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GadW DNA-binding transcriptional dual regulator

Synonyms: GadW
Summary:
The transcription factor GadW, for Glutamic acid decarboxylase, is negatively autoregulated and controls the transcription of the genes involved in the principal acid resistance system, is glutamate dependent (GAD), and is also referred to as the GAD system [1, 2, 3, 4, 5] In addition, GadW also activates the transcription of the central activator involved in the acid response [5] The physiological inducer is unknown. Richard et al. proposed that GadW can sense intracellular Na+ concentrations, but the mechanism is not known [7]
GadW is one of the regulators in the acid resistance system and is encoded by the unusual gadXW operon, which is located in the region called the acid fitness island [2] This operon encodes two transcriptional regulators, GadX and GadW, both of which are members of the AraC/XylS family of transcriptional regulators [2, 8, 9]
The activities of GadW and GadX are indispensable upon entry into the stationary phase in response to acid pH [1, 10] In addition, Tramonti et al.
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Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
GadW     nd nd
Evolutionary Family: AraC/XylS
Connectivity class: Local Regulator
Gene name: gadW
  Genome position: 3663890-3664618
  Length: 729 bp / 242 aa
Operon name: gadAXW
TU(s) encoding the TF:
Transcription unit        Promoter
gadW
gadWp1
gadW
gadWp2
gadXW
gadXp


Regulon       
Regulated gene(s) dctR, gadA, gadB, gadC, gadE, gadW, gadX, gadY, hdeA, hdeB, mdtE, mdtF, slp, yhiD
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
pH (6)
Transcription related (3)
Porters (Uni-, Sym- and Antiporters) (2)
membrane (2)
activator (2)
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Regulated operon(s) gadAXW, gadBC, gadE-mdtEF, gadY, hdeAB-yhiD, slp-dctR
First gene in the operon(s) gadA, gadB, gadE, gadW, gadX, gadX, gadY, hdeA, slp
Simple and complex regulons AdiY,ArcA,CRP,FNR,Fis,GadE-RcsB,GadW,GadX,H-NS,RcsB,TorR
AdiY,CRP,Fis,FliZ,GadE,GadW,GadX,RcsB
CRP,EvgA,FliZ,GadE,GadW,GadX,H-NS,YdeO
FNR,GadE,GadW,GadX,H-NS,PhoB,RutR
FliZ,GadE,GadW,GadX,H-NS,Lrp,MarA,PhoP,RcsB,TorR
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Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[GadW,+-](3)
[GadW,-](3)
[GadW,+](1)


Transcription factor binding sites (TFBSs) arrangements       

  Functional conformation Function Promoter Sigma factor Central Rel-Pos Distance to first Gene Genes Sequence LeftPos RightPos Evidence (Confirmed, Strong, Weak) References
  GadW dual gadAp Sigma38 -121.5 -148.5 gadA, gadX
tacgataataAAGTCTGTTTTTAATATTATcatgttaaat
3667719 3667738 [BPP], [GEA], [HIBSCS] [1], [2], [3], [4]
  GadW dual gadAp Sigma38 -100.5 -127.5 gadA, gadX
taatattatcATGTTAAATGTTTATATTATaaaaagtcgt
3667698 3667717 [BPP], [GEA], [HIBSCS] [1], [2], [3], [4]
  GadW dual gadAp Sigma38 -78.0 -105.0 gadA, gadX
atattataaaAAGTCGTTTTTCTGCTTAGgattttgtta
3667676 3667694 [BPP], [GEA] [1], [4]
  GadW dual gadAp Sigma38 -57.5 -84.5 gadA, gadX
tctgcttaggATTTTGTTATTTAAATTAAGcctgtaatgc
3667655 3667674 [BPP], [GEA] [1], [4]
  GadW dual gadBp Sigma38 -231.5 -258.5 gadB, gadC
ataataatcaAGTACTAATAGTGATATTTTaaggtctgat
1572294 1572313 [BPP], [GEA], [HIBSCS] [1], [2], [3], [4]
  GadW dual gadBp Sigma38 -210.5 -237.5 gadB, gadC
tgatattttaAGGTCTGATTTTTACGTGATaattcaggag
1572273 1572292 [BPP], [GEA], [HIBSCS] [1], [2], [3], [4]
  GadW dual gadBp Sigma38 -119.5 -146.5 gadB, gadC
gaatttcataTTGTATTGTTTTTCAATGAAaaaatattat
1572182 1572201 [BPP], [GEA] [1], [3], [4]
  GadW dual gadBp Sigma38 -98.5 -125.5 gadB, gadC
ttcaatgaaaAAATATTATTCGCGTAATATctcacgataa
1572161 1572180 [BPP], [GEA] [1], [3], [4]
  GadW activator gadEp Sigma38 -595.5 -616.5 gadE, mdtE, mdtF
ctatggcaaaTTAGCCATTTCAAACATTATcatggctgat
3657740 3657759 [AIBSCS], [GEA] [2], [5]
  GadW activator gadEp Sigma38 -574.5 -595.5 gadE, mdtE, mdtF
aaacattatcATGGCTGATATTTTCCGTAGtcaggtttaa
3657761 3657780 [GEA], [HIBSCS] [2], [5]
  GadW repressor gadWp2 nd -53.5 -216.5 gadW
ataacttttaCTGGAAATAAGATCAGCCATttttttataa
3664825 3664844 [GEA] [2]
  GadW repressor gadWp2 nd -32.5 -195.5 gadW
atcagccattTTTTTATAAACATAAGCTATacgctgtgcg
3664804 3664823 [GEA] [2]
  GadW repressor gadXp Sigma38 nd nd gadX, gadW nd nd [GEA] [1]
  GadW repressor gadYp Sigma38 -50.5 -50.5 gadY
cgcacagcgtATAGCTTATGTTTATAAAAAaatggctgat
3664804 3664823 [GEA] [2]
  GadW repressor gadYp Sigma38 -29.5 -29.5 gadY
ttataaaaaaATGGCTGATCTTATTTCCAGtaaaagttat
3664825 3664844 [GEA] [2]
  GadW dual hdeAp Sigma38 -126.5 -177.5 hdeA, hdeB, yhiD
gcgtctaagaATGCAGTCGATTTAATAAAAatttcctaat
3656908 3656927 [AIBSCS], [GEA] [4], [6]
  GadW dual hdeAp Sigma38 -74.5 -125.5 hdeA, hdeB, yhiD
tgcatctgtaACTCATTGTATTGAAATAAAaatatctgat
3656856 3656875 [BPP], [GEA], [HIBSCS] [2], [4], [6]
  GadW dual hdeAp Sigma38 -53.5 -104.5 hdeA, hdeB, yhiD
tgaaataaaaATATCTGATTTTGATATTTTccatcaacat
3656835 3656854 [AIBSCS], [BPP], [GEA], [HIBSCS] [2], [4], [6]
  GadW repressor slpp Sigma70 -81.5 -106.5 slp, dctR
ctaaacagaaAGGATATAAACATCAGACAGgtttacgtta
3653845 3653864 [GEA], [HIBSCS] [2], [4]
  GadW repressor slpp Sigma70 -60.5 -85.5 slp, dctR
atcagacaggTTTACGTTACTATCAGGCATatcacctcag
3653866 3653885 [AIBSCS], [GEA] [2], [4]


