The Rumen-Originating, Ornate, Large (ROOL) RNA motif was originally discovered by bioinformatics by analyzing

metagenomic Metagenomics is the study of genetic material recovered directly from environmental or clinical samples by a method called sequencing. The broad field may also be referred to as environmental genomics, ecogenomics, community genomics or micro ...

sequences from

cow Cattle (''Bos taurus'') are large, domesticated, cloven-hooved, herbivores. They are a prominent modern member of the subfamily Bovinae and the most widespread species of the genus '' Bos''. Adult females are referred to as cows and adult ...

rumen The rumen, also known as a paunch, is the largest stomach compartment in ruminants and the larger part of the reticulorumen, which is the first chamber in the alimentary canal of ruminant animals. The rumen's microbial favoring environment allow ...

. ROOL RNAs are found in a variety of

bacteria Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were am ...

l species and apparently do not code for

protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, respon ...

s. The RNA has a complex

RNA secondary structure Nucleic acid secondary structure is the basepairing interactions within a single nucleic acid polymer or between two polymers. It can be represented as a list of bases which are paired in a nucleic acid molecule. The secondary structures of biolo ...

and its average size of 581 nucleotides is unusually large for bacterial non-coding RNAs. This large size and structural complexity for a bacterial RNA is consistent with properties of large

ribozyme Ribozymes (ribonucleic acid enzymes) are RNA molecules that have the ability to catalyze specific biochemical reactions, including RNA splicing in gene expression, similar to the action of protein enzymes. The 1982 discovery of ribozymes demonst ...

s. ROOL RNAs are present in

prophage A prophage is a bacteriophage (often shortened to "phage") genome that is integrated into the circular bacterial chromosome or exists as an extrachromosomal plasmid within the bacterial cell. Integration of prophages into the bacterial host is the ...

s and purified

phages A bacteriophage (), also known informally as a ''phage'' (), is a duplodnaviria virus that infects and replicates within bacteria and archaea. The term was derived from "bacteria" and the Greek φαγεῖν ('), meaning "to devour". Bacter ...

, but also in bacterial

genomic Genomics is an interdisciplinary field of biology focusing on the structure, function, evolution, mapping, and editing of genomes. A genome is an organism's complete set of DNA, including all of its genes as well as its hierarchical, three-dim ...

locations that do not appear to be related to phages. ROOL RNAs are also frequently located nearby to

tRNA Transfer RNA (abbreviated tRNA and formerly referred to as sRNA, for soluble RNA) is an adaptor molecule composed of RNA, typically 76 to 90 nucleotides in length (in eukaryotes), that serves as the physical link between the mRNA and the amino a ...

s. The large size and complicated secondary structure of ROOL RNAs, combined with their association with tRNAs and phages are properties that are shared by the

GOLLD RNA motif Giant, Ornate, Lake- and Lactobacillales-Derived (GOLLD) RNA is a conserved RNA structure present in bacteria. GOLLD RNAs were originally detected based on metagenome sequences of DNA isolated from Lake Gatun in Panama. However, they are know ...

, another bacterial non-coding RNA. These shared properties could suggest a related function, but the commonalities could arise for other reasons. ROOL RNAs are present in bacteria in the

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 Phyl ...

Bacillota The Bacillota (synonym Firmicutes) are a phylum of bacteria, most of which have gram-positive cell wall structure. The renaming of phyla such as Firmicutes in 2021 remains controversial among microbiologists, many of whom continue to use the ea ...

, Fusobacteriota and

Mycoplasmatota Mycoplasmatota is a phylum of bacteria that contains the class Mollicutes. The phylum was originally named "Tenericutes" (''tener cutis'': soft skin). Notable genera include ''Mycoplasma'', ''Spiroplasma'', ''Ureaplasma'', and ''Candidatus'' Phyt ...

, in addition to phages and cow rumen metagenomes, as mentioned above. Within the Bacillota, they are present in a few species of

Clostridia The Clostridia are a highly polyphyletic class of Bacillota, including '' Clostridium'' and other similar genera. They are distinguished from the Bacilli by lacking aerobic respiration. They are obligate anaerobes and oxygen is toxic to them. S ...

and many

lactic acid bacteria Lactobacillales are an order of gram-positive, low-GC, acid-tolerant, generally nonsporulating, nonrespiring, either rod-shaped ( bacilli) or spherical ( cocci) bacteria that share common metabolic and physiological characteristics. These bact ...

, especially those in the

genus Genus ( plural genera ) is a taxonomic rank used in the biological classification of living and fossil organisms as well as viruses. In the hierarchy of biological classification, genus comes above species and below family. In binomial n ...

Lactobacillus ''Lactobacillus'' is a genus of Gram-positive, aerotolerant anaerobes or microaerophilic, rod-shaped, non-spore-forming bacteria. Until 2020, the genus ''Lactobacillus'' comprised over 260 phylogenetically, ecologically, and metabolically di ...

''. ROOL RNAs in ''

Lactobacillus salivarius ''Ligilactobacillus salivarius'' is a probiotic bacteria species that has been found to live in the gastrointestinal tract and exert a range of therapeutic properties including suppression of pathogenic bacteria. Therapeutic research Irritab ...

'' were independently discovered based on their extremely high rates of expression in ''Lactobacillus salivarius'' UCC118 ROOL RNAs in various strains of ''Lactobacillus salivarius'' were then studied; there is a very large range in the expression levels of ROOL RNAs in different strains, and some strains do not appear to have these RNAs in their genome. ROOL RNAs in ''L. salivarius'' UC118 are so abundant in some growth conditions that in late stationary phase they exceed even

16S ribosomal RNA 16 S ribosomal RNA (or 16 S rRNA) is the RNA component of the 30S subunit of a prokaryotic ribosome ( SSU rRNA). It binds to the Shine-Dalgarno sequence and provides most of the SSU structure. The genes coding for it are referred to as 16S r ...

s. The experimentally determined size for ROOL RNAs in ''L. salivarius'' closely matches the size of the proposed RNA structure based on bioinformatics.

References

Non-coding RNA {{molecular-cell-biology-stub