U12 type introns were lost at multiple occasions during evolution

Abstract

Background: Two categories of introns are known, a common U2 type and a rare U12 type. These two types of introns are removed by distinct spliceosomes. The phylogenetic distribution of spliceosomal RNAs that are characteristic of the U12 spliceosome, i.e. the U11, U12, U4atac and U6atac RNAs, suggest that U12 spliceosomes were lost in many phylogenetic groups. We have now examined the distribution of U2 and U12 introns in many of these groups.

Results: U2 and U12 introns were predicted by making use of available EST and genomic sequences. The results show that in species or branches where U12 spliceosomal components are missing, also U12 type of introns are lacking. Examples are the choanoflagellate Monosiga brevicollis, Entamoeba histolytica, green algae, diatoms, and the fungal lineage Basidiomycota. Furthermore, whereas U12 splicing does not occur in Caenorhabditis elegans, U12 introns as well as U12 snRNAs are present in Trichinella spiralis, which is deeply branching in the nematode tree. A comparison of homologous genes in T. spiralis and C. elegans revealed different mechanisms whereby U12 introns were lost.

Conclusions: The phylogenetic distribution of U12 introns and spliceosomal RNAs give further support to an early origin of U12 dependent splicing. In addition, this distribution identifies a large number of instances during eukaryotic evolution where such splicing was lost.

Figure 1

Plot of splice site scores of introns identified in Phytophthora sojae. The scores of 5' splice sites and branch sites are compared to those of a reference set of U12 introns as used by Burge et al [5] (within blue rectangle). Introns in P. sojae predicted to be of the U12 type have both 5' splice site and branch site scores equal to or larger than the minimum values of the reference set. Arrows indicate one GT-AG and two AT-AC introns.

Figure 2

Schematic phylogenetic tree showing instances where U12 introns were lost. Presence or absence of U12 snRNAs and U12 introns are shown as well as paths where U12 splicing seem to have been lost (dashed lines). Figure is based on previous information regarding the phylogenetic distribution of U12 snRNAs [7,8] as well as results regarding U12 intron distribution described here.

Figure 3

Conserved sequence elements of U12 introns in A. castellanii. Position 6 in alignment corresponds to the 5' terminal position of the intron. The majority of these introns were identified by Russell et al [7], whereas the introns of lipid transfer protein and carnitine/acylcarnitine carrier protein was identified in this work.