A conserved alternative splicing event in plants reveals an ancient exonization of 5S rRNA that regulates TFIIIA

Abstract

Uncovering conserved alternative splicing (AS) events can identify AS events that perform important functions. This is especially useful for identifying premature stop codon containing (PTC) AS isoforms that may regulate protein expression by being targets for nonsense mediated decay. This report discusses the identification of a PTC containing splice isoform of the TFIIIA gene that is highly conserved in land plants. TFIIIA is essential for RNA Polymerase III-based transcription of 5S rRNA in eukaryotes. Two independent groups have determined that the PTC containing alternative exon is ultraconserved and is coupled with nonsense-mediated mRNA decay. The alternative exon appears to have been derived by the exonization of 5S ribosomal RNA (5S rRNA) within the gene of its own transcription regulator, TFIIIA. This provides the first evidence of ancient exaptation of 5S rRNA in plants, suggesting a novel gene regulation model mediated by the AS of an anciently exonized non-coding element.

Acknowledgements

Thanks to Yan Fu for supplying data and analysis included in Figure 1.

Figures and Tables

Figure 1 An example of sequence conservation between the alternative exons in a selection of plant TFIIIA genes. (A) Vista plots of pair-wise alignments between TFIIIA from Arabidopsis and its orthologue in medicago, poplar, tomato, rice maize and sorghum. The alternative exon (boxed) is the most conserved feature between Arabidopsis TFIIIA and its orthologues in other plant species. Levels of sequence identity between Arabidopsis TFIIIA and its orthologues in the six other plants species displayed are depicted as blue peaks. Brown bars signify segments that pass the alignment criteria of 70% identity over a window of 100 bp. (B) Detailed sequence alignment between the PTC containing alternative exon of Arabidopsis TFIIIA and one of the PTC containing alternative exons of rice TFIIIA—rice contains a duplication of the alternatively spliced exon (see text). Sequence identity across the alternatively splice exon is 74%. The in-frame stop codon introduced when this exon is included in the transcript is represented by red text.

Figure 2 Alignment of the alternative exon of Arabidopsis TFIIIA to Arabidopsis 5SrRNA. The alternative exon sequence is represented within Gen-Bank accession NM_105863 from nucleotide position 380 to 479. Regions corresponding to 5SrRNA secondary structure features are depicted above the sequence segment in which they are found. Elements are named according to the standard 5S rRNA nomenclature: helices are designated by roman numerals (III–V) in colored boxes; loop regions are designated by letters (C–E) in open boxes.