RegulonDB RegulonDB 10.7: Operon Form
   

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




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


Transcription unit          
Name: nagE
Gene(s): nagE   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
[PM] Polar mutation
Reference(s): [1] Peri KG., et al., 1988
[2] Plumbridge J., et al., 1991
[3] Plumbridge JA. 1991
[4] Rogers MJ., et al., 1988
Promoter
Name: nagEp
+1: 703840
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 104
Sequence: actcacaaaagacacgcgtttaatttgcgatacgaattaaattttcacacactctgtagcAgatgatctaacaatctgatt
                         -35                    -10         +1                   
Evidence: [RS-EPT-CBR]
[TIM]
Reference(s): [2] Plumbridge J., et al., 1991
[5] Plumbridge J., et al., 1993
[6] Plumbridge J., et al., 1998
[4] Rogers MJ., et al., 1988
[7] Salgado H, et al., 2012
Terminator(s)
Type: rho-independent
Sequence: caacaatgacAAGCGGTGGAGATCTTCTCTGCCGCTTtttttttcat
Reference(s): [4] Rogers MJ., et al., 1988
TF binding sites (TFBSs)
[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-cAMP activator nagEp 703768 703789 -61.5 aataacgataTTTGGTGACAAAACTCACAAAAgacacgcgtt nd [APIORCISFBSCS], [BCE], [BPP], [GEA] [2], [4], [5], [6], [9]
proximal CRP-cAMP repressor nagEp 703768 703789 -61.5 aataacgataTTTGGTGACAAAACTCACAAAAgacacgcgtt nd [APIORCISFBSCS], [BCE], [BPP], [GEA] [2], [4], [5], [6], [9]
proximal CRP-cAMP repressor nagEp 703802 703823 -27.5 cacgcgtttaATTTGCGATACGAATTAAATTTtcacacactc nd [APIORCISFBSCS], [BPP] [2]
proximal CRP-cAMP activator nagEp 703802 703823 -27.5 cacgcgtttaATTTGCGATACGAATTAAATTTtcacacactc nd [APIORCISFBSCS], [BPP] [2]
[NagC,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote NagC repressor nagEp 703704 703726 -125.0 aatccgacctGATTTTTTGAATGATAAAATAAGttttctggtt nd [BPP], [GEA], [SM] [2], [5], [6], [8], [9]
proximal NagC repressor nagEp 703798 703820 -31.0 aagacacgcgTTTAATTTGCGATACGAATTAAAttttcacaca nd [BPP], [GEA], [SM] [2], [5], [6], [8], [9]


Evidence    

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

 [TIM] Transcription initiation mapping

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

 [BCE] Binding of cellular extracts

 [BPP] Binding of purified proteins

 [GEA] Gene expression analysis

 [SM] Site mutation


Reference(s)    

 [1] Peri KG., Waygood EB., 1988, Sequence of cloned enzyme IIN-acetylglucosamine of the phosphoenolpyruvate:N-acetylglucosamine phosphotransferase system of Escherichia coli., Biochemistry 27(16):6054-61

 [2] Plumbridge J., Kolb A., 1991, CAP and Nag repressor binding to the regulatory regions of the nagE-B and manX genes of Escherichia coli., J Mol Biol 217(4):661-79

 [3] Plumbridge JA., 1991, Repression and induction of the nag regulon of Escherichia coli K-12: the roles of nagC and nagA in maintenance of the uninduced state., Mol Microbiol 5(8):2053-62

 [4] Rogers MJ., Ohgi T., Plumbridge J., Soll D., 1988, Nucleotide sequences of the Escherichia coli nagE and nagB genes: the structural genes for the N-acetylglucosamine transport protein of the bacterial phosphoenolpyruvate: sugar phosphotransferase system and for glucosamine-6-phosphate deaminase., Gene 62(2):197-207

 [5] Plumbridge J., Kolb A., 1993, DNA loop formation between Nag repressor molecules bound to its two operator sites is necessary for repression of the nag regulon of Escherichia coli in vivo., Mol Microbiol 10(5):973-81

 [6] Plumbridge J., Kolb A., 1998, DNA bending and expression of the divergent nagE-B operons., Nucleic Acids Res 26(5):1254-60

 [7] 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.

 [8] Fernandez M., Plumbridge J., 2019, Complex synergistic amino acid-nucleotide interactions contribute to the specificity of NagC operator recognition and induction., Microbiology 165(7):792-803

 [9] Plumbridge J., 2001, DNA binding sites for the Mlc and NagC proteins: regulation of nagE, encoding the N-acetylglucosamine-specific transporter in Escherichia coli., Nucleic Acids Res 29(2):506-14

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