| Summary: | <p>Abstract</p> <p>Background</p> <p>In protozoa, the identification of preserved motifs by comparative genomics is often impeded by difficulties to generate reliable alignments for non-coding sequences. Moreover, the evolutionary dynamics of regulatory elements in 3' untranslated regions (both in protozoa and metazoa) remains a virtually unexplored issue.</p> <p>Results</p> <p>By screening <it>Paramecium tetraurelia</it>'s 3' untranslated regions for <it>8-mers </it>that were previously found to be preserved in mammalian 3' UTRs, we detect and characterize a motif that is distinctly conserved in the ribosomal genes of this ciliate. The motif appears to be conserved across <it>Paramecium aurelia </it>species but is absent from the ribosomal genes of four additional non-<it>Paramecium </it>species surveyed, including another ciliate, <it>Tetrahymena thermophila</it>. Motif-free ribosomal genes retain fewer paralogs in the genome and appear to be lost more rapidly relative to motif-containing genes. Features associated with the discovered preserved motif are consistent with this <it>8-mer </it>playing a role in post-transcriptional regulation.</p> <p>Conclusions</p> <p>Our observations 1) shed light on the evolution of a putative regulatory motif across large phylogenetic distances; 2) are expected to facilitate the understanding of the modulation of ribosomal genes expression in <it>Paramecium</it>; and 3) reveal a largely unexplored--and presumably not restricted to <it>Paramecium</it>--association between the presence/absence of a DNA motif and the evolutionary fate of its host genes.</p>
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