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Eukaryotic penelope-like retroelements encode hammerhead ribozyme motifs.

Cervera A, De la Peña M - Mol. Biol. Evol. (2014)

Bottom Line: Small self-cleaving RNAs, such as the paradigmatic Hammerhead ribozyme (HHR), have been recently found widespread in DNA genomes across all kingdoms of life.In this work, we found that new HHR variants are preserved in the ancient family of Penelope-like elements (PLEs), a group of eukaryotic retrotransposons regarded as exceptional for encoding telomerase-like retrotranscriptases and spliceosomal introns.Overall, our data confirm the connection of self-cleaving RNAs with eukaryotic retroelements and unveil these motifs as a significant fraction of the encoded information in eukaryotic genomes.

View Article: PubMed Central - PubMed

Affiliation: Instituto de Biología Molecular y Celular de Plantas (UPV-CSIC), Valencia, Spain.

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(A) Canonical HHRs found in the PLTRs of PLEs from the plant Selaginella moellendorffii. In the right inset, the HHRs found in Schistosoma mansoni and humans are shown for comparison, with differences in gray (De la Peña and Garcia-Robles 2010a). (B) HHR variants found in retroelements of fungi (inset shows a kinetic analysis of self-cleavage at 1 mM Mg2+ of the Serpula lacrymans HHR, sequence in black) and (C) protists (inset shows a second HHR variant found in the genome of Thalassiosira oceanica). Sequence variability is depicted with nucleotides in red.
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msu232-F3: (A) Canonical HHRs found in the PLTRs of PLEs from the plant Selaginella moellendorffii. In the right inset, the HHRs found in Schistosoma mansoni and humans are shown for comparison, with differences in gray (De la Peña and Garcia-Robles 2010a). (B) HHR variants found in retroelements of fungi (inset shows a kinetic analysis of self-cleavage at 1 mM Mg2+ of the Serpula lacrymans HHR, sequence in black) and (C) protists (inset shows a second HHR variant found in the genome of Thalassiosira oceanica). Sequence variability is depicted with nucleotides in red.

Mentions: EN-deficient PLEs have been reported within telomeric regions of plants, fungi or protist, and postulated as possible antecessors of present-day telomerases (Gladyshev and Arkhipova 2007). Inspection of PLEs from the plant Selaginella moellendorfii allowed us to find canonical type-I HHRs in their PLTRs showing typical Helixes I, II, and III, as well as the conserved nucleotides involved in tertiary interactions (fig. 3A). PLEs from diverse fungi (fig. 3B) and protists (fig. 3C), however, showed new type-I HHR variants similar to bacterial motifs (De la Peña and Garcia-Robles 2010b; Jimenez et al. 2011; Perreault et al. 2011), characterized by a large Helix III, whereas Helixes I and II had diverse sizes with no recognizable tertiary interactions between them.Fig. 3.


Eukaryotic penelope-like retroelements encode hammerhead ribozyme motifs.

Cervera A, De la Peña M - Mol. Biol. Evol. (2014)

(A) Canonical HHRs found in the PLTRs of PLEs from the plant Selaginella moellendorffii. In the right inset, the HHRs found in Schistosoma mansoni and humans are shown for comparison, with differences in gray (De la Peña and Garcia-Robles 2010a). (B) HHR variants found in retroelements of fungi (inset shows a kinetic analysis of self-cleavage at 1 mM Mg2+ of the Serpula lacrymans HHR, sequence in black) and (C) protists (inset shows a second HHR variant found in the genome of Thalassiosira oceanica). Sequence variability is depicted with nucleotides in red.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4209133&req=5

msu232-F3: (A) Canonical HHRs found in the PLTRs of PLEs from the plant Selaginella moellendorffii. In the right inset, the HHRs found in Schistosoma mansoni and humans are shown for comparison, with differences in gray (De la Peña and Garcia-Robles 2010a). (B) HHR variants found in retroelements of fungi (inset shows a kinetic analysis of self-cleavage at 1 mM Mg2+ of the Serpula lacrymans HHR, sequence in black) and (C) protists (inset shows a second HHR variant found in the genome of Thalassiosira oceanica). Sequence variability is depicted with nucleotides in red.
Mentions: EN-deficient PLEs have been reported within telomeric regions of plants, fungi or protist, and postulated as possible antecessors of present-day telomerases (Gladyshev and Arkhipova 2007). Inspection of PLEs from the plant Selaginella moellendorfii allowed us to find canonical type-I HHRs in their PLTRs showing typical Helixes I, II, and III, as well as the conserved nucleotides involved in tertiary interactions (fig. 3A). PLEs from diverse fungi (fig. 3B) and protists (fig. 3C), however, showed new type-I HHR variants similar to bacterial motifs (De la Peña and Garcia-Robles 2010b; Jimenez et al. 2011; Perreault et al. 2011), characterized by a large Helix III, whereas Helixes I and II had diverse sizes with no recognizable tertiary interactions between them.Fig. 3.

Bottom Line: Small self-cleaving RNAs, such as the paradigmatic Hammerhead ribozyme (HHR), have been recently found widespread in DNA genomes across all kingdoms of life.In this work, we found that new HHR variants are preserved in the ancient family of Penelope-like elements (PLEs), a group of eukaryotic retrotransposons regarded as exceptional for encoding telomerase-like retrotranscriptases and spliceosomal introns.Overall, our data confirm the connection of self-cleaving RNAs with eukaryotic retroelements and unveil these motifs as a significant fraction of the encoded information in eukaryotic genomes.

View Article: PubMed Central - PubMed

Affiliation: Instituto de Biología Molecular y Celular de Plantas (UPV-CSIC), Valencia, Spain.

Show MeSH