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Name: | gltBDF | |||||||||
Synonym(s): | OP00253, gltD | |||||||||
Gene(s): | gltB, gltD, gltF Genome Browser M3D Gene expression COLOMBOS | |||||||||
Note(s): | The gltBDF operon codes for the glutamate synthase, the large (gltB) and small (gltD) subunits, and a protein that is implied in the self-operon regulation (gltF) Castano I,1988. Castano I,1992 The operon is the target of Lrp (global modulator in response to leucine levels, related to nitrogen metabolism) Wiese DE,1997. Oliver G,1987 IHF (global DNA-bending protein), and GadE (regulator for resistance to low pH) Hommais F,2004activation, and Nac (regulator for the histidine and nitrogen utilization) Zimmer DP,2000 and Fnr (global regulator in response to respiration changes) Constantinidou C,2006repression. The Lrp activation is helped by the IHF binding between the promoter and its proximal Lrp site (the one centered at ?152 bp), by which Lrp gets closer to the σ70 to activate Paul L,2001 An important detail about the proximal Lrp and IHF sites is that the same order and approximate distances and sequences of the sites and the promoter are conserved among several related organisms of the Enterobacteriaceae genera Paul L,2001 A new site for Lrp controlling positively the gltBp promoter has been identified Lintner RE,2008 However, it was not considered, since it is 42 bp downstream from the transcriptional start site of gltB Lintner RE,2008 Under nitrogen-rich growth conditions, the expression of this operon was increased in mutants for two genes that encode two terminal oxidases, cyoA and cydB, and in mutants for two transcriptional regulators, Fnr and Fur Kumar R,2011 |
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Evidence: | [CV(LTED/PM)] cross validation(LTED/PM) [LTED] Length of transcript experimentally determined [PM] Polar mutation |
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Reference(s): |
[1] Castano I., et al., 1988 [2] Castano I., et al., 1992 [3] Grassl G., et al., 1999 [4] Paul L., et al., 2007 |
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Promoter | ||||||||||
Name: | gltBp2 | |||||||||
+1: | 3354509 | |||||||||
Sigma Factor: | Sigma38 Sigmulon | |||||||||
Distance from start of the gene: | 216 | |||||||||
Sequence: |
acatttctgtaccaataagcttgccatttgacctgtatcagctttcccgataagttggaaAtccgctggaagctttctgga |
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Evidence: |
[HIPP] [IPI] [TIM] |
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Reference(s): |
[5] Oliver G., et al., 1987 [6] Seo SW., et al., 2015 [7] Velazquez L., et al., 1991 |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
remote | ArgR-L-arginine | repressor | gltBp2 | 3354148 | 3354165 | -352.0 | gcttttatcaACTGCATAATCAATCAAAattaccgaaa | nd | [GEA], [APIORCISFBSCS], [BPP] | [4], [8] |
remote | ArgR-L-arginine | repressor | gltBp2 | 3354169 | 3354186 | -331.5 | aatcaaaattACCGAAATTTCATGCATAatcacataaa | nd | [GEA], [APIORCISFBSCS], [BPP] | [4], [8] |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
proximal | CRP-cyclic-AMP | repressor | gltBp2 | 3354433 | 3354454 | -65.5 | tttaataaagAATTTTGCGCTAAAGCACATTTctgtaccaat | nd | [GEA], [APIORCISFBSCS], [BPP], [SM] | [4] |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
remote | GadE | activator | gltBp2 | 3354215 | 3354234 | -284.0 | gcttatcttgTGTCAGATTTTTTTATCTCCtgatggattt | nd | [GEA], [RSE], [BPP], [CEEUMA], [IHBCE] | [6], [9] |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
proximal | IHF | activator | gltBp2 | 3354414 | 3354426 | -89.0 | tccattttaaTTTCAGTCATTTAataaagaatt | nd | [GEA], [BPP] | [4], [14] |
proximal | IHF | activator | gltBp2 | 3354418 | 3354430 | -85.0 | ttttaatttcAGTCATTTAATAAagaattttgc | nd | [GEA], [BPP] | [4], [14] |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
remote | Lrp | activator | gltBp2 | 3354256 | 3354270 | -246.0 | aggcaaaaacAGTAGCATGAAACGTcattaccaat | nd | [RSE], [APIORCISFBSCS], [BPP], [CSE], [SM] | [4], [10], [11] |
remote | Lrp | activator | gltBp2 | 3354287 | 3354301 | -215.0 | caattaaggcAGTATAAAATGCTGGttttgtcgtc | nd | [EME], [RSE], [AIBSPD], [APIORCISFBSCS], [BPP], [CCE], [CSE], [SM] | [4], [5], [10], [11], [12] |
remote | Lrp | activator | gltBp2 | 3354350 | 3354364 | -152.0 | cctttatgacAGTCAGGAATTGACTgtttctctaa | nd | [RSE], [APIORCISFBSCS], [BPP], [CSE], [SM] | [4], [5], [10], [11] |
remote | Lrp-L-leucine | activator | gltBp2 | 3354394 | 3354409 | -108.0 | ttttagccttAAAGATAAAATCCATTttaatttcag | nd | [GEA], [RSE], [AIBSCS], [CSE] | [10], [13] |
Name: | gltBDF | |||||||||
