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Name: | gadBC |
Gene(s): | gadC, gadB Genome Browser M3D Gene expression COLOMBOS |
Note(s): | De Biase D,1999and Yoshida T,1993have reported evidence of a negative effect of Hns protein on the gadBC operon. However, Giangrossi M,2005demonstrated that Hns does not bind the regulatory region of the operon. Therefore, the HNS effect on gadBC is indirect. Genes involved in the gad (gadABCDEWX) system are common under many adverse conditions, as determined by microarray analyses and Fourier transform-infrared spectroscopy. Although they are known to be important for the acid stress response, it has also been shown that part of this system is also upregulated by NaCl, cold stress, ethanol, and heat stress Moen B,2009 Basal GadE activity is required for activation of gadA and gadBC expression during stationary-phase growth Castanie-Cornet MP,2007 The transcription of gadB appears to be increased under acidic growth conditions during the exponential phase in a RcsB-dependent manner, but not during stationary phase Johnson MD,2011 gadB is induced during biofilm formation Giangrossi M,2005. 12657059 RcsB activity through both the RcsCD phosphorelay pathway and the RcsA pathway lowers the acid resistance Castanie-Cornet MP,2007 The role of this negative regulation might be to prevent costly runaway expression of the gad genes or to shut off the response, once the acid stress is over Castanie-Cornet MP,2007 Indole enhances the expression of several genes related to acid resistance, such as gadA, gadB, gadC, hdeA, hdeB, hdeD, slp, and gadE 20470880 The acid resistance phenotype induced by indoles is mainly due to increased expression of the glutamine decarboxylase system 20470880 The mdtEF-tolC, malEFG, gadBC, treBC, entCEBA-ybdB, hdeAB-yhiD, and alaE operons were differentially regulated after induction of the nonnative organic acid citramalate Webb J,2019 |
Evidence: | [BTEI] Boundaries of transcription experimentally identified [LTED] Length of transcript experimentally determined |
Reference(s): |
[1] Castanie-Cornet MP., et al., 2001 [2] De Biase D., et al., 1999 [3] Shimada T., et al., 2007 [4] Waterman SR., et al., 2003 |
Promoter | |
Name: | gadBp |
+1: | 1572072 |
Sigma Factor: | Sigma38, Sigma70, Sigma38, Sigma70 |
Distance from start of the gene: | 27 |
Sequence: |
tatttaaacacgagtcctttgcacttgcttactttatcgataaatcctacttttttaatgCgatccaatcattttaaggag -35 -10 +1 |
Note(s): | The σ38 factor is required for stationary-phase induction but not acid induction of the gadB promoter Castanie-Cornet MP,2001. Waterman SR,2003 were able to detect transcripts of gadBC in an hns rpoS double mutant, suggesting that the gadBp promoter is also recognized by σ70. |
Evidence: |
[HIPP] [TIM] |
Reference(s): |
[1] Castanie-Cornet MP., et al., 2001 [5] Itou J., et al., 2009 [4] Waterman SR., et al., 2003 |
Terminator(s) | |
Type: | rho-independent |
Sequence: | aagcacgaaaAAGGGAGCGATGAATTATCGCTCCCTTgtcttataac |
Reference(s): | [2] De Biase D., et al., 1999 |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
proximal | CRP-cAMP1 | repressor | gadBp | 1572125 | 1572146 | -63.5 | cgataaataaCATTAGGATTTTGTTATTTAAAcacgagtcct | nd | [APIORCISFBSCS], [CV(GEA/ROMA)], [GEA] | [1] |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
remote | Fis | repressor | gadBp | 1572029 | 1572043 | 37.0 | agtttaaaatGGATAAGAAGCAAGTaacggattta | nd | [AIBSCS], [CV(GEA/ROMA)], [GEA] | [13] |
proximal | Fis | repressor | gadBp | 1572092 | 1572106 | -27.0 | ctttgcacttGCTTACTTTATCGATaaatcctact | nd | [AIBSCS], [CV(GEA/ROMA)], [GEA] | [13] |
proximal | Fis | repressor | gadBp | 1572124 | 1572138 | -59.0 | aacattaggaTTTTGTTATTTAAACacgagtcctt | nd | [AIBSCS], [CV(GEA/ROMA)], [GEA] | [13] |
