IMES-2 RNA motif

The IMES-2 RNA motif is a conserved RNA structure that was identified by a study based on metagenomics and bioinformatics,^[1] and the underlying RNA sequences were identified independently by a similar earlier study.^[2] These RNAs are present in environmental sequences, and when discovered were not known to be present in any cultivated species. However, an IMES-2 RNA has been detected in alphaproteobacterium HIMB114, which is classified in the SAR11 clade of marine bacteria. This finding fits with earlier predictions that species that use IMES-2 RNAs are most closely related to alphaproteobacteria.^[2] IMES-2 RNAs are exceptionally abundant, as twice as many IMES-2 RNAs were found as ribosomes^[1] in RNAs sampled from the Pacific Ocean.^[2][3] Only two bacterial RNAs are known (6S RNA and transfer RNA) to be more highly transcribed than ribosomes.

Consensus secondary structure of IMES-2 RNAs. This figure is adapted from supplementary data of a previous publication.^[1]

Predicted IMES-2 RNA secondary structure in alphaproteobacterium HIMB114. Nucleotides are numbered starting at the 5′ end. Lines labeled "0 nt" do not contain any nucleotides.

The IMES-2 RNA secondary structure contains four stem-loop structures and one pseudoknot.