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. 2013 Jan 18;5(2):418–438. doi: 10.1093/gbe/evt008

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© The Author(s) 2013. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Fig. 4.— — Comparison of tmRNA secondary structures from Andalucia, Reclinomonas-94, and Jakoba libera. Nucleotides marked blue are conserved in bacterial and jakobid tmRNAs. Nucleotides in red are identical among jakobid homologs. Yellow highlighting indicates the typical tRNA^Ala identity element that is common to tRNA^Ala and tmRNAs. This element is characterized by a GċU base pair (at the third position of the acceptor stem in the tRNA) and an A (the discriminator nucleotide in the tRNA) preceding the CCA tail (Komine et al. 1994). The blue line shows the processing sites corresponding to tRNA 5′- and 3′-termini, and the site of post-transcriptional CCA addition is indicated. The Andalucia tmRNA is characterized by a short, compact structure and a shortened T-loop with an unusual sequence compared with the other counterparts.