Rsa RNAs are

non-coding RNA A non-coding RNA (ncRNA) is a functional RNA molecule that is not translated into a protein. The DNA sequence from which a functional non-coding RNA is transcribed is often called an RNA gene. Abundant and functionally important types of non-c ...

s found in the bacterium ''

Staphylococcus aureus ''Staphylococcus aureus'' is a Gram-positive spherically shaped bacterium, a member of the Bacillota, and is a usual member of the microbiota of the body, frequently found in the upper respiratory tract and on the skin. It is often positive ...

''. The shared name comes from their discovery, and does not imply

homology Homology may refer to: Sciences Biology *Homology (biology), any characteristic of biological organisms that is derived from a common ancestor * Sequence homology, biological homology between DNA, RNA, or protein sequences *Homologous chrom ...

Bioinformatics Bioinformatics () is an interdisciplinary field that develops methods and software tools for understanding biological data, in particular when the data sets are large and complex. As an interdisciplinary field of science, bioinformatics combi ...

scans identified the 16 Rsa RNA families named RsaA-K and RsaOA-OG. Others, RsaOH-OX, were found thanks to an RNomic approach. Although the RNAs showed varying expression patterns, many of the newly discovered RNAs were shown to be

Hfq The Hfq protein (also known as HF-I 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 RN ...

-independent and most carried a C-rich motif (UCCC).

RsaA

Represses the translation of the transcriptional regulator MgrA by binding to its mRNA, enhances biofilm formation and decreases bacterial virulence. Other mRNAs: including SsaA-like enzymes involved in peptidoglycan metabolism and the secreted anti-inflammatory FLIPr protein were validated as direct targets of RsaA.

RsaE

RsaE is found in other members of the genus ''

Staphylococcus ''Staphylococcus'' is a genus of Gram-positive bacteria in the family Staphylococcaceae from the order Bacillales. Under the microscope, they appear spherical (cocci), and form in grape-like clusters. ''Staphylococcus'' species are facultative ...

'' such as ''

Staphylococcus epidermidis ''Staphylococcus epidermidis'' is a Gram-positive bacterium, and one of over 40 species belonging to the genus '' Staphylococcus''. It is part of the normal human microbiota, typically the skin microbiota, and less commonly the mucosal microbio ...

'' and ''

Staphylococcus saprophyticus ''Staphylococcus saprophyticus'' is a Gram-positive coccus belonging to the genus '' Staphylococcus''. ''S. saprophyticus'' is a common cause of community-acquired urinary tract infections. History ''Staphylococcus saprophyticus'' was not recogn ...

'' and is the only Rsa RNA to be found outside of this genus, in '' Macrococcus caseolyticus'' and ''

Bacillus ''Bacillus'' (Latin "stick") is a genus of Gram-positive, rod-shaped bacteria, a member of the phylum ''Bacillota'', with 266 named species. The term is also used to describe the shape (rod) of other so-shaped bacteria; and the plural ''Bacilli ...

''. In ''

Bacillus subtilis ''Bacillus subtilis'', known also as the hay bacillus or grass bacillus, is a Gram-positive, catalase-positive bacterium, found in soil and the gastrointestinal tract of ruminants, humans and marine sponges. As a member of the genus ''Bacillu ...

'', RsaE had previously been identified as ncr22. RsaE is also consistently found downstream of ''PepF'' which codes for oligoendopeptidase F. The function of RsaE was discovered using

gene knockout A gene knockout (abbreviation: KO) is a genetic technique in which one of an organism's genes is made inoperative ("knocked out" of the organism). However, KO can also refer to the gene that is knocked out or the organism that carries the gene kno ...

analysis and gene overexpression - it was found to regulate the

expression Expression may refer to: Linguistics * Expression (linguistics), a word, phrase, or sentence * Fixed expression, a form of words with a specific meaning * Idiom, a type of fixed expression * Metaphorical expression, a particular word, phrase, o ...

