OxyS RNA

OxyS RNA
OxyS RNA
	Predicted secondary structure and sequence conservation of OxyS
Identifiers
Symbol	OxyS
Rfam	RF00035
Other data
RNA type	Gene; sRNA
Domain(s)	Bacteria
SO	SO:0000384
PDB structures	PDBe

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[]

^ 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.
^ 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.
^ 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.
^ 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.
^ 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.
^ 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.

External links[]

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[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.

[pmid27044921-3] 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.

[pmid16717284-5] 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.

[pmid29237698-6] 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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