YjdF RNA motif

Consensus secondary structure of yjdF RNAs. This figure is adapted from a previous publication.^[1]

Protein of unknown function (DUF2992)
Identifiers
Symbol	DUF2992
Pfam	PF11208
Available protein structures: Pfam structures PDB RCSB PDB; PDBe PDBsum structure summary

yjdF RNA
Identifiers
Symbol	yjdF
Rfam	RF01764
Other data
RNA type	Cis-reg;
Domain(s)	Bacteria;
SO	0005836

The yjdF RNA motif is a conserved RNA structure identified using bioinformatics.^[1] Most yjdF RNAs are located in bacteria classified within the phylum Firmicutes. 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.^[2]

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.^[1] The biochemical function of yjdF RNAs remains unknown.

A number of other RNAs were identified in the same study, including:

Bacteroidales-1 RNA motif CrcB RNA Motif Chlorobi-1 RNA motif Gut-1 RNA motif JUMPstart RNA motif Lactis-plasmid RNA motif

Lacto-usp RNA motif MraW RNA motif Ocean-V RNA motif PotC RNA motif PsaA RNA motif Pseudomon-Rho RNA motif

Rne-II RNA motif STAXI RNA motif TwoAYGGAY RNA motif Whalefall-1 RNA motif WcaG RNA motif YkkC-yxkD leader

References

1. ^ ^{a b c} Weinberg Z, Wang JX, Bogue J, et al. (March 2010). "Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea and their metagenomes". Genome Biol 11 (3): R31. doi:10.1186/gb-2010-11-3-r31. PMC 2864571. PMID 20230605. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2864571. 
2. ^ http://pfam.sanger.ac.uk/family/PF11208.1

External links

• Rfam page for yjdF RNA