The ''pemK'' 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. ''pemK'' motif RNAs are found in organisms within the

phylum In biology, a phylum (; : phyla) is a level of classification, or taxonomic rank, that is below Kingdom (biology), kingdom and above Class (biology), class. Traditionally, in botany the term division (taxonomy), division has been used instead ...

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 is very widespread in this phylum. ''pemK'' motif RNAs likely 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, in view of their positions upstream of protein-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. Indeed, the RNAs are upstream of multiple genes that encode non- homologous

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 ...

s. If all examples of the RNA were upstream of homologous genes, there is the possibility that the RNAs were conserved in that position simply by inheritance. The non-homology of the genes downstream of ''pemK'' RNAs makes this scenario less likely. ''cis''-regulatory RNAs such as

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 ...

es in Bacillota are often followed by Rho-independent transcription terminators, and they use these transcription terminators as part of a regulatory mechanism. Specifically, depending on the regulatory state of the ''cis''-regulatory RNA, formation of the transcription terminator is either prevented or allowed via alternate secondary structures. ''pemK'' RNAs, however, are very rarely followed by a transcription terminator. This fact could raise the possibility that these RNAs are not ''cis''-regulatory, but rather function as

small RNA Small RNA (sRNA) are polymeric RNA molecules that are less than 200 nucleotides in length, and are usually non-coding RNA, non-coding. RNA silencing is often a function of these molecules, with the most common and well-studied example being RNA int ...

s. However, there are some ''cis''-regulatory RNAs in Bacillota that do not use Rho-independent transcription terminations as a regulatory mechanism, e.g., the yjdF RNA motif.

References

{{reflist Non-coding RNA