RegulonDB RegulonDB 11.2: Operon Form
   

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




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


Transcription unit          
Name: argO
Gene(s): argO   Genome Browser M3D Gene expression COLOMBOS
Note(s): The activation by both Lrp and ArgP in the argO operator is intertwined, each activator being more potent in the absence of the other Peeters E,2009 The competitive activation of a single promoter by two activator proteins, as described by Peeters et al., appears to be rare Peeters E,2009 The three sites of the Lrp activator act cooperatively and normally in wrapping of the operator DNA in the argO promoter region Peeters E,2009 Expression of argO is modulated by the effectors of both activators, which ensures an adapted and fine-tuned synthesis of the transporter in response to environmental conditions Peeters E,2009
In 1999 Laishram et al. proposed that ArgP binds to a region of approximately 60 bp in the intergenic region of argO Laishram RS,2007. Peeters E,2009. The curator assigned two binding sites of 20 bp for ArgP, located at -33.5 and -53.5, and proposes that in this intergenic region this regulator binds as dimer of dimers to two contiguous degenerated inverted repeat sites. The curator identified the consensus sequence of ArgP and assigned the possible central position of these binding sites, based on similarity to consensus sequences.
ArgP has been identified as binding as a dimer of dimers in the intergenic region of dnaA in E. coli Lee Y,1997 and also in the regulatory region of gdhA of Klebsiella pneumoniae Goss TJ,2008. For this reason, there is a possibility that this regulator transcriptionally regulates as a dimer of dimers.
Evidence: [COMP-AINF] Inferred computationally without human oversight
Promoter
Name: argOp
+1: 3068836
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 28
Sequence: ctgattgccaattaatattatcaatttccgctaataacaatcccgcgatatagtctctgcAtcagatacttaattcggaat
                              -35                     -10   +1                   
Note(s): In the argO and dapB promoters, the lysine repression of ArgP-dependent transcription between argO and dapB is apparently different. In the dapBp1 promoter, lysine prevents binding of ArgP Bouvier J,2008 whereas in the argO promoter, lysine traps RNA polymerase recruitment by ArgP Laishram RS,2007.
Evidence: [COMP-AINF]
[COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP]
[EXP-IDA-RNA-POLYMERASE-FOOTPRINTING]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [1] Huerta AM., et al., 2003
[2] Laishram RS., et al., 2007
[3] Mendoza-Vargas A., et al., 2009
[4] Peeters E., et al., 2009
TF binding sites (TFBSs)
[ArgP,+] 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 ArgP-L-arginine activator argOp 3068860 3068879 -33.5 ccaattaataTTATCAATTTCCGCTAATAAcaatcccgcg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [2], [4], [5], [6], [7], [8]
proximal ArgP-L-arginine activator argOp 3068880 3068900 -53.5 tcttattagtTTTTCTGATTGCCAATTAATAttatcaattt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [IC], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION], [IC] C [2], [4], [5], [6], [7]
[Lrp,+] 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 Lrp-L-leucine activator argOp 3068873 3068889 -44.5 tttctgattgCCAATTAATATTATCAAtttccgctaa nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [4]
proximal Lrp-L-leucine activator argOp 3068894 3068910 -65.5 ctggcctctcTCTTATTAGTTTTTCTGattgccaatt nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [4]
proximal Lrp-L-leucine activator argOp 3068918 3068934 -89.5 aacgctgaggCCAGATAATACTCTCTGgcctctctct nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [4]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

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

 [EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP] High-throughput transcription initiation mapping

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

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

 [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-DAP-SEQ] high throughput DNA Affinity Purification (DAP) Sequencing

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

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

 [EXP-IMP-SITE-MUTATION] Site mutation

 [IC] Inferred by curator


Reference(s)    

 [1] 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

 [2] Laishram RS., Gowrishankar J., 2007, Environmental regulation operating at the promoter clearance step of bacterial transcription., Genes Dev 21(10):1258-72

 [3] Mendoza-Vargas A., Olvera L., Olvera M., Grande R., Vega-Alvarado L., Taboada B., Jimenez-Jacinto V., Salgado H., Juarez K., Contreras-Moreira B., Huerta AM., Collado-Vides J., Morett E., 2009, Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli., PLoS One 4(10):e7526

 [4] Peeters E., Nguyen Le Minh P., Foulquie-Moreno M., Charlier D., 2009, Competitive activation of the Escherichia coli argO gene coding for an arginine exporter by the transcriptional regulators Lrp and ArgP., Mol Microbiol 74(6):1513-26

 [5] Marbaniang CN., Gowrishankar J., 2011, Role of ArgP (IciA) in Lysine-Mediated Repression in Escherichia coli., J Bacteriol 193(21):5985-96

 [6] Nandineni MR., Gowrishankar J., 2004, Evidence for an arginine exporter encoded by yggA (argO) that is regulated by the LysR-type transcriptional regulator ArgP in Escherichia coli., J Bacteriol 186(11):3539-46

 [7] Nguyen Le Minh P., Velazquez Ruiz C., Vandermeeren S., Abwoyo P., Bervoets I., Charlier D., 2018, Differential protein-DNA contacts for activation and repression by ArgP, a LysR-type (LTTR) transcriptional regulator in Escherichia coli., Microbiol Res 206:141-158

 [8] Bouvier J., Stragier P., Morales V., Remy E., Gutierrez C., 2008, Lysine represses transcription of the Escherichia coli dapB gene by preventing its activation by the ArgP activator., J Bacteriol 190(15):5224-9

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