Hfq binding sRNA
RNA family
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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
