RegulonDB RegulonDB 10.8: Operon Form
   

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




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


Transcription unit          
Name: gdhA
Gene(s): gdhA   Genome Browser M3D Gene expression COLOMBOS
Note(s): Under nitrogen-limiting growth conditions, the transcription of the gdhA gene is repressed by the Nac protein Camarena L,1998.
Under nitrogen-rich growth conditions, the expression of the gdhA gene was decreased in mutants for two genes that encode two terminal oxidases, cyoA and cydB, and in mutants for two transcriptional regulators, Fnr and Fur. However, under nitrogen-limited growth conditions, the gene expression was increased in the Fur mutant Kumar R,2011
Evidence: [LTED] Length of transcript experimentally determined
Reference(s): [1] Riba L., et al., 1988
Promoter
Name: gdhAp1
+1: 1842308
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 63
Sequence: ctttcctgggtcatttttttcttgcttaccgtcacattcttgatggtatagtcgaaaactGcaaaagcacatgacataaac
                      -35                      -10          +1                   
Note(s): There are 19 bp between the -10 (TATAGT) box and the -35 box (TTGCTT) in the gdhAp promoter. The optimum distance between the boxes of the promoters is 17 bp Riba L,1988.
Evidence: [CV(RS-EPT-CBR)]
[CV(TIM)]
[HIPP]
[HTIM]
[IMP]
[RS-EPT-CBR]
[TIM]
Reference(s): [2] Mendoza-Vargas A., et al., 2009
[1] Riba L., et al., 1988
[3] Salgado H, et al., 2012
TF binding sites (TFBSs)
[ArgP,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal ArgP activator gdhAp1 1842219 1842238 -79.5 atcgcatttgGTTATGAGATTACTCTCGTTattaatttgc nd [BPP], [CV(SM)], [GEA], [SM] [5], [6]
proximal ArgP activator gdhAp1 1842239 1842258 -59.5 tactctcgttATTAATTTGCTTTCCTGGGTcatttttttc nd [BPP], [CV(SM)], [GEA], [SM] [6]
[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 gdhAp1 1842265 1842286 -32.5 gggtcattttTTTCTTGCTTACCGTCACATTCttgatggtat nd [APIORCISFBSCS] [1]
[FNR,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd FNR activator gdhAp1 nd nd nd nd nd [GEA] [7]
[Fur,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd Fur-Fe2+ activator gdhAp1 nd nd nd nd nd [GEA] [7]
[Fur,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd Fur-Fe2+ repressor gdhAp1 nd nd nd nd nd [GEA] [7]
[Nac,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal Nac repressor gdhAp1 1842220 1842234 -81.0 tcgcatttggTTATGAGATTACTCTcgttattaat nd [APIORCISFBSCS], [CV(GEA)], [GEA] [4]
proximal Nac repressor gdhAp1 1842276 1842290 -25.0 ttcttgcttaCCGTCACATTCTTGAtggtatagtc nd [APIORCISFBSCS], [CV(GEA)], [GEA] [4]
proximal Nac repressor gdhAp1 1842325 1842339 25.0 cacatgacatAAACAACATAAGCACaatcgtatta nd [APIORCISFBSCS], [CV(GEA)], [GEA] [4]
remote Nac repressor gdhAp1 1842345 1842359 45.0 agcacaatcgTATTAATATATAAGGgttttatatc nd [APIORCISFBSCS], [CV(GEA)], [GEA] [4]
Note(s): 1A putative CRP-bindig site was identified at bp -32.5 upstream of gdhAp. The regulatory effect of this possible interaction of CRP with the site is not known. However, we assigned a negative effect to this regulatory interaction based on the fact that the position of the site is not optimal for activation of transcription by CRP. This site is located between the -10 and -35 boxes of the promoter Riba L,1988.4A putative CRP-bindig site was identified at bp -32.5 upstream of gdhAp. The regulatory effect of this possible interaction of CRP with the site is not known. However, we assigned a negative effect to this regulatory interaction based on the fact that the position of the site is not optimal for activation of transcription by CRP. This site is located between the -10 and -35 boxes of the promoter Riba L,1988.


Regulation by sRNA    
  Small RNA name (Regulator) Regulation type Mechanism Function Binding Sites Evidence Reference
LeftPos RightPos Sequence (RNA-strand)
  gcvB unknown unknown activator       [IMP] [8]
Notes: "The provided sequence is that of the RNA strand,i.e. 'U's are showed instead the 'T'"


Evidence    

 [CV(RS-EPT-CBR)] cross validation(RS-EPT-CBR)

 [CV(TIM)] cross validation(TIM)

 [HIPP] Human inference of promoter position

 [HTIM] High-throughput transcription initiation mapping

 [IMP] Inferred from mutant phenotype

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

 [TIM] Transcription initiation mapping

 [BPP] Binding of purified proteins

 [CV(SM)] cross validation(SM)

 [GEA] Gene expression analysis

 [SM] Site mutation

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

 [CV(GEA)] cross validation(GEA)


Reference(s)    

 [1] Riba L., Becerril B., Servin-Gonzalez L., Valle F., Bolivar F., 1988, Identification of a functional promoter for the Escherichia coli gdhA gene and its regulation., Gene 71(2):233-46

 [2] Mendoza-Vargas A., Olvera L., Olvera M., Grande R., Vega-Alvarado L., Taboada B., Jimenez-Jacinto V., Salgado H., Juarez K., Contreras-Moreira B., Huerta AM., Collado-Vides J., Morett E., 2009, Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli., PLoS One 4(10):e7526

 [3] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

 [4] Camarena L., Poggio S., Garcia N., Osorio A., 1998, Transcriptional repression of gdhA in Escherichia coli is mediated by the Nac protein., FEMS Microbiol Lett 167(1):51-6

 [5] Marbaniang CN., Gowrishankar J., 2011, Role of ArgP (IciA) in Lysine-Mediated Repression in Escherichia coli., J Bacteriol 193(21):5985-96

 [6] Nguyen Le Minh P., Velazquez Ruiz C., Vandermeeren S., Abwoyo P., Bervoets I., Charlier D., 2018, Differential protein-DNA contacts for activation and repression by ArgP, a LysR-type (LTTR) transcriptional regulator in Escherichia coli., Microbiol Res 206:141-158

 [7] Kumar R., Shimizu K., 2011, Transcriptional regulation of main metabolic pathways of cyoA, cydB, fnr, and fur gene knockout Escherichia coli in C-limited and N-limited aerobic continuous cultures., Microb Cell Fact 10:3

 [8] Pulvermacher SC., Stauffer LT., Stauffer GV., 2009, Role of the sRNA GcvB in regulation of cycA in Escherichia coli., Microbiology 155(Pt 1):106-14

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