The ''raiA'' 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'' motif RNAs are found 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 ...
and
Bacillota
The Bacillota (synonym Firmicutes) are a phylum of bacteria, most of which have Gram-positive cell wall structure. They have round cells, called cocci (singular coccus), or rod-like forms (bacillus). A few Bacillota, such as '' Megasphaera'', ...
, and have many conserved features—including conserved
nucleotide
Nucleotides are Organic compound, organic molecules composed of a nitrogenous base, a pentose sugar and a phosphate. They serve as monomeric units of the nucleic acid polymers – deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), both o ...
positions, conserved
secondary structures and associated
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 ...
-coding
gene
In biology, the word gene has two meanings. The Mendelian gene is a basic unit of heredity. The molecular gene is a sequence of nucleotides in DNA that is transcribed to produce a functional RNA. There are two types of molecular genes: protei ...
s—in both of these
phyla
Phyla, the plural of ''phylum'', may refer to:
* Phylum, a biological taxon between Kingdom and Class
* by analogy, in linguistics, a large division of possibly related languages, or a major language family which is not subordinate to another
Phy ...
.
Some conserved features of the ''raiA'' RNA motif suggest that they function as
cis-regulatory elements
''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 morphogen ...
, but other aspects of the motif suggest otherwise.
''raiA'' RNAs usually occur upstream of protein-coding genes. Although this association could suggest a ''cis''-regulatory function, the ''raiA'' RNAs are fairly often located unusually far (more than 600 bp) from the genes compared to typical ''cis''-regulatory RNAs. Moreover, although most ''raiA'' RNAs are located upstream of protein-coding genes, many are not.
In both Bacillota and Actinomycetota, ''raiA'' RNAs commonly occur upstream of genes encoding RaiA, a protein that binds to the
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 ...
as part of a stress response, and upstream of genes encoding
periplasmic-binding proteins, which are
transporters of unknown specificity. Also in both Bacillota and Actinomycetota, ''raiA'' RNAs commonly occur downstream of genes encoding ComFC domains, although not necessarily immediately downstream of such genes. ComFC domains likely function as part of genetic
natural competence
In microbiology, genetics, cell biology, and molecular biology, competence is the ability of a cell to alter its genetics by taking up extracellular DNA from its environment through a process called transformation. Competence can be differentiat ...
. The RNA's association with an upstream gene is highly unusual for bacterial ''cis''-regulatory elements. Although some bacterial regulatory elements reside in the 3′
untranslated region
In molecular genetics, an untranslated region (or UTR) refers to either of two sections, one on each side of a coding sequence on a strand of mRNA. If it is found on the Directionality (molecular biology), 5' side, it is called the Five prime ...
s of genes, such elements have no association with downstream genes.
Therefore, it is unclear whether ''raiA'' are ''cis''-regulatory or not.
ely that raiA motif RNAs regulate expression of the upstream ORF. However, because of the motif's complex secondary structure and highly conserved nucleotide positions, it was proposed
that the motif could be a
riboswitch
In molecular biology, a riboswitch is a regulatory segment of a messenger RNA molecule that binds a small molecule, resulting in a change in Translation (biology), production of the proteins encoded by the mRNA. Thus, an mRNA that contains a ribo ...
, if it is indeed ''cis'' regulatory.
References
{{reflist
Non-coding RNA