RegulonDB RegulonDB 10.9: Operon Form
   

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




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


Transcription unit          
Name: leuO
Gene(s): leuO   Genome Browser M3D Gene expression COLOMBOS
Note(s): LrhA binds to a region which overlaps with the HNS-binding site and one of the LeuO-binding sites, activating the promoters leuOp1, leuOp, and leuOp3 Breddermann H,2017
The transcription of the leuO gene is induced during the first 24 h after the induction of nitrogen starvation 32571968.
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [1] Stratmann T., et al., 2012
Promoter
Name: leuOp1
+1: 84154
Distance from start of the gene: 214
Sequence: cacatttaatccattttgtagatgattgagtattcgcggtagttatgattagattgttttCgcaacaaaaacattatggat
Evidence: [TIM]
Reference(s): [2] Breddermann H., et al., 2017
[1] Stratmann T., et al., 2012
TF binding sites (TFBSs)
[LrhA,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote LrhA activator leuOp1 84000 84091 -109.0 attatatgttTTGCGATTTTTTTTGATATTGATTTGGTGAATATTATTGATCAATTAATGTTAAGAATTAATGCATTAAATATATAAATTAATTATTAAATAagcacattta nd [BPP], [GEA], [BPP], [GEA] [2]


Transcription unit          
Name: leuO
Gene(s): leuO   Genome Browser M3D Gene expression COLOMBOS
Note(s): The leuO gene is one of the genes naturally regulated by the gene silencer. It is, together with the ilvIH and leuABCD operons, regulated via the promoter-relay mechanism. It was demonstrated by primer extension experiments that ilvIH promoter activity is required for activation of the leuO gene via this mechanism. The AT-rich DNA regions flanking leuO are named locus control regions LCR-I and LCR-II, respectively. LCR-I (gene silencer) corresponds to the H-NS (cis-element with little DNA sequence specificity), and LCR-II-binding sites regulate negatively and positively the leuO gene expression Chen CC,2005.
Expression of the leuO gene is coupled to the expression of the ilvIH operon located downstream of the leuO gene Stratmann T,2008.
LrhA binds to a region which overlaps with the HNS-binding site and one of the LeuO-binding sites, activating the promoters leuOp1, leuOp, and leuOp3 Breddermann H,2017
The transcription of the leuO gene is induced during the first 24 h after the induction of nitrogen starvation 32571968.
Evidence: [LTED] Length of transcript experimentally determined
Reference(s): [3] Chen CC., et al., 2005
Promoter
Name: leuOp
+1: 84188
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 180
Sequence: cgcggtagttatgattagattgttttcgcaacaaaaacattatggattattatgctgtggTaaatgactcattccacggca
                         -35                    -10         +1                   
Note(s): The transcription start site leuOp has been mapped 1 bp upstream of the site mapped here Breddermann H,2017
Evidence: [HIPP]
[ICWHO]
[TIM]
Reference(s): [2] Breddermann H., et al., 2017
[3] Chen CC., et al., 2005
[4] Huerta AM., et al., 2003
TF binding sites (TFBSs)
[H-NS,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote H-NS1 repressor leuOp 84085 84099 -96.0 aaattaattaTTAAATAAGCACATTTaatccatttt nd [APIORCISFBSCS], [GEA] [3]
[LeuO,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal LeuO activator leuOp 84122 84142 -56.0 tagatgattgAGTATTCGCGGTAGTTATGATTagattgtttt nd [BPP], [GEA], [IC], [BPP], [GEA] [1]
[LrhA,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote LrhA activator leuOp 84000 84091 -143.0 attatatgttTTGCGATTTTTTTTGATATTGATTTGGTGAATATTATTGATCAATTAATGTTAAGAATTAATGCATTAAATATATAAATTAATTATTAAATAagcacattta nd [BPP], [GEA] [2]
[SlyA,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote SlyA activator leuOp 84063 84062 -125.5 agaattaatgCattaaatata nd [AIBSCS], [BPP], [GEA] [5]
remote SlyA activator leuOp 84071 84070 -117.5 tgcattaaatAtataaattaa nd [AIBSCS], [BPP], [GEA] [5]
Note(s): 1H-NS acts as trans-acting factor upstream of the leuO gene, and it is responsible for the transcriptional repression mediated by a gene silencer. Chen et al. (2005) concluded that the gene silencer site is important for the relay mechanism and that there must be an H-NS nucleation site for its propagation, rather than an ordinary H-NS-preferred DNA-binding sequence Chen CC,2005.4H-NS acts as trans-acting factor upstream of the leuO gene, and it is responsible for the transcriptional repression mediated by a gene silencer. Chen et al. (2005) concluded that the gene silencer site is important for the relay mechanism and that there must be an H-NS nucleation site for its propagation, rather than an ordinary H-NS-preferred DNA-binding sequence Chen CC,2005.
Allosteric regulation of RNA-polymerase
  Regulator Function Promoter target of RNApol Growth Conditions Note Evidence Reference
  ppGpp activation leuOp nd leuO expression is induced indirectly via an increase in the cellular Lrp level in response to a ppGpp level increase, which is caused by the slow growth rate as cells enter stationary phase Fang M,2000 [GEA]
[IMP] 		[6]
Evidence: [GEA] Gene expression analysis
[IMP] Inferred from mutant phenotype
Reference(s): [6] Fang M., et al., 2000


