YjdF RNA Motif

The ''yjdF'' RNA motif is a conserved RNA structure identified using bioinformatics. Most ''yjdF'' RNAs are located in bacteria classified within the phylum Bacillota. A ''yjdF'' RNA is found in the presumed 5' untranslated region (5' UTR) of the ''yjdF'' gene in '' Bacillus subtilis'', and almost all ''yjdF'' RNAs are found in the 5' UTRs of homologs of this gene. The function of the ''yjdF'' gene is unknown, but the protein that it is predicted to encode is classified by the Pfam Database as DUF2992.

The moderately complex secondary structure and nucleotide positions conserved in the ''yjdF'' RNA motif and the fact that it is likely to be present in 5' UTRs led to the hypothesis that ''yjdF'' RNAs function as riboswitches. One ''yjdF'' RNA is found instead in the presumed 5' UTR of genes encoding enzymes involved in the synthesis of nicotinamide adenine dinucleotide (NAD). These RNAs lack a region of the otherwise conserved ''yjdF'' RNA motif and might be non-functional, or conform to a distinct structure that achieves the same function. If ''yjdF'' RNAs are riboswitches, this other RNA might bind a distinct small molecule ligand.

Experiments support the conclusion that the ''yjdF'' RNA in ''B. subtilis'' is indeed in the 5' UTR of the ''yjdF'' gene, and that the ''yjdF'' genes are transcribed separately from the upstream ''manPA'' operon. The biochemical function of ''yjdF'' RNAs remains unknown.

''yjdF'' RNAs appear to function as riboswitches that sense azaaromatic compounds, although the precise compound or set of compounds that is sensed by this riboswitch in the cell remains unclear.

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{{Rfam, id=RF01764, name=yjdF RNA

Cis-regulatory RNA elements