RegulonDB RegulonDB 10.7: Operon Form
   

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




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


Transcription unit          
Name: gadBC
Gene(s): gadC, gadB   Genome Browser M3D Gene expression COLOMBOS
Note(s): |CITS:[10383761]| and |CITS:[8455549]| have reported evidence of a negative effect of Hns protein on the gadBC operon. However, |CITS:[15795232]| demonstrated 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 |CITS:[19767843]|.
Basal GadE activity is required for activation of gadA and gadBC expression during stationary-phase growth |CITS:[17185552]|.
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 |CITS:[21571995]|. gadB is induced during biofilm formation |CITS:[15795232][12657059]|.
RcsB activity through both the RcsCD phosphorelay pathway and the RcsA pathway lowers the acid resistance |CITS:[17185552]|. 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 |CITS:[17185552]|.
Indole enhances the expression of several genes related to acid resistance, such as gadA, gadB, gadC, hdeA, hdeB, hdeD, slp, and gadE |CITS:[20470880]|. The acid resistance phenotype induced by indoles is mainly due to increased expression of the glutamine decarboxylase system |CITS:[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 |CITS:[31186337]|.
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
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 gadBp nd nd nd nd nd [BPP] [17]
[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 gadBp 1572125 1572146 -63.5 cgataaataaCATTAGGATTTTGTTATTTAAAcacgagtcct nd [APIORCISFBSCS], [GEA] [1]
[Fis,-] Phrase
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], [GEA] [13]
proximal Fis repressor gadBp 1572092 1572106 -27.0 ctttgcacttGCTTACTTTATCGATaaatcctact nd [AIBSCS], [GEA] [13]
proximal Fis repressor gadBp 1572124 1572138 -59.0 aacattaggaTTTTGTTATTTAAACacgagtcctt nd [AIBSCS], [GEA] [13]
remote Fis repressor gadBp 1572170 1572184 -105.0 gtttttcaatGAAAAAATATTATTCgcgtaatatc nd [AIBSCS], [GEA] [13]
[FliZ,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd FliZ repressor gadBp nd nd nd nd nd [BPP], [GEA] [18], [19]
[GadE,+] Phrase
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], , [GEA], [IHBCE], [1], [5], [6], [9], [10], [16]
[GadW,+-] Phrase
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 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 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], [GEA] [7], [8], [9], [10]
remote GadW repressor gadBp 1572273 1572292 -210.5 tgatattttaAGGTCTGATTTTTACGTGATaattcaggag nd [APIORCISFBSCS], [BPP], [GEA] [7], [8], [9], [10]
remote GadW repressor gadBp 1572294 1572313 -231.5 ataataatcaAGTACTAATAGTGATATTTTaaggtctgat nd [APIORCISFBSCS], [BPP], [GEA] [7], [8], [9], [10]
remote GadW activator gadBp 1572294 1572313 -231.5 ataataatcaAGTACTAATAGTGATATTTTaaggtctgat nd [APIORCISFBSCS], [BPP], [GEA] [7], [8], [9], [10]
[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 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], [GEA] [7], [8], [9]
remote GadX activator gadBp 1572294 1572313 -231.5 ataataatcaAGTACTAATAGTGATATTTTaaggtctgat nd [APIORCISFBSCS], [BPP], , [GEA], [IHBCE], [6], [7], [8], [9]
remote GadX activator gadBp 1572330 1572349 -268.0 ctatttttatGTAATAATTTTATAAATGCGttcaaaataa nd , [IHBCE], [6]
[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 activator gadBp 1572130 1572144 -64.5 ataaataacaTTAGGATTTTGTTATttaaacacga nd [APIORCISFBSCS], [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.


Transcription unit       
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 |CITS:[23274360]|. The increased expression under aerobiosis appears to be caused by the transcription factor PhoB |CITS:[23274360]|, 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


Transcription unit       
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 |CITS:[23274360]|. The increased expression under aerobiosis appears to be caused by the transcription factor PhoB |CITS:[23274360]|, 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


Transcription unit       
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 |CITS:[23274360]|. The increased expression under aerobiosis appears to be caused by the transcription factor PhoB |CITS:[23274360]|, 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    
  Small RNA name (Regulator) Regulation type Mechanism Function Binding Sites Evidence Reference
LeftPos RightPos Sequence (RNA-strand)
  oxyS antisense post-transcriptional regulation repressor       [GEA]
[IMP]
[IPI]		 [20]
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: Translational
Strand: reverse
Evidence: [ICA] Inferred by computational analysis
Reference(s): [21] Merino E, et al., 2005
  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"


Evidence    

 [HIPP] Human inference of promoter position

 [TIM] Transcription initiation mapping

 [BPP] Binding of purified proteins

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

 [GEA] Gene expression analysis

 [AIBSCS] Automated inference based on similarity to consensus sequences

 [CEUMA] ChIP-exo evidence used in manual assertion

 [IHBCE] Inferred by a human based on computational evidence

 [RE] RNA-seq evidence


Reference(s)    

 [1] 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

 [2] De Biase D., Tramonti A., Bossa F., Visca P., 1999, The response to stationary-phase stress conditions in Escherichia coli: role and regulation of the glutamic acid decarboxylase system., Mol Microbiol 32(6):1198-211

 [3] 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

 [4] 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

 [5] 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

 [6] 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

 [7] 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

 [8] 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

 [9] 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

 [10] 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

 [11] 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

 [12] 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

 [13] 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

 [14] 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

 [15] 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

 [16] 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

 [17] 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

 [18] Pesavento C., Becker G., Sommerfeldt N., Possling A., Tschowri N., Mehlis A., Hengge R., 2008, Inverse regulatory coordination of motility and curli-mediated adhesion in Escherichia coli., Genes Dev 22(17):2434-46

 [19] Pesavento C., Hengge R., 2012, The global repressor FliZ antagonizes gene expression by σS-containing RNA polymerase due to overlapping DNA binding specificity., Nucleic Acids Res 40(11):4783-93

 [20] Altuvia S, Zhang A, Argaman L, Tiwari A, Storz G, 1998, The Escherichia coli OxyS regulatory RNA represses fhlA translation by blocking ribosome binding., EMBO J, 1998 Oct 15

 [21] Merino E, Yanofsky C., 2005, Transcription attenuation: a highly conserved regulatory strategy used by bacteria., Trends Genet. 2005 May;21(5):260-4.

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