RegulonDB RegulonDB 10.9: Operon Form
   

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




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


Transcription unit          
Name: oxyR
Synonym(s): OP00067
Gene(s): oxyR   Genome Browser M3D Gene expression COLOMBOS
Note(s): Jung IL,2003demonstrated that both the oxyR and ahpC genes, which codify a transcriptional regulator and a product essential for the detoxification against H2O2-induced stress, respectively, were absolutely dependent on polyamines during entry into the stationary phase. These data suggest that polyamines could be directly participating in the defense mechanism against oxidative stress. Both putrecine and spermidine polyamines increase expression of of the oxyR and katG genes, which are responsible for defense against oxidative stress 12948384.
Overlapping the -35 region of oxyRp is another possible binding site, located at bp -27 of the TSS, with the following sequence: GATAGGATAATCGTTC. This sequence was identified by the curator, who used a new predictive methodology, PhyPIR (Phylogenetic Profile of Inverted Repeated patterns), which was developed in the laboratory of Dr. Enrique Merino of the Institute of Biotechnology, UNAM.
OxyR binds in tandem at the oxyS/oxyR intergenic region, and it acts to repress its own expression in its oxidized and reduced forms. Oxidized OxyR activates the transcription overlapping the -35 box of the promoter oxySp.
The transcription of the gene oxyR is enhanced under high oxygen saturation (300%) Baez A,2013
Hepcidin, an antimicrobial peptide, increases the expression of oxyR under conditions of iron availability 29659799
Reference(s): [1] Vasil'eva SV., et al., 1991
Promoter
Name: oxyRp
+1: 4158457
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 33
Sequence: tgagcaattatcagtcagaatgcttgatagggataatcgttcattgctattctacctatcGccatgaactatcgtggcgat
                        -35                     -10         +1                   
Note(s): In a mutant strain lacking the rpoS gene, the expression of the oxyR gene is increased Gonzalez-Flecha B,1997.
Evidence: [HIPP]
[ICWHO]
[TIM]
Reference(s): [2] Christman MF., et al., 1989
[3] Gonzalez-Flecha B., et al., 1997
[4] Huerta AM., et al., 2003
TF binding sites (TFBSs)
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd CRP-cAMP activator oxyRp nd nd nd nd nd [BPP], [GEA], [IGI] [3]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal OxyR repressor oxyRp 4158431 4158447 -18.0 tgatagggatAATCGTTCATTGCTATTCtacctatcgc [APIORCISFBSCS], [BPP], [GEA] [2], [5], [6]
proximal OxyR repressor oxyRp 4158453 4158469 5.0 ctattctaccTATCGCCATGAACTATCGtggcgatgga [APIORCISFBSCS], [BPP], [CEEUMA], [GEA], [IHBCE], [RSE] [2], [5], [7]


Transcription unit          
Name: oxyR
Synonym(s): OP00067
Gene(s): oxyR   Genome Browser M3D Gene expression COLOMBOS
Note(s): Jung IL,2003demonstrated that both the oxyR and ahpC genes, which codify a transcriptional regulator and a product essential for the detoxification against H2O2-induced stress, respectively, were absolutely dependent on polyamines during entry into the stationary phase. These data suggest that polyamines could be directly participating in the defense mechanism against oxidative stress. Both putrecine and spermidine polyamines increase expression of of the oxyR and katG genes, which are responsible for defense against oxidative stress 12948384.
Overlapping the -35 region of oxyRp is another possible binding site, located at bp -27 of the TSS, with the following sequence: GATAGGATAATCGTTC. This sequence was identified by the curator, who used a new predictive methodology, PhyPIR (Phylogenetic Profile of Inverted Repeated patterns), which was developed in the laboratory of Dr. Enrique Merino of the Institute of Biotechnology, UNAM.
OxyR binds in tandem at the oxyS/oxyR intergenic region, and it acts to repress its own expression in its oxidized and reduced forms. Oxidized OxyR activates the transcription overlapping the -35 box of the promoter oxySp.
The transcription of the gene oxyR is enhanced under high oxygen saturation (300%) Baez A,2013
Hepcidin, an antimicrobial peptide, increases the expression of oxyR under conditions of iron availability 29659799
Reference(s): [1] Vasil'eva SV., et al., 1991
Promoter
Name: oxyRp2
+1: 4158457
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 33
Sequence: tgagcaattatcagtcagaatgcttgatagggataatcgttcattgctattctacctatcGccatgaactatcgtggcgat
                        -35                -10              +1                   
Note(s): In a mutant strain lacking the rpoS gene, the expression of the oxyR gene is increased Gonzalez-Flecha B,1997.
Evidence: [HIPP]
[ICWHO]
[TIM]
Reference(s): [2] Christman MF., et al., 1989
[3] Gonzalez-Flecha B., et al., 1997
[4] Huerta AM., et al., 2003
TF binding sites (TFBSs)
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd CRP-cAMP activator oxyRp2 nd nd nd nd nd [BPP], [GEA], [IGI] [3]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal OxyR repressor oxyRp2 4158431 4158447 -18.0 tgatagggatAATCGTTCATTGCTATTCtacctatcgc nd [APIORCISFBSCS], [BPP], [GEA] [2], [5], [6]
proximal OxyR repressor oxyRp2 4158453 4158469 5.0 ctattctaccTATCGCCATGAACTATCGtggcgatgga nd [APIORCISFBSCS], [BPP], [CEEUMA], [GEA], [IHBCE], [RSE] [2], [5], [7]


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Translational
Strand: forward
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -23.9 4158443 4158486 cgttcattgcTATTCTACCTATCGCCATGAACTATCGTGGCGATGGAGGATGGataatgaata
Notes: "The provided "Sequence" is that of the RNA strand, i.e. U's are shown instead of T's and regulators on the reverse strand will appear as the reverse complement of the sequence delimited by LeftPos-RigtPos"





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