RegulonDB RegulonDB 10.9: Operon Form
   

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




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


Transcription unit       
Name: dapB
Gene(s): dapB   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
[IHBCE] Inferred by a human based on computational evidence
Reference(s): [1] Bouvier J., et al., 1984
Promoter
Name: dapBp2
+1: 28288
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 86
Sequence: tgcagtcattcatcgactcatgcctttcactgatatccctccctgtttatcattaatttcTaattatcagcgtttttggct
                          -35                   -10         +1                   
Evidence: [ICWHO]
[RS-EPT-CBR]
[TIM]
Reference(s): [1] Bouvier J., et al., 1984
[2] Huerta AM., et al., 2003
[3] Salgado H, et al., 2012
Terminator(s)
Type: rho-independent
Sequence: tattgattatAAAGGGCTTTAATTTTTGGCCCTTTtatttttggt
Reference(s): [1] Bouvier J., et al., 1984


Transcription unit          
Name: dapB
Gene(s): dapB   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
[IHBCE] Inferred by a human based on computational evidence
Reference(s): [1] Bouvier J., et al., 1984
Promoter
Name: dapBp1
+1: 28343
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 31
Sequence: atttctaattatcagcgtttttggctggcggcgtagcgatgcgctggttactctgaaaacGgtctatgcaaattaacaaaa
                         -35                     -10        +1                   
Note(s): In the argO and dapB promoters, the lysine repression of ArgP-dependent transcription between argO and dapB is apparently different. In the dapBp1 promoter, lysine prevents binding of ArgP Bouvier J,2008 whereas in the argO promoter, lysine traps RNA polymerase recruitment by ArgP Laishram RS,2007.
Evidence: [HIPP]
[ICWHO]
[RS-EPT-CBR]
[TIM]
Reference(s): [1] Bouvier J., et al., 1984
[4] Bouvier J., et al., 1991
[2] Huerta AM., et al., 2003
[3] Salgado H, et al., 2012
Terminator(s)
Type: rho-independent
Sequence: tattgattatAAAGGGCTTTAATTTTTGGCCCTTTtatttttggt
Reference(s): [1] Bouvier J., et al., 1984
TF binding sites (TFBSs)
[ArgP,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal ArgP1 activator dapBp1 28252 28271 -81.5 gactcatgccTTTCACTGATATCCCTCCCTGtttatcatta nd [APIORCISFBSCS], [BCE], [BPP], [GEA], [IC], [SM] [5], [6], [7]
proximal ArgP activator dapBp1 28272 28291 -61.5 atccctccctGTTTATCATTAATTTCTAATTatcagcgttt nd [BPP], [GEA], [SM] [7]
Note(s): 1Based on EMSE, it was demonstrated that His6-ArgP has an apparent Kd of 35 nM for the binding of ArgP to the dapB regulatory region Bouvier J,2008
1Based on EMSE, it was demonstrated that His6-ArgP has an apparent Kd of 35 nM for the binding of ArgP to the dapB regulatory region Bouvier J,2008


Evidence    

 [ICWHO] Inferred computationally without human oversight

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

 [TIM] Transcription initiation mapping

 [HIPP] Human inference of promoter position

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

 [BCE] Binding of cellular extracts

 [BPP] Binding of purified proteins

 [GEA] Gene expression analysis

 [IC] Inferred by curator

 [SM] Site mutation


Reference(s)    

 [1] Bouvier J., Richaud C., Richaud F., Patte JC., Stragier P., 1984, Nucleotide sequence and expression of the Escherichia coli dapB gene., J Biol Chem 259(23):14829-34

 [2] 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

 [3] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

 [4] Bouvier J., Stragier P., 1991, Nucleotide sequence of the lsp-dapB interval in Escherichia coli., Nucleic Acids Res 19(1):180

 [5] Bouvier J., Stragier P., Morales V., Remy E., Gutierrez C., 2008, Lysine represses transcription of the Escherichia coli dapB gene by preventing its activation by the ArgP activator., J Bacteriol 190(15):5224-9

 [6] Marbaniang CN., Gowrishankar J., 2011, Role of ArgP (IciA) in Lysine-Mediated Repression in Escherichia coli., J Bacteriol 193(21):5985-96

 [7] Nguyen Le Minh P., Velazquez Ruiz C., Vandermeeren S., Abwoyo P., Bervoets I., Charlier D., 2018, Differential protein-DNA contacts for activation and repression by ArgP, a LysR-type (LTTR) transcriptional regulator in Escherichia coli., Microbiol Res 206:141-158

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