Numerous Fragmented Spliceosomal Introns, AT-AC Splicing, and an Unusual Dynein Gene Expression Pathway in Giardia lamblia

Abstract

Spliceosomal introns are hallmarks of eukaryotic genomes, dividing coding regions into separate exons, which are joined during mRNA intron removal catalyzed by the spliceosome. With few known exceptions, spliceosomal introns are cis-spliced, that is, removed from one contiguous pre-mRNA transcript. The protistan intestinal parasite Giardia lamblia exhibits one of the most reduced eukaryotic genomes known, with short intergenic regions and only four known spliceosomal introns. Our genome-wide search for additional introns revealed four unusual cases of spliceosomal intron fragmentation, with consecutive exons of conserved protein-coding genes being dispersed to distant genomic sites. Independent transcripts are trans-spliced to yield contiguous mature mRNAs. Most strikingly, a dynein heavy chain subunit is both interrupted by two fragmented introns and also predicted to be assembled as two separately translated polypeptides, a remarkably complex expression pathway for a nuclear-encoded sequence. For each case, we observe extensive base-pairing potential between intron halves. This base pairing provides both a rationale for the in vivo association of independently transcribed mRNAs transcripts and the apparent specificity of splicing. Similar base-pairing potential in two cis-spliced G. lamblia introns suggests an evolutionary pathway whereby intron fragmentation of cis-spliced introns is permissible and a preliminary evolutionary step to complete gene fission. These results reveal remarkably complex genome dynamics in a severely genomically reduced parasite.

Alternative splicing and trans-splicing events revealed by analysis of the Bombyx mori transcriptome

“…S2A). Furthermore, it has been revealed that RNA base-pairing is critical for the trans-splicing (Fischer et al 2008;Kamikawa et al 2011;Roy et al 2011). We assembled each set of the 59 and 39 trans-introns to reveal potential RNA base-pairings.…”

Transcriptomic analysis of diplomonad parasites reveals a trans-spliced intron in a helicase gene inGiardia

“…1D); and (iii) the recently-discovered G. lamblia cleavage motif (with consensus TCCTTTACTCAA; Fig. 1D; Hudson et al, 2012). A BLASTX search of the mature trans-spliced transcript against Genbank revealed homology to p68 helicase (Fig.…”

“…Recently, the first case in which a substantial fraction of introns in an organism are trans-spliced was reported. In the genome of the diplomonad intestinal parasite G. lamblia, systematic studies have revealed only six cis-spliced introns to date (Nixon et al, 2002;Russell et al, 2005;Morrison et al, 2007;Roy et al, 2012;Franzén et al, 2013); intriguingly small-scale studies revealed four cases of genic trans-splicing, including two in a single gene (Nageshan et al, 2011;Kamikawa et al, 2011;Roy et al, 2012;Hudson et al, 2015). These cases showed distinctive sequence featuresmost notably extended basepairing potential between the pairs of trans-spliced transcripts.…”

A novel spliceosome-mediated trans-splicing can change our view on genome complexity of the divergent eukaryote Giardia intestinalis

“…For a long time, it was believed that G. intestinalis possesses neither a typical mitochondrion with respiratory function nor spliceosomal introns (Adam 2000). We now know that G. intestinalis secondarily lost its mitochondria (Roger et al 1998;Hashimoto et al 1998;Tovar et al 2003), and five genes had been found to bear canonical (cis-spliced) spliceosomal introns in its genome (Nixon et al 2002;Morrison et al 2007;Roy et al 2011). These findings suggest that this organism does not necessarily represent the ancestral eukaryotes; rather, they lost the typical mitochondria because of their anaerobic lifestyle, and spliceosomal introns in the G. intestinalis genome are merely more sparse than those in other eukaryotic genomes.…”