Hfq binding sRNA
Encyclopedia
Bacterial small RNA
Bacterial small RNAs are small non-coding RNA molecules produced by bacteria, they are highly structured and contain several stem-loops...
that binds the bacterial
Bacteria
Bacteria are a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a wide range of shapes, ranging from spheres to rods and spirals...
RNA binding protein
Protein
Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...
called Hfq
Hfq protein
The Hfq protein encoded by the hfq gene was discovered in 1968 as an Escherichia. coli host factor that was essential for replication of the bacteriophage Qβ. It is now clear that Hfq is an abundant bacterial RNA binding protein which has many important physiological roles. Usually mediated by...
. A number of bacterial small RNAs which have been shown to bind to Hfq have been characterised (see list).
Many of these RNA
RNA
Ribonucleic acid , or RNA, is one of the three major macromolecules that are essential for all known forms of life....
s share a similar structure
Secondary structure
In biochemistry and structural biology, secondary structure is the general three-dimensional form of local segments of biopolymers such as proteins and nucleic acids...
composed of three stem-loop
Stem-loop
Stem-loop intramolecular base pairing is a pattern that can occur in single-stranded DNA or, more commonly, in 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 read in opposite directions,...
s. Recent studies have expanded this list and experimentally validated a total of 64 Hfq binding sRNA in Salmonella Typhimurium. Genomic SELEX has been used to show that Hfq binding RNAs are enriched in the sequence motif
Sequence motif
In genetics, a sequence motif is a nucleotide or amino-acid sequence pattern that is widespread and has, or is conjectured to have, a biological significance...
5'-AAYAAYAA-3'.
Bacterial Hfq binding sRNAs
- DicF RNADicF RNADicF RNA is a non-coding RNA that is an antisense inhibitor of cell division gene ftsZ. DicF is bound by the Hfq protein which enhances its interaction with its targets....
- DsrA RNADsrA RNADsrA 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...
- FnrS RNAFnrS RNAFnrS RNA is a family of Hfq-binding small RNA whose expression is upregulated in response to anaerobic conditions. It is named FnrS because its expression is strongly dependant on fumarate and nitrate reductase regulator , a direct oxygen availability sensor.A conserved intergenic region between...
- GadY RNA
- GcvB RNAGcvB RNAThe gcvB RNA gene encodes a small non-coding RNA involved in the regulation of a number of amino acid transport systems as well as amino acid biosynthetic genes. The GcvB gene is found in enteric bacteria such as Escherichia coli. GcvB regulates genes by acting as an antisense binding partner of...
- IsrJ RNA
- MicA RNA / SraD RNASraD RNAThe MicA RNA is a small non-coding RNA that was discovered in E. coli during a large scale screen. Expression of SraD is highly abundant in stationary phase, but low levels could be detected in exponentially growing cells as well....
- MicC RNAMicC RNAThe MicC non-coding RNA is located between the ompN and ydbK genes in E. coli. This RNA is thought to be a regulator of the expression level of the OmpC porin protein, with a 5' region of 22 nucleotides potentially forming an antisense interaction with the ompC mRNA...
- MicF RNAMicF RNAThe micF RNA is a non-coding RNA stress response gene found in Escherichia coli and related bacteria that post-transcriptionally controls expression of the outer membrane porin gene ompF. The micF gene encodes a non-translated 93 nucleotide antisense RNA that binds its target ompF mRNA and...
- OmrA RNA / OmrB RNA / RygA RNA / RygB RNA / SraE RNA
- OxyS RNAOxyS RNAOxyS 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 fhlA-encoded transcriptional activator and the...
- Qrr RNAQrr RNAQrr is a non-coding RNA that is thought to be involved in the regulation of quorum sensing in Vibrio species. It is believed that these RNAs, guided by a protein, Hfq, can mediate the destabilisation of the quorum-sensing master regulators LuxR/HapR/VanT mRNAs.Qrr operates as part of a negative...
- RprA RNARprA RNAThe 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 messenger RNA, occluding the translation initiation...
- RybB RNARybB RNARybB is a small non-coding RNA was identified in a large scale screen of E. coli. The function of this short RNA has been studied using a transcriptomic approach and kinetic analyses of target mRNA decay in vivo. RybB was identified as a factor that selectively accelerates the decay of multiple...
- RydC RNARydC RNARydC is a bacterial non-coding RNA. RydC is thought to regulate a mRNA, yejABEF, which encodes an ABC transporter protein. RydC is known to bind the Hfq protein, which causes a conformational change in the RNA molecule. The Hfq/RydC complex is then thought to bind to the target mRNA and induce its...
- RyeB RNARyeB RNAThe RyeB RNA is a non-coding RNA that was identified in a large scale screen of E. coli. The exact 5' and 3' ends of this RNA are uncertain. This RNA overlaps the SraC/RyeA RNA on the opposite strand suggesting that the two may act in a concerted manner....
- CyaR RNARyeE RNAThe CyaR RNA non-coding RNA was identified in a large scale screen of E. coli and was called candidate 14. The exact 5' and 3' ends of this RNA are uncertain. This gene lies between yegQ and orgK in E. coli. This small RNA was shown to be bound by the Hfq protein. This RNA has been renamed as CyaR...
- RyeF
- RyhB RNARyhB RNARyhB RNA is a 90 nucleotide non-coding 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 . This ncRNA gene was independently identified in two screens, named RyhB by Wasserman et...
- SgrS RNASgrS RNASgrS is a 227 nucleotide small RNA that is activated by SgrR in Escherichia coli during glucose-phosphate stress. The nature of glucose-phosphate stress is not fully understood, but is correlated with intracellular accumulation of glucose-6-phosphate...
- Spot 42 RNASpot 42 RNAThe Spot 42 RNA is a non-coding RNA molecule discovered over three decades ago. Escherichia coli Spot 42 RNA is 109 nucleotides in length. Its physiological role has remained obscure, but Spot 42 seems to have a regulatory role on the galactose operon. It is proposed that Spot 42 acts by an...
- SraH RNASraH RNAIn molecular biology the ArcZ RNA is a small non-coding RNA . It is the functional product of a gene which is not translated into protein...
- SraJ RNASraJ RNAGlmZ is a is a small non-coding RNA . It is the functional product of a gene which is not translated into protein....
- SroB RNA / MicM RNA / RybCSroB RNAThe sroB RNA is a non-coding RNA gene of 90 nucleotides in length. sroB is found in several Enterobacterial species but its function is unknown.SroB is found in the intergenic region on the opposite strand to the ybaK and ybaP genes...
- SroC RNASroC RNAThe bacterial SroC RNA is an non-coding RNA gene of around 160 nucleotides in length. sroC is found in several Enterobacterial species but its function is unknown. This RNA interacts with the Hfq protein....