Hfq binding sRNA

isrA Hfq binding RNA
Predicted secondary structure of isrA Hfq binding RNA
Identifiers
Symbol	isrA
Rfam	RF01385
Other data
RNA type	gene, sRNA
Domain(s)	Enterobacteriaceae
PDB structures	PDBe

Hfq protein from S. aureus with a bound sRNA.

An Hfq binding sRNA is an sRNA that binds the bacterial RNA binding protein called Hfq. A number of bacterial small RNAs which have been shown to bind to Hfq have been characterised (see list). Many of these RNAs share a similar structure composed of three stem-loops.[1] Several studies have expanded this list, and experimentally validated a total of 64 Hfq binding sRNA in Salmonella Typhimurium.[2][3][4] A transcriptome wide study on Hfq binding sites in Salmonella mapped 126 Hfq binding sites within sRNAs.[5] Genomic SELEX has been used to show that Hfq binding RNAs are enriched in the sequence motif 5′-AAYAAYAA-3′.[6] Genome-wide study identified 40 candidate Hfq-dependent sRNAs in plant pathogen Erwinia amylovora. 12 of them were confirmed by Northern blot.[7]

Bacterial Hfq binding sRNAs

• DicF RNA
• DsrA RNA
• FnrS RNA
• GadY RNA
• GcvB RNA
• IsrJ RNA[4]
• MicA RNA / SraD RNA
• MicC RNA
• MicF RNA
• OmrA RNA / OmrB RNA / RygA RNA / RygB RNA / SraE RNA
• OxyS RNA
• Qrr RNA
• RmA RNA
• RprA RNA
• RybB RNA
• RydC RNA
• RyeB RNA
• CyaR RNA
• RyeF
• RyhB RNA
• SgrS RNA
• Spot 42 RNA
• SraH RNA
• SraJ RNA
• SroB RNA / MicM RNA / RybC
• SroC RNA

References

1. Zhang A, Wassarman KM, Rosenow C, Tjaden BC, Storz G, Gottesman S (2003). "Global analysis of small RNA and mRNA targets of Hfq". Mol. Microbiol. 50 (4): 1111–1124. doi:10.1046/j.1365-2958.2003.03734.x. PMID 14622403. S2CID 40056275.
2. Pfeiffer V, Sittka A, Tomer R, Tedin K, Brinkmann V, Vogel J (December 2007). "A small non-coding RNA of the invasion gene island (SPI-1) represses outer membrane protein synthesis from the Salmonella core genome". Molecular Microbiology. 66 (5): 1174–1191. doi:10.1111/j.1365-2958.2007.05991.x. PMID 17971080.
3. Sittka A, Lucchini S, Papenfort K, et al. (2008). Burkholder WF (ed.). "Deep Sequencing Analysis of Small Noncoding RNA and mRNA Targets of the Global Post-Transcriptional Regulator, Hfq". PLOS Genetics. 4 (8): e1000163. doi:10.1371/journal.pgen.1000163. PMC 2515195. PMID 18725932.
4. Padalon-Brauch G, Hershberg R, Elgrably-Weiss M, et al. (April 2008). "Small RNAs encoded within genetic islands of Salmonella typhimurium show host-induced expression and role in virulence". Nucleic Acids Research. 36 (6): 1913–1927. doi:10.1093/nar/gkn050. PMC 2330248. PMID 18267966.
5. 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.
6. Lorenz C, Gesell T, Zimmermann B, Schoeberl U, Bilusic I, Rajkowitsch L, Waldsich C, von Haeseler A, Schroeder R (2010). "Genomic SELEX for Hfq-binding RNAs identifies genomic aptamers predominantly in antisense transcripts". Nucleic Acids Res. 38 (11): 3794–3808. doi:10.1093/nar/gkq032. PMC 2887942. PMID 20348540.
7. Zeng, Quan; Sundin, George W. (2014-01-01). "Genome-wide identification of Hfq-regulated small RNAs in the fire blight pathogen Erwinia amylovora discovered small RNAs with virulence regulatory function". BMC Genomics. 15 (1): 414. doi:10.1186/1471-2164-15-414. ISSN 1471-2164. PMC 4070566. PMID 24885615.

Further reading

• De Lay, N.; Schu, D. J.; Gottesman, S. (2013). "Bacterial Small RNA-based Negative Regulation: Hfq and Its Accomplices". Journal of Biological Chemistry. 288 (12): 7996–8003. doi:10.1074/jbc.R112.441386. PMC 3605619. PMID 23362267.
• Peng, Y.; Soper, T. J.; Woodson, S. A. (2013). "Positional effects of AAN motifs in rpoS regulation by sRNAs and Hfq". Journal of Molecular Biology. 426 (2): 275–285. doi:10.1016/j.jmb.2013.08.026. PMC 3947347. PMID 24051417.

External links

• Rfam database