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

A 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] Recent studies have expanded this list and experimentally validated a total of 64 Hfq binding sRNA in Salmonella Typhimurium.[2][3][4] Genomic SELEX has been used to show that Hfq binding RNAs are enriched in the sequence motif 5'-AAYAAYAA-3'.[5]

Bacterial Hfq binding sRNAs

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): 1111–24. doi:10.1046/j.1365-2958.2003.03734.x. PMID 14622403. 
  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): 1174–91. doi:10.1111/j.1365-2958.2007.05991.x. PMID 17971080. 
  3. ^ Sittka A, Lucchini S, Papenfort K, et al. (2008). Burkholder, William F.. 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. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2515195. 
  4. ^ a b 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): 1913–27. doi:10.1093/nar/gkn050. PMC 2330248. PMID 18267966. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2330248. 
  5. ^ 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): 3794–808. doi:10.1093/nar/gkq032. PMC 2887942. PMID 20348540. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2887942. 

External links

Gallery of secondary structure images
isrA Hfq binding RNA: Predicted secondary structure taken from the Rfam database. Family RF01385.  
isrB Hfq binding RNA: Predicted secondary structure taken from the Rfam database. Family RF01386.  
isrC Hfq binding RNA: Predicted secondary structure taken from the Rfam database. Family RF01387.  
isrD Hfq binding RNA: Predicted secondary structure taken from the Rfam database. Family RF01388.  
isrF Hfq binding RNA: Predicted secondary structure taken from the Rfam database. Family RF01389.  
isrG Hfq binding RNA: Predicted secondary structure taken from the Rfam database. Family RF01390.  
isrH Hfq binding RNA: Predicted secondary structure taken from the Rfam database. Family RF01391.  
isrI Hfq binding RNA: Predicted secondary structure taken from the Rfam database. Family RF01392.  
isrJ Hfq binding RNA: Predicted secondary structure taken from the Rfam database. Family RF01393.  
isrK Hfq binding RNA: Predicted secondary structure taken from the Rfam database. Family RF01394.  
isrL Hfq binding RNA: Predicted secondary structure taken from the Rfam database. Family RF01395.  
isrN Hfq binding RNA: Predicted secondary structure taken from the Rfam database. Family RF01396.  
isrO Hfq binding RNA: Predicted secondary structure taken from the Rfam database. Family RF01397.  
isrP Hfq binding RNA: Predicted secondary structure taken from the Rfam database. Family RF01398.  
isrQ Hfq binding RNA: Predicted secondary structure taken from the Rfam database. Family RF01399.  
istR Hfq binding RNA: Predicted secondary structure taken from the Rfam database. Family RF01400.  
rseX Hfq binding RNA: Predicted secondary structure taken from the Rfam database. Family RF01401.  
STnc150 Hfq binding RNA: Predicted secondary structure taken from the Rfam database. Family RF01402.  
STnc290 Hfq binding RNA: Predicted secondary structure taken from the Rfam database. Family RF01403.  
STnc440 Hfq binding RNA: Predicted secondary structure taken from the Rfam database. Family RF01404.  
STnc490k Hfq binding RNA: Predicted secondary structure taken from the Rfam database. Family RF01405.  
STnc500 Hfq binding RNA: Predicted secondary structure taken from the Rfam database. Family RF01406.  
STnc560 Hfq binding RNA: Predicted secondary structure taken from the Rfam database. Family RF01407.  
sraL Hfq binding RNA: Predicted secondary structure taken from the Rfam database. Family RF01408.  
STnc250 Hfq binding RNA: Predicted secondary structure taken from the Rfam database. Family RF01409.