Plasmodium interspersed repeats: the major multigene superfamily of malaria parasites

Abstract

Functionally related homologues of known genes can be difficult to identify in divergent species. In this paper, we show how multi-character analysis can be used to elucidate the relationships among divergent members of gene superfamilies. We used probabilistic modelling in conjunction with protein structural predictions and gene-structure analyses on a whole-genome scale to find gene homologies that are missed by conventional similarity-search strategies and identified a variant gene superfamily in six species of malaria (Plasmodium interspersed repeats, pir). The superfamily includes rif in P.falciparum, vir in P.vivax, a novel family kir in P.knowlesi and the cir/bir/yir family in three rodent malarias. Our data indicate that this is the major multi-gene family in malaria parasites. Protein localization of products from pir members to the infected erythrocyte membrane in the rodent malaria parasite P.chabaudi, demonstrates phenotypic similarity to the products of pir in other malaria species. The results give critical insight into the evolutionary adaptation of malaria parasites to their host and provide important data for comparative immunology between malaria parasites obtained from laboratory models and their human counterparts.

Figure 1

Plots of sequence conservation in alignments of (A) 276 rif amino acid sequences and (B) 1016 cir, yir and bir amino acid sequences, measured with the PAM250 scoring matrix, using a window size of four amino acids. The hypervariable regions are artificially long due to extensive gapping in the alignments. The predicted conserved secondary structure is given beneath each conservation plot (see key). Sequence motifs conserved among rifins and rodent malaria cir protein homologues, identified using neural network analysis (see Table 1), are shown in open boxes containing motif numbers.

Figure 2

A total of 157 amino acid sequences of superfamily members from P.falciparum, P.vivax, P.knowlesi, P.yoelii and P.chabaudi were aligned using ClustalW. Poorly aligned positions and divergent regions of the alignment were eliminated (see text), and a tree generated using the maximum parsimony method implemented by the protpars algorithm of the Phylip package (23).