title: Evolutionary dynamics of a conserved sequence motif in the ribosomal genes of the ciliate Paramecium.
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.
authors.affiliation: Department of Biology, Indiana University, 1001E 3rd Street, Bloomington, IN 47405, USA. fcatania@indiana.edu
authors.forename: Francesco
authors.initials: F
authors.lastname: Catania
authors.forename: Michael
authors.initials: M
authors.lastname: Lynch
mesh_terms: D001483:Base Sequence; D017124:Conserved Sequence; D017125:Genes, Protozoan; D035683:MicroRNAs / Q000378:metabolism; D010247:Paramecium / Q000235:genetics*; D012269:Ribosomal Proteins / Q000235:genetics*
chemical_list: D035683:MicroRNAs; D012269:Ribosomal Proteins