RegulonDB RegulonDB 10.8: Operon Form
   

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




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


Transcription unit          
Name: gadW
Gene(s): gadW   Genome Browser M3D Gene expression COLOMBOS
Note(s): 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
The sequence of the putative stem-loop structure located 334 nt downstream of the gadW stop codon reportedly may function as a rho-independent terminator Tramonti A,2008 however, the putative terminator sequence was not shown in the paper.
The expression of the gene gadW is increased under acidic growth conditions in either aerobiosis or microaerobiosis Marzan LW,2013
Evidence: [LTED] Length of transcript experimentally determined
Reference(s): [1] Tramonti A., et al., 2008
Promoter
Name: gadWp1
+1: 3664651
Distance from start of the gene: 33
Sequence:
Evidence: [TIM]
Reference(s): [1] Tramonti A., et al., 2008
Terminator(s)
Type: rho-independent
Sequence: gtaaatgagaGTAAGGTTGAACATGAAGGTTCAGCCTTACTctttcctgct
Reference(s): [1] Tramonti A., et al., 2008
TF binding sites (TFBSs)
[YdeO,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal YdeO activator gadWp1 3664654 3664675 -13.0 agtctggcatCATTTCATTAGTATACTGAAATtgaaataatc nd [BPP], [CV(GEA)], [CV(GEA)], [GEA], [IHBCE] [2]


Transcription unit          
Name: gadW
Gene(s): gadW   Genome Browser M3D Gene expression COLOMBOS
Note(s): 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
The expression of the gadW gene was induced by SidA in the presence of N-(3-oxo-hexanoyl)-L-homoserine lactone (AHL) at 30 C, although the expression was negatively responsive in the presence of ethyl acetate (EA) at 37 C Dyszel JL,2010 It is not known if the regulation of the gadW gene by SdiA is dependent on the gadWp1 or gadWp2 promoter or both.
The transcription of gadW 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. Marzan LW,2013 However, it is not known which of the three promoters that transcribe this gene is affected by RcsB.
The sequence of the putative stem-loop structure located 334 nt downstream of the gadW stop codon reportedly may function as a rho-independent terminator Tramonti A,2008 however, the putative terminator sequence was not shown in the paper.
Evidence: [LTED] Length of transcript experimentally determined
Reference(s): [1] Tramonti A., et al., 2008
Promoter
Name: gadWp2
+1: 3664781
Distance from start of the gene: 163
Sequence:
Evidence: [TIM]
Reference(s): [1] Tramonti A., et al., 2008
Terminator(s)
Type: rho-independent
Sequence: gtaaatgagaGTAAGGTTGAACATGAAGGTTCAGCCTTACTctttcctgct
Reference(s): [1] Tramonti A., et al., 2008
TF binding sites (TFBSs)
[GadW,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal GadW repressor gadWp2 3664804 3664823 -32.5 atcagccattTTTTTATAAACATAAGCTATacgctgtgcg nd [GEA] [1]
proximal GadW repressor gadWp2 3664825 3664844 -53.5 ataacttttaCTGGAAATAAGATCAGCCATttttttataa nd [GEA] [1]
[GadX,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal GadX repressor gadWp2 3664804 3664823 -32.5 atcagccattTTTTTATAAACATAAGCTATacgctgtgcg nd [GEA] [1]
proximal GadX repressor gadWp2 3664825 3664844 -53.5 ataacttttaCTGGAAATAAGATCAGCCATttttttataa nd [GEA] [1]
proximal GadX repressor gadWp2 3664840 3664859 -68.5 ctcagtaagtTAAATATAACTTTTACTGGAaataagatca nd , [IHBCE], [3]
remote GadX repressor gadWp2 3664868 3664887 -96.5 tccctgttggCACGGGAAACTTTGTGCTCTcagtaagtta nd , [IHBCE], [3]
[H-NS,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd H-NS repressor gadWp2 nd nd nd nd nd [BPP] [6]
[PhoP,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal PhoP-Phosphorylated activator gadWp2 3664801 3664817 -28.0 catttttttaTAAACATAAGCTATACGctgtgcgaaa nd [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA] [4]
[SdiA,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd SdiA activator gadWp2 nd nd nd nd nd [GEA] [5]


