RegulonDB RegulonDB 10.9: Gene Form
   

soxS gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

pdeC soxR soxS ryjA AcrR SoxR SoxS SoxR anti-anti-terminator anti-terminator terminator soxRp soxRp soxSp soxSp

Gene      
Name: soxS    Texpresso search in the literature
Synonym(s): ECK4054, EG10958, b4062
Genome position(nucleotides): 4277060 <-- 4277383 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
50.93
External database links:  
ASAP:
ABE-0013311
CGSC:
27801
ECHOBASE:
EB0951
ECOLIHUB:
soxS
OU-MICROARRAY:
b4062
STRING:
511145.b4062
COLOMBOS: soxS


Shine dalgarno      
Sequence: tgaacactgaAAAGAGgcagattTAT


Product      
Name: DNA-binding transcriptional dual regulator SoxS
Synonym(s): SoxS, regulation of superoxide response regulon
Sequence: Get amino acid sequence Fasta Format
Regulator Family: AraC/XylS
Cellular location: cytosol
Molecular weight: 12.911
Isoelectric point: 10.277
Motif(s):
 
Type Positions Sequence
2 -> 107 SHQKIIQDLIAWIDEHIDQPLNIDVVAKKSGYSKWYLQRMFRTVTHQTLGDYIRQRRLLLAAVELRTTERPIFDIAMDLGYVSQQTFSRVFRRQFDRTPSDYRHRL
8 -> 106 QDLIAWIDEHIDQPLNIDVVAKKSGYSKWYLQRMFRTVTHQTLGDYIRQRRLLLAAVELRTTERPIFDIAMDLGYVSQQTFSRVFRRQFDRTPSDYRHR
27 -> 106 VAKKSGYSKWYLQRMFRTVTHQTLGDYIRQRRLLLAAVELRTTERPIFDIAMDLGYVSQQTFSRVFRRQFDRTPSDYRHR
25 -> 46 DVVAKKSGYSKWYLQRMFRTVT
73 -> 96 IFDIAMDLGYVSQQTFSRVFRRQF

 

Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.2 - RNA related --> 2.2.2 - Transcription related
  3 - regulation --> 3.1 - type of regulation --> 3.1.2 - transcriptional level --> 3.1.2.2 - activator
  3 - regulation --> 3.1 - type of regulation --> 3.1.2 - transcriptional level --> 3.1.2.3 - repressor
  3 - regulation --> 3.3 - genetic unit regulated --> 3.3.2 - regulon
  5 - cell processes --> 5.5 - adaptations --> 5.5.6 - other (mechanical, nutritional, oxidative stress)
  5 - cell processes --> 5.6 - protection --> 5.6.2 - detoxification
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0005829 - cytosol
molecular_function GO:0003677 - DNA binding
GO:0003700 - DNA-binding transcription factor activity
GO:0043565 - sequence-specific DNA binding
GO:0000986 - bacterial-type cis-regulatory region sequence-specific DNA binding
GO:0001108 - bacterial-type RNA polymerase holo enzyme binding
biological_process GO:0006355 - regulation of transcription, DNA-templated
Note(s): Note(s): ...[more].
Evidence: [IE] Inferred from experiment
Reference(s): [1] Amabile-Cuevas CF., et al., 1991
[2] Blattner FR., et al., 1993
[3] Fawcett WP., et al., 1994
[4] Fawcett WP., et al., 1995
[5] Li Z., et al., 1994
[6] Nunoshiba T., et al., 1993
[7] Wu J., et al., 1991
External database links:  
DIP:
DIP-10904N
ECOCYC:
PD00406
ECOLIWIKI:
b4062
INTERPRO:
IPR018060
INTERPRO:
IPR020449
INTERPRO:
IPR018062
INTERPRO:
IPR009057
PFAM:
PF12833
PRIDE:
P0A9E2
PRINTS:
PR00032
PRODB:
PRO_000023970
PROSITE:
PS01124
PROSITE:
PS00041
REFSEQ:
NP_418486
SMART:
SM00342
SMR:
P0A9E2
SWISSMODEL:
P0A9E2
UNIPROT:
P0A9E2


