Spliced leader RNA-mediated trans-splicing in phylum Rotifera

Area of Science:

• Molecular Biology
• Evolutionary Biology
• Genetics

Background:

• Trans-splicing generates mature messenger RNAs (mRNAs) by replacing precursor mRNA 5'-ends with a spliced leader (SL) exon from small SL RNA.
• This process occurs in kinetoplastids, Euglena, and four metazoan phyla but is absent in vertebrates, insects, plants, and yeast.
• The sporadic phylogenetic distribution and lack of SL RNA homology have fueled debate regarding its evolutionary origin.

Purpose of the Study:

• To investigate the presence and characteristics of trans-splicing in bdelloid rotifers.
• To analyze the SL RNA sequences and structures in bdelloid rotifers.
• To assess the evolutionary implications of trans-splicing in Rotifera.

Main Methods:

• Identification of a common 23-nt SL exon sequence at the 5'-end of mRNAs in Adineta ricciae and Philodina sp.
• Analysis of SL RNA length (105-106 nt) and composition, including SL sequence, splice donor site, and intron with a putative spliceosome-binding motif.
• Comparison of rotifer SL RNA sequences and predicted secondary structures with nematode SL1 RNA.

Main Results:

• Evidence for SL RNA-mediated trans-splicing found in 50%-65% of mRNAs from bdelloid rotifers.
• Observed complex trans-splicing patterns, including alternative SL exon splicing in hsp82-1 transcripts.
• Identified similarities between rotifer SL RNA and nematode SL1 RNA, though homology is unlikely.
• Detected rotifer SL exon sequences in rice cDNA databases, suggesting cross-kingdom contamination.

Conclusions:

• The discovery of trans-splicing in bdelloid rotifers expands its known metazoan distribution to at least five phyla.
• This finding strengthens the hypothesis that trans-splicing is a phylogenetically widespread and ancient phenomenon.
• The study highlights the potential for cross-kingdom sequence contamination in genomic databases.