Transcription unit          
Name: gadXW
Gene(s): gadW, gadX   Genome Browser M3D Gene expression COLOMBOS
Evidence: [ITC] Inferred through co-regulation
[LTED] Length of transcript experimentally determined
Reference(s): [1] Tramonti A., et al., 2008
[7] Tucker DL., et al., 2003
Promoter
Name: gadXp
+1: 3665839
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 29
Sequence: tttaaatttatttatcaatcaatttgacttaagagggcggcgtgctacattaataaacagTaatatgtttatgtaatatta
                        -35              -10                +1                   
Evidence: [HIPP]
[TIM]
Reference(s): [8] Tramonti A., et al., 2002
Terminator(s)
Type: rho-independent
Sequence: gtaaatgagaGTAAGGTTGAACATGAAGGTTCAGCCTTACTctttcctgct
Reference(s): [1] Tramonti A., et al., 2008
TF binding sites (TFBSs)
[FNR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote FNR repressor gadXp 3665992 3666005 -159.5 aagggattatTTGCTTACTATTAAtttccctgtg nd [AIBSCS], [CV(GEA)], [GEA] [10]
[GadE,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd GadE activator gadXp nd nd nd nd nd [BPP], [GEA] [11]
[GadW,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd GadW repressor gadXp nd nd nd nd nd [GEA] [12]
[GadX,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd GadX activator gadXp nd nd nd nd nd [GEA] [1], [11], [12]
[H-NS,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd H-NS1 repressor gadXp nd nd nd nd nd [BPP], [GEA] [14], [15]
[PhoB,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd PhoB-Phosphorylated activator gadXp nd nd nd nd nd [GEA] [13]
[RutR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote RutR repressor gadXp 3666654 3666674 -824.5 ggtgttcaacGTTGACTACCTGGGTGGTCAAattggtactt nd [BPP], [GEA] [9]
Note(s): 1Two large footprinting regions for Hns binding, which are necessary for full repression, were identified around the regulatory region of the gadXp promoter (from +1 to -67 and from -86 to -153 ) . These regions may contain sites for several Hns molecules, but these specific sites have
not been identified Giangrossi M,2005
The RNA polymerase binding to the gadXp promoter can be prevented by Hns protein that binds around the promoter region Giangrossi M,20056Two large footprinting regions for Hns binding, which are necessary for full repression, were identified around the regulatory region of the gadXp promoter (from +1 to -67 and from -86 to -153 ) . These regions may contain sites for several Hns molecules, but these specific sites have
not been identified Giangrossi M,2005
The RNA polymerase binding to the gadXp promoter can be prevented by Hns protein that binds around the promoter region Giangrossi M,2005


