RegulonDB RegulonDB 11.2: Operon Form
   

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




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


Transcription unit          
Name: argF
Synonym(s): OP00007
Gene(s): argF   Genome Browser M3D Gene expression COLOMBOS
Note(s): argF gene expression is downregulated upon L-valine addition (isoleucine starvation) in the cellular growth medium Gummesson B, Shah SA, Borum AS, Fessler M, Mitarai N, Sørensen MA, Svenningsen SL,2020.
Reference(s): [1] Cunin R., et al., 1983
Promoter
Name: argFp
+1: 290340
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 35
Sequence: gtaagaaagaattgtgaaatggggttgcaaatgaataattacacatataaagtgaattttAattcaataagtggcgttcgc
                              -35                  -10      +1                   
Evidence: [COMP-AINF]
[EXP-IDA-RNA-POLYMERASE-FOOTPRINTING]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[RS-EPT-CBR]
Reference(s): [2] Huerta AM., et al., 2003
[3] Moore SK., et al., 1978
[4] Piette J., et al., 1982
[5] Salgado H, et al., 2012
TF binding sites (TFBSs)
[ArgR,-] 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 ArgR-L-arginine repressor argFp 290333 290350 -1.5 acacatataaAGTGAATTTTAATTCAATaagtggcgtt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IEP-MICROARRAY], [COMP-AINF-PATTERN-DISCOVERY], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-EXO], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [6], [7], [9]
proximal ArgR-L-arginine repressor argFp 290354 290371 -22.5 tggggttgcaAATGAATAATTACACATAtaaagtgaat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [6], [7], [8]


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: reverse
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -14.5 290430 290474 tcgatccaatGTCTTTCTGCTTCTGCAGAGAATCGGAGGCAGATACGATTATTTtcacacacgg
  anti-terminator -5.9 290456 290469 ccaatgtcttTCTGCTTCTGCAGagaatcggag
  anti-anti-terminator -5.4 290461 290495 gactcgacctGGTTGTAGAATTCGATCCAATGTCTTTCTGCTTCtgcagagaat
Notes: "The provided "Sequence" is that of the RNA strand, i.e. U's are shown instead of T's and regulators on the reverse strand will appear as the reverse complement of the sequence delimited by LeftPos-RigtPos"


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

 [EXP-IDA-RNA-POLYMERASE-FOOTPRINTING] RNA polymerase footprinting

 [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

 [EXP-IEP-MICROARRAY] high throughput expression microarray evidence

 [COMP-AINF-PATTERN-DISCOVERY] Automated inference based on sequence pattern discovery

 [COMP-AINF-SIMILAR-TO-CONSENSUS] Automated inference based on similarity to consensus sequences

 [EXP-CHIP-EXO] high throughput ChIP-exo evidence

 [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] Binding of purified proteins

 [EXP-IMP-SITE-MUTATION] Site mutation

 [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] Binding of cellular extracts


Reference(s)    

 [1] Cunin R., Eckhardt T., Piette J., Boyen A., Pierard A., Glansdorff N., 1983, Molecular basis for modulated regulation of gene expression in the arginine regulon of Escherichia coli K-12., Nucleic Acids Res 11(15):5007-19

 [2] 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

 [3] Moore SK., James E., James PM., Fareed G., 1978, Isolation, cloning and characterization of argF gene DNA from Escherichia coli K-12., Gene 4(3):261-78

 [4] Piette J., Cunin R., Van Vliet F., Charlier D., Crabeel M., Ota Y., Glansdorff N., 1982, Homologous control sites and DNA transcription starts in the related argF and argI genes of Escherichia coli K12., EMBO J 1(7):853-7

 [5] 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.

 [6] Caldara M., Charlier D., Cunin R., 2006, The arginine regulon of Escherichia coli: whole-system transcriptome analysis discovers new genes and provides an integrated view of arginine regulation., Microbiology 152(Pt 11):3343-54

 [7] Charlier D., Roovers M., Van Vliet F., Boyen A., Cunin R., Nakamura Y., Glansdorff N., Pierard A., 1992, Arginine regulon of Escherichia coli K-12. A study of repressor-operator interactions and of in vitro binding affinities versus in vivo repression., J Mol Biol 226(2):367-86

 [8] Levitt M., 1992, Accurate modeling of protein conformation by automatic segment matching., J Mol Biol 226(2):507-33

 [9] Tian G., Maas WK., 1994, Mutational analysis of the arginine repressor of Escherichia coli., Mol Microbiol 13(4):599-608

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