remote | Fis | repressor | gadBp | 1572170 | 1572184 | -105.0 | gtttttcaatGAAAAAATATTATTCgcgtaatatc | nd | [AIBSCS], [CV(GEA/ROMA)], [GEA] | [13] |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
proximal | GadE1 | activator | gadBp | 1572125 | 1572144 | -62.5 | ataaataacaTTAGGATTTTGTTATTTAAAcacgagtcct | nd | [APIORCISFBSCS], [BPP], , [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA], [IHBCE], | [1], [5], [6], [9], [10], [16] |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
remote | GadW | activator | gadBp | 1572161 | 1572180 | -98.5 | ttcaatgaaaAAATATTATTCGCGTAATATctcacgataa | nd | [BPP], [GEA] | [7], [9], [10] |
remote | GadW | activator | gadBp | 1572182 | 1572201 | -119.5 | gaatttcataTTGTATTGTTTTTCAATGAAaaaatattat | nd | [BPP], [GEA] | [7], [9], [10] |
remote | GadW | activator | gadBp | 1572273 | 1572292 | -210.5 | tgatattttaAGGTCTGATTTTTACGTGATaattcaggag | nd | [APIORCISFBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA] | [7], [8], [9], [10] |
remote | GadW | activator | gadBp | 1572294 | 1572313 | -231.5 | ataataatcaAGTACTAATAGTGATATTTTaaggtctgat | nd | [APIORCISFBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA] | [7], [8], [9], [10] |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
remote | GadW | repressor | gadBp | 1572161 | 1572180 | -98.5 | ttcaatgaaaAAATATTATTCGCGTAATATctcacgataa | nd | [BPP], [GEA] | [7], [9], [10] |
remote | GadW | repressor | gadBp | 1572182 | 1572201 | -119.5 | gaatttcataTTGTATTGTTTTTCAATGAAaaaatattat | nd | [BPP], [GEA] | [7], [9], [10] |
remote | GadW | repressor | gadBp | 1572273 | 1572292 | -210.5 | tgatattttaAGGTCTGATTTTTACGTGATaattcaggag | nd | [APIORCISFBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA] | [7], [8], [9], [10] |
remote | GadW | repressor | gadBp | 1572294 | 1572313 | -231.5 | ataataatcaAGTACTAATAGTGATATTTTaaggtctgat | nd | [APIORCISFBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA] | [7], [8], [9], [10] |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
proximal | GadX | activator | gadBp | 1572080 | 1572099 | -17.5 | cttgcttactTTATCGATAAATCCTACTTTtttaatgcga | nd | [BPP], [GEA] | [7], [9], [10], [11], [12] |
proximal | GadX | activator | gadBp | 1572102 | 1572121 | -39.5 | atttaaacacGAGTCCTTTGCACTTGCTTActttatcgat | nd | [BPP], [GEA] | [7], [9], [10], [11], [12] |
remote | GadX | activator | gadBp | 1572161 | 1572180 | -98.5 | ttcaatgaaaAAATATTATTCGCGTAATATctcacgataa | nd | [BPP], [GEA] | [7], [9], [10], [11], [12] |
remote | GadX | activator | gadBp | 1572182 | 1572201 | -119.5 | gaatttcataTTGTATTGTTTTTCAATGAAaaaatattat | nd | [BPP], [GEA] | [7], [9], [10], [11], [12] |
remote | GadX | activator | gadBp | 1572246 | 1572265 | -184.0 | gataattcagGAGACACAGAATGCGCATAAaaataacagc | nd | , [IHBCE], | [6] |
remote | GadX | activator | gadBp | 1572273 | 1572292 | -210.5 | tgatattttaAGGTCTGATTTTTACGTGATaattcaggag | nd | [APIORCISFBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA] | [7], [8], [9] |
remote | GadX | activator | gadBp | 1572294 | 1572313 | -231.5 | ataataatcaAGTACTAATAGTGATATTTTaaggtctgat | nd | [APIORCISFBSCS], [BPP], , [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA], [IHBCE], | [6], [7], [8], [9] |
remote | GadX | activator | gadBp | 1572330 | 1572349 | -268.0 | ctatttttatGTAATAATTTTATAAATGCGttcaaaataa | nd | , [IHBCE], | [6] |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
proximal | RcsB-Pasp56 | activator | gadBp | 1572130 | 1572144 | -64.5 | ataaataacaTTAGGATTTTGTTATttaaacacga | nd | [APIORCISFBSCS], [CV(GEA/ROMA)], [GEA] | [14], [15] |
Note(s): |
