RegulonDB RegulonDB 11.2: Operon Form
   

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




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


Transcription unit          
Name: rob
Gene(s): rob   Genome Browser M3D Gene expression COLOMBOS
Note(s): RpoS is involved in the transcription of the rob gene, but it appears that another σ factor, probably σ70 also regulates rob expression Kakeda M, Ueguchi C, Yamada H, Mizuno T,1995
The rob gene is expressed predominantly in the stationary phase Kakeda M, Ueguchi C, Yamada H, Mizuno T,1995 In addition, it was proved in an experiment with increasing concentrations of the tetracycline antibiotic that rob gene expression was induced in low concentrations (1.5 and 4 mg/L) but not in high ones (10 mg/L); this suggests that the product of this gene plays a role under this condition Viveiros M, Dupont M, Rodrigues L, Couto I, Davin-Regli A, Martins M, Pagès JM, Amaral L,2007 The rob gene is also induced in the presence of norfloxacin Reyes-Fernández EZ, Schuldiner S,2020.

Decanoate represses the robp promoter independently of Rob Chubiz LM, Glekas GD, Rao CV,2012 Rob does not directly bind salicylate; instead, salicylate may regulate Rob at the transcriptional level Chubiz LM, Glekas GD, Rao CV,2012 Salicylate activates the rob promoter independently of the marRAB operon Chubiz LM, Glekas GD, Rao CV,2012
Evidence: [COMP-AINF-SINGLE-DIRECTON] Automated inference that a single-gene directon is a transcription unit
[EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] Schneiders T., et al., 2006
Promoter
Name: robp
+1: 4635353
Distance from start of the gene: 43
Sequence: atactctactaagaaaaaaacactgaatgctaaaacagcaaaaaatgctattatccaattAcctgatgtcaggtgctcgtt
Evidence: [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[RS-EPT-CBR]
Reference(s): [2] Salgado H, et al., 2012
[1] Schneiders T., et al., 2006
TF binding sites (TFBSs)
[MarA,-] 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 MarA repressor robp 4635363 4635382 -20.0 actgaatgctAAAACAGCAAAAAATGCTATtatccaatta nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [1]
[Rob,-] 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 Rob repressor robp 4635363 4635382 -19.5 actgaatgctAAAACAGCAAAAAATGCTATtatccaatta nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-EXO], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [1]
[SoxS,-] 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 SoxS repressor robp 4635363 4635382 -19.5 actgaatgctAAAACAGCAAAAAATGCTATtatccaatta nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-EXO], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [1]


Evidence    

 [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

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

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

 [EXP-IMP-SITE-MUTATION] Site mutation

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

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


Reference(s)    

 [1] Schneiders T., Levy SB., 2006, MarA-mediated transcriptional repression of the rob promoter., J Biol Chem 281(15):10049-55

 [2] 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.

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