RegulonDB RegulonDB 10.8: Operon Form
   

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




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


Transcription unit          
Name: argD
Synonym(s): OP00151
Gene(s): argD   Genome Browser M3D Gene expression COLOMBOS
Reference(s): [1] Riley M., et al., 1983
Promoter
Name: argDp
+1: 3490221
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 41
Sequence: tttcctgcatcgctgatttctgattgccatttagtgattttttatgcatattttgtggttAtaatttcacatttgtttatg
                        -35                      -10        +1                   
Evidence: [RS-EPT-CBR]
[TAS]
Reference(s): [2] Charlier D., et al., 1992
[3] Salgado H, et al., 2012
TF binding sites (TFBSs)
[ArgR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal ArgR-L-arginine repressor argDp 3490211 3490228 2.5 atgcatatttTGTGGTTATAATTTCACAtttgtttatg nd [AIBSCS], [BPP] [2], [4], [5]
proximal ArgR-L-arginine repressor argDp 3490232 3490249 -19.5 attgccatttAGTGATTTTTTATGCATAttttgtggtt nd [AIBSCS], [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA] [2], [4], [5]
[PhoP,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal PhoP-Phosphorylated1 repressor argDp 3490203 3490219 11.0 ttgtggttatAATTTCACATTTGTTTAtgcgtaacag nd [AIBSCS], [CV(GEA)], [GEA] [6]
Note(s): 1This regulatory interaction was identified by means of PhoPQ-related microarray experiments, and the investigators checked for the presence of its regulatory motif in the promoter region Monsieurs P,2005. A repressor function for argD gene transcription can be clearly anticipated from the localization of the PhoP-binding site, very close to the argDp promoter core region.3This regulatory interaction was identified by means of PhoPQ-related microarray experiments, and the investigators checked for the presence of its regulatory motif in the promoter region Monsieurs P,2005. A repressor function for argD gene transcription can be clearly anticipated from the localization of the PhoP-binding site, very close to the argDp promoter core region.


Evidence    

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

 [TAS] Traceable author statement

 [AIBSCS] Automated inference based on similarity to consensus sequences

 [BPP] Binding of purified proteins

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

 [CV(GEA)] cross validation(GEA)

 [GEA] Gene expression analysis


Reference(s)    

 [1] Riley M., Glansdorff N., 1983, Cloning the Escherichia coli K-12 argD gene specifying acetylornithine delta-transaminase., Gene 24(2-3):335-9

 [2] Charlier D., Roovers M., Van Vliet F., Boyen A., Cunin R., Nakamura Y., Glansdorff N., Pierard A., 1992, Arginine regulon of Escherichia coli K-12. A study of repressor-operator interactions and of in vitro binding affinities versus in vivo repression., J Mol Biol 226(2):367-86

 [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] Caldara M., Charlier D., Cunin R., 2006, The arginine regulon of Escherichia coli: whole-system transcriptome analysis discovers new genes and provides an integrated view of arginine regulation., Microbiology 152(Pt 11):3343-54

 [5] Makarova KS., Mironov AA., Gelfand MS., 2001, Conservation of the binding site for the arginine repressor in all bacterial lineages., Genome Biol 2(4):RESEARCH0013

 [6] Monsieurs P., De Keersmaecker S., Navarre WW., Bader MW., De Smet F., McClelland M., Fang FC., De Moor B., Vanderleyden J., Marchal K., 2005, Comparison of the PhoPQ regulon in Escherichia coli and Salmonella typhimurium., J Mol Evol 60(4):462-74

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