Operon      
Name: soxS         
Operon arrangement:
Transcription unit        Promoter
soxS


Transcriptional Regulation      
Display Regulation             
Activated by: SoxR
Repressed by: FNR, Fur, SoxS, AcrR
Growth Conditions:

[1] 

C: Escherichia coli| paraquat 50 µM| oxygen atom| 37.0 C
E: Escherichia coli| paraquat 50 µM| 37.0 C

[2] 

C: Escherichia coli| copper(II) sulfate 3 mM| oxygen atom| 37.0 C
E: Escherichia coli| copper(II) sulfate 3 mM| 37.0 C

[3] 

C: Escherichia coli| exponential phase
E: Escherichia coli| paraquat 0.25 mM| exponential phase

[4] 

C: Escherichia coli| M9 minimal medium| oxygen atom| 37.0 C
E: Escherichia coli| M9 minimal medium| paraquat 50 µM| oxygen atom| 37.0 C

[5] 

C: Escherichia coli| copper(II) sulfate 3 mM| 37.0 C
E: Escherichia coli| soxR knockout mutant| copper(II) sulfate 3 mM| 37.0 C

[6] 

C: Escherichia coli| M9 minimal medium| oxygen atom| 37.0 C
E: Escherichia coli| M9 minimal medium| copper(II) sulfate 3 mM| oxygen atom| 37.0 C

[7] 

C: Escherichia coli| LB broth| 37.0 C
E: Escherichia coli| LB broth| paraquat 0.25 mM| 37.0 C

[8] 

C: Escherichia coli| soxR knockout mutant; soxS knockout mutant; ?(soxR)| LB medium| 37.0 C
E: Escherichia coli| soxR knockout mutant; soxS knockout mutant; ?(soxR)| LB medium| paraquat 50 µM| 37.0 C

[9] 

C: Escherichia coli| soxR knockout mutant; soxS knockout mutant; ?(soxR)| exponential phase
E: Escherichia coli| soxR knockout mutant; soxS knockout mutant; ?(soxR)| paraquat 0.25 mM| exponential phase



RNA cis-regulatory element    
Attenuation: Transcriptional


Elements in the selected gene context region unrelated to any object in RegulonDB      

  Type Name Post Left Post Right Strand Notes Evidence (Confirmed, Strong, Weak) References


Reference(s)    

 [1] Amabile-Cuevas CF., Demple B., 1991, Molecular characterization of the soxRS genes of Escherichia coli: two genes control a superoxide stress regulon., Nucleic Acids Res 19(16):4479-84

 [2] Blattner FR., Burland V., Plunkett G., Sofia HJ., Daniels DL., 1993, Analysis of the Escherichia coli genome. IV. DNA sequence of the region from 89.2 to 92.8 minutes., Nucleic Acids Res 21(23):5408-17

 [3] Fawcett WP., Wolf RE., 1994, Purification of a MalE-SoxS fusion protein and identification of the control sites of Escherichia coli superoxide-inducible genes., Mol Microbiol 14(4):669-79

 [4] Fawcett WP., Wolf RE., 1995, Genetic definition of the Escherichia coli zwf "soxbox," the DNA binding site for SoxS-mediated induction of glucose 6-phosphate dehydrogenase in response to superoxide., J Bacteriol 177(7):1742-50

 [5] Li Z., Demple B., 1994, SoxS, an activator of superoxide stress genes in Escherichia coli. Purification and interaction with DNA., J Biol Chem 269(28):18371-7

 [6] Nunoshiba T., Hidalgo E., Li Z., Demple B., 1993, Negative autoregulation by the Escherichia coli SoxS protein: a dampening mechanism for the soxRS redox stress response., J Bacteriol 175(22):7492-4

 [7] 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


RegulonDB