Transcription unit          
Name: gadX
Gene(s): gadX   Genome Browser M3D Gene expression COLOMBOS
Note(s): gadX gene expression is induced under exposure to hydrogen peroxide Hodges AP,2010
UspE regulates positively the transcription of the gadX gene in an unknown way, and GadX induces the transcription of uspE Hodges AP,2010
The expression of the gene gadX is increased by PhoB under acidic growth conditions Marzan LW,2013
The mRNA produced by the gadX gene has been observed mainly in the poles of the cell 31540875.
Evidence: [LTED] Length of transcript experimentally determined
Reference(s): [8] Tramonti A., et al., 2002
Promoter
Name: gadXp
+1: 3665839
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 29
Sequence: tttaaatttatttatcaatcaatttgacttaagagggcggcgtgctacattaataaacagTaatatgtttatgtaatatta
                        -35              -10                +1                   
Evidence: [HIPP]
[TIM]
Reference(s): [8] Tramonti A., et al., 2002
Terminator(s)
Type: rho-independent
Sequence: aacggtttatTAGTCTGGAGACGGCAGACTAtcctcttccc
Reference(s): [8] Tramonti A., et al., 2002
TF binding sites (TFBSs)
[FNR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote FNR repressor gadXp 3665992 3666005 -159.5 aagggattatTTGCTTACTATTAAtttccctgtg nd [AIBSCS], [CV(GEA)], [GEA] [10]
[GadE,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd GadE activator gadXp nd nd nd nd nd [BPP], [GEA] [11]
[GadW,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd GadW repressor gadXp nd nd nd nd nd [GEA] [12]
[GadX,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd GadX activator gadXp nd nd nd nd nd [GEA] [1], [11], [12]
[H-NS,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd H-NS1 repressor gadXp nd nd nd nd nd [BPP], [GEA] [14], [15]
[PhoB,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd PhoB-Phosphorylated activator gadXp nd nd nd nd nd [GEA] [13]
[RutR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote RutR repressor gadXp 3666654 3666674 -824.5 ggtgttcaacGTTGACTACCTGGGTGGTCAAattggtactt nd [BPP], [GEA] [9]
Note(s): 1Two large footprinting regions for Hns binding, which are necessary for full repression, were identified around the regulatory region of the gadXp promoter (from +1 to -67 and from -86 to -153 ) . These regions may contain sites for several Hns molecules, but these specific sites have
not been identified Giangrossi M,2005
The RNA polymerase binding to the gadXp promoter can be prevented by Hns protein that binds around the promoter region Giangrossi M,20056Two large footprinting regions for Hns binding, which are necessary for full repression, were identified around the regulatory region of the gadXp promoter (from +1 to -67 and from -86 to -153 ) . These regions may contain sites for several Hns molecules, but these specific sites have
not been identified Giangrossi M,2005
The RNA polymerase binding to the gadXp promoter can be prevented by Hns protein that binds around the promoter region Giangrossi M,2005


