RegulonDB RegulonDB 10.10: Gene Form
   

oxyS gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

argH oxyR oxyS sthA OxyR OxyR terminator oxyRp oxyRp oxySp oxySp TSS_4687 (cluster) TSS_4687 (cluster)

Gene      
Name: oxyS    Texpresso search in the literature
Synonym(s): ECK3952, EG31116, b4458
Genome position(nucleotides): 4158278 <-- 4158394 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
46.15
External database links:  
ASAP:
ABE-0047276
CGSC:
28844
ECHOBASE:
EB4279
ECOLIHUB:
oxyS
COLOMBOS: oxyS


Product      
Name: small regulatory RNA OxyS
Synonym(s): OxyS
Type: small RNA
Cellular location: bacterial nucleoid,cytosol
Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.2 - RNA related --> 2.2.7 - antisense RNA
  2 - information transfer --> 2.3 - protein related --> 2.3.2 - translation
  3 - regulation --> 3.1 - type of regulation --> 3.1.3 - posttranscriptional --> 3.1.3.1 - translation attenuation and efficiency
  3 - regulation --> 3.1 - type of regulation --> 3.1.3 - posttranscriptional --> 3.1.3.6 - antisense RNA
  5 - cell processes --> 5.5 - adaptations --> 5.5.6 - other (mechanical, nutritional, oxidative stress)
  5 - cell processes --> 5.6 - protection
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0043590 - bacterial nucleoid
molecular_function GO:0005515 - protein binding
GO:0003729 - mRNA binding
GO:0048027 - mRNA 5'-UTR binding
biological_process GO:0006979 - response to oxidative stress
GO:0040033 - negative regulation of translation, ncRNA-mediated
GO:1902201 - negative regulation of bacterial-type flagellum-dependent cell motility
Note(s): Note(s): ...[more].
Evidence: [IMP] Inferred from mutant phenotype
Reference(s): [1] Akay A., et al., 2015
[2] Alkan C., et al., 2006
[3] Altuvia S., et al., 1997
[4] Cho H., et al., 2018
[5] Doi H., et al., 2014
[6] Fratczak A., et al., 2009
[7] Goeser L., et al., 2015
[8] Haridas V., et al., 2005
[9] Idil O., et al., 2016
[10] Kim T., et al., 2015
[11] Liu H., et al., 2012
[12] Malecka EM., et al., 2015
[13] Rosner JL., et al., 1994
[14] Sheng H., et al., 2017
[15] Sridhar J., et al., 2007
[16] Storz G. 2016
[17] Updegrove TB., et al., 2011
[18] Wu TH., et al., 2010
External database links:  
ECOCYC:
OXYS-RNA
ECOLIWIKI:
b4458


Operon      
Name: oxyS         
Operon arrangement:
Transcription unit        Promoter
oxyS


Transcriptional Regulation      
Display Regulation             
Activated by: OxyR


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
  promoter TSS_4687 (cluster) 4157619 forward nd [RS-EPT-CBR] [19]


Evidence    

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



Reference(s)    

 [1] Akay A., Sarkies P., Miska EA., 2015, E. coli OxyS non-coding RNA does not trigger RNAi in C. elegans., Sci Rep 5:9597

 [2] Alkan C., Karakoc E., Nadeau JH., Sahinalp SC., Zhang K., 2006, RNA-RNA interaction prediction and antisense RNA target search., J Comput Biol 13(2):267-82

 [3] Altuvia S., Weinstein-Fischer D., Zhang A., Postow L., Storz G., 1997, A small, stable RNA induced by oxidative stress: role as a pleiotropic regulator and antimutator., Cell 90(1):43-53

 [4] Cho H., Kim KS., 2018, Escherichia coli OxyS RNA triggers cephalothin resistance by modulating the expression of CRP-associated genes., Biochem Biophys Res Commun 506(1):66-72

 [5] Doi H., Hoshino Y., Nakase K., Usuda Y., 2014, Reduction of hydrogen peroxide stress derived from fatty acid beta-oxidation improves fatty acid utilization in Escherichia coli., Appl Microbiol Biotechnol 98(2):629-39

 [6] Fratczak A., Kierzek R., Kierzek E., 2009, LNA-modified primers drastically improve hybridization to target RNA and reverse transcription., Biochemistry 48(3):514-6

 [7] Goeser L., Fan TJ., Tchaptchet S., Stasulli N., Goldman WE., Sartor RB., Hansen JJ., 2015, Small heat-shock proteins, IbpAB, protect non-pathogenic Escherichia coli from killing by macrophage-derived reactive oxygen species., PLoS One 10(3):e0120249

 [8] Haridas V., Kim SO., Nishimura G., Hausladen A., Stamler JS., Gutterman JU., 2005, Avicinylation (thioesterification): a protein modification that can regulate the response to oxidative and nitrosative stress., Proc Natl Acad Sci U S A 102(29):10088-93

 [9] Idil O., Macit I., Kaygusuz O., Darcan C., 2016, The role of oxidative stress genes and effect of pH on methylene blue sensitized photooxidation of Escherichia coli., Acta Biol Hung 67(1):85-98

 [10] Kim T., Bak G., Lee J., Kim KS., 2015, Systematic analysis of the role of bacterial Hfq-interacting sRNAs in the response to antibiotics., J Antimicrob Chemother 70(6):1659-68

 [11] Liu H., Wang X., Wang HD., Ren J., Meng L., Wu Q., Dong H., Wu J., Kao TY., Ge Q., Wu ZX., Yuh CH., Shan G., 2012, Escherichia coli noncoding RNAs can affect gene expression and physiology of Caenorhabditis elegans., Nat Commun 3:1073

 [12] Malecka EM., Strozecka J., Sobanska D., Olejniczak M., 2015, Structure of bacterial regulatory RNAs determines their performance in competition for the chaperone protein Hfq., Biochemistry 54(5):1157-70

 [13] Rosner JL., Storz G., 1994, Effects of peroxides on susceptibilities of Escherichia coli and Mycobacterium smegmatis to isoniazid., Antimicrob Agents Chemother 38(8):1829-33

 [14] Sheng H., Stauffer WT., Hussein R., Lin C., Lim HN., 2017, Nucleoid and cytoplasmic localization of small RNAs in Escherichia coli., Nucleic Acids Res 45(5):2919-2934

 [15] Sridhar J., Rafi ZA., 2007, Identification of novel genomic islands associated with small RNAs., In Silico Biol 7(6):601-11

 [16] Storz G., 2016, New perspectives: Insights into oxidative stress from bacterial studies., Arch Biochem Biophys 595:25-7

 [17] Updegrove TB., Correia JJ., Chen Y., Terry C., Wartell RM., 2011, The stoichiometry of the Escherichia coli Hfq protein bound to RNA., RNA 17(3):489-500

 [18] Wu TH., Chang IY., Chu LC., Huang HC., Ng WV., 2010, Modularity of Escherichia coli sRNA regulation revealed by sRNA-target and protein network analysis., BMC Bioinformatics 11 Suppl 7:S11

 [19] 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.


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