RegulonDB RegulonDB 10.9: Operon Form
   

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




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


Transcription unit          
Name: soxR
Gene(s): soxR   Genome Browser M3D Gene expression COLOMBOS
Note(s): It was originally thought that soxR mRNA overlaps soxS, which is transcribed in the opposite direction Wu J,1991. However, further experiments have shown that the soxR and soxS promoter regions, but not the mRNAs, overlap Hidalgo E,1998.
Under nitrogen-rich growth conditions, the expression of the soxR gene was increased in mutants for two genes that encode two terminal oxidases, cyoA and cydB, and in mutants for two transcriptional regulators, Fnr and Fur Kumar R,2011

The expression of the gene soxR is increased under acidic growth conditions in either aerobiosis or microaerobiosis Marzan LW,2013 it is enhanced under high oxygen saturation (300%) in the absence of the superoxide dismutase proteins SodA and SodB Baez A,2013 and it is induced in the presence of norfloxacin 32561799.
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [1] Wu J., et al., 1991
Promoter
Name: soxRp
+1: 4277447
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 22
Sequence: tctgcctcttttcagtgttcagttcgttaattcatctgttggggagtataattcctcaagTtaacttgaggtaaagcgatt
                       -35                     -10          +1                   
Note(s): Wu and Weiss Wu J,1991 initially mapped the soxR transcription start site by primer extension to 218 bp upstream from the soxR gene. Hidalgo et al. Hidalgo E,1998 later determined a different transcription start site, shown here.
Evidence: [HIPP]
[ICWHO]
[TIM]
Reference(s): [2] Hidalgo E., et al., 1998
[3] Huerta AM., et al., 2003
Terminator(s)
Type: rho-independent
Sequence: aagatgaacaAAACTAAAGCGCCACAAGGGCGCTTTAGTTTgttttccggt
Reference(s): [4] Argaman L., et al., 2001
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
proximal AcrR repressor soxRp 4277444 4277454 2.5 ataattcctcAAGTTAACTTGaggtaaagcg nd [APIORCISFBSCS], [BPP], [GEA] [7]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd FNR repressor soxRp nd nd nd nd nd [BPP], [GEA], [IGI] [8]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd Fur-Fe2+ repressor soxRp nd nd nd nd nd [BPP], [GEA], [IGI] [8]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal SoxR repressor soxRp 4277440 4277457 2.5 gagtataattCCTCAAGTTAACTTGAGGTaaagcgattt nd [BPP], [CEEUMA], [GEA], [IHBCE], [RSE] [2], [5], [6]




Reference(s)    

 [1] Wu J., Weiss B., 1991, Two divergently transcribed genes, soxR and soxS, control a superoxide response regulon of Escherichia coli., J Bacteriol 173(9):2864-71

 [2] Hidalgo E., Leautaud V., Demple B., 1998, The redox-regulated SoxR protein acts from a single DNA site as a repressor and an allosteric activator., EMBO J 17(9):2629-36

 [3] 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

 [4] Argaman L., Hershberg R., Vogel J., Bejerano G., Wagner EG., Margalit H., Altuvia S., 2001, Novel small RNA-encoding genes in the intergenic regions of Escherichia coli., Curr Biol 11(12):941-50

 [5] Hidalgo E., Bollinger JM., Bradley TM., Walsh CT., Demple B., 1995, Binuclear [2Fe-2S] clusters in the Escherichia coli SoxR protein and role of the metal centers in transcription., J Biol Chem 270(36):20908-14

 [6] 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

 [7] Lee JO., Cho KS., Kim OB., 2014, Overproduction of AcrR increases organic solvent tolerance mediated by modulation of SoxS regulon in Escherichia coli., Appl Microbiol Biotechnol 98(20):8763-73

 [8] Kumar R., Shimizu K., 2011, Transcriptional regulation of main metabolic pathways of cyoA, cydB, fnr, and fur gene knockout Escherichia coli in C-limited and N-limited aerobic continuous cultures., Microb Cell Fact 10:3


RegulonDB