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Spliced leader RNAs, mitochondrial gene frameshifts and multi-protein phylogeny expand support for the genus Perkinsus as a unique group of alveolates.

Zhang H, Campbell DA, Sturm NR, Dungan CF, Lin S - PLoS ONE (2011)

Bottom Line: In contrast to the canonical 22-nt SL found in dinoflagellates (DinoSL), P. marinus has a shorter (21-nt) and a longer (22-nt) SL with slightly different sequences than DinoSL.The major SL RNA transcripts range in size between 80-83 nt in P. marinus, and ∼ 83 nt in P. chesapeaki, significantly larger than the typical ≤ 56-nt dinoflagellate SL RNA.These results, along with the presence of the numerous uncharacterized 'marine alveolate group I' and Perkinsus-like lineages separating perkinsids from core dinoflagellates, expand support for the affiliation of the genus Perkinsus with an independent lineage (Perkinsozoa) positioned between the phyla of Apicomplexa and Dinoflagellata.

View Article: PubMed Central - PubMed

Affiliation: Department of Marine Sciences, University of Connecticut, Groton, Connecticut, United States of America. huan.zhang@uconn.edu

ABSTRACT
The genus Perkinsus occupies a precarious phylogenetic position. To gain a better understanding of the relationship between perkinsids, dinoflagellates and other alveolates, we analyzed the nuclear-encoded spliced-leader (SL) RNA and mitochondrial genes, intron prevalence, and multi-protein phylogenies. In contrast to the canonical 22-nt SL found in dinoflagellates (DinoSL), P. marinus has a shorter (21-nt) and a longer (22-nt) SL with slightly different sequences than DinoSL. The major SL RNA transcripts range in size between 80-83 nt in P. marinus, and ∼ 83 nt in P. chesapeaki, significantly larger than the typical ≤ 56-nt dinoflagellate SL RNA. In most of the phylogenetic trees based on 41 predicted protein sequences, P. marinus branched at the base of the dinoflagellate clade that included the ancient taxa Oxyrrhis and Amoebophrya, sister to the clade of apicomplexans, and in some cases clustered with apicomplexans as a sister to the dinoflagellate clade. Of 104 Perkinsus spp. genes examined 69.2% had introns, a higher intron prevalence than in dinoflagellates. Examination of Perkinsus spp. mitochondrial cytochrome B and cytochrome C oxidase subunit I genes and their cDNAs revealed no mRNA editing, but these transcripts can only be translated when frameshifts are introduced at every AGG and CCC codon as if AGGY codes for glycine and CCCCU for proline. These results, along with the presence of the numerous uncharacterized 'marine alveolate group I' and Perkinsus-like lineages separating perkinsids from core dinoflagellates, expand support for the affiliation of the genus Perkinsus with an independent lineage (Perkinsozoa) positioned between the phyla of Apicomplexa and Dinoflagellata.

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Perkinsus marinus SL RNA secondary structure similar to DinoSL RNA.Predicted structures of SL RNA for P. marinus L-type (A) and S-type (B) based on the most abundant cDNAs obtained. Model simulation was run using MFOLD: Prediction of RNA secondary structure modeling program (http://bioweb.pasteur.fr/seqanal/interfaces/mfold-simple.html) under default settings except that the folding temperature was set at 27°C, the culture temperature.
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pone-0019933-g003: Perkinsus marinus SL RNA secondary structure similar to DinoSL RNA.Predicted structures of SL RNA for P. marinus L-type (A) and S-type (B) based on the most abundant cDNAs obtained. Model simulation was run using MFOLD: Prediction of RNA secondary structure modeling program (http://bioweb.pasteur.fr/seqanal/interfaces/mfold-simple.html) under default settings except that the folding temperature was set at 27°C, the culture temperature.

Mentions: Similar to the situation in dinoflagellates, no apparent Sm-binding site sequence was found in the predicted intron regions of either of the PmaSLRNAs. Instead, AUUCUGG (L-type) or AUCUGG (S-type) found within the SL was the only recognizable candidate Sm-binding site, as in the DinoSL (AUUUUGG). The predicted intron region was similar between the two PmaSLRNAs, in contrast to the conserved intron in DinoSL RNAs, with the exception of the ancient parasitic genus of dinoflagellates Amoebophrya that showed considerable variation (Figure 1B). In the structural simulation using the default conditions for all but temperature, which was adjusted to the culture temperature of 27°C, the splice-donor dinucleotide (‘gu’ in ‘Gguag’) was double-stranded and the putative Sm-binding site (AUUCUGG/AUCUGG) single-stranded, forming a small terminal loop. The simulation yielded one comparable structure for both types of PmaSLRNAs (Figure 3). The predicted structures were similar to typical dinoflagellate SL RNA structures, having two stem-loops [8], [9], with the ‘extra’ intron region situated in a bulge of unpaired sequence connecting the two stem loops.


