RegulonDB RegulonDB 11.0: Operon Form
   

atoDAEB operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: atoDAEB
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit          
Name: atoDAEB
Synonym(s): OP00154, atoDAB
Gene(s): atoD, atoA, atoE, atoB   Genome Browser M3D Gene expression COLOMBOS
Note(s): The expression of the atoDAEB operon is required for short -chain poly-(R)-3-hydroxybutyrate synthesis. This expression is dependent on the AtoC transcriptional regulator, which is a protein that appears to be active when it senses the presence of spermidine and acetoacetate. Therefore, spermidine and acetoacetate are inducers of the atoDAEB expression, although if both inducers are present, spermidine counteracts the acetate effect on the operon Theodorou MC, Theodorou EC, Panagiotidis CA, Kyriakidis DA,2007. Theodorou MC, Panagiotidis CA, Panagiotidis CH, Pantazaki AA, Kyriakidis DA,2006
In an AckA mutant, the atoDAEB operon is significantly upregulated under anaerobic conditions, hinting to the production of acetoacetate Schütze A, Benndorf D, Püttker S, Kohrs F, Bettenbrock K,2020
Reference(s): [1] Jenkins LS., et al., 1987
[2] Jenkins LS., et al., 1987
Promoter
Name: atoDp
+1: 2323412
Sigma Factor: Sigma54 Sigmulon
Distance from start of the gene: 35
Sequence: attagttaaataactaaatccaataatctcattctggcactccccttgctattgcctgacTgtacccacaacggtgtatgc
                                   -24         -12          +1                   
Note(s): We assigned a putative transcription start site to this promoter based on the observation that the majority of the σ54-dependent promoters, whose transcription start sites were determined experimentally, present a distance of 11 nucleotides between the transcription start site and the -12 box Barrios H,1999
Evidence: [AIBSCS]
[AIPP]
[ICWHO]
[IMP]
Reference(s): [3] Huerta AM., et al., 2003
[4] Matta MK., et al., 2007
[5] Reitzer L., et al., 2001
TF binding sites (TFBSs)
[AtoC,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote AtoC-phosphorylated activator atoDp 2323264 2323283 -138.5 ccaaaacttgCTATGCAGAAATTTGCACAGtgcgcaattt nd [GEA], [APIORCISFBSCS], [BPP], [SM] [1], [2], [4], [6]
remote AtoC-phosphorylated activator atoDp 2323283 2323302 -119.5 aatttgcacaGTGCGCAATTTTCTGCATAGccgctcattc nd [GEA], [APIORCISFBSCS], [BPP], [SM] [1], [2], [4], [6]
[IHF,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal IHF activator atoDp 2323349 2323361 -57.0 cccttcatatTCAATTAGTTAAAtaactaaatc nd [GEA], [APIORCISFBSCS] [4]
proximal IHF activator atoDp 2323374 2323386 -32.0 actaaatccaATAATCTCATTCTggcactcccc nd [GEA], [APIORCISFBSCS], [SM] [4]


Evidence    

 [AIBSCS] Automated inference based on similarity to consensus sequences

 [AIPP] Automated inference of promoter position

 [ICWHO] Inferred computationally without human oversight

 [IMP] Inferred from mutant phenotype

 [GEA] Gene expression analysis

 [APIORCISFBSCS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [BPP] Binding of purified proteins

 [SM] Site mutation


Reference(s)    

 [1] Jenkins LS., Nunn WD., 1987, Regulation of the ato operon by the atoC gene in Escherichia coli., J Bacteriol 169(5):2096-102

 [2] Jenkins LS., Nunn WD., 1987, Genetic and molecular characterization of the genes involved in short-chain fatty acid degradation in Escherichia coli: the ato system., J Bacteriol 169(1):42-52

 [3] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78

 [4] Matta MK., Lioliou EE., Panagiotidis CH., Kyriakidis DA., Panagiotidis CA., 2007, Interactions of the antizyme AtoC with regulatory elements of the Escherichia coli atoDAEB operon., J Bacteriol 189(17):6324-32

 [5] Reitzer L., Schneider BL., 2001, Metabolic context and possible physiological themes of sigma(54)-dependent genes in Escherichia coli., Microbiol Mol Biol Rev 65(3):422-44, table of contents

 [6] Lioliou EE., Mimitou EP., Grigoroudis AI., Panagiotidis CH., Panagiotidis CA., Kyriakidis DA., 2005, Phosphorylation activity of the response regulator of the two-component signal transduction system AtoS-AtoC in E. coli., Biochim Biophys Acta 1725(3):257-68

 [7] Beisel CL., Updegrove TB., Janson BJ., Storz G., 2012, Multiple factors dictate target selection by Hfq-binding small RNAs., EMBO J 31(8):1961-74

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