Supplementary materials for PhD thesis “Transcriptional regulation of yir genes in Plasmodium yoelii yoelii infected erythrocytes”

This dataset comprises the files contained on a CD-ROM which was attached to the thesis when it was submitted in 2006. It was uploaded to ORDO in 2024 for preservation purposes. For more information, please refer to the thesis Transcriptional regulation of yir genes in Plasmodium yoelii yoelii infected erythrocytes.

In 1998, a large multi gene family was discovered in Plasmodium vivax (del Portillo et al., 1998). This multigene family was termed vir, and later studies showed that vir homologues existed in the three rodent malaria species, Plasmodium chabaudi (cir), Plasmodium berghei (bir) and Plasmodium yoelii (yir). By 5x coverage sequencing of Plasmodium yoelii 17X, 838 yir genes were predicted (Carlton et al., 2002), making this the largest known multi gene family in Plasmodium. YIR proteins are expressed at the surface of infected erythrocytes (Cunningham et al., 2005), and therefore this family is thought to be involved in antigenic variation.

The aim of this thesis was to examine how P.yoelii regulates transcription of the yir family. The yir gene structure was verified experimentally, and phylogenetic analysis showed that yir genes could be divided into five supergroups consisting of yir genes with different sizes and subtelomeric localisation. In the blood stages, numerous yir genes were transcribed from all the supergroups in immunocompromised mice. However, a maximum of two yir genes were transcribed in single infected erythrocytes at the Schizont stage, which suggested strong silencing mechanisms. The transcriptional start and polyadenylation sites were identified experimentally, and it was found that both occurred at highly conserved motifs. In addition, the transcription initiation site was located close to an unusual and universally conserved triple-repeat motif, and it was found that all yir transcripts in two populations of parasites initiated downstream of this motif. Transfection experiments were performed in order to examine the role of this motif, but no solid conclusions could be drawn from these. Several alternative splicing events were detected in the yir 5'UTRs, and one of these led to exon 1 skipping of a yir gene. Through bioinformatic analysis of yir 5' intergenic regions, it was found that the UTR introns had a discrete distribution amongst the yir supergroups.