Spliceosomal small nuclear RNA genes in 11 insect genomes

Abstract

The removal of introns from the primary transcripts of protein-coding genes is accomplished by the spliceosome, a large macromolecular complex of which small nuclear RNAs (snRNAs) are crucial components. Following the recent sequencing of the honeybee (Apis mellifera) genome, we used various computational methods, ranging from sequence similarity search to RNA secondary structure prediction, to search for putative snRNA genes (including their promoters) and to examine their pattern of conservation among 11 available insect genomes (A. mellifera, Tribolium castaneum, Bombyx mori, Anopheles gambiae, Aedes aegypti, and six Drosophila species). We identified candidates for all nine spliceosomal snRNA genes in all the analyzed genomes. All the species contain a similar number of snRNA genes, with the exception of A. aegypti, whose genome contains more U1, U2, and U5 genes, and A. mellifera, whose genome contains fewer U2 and U5 genes. We found that snRNA genes are generally more closely related to homologs within the same genus than to those in other genera. Promoter regions for all spliceosomal snRNA genes within each insect species share similar sequence motifs that are likely to correspond to the PSEA (proximal sequence element A), the binding site for snRNA activating protein complex, but these promoter elements vary in sequence among the five insect families surveyed here. In contrast to the other insect species investigated, Dipteran genomes are characterized by a rapid evolution (or loss) of components of the U12 spliceosome and a striking loss of U12-type introns.

Evolution of Spliceosomal snRNA Genes in Metazoan Animals

“…For Drosophilids, on the other hand, our analysis is almost identical to the results of [53,Tab.1] and the data reported in [77]. Furthermore, we come close the results of a comparative genomics screen for non-coding RNAs in C. elegans [49], which reported 12 U1, 19 U2, 5 U4, 13 U5, and 23 U6, i.e., only a few more candidates than our present purely homology-based approach.…”

“…Only a few sequences of minor spliceosomal snRNAs have been reported so far, mostly in a few model mammals [82] and in Drosophilids [69,53].…”

“…They were manually compared with previously published sequence elements. We visually compared the MEME -patterns with the upstream elements in related species from the following literature sources: [26] (general motifs), [14,82,2,38] (human), [36,5] (chicken), [53] (insects), [77] (Bombyx mori), [81] (Strongylocentrotus purpuratus), [84] (Caenorhabditis elegans).…”

“…Our analysis agrees with the recent observation that in Drosophilids there is a rapid turnover in the upstream sequences. Even though the PSE is fairly well-conserved within Drosophilids, it already differs substantially between the major insect groups [53]. Sim-ilarly, within the nematodes conservation of upstream elements is limited to the genus level.…”

“…[64,8,39,77,29,78] and the references therein. The only systematic study that we are aware of is the recent comprehensive analysis of 11 insect genomes [53] which reported that phylogenetic gene trees of insect snRNAs do not provide clear support for discernible paralog groups of U1 and/or U5 snRNAs that would correspond to the variants with tissue-specific expression patterns. Instead, the analysis supports a concerted mode of evolution and/or extreme purifying selection, a scenario previously described for snRNA evolution [42,40,57].…”