RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit          
Name: gnd
Gene(s): gnd   Genome Browser M3D Gene expression COLOMBOS
Note(s): Under nitrogen-rich growth conditions, the expression of the gnd gene was increased in mutants for two genes that encode two terminal oxidases, cyoA and cydB, and in mutants for two transcriptional regulators, Fnr and Fur. However, it is unknown if the effects of the transcriptional regulators act directly on gene expressionKumar R,2011
The expression of the gene gnd is increased under acidic growth conditions in microaerobiosis Marzan LW,2013
A potential RNA G-quadruplex structure, formed by guanine-rich sequences located in the coding sequence region of the gene, was identified for gnd . This structure could regulate the expression of the gene, as observed for hemL gene expression Shao X, Zhang W, Umar MI, Wong HY, Seng Z, Xie Y, Zhang Y, Yang L, Kwok CK, Deng X,2020.
The expression of the gene gnd is enhanced under oxygen limitation Kawaguchi H, Miyagawa H, Nakamura-Tsuruta S, Takaya N, Ogino C, Kondo A,2019.
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s): [1] Nasoff MS., et al., 1984
Promoter
Name: gndp
+1: 2101324
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 56
Sequence: aagcatataagcatggataagctatttatactttaataagtactttgtatacttatttgcGaacattccaggccgcgagca
                              -35                    -10    +1                   
Evidence: [COMP-AINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[RS-EPT-CBR]
Reference(s): [2] Baker HV., et al., 1984
[3] Huerta AM., et al., 2003
[1] Nasoff MS., et al., 1984
[4] Salgado H, et al., 2012
TF binding sites (TFBSs)
[FNR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd FNR repressor gndp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [6]
[Fur,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd Fur-Fe2+ repressor gndp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [6]
[GadE,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd GadE activator gndp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [5]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

 [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] Transcription initiation mapping

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

 [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis


Reference(s)    

 [1] Nasoff MS., Baker HV., Wolf RE., 1984, DNA sequence of the Escherichia coli gene, gnd, for 6-phosphogluconate dehydrogenase., Gene 27(3):253-64

 [2] Baker HV., Wolf RE., 1984, Essential site for growth rate-dependent regulation within the Escherichia coli gnd structural gene., Proc Natl Acad Sci U S A 81(24):7669-73

 [3] 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

 [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] 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

 [6] 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

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