(s)    

 [1] Buoncristiani MR., Howard PK., Otsuka AJ., 1986, DNA-binding and enzymatic domains of the bifunctional biotin operon repressor (BirA) of Escherichia coli., Gene 44(2-3):255-61

 [2] Wilson KP, Shewchuk LM, Brennan RG, Otsuka AJ, Matthews BW, 1992, Escherichia coli biotin holoenzyme synthetase/bio repressor crystal structure delineates the biotin- and DNA-binding domains., Proc Natl Acad Sci U S A, 1992 Oct 1

 [3] Cronan JE., 1989, The E. coli bio operon: transcriptional repression by an essential protein modification enzyme., Cell 58(3):427-9

 [4] Lin KC., Campbell A., Shiuan D., 1991, Binding characteristics of Escherichia coli biotin repressor-operator complex., Biochim Biophys Acta 1090(3):317-25

 [5] Otsuka A., Abelson J., 1978, The regulatory region of the biotin operon in Escherichia coli., Nature 276(5689):689-94

 [6] Eisenberg MA, Prakash O, Hsiung SC, 1982, Purification and properties of the biotin repressor. A bifunctional protein., J Biol Chem, 1982 Dec 25

 [7] Beckett D., 1998, Energetic methods to study bifunctional biotin operon repressor., Methods Enzymol 295:424-50

 [8] Abbott J, Beckett D, 1993, Cooperative binding of the Escherichia coli repressor of biotin biosynthesis to the biotin operator sequence., Biochemistry, 1993 Sep 21

 [9] Streaker ED, Beckett D, 1998, Coupling of site-specific DNA binding to protein dimerization in assembly of the biotin repressor-biotin operator complex., Biochemistry, 1998 Mar 3

 [10] Subrahmanyam S, Cronan JE Jr, 1999, Isolation from genomic DNA of sequences binding specific regulatory proteins by the acceleration of protein electrophoretic mobility upon DNA binding., Gene, 1999 Jan 21

 [11] Streaker ED, Beckett D, 2003, Coupling of protein assembly and DNA binding: biotin repressor dimerization precedes biotin operator binding., J Mol Biol, 2003 Jan 31

 [12] Weaver LH, Kwon K, Beckett D, Matthews BW, 2001, Competing protein:protein interactions are proposed to control the biological switch of the E coli biotin repressor., Protein Sci, 2001 Dec

 [13] Eisenstein E, Beckett D, 1999, Dimerization of the Escherichia coli biotin repressor: corepressor function in protein assembly., Biochemistry, 1999 Oct 5

 [14] Weaver LH, Kwon K, Beckett D, Matthews BW, 2001, Corepressor-induced organization and assembly of the biotin repressor: a model for allosteric activation of a transcriptional regulator., Proc Natl Acad Sci U S A, 2001 May 22

 [15] Prakash O, Eisenberg MA, 1978, In vitro synthesis and and regulation of the biotin enzymes of Escherichia coli K-12., J Bacteriol, 1978 Jun

 [16] Brennan RG, Vasu S, Matthews BW, Otsuka AJ, 1989, Crystallization of the bifunctional biotin operon repressor., J Biol Chem, 1989 Jan 5

 [17] Xu Y, Nenortas E, Beckett D, 1995, Evidence for distinct ligand-bound conformational states of the multifunctional Escherichia coli repressor of biotin biosynthesis., Biochemistry, 1995 Dec 26

 [18] Streaker ED, Beckett D, 1999, Ligand-linked structural changes in the Escherichia coli biotin repressor: the significance of surface loops for binding and allostery., J Mol Biol, 1999 Sep 24

 [19] Kwon K, Streaker ED, Ruparelia S, Beckett D, 2000, Multiple disordered loops function in corepressor-induced dimerization of the biotin repressor., J Mol Biol, 2000 Dec 15

 [20] Kwon K, Streaker ED, Beckett D, 2002, Binding specificity and the ligand dissociation process in the E. coli biotin holoenzyme synthetase., Protein Sci, 2002 Mar

 [21] Xu Y, Beckett D, 1994, Kinetics of biotinyl-5'-adenylate synthesis catalyzed by the Escherichia coli repressor of biotin biosynthesis and the stability of the enzyme-product complex., Biochemistry, 1994 Jun 14

 [22] Nenortas E, Beckett D, 1996, Purification and characterization of intact and truncated forms of the Escherichia coli biotin carboxyl carrier subunit of acetyl-CoA carboxylase., J Biol Chem, 1996 Mar 29

 [23] Xu Y, Johnson CR, Beckett D, 1996, Thermodynamic analysis of small ligand binding to the Escherichia coli repressor of biotin biosynthesis., Biochemistry, 1996 Apr 30

 [24] Streaker ED, Gupta A, Beckett D, 2002, The biotin repressor: thermodynamic coupling of corepressor binding, protein assembly, and sequence-specific DNA binding., Biochemistry, 2002 Dec 3

 [25] Schatz PJ, 1993, Use of peptide libraries to map the substrate specificity of a peptide-modifying enzyme: a 13 residue consensus peptide specifies biotinylation in Escherichia coli., Biotechnology (N Y), 1993 Oct

 [26] Cronan JE Jr, 1990, Biotination of proteins in vivo. A post-translational modification to label, purify, and study proteins., J Biol Chem, 1990 Jun 25

 [27] Beckett D, Kovaleva E, Schatz PJ, 1999, A minimal peptide substrate in biotin holoenzyme synthetase-catalyzed biotinylation., Protein Sci, 1999 Apr

 [28] Reche PA, Howard MJ, Broadhurst RW, Perham RN, 2000, Heteronuclear NMR studies of the specificity of the post-translational modification of biotinyl domains by biotinyl protein ligase., FEBS Lett, 2000 Aug 18

