RegulonDB RegulonDB 11.1: Operon Form
   

aroF-tyrA operon and associated TUs in Escherichia coli K-12 genome




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


Transcription unit          
Name: aroF-tyrA
Synonym(s): OP00010, aroF
Gene(s): tyrA, aroF   Genome Browser M3D Gene expression COLOMBOS
Note(s): The aroF-tyrA operon is repressed by TyrR in the presence of tyrosine and, to a lesser extent, in the presence of high concentrations of phenylalanine. For full repression, the protein binds to three TyrR boxes Cobbett CS.,1988 Two of them, located at positions -29.5 and -52.5 bp from the transcriptional start site (TSS), are adjacent to each other and overlap the promoter; the third is located further upstream of the promoter (-104.5 bp from the TSS) Cobbett CS,1987. DeFeyter RC,1986 All three boxes are aligned on the same face of the DNA helix, and it was proposed that they form a repression loop Cobbett CS.,1988
A potential RNA G-quadruplex structure, formed by guanine-rich sequences located in the coding sequence region of the gene, was identified for tyrA. 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 aroF 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
[IC-ADJ-GENES-SAME-BIO-PROCESS] Products of adjacent genes in the same biological process
Reference(s): [1] Garner CC., et al., 1985
[2] Hudson GS., et al., 1984
Promoter
Name: aroFp
+1: 2741201
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 51
Sequence: gtaaataaaaatgtacgaaatatggattgaaaactttactttatgtgttatcgttacgtcAtcctcgctgaggatcaacta
                                -35                   -10   +1                   
Note(s): A total of 554 promoter regions from Escherichia coli were aligned in order to analyze their sequence similarities. Mitchell JE,2003focused on conservation, patterns, similarities, and differences between promoters with or without an extended -10 5'-TG-3' element and other conserved elements. They experimentally showed that, for several naturally occurring extended -10 promoters, the 5'-TRTG-3' motif is an important determinant for promoter activity. Eleven promoters were selected for further experimental study. Of those, the seven most active (aroF > ompF > envA > purFp1 > purEF > purMN > gyrA) were investigated for the contribution of the extended -10 motif by changing the 5'-TG-3' element. Promoters with poor matches to the -10 and -35 consensus hexamers are more dependent on the 5'-TG-3' motif, and this plays a similar role on different promoters. The dinucleotide at -17 and -16 in aroFp results in similar patterns of activity, suggesting that these bases play a similar role on different promoters Mitchell JE,2003
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[RS-EPT-CBR]
Reference(s): [1] Garner CC., et al., 1985
[3] Huerta AM., et al., 2003
[4] Salgado H, et al., 2012
Terminator(s)
Type: rho-independent
Sequence: ctgatgaaaaGGTGCCGGATGATGTGAATCATCCGGCACtggattatta
Reference(s): [2] Hudson GS., et al., 1984
TF binding sites (TFBSs)
[SoxR,+] 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
proximal SoxR activator aroFp 2741185 2741202 8.5 atcgttacgtCATCCTCGCTGAGGATCAactatcgcaa nd [EXP-IEP-RNA-SEQ], [COMP-HINF], [EXP-CHIP-EXO-MANUAL] S [8]
[TyrR,-] 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
proximal TyrR-L-tyrosine repressor aroFp 2741222 2741239 -29.5 gtacgaaataTGGATTGAAAACTTTACTttatgtgtta nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IMP-SITE-MUTATION] W [1], [5], [6], [7]
proximal TyrR-L-tyrosine repressor aroFp 2741245 2741262 -52.5 aaattgcctgTGTAAATAAAAATGTACGaaatatggat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IMP-SITE-MUTATION] W [1], [5], [6]
remote TyrR-L-tyrosine repressor aroFp 2741297 2741314 -104.5 tcaaagggagTGTAAATTTATCTATACAgaggtaaggg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IMP-SITE-MUTATION] W [1], [5], [6]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

 [COMP-HINF-POSITIONAL-IDENTIFICATION] Human inference of promoter position

 [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-RNA-SEQ] high throughput RNA-seq evidence

 [COMP-HINF] Inferred by a human based on computational evidence

 [EXP-CHIP-EXO-MANUAL] ChIP-exo evidence used in manual assertion

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

 [COMP-HINF-SIMILAR-TO-CONSENSUS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [EXP-IMP-SITE-MUTATION] Site mutation


Reference(s)    

 [1] Garner CC., Herrmann KM., 1985, Operator mutations of the Escherichia coli aroF gene., J Biol Chem 260(6):3820-5

 [2] Hudson GS., Davidson BE., 1984, Nucleotide sequence and transcription of the phenylalanine and tyrosine operons of Escherichia coli K12., J Mol Biol 180(4):1023-51

 [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] Cobbett CS., 1988, Repression of the aroF promoter by the TyrR repressor in Escherichia coli K-12: role of the 'upstream' operator site., Mol Microbiol 2(3):377-83

 [6] Cobbett CS., Delbridge ML., 1987, Regulatory mutants of the aroF-tyrA operon of Escherichia coli K-12., J Bacteriol 169(6):2500-6

 [7] DeFeyter RC., Davidson BE., Pittard J., 1986, Nucleotide sequence of the transcription unit containing the aroL and aroM genes from Escherichia coli K-12., J Bacteriol 165(1):233-9

 [8] 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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