RegulonDB RegulonDB 10.9: Operon Form
   

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




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


Transcription unit          
Name: leuE
Gene(s): leuE   Genome Browser M3D Gene expression COLOMBOS
Evidence: [ICWHO] Inferred computationally without human oversight
Promoter
Name: leuEp
+1: 1880800
Distance from start of the gene: 41
Sequence:
Evidence: [RS-EPT-CBR]
[TIM]
Reference(s): [1] Kutukova EA., et al., 2005
[2] Salgado H, et al., 2012
TF binding sites (TFBSs)
[Lrp,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote Lrp-leucine1 repressor leuEp 1880764 1880775 31.5 gatcgaaagaTAATTAAAGAGGTtaatgtgttc nd [RSE], [AIBSCS], [CSE] [3], [4]
proximal Lrp-leucine2 repressor leuEp 1880801 1880812 -6.5 tacagattggTTAGCATATTCACctttaatcgc nd [RSE], [AIBSCS], [CSE] [3], [4]
proximal Lrp-leucine3 repressor leuEp 1880835 1880846 -40.5 aggttaaaacCTGATTTTCTCCTttctaagccg nd [RSE], [AIBSCS], [CSE] [3], [4]
proximal Lrp-leucine4 repressor leuEp 1880868 1880879 -73.5 cctgattaatGATTCAATTATCGggttgatatc nd [RSE], [AIBSCS], [CSE] [3], [4]
Note(s): 1Additional evidence supports this TF-gene interaction with no precise position defined.
GCs_GeneExpression_EXP: lrp knockout mutant| MOPS| 0.2% glycerol| | 37.0 C| | | OD600 from 0.15 to 0.25| exponential phase| | |200 rpm. GCs_GeneExpression_CONTROL: wild-type| MOPS| 0.2% glycerol| | 37.0 C| | | OD600 from 0.15 to 0.25| exponential phase| | |200 rpm Kroner GM,2019br>GCs_GeneExpression_EXP: lrp knockout mutant| MOPS| 0.2% glycerol| | 37.0 C| | | OD600 from 1.8 to 2.2| transition point| | |200 rpm. GCs_GeneExpression_CONTROL: wild-type| MOPS| 0.2% glycerol| | 37.0 C| | | OD600 from 1.8 to 2.2| transition point| | |200 rpm Kroner GM,2019
2Additional evidence supports this TF-gene interaction with no precise position defined.
GCs_GeneExpression_EXP: lrp knockout mutant| MOPS| 0.2% glycerol| | 37.0 C| | | OD600 from 0.15 to 0.25| exponential phase| | |200 rpm. GCs_GeneExpression_CONTROL: wild-type| MOPS| 0.2% glycerol| | 37.0 C| | | OD600 from 0.15 to 0.25| exponential phase| | |200 rpm Kroner GM,2019br>GCs_GeneExpression_EXP: lrp knockout mutant| MOPS| 0.2% glycerol| | 37.0 C| | | OD600 from 1.8 to 2.2| transition point| | |200 rpm. GCs_GeneExpression_CONTROL: wild-type| MOPS| 0.2% glycerol| | 37.0 C| | | OD600 from 1.8 to 2.2| transition point| | |200 rpm Kroner GM,2019
3Additional evidence supports this TF-gene interaction with no precise position defined.
GCs_GeneExpression_EXP: lrp knockout mutant| MOPS| 0.2% glycerol| | 37.0 C| | | OD600 from 0.15 to 0.25| exponential phase| | |200 rpm. GCs_GeneExpression_CONTROL: wild-type| MOPS| 0.2% glycerol| | 37.0 C| | | OD600 from 0.15 to 0.25| exponential phase| | |200 rpm Kroner GM,2019br>GCs_GeneExpression_EXP: lrp knockout mutant| MOPS| 0.2% glycerol| | 37.0 C| | | OD600 from 1.8 to 2.2| transition point| | |200 rpm. GCs_GeneExpression_CONTROL: wild-type| MOPS| 0.2% glycerol| | 37.0 C| | | OD600 from 1.8 to 2.2| transition point| | |200 rpm Kroner GM,2019
4Additional evidence supports this TF-gene interaction with no precise position defined.
GCs_GeneExpression_EXP: lrp knockout mutant| MOPS| 0.2% glycerol| | 37.0 C| | | OD600 from 0.15 to 0.25| exponential phase| | |200 rpm. GCs_GeneExpression_CONTROL: wild-type| MOPS| 0.2% glycerol| | 37.0 C| | | OD600 from 0.15 to 0.25| exponential phase| | |200 rpm Kroner GM,2019br>GCs_GeneExpression_EXP: lrp knockout mutant| MOPS| 0.2% glycerol| | 37.0 C| | | OD600 from 1.8 to 2.2| transition point| | |200 rpm. GCs_GeneExpression_CONTROL: wild-type| MOPS| 0.2% glycerol| | 37.0 C| | | OD600 from 1.8 to 2.2| transition point| | |200 rpm Kroner GM,20191Additional evidence supports this TF-gene interaction with no precise position defined.
GCs_GeneExpression_EXP: lrp knockout mutant| MOPS| 0.2% glycerol| | 37.0 C| | | OD600 from 0.15 to 0.25| exponential phase| | |200 rpm. GCs_GeneExpression_CONTROL: wild-type| MOPS| 0.2% glycerol| | 37.0 C| | | OD600 from 0.15 to 0.25| exponential phase| | |200 rpm Kroner GM,2019br>GCs_GeneExpression_EXP: lrp knockout mutant| MOPS| 0.2% glycerol| | 37.0 C| | | OD600 from 1.8 to 2.2| transition point| | |200 rpm. GCs_GeneExpression_CONTROL: wild-type| MOPS| 0.2% glycerol| | 37.0 C| | | OD600 from 1.8 to 2.2| transition point| | |200 rpm Kroner GM,2019
2Additional evidence supports this TF-gene interaction with no precise position defined.
GCs_GeneExpression_EXP: lrp knockout mutant| MOPS| 0.2% glycerol| | 37.0 C| | | OD600 from 0.15 to 0.25| exponential phase| | |200 rpm. GCs_GeneExpression_CONTROL: wild-type| MOPS| 0.2% glycerol| | 37.0 C| | | OD600 from 0.15 to 0.25| exponential phase| | |200 rpm Kroner GM,2019br>GCs_GeneExpression_EXP: lrp knockout mutant| MOPS| 0.2% glycerol| | 37.0 C| | | OD600 from 1.8 to 2.2| transition point| | |200 rpm. GCs_GeneExpression_CONTROL: wild-type| MOPS| 0.2% glycerol| | 37.0 C| | | OD600 from 1.8 to 2.2| transition point| | |200 rpm Kroner GM,2019
3Additional evidence supports this TF-gene interaction with no precise position defined.
GCs_GeneExpression_EXP: lrp knockout mutant| MOPS| 0.2% glycerol| | 37.0 C| | | OD600 from 0.15 to 0.25| exponential phase| | |200 rpm. GCs_GeneExpression_CONTROL: wild-type| MOPS| 0.2% glycerol| | 37.0 C| | | OD600 from 0.15 to 0.25| exponential phase| | |200 rpm Kroner GM,2019br>GCs_GeneExpression_EXP: lrp knockout mutant| MOPS| 0.2% glycerol| | 37.0 C| | | OD600 from 1.8 to 2.2| transition point| | |200 rpm. GCs_GeneExpression_CONTROL: wild-type| MOPS| 0.2% glycerol| | 37.0 C| | | OD600 from 1.8 to 2.2| transition point| | |200 rpm Kroner GM,2019
4Additional evidence supports this TF-gene interaction with no precise position defined.
GCs_GeneExpression_EXP: lrp knockout mutant| MOPS| 0.2% glycerol| | 37.0 C| | | OD600 from 0.15 to 0.25| exponential phase| | |200 rpm. GCs_GeneExpression_CONTROL: wild-type| MOPS| 0.2% glycerol| | 37.0 C| | | OD600 from 0.15 to 0.25| exponential phase| | |200 rpm Kroner GM,2019br>GCs_GeneExpression_EXP: lrp knockout mutant| MOPS| 0.2% glycerol| | 37.0 C| | | OD600 from 1.8 to 2.2| transition point| | |200 rpm. GCs_GeneExpression_CONTROL: wild-type| MOPS| 0.2% glycerol| | 37.0 C| | | OD600 from 1.8 to 2.2| transition point| | |200 rpm Kroner GM,2019