of several enzymes involved in

metabolism Metabolism (, from el, μεταβολή ''metabolē'', "change") is the set of life-sustaining chemical reactions in organisms. The three main functions of metabolism are: the conversion of the energy in food to energy available to run cell ...

via

antisense In molecular biology and genetics, the sense of a nucleic acid molecule, particularly of a strand of DNA or RNA, refers to the nature of the roles of the strand and its complement in specifying a sequence of amino acids. Depending on the context, ...

binding of their

mRNA In molecular biology, messenger ribonucleic acid (mRNA) is a single-stranded molecule of RNA that corresponds to the genetic sequence of a gene, and is read by a ribosome in the process of Protein biosynthesis, synthesizing a protein. mRNA is ...

. RsaE was shown to be regulated by the presence of nitric oxide (NO). In ''Bacillus subtilis'' it controls expression of genes with functions related to oxidative stress and oxidation-reduction reactions and it was renamed RoxS (for related to oxidative stress).

RsaF

In ''S.aureus'' species RsaF is located in the same intergenic region as RsaE and overlaps with 3′ end of RsaE by approximately 20bp. In contrast to RsaE, RsaF and its upstream gene have only been identified in ''S.aureus species''.

RsaK

RsaK is found in the leader sequence of ''glcA'' mRNA which encodes an

enzyme Enzymes () are proteins that act as biological catalysts by accelerating chemical reactions. The molecules upon which enzymes may act are called substrates, and the enzyme converts the substrates into different molecules known as products. A ...

involved in the glucose-specific

phosphotransferase system PEP group translocation, also known as the phosphotransferase system or PTS, is a distinct method used by bacteria for sugar uptake where the source of energy is from phosphoenolpyruvate (PEP). It is known to be a multicomponent system that always i ...

. RsaK also contains a conserved ribonucleic

antiterminator Antitermination is the prokaryotic cell's aid to fix premature termination of RNA synthesis during the transcription of RNA. It occurs when the RNA polymerase ignores the termination signal and continues elongating its transcript until a second sign ...

system, as recognised by GclT protein.

RsaI

RsaOG also renamed RsaI is thought to fine-tune the regulation of toxin or invasion mechanisms in ''S. aureus'' via

trans-acting In the field of molecular biology, ''trans''-acting (''trans''-regulatory, ''trans''-regulation), in general, means "acting from a different molecule" (''i.e.'', intermolecular). It may be considered the opposite of ''cis''-acting (''cis''-regulat ...

mechanisms. Its

secondary structure Protein secondary structure is the three dimensional conformational isomerism, form of ''local segments'' of proteins. The two most common Protein structure#Secondary structure, secondary structural elements are alpha helix, alpha helices and beta ...

contains a

pseudoknot __NOTOC__ A pseudoknot is a nucleic acid secondary structure containing at least two stem-loop structures in which half of one stem is intercalated between the two halves of another stem. The pseudoknot was first recognized in the turnip yellow ...

formed between two highly conserved unpaired sequences.

Expression patterns

RsaD, E H and I were found to be highly expressed in ''S. aureus''. Expression levels of other Rsa RNAs varied under various environmental conditions, for example RsaC was induced by

cold shock Cold shock response is a series of neurogenic cardio-respiratory responses caused by sudden immersion in cold water. In cold water immersions, such as by falling through thin ice, cold shock response is perhaps the most common cause of death. Als ...

and RsaA is induced in response to

osmotic stress Osmotic shock or osmotic stress is physiologic dysfunction caused by a sudden change in the solute concentration around a cell, which causes a rapid change in the movement of water across its cell membrane. Under hypertonic conditions - conditions ...

. RsaE and RsaF genes overlap in ''S.aureus'' species but appear to have opposite expression patterns. Transcriptional interference due to an overlap between a σ^A recognition motif and a potential σ^B binding site is proposed as a mechanism causing the differential expression of the two transcripts

RsaA

RsaE

RsaF

RsaK

RsaI

Expression patterns

See also

References

Further reading