title: Structural and functional characterization of ribosomal protein gene introns in sponges.
abstract: Ribosomal protein genes (RPGs) are a powerful tool for studying intron evolution. They exist in all three domains of life and are much conserved. Accumulating genomic data suggest that RPG introns in many organisms abound with non-protein-coding-RNAs (ncRNAs). These ancient ncRNAs are small nucleolar RNAs (snoRNAs) essential for ribosome assembly. They are also mobile genetic elements and therefore probably important in diversification and enrichment of transcriptomes through various mechanisms such as intron/exon gain/loss. snoRNAs in basal metazoans are poorly characterized. We examined 449 RPG introns, in total, from four demosponges: Amphimedon queenslandica, Suberites domuncula, Suberites ficus and Suberites pagurorum and showed that RPG introns from A. queenslandica share position conservancy and some structural similarity with "higher" metazoans. Moreover, our study indicates that mobile element insertions play an important role in the evolution of their size. In four sponges 51 snoRNAs were identified. The analysis showed discrepancies between the snoRNA pools of orthologous RPG introns between S. domuncula and A. queenslandica. Furthermore, these two sponges show as much conservancy of RPG intron positions between each other as between themselves and human. Sponges from the Suberites genus show consistency in RPG intron position conservation. However, significant differences in some of the orthologous RPG introns of closely related sponges were observed. This indicates that RPG introns are dynamic even on these shorter evolutionary time scales.
authors.affiliation: Department of Molecular Biology, Rudjer Boskovic Institute, Zagreb, Croatia.
authors.forename: Drago
authors.initials: D
authors.lastname: Perina
authors.forename: Marina
authors.initials: M
authors.lastname: Korolija
authors.forename: Andreja
authors.initials: A
authors.lastname: Mikoč
authors.forename: Maša
authors.initials: M
authors.lastname: Roller
authors.forename: Bruna
authors.initials: B
authors.lastname: Pleše
authors.forename: Mirna
authors.initials: M
authors.lastname: Imešek
authors.forename: Christine
authors.initials: C
authors.lastname: Morrow
authors.forename: Renato
authors.initials: R
authors.lastname: Batel
authors.forename: Helena
authors.initials: H
authors.lastname: Ćetković
mesh_terms: D000818:Animals; D001483:Base Sequence; D017124:Conserved Sequence; D006801:Humans; D007438:Introns / Q000235:genetics*; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D059372:Nucleotide Motifs / Q000235:genetics; D011161:Porifera / Q000235:genetics*; D012339:RNA, Ribosomal, 28S / Q000235:genetics; D020537:RNA, Small Nucleolar / Q000737:chemistry / Q000235:genetics; D012269:Ribosomal Proteins / Q000235:genetics*; D016415:Sequence Alignment; D013045:Species Specificity
chemical_list: D012339:RNA, Ribosomal, 28S; D020537:RNA, Small Nucleolar; D012269:Ribosomal Proteins