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Evolutionary dynamics of a conserved sequence motif in the ribosomal genes of the ciliate Paramecium.

Catania F, Lynch M - BMC Evol. Biol. (2010)

Bottom Line: By screening Paramecium tetraurelia's 3' untranslated regions for 8-mers 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.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 8-mer playing a role in post-transcriptional regulation.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biology, Indiana University, 1001E 3rd Street, Bloomington, IN 47405, USA. fcatania@indiana.edu

ABSTRACT

Background: 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.

Results: By screening Paramecium tetraurelia's 3' untranslated regions for 8-mers 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 Paramecium aurelia species but is absent from the ribosomal genes of four additional non-Paramecium species surveyed, including another ciliate, Tetrahymena thermophila. 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 8-mer playing a role in post-transcriptional regulation.

Conclusions: 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 Paramecium; and 3) reveal a largely unexplored--and presumably not restricted to Paramecium--association between the presence/absence of a DNA motif and the evolutionary fate of its host genes.

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Structure of the two candidate precursor miRNAs in P. tetraurelia. a) candidate pre-miRNA (location in macronuclear genome: scaffold_567:869-915); b) candidate pre-miRNA (this is a portion of an EST [cDNA clone LK0ADA28YP05; collected at conjugation (beginning of meiosis)] that can be only partially mapped to the 3' end region of three 60S ribosomal protein-coding gene L1 that are located in scaffold_161: 34738-35490; scaffold_253: 730-1589; and scaffold_151: 51790-52544). Color scale displays base-pairs probability.
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Figure 3: Structure of the two candidate precursor miRNAs in P. tetraurelia. a) candidate pre-miRNA (location in macronuclear genome: scaffold_567:869-915); b) candidate pre-miRNA (this is a portion of an EST [cDNA clone LK0ADA28YP05; collected at conjugation (beginning of meiosis)] that can be only partially mapped to the 3' end region of three 60S ribosomal protein-coding gene L1 that are located in scaffold_161: 34738-35490; scaffold_253: 730-1589; and scaffold_151: 51790-52544). Color scale displays base-pairs probability.

Mentions: This screening yielded a total of 284 candidate pre-miRNAs. For each of these candidate elements we assessed the stability of the secondary structure by measuring: 1) the minimum free energies (MFE), as predicted by the RNAfold program [21]; the parameter AMFE ([MFE/length]*100)), which provides an estimate of stability that is not influenced by differences in RNA sequences length; and MFEI (AMFE/(G+C)%), an index that appears to be valuable in distinguishing miRNAs from other coding and non-coding RNAs [22], and whose absolute values are consistently close or higher than 0.85 when experimentally confirmed miRNAs in metazoans are examined [19,22]. The study of these parameters across the candidate pre-miRNAs led to the identification of a putative pre-miRNA that, irrespective of the arbitrary number of flanking bases, showed consistently both low AMFE values (-28.69 ± 7.25), which are comparable to those detected for confirmed miRNAs in metazoans [19], and absolute values of MFEI close to or higher than 0.85 (0.98 ± 0.20). This candidate pre-miRNA, whose MFE structure is shown in Figure 3a, matches none of the currently available P. tetraurelia ESTs, has a single hit in the P. tetraurelia genome and is located in a region that is devoid of genes.


Evolutionary dynamics of a conserved sequence motif in the ribosomal genes of the ciliate Paramecium.

Catania F, Lynch M - BMC Evol. Biol. (2010)

Structure of the two candidate precursor miRNAs in P. tetraurelia. a) candidate pre-miRNA (location in macronuclear genome: scaffold_567:869-915); b) candidate pre-miRNA (this is a portion of an EST [cDNA clone LK0ADA28YP05; collected at conjugation (beginning of meiosis)] that can be only partially mapped to the 3' end region of three 60S ribosomal protein-coding gene L1 that are located in scaffold_161: 34738-35490; scaffold_253: 730-1589; and scaffold_151: 51790-52544). Color scale displays base-pairs probability.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2874801&req=5

Figure 3: Structure of the two candidate precursor miRNAs in P. tetraurelia. a) candidate pre-miRNA (location in macronuclear genome: scaffold_567:869-915); b) candidate pre-miRNA (this is a portion of an EST [cDNA clone LK0ADA28YP05; collected at conjugation (beginning of meiosis)] that can be only partially mapped to the 3' end region of three 60S ribosomal protein-coding gene L1 that are located in scaffold_161: 34738-35490; scaffold_253: 730-1589; and scaffold_151: 51790-52544). Color scale displays base-pairs probability.
Mentions: This screening yielded a total of 284 candidate pre-miRNAs. For each of these candidate elements we assessed the stability of the secondary structure by measuring: 1) the minimum free energies (MFE), as predicted by the RNAfold program [21]; the parameter AMFE ([MFE/length]*100)), which provides an estimate of stability that is not influenced by differences in RNA sequences length; and MFEI (AMFE/(G+C)%), an index that appears to be valuable in distinguishing miRNAs from other coding and non-coding RNAs [22], and whose absolute values are consistently close or higher than 0.85 when experimentally confirmed miRNAs in metazoans are examined [19,22]. The study of these parameters across the candidate pre-miRNAs led to the identification of a putative pre-miRNA that, irrespective of the arbitrary number of flanking bases, showed consistently both low AMFE values (-28.69 ± 7.25), which are comparable to those detected for confirmed miRNAs in metazoans [19], and absolute values of MFEI close to or higher than 0.85 (0.98 ± 0.20). This candidate pre-miRNA, whose MFE structure is shown in Figure 3a, matches none of the currently available P. tetraurelia ESTs, has a single hit in the P. tetraurelia genome and is located in a region that is devoid of genes.

Bottom Line: By screening Paramecium tetraurelia's 3' untranslated regions for 8-mers 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.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 8-mer playing a role in post-transcriptional regulation.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biology, Indiana University, 1001E 3rd Street, Bloomington, IN 47405, USA. fcatania@indiana.edu

ABSTRACT

Background: 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.

Results: By screening Paramecium tetraurelia's 3' untranslated regions for 8-mers 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 Paramecium aurelia species but is absent from the ribosomal genes of four additional non-Paramecium species surveyed, including another ciliate, Tetrahymena thermophila. 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 8-mer playing a role in post-transcriptional regulation.

Conclusions: 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 Paramecium; and 3) reveal a largely unexplored--and presumably not restricted to Paramecium--association between the presence/absence of a DNA motif and the evolutionary fate of its host genes.

Show MeSH
Related in: MedlinePlus