RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit          
Name: argI
Synonym(s): OP00008
Gene(s): argI   Genome Browser M3D Gene expression COLOMBOS
Note(s): argI 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: argIp
+1: 4478344
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 33
Sequence: gtgacaaagatttatgctttagacttgcaaatgaataatcatccatataaattgaattttAattcattgaggcgttagcca
                              -35                  -10      +1                   
Evidence: [COMP-AINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [2] Huerta AM., et al., 2003
[3] Piette J., et al., 1982
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 argIp 4478337 4478354 -1.5 atccatataaATTGAATTTTAATTCATTgaggcgttag 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-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [4], [5]
proximal ArgR-L-arginine repressor argIp 4478358 4478375 -22.5 tagacttgcaAATGAATAATCATCCATAtaaattgaat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [4], [5]
Allosteric regulation of RNA-polymerase
  Regulator Function Promoter target of RNApol Growth Conditions Note Evidence Reference
  DksA-ppGpp activation argIp nd   [EXP-IDA-PURIFIED-PROTEIN]
[EXP-IMP] 		[6]
  ppGpp activation argIp nd   [EXP-IEP-GENE-EXPRESSION-ANALYSIS] [7]
Evidence: [EXP-IDA-PURIFIED-PROTEIN] Assay of protein purified to homogeneity
[EXP-IMP] Inferred from mutant phenotype
[EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis
Reference(s): [6] Paul BJ., et al., 2005
[7] Barker MM., et al., 2001


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

 [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] Transcription initiation mapping

 [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-CELLULAR-EXTRACTS] Binding of cellular extracts

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


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] 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

 [4] 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

 [5] 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

 [6] Paul BJ., Berkmen MB., Gourse RL., 2005, DksA potentiates direct activation of amino acid promoters by ppGpp., Proc Natl Acad Sci U S A 102(22):7823-8

 [7] Barker MM., Gaal T., Josaitis CA., Gourse RL., 2001, Mechanism of regulation of transcription initiation by ppGpp. I. Effects of ppGpp on transcription initiation in vivo and in vitro., J Mol Biol 305(4):673-88

RegulonDB