Transcription unit          
Name: gadAX
Gene(s): gadX, gadA   Genome Browser M3D Gene expression COLOMBOS
Note(s): 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 gadAX appears to be increased under acidic growth conditions during stationary and exponential phases in a RcsB-dependent manner Johnson MD,2011. Marzan LW,2013
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 gadAp promoter is strongly induced by GreA overproduction only when DksA is absent, as are many other genes 22056927. gadA is induced during biofilm formation Giangrossi M,2005. 12657059
Evidence: [BTEI] Boundaries of transcription experimentally identified
[LTED] Length of transcript experimentally determined
Reference(s): [9] Shimada T., et al., 2007
[8] Tramonti A., et al., 2002
[16] Waterman SR., et al., 2003
Promoter
Name: gadAp
+1: 3667607
Sigma Factor: Sigma38, Sigma70, Sigma38, Sigma70
Distance from start of the gene: 27
Sequence: tatttaaattaagcctgtaatgccttgcttccattgcggataaatcctacttttttattgCcttcaaataaatttaaggag
                         -35                    -10         +1                   
Note(s): σ38 factor is required for stationary phase induction but not acid induction of the gadA promoter Castanie-Cornet MP,2001. Waterman SR,2003 were able to detect transcripts of gadA in an hns rpoS double mutant, suggesting that the gadAp promoter can also be recognized by σ70.
Evidence: [HIPP]
[TIM]
Reference(s): [17] Castanie-Cornet MP., et al., 2001
[18] Itou J., et al., 2009
[16] Waterman SR., et al., 2003
Terminator(s)
Type: rho-independent
Sequence: aacggtttatTAGTCTGGAGACGGCAGACTAtcctcttccc
Reference(s): [8] Tramonti A., et al., 2002
TF binding sites (TFBSs)
[AdiY,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd AdiY activator gadAp nd nd nd nd nd [BPP] [6]
[ArcA,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd ArcA-Phosphorylated1 activator gadAp nd nd nd nd nd [AIBSCS], [CV(GEA)], [GEA] [27]
[CRP,-] Phrase
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 gadAp 3667659 3667680 -62.5 cgtttttctgCTTAGGATTTTGTTATTTAAATtaagcctgta nd [APIORCISFBSCS], [CV(GEA)], [GEA] [17]
[FNR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal FNR repressor gadAp 3667590 3667603 11.5 ttattgccttCAAATAAATTTAAGgagttcgaaa nd [AIBSCS], [CV(GEA)], [GEA] [10]
[Fis,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal Fis repressor gadAp 3667616 3667635 -18.0 ccttgcttccATTGCGGATAAATCCTACTTttttattgcc nd [AIBSCS], [CV(GEA)], [GEA] [19]
remote Fis repressor gadAp 3667692 3667711 -94.0 tatcatgttaAATGTTTATATTATAAAAAGtcgtttttct nd [AIBSCS], [CV(GEA)], [GEA] [19]
remote Fis repressor gadAp 3667716 3667735 -118.0 gataataaagTCTGTTTTTAATATTATCATgttaaatgtt nd [AIBSCS], [CV(GEA)], [GEA] [19]
remote Fis repressor gadAp 3667745 3667764 -147.0 aacagcaatgTTTGGGCGATTTTTATTACGataataaagt nd [AIBSCS], [CV(GEA)], [GEA] [19]
[GadRcs,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal GadE-RcsB1 activator gadAp 3667660 3667680 -62.5 cgtttttctgCTTAGGATTTTGTTATTTAAAttaagcctgt nd [APIORCISFBSCS], [BPP], , [CV(GEA)], [CV(GEA)], [CV(GEA/SM)], [CV(SM)], [GEA], [IHBCE], , [SM] [3], [11], [17], [18], [21], [22], [23], [24], [25]
[GadW,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal GadW activator gadAp 3667655 3667674 -57.5 tctgcttaggATTTTGTTATTTAAATTAAGcctgtaatgc nd [BPP], [GEA] [7], [12]
proximal GadW activator gadAp 3667676 3667695 -78.0 tatattataaAAAGTCGTTTTTCTGCTTAGgattttgtta nd [BPP], [GEA] [7], [12]
remote GadW activator gadAp 3667698 3667717 -100.5 taatattatcATGTTAAATGTTTATATTATaaaaagtcgt nd [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA] [1], [7], [12], [21]
remote GadW4 activator gadAp 3667719 3667738 -121.5 tacgataataAAGTCTGTTTTTAATATTATcatgttaaat nd [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA] [1], [7], [12], [21]
[GadW,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal GadW repressor gadAp 3667655 3667674 -57.5 tctgcttaggATTTTGTTATTTAAATTAAGcctgtaatgc nd [BPP], [GEA] [7], [12]
proximal GadW repressor gadAp 3667676 3667695 -78.0 tatattataaAAAGTCGTTTTTCTGCTTAGgattttgtta nd [BPP], [GEA] [7], [12]
remote GadW repressor gadAp 3667698 3667717 -100.5 taatattatcATGTTAAATGTTTATATTATaaaaagtcgt nd [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA] [1], [7], [12], [21]
remote GadW4 repressor gadAp 3667719 3667738 -121.5 tacgataataAAGTCTGTTTTTAATATTATcatgttaaat nd [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA] [1], [7], [12], [21]
[GadX,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal GadX activator gadAp 3667608 3667627 -10.5 ccattgcggaTAAATCCTACTTTTTTATTGccttcaaata nd [BPP], [GEA] [7], [8], [12], [14], [21]
