An Hfq binding sRNA is an sRNA that binds the

bacteria Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were among ...

l RNA binding

protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, respo ...

called Hfq. A number of bacterial small RNAs which have been shown to bind to Hfq have been characterised (see list). Many of these

RNA Ribonucleic acid (RNA) is a polymeric molecule essential in various biological roles in coding, decoding, regulation and expression of genes. RNA and deoxyribonucleic acid ( DNA) are nucleic acids. Along with lipids, proteins, and carbohydra ...

s share a similar

structure A structure is an arrangement and organization of interrelated elements in a material object or system, or the object or system so organized. Material structures include man-made objects such as buildings and machines and natural objects such as ...

composed of three

stem-loop Stem-loop intramolecular base pairing is a pattern that can occur in single-stranded RNA. The structure is also known as a hairpin or hairpin loop. It occurs when two regions of the same strand, usually complementary in nucleotide sequence when ...

s. Several studies have expanded this list, and experimentally validated a total of 64 Hfq binding sRNA in ''

Salmonella Typhimurium ''Salmonella enterica'' subsp. ''enterica'' is a subspecies of ''Salmonella enterica'', the rod-shaped, flagellated, aerobic, Gram-negative bacterium. Many of the pathogenic serovars of the ''S. enterica'' species are in this subspecies, includin ...

''. A transcriptome wide study on Hfq binding sites in ''Salmonella'' mapped 126 Hfq binding sites within sRNAs. Genomic SELEX has been used to show that Hfq binding RNAs are enriched in the

sequence motif In biology, a sequence motif is a nucleotide or amino-acid sequence pattern that is widespread and usually assumed to be related to biological function of the macromolecule. For example, an ''N''-glycosylation site motif can be defined as ''As ...

5′-AAYAAYAA-3′. Genome-wide study identified 40 candidate Hfq-dependent sRNAs in plant pathogen ''

Erwinia amylovora Fire blight, also written fireblight, is a contagious disease affecting apples, pears, and some other members of the family Rosaceae. It is a serious concern to apple and pear producers. Under optimal conditions, it can destroy an entire orchard ...

.'' 12 of them were confirmed by Northern blot.

Bacterial Hfq binding sRNAs

* DicF RNA *

DsrA RNA DsrA RNA is a non-coding RNA that regulates both transcription, by overcoming transcriptional silencing by the nucleoid-associated H-NS protein, and translation, by promoting efficient translation of the stress sigma factor, RpoS. These two acti ...

* FnrS RNA * GadY RNA * GcvB RNA * IsrJ RNA * MicA RNA / SraD RNA * MicC RNA * MicF RNA * OmrA RNA / OmrB RNA / RygA RNA / RygB RNA / SraE RNA *

OxyS RNA 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 ...

Qrr RNA Introduction Qrr (Quorum regulatory RNA) is a small non-coding RNA that is thought to be involved in the regulation of quorum sensing in ''Vibrio'' species. The use of small RNAs for vital functions like metabolism, infection cycling, and stre ...

* RmA RNA *

RprA RNA The RprA RNA gene encodes a 106 nucleotide regulatory non-coding RNA. Translational regulation of the stationary phase sigma factor RpoS is mediated by the formation of a double-stranded RNA stem-loop structure in the upstream region of the rpoS ...

* RybB RNA * RydC RNA * RyeB RNA * CyaR RNA * RyeF *

RyhB RNA RyhB RNA is a 90 nucleotide RNA that down-regulates a set of iron-storage and iron-using proteins when iron is limiting; it is itself negatively regulated by the ferric uptake repressor protein, Fur ( Ferric uptake regulator). Discovery The gene ...

* SgrS RNA * Spot 42 RNA * SraH RNA * SraJ RNA * SroB RNA / MicM RNA / RybC * SroC RNA

References

External links

Rfam database
Non-coding RNA {{molecular-cell-biology-stub

Bacterial Hfq binding sRNAs

References

Further reading

External links