Constrained intron structures in a microsporidian

Abstract

The 2.9-Mbp genome of the microsporidian Encephalitozoon cuniculi is severely reduced and compacted, possessing only 16 known tiny spliceosomal introns. Based on motif and expression data, intron profiles were constructed to screen the genome. Twenty additional introns were predicted and verified, doubling the previous estimate. We further predict that accurate 3' splice site (3'SS) selection is accomplished via a scanning mechanism with specificity achieved by maintaining a constrained variable length between the branch point motif and 3'SS. Only introns in ribosomal protein genes exhibit positional bias, and we hypothesize that splicing could be regulating expression of these genes. The large set of new introns in non-ribosomal protein genes suggests that current models of intron loss are unlikely sufficient to explain the distribution of introns. Together, these results extend our understanding of the role of intron loss in genome evolution and contribute to a novel model for splice site selection.

FIG. 1.

Encephalitozoon cuniculi introns are aligned and listed in order of increasing length. New introns are shown in bold; an asterisk indicates those shorter than annotated. Poly-A binder bases 9–36 are shown as “N.”

FIG. 2.

Intron (lowercase) and exon (uppercase) bases with the trinucleotide threshold (pink) and bpA motif (blue) indicated. (a) Intron sequences with all possible bpA-3′SS distances. (b) Sample of sequences that contain all splicing motifs but are not introns.

FIG. 3.

Positional distribution of original (above ORF) and new (below ORF) introns. Arrowheads indicate RPG (black) and non-RPG (pink) introns.