Limits...
Structural and functional characterization of ribosomal protein gene introns in sponges.

Perina D, Korolija M, Mikoč A, Roller M, Pleše B, Imešek M, Morrow C, Batel R, Ćetković H - PLoS ONE (2012)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Biology, Rudjer Boskovic Institute, Zagreb, Croatia.

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.

Show MeSH

Related in: MedlinePlus

A potential 28S rRNA target (A) and secondary structure of a novel snoRNA found in the last intron of the RPS19 gene in S. domuncula (B), S. ficus (C) and S. pagurorum (D).
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC3412847&req=5

pone-0042523-g006: A potential 28S rRNA target (A) and secondary structure of a novel snoRNA found in the last intron of the RPS19 gene in S. domuncula (B), S. ficus (C) and S. pagurorum (D).

Mentions: Many snoRNAs were found within introns of vertebrate RPGs. In human, 57 snoRNAs were identified within introns of 28 RPGs [36]. The initial search in 316 introns of 79 sponge AQ RPGs, for which we used snoSeeker, with non-stringent search parameters, produced a candidate set of 16 C/D box snoRNAs and 2 H/ACA snoRNAs (Table S7). The corresponding 17 introns, as well as the neighboring ones, were sequenced in sponge SD to determinate dynamics of snoRNAs in sponges. The total set of 53 introns produced a candidate set of 9 C/D box snoRNAs and 2 H/ACA snoRNAs (Table S7). Furthermore, the corresponding 40 introns were sequenced in S. ficus (SF) and S. pagurorum (SP) which produced a candidate set of 9 C/D box snoRNAs and 2 H/ACA snoRNAs in each of the sponge (Table S7). With a more detailed analysis we were able to identified only three snoRNAs in all four sponges that match a sequence motif of known snoRNAs available on Rfam, the snOPY database and/or the snoRNA-LBME database. The first snoRNA is the sponge ortholog of the human C/D box snoRNA SNORD100 (HBII-429) found in the RPS12 gene. We analyzed introns of RPS12 genes in vertebrates (Rattus norvegicus, Gallus gallus, Danio rerio, Takifugu rubripes) and invertebrates (D. melanogaster, C. elegans, N. vectensis, T. adhaerens) and checked for the presence and the position of the SNORD100 ortholog. There is an obvious tendency of this snoRNA to colonize the RPS12 gene from basal metazoans to “higher” vertebrates (Fig. 4A). Only in animals with intensive intron loss, SNORD100 was not identified in the RPS12 gene. Its expression was verified experimentally. SNORD100 is predicted to guide the 2′-O-ribose methylation of guanine at position 436 in human 18S rRNA [45]. This target sequence of 18S rRNA is highly conserved between human and sponges investigated (Fig. 4B). The sponge SNORD100 methylation guide sequence as well as the C/D box were also well conserved (Fig. 4C). The other conserved snoRNA was found in the third intron of the RPL5 gene in sponge AQ and in the same intron of SD, SF and SP RPL5. This snoRNA is an ortholog of the human C/D box snoRNA SNORD24 (U24), found in the second intron of the RPL7A gene. It is predicted to guide the 2′-O-ribose methylation of 28S rRNA cytosines at position 2338 and 2352 in human [46]. Sponge orthologs show different levels of conservation with human SNORD24 elements (Fig. 4D). Only one methylation guide site is conserved in all four sponges while target sequences of 28S rRNAs are well conserved in all of them. Interestingly, we confirm expression of this snoRNA in SD, which indicates a possible appearance of a novel snoRNA target or just loss of an old one. The third conserved snoRNA was found in the fourth intron of the sponge AQ RPP0 gene and is most similar to human SNORD83A/SNORD83B (U83A/U83B) found in the fifth and seventh intron of the human RPL3 gene, respectively (Fig. 4F). In SD, SF and SP this snoRNA was found in the second and last introns of the RPP0 gene, but not in the intron that contains this snoRNA in AQ. More interestingly, another snoRNA is located in the last intron of the RPP0 gene of AQ. Target RNA(s) of this snoRNA are still unknown [36]. All sponges have H/ACA box snoRNAs conserved in the RPL13A gene. While AQ possesses only one copy, in SD, SF and SP this snoRNA was found duplicated in the neighboring intron. The SD copies are 94% identical to each other, while one shares only 48% and the other 49% identical nucleotides with those from AQ. Although overall not well conserved, all essential snoRNA elements and target sites are maintained (Fig. 5). Some of the other snoRNAs, whose expression was verified experimentally show stable snoRNA secondary structures with conserved snoRNA parts. In the last intron of the RPS19 gene the single snoRNA with a potential target rRNA was found (Fig. 6). This target has not yet been described as a methylation site in human so we can only speculate about the possible function of this snoRNA.


