TY - JOUR
T1 - Evolutionary dynamics of a conserved sequence motif in the ribosomal genes of the ciliate Paramecium
AU - Catania, Francesco
AU - Lynch, Michael
N1 - Funding Information:
We thank Eric Meyer, Jean-François Gout and two anonymous reviewers for their comments and suggestions on how to improve our study. This work was supported by MetaCyte funding from the Lilly Foundation to Indiana University and the National Science Foundation grantsEF -0827411 to M.L.
PY - 2010
Y1 - 2010
N2 - 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.
AB - 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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U2 - 10.1186/1471-2148-10-129
DO - 10.1186/1471-2148-10-129
M3 - Article
C2 - 20441586
AN - SCOPUS:77952840944
SN - 1472-6785
VL - 10
JO - BMC Evolutionary Biology
JF - BMC Evolutionary Biology
IS - 1
M1 - 129
ER -