SraH RNA
Encyclopedia
In molecular biology the ArcZ RNA (also known as RyhA and SraH) is a small non-coding RNA
(ncRNA). It is the functional product of a gene
which is not translated into protein
. ArcZ is an Hfq binding RNA that functions as an antisense regulator of a number of protein coding genes.
during a large scale computational screen for transcription signals and genomic features of known small RNA-encoding genes. During this screen 14 novel ncRNA genes were identified, including GlmZ, SraB
, SraC
and SraD
. The expression of SraH was experimentally confirmed by Northern blotting. Its expression is highly abundant in stationary growth phase
but low levels of expression can still be detected in exponentially growing cells
.
it has been shown to repress the expression
of protein coding genes sdaCB (involved in serine
uptake) and tpx
(involved in oxidative stress
) genes, and of the horizontally acquired gene methyl-accepting chemotaxis protein
(MCP). Both sdaCB and STM3216 are regulated by ArcZ binding the ribosome binding site, the tpx mRNA is targeted in the coding sequence (CDS).
ArcZ positively stimulates expression of RpoS stationary phase sigma factor.
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...
(ncRNA). It is the functional product of a gene
Gene
A gene is a molecular unit of heredity of a living organism. It is a name given to some stretches of DNA and RNA that code for a type of protein or for an RNA chain that has a function in the organism. Living beings depend on genes, as they specify all proteins and functional RNA chains...
which is not translated into 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...
. ArcZ is an Hfq binding RNA that functions as an antisense regulator of a number of protein coding genes.
Discovery
This non-coding RNA was discovered in the bacteria Escherichia coliEscherichia coli
Escherichia coli is a Gram-negative, rod-shaped bacterium that is commonly found in the lower intestine of warm-blooded organisms . Most E. coli strains are harmless, but some serotypes can cause serious food poisoning in humans, and are occasionally responsible for product recalls...
during a large scale computational screen for transcription signals and genomic features of known small RNA-encoding genes. During this screen 14 novel ncRNA genes were identified, including GlmZ, SraB
SraB RNA
The SraB RNA is a small non-coding RNA discovered in E. coli during a large scale experimental screen. The 14 novel RNAs discovered were named 'sra' for small RNA, examples include SraC, SraD and SraG. This ncRNA was found to be expressed only in stationary phase...
, SraC
SraC/RyeA RNA
The SraC/RyeA RNA is a non-coding RNA that was discovered in E. coli during two large scale screens for RNAs. The function of this RNA is currently unknown. This RNA overlaps the RyeB RNA on the opposite strand suggesting that the two RNAs may act in a concerted manner....
and SraD
SraD RNA
The 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....
. The expression of SraH was experimentally confirmed by Northern blotting. Its expression is highly abundant in stationary growth phase
Bacterial growth
250px|right|thumb|Growth is shown as L = log where numbers is the number of colony forming units per ml, versus T Bacterial growth is the division of one bacterium into two daughter cells in a process called binary fission. Providing no mutational event occurs the resulting daughter cells are...
but low levels of expression can still be detected in exponentially growing cells
Bacterial growth
250px|right|thumb|Growth is shown as L = log where numbers is the number of colony forming units per ml, versus T Bacterial growth is the division of one bacterium into two daughter cells in a process called binary fission. Providing no mutational event occurs the resulting daughter cells are...
.
Processing
Although ArcZ is initially transcribed as a transcript of ~120 nucleotides. This precursor is unstable and is processed into an abundant fragment ~58 nucleotides which represents the 3' end of the initial transcript. The stability and abundance of the shorter 3' transcript is confirmed in both Northern blotting and deep sequencing analysis.Function
ArcZ has been shown to strongly bind the global post-transcriptional regulator protein Hfq. In SalmonellaSalmonella
Salmonella is a genus of rod-shaped, Gram-negative, non-spore-forming, predominantly motile enterobacteria with diameters around 0.7 to 1.5 µm, lengths from 2 to 5 µm, and flagella which grade in all directions . They are chemoorganotrophs, obtaining their energy from oxidation and reduction...
it has been shown to repress the expression
Gene expression
Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product. These products are often proteins, but in non-protein coding genes such as ribosomal RNA , transfer RNA or small nuclear RNA genes, the product is a functional RNA...
of protein coding genes sdaCB (involved in serine
Serine
Serine is an amino acid with the formula HO2CCHCH2OH. It is one of the proteinogenic amino acids. By virtue of the hydroxyl group, serine is classified as a polar amino acid.-Occurrence and biosynthesis:...
uptake) and tpx
TPX
The TPX is a line of baseball gloves and bats produced by Louisville Slugger. Some of the most popular of the baseball bats are the EXOgrid, Omaha, Triton, and the Catalyst. Major League endorsers include ShortStop Derek Jeter....
(involved in oxidative stress
Oxidative stress
Oxidative stress represents an imbalance between the production and manifestation of reactive oxygen species and a biological system's ability to readily detoxify the reactive intermediates or to repair the resulting damage...
) genes, and of the horizontally acquired gene methyl-accepting chemotaxis protein
Methyl-accepting chemotaxis protein
Methyl-accepting chemotaxis protein is a transmembrane sensor protein of bacteria. Use of the MCP allows bacteria to detect concentrations of molecules in the extracellular matrix so that the bacteria may smooth swim or tumble accordingly...
(MCP). Both sdaCB and STM3216 are regulated by ArcZ binding the ribosome binding site, the tpx mRNA is targeted in the coding sequence (CDS).
ArcZ positively stimulates expression of RpoS stationary phase sigma factor.