proximal GadX activator gadAp 3667629 3667648 -31.5 taagcctgtaATGCCTTGCTTCCATTGCGGataaatccta nd [BPP], [GEA] [7], [8], [12], [14], [21]
proximal GadX activator gadAp 3667655 3667674 -57.5 tctgcttaggATTTTGTTATTTAAATTAAGcctgtaatgc nd [BPP], [GEA] [7], [8], [12], [14], [21]
proximal GadX activator gadAp 3667676 3667695 -78.0 tatattataaAAAGTCGTTTTTCTGCTTAGgattttgtta nd [BPP], [GEA] [7], [8], [12], [14], [21]
remote GadX activator gadAp 3667698 3667717 -100.5 taatattatcATGTTAAATGTTTATATTATaaaaagtcgt nd [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA] [1], [7], [8], [12], [14], [21]
remote GadX activator gadAp 3667719 3667738 -121.5 tacgataataAAGTCTGTTTTTAATATTATcatgttaaat nd [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA] [1], [7], [8], [12], [14], [21]
[H-NS,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd H-NS1 repressor gadAp nd nd nd nd nd [BPP], [GEA] [8], [12], [14]
[RcsB,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal RcsB-Pasp56 repressor gadAp 3667619 3667632 -18.5 tgcttccattGCGGATAAATCCTActtttttatt nd [BPP], [CV(GEA)], [CV(GEA)], [CV(GEA/SM)], [CV(SM)], [GEA], [IHBCE], [SM] [22], [23], [26]
[TorR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote TorR-Pasp repressor gadAp 3667530 3667539 73.5 cagaactactCGATTCACGTtttggcgcaa nd [AIBSCS], [CV(GEA)], [GEA] [20]
remote TorR-Pasp repressor gadAp 3667725 3667734 -122.5 ataataaagtCTGTTTTTAAtattatcatg nd [AIBSCS], [CV(GEA)], [GEA] [20]
Note(s): 1ArcA appears to activate gadAX operon expression under anaerobiosis. A putative ArcA-binding site was identified 567 bp upstream of this operon Salmon KA,2005, but the sequence was not shown.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 gadA expression during growth both 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 may be one of the most intensively regulated systems in Escherichia coli, since it is regulated by different factors. GadE and GadX may simultaneously bind to the GAD box region of gadA/gadBC and form a complex Ma Z,2003.4GadW regulates positively the expression of gadA in the absence of GadX only to pH 8 Ma Z,2002.4GadW regulates positively the expression of gadA in the absence of GadX only to pH 8 Ma Z,2002.1Two large footprinting regions for Hns binding, which are necessary for full repression, were identified around the regulatory region of the gadAp promoter (from +43 to -55 and from -86 to -133). These regions may contain sites for several Hns molecules, but these specific sites have not been identified Giangrossi M,2005
The RNA polymerase binding to the gadAp promoter can be prevented by the Hns protein which binds around the promoter region. Also, on the same region GadX can bind, competing with Hns for the same site; even GadX can remove the already-bound Hns Giangrossi M,2005.4GadW regulates positively the expression of gadA in the absence of GadX only to pH 8 Ma Z,2002.
5GadW regulates positively the expression of gadA in the absence of GadX only to pH 8 Ma Z,2002.
14GadE 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 may be one of the most intensively regulated systems in Escherichia coli, since it is regulated by different factors. GadE and GadX may simultaneously bind to the GAD box region of gadA/gadBC and form a complex Ma Z,2003.
15This 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 gadA expression during growth both under acidic conditions and in stationary phase.
25ArcA appears to activate gadAX operon expression under anaerobiosis. A putative ArcA-binding site was identified 567 bp upstream of this operon Salmon KA,2005, but the sequence was not shown.
27Two large footprinting regions for Hns binding, which are necessary for full repression, were identified around the regulatory region of the gadAp promoter (from +43 to -55 and from -86 to -133). These regions may contain sites for several Hns molecules, but these specific sites have not been identified Giangrossi M,2005
The RNA polymerase binding to the gadAp promoter can be prevented by the Hns protein which binds around the promoter region. Also, on the same region GadX can bind, competing with Hns for the same site; even GadX can remove the already-bound Hns Giangrossi M,2005.
Allosteric regulation of RNA-polymerase
  Regulator Function Promoter target of RNApol Growth Conditions Note Evidence Reference
  ppGpp activation gadAp   [EME] [28]
Evidence: [EME] Expression microarray evidence
Reference(s): [28] Traxler MF., et al., 2008


