RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit          
Name: soxS
Synonym(s): OP00296
Gene(s): soxS   Genome Browser M3D Gene expression COLOMBOS
Note(s): The expression of the soxS gene is induced quickly under oxidative stress Lu C,2003 In addition, it was proved in an experiment with increasing concentrations of the antibiotic tetracycline that the soxS gene is 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 soxS is also induced in the presence of menadione, salicylic acid, and norfloxacin in a MarR-dependent way Reyes-Fernández EZ, Schuldiner S,2020.
Under nitrogen-rich growth conditions, the expression of the soxS 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
Overexpression of MarA and Rob represses the soxSp promoter Chubiz LM, Glekas GD, Rao CV,2012 SoxS represses the soxSp promoter in response to paraquat Chubiz LM, Glekas GD, Rao CV,2012 Decanoate represses the soxSp promoter independently of Rob Chubiz LM, Glekas GD, Rao CV,2012
The expression of the gene soxS is increased under acidic growth conditions in either aerobiosis or microaerobiosis Marzan LW,2013
The transcription of the gene soxS is enhanced under high oxygen saturation (300%) in the absence of the superoxide dismutase proteins SodA and SodB Baez A,2013
Evidence: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] Fozo EM., et al., 2008
[2] Nunoshiba T., et al., 1993
[3] Wu J., et al., 1991
Promoter
Name: soxSp
+1: 4277423
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 40
Sequence: taatttcttttccataaatcgctttacctcaagttaacttgaggaattatactccccaacAgatgaattaacgaactgaac
                             -35                     -10    +1                   
Note(s): The soxS promoter is induced by the presence of salicylate Jain K, Saini S,2016
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[RS-EPT-CBR]
Reference(s): [4] Huerta AM., et al., 2003
[5] Salgado H, et al., 2012
[3] Wu J., et al., 1991
TF binding sites (TFBSs)
[AcrR,-] 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 AcrR repressor soxSp 4277444 4277454 -25.5 cgctttacctCAAGTTAACTTgaggaattat nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [10]
[FNR,-] 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
nd FNR repressor soxSp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [11]
[Fur,-] 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
nd Fur-Fe2+ repressor soxSp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [11]
[SoxR,+] 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 SoxR activator soxSp 4277409 4277426 6.0 tatactccccAACAGATGAATTAACGAActgaacactg nd [EXP-IEP-RNA-SEQ], [COMP-HINF], [EXP-CHIP-EXO-MANUAL] S [9]
proximal SoxR activator soxSp 4277440 4277457 -25.5 aatcgctttaCCTCAAGTTAACTTGAGGaattatactc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IEP-RNA-SEQ], [COMP-HINF], [EXP-CHIP-EXO-MANUAL], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [7], [8], [9]
[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 soxSp 4277411 4277430 3.0 gaattatactCCCCAACAGATGAATTAACGaactgaacac nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IEP-RNA-SEQ], [COMP-HINF], [EXP-CHIP-EXO-MANUAL], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [2], [9]
sRNA Interaction TU
sRNA TU Regulated Function Binding Sites Regulatory Mechanism Evidence (Confirmed, Strong, Weak) Reference(s)
PosLeft PosRight Target sequence (mRNA)
small regulatory RNA MgrR soxS repressor 4277340 4277355 UCAAUCCAUGCGAUAA nd [EXP-IMP], [EXP-IMP-SITE-MUTATION] [6]


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: reverse
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -9.5 4277473 4277518 gcgtttcgccACTTCGCCGGGGGTTAGCAGCGCTTTAATGCGGGGTAATTTCTTTtccataaatc
  anti-terminator -8.4 4277505 4277539 cgccgataccGCCACACCGCTGCGTTTCGCCACTTCGCCGGGGGttagcagcgc
  anti-anti-terminator -14.16 4277522 4277558 tactttcataGAAATGCAGCGCCGATACCGCCACACCGCTGCGTTTcgccacttcg
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"


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

 [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] Transcription initiation mapping

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

 [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-GENE-EXPRESSION-ANALYSIS] Gene expression analysis

 [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

 [EXP-IMP] Inferred from mutant phenotype

 [EXP-IMP-SITE-MUTATION] Site mutation


Reference(s)    

 [1] Fozo EM., Kawano M., Fontaine F., Kaya Y., Mendieta KS., Jones KL., Ocampo A., Rudd KE., Storz G., 2008, Repression of small toxic protein synthesis by the Sib and OhsC small RNAs., Mol Microbiol 70(5):1076-93

 [2] 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

 [3] 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

 [4] 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

 [5] 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.

 [6] Lee HJ., Gottesman S., 2016, sRNA roles in regulating transcriptional regulators: Lrp and SoxS regulation by sRNAs., Nucleic Acids Res 44(14):6907-23

 [7] 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

 [8] 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

 [9] 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

 [10] 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

 [11] 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