RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit          
Name: oxyS
Gene(s): oxyS   Genome Browser M3D Gene expression COLOMBOS
Note(s): The transcription of the gene oxyS is enhanced under high oxygen saturation (300%) Baez A,2013
Evidence: [COMP-AINF-SINGLE-DIRECTON] Automated inference that a single-gene directon is a transcription unit
Promoter
Name: oxySp
+1: 4158394
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 0
Sequence: taggtagaatagcaatgaacgattatccctatcaagcattctgactgataattgctcacaGaaacggagcggcacctcttt
                            -35                     -10     +1                   
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
Reference(s): [1] Huerta AM., et al., 2003
[2] Toledano MB., et al., 1994
TF binding sites (TFBSs)
[OxyR,+] 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 OxyR activator oxySp 4158431 4158447 -45.0 cgataggtagAATAGCAATGAACGATTatccctatca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [2], [3]
proximal OxyR activator oxySp 4158453 4158469 -67.0 ccatcgccacGATAGTTCATGGCGATAggtagaatag nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IEP-RNA-SEQ], [COMP-HINF], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-EXO-MANUAL], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [2], [3], [4]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

 [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-IEP-RNA-SEQ] RNA-seq evidence

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

 [EXP-CHIP-EXO-MANUAL] ChIP-exo evidence used in manual assertion


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] Toledano MB., Kullik I., Trinh F., Baird PT., Schneider TD., Storz G., 1994, Redox-dependent shift of OxyR-DNA contacts along an extended DNA-binding site: a mechanism for differential promoter selection., Cell 78(5):897-909

 [3] Kullik I., Toledano MB., Tartaglia LA., Storz G., 1995, Mutational analysis of the redox-sensitive transcriptional regulator OxyR: regions important for oxidation and transcriptional activation., J Bacteriol 177(5):1275-84

 [4] Seo SW., Kim D., Szubin R., Palsson BO., 2015, Genome-wide Reconstruction of OxyR and SoxRS Transcriptional Regulatory Networks under Oxidative Stress in Escherichia coli K-12 MG1655., Cell Rep 12(8):1289-99

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