Transcription unit          
Name: leuO
Gene(s): leuO   Genome Browser M3D Gene expression COLOMBOS
Note(s): LrhA binds to a region which overlaps with the HNS-binding site and one of the LeuO-binding sites, activating the promoters leuOp1, leuOp, and leuOp3 Breddermann H,2017
The transcription of the leuO gene is induced during the first 24 h after the induction of nitrogen starvation 32571968.
Evidence: [LTED] Length of transcript experimentally determined
Reference(s): [3] Chen CC., et al., 2005
Promoter
Name: leuOp3
+1: 84298
Distance from start of the gene: 70
Sequence: ctttatgttttccgaattttactcattttgctttttcttattttatatgcatgataaatcAtattcttcaggattatttct
Note(s): The transcription start site leuOp3 presents an additional site mapped 4 bp upstream of leuOp2 Breddermann H,2017
Evidence: [TIM]
Reference(s): [2] Breddermann H., et al., 2017
TF binding sites (TFBSs)
[LrhA,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote LrhA activator leuOp3 84000 84091 -253.0 attatatgttTTGCGATTTTTTTTGATATTGATTTGGTGAATATTATTGATCAATTAATGTTAAGAATTAATGCATTAAATATATAAATTAATTATTAAATAagcacattta nd [BPP], [GEA], [BPP], [GEA] [2]


