The ''raiA''-hairpin RNA motif is a conserved

RNA Ribonucleic acid (RNA) is a polymeric molecule that is essential for most biological functions, either by performing the function itself (non-coding RNA) or by forming a template for the production of proteins (messenger RNA). RNA and deoxyrib ...

structure that was discovered by bioinformatics. ''raiA''-hairpin motif RNAs are found in organism classified within the

genus Genus (; : genera ) is a taxonomic rank above species and below family (taxonomy), family as used in the biological classification of extant taxon, living and fossil organisms as well as Virus classification#ICTV classification, viruses. In bino ...

Streptomyces ''Streptomyces'', from στρεπτός (''streptós''), meaning "twisted", and μύκης (''múkés''), meaning "fungus", is the largest genus of Actinomycetota, and the type genus of the family Streptomycetaceae. Over 700 species of ''St ...

''. This motif is consistently located upstream of ''raiA'' genes, which encode a

ribosome Ribosomes () are molecular machine, macromolecular machines, found within all cell (biology), cells, that perform Translation (biology), biological protein synthesis (messenger RNA translation). Ribosomes link amino acids together in the order s ...

-binding

protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residue (biochemistry), residues. Proteins perform a vast array of functions within organisms, including Enzyme catalysis, catalysing metab ...

that is involved in a bacterial stress response process. This association is shared with the raiA RNA motif. However, where the ''rai'' RNA motif exhibits a highly conserved and complex

secondary structure Protein secondary structure is the local spatial conformation of the polypeptide backbone excluding the side chains. The two most common Protein structure#Secondary structure, secondary structural elements are alpha helix, alpha helices and beta ...

, the ''raiA''-hairpin's secondary structure consists of a simple hairpin. The positioning of ''raiA''-hairpin RNAs suggest that they function as

cis-regulatory element ''Cis''-regulatory elements (CREs) or ''cis''-regulatory modules (CRMs) are regions of non-coding DNA which regulate the transcription of neighboring genes. CREs are vital components of genetic regulatory networks, which in turn control morpho ...

s. However, the fact that the ''raiA'' motif is also located in such positions, and that it is unclear whether the ''raiA'' RNA motif functions in ''cis'' calls into question whether the ''raiA''-hairpin RNA motif functions as a ''cis'' regulator. There is also a possibility, based on computational predictions, that ''raiA''-hairpin RNAs function as Rho-independent transcription termination hairpins. Such hairpins have less specific properties in

Actinomycetota The Actinomycetota (or Actinobacteria) are a diverse phylum of Gram-positive bacteria with high GC content. They can be terrestrial or aquatic. They are of great importance to land flora because of their contributions to soil systems. In soil t ...

, such as ''Streptomyces''. However, only some ''rai''-hairpin RNAs are predicted as transcription termination hairpins.

References

{{reflist Non-coding RNA