pemK RNA motif

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pemK
Consensus secondary structure and sequence conservation of pemK RNA
Identifiers
Symbol	pemK
Rfam	RF02913
Other data
RNA type	Cis-reg
SO	SO:0005836
PDB structures	PDBe

The pemK RNA motif is a conserved RNA structure that was discovered by bioinformatics.^[1]pemK motif RNAs are found in organisms within the phylum Bacillota, and is very widespread in this phylum.

pemK motif RNAs likely function as cis-regulatory elements, in view of their positions upstream of protein-coding genes. Indeed, the RNAs are upstream of multiple genes that encode non-homologous proteins. 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 riboswitches 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 RNAs. 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.