RegulonDB RegulonDB 10.9: Operon Form
   

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




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


Transcription unit          
Name: fnr
Synonym(s): OP00029
Gene(s): fnr   Genome Browser M3D Gene expression COLOMBOS
Note(s): The expression of the fnr gene was increased in mutants for two genes that encode two terminal oxidases, cyoA and cydB, and in mutant for the transcriptional regulator Fur Kumar R,2011
The expression of fnr is increased under acidic growth conditions in either aerobiosis or microaerobiosis Marzan LW,2013
Based on genome-wide analysis, 472 single-gene knockouts were studied to determine their anaerobic fermentation products, based on the control of redox reactions. It was determined that the combined knockout of the guaB, pyrD, serA, fnr, arcA, and arcB genes enhanced D-lactate overproduction Kim HJ,2013
Reference(s): [1] Shaw DJ., et al., 1982
[2] Shaw DJ., et al., 1982
Promoter
Name: fnrp
+1: 1399552
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 26
Sequence: ctctgctgttaaggtttgcttagacttacttgctccctaaaaagatgttaaaattgacaaAtatcaattacggcttgagca
                          -35                    -10        +1                   
Evidence: [HIPP]
[ICWHO]
[RS-EPT-CBR]
Reference(s): [3] Huerta AM., et al., 2003
[4] Salgado H, et al., 2012
[1] Shaw DJ., et al., 1982
TF binding sites (TFBSs)
[ArcA,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd ArcA-phosphorylated1 repressor fnrp nd nd nd nd nd [BPP], [GEA], [IGI] [6]
[FNR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal FNR repressor fnrp 1399546 1399559 -0.5 agatgttaaaATTGACAAATATCAAttacggcttg nd [APIORCISFBSCS], [BCE], [BPP], [GEA] [5]
[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 fnrp nd nd nd nd nd [BPP], [GEA], [IGI] [7]
[IHF,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote IHF activator fnrp 1399649 1399663 -104.0 cccttaacaaCTTAAGGGTTTTCAAatagatagac nd [BPP], [GEA], [SM] [5]
Note(s): 1The negative effect of ArcA on fnr expression is slight; this was found using QRT-PCR.3The negative effect of ArcA on fnr expression is slight; this was found using QRT-PCR.


Evidence    

 [HIPP] Human inference of promoter position

 [ICWHO] Inferred computationally without human oversight

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

 [BPP] Binding of purified proteins

 [GEA] Gene expression analysis

 [IGI] Inferred from genetic interaction

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

 [BCE] Binding of cellular extracts

 [SM] Site mutation


Reference(s)    

 [1] Shaw DJ., Guest JR., 1982, Nucleotide sequence of the fnr gene and primary structure of the Enr protein of Escherichia coli., Nucleic Acids Res 10(19):6119-30

 [2] Shaw DJ., Guest JR., 1982, Amplification and product identification of the fnr gene of Escherichia coli., J Gen Microbiol 128(10):2221-8

 [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] Mettert EL., Kiley PJ., 2007, Contributions of [4Fe-4S]-FNR and integration host factor to fnr transcriptional regulation., J Bacteriol 189(8):3036-43

 [6] Shalel-Levanon S., San KY., Bennett GN., 2005, Effect of ArcA and FNR on the expression of genes related to the oxygen regulation and the glycolysis pathway in Escherichia coli under microaerobic growth conditions., Biotechnol Bioeng 92(2):147-59

 [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

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