Spliced leader RNAs, mitochondrial gene frameshifts and multi-protein phylogeny expand support for the genus Perkinsus as a unique group of alveolates.

Zhang H, Campbell DA, Sturm NR, Dungan CF, Lin S - PLoS ONE (2011)

Perkinsus marinus SL RNA secondary structure similar to DinoSL RNA.Predicted structures of SL RNA for P. marinus L-type (A) and S-type (B) based on the most abundant cDNAs obtained. Model simulation was run using MFOLD: Prediction of RNA secondary structure modeling program (http://bioweb.pasteur.fr/seqanal/interfaces/mfold-simple.html) under default settings except that the folding temperature was set at 27°C, the culture temperature.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3101222&req=5

pone-0019933-g003: Perkinsus marinus SL RNA secondary structure similar to DinoSL RNA.Predicted structures of SL RNA for P. marinus L-type (A) and S-type (B) based on the most abundant cDNAs obtained. Model simulation was run using MFOLD: Prediction of RNA secondary structure modeling program (http://bioweb.pasteur.fr/seqanal/interfaces/mfold-simple.html) under default settings except that the folding temperature was set at 27°C, the culture temperature.
Mentions: Similar to the situation in dinoflagellates, no apparent Sm-binding site sequence was found in the predicted intron regions of either of the PmaSLRNAs. Instead, AUUCUGG (L-type) or AUCUGG (S-type) found within the SL was the only recognizable candidate Sm-binding site, as in the DinoSL (AUUUUGG). The predicted intron region was similar between the two PmaSLRNAs, in contrast to the conserved intron in DinoSL RNAs, with the exception of the ancient parasitic genus of dinoflagellates Amoebophrya that showed considerable variation (Figure 1B). In the structural simulation using the default conditions for all but temperature, which was adjusted to the culture temperature of 27°C, the splice-donor dinucleotide (‘gu’ in ‘Gguag’) was double-stranded and the putative Sm-binding site (AUUCUGG/AUCUGG) single-stranded, forming a small terminal loop. The simulation yielded one comparable structure for both types of PmaSLRNAs (Figure 3). The predicted structures were similar to typical dinoflagellate SL RNA structures, having two stem-loops [8], [9], with the ‘extra’ intron region situated in a bulge of unpaired sequence connecting the two stem loops.

Bottom Line: In contrast to the canonical 22-nt SL found in dinoflagellates (DinoSL), P. marinus has a shorter (21-nt) and a longer (22-nt) SL with slightly different sequences than DinoSL.The major SL RNA transcripts range in size between 80-83 nt in P. marinus, and ∼ 83 nt in P. chesapeaki, significantly larger than the typical ≤ 56-nt dinoflagellate SL RNA.These results, along with the presence of the numerous uncharacterized 'marine alveolate group I' and Perkinsus-like lineages separating perkinsids from core dinoflagellates, expand support for the affiliation of the genus Perkinsus with an independent lineage (Perkinsozoa) positioned between the phyla of Apicomplexa and Dinoflagellata.

View Article: PubMed Central - PubMed

Affiliation: Department of Marine Sciences, University of Connecticut, Groton, Connecticut, United States of America. huan.zhang@uconn.edu

ABSTRACT
The genus Perkinsus occupies a precarious phylogenetic position. To gain a better understanding of the relationship between perkinsids, dinoflagellates and other alveolates, we analyzed the nuclear-encoded spliced-leader (SL) RNA and mitochondrial genes, intron prevalence, and multi-protein phylogenies. In contrast to the canonical 22-nt SL found in dinoflagellates (DinoSL), P. marinus has a shorter (21-nt) and a longer (22-nt) SL with slightly different sequences than DinoSL. The major SL RNA transcripts range in size between 80-83 nt in P. marinus, and ∼ 83 nt in P. chesapeaki, significantly larger than the typical ≤ 56-nt dinoflagellate SL RNA. In most of the phylogenetic trees based on 41 predicted protein sequences, P. marinus branched at the base of the dinoflagellate clade that included the ancient taxa Oxyrrhis and Amoebophrya, sister to the clade of apicomplexans, and in some cases clustered with apicomplexans as a sister to the dinoflagellate clade. Of 104 Perkinsus spp. genes examined 69.2% had introns, a higher intron prevalence than in dinoflagellates. Examination of Perkinsus spp. mitochondrial cytochrome B and cytochrome C oxidase subunit I genes and their cDNAs revealed no mRNA editing, but these transcripts can only be translated when frameshifts are introduced at every AGG and CCC codon as if AGGY codes for glycine and CCCCU for proline. These results, along with the presence of the numerous uncharacterized 'marine alveolate group I' and Perkinsus-like lineages separating perkinsids from core dinoflagellates, expand support for the affiliation of the genus Perkinsus with an independent lineage (Perkinsozoa) positioned between the phyla of Apicomplexa and Dinoflagellata.

Show MeSH