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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 Switzer A, Burchell L, McQuail J, Wigneshweraraj S,2020. |
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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 |
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Evidence: | [TIM] | |||||||||
Reference(s): |
[2] Breddermann H., et al., 2017 [1] Stratmann T., et al., 2012 |
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] | [2] |
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 Switzer A, Burchell L, McQuail J, Wigneshweraraj S,2020. |
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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 |
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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] |
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Reference(s): |
[2] Breddermann H., et al., 2017 [3] Chen CC., et al., 2005 [4] Huerta AM., et al., 2003 |
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 | leuOp | 84085 | 84099 | -96.0 | aaattaattaTTAAATAAGCACATTtaatccattt | nd | [GEA], [APIORCISFBSCS] | [1], [3] |
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 | [GEA], [BPP] | [2] |
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 | 84062 | 84063 | -125.5 | agaattaatgCattaaatata | nd | [GEA], [AIBSCS], [BPP] | [5] |
remote | SlyA | activator | leuOp | 84070 | 84071 | -117.5 | tgcattaaatAtataaattaa | nd | [GEA], [AIBSCS], [BPP] | [5] |
Evidence: |
[GEA] Gene expression analysis [IMP] Inferred from mutant phenotype |
Reference(s): | [6] Fang M., et al., 2000 |
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 Switzer A, Burchell L, McQuail J, Wigneshweraraj S,2020. |
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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 |
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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 |
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] | [2] |
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 Breddermann H, Schnetz K,2016. Growth under steady-state conditions revealed uniform expression of both regulators, which have antagonistic regulation activities that act independently of each other Breddermann H, Schnetz K,2016. 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 Switzer A, Burchell L, McQuail J, Wigneshweraraj S,2020. |
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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 |
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Evidence: |
[RS-EPT-CBR] [TIM] |
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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 |
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 | aaattaattaTTAAATAAGCACATTtaatccattt | nd | [BPP], [GEA], [APIORCISFBSCS] | [1], [3] |
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 | gattttttttGATATTGATTTGGTGAATATTattgatcaat | nd | [GEA], [IC], [AIBSCS], [BPP], [GS], [IC] | [1] |
remote | LeuO | activator | leuOp2 | 84040 | 84060 | -254.0 | atattattgaTCAATTAATGTTAAGAATTAAtgcattaaat | nd | [GEA], [IC], [BPP], [IC] | [1] |
remote | LeuO | activator | leuOp2 | 84099 | 84119 | -195.0 | ataagcacatTTAATCCATTTTGTAGATGATtgagtattcg | nd | [GEA], [IC], [BPP], [IC] | [1] |
remote | LeuO | activator | leuOp2 | 84122 | 84142 | -172.0 | tagatgattgAGTATTCGCGGTAGTTATGATtagattgttt | nd | [GEA], [BPP] | [1], [3] |
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 | gattttttttGATATTGATTTGGTGAATATTattgatcaat | nd | [GEA], [IC], [AIBSCS], [BPP], [GS], [IC] | [1] |
remote | LeuO | repressor | leuOp2 | 84040 | 84060 | -254.0 | atattattgaTCAATTAATGTTAAGAATTAAtgcattaaat | nd | [GEA], [IC], [BPP], [IC] | [1] |
remote | LeuO | repressor | leuOp2 | 84099 | 84119 | -195.0 | ataagcacatTTAATCCATTTTGTAGATGATtgagtattcg | nd | [GEA], [IC], [BPP], [IC] | [1] |
remote | LeuO | repressor | leuOp2 | 84122 | 84142 | -172.0 | tagatgattgAGTATTCGCGGTAGTTATGATtagattgttt | nd | [GEA], [BPP] | [1], [3] |
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 | cagaacccgtATCTTTATGTTTTCCGAATTttactcattt | nd | [GEA], [APIORCISFBSCS], [SM] | [1] |
Reference(s) |
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