Nucleic Acids Research Advance Access published online on April 4, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn142
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Computational Biology |
Computational screen for spliceosomal RNA genes aids in defining the phylogenetic distribution of major and minor spliceosomal components
1Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, Box 440 and 2Department of Cell and Molecular Biology, University of Gothenburg, Box 462, SE-405 30 Göteborg, Sweden
*To whom correspondence should be addressed. Tel: +46 31 786 3468; Fax: +46 31 41 6108; Email: Tore.Samuelsson{at}medkem.gu.se
Received February 8, 2008. Revised March 13, 2008. Accepted March 14, 2008.
The RNA molecules of the spliceosome are critical for specificity and catalysis during splicing of eukaryotic pre-mRNA. In order to examine the evolution and phylogenetic distribution of these RNAs, we analyzed 149 eukaryotic genomes representing a broad range of phylogenetic groups. RNAs were predicted using high-sensitivity local alignment methods and profile HMMs in combination with covariance models. The results provide the most comprehensive view so far of the phylogenetic distribution of spliceosomal RNAs. RNAs were predicted in many phylogenetic groups where these RNA were not previously reported. Examples are RNAs of the major (U2-type) spliceosome in all fungal lineages, in lower metazoa and many protozoa. We also identified the minor (U12-type) spliceosomal U11 and U6atac RNAs in Acanthamoeba castellanii, where U12 spliceosomal RNA as well as minor introns were reported recently. In addition, minor-spliceosome-specific RNAs were identified in a number of phylogenetic groups where previously such RNAs were not observed, including the nematode Trichinella spiralis, the slime mold Physarum polycephalum and the fungal lineages Zygomycota and Chytridiomycota. The detailed map of the distribution of the U12-type RNA genes supports an early origin of the minor spliceosome and points to a number of occasions during evolution where it was lost.
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