RegulonDB RegulonDB 10.8: Operon Form
   

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




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


Transcription unit          
Name: nfo
Synonym(s): OP00263
Gene(s): nfo   Genome Browser M3D Gene expression COLOMBOS
Reference(s): [1] Ariza RR., et al., 1995
Promoter
Name: nfop
+1: 2250806
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 34
Sequence: attcaaagcgtcatcgcataaaccactacatcttgctcctgttaacccgctatcattaccGttttcctccagcgggtttaa
                          -35                      -10      +1                   
Evidence: [HIPP]
[TIM]
Reference(s): [2] Saporito SM., et al., 1988
TF binding sites (TFBSs)
[MarA,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal MarA activator nfop 2250758 2250777 -38.5 tcaaagcgtcATCGCATAAACCACTACATCttgctcctgt nd [AIBSCS], [APIORCISFBSCS], [CV(GEA)], [GEA] [3], [4], [5]
[Rob,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal Rob activator nfop 2250758 2250777 -38.5 tcaaagcgtcATCGCATAAACCACTACATCttgctcctgt nd [APIORCISFBSCS], [CV(GEA)], [GEA] [1], [4]
[SoxS,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal SoxS1 activator nfop 2250759 2250778 -37.0 caaagcgtcaTCGCATAAACCACTACATCTtgctcctgtt nd [APIORCISFBSCS], [BCE], [CV(GEA)], [GEA] [4], [6], [7], [8]
proximal SoxS activator nfop 2250770 2250789 -26.0 cgcataaaccACTACATCTTGCTCCTGTTAacccgctatc nd , [IHBCE], [9]
Note(s): 1Stimulation of the nfop promoter was independent of the C-terminal domain of the RNA polymerase α-subunit. The binding site overlaps the -35 promoter hexamer.
3Stimulation of the nfop promoter was independent of the C-terminal domain of the RNA polymerase α-subunit. The binding site overlaps the -35 promoter hexamer.


Evidence    

 [HIPP] Human inference of promoter position

 [TIM] Transcription initiation mapping

 [AIBSCS] Automated inference based on similarity to consensus sequences

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

 [CV(GEA)] cross validation(GEA)

 [GEA] Gene expression analysis

 [BCE] Binding of cellular extracts

 [CEUMA] ChIP-exo evidence used in manual assertion

 [IHBCE] Inferred by a human based on computational evidence

 [RE] RNA-seq evidence


Reference(s)    

 [1] Ariza RR., Li Z., Ringstad N., Demple B., 1995, Activation of multiple antibiotic resistance and binding of stress-inducible promoters by Escherichia coli Rob protein., J Bacteriol 177(7):1655-61

 [2] Saporito SM., Cunningham RP., 1988, Nucleotide sequence of the nfo gene of Escherichia coli K-12., J Bacteriol 170(11):5141-5

 [3] Jair KW., Martin RG., Rosner JL., Fujita N., Ishihama A., Wolf RE., 1995, Purification and regulatory properties of MarA protein, a transcriptional activator of Escherichia coli multiple antibiotic and superoxide resistance promoters., J Bacteriol 177(24):7100-4

 [4] Martin RG., Gillette WK., Rhee S., Rosner JL., 1999, Structural requirements for marbox function in transcriptional activation of mar/sox/rob regulon promoters in Escherichia coli: sequence, orientation and spatial relationship to the core promoter., Mol Microbiol 34(3):431-41

 [5] Rodionov DA., Gelfand MS., Mironov AA., Rakhmaninova AB., 2001, Comparative approach to analysis of regulation in complete genomes: multidrug resistance systems in gamma-proteobacteria., J Mol Microbiol Biotechnol 3(2):319-24

 [6] Fawcett WP., Wolf RE., 1995, Genetic definition of the Escherichia coli zwf "soxbox," the DNA binding site for SoxS-mediated induction of glucose 6-phosphate dehydrogenase in response to superoxide., J Bacteriol 177(7):1742-50

 [7] Jair KW., Fawcett WP., Fujita N., Ishihama A., Wolf RE., 1996, Ambidextrous transcriptional activation by SoxS: requirement for the C-terminal domain of the RNA polymerase alpha subunit in a subset of Escherichia coli superoxide-inducible genes., Mol Microbiol 19(2):307-17

 [8] Li Z., Demple B., 1994, SoxS, an activator of superoxide stress genes in Escherichia coli. Purification and interaction with DNA., J Biol Chem 269(28):18371-7

 [9] Seo SW., Kim D., Szubin R., Palsson BO., 2015, Genome-wide Reconstruction of OxyR and SoxRS Transcriptional Regulatory Networks under Oxidative Stress in Escherichia coli K-12 MG1655., Cell Rep 12(8):1289-99

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