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: reverse
Evidence: [ICA] Inferred by computational analysis
Reference(s): [5] Merino E, et al., 2005
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -6.3 1880838 1880859 cgggttgataTCAGGTTAAAACCTGATTTTCtcctttctaa
  anti-terminator -10.0 1880854 1880891 actggagcatGCCTGATTAATGATTCAATTATCGGGTTGATATCAGGttaaaacctg
Notes: "The provided "Sequence" is that of the RNA strand, i.e. U's are shown instead of T's and regulators on the reverse strand will appear as the reverse complement of the sequence delimited by LeftPos-RigtPos"


Evidence    

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

 [TIM] Transcription initiation mapping

 [RSE] RNA-seq evidence

 [AIBSCS] Automated inference based on similarity to consensus sequences

 [CSE] ChIP-seq evidence


Reference(s)    

 [1] Kutukova EA., Livshits VA., Altman IP., Ptitsyn LR., Zyiatdinov MH., Tokmakova IL., Zakataeva NP., 2005, The yeaS (leuE) gene of Escherichia coli encodes an exporter of leucine, and the Lrp protein regulates its expression., FEBS Lett 579(21):4629-34

 [2] 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.

 [3] Kroner GM., Wolfe MB., Freddolino PL., 2019, Escherichia coli Lrp Regulates One-Third of the Genome via Direct, Cooperative, and Indirect Routes., J Bacteriol 201(3)

 [4] Robison K., McGuire AM., Church GM., 1998, A comprehensive library of DNA-binding site matrices for 55 proteins applied to the complete Escherichia coli K-12 genome., J Mol Biol 284(2):241-54

 [5] Merino E, Yanofsky C., 2005, Transcription attenuation: a highly conserved regulatory strategy used by bacteria., Trends Genet. 2005 May;21(5):260-4.

RegulonDB