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.

References
  1. Weinberg Z, Perreault J, Meyer MM, Breaker RR (December 2009). "Exceptional structured noncoding RNAs revealed by bacterial metagenome analysis". Nature. 462 (7273): 656–659. doi:10.1038/nature08586. PMC 4140389. PMID 19956260.
  2. Shi Y, Tyson GW, DeLong EF (May 2009). "Metatranscriptomics reveals unique microbial small RNAs in the ocean's water column". Nature. 459 (7244): 266–269. doi:10.1038/nature08055. PMID 19444216.
  3. Frias-Lopez J, Shi Y, Tyson GW, et al. (March 2008). "Microbial community gene expression in ocean surface waters". Proc. Natl. Acad. Sci. U.S.A. 105 (10): 3805–3810. doi:10.1073/pnas.0708897105. PMC 2268829. PMID 18316740.
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