Regulation by sRNA    
  Small RNA name (Regulator) Regulation type Mechanism Function Binding Sites Evidence Reference
LeftPos RightPos Sequence (RNA-strand)
  gadY base-pairing post-transcriptional regulation activator 3665727 3665792 AATTGTCTAATTGCGTATGCAAGACATAAATATATTCTCACCATGGTTAATGGTGAATATCGCTA [GEA]
[HIFS]
[IMP]
[IPI]		 [29]
Notes: "The provided sequence is that of the RNA strand,i.e. 'U's are showed instead the 'T'"


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: reverse
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -21.6 3667748 3667783 taattaatttGATCGCCCGAACAGCAATGTTTGGGCGATTTTTATtacgataata
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    

 [TIM] Transcription initiation mapping

 [BPP] Binding of purified proteins

 [CV(GEA)] cross validation(GEA)

 [GEA] Gene expression analysis

 [IHBCE] Inferred by a human based on computational evidence

 [CEUMA] ChIP-exo evidence used in manual assertion

 [RE] RNA-seq evidence

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

 [HIPP] Human inference of promoter position

 [AIBSCS] Automated inference based on similarity to consensus sequences

 [CV(GEA/SM)] cross validation(GEA/SM)

 [CV(SM)] cross validation(SM)

 [SM] Site mutation


Reference(s)    

 [1] Tramonti A., De Canio M., De Biase D., 2008, GadX/GadW-dependent regulation of the Escherichia coli acid fitness island: transcriptional control at the gadY-gadW divergent promoters and identification of four novel 42 bp GadX/GadW-specific binding sites., Mol Microbiol 70(4):965-82

 [2] Yamanaka Y., Oshima T., Ishihama A., Yamamoto K., 2014, Characterization of the YdeO regulon in Escherichia coli., PLoS One 9(11):e111962

 [3] Seo SW., Kim D., O'Brien EJ., Szubin R., Palsson BO., 2015, Decoding genome-wide GadEWX-transcriptional regulatory networks reveals multifaceted cellular responses to acid stress in Escherichia coli., Nat Commun 6:7970

 [4] Zwir I., Shin D., Kato A., Nishino K., Latifi T., Solomon F., Hare JM., Huang H., Groisman EA., 2005, Dissecting the PhoP regulatory network of Escherichia coli and Salmonella enterica., Proc Natl Acad Sci U S A 102(8):2862-7

 [5] Dyszel JL., Soares JA., Swearingen MC., Lindsay A., Smith JN., Ahmer BM., 2010, E. coli K-12 and EHEC genes regulated by SdiA., PLoS One 5(1):e8946

 [6] Krin E., Danchin A., Soutourina O., 2010, Decrypting the H-NS-dependent regulatory cascade of acid stress resistance in Escherichia coli., BMC Microbiol 10:273

 [7] Tucker DL., Tucker N., Ma Z., Foster JW., Miranda RL., Cohen PS., Conway T., 2003, Genes of the GadX-GadW regulon in Escherichia coli., J Bacteriol 185(10):3190-201

 [8] Tramonti A., Visca P., De Canio M., Falconi M., De Biase D., 2002, Functional characterization and regulation of gadX, a gene encoding an AraC/XylS-like transcriptional activator of the Escherichia coli glutamic acid decarboxylase system., J Bacteriol 184(10):2603-13

 [9] Shimada T., Hirao K., Kori A., Yamamoto K., Ishihama A., 2007, RutR is the uracil/thymine-sensing master regulator of a set of genes for synthesis and degradation of pyrimidines., Mol Microbiol 66(3):744-57

 [10] Constantinidou C., Hobman JL., Griffiths L., Patel MD., Penn CW., Cole JA., Overton TW., 2006, A reassessment of the FNR regulon and transcriptomic analysis of the effects of nitrate, nitrite, NarXL, and NarQP as Escherichia coli K12 adapts from aerobic to anaerobic growth., J Biol Chem 281(8):4802-15

 [11] Hommais F., Krin E., Coppee JY., Lacroix C., Yeramian E., Danchin A., Bertin P., 2004, GadE (YhiE): a novel activator involved in the response to acid environment in Escherichia coli., Microbiology 150(Pt 1):61-72

 [12] Ma Z., Richard H., Tucker DL., Conway T., Foster JW., 2002, Collaborative regulation of Escherichia coli glutamate-dependent acid resistance by two AraC-like regulators, GadX and GadW (YhiW)., J Bacteriol 184(24):7001-12

 [13] Marzan LW., Hasan CM., Shimizu K., 2013, Effect of acidic condition on the metabolic regulation of Escherichia coli and its phoB mutant., Arch Microbiol 195(3):161-71

