Alternative Splicing in Apicomplexan Parasites

Abstract

Alternative splicing is a widespread, essential, and complex component of gene regulation. Apicomplexan parasites have long been recognized to produce alternatively spliced transcripts for some genes and can produce multiple protein products that are essential for parasite growth. Recent approaches are now providing more wide-ranging surveys of the extent of alternative splicing; some indicate that alternative splicing is less widespread than in other model eukaryotes, whereas others suggest levels comparable to those of previously studied groups. In many cases, apicomplexan alternative splicing events appear not to generate multiple alternative proteins but instead produce aberrant or noncoding transcripts. Nonetheless, appropriate regulation of alternative splicing is clearly essential in Plasmodium and Toxoplasma parasites, suggesting a biological role for at least some of the alternative splicing observed. Several studies have now disrupted conserved regulators of alternative splicing and demonstrated lethal effects in apicomplexans. This minireview discusses methods to accurately determine the extent of alternative splicing in Apicomplexa and discuss potential biological roles for this conserved process in a phylum of parasites with compact genomes.

Keywords: Plasmodium; RNA splicing; Toxoplasma; apicomplexan parasites; posttranscriptional control mechanisms.

FIG 1

Gene structure in Apicomplexa. (A) Gene structure in Cryptosporidium parvum, Eimeria tenella, Toxoplasma gondii, Plasmodium falciparum, Theileria annulata, and Babesia bigemina. Whereas some apicomplexan genera have very few introns, others have many introns in some genes and at least one intron in most genes. Exon number in the phylum tends to track with genome size. (B) Gene structure varies widely within the phylum Apicomplexa, even between closely related genera. Apicomplexan orthologues of a representative gene, serine hydroxymethyltransferase 2, are depicted as one example. The transcripts are similar but not exactly equal lengths, but all are drawn to scale relative to the length of each gene. Gene IDs are listed below each gene.

FIG 2

Examples of alternatively spliced genes in Apicomplexa. Boxes represent exons, and thin lines represent introns. Gray or colored regions are common or variable between isoforms, respectively. The structures are not always drawn to scale to emphasize differences in isoforms. For ALAD/SPP (P. falciparum), alternative 3′ splicing targets two unrelated proteins to the same location (60). CysRS (T. gondii and P. falciparum, the latter depicted) shows the opposite of ALAD/SPP. Intron retention (and possibly alternative transcriptional start site) results in one mature protein with two locations, the apicoplast and cytosol (63, 106). Lighter colors denote untranslated regions. Myosin B/C (T. gondii) shows similar functional results to CysRS but at the C-terminal end. Intron retention (and possibly alternative transcriptional stop site) results in one mature protein with two locations (61). For Maebl (P. falciparum), alternative 3′ splicing results in a frameshift and different stop codons, encoding either soluble or membrane-bound variants (62). For HXGPRT (T. gondii), exon skipping induces localization in either the cytosol or inner membrane complex (44).

FIG 3

Alternative splicing factors can regulate spliceosomal components. Part of the spliceosome, U2AF65, binds to mRNA, mediating canonical splicing. SR proteins and PTB interact with neighboring sequences and can repress the binding of this component. SR proteins can also enrich this activity.

FIG 4

A phylogenetic tree inferred for putative apicomplexan and human SR proteins. Numbers denote bootstrap values above 50 for a neighbor-joining distance tree. Sequences from Plasmodium falciparum (PF) (black), Babesia bovis (BB) (purple), Toxoplasma gondii (TG) (blue), Theileria parva (TP) (orange), Cryptosporidium muris (CM) (green), and Homo sapiens (Hs) (red) are indicated. Some apicomplexan SRs group strongly with one or more human SR counterparts, whereas others are clearly paralogous or only weakly allied with a human SR.