RegulonDB RegulonDB 11.2: Operon Form
   

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




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


Transcription unit          
Name: lysP
Gene(s): lysP   Genome Browser M3D Gene expression COLOMBOS
Note(s): In 2011 Ruiz et al. proposed that ArgP binds to a region of 15 bp (ATGAAGGTGTCTTAT) in the intergenic region of lysP Ruiz J,2011. DNase I digestion patterns showed that ArgP binds approximately 50 bp upstream of the transcription start site of lysP Ruiz J,2011. According to this evidence, and electrophoretic mobility shift assay results Ruiz J,2011. Marbaniang CN,2011, the curator assigned two possible binding sites of 20 bp for ArgP, located at -62.5 and -82.5 relative to the transcription start site of lysP.
The curator identified the consensus sequence of ArgP and assigned the possible central position of these binding sites, based on similarity to consensus sequences. The sequence proposed by Ruiz and colleagues is included in the binding site located at -62.5 Ruiz J,2011.
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: lysPp
+1: 2248560
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 28
Sequence: gtgtcttataaccgtgtatttctgccggaaggattgccaatcgtctgctacaatcgcgccTcatttttaagatggatagca
                           -35                        -10   +1                   
Evidence: [COMP-AINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [1] Huerta AM., et al., 2003
[2] Neely MN., et al., 1996
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 activator lysPp 2248613 2248632 -62.5 taatccctggGCGATCATGAAGGTGTCTTAtaaccgtgta 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 [3], [4], [5]
proximal ArgP activator lysPp 2248633 2248652 -82.5 gagattggctGCTTTACTTATAATCCCTGGgcgatcatga 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 [3], [4], [5]
[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
nd Lrp activator lysPp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [5]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

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

 [IC] Inferred by curator

 [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-PURIFIED-PROTEINS] Binding of purified proteins

 [EXP-IMP-SITE-MUTATION] Site mutation


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] Neely MN., Olson ER., 1996, Kinetics of expression of the Escherichia coli cad operon as a function of pH and lysine., J Bacteriol 178(18):5522-8

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

 [4] 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

 [5] Ruiz J., Haneburger I., Jung K., 2011, Identification of ArgP and Lrp as transcriptional regulators of lysP, the gene encoding the specific lysine permease of Escherichia coli., J Bacteriol 193(10):2536-48

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