Synonym(s): | OP00253, gltD | |||||||||
Gene(s): | gltB, gltD, gltF Genome Browser M3D Gene expression COLOMBOS | |||||||||
Note(s): | The gltBDF operon codes for the glutamate synthase, the large (gltB) and small (gltD) subunits, and a protein that is implied in the self-operon regulation (gltF) Castano I,1988. Castano I,1992 The operon is the target of Lrp (global modulator in response to leucine levels, related to nitrogen metabolism) Wiese DE,1997. Oliver G,1987 IHF (global DNA-bending protein), and GadE (regulator for resistance to low pH) Hommais F,2004activation, and Nac (regulator for the histidine and nitrogen utilization) Zimmer DP,2000 and Fnr (global regulator in response to respiration changes) Constantinidou C,2006repression. The Lrp activation is helped by the IHF binding between the promoter and its proximal Lrp site (the one centered at ?152 bp), by which Lrp gets closer to the σ70 to activate Paul L,2001 An important detail about the proximal Lrp and IHF sites is that the same order and approximate distances and sequences of the sites and the promoter are conserved among several related organisms of the Enterobacteriaceae genera Paul L,2001 A new site for Lrp controlling positively the gltBp promoter has been identified Lintner RE,2008 However, it was not considered, since it is 42 bp downstream from the transcriptional start site of gltB Lintner RE,2008 Under nitrogen-rich growth conditions, the expression of this operon was increased in mutants for two genes that encode two terminal oxidases, cyoA and cydB, and in mutants for two transcriptional regulators, Fnr and Fur Kumar R,2011 |
|||||||||
Evidence: | [CV(LTED/PM)] cross validation(LTED/PM) [LTED] Length of transcript experimentally determined [PM] Polar mutation |
|||||||||
Reference(s): |
[1] Castano I., et al., 1988 [2] Castano I., et al., 1992 [3] Grassl G., et al., 1999 [4] Paul L., et al., 2007 |
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Promoter | ||||||||||
Name: | gltBp | |||||||||
+1: | 3354509 | |||||||||
Sigma Factor: | Sigma70 Sigmulon | |||||||||
Distance from start of the gene: | 216 | |||||||||
Sequence: |
acatttctgtaccaataagcttgccatttgacctgtatcagctttcccgataagttggaaAtccgctggaagctttctgga -35 -10 +1 |
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Evidence: |
[HIPP] [ICWHO] [TIM] |
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Reference(s): |
[19] Huerta AM., et al., 2003 [5] Oliver G., et al., 1987 [6] Seo SW., et al., 2015 [7] Velazquez L., et al., 1991 |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
remote | ArgR-L-arginine | repressor | gltBp | 3354148 | 3354165 | -352.0 | gcttttatcaACTGCATAATCAATCAAAattaccgaaa | nd | [GEA], [APIORCISFBSCS], [BPP] | [4], [8] |
remote | ArgR-L-arginine | repressor | gltBp | 3354169 | 3354186 | -331.5 | aatcaaaattACCGAAATTTCATGCATAatcacataaa | nd | [GEA], [APIORCISFBSCS], [BPP] | [4], [8] |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
proximal | CRP-cyclic-AMP | repressor | gltBp | 3354433 | 3354454 | -65.5 | tttaataaagAATTTTGCGCTAAAGCACATTTctgtaccaat | nd | [GEA], [APIORCISFBSCS], [BPP], [SM] | [4] |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
remote | GadE | activator | gltBp | 3354215 | 3354234 | -284.0 | gcttatcttgTGTCAGATTTTTTTATCTCCtgatggattt | nd | [GEA], [RSE], [BPP], [CEEUMA], [IHBCE] | [6], [9] |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
proximal | IHF | activator | gltBp | 3354414 | 3354426 | -89.0 | tccattttaaTTTCAGTCATTTAataaagaatt | nd | [GEA], [BPP] | [4], [14] |
proximal | IHF | activator | gltBp | 3354418 | 3354430 | -85.0 | ttttaatttcAGTCATTTAATAAagaattttgc | nd | [GEA], [BPP] | [4], [14] |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
remote | Lrp | activator | gltBp | 3354256 | 3354270 | -246.0 | aggcaaaaacAGTAGCATGAAACGTcattaccaat | nd | [RSE], [APIORCISFBSCS], [BPP], [CSE], [SM] | [4], [10], [11] |
remote | Lrp | activator | gltBp | 3354287 | 3354301 | -215.0 | caattaaggcAGTATAAAATGCTGGttttgtcgtc | nd | [EME], [RSE], [AIBSPD], [APIORCISFBSCS], [BPP], [CCE], [CSE], [SM] | [4], [5], [10], [11], [12] |
remote | Lrp | activator | gltBp | 3354350 | 3354364 | -152.0 | cctttatgacAGTCAGGAATTGACTgtttctctaa | nd | [RSE], [APIORCISFBSCS], [BPP], [CSE], [SM] | [4], [5], [10], [11] |
remote | Lrp-L-leucine | activator | gltBp | 3354394 | 3354409 | -108.0 | ttttagccttAAAGATAAAATCCATTttaatttcag | nd | [GEA], [RSE], [AIBSCS], [CSE] | [10], [13] |
Name: | gltF |
Gene(s): | gltF Genome Browser M3D Gene expression COLOMBOS |
Evidence: | [NTAS] Non-traceable author statement |
Reference(s) |
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