RyhB RNA is a 90 nucleotide

Nucleotide

Nucleotides are molecules that, when joined together, make up the structural units of RNA and DNA. In addition, nucleotides participate in cellular signaling , and are incorporated into important cofactors of enzymatic reactions...

 non-coding RNA

Non-coding RNA

A non-coding RNA is a functional RNA molecule that is not translated into a protein. Less-frequently used synonyms are non-protein-coding RNA , non-messenger RNA and functional RNA . The term small RNA is often used for short bacterial ncRNAs...

 that down-regulates a set of iron-storage and iron-using 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...

s when iron is limiting; it is itself negatively regulated by the ferric uptake repressor protein, Fur (Ferric uptake regulator). This ncRNA gene was independently identified in two screens, named RyhB by Wasserman et al. and called SraI by Argaman et al. and was found to be expressed only in stationary phase. RyhB RNA levels are inversely correlated with mRNA levels for the sdhCDAB operon, encoding succinate dehydrogenase, as well as five other genes previously shown to be positively regulated by Fur by an unknown mechanism. These include two other genes encoding enzymes in the tricarboxylic acid cycle

Citric acid cycle

The citric acid cycle — also known as the tricarboxylic acid cycle , the Krebs cycle, or the Szent-Györgyi-Krebs cycle — is a series of chemical reactions which is used by all aerobic living organisms to generate energy through the oxidization of acetate derived from carbohydrates, fats and...

, acnA and fumA, two ferritin

Ferritin

Ferritin is a ubiquitous intracellular protein that stores iron and releases it in a controlled fashion. The amount of ferritin stored reflects the amount of iron stored. The protein is produced by almost all living organisms, including bacteria, algae and higher plants, and animals...

 genes, ftnA and bfr, and a gene for superoxide dismutase

Superoxide dismutase

Superoxide dismutases are a class of enzymes that catalyze the dismutation of superoxide into oxygen and hydrogen peroxide. As such, they are an important antioxidant defense in nearly all cells exposed to oxygen...

, sodB. A number of other genes have been predicted computationally and verified as targets by microarray

Microarray

A microarray is a multiplex lab-on-a-chip. It is a 2D array on a solid substrate that assays large amounts of biological material using high-throughput screening methods.Types of microarrays include:...

 analysis: napF, sodA, cysE, yciS, acpS, nagZ and dadA. RyhB is bound by the Hfq protein

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...

, that increases its interaction with its target messages.

It has been shown that RyhB has a role in targeting the polycistronic transcript iscRSUA for differential degradation. RyhB binds to the second cistron of iscRSUA, which encodes machinery for biosynthesis of Fe-S clusters. This binding promotes cleavage of the downstream iscSUA transcript. This cleavage leaves the 5' IscR transcript which is a transcriptional regulator responsible regulating several genes that depend on cellular Fe-S level.

RyhB is an analog

Analogy (biology)

An analogy is a trait or an organ that appears similar in two unrelated organisms. The cladistic term for the same phenomenon is homoplasy, from Greek for same form. Biological anologies are often the result of convergent evolution....

 of the sRNA PrrF RNA

PrrF RNA

PrrF RNA is a small non-coding RNA involved in iron homeostasis and is found exclusively in Pseudomonas species. PrrF sequences are the analogs of the sRNA RyhB RNA and are found in tandem. Their expression is induced under iron limitation by the ferric uptake regulator and they act to negatively...

 found in Pseudomonas aeruginosa.

Naming

The RyhB gene name is an acronym composed of R for RNA, y for unknown function (after the protein naming convention), with the h representing the ten minute interval section of the E. coli map the gene is found in. The B comes from the fact that this was one of two RNA genes identified in this interval. Other RNAs using this nomenclature include RydB RNA

RydB RNA

The RydB RNA is a non-coding RNA originally identified in E. coli in an RNA screen. This gene is only 67 nucleotides in length and is composed of a hairpin like structure. RydB lies between the ydiC and ydiH in E. coli. Homologous RNA genes have been found in other species such as Shigella...

, RyeB RNA

RyeB RNA

The 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....

, RyeE RNA

RyeE RNA

The 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...

 and RyfA RNA

RyfA RNA

The ryfA RNA gene is a non-coding RNA present in E. coli, Shigella flexneri and Salmonella species where it is found between the ydaN and dbpA genes. These RNA genes are about 300 nucleotides in length. The function of this RNA is unknown....

.