 [29] Polyak SW, Chapman-Smith A, Mulhern TD, Cronan JE Jr, Wallace JC, 2001, Mutational analysis of protein substrate presentation in the post-translational attachment of biotin to biotin domains., J Biol Chem, 2001 Feb 2

 [30] Murtif VL, Samols D, 1987, Mutagenesis affecting the carboxyl terminus of the biotinyl subunit of transcarboxylase. Effects on biotination., J Biol Chem, 1987 Aug 25

 [31] Val DL, Chapman-Smith A, Walker ME, Cronan JE Jr, Wallace JC, 1995, Polymorphism of the yeast pyruvate carboxylase 2 gene and protein: effects on protein biotinylation., Biochem J, 1995 Dec 15

 [32] He C, Custer G, Wang J, Matysiak S, Beckett D, 2018, Superrepression through Altered Corepressor-Activated Protein:Protein Interactions., Biochemistry, 2018 Feb 20

 [33] Howard PK., Shaw J., Otsuka AJ., 1985, Nucleotide sequence of the birA gene encoding the biotin operon repressor and biotin holoenzyme synthetase functions of Escherichia coli., Gene 35(3):321-31

 [34] Barker DF, Campbell AM, 1980, Use of bio-lac fusion strains to study regulation of biotin biosynthesis in Escherichia coli., J Bacteriol, 1980 Aug

 [35] Campbell A., Chang R., Barker D., Ketner G., 1980, Biotin regulatory (bir) mutations of Escherichia coli., J Bacteriol 142(3):1025-8

 [36] Eisenburg MA., Mee B., Prakash O., Eisenburg MR., 1975, Properties of alpha-dehydrobiotin-resistant mutants of Escherichia coli K-12., J Bacteriol 122(1):66-72

 [37] Xu Y, Beckett D, 1996, Evidence for interdomain interaction in the Escherichia coli repressor of biotin biosynthesis from studies of an N-terminal domain deletion mutant., Biochemistry, 1996 Feb 13

 [38] Kwon K, Beckett D, 2000, Function of a conserved sequence motif in biotin holoenzyme synthetases., Protein Sci, 2000 Aug

 [39] Chapman-Smith A, Mulhern TD, Whelan F, Cronan JE Jr, Wallace JC, 2001, The C-terminal domain of biotin protein ligase from E. coli is required for catalytic activity., Protein Sci, 2001 Dec

 [40] Buoncristiani MR, Otsuka AJ, 1988, Overproduction and rapid purification of the biotin operon repressor from Escherichia coli., J Biol Chem, 1988 Jan 15

 [41] Saviranta P, Haavisto T, Rappu P, Karp M, Lövgren T, 1998, In vitro enzymatic biotinylation of recombinant fab fragments through a peptide acceptor tail., Bioconjug Chem, 1998 Nov-Dec

 [42] Wu SC, Yeung JC, Hwang PM, Wong SL, 2002, Design, production, and characterization of an engineered biotin ligase (BirA) and its application for affinity purification of staphylokinase produced from Bacillus subtilis via secretion., Protein Expr Purif, 2002 Apr

 [43] Reche PA., 2000, Lipoylating and biotinylating enzymes contain a homologous catalytic module., Protein Sci 9(10):1922-9

 [44] Duffy S, Tsao KL, Waugh DS, 1998, Site-specific, enzymatic biotinylation of recombinant proteins in Spodoptera frugiperda cells using biotin acceptor peptides., Anal Biochem, 1998 Sep 10

 [45] Smith PA, Tripp BC, DiBlasio-Smith EA, Lu Z, LaVallie ER, McCoy JM, 1998, A plasmid expression system for quantitative in vivo biotinylation of thioredoxin fusion proteins in Escherichia coli., Nucleic Acids Res, 1998 Mar 15

 [46] Parrott MB, Barry MA, 2001, Metabolic biotinylation of secreted and cell surface proteins from mammalian cells., Biochem Biophys Res Commun, 2001 Mar 9

 [47] Jander G, Cronan JE Jr, Beckwith J, 1996, Biotinylation in vivo as a sensitive indicator of protein secretion and membrane protein insertion., J Bacteriol, 1996 Jun

 [48] Cloutier SM, Couty S, Terskikh A, Marguerat L, Crivelli V, Pugnières M, Mani JC, Leisinger HJ, Mach JP, Deperthes D, 2000, Streptabody, a high avidity molecule made by tetramerization of in vivo biotinylated, phage display-selected scFv fragments on streptavidin., Mol Immunol, 2000 Dec

 [49] Skowronek K, Kasprzak AA, 2002, A two-plasmid system for independent genetic manipulation of subunits of homodimeric proteins and selective isolation of chimeric dimers., Anal Biochem, 2002 Jan 15

 [50] Steinkühler C, Biasiol G, Cerretani M, Di Renzo L, Brunetti M, Ingallinella P, De Francesco R, Altamura S, 2002, A scintillation proximity active site binding assay for the hepatitis C virus serine protease., Anal Biochem, 2002 Aug 1

 [51] Commichau FM, Stülke J, 2008, Trigger enzymes: bifunctional proteins active in metabolism and in controlling gene expression., Mol Microbiol, 2008 Feb

 [52] Beckett D, 2007, Biotin sensing: universal influence of biotin status on transcription., Annu Rev Genet, 2007

 [53] Chapman-Smith A, Cronan JE Jr, 1999, The enzymatic biotinylation of proteins: a post-translational modification of exceptional specificity., Trends Biochem Sci, 1999 Sep

 [54] Chapman-Smith A, Cronan JE Jr, 1999, In vivo enzymatic protein biotinylation., Biomol Eng, 1999 Dec 31



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