 [14] Giangrossi M., Zattoni S., Tramonti A., De Biase D., Falconi M., 2005, Antagonistic role of H-NS and GadX in the regulation of the glutamate decarboxylase-dependent acid resistance system in Escherichia coli., J Biol Chem 280(22):21498-505

 [15] Hommais F., Krin E., Laurent-Winter C., Soutourina O., Malpertuy A., Le Caer JP., Danchin A., Bertin P., 2001, Large-scale monitoring of pleiotropic regulation of gene expression by the prokaryotic nucleoid-associated protein, H-NS., Mol Microbiol 40(1):20-36

 [16] Waterman SR., Small PL., 2003, Transcriptional expression of Escherichia coli glutamate-dependent acid resistance genes gadA and gadBC in an hns rpoS mutant., J Bacteriol 185(15):4644-7

 [17] Castanie-Cornet MP., Foster JW., 2001, Escherichia coli acid resistance: cAMP receptor protein and a 20 bp cis-acting sequence control pH and stationary phase expression of the gadA and gadBC glutamate decarboxylase genes., Microbiology 147(Pt 3):709-15

 [18] Itou J., Eguchi Y., Utsumi R., 2009, Molecular mechanism of transcriptional cascade initiated by the EvgS/EvgA system in Escherichia coli K-12., Biosci Biotechnol Biochem 73(4):870-8

 [19] Bradley MD., Beach MB., de Koning AP., Pratt TS., Osuna R., 2007, Effects of Fis on Escherichia coli gene expression during different growth stages., Microbiology 153(Pt 9):2922-40

 [20] Bordi C., Theraulaz L., Mejean V., Jourlin-Castelli C., 2003, Anticipating an alkaline stress through the Tor phosphorelay system in Escherichia coli., Mol Microbiol 48(1):211-23

 [21] Tramonti A., De Canio M., Delany I., Scarlato V., De Biase D., 2006, Mechanisms of transcription activation exerted by GadX and GadW at the gadA and gadBC gene promoters of the glutamate-based acid resistance system in Escherichia coli., J Bacteriol 188(23):8118-27

 [22] Castanie-Cornet MP., Cam K., Bastiat B., Cros A., Bordes P., Gutierrez C., 2010, Acid stress response in Escherichia coli: mechanism of regulation of gadA transcription by RcsB and GadE., Nucleic Acids Res 38(11):3546-54

 [23] Castanie-Cornet MP., Treffandier H., Francez-Charlot A., Gutierrez C., Cam K., 2007, The glutamate-dependent acid resistance system in Escherichia coli: essential and dual role of the His-Asp phosphorelay RcsCDB/AF., Microbiology 153(Pt 1):238-46

 [24] Johnson MD., Burton NA., Gutierrez B., Painter K., Lund PA., 2011, RcsB Is Required for Inducible Acid Resistance in Escherichia coli and Acts at gadE-Dependent and -Independent Promoters., J Bacteriol 193(14):3653-6

 [25] Ma Z., Gong S., Richard H., Tucker DL., Conway T., Foster JW., 2003, GadE (YhiE) activates glutamate decarboxylase-dependent acid resistance in Escherichia coli K-12., Mol Microbiol 49(5):1309-20

 [26] Krin E., Danchin A., Soutourina O., 2010, RcsB plays a central role in H-NS-dependent regulation of motility and acid stress resistance in Escherichia coli., Res Microbiol 161(5):363-371

 [27] Salmon KA., Hung SP., Steffen NR., Krupp R., Baldi P., Hatfield GW., Gunsalus RP., 2005, Global gene expression profiling in Escherichia coli K12: effects of oxygen availability and ArcA., J Biol Chem 280(15):15084-96

 [28] Traxler MF., Summers SM., Nguyen HT., Zacharia VM., Hightower GA., Smith JT., Conway T., 2008, The global, ppGpp-mediated stringent response to amino acid starvation in Escherichia coli., Mol Microbiol 68(5):1128-48

 [29] Opdyke JA., Kang JG., Storz G., 2004, GadY, a small-RNA regulator of acid response genes in Escherichia coli., J Bacteriol 186(20):6698-705

RegulonDB