RegulonDB RegulonDB 10.9: 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: [HIPP]
[HTTIM]
[ICWHO]
[IMP]
[RS-EPT-CBR]
[TIM]
Reference(s): [2] Huerta AM., et al., 2003
[3] Mendoza-Vargas A., et al., 2009
[1] Riba L., et al., 1988
[4] Salgado H, et al., 2012
TF binding sites (TFBSs)
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 atcgcatttgGTTATGAGATTACTCTCGTTAttaatttgct nd [BPP], [GEA], [SM] [6], [7]
proximal ArgP activator gdhAp1 1842239 1842258 -59.5 nd nd [BPP], [GEA], [SM] [7]
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 gggtcattttTTTCTTGCTTACCGTCACATTCTtgatggtata nd [APIORCISFBSCS] [1]
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 [BPP], [GEA], [IGI] [9]
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 [BPP], [GEA], [IGI] [9]
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 [BPP], [GEA], [IGI] [9]
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 tcgcatttggTTATGAGATTACTCTCgttattaatt nd [APIORCISFBSCS], [GEA] [5]
proximal Nac repressor gdhAp1 1842276 1842290 -25.0 ttcttgcttaCCGTCACATTCTTGATggtatagtcg nd [APIORCISFBSCS], [GEA] [5]
proximal Nac repressor gdhAp1 1842325 1842339 25.0 cacatgacatAAACAACATAAGCACAatcgtattaa nd [APIORCISFBSCS], [GEA] [5]
remote Nac repressor gdhAp1 1842345 1842359 45.0 agcacaatcgTATTAATATATAAGGGttttatatct nd [RSE], [AIBSPD], [APIORCISFBSCS], [CSE], [GEA] [5], [8]
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.




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] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78

 [3] 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

 [4] 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.

 [5] 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

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

 [7] 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

 [8] Aquino P., Honda B., Jaini S., Lyubetskaya A., Hosur K., Chiu JG., Ekladious I., Hu D., Jin L., Sayeg MK., Stettner AI., Wang J., Wong BG., Wong WS., Alexander SL., Ba C., Bensussen SI., Bernstein DB., Braff D., Cha S., Cheng DI., Cho JH., Chou K., Chuang J., Gastler DE., Grasso DJ., Greifenberger JS., Guo C., Hawes AK., Israni DV., Jain SR., Kim J., Lei J., Li H., Li D., Li Q., Mancuso CP., Mao N., Masud SF., Meisel CL., Mi J., Nykyforchyn CS., Park M., Peterson HM., Ramirez AK., Reynolds DS., Rim NG., Saffie JC., Su H., Su WR., Su Y., Sun M., Thommes MM., Tu T., Varongchayakul N., Wagner TE., Weinberg BH., Yang R., Yaroslavsky A., Yoon C., Zhao Y., Zollinger AJ., Stringer AM., Foster JW., Wade J., Raman S., Broude N., Wong WW., Galagan JE., 2017, Coordinated regulation of acid resistance in Escherichia coli., BMC Syst Biol 11(1):1

 [9] 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

 [10] Wright PR., Richter AS., Papenfort K., Mann M., Vogel J., Hess WR., Backofen R., Georg J., 2013, Comparative genomics boosts target prediction for bacterial small RNAs., Proc Natl Acad Sci U S A 110(37):E3487-96


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