Transcription unit          
Name: leuO
Gene(s): leuO   Genome Browser M3D Gene expression COLOMBOS
Note(s): A double-positive feedback network between LeuO and BglJ antagonistic regulators results in bistability and heterogeneity, or it can be maintained in stable OFF or ON states by an additional signal 27695690. Growth under steady-state conditions revealed uniform expression of both regulators, which have antagonistic regulation activities that act independently of each other 27695690.
The effect of BglJ and LrhA together on leuOp2 activation is additive Breddermann H,2017
The expression of lrhA from a plasmid can activate leuO transcription; however, the expression of leuO is dependent on more than the presence of LrhA. In addition, the activation by LrhA is affected negatively by the LeuO regulator Breddermann H,2017
The transcription of the leuO gene is induced during the first 24 h after the induction of nitrogen starvation 32571968.
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [1] Stratmann T., et al., 2012
Promoter
Name: leuOp2
+1: 84304
Distance from start of the gene: 64
Sequence: gttttccgaattttactcattttgctttttcttattttatatgcatgataaatcatattcTtcaggattatttctctgcat
Evidence: [RS-EPT-CBR]
[TIM]
Reference(s): [2] Breddermann H., et al., 2017
[7] Salgado H, et al., 2012
[8] Salscheider SL., et al., 2014
[1] Stratmann T., et al., 2012
TF binding sites (TFBSs)
[H-NS,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote H-NS repressor leuOp2 84085 84099 -212.0 aaattaattaTTAAATAAGCACATTTaatccatttt nd [BPP], [APIORCISFBSCS], [GEA] [3]
[LeuO,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote LeuO activator leuOp2 84014 84034 -280.0 gattttttttGATATTGATTTGGTGAATATTAttgatcaatt nd [AIBSCS], [BPP], [GEA], [GS], [IC] [1]
remote LeuO activator leuOp2 84040 84060 -254.0 atattattgaTCAATTAATGTTAAGAATTAATgcattaaata nd [BPP], [GEA], [IC] [1]
remote LeuO activator leuOp2 84099 84119 -195.0 ataagcacatTTAATCCATTTTGTAGATGATTgagtattcgc nd [BPP], [GEA], [IC] [1]
remote LeuO activator leuOp2 84122 84142 -172.0 tagatgattgAGTATTCGCGGTAGTTATGATTagattgtttt nd [BPP], [GEA] [1]
[LeuO,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote LeuO repressor leuOp2 84014 84034 -280.0 gattttttttGATATTGATTTGGTGAATATTAttgatcaatt nd [AIBSCS], [BPP], [GEA], [GS], [IC] [1]
remote LeuO repressor leuOp2 84040 84060 -254.0 atattattgaTCAATTAATGTTAAGAATTAATgcattaaata nd [BPP], [GEA], [IC] [1]
remote LeuO repressor leuOp2 84099 84119 -195.0 ataagcacatTTAATCCATTTTGTAGATGATTgagtattcgc nd [BPP], [GEA], [IC] [1]
remote LeuO repressor leuOp2 84122 84142 -172.0 tagatgattgAGTATTCGCGGTAGTTATGATTagattgtttt nd [BPP], [GEA] [1]
[RcsB-BglJ,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal RcsB-BglJ activator leuOp2 84236 84255 -58.5 cagaacccgtATCTTTATGTTTTCCGAATTTtactcatttt nd [APIORCISFBSCS], [GEA], [SM] [1]
[StpA,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd StpA repressor leuOp2 nd nd nd nd nd [BPP], [GEA], [IGI] [1]


Evidence    

 [TIM] Transcription initiation mapping

 [BPP] Binding of purified proteins

 [GEA] Gene expression analysis

 [HIPP] Human inference of promoter position

 [ICWHO] Inferred computationally without human oversight

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

 [IC] Inferred by curator

 [AIBSCS] Automated inference based on similarity to consensus sequences

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

 [GS] genomic SELEX

 [SM] Site mutation

 [IGI] Inferred from genetic interaction


Reference(s)    

 [1] Stratmann T., Pul U., Wurm R., Wagner R., Schnetz K., 2012, RcsB-BglJ activates the Escherichia coli leuO gene, encoding an H-NS antagonist and pleiotropic regulator of virulence determinants., Mol Microbiol 83(6):1109-23

 [2] Breddermann H., Schnetz K., 2017, Activation of leuO by LrhA in Escherichia coli., Mol Microbiol 104(4):664-676

 [3] Chen CC., Chou MY., Huang CH., Majumder A., Wu HY., 2005, A cis-spreading nucleoprotein filament is responsible for the gene silencing activity found in the promoter relay mechanism., J Biol Chem 280(6):5101-12

 [4] 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

 [5] Curran TD., Abacha F., Hibberd SP., Rolfe MD., Lacey MM., Green J., 2017, Identification of new members of the Escherichia coli K-12 MG1655 SlyA regulon., Microbiology 163(3):400-409

 [6] Fang M., Majumder A., Tsai KJ., Wu HY., 2000, ppGpp-dependent leuO expression in bacteria under stress., Biochem Biophys Res Commun 276(1):64-70

 [7] 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.

 [8] Salscheider SL., Jahn A., Schnetz K., 2014, Transcriptional regulation by BglJ-RcsB, a pleiotropic heteromeric activator in Escherichia coli., Nucleic Acids Res 42(5):2999-3008

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