Alignment and PSSM for GadW TFBSs    

Aligned TFBS of GadW   
  Sequence
  AAAATATTATTCGCGTAATA
  CATATTGTATTGTTTTTCAA
  CTGATTTTTACGTGATAATT
  CTAATAGTGATATTTTAAGG
  AGGATATAAACATCAGACAG
  CTGATAGTAACGTAAACCTG
  CTGATTTTGATATTTTCCAT
  CTCATTGTATTGAAATAAAA
  AGAATGCAGTCGATTTAATA
  CCATTTCAAACATTATCATG
  CTGATATTTTCCGTAGTCAG
  CTTATGTTTATAAAAAAATG
  CTGATCTTATTTCCAGTAAA
  AGGATTTTGTTATTTAAATT
  AAGTCGTTTTTCTGCTTAGG
  ATAATATAAACATTTAACAT
  CTGTTTTTAATATTATCATG

Position weight matrix (PWM).   
A	6	3	5	14	0	6	0	4	9	9	0	8	3	3	9	4	9	11	7	5
C	11	1	1	0	1	1	2	0	0	0	7	3	1	3	1	0	4	6	0	0
G	0	3	9	0	0	3	4	0	4	0	0	5	2	2	1	3	0	0	2	8
T	0	10	2	3	16	7	11	13	4	8	10	1	11	9	6	10	4	0	8	4

PWM logo   


 


Evolutionary conservation of regulatory elements    
     Note: Evolutionary conservation of regulatory interactions and promoters is limited to gammaproteobacteria.
TF-target gene evolutionary conservation
Promoter-target gene evolutionary conservation


Evidence    

 [BPP] Binding of purified proteins

 [GEA] Gene expression analysis

 [HIBSCS] Human inference based on similarity to consensus sequences

 [AIBSCS] Automated inference based on similarity to consensus sequences



Reference(s)    

 [1] 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

 [2] 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

 [3] 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

 [4] 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

 [5] Sayed AK., Odom C., Foster JW., 2007, The Escherichia coli AraC-family regulators GadX and GadW activate gadE, the central activator of glutamate-dependent acid resistance., Microbiology. 153(Pt 8):2584-92

 [6] Ruiz C., McMurry LM., Levy SB., 2008, Role of the multidrug resistance regulator MarA in global regulation of the hdeAB acid resistance operon in Escherichia coli., J Bacteriol. 190(4):1290-7

 [7] Richard H., Foster JW., 2007, Sodium regulates Escherichia coli acid resistance, and influences GadX- and GadW-dependent activation of gadE., Microbiology. 153(Pt 9):3154-61

 [8] Gallegos MT., Schleif R., Bairoch A., Hofmann K., Ramos JL., 1997, Arac/XylS family of transcriptional regulators., Microbiol Mol Biol Rev. 61(4):393-410

 [9] Martin RG., Rosner JL., 2001, The AraC transcriptional activators., Curr Opin Microbiol. 4(2):132-7

 [10] 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

 [11] 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

 [12] Gallegos MT., Michan C., Ramos JL., 1993, The XylS/AraC family of regulators., Nucleic Acids Res. 21(4):807-10



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