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