Structural and functional characterization of ribosomal protein gene introns in sponges.

Perina D, Korolija M, Mikoč A, Roller M, Pleše B, Imešek M, Morrow C, Batel R, Ćetković H - PLoS ONE (2012)

A potential 28S rRNA target (A) and secondary structure of a novel snoRNA found in the last intron of the RPS19 gene in S. domuncula (B), S. ficus (C) and S. pagurorum (D).
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3412847&req=5

pone-0042523-g006: A potential 28S rRNA target (A) and secondary structure of a novel snoRNA found in the last intron of the RPS19 gene in S. domuncula (B), S. ficus (C) and S. pagurorum (D).
Mentions: Many snoRNAs were found within introns of vertebrate RPGs. In human, 57 snoRNAs were identified within introns of 28 RPGs [36]. The initial search in 316 introns of 79 sponge AQ RPGs, for which we used snoSeeker, with non-stringent search parameters, produced a candidate set of 16 C/D box snoRNAs and 2 H/ACA snoRNAs (Table S7). The corresponding 17 introns, as well as the neighboring ones, were sequenced in sponge SD to determinate dynamics of snoRNAs in sponges. The total set of 53 introns produced a candidate set of 9 C/D box snoRNAs and 2 H/ACA snoRNAs (Table S7). Furthermore, the corresponding 40 introns were sequenced in S. ficus (SF) and S. pagurorum (SP) which produced a candidate set of 9 C/D box snoRNAs and 2 H/ACA snoRNAs in each of the sponge (Table S7). With a more detailed analysis we were able to identified only three snoRNAs in all four sponges that match a sequence motif of known snoRNAs available on Rfam, the snOPY database and/or the snoRNA-LBME database. The first snoRNA is the sponge ortholog of the human C/D box snoRNA SNORD100 (HBII-429) found in the RPS12 gene. We analyzed introns of RPS12 genes in vertebrates (Rattus norvegicus, Gallus gallus, Danio rerio, Takifugu rubripes) and invertebrates (D. melanogaster, C. elegans, N. vectensis, T. adhaerens) and checked for the presence and the position of the SNORD100 ortholog. There is an obvious tendency of this snoRNA to colonize the RPS12 gene from basal metazoans to “higher” vertebrates (Fig. 4A). Only in animals with intensive intron loss, SNORD100 was not identified in the RPS12 gene. Its expression was verified experimentally. SNORD100 is predicted to guide the 2′-O-ribose methylation of guanine at position 436 in human 18S rRNA [45]. This target sequence of 18S rRNA is highly conserved between human and sponges investigated (Fig. 4B). The sponge SNORD100 methylation guide sequence as well as the C/D box were also well conserved (Fig. 4C). The other conserved snoRNA was found in the third intron of the RPL5 gene in sponge AQ and in the same intron of SD, SF and SP RPL5. This snoRNA is an ortholog of the human C/D box snoRNA SNORD24 (U24), found in the second intron of the RPL7A gene. It is predicted to guide the 2′-O-ribose methylation of 28S rRNA cytosines at position 2338 and 2352 in human [46]. Sponge orthologs show different levels of conservation with human SNORD24 elements (Fig. 4D). Only one methylation guide site is conserved in all four sponges while target sequences of 28S rRNAs are well conserved in all of them. Interestingly, we confirm expression of this snoRNA in SD, which indicates a possible appearance of a novel snoRNA target or just loss of an old one. The third conserved snoRNA was found in the fourth intron of the sponge AQ RPP0 gene and is most similar to human SNORD83A/SNORD83B (U83A/U83B) found in the fifth and seventh intron of the human RPL3 gene, respectively (Fig. 4F). In SD, SF and SP this snoRNA was found in the second and last introns of the RPP0 gene, but not in the intron that contains this snoRNA in AQ. More interestingly, another snoRNA is located in the last intron of the RPP0 gene of AQ. Target RNA(s) of this snoRNA are still unknown [36]. All sponges have H/ACA box snoRNAs conserved in the RPL13A gene. While AQ possesses only one copy, in SD, SF and SP this snoRNA was found duplicated in the neighboring intron. The SD copies are 94% identical to each other, while one shares only 48% and the other 49% identical nucleotides with those from AQ. Although overall not well conserved, all essential snoRNA elements and target sites are maintained (Fig. 5). Some of the other snoRNAs, whose expression was verified experimentally show stable snoRNA secondary structures with conserved snoRNA parts. In the last intron of the RPS19 gene the single snoRNA with a potential target rRNA was found (Fig. 6). This target has not yet been described as a methylation site in human so we can only speculate about the possible function of this snoRNA.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Biology, Rudjer Boskovic Institute, Zagreb, Croatia.

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.

Show MeSH
Related in: MedlinePlus