OxyS RNA

OxyS RNA
Predicted secondary structure and sequence conservation of OxyS
Identifiers
SymbolOxyS
RfamRF00035
Other data
RNA typeGene; sRNA
Domain(s)Bacteria
SOSO:0000384
PDB structuresPDBe

OxyS RNA is a small non-coding RNA which is induced in response to oxidative stress in Escherichia coli. This RNA acts as a global regulator to activate or repress the expression of as many as 40 genes, by an antisense mechanism, including the fhlA-encoded transcriptional activator and the rpoS-encoded sigma(s) subunit of RNA polymerase.[1] OxyS is bound by the Hfq protein, that increases the OxyS RNA interaction with its target messages.[2][3] Binding to Hfq alters the conformation of OxyS.[4] The 109 nucleotide RNA is thought to be composed of three stem-loops.

Target genes

A number of additional targets were predicted and verified using microarray analysis.[5] These are listed below:

  • yobF – confirmed by Northern analysis
  • yaiZ
  • rumA
  • wrbA – confirmed by Northern analysis
  • ybaY – confirmed by Northern analysis

Furthermore, the mRNA encoded by the nusG gene is a direct target of OxyS.[6]

References

  1. ^ Altuvia, S; Zhang A; Argaman L; Tiwari A; Storz G (1998). "The Escherichia coli OxyS regulatory RNA represses fhlA translation by blocking ribosome binding". EMBO J. 17 (20): 6069–6075. doi:10.1093/emboj/17.20.6069. PMC 1170933. PMID 9774350.
  2. ^ Zhang, A; Wassarman KM; Ortega J; Steven AC; Storz G (2002). "The Sm-like Hfq protein increases OxyS RNA interaction with target mRNAs". Mol Cell. 9 (1): 11–22. doi:10.1016/S1097-2765(01)00437-3. PMID 11804582.
  3. ^ Holmqvist E, Wright PR, Li L, Bischler T, Barquist L, Reinhardt R, Backofen R, Vogel J (2016). "Global RNA recognition patterns of post-transcriptional regulators Hfq and CsrA revealed by UV crosslinking in vivo". EMBO J. 35 (9): 991–1011. doi:10.15252/embj.201593360. PMC 5207318. PMID 27044921.
  4. ^ Henderson, CA; Vincent, HA; Casamento, A; Stone, CM; Phillips, JO; Cary, PD; Sobott, F; Gowers, DM; Taylor, JE; Callaghan, AJ (August 2013). "Hfq binding changes the structure of Escherichia coli small noncoding RNAs OxyS and RprA, which are involved in the riboregulation of rpoS". RNA. 19 (8): 1089–1104. doi:10.1261/rna.034595.112. PMC 3708529. PMID 23804244.
  5. ^ Tjaden B, Goodwin SS, Opdyke JA, et al. (2006). "Target prediction for small, noncoding RNAs in bacteria". Nucleic Acids Res. 34 (9): 2791–2802. doi:10.1093/nar/gkl356. PMC 1464411. PMID 16717284.
  6. ^ Barshishat S, Elgrably-Weiss M, Edelstein J, Georg J, Govindarajan S, Haviv M, Wright PR, Hess WR, Altuvia S (2018). "OxyS small RNA induces cell cycle arrest to allow DNA damage repair". EMBO J. 37 (3): 413–426. doi:10.15252/embj.201797651. PMC 5793797. PMID 29237698.
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