Evolutionary dynamics of a conserved sequence motif in the ribosomal genes of the ciliate <it>Paramecium</it>
<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�...
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| Format: | Article |
| Language: | English |
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BMC
2010-05-01
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| Series: | BMC Evolutionary Biology |
| Online Access: | http://www.biomedcentral.com/1471-2148/10/129 |
| _version_ | 1818978567639269376 |
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| author | Lynch Michael Catania Francesco |
| author_facet | Lynch Michael Catania Francesco |
| author_sort | Lynch Michael |
| collection | DOAJ |
| description | <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> |
| first_indexed | 2024-12-20T16:45:42Z |
| format | Article |
| id | doaj.art-feef3dfa418949f18332c406fa6a2e1f |
| institution | Directory Open Access Journal |
| issn | 1471-2148 |
| language | English |
| last_indexed | 2024-12-20T16:45:42Z |
| publishDate | 2010-05-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Evolutionary Biology |
| spelling | doaj.art-feef3dfa418949f18332c406fa6a2e1f2022-12-21T19:32:56ZengBMCBMC Evolutionary Biology1471-21482010-05-0110112910.1186/1471-2148-10-129Evolutionary dynamics of a conserved sequence motif in the ribosomal genes of the ciliate <it>Paramecium</it>Lynch MichaelCatania Francesco<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>http://www.biomedcentral.com/1471-2148/10/129 |
| spellingShingle | Lynch Michael Catania Francesco Evolutionary dynamics of a conserved sequence motif in the ribosomal genes of the ciliate <it>Paramecium</it> BMC Evolutionary Biology |
| title | Evolutionary dynamics of a conserved sequence motif in the ribosomal genes of the ciliate <it>Paramecium</it> |
| title_full | Evolutionary dynamics of a conserved sequence motif in the ribosomal genes of the ciliate <it>Paramecium</it> |
| title_fullStr | Evolutionary dynamics of a conserved sequence motif in the ribosomal genes of the ciliate <it>Paramecium</it> |
| title_full_unstemmed | Evolutionary dynamics of a conserved sequence motif in the ribosomal genes of the ciliate <it>Paramecium</it> |
| title_short | Evolutionary dynamics of a conserved sequence motif in the ribosomal genes of the ciliate <it>Paramecium</it> |
| title_sort | evolutionary dynamics of a conserved sequence motif in the ribosomal genes of the ciliate it paramecium it |
| url | http://www.biomedcentral.com/1471-2148/10/129 |
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