1This potential site could belong to the CRP regulator since it possesses 9 of the 16 consensus nucleotides associated with CRP binding Castanie-Cornet MP,2001. GadE and CRP bind to this site, controlling gadB expression during both growth under acidic conditions and in stationary phase.1GadE is required both for gadA/gadBC expression during exponential growth and stationary phase expression. GadE is an acid-induced regulator, since it is involved in the acid induction of gadA/gadBC operons during exponential growth. The expression of these operons is maybe one of the most intensively regulated systems in Escherichia coli since it is regulated by different factors. GadE and GadX could simultaneously bind to the GAD box region of gadA/gadBC and form a complex Ma Z,2003.17This potential site could belong to the CRP regulator since it possesses 9 of the 16 consensus nucleotides associated with CRP binding Castanie-Cornet MP,2001. GadE and CRP bind to this site, controlling gadB expression during both growth under acidic conditions and in stationary phase. 18GadE is required both for gadA/gadBC expression during exponential growth and stationary phase expression. GadE is an acid-induced regulator, since it is involved in the acid induction of gadA/gadBC operons during exponential growth. The expression of these operons is maybe one of the most intensively regulated systems in Escherichia coli since it is regulated by different factors. GadE and GadX could simultaneously bind to the GAD box region of gadA/gadBC and form a complex Ma Z,2003. |
Gene(s): | gadC Genome Browser M3D Gene expression COLOMBOS |
Note(s): | The expression of the gene gadC is increased under acidic growth conditions in either aerobiosis or microaerobiosis Marzan LW,2013 The increased expression under aerobiosis appears to be caused by the transcription factor PhoB Marzan LW,2013 but it is not known which promoter, of four transcribing gadC, is affected by PhoB. |
Evidence: | [IC] Inferred by curator |
Terminator(s) | |
Type: | rho-independent |
Sequence: | aagcacgaaaAAGGGAGCGATGAATTATCGCTCCCTTgtcttataac |
Reference(s): | [2] De Biase D., et al., 1999 |
Gene(s): | gadC Genome Browser M3D Gene expression COLOMBOS |
Note(s): | The expression of the gene gadC is increased under acidic growth conditions in either aerobiosis or microaerobiosis Marzan LW,2013 The increased expression under aerobiosis appears to be caused by the transcription factor PhoB Marzan LW,2013 but it is not known which promoter, of four transcribing gadC, is affected by PhoB. |
Evidence: | [IC] Inferred by curator |
Terminator(s) | |
Type: | rho-independent |
Sequence: | aagcacgaaaAAGGGAGCGATGAATTATCGCTCCCTTgtcttataac |
Reference(s): | [2] De Biase D., et al., 1999 |
Gene(s): | gadC Genome Browser M3D Gene expression COLOMBOS |
Note(s): | The expression of the gene gadC is increased under acidic growth conditions in either aerobiosis or microaerobiosis Marzan LW,2013 The increased expression under aerobiosis appears to be caused by the transcription factor PhoB Marzan LW,2013 but it is not known which promoter, of four transcribing gadC, is affected by PhoB. |
Evidence: | [IC] Inferred by curator |
Terminator(s) | |
Type: | rho-independent |
Sequence: | aagcacgaaaAAGGGAGCGATGAATTATCGCTCCCTTgtcttataac |
Reference(s): | [2] De Biase D., et al., 1999 |
Regulation by sRNA | ![]() |
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RNA cis-regulatory element | ![]() |
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Regulation, transcriptional elongation | |
Attenuator type: | Translational |
Strand: | reverse |
Structure type | Energy | LeftPos | RightPos | Sequence (RNA-strand) | |
---|---|---|---|---|---|
terminator | -8.9 | 1570501 | 1570534 | gcttcagaacAAAACAGGTGCGGTTCCGACAGGAATACCGTTTtagggggata |
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" |
Reference(s) |
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