Chapter 20 : Recombination and Diversification of the Variant Antigen Encoding Genes in the Malaria Parasite Plasmodium falciparum

Schematic representation of the Plasmodium life cycle highlighting major points of morphological transition and replication. (1) Asexual replication within the erythrocytes of the mammalian host. (2) Male and female gametocytes circulating within the blood stream of the mammalian host prior to being acquired by the mosquito vector during a blood meal. (3) Male and female parasites as they leave the red blood cells prior to fusion and sexual division. The “rounded up” female is shown on the left and the male undergoing exflagellation is shown on the right. (4) The motile ookinete that crosses the gut wall of the blood fed mosquito. (5) An oocyst that forms after the ookinete crosses the gut wall. The parasite undergoes numerous asexual divisions at this point, giving rise to thousands of sporozoites. (6) Sporozoites that infect the salivary glands of the mosquito and are injected into a mammalian host during a subsequent blood meal. They then travel to and invade cells within the liver. (7) A liver cell infected with asexually replicating parasites. These parasites leave the liver and infect circulating red blood cells, thus completing the cycle. Figure adapted with permission from reference 83 .

Structure and genomic arrangement of the var gene family in P. falciparum. (A) Schematic showing the two exon structure of all var genes. Note that the 5′ UTR, intron, exon 2 and 3′ UTR are all highly conserved (gray). The sequence of the 5′ UTR and upstream regulatory domains can be classified into three basic types called A, B and C. Exon 1 encodes the polymorphic portion of PfEMP1 and is arranged as an alternating series of highly diverse sequences separating regions of higher similarity. Overall the greatest degree of sequence diversity is found at the 3′ end of exon 1 as represented by the color gradient. Exon 2 encodes a highly conserved region of PfEMP1 that is not exposed to the immune system. (B) General chromosomal arrangement of var genes, with type C genes typically found in tandem arrangement in the internal regions of the chromosomes while types A and B genes are located next to the telomere repeats. The telomeres are known to cluster into “bouquets” which align the genes in a way that is proposed to facilitate recombination and gene conversion events. (C) Illustration (left) showing the subnuclear localization of the telomere bouquets (yellow spots) that are found near the nuclear envelope within regions of dense heterochromatin (dark blue). Regions of less dense euchromatin are typically found near the center of the nucleus (light blue). Fluorescent in situ hybridization showing the location of the var gene clusters within the parasite’s nucleus. A probe that hybridizes to the conserved exon 2 of var genes is shown in yellow while the nuclear DNA is stained with DAPI (4′,6-diamidino-2-phenylindole) and is shown in blue. Image in Fig. 2(B) modified with permission from reference 84 . Image in Fig. 2(C) modified with permission from reference 85 .

Phylogenetic tree of the Apicomplexan lineage. The different colors highlight several groups of obligate, Apicomplexan parasites. The Haemosporidia (orange) include parasites that cause malaria in humans (P. falciparum and P. vivax), nonhuman primates (P. knowlesi) and rodents (P. berghei and P. chabaudi). The Piroplasmida (green) are parasites transmitted by ticks that infect either red blood cells (Babesia bovis) or white blood cells (T. annulata and T. parva). The Coccidia (blue) are cyst forming parasites that do not undergo antigenic variation. The Cryptospiridia (purple) also form cysts and have a highly reduced genome. The ciliates, as exemplified by P. tetraurelia and T. thermophila, are nonparasitic, free living organisms. The ability of the organisms to utilize the C-NHEJ pathway for DSB repair is inferred by the presence or absence of proteins of the Ku family. Note that, of the Apicomplexans, only the Coccidia have retained these genes within their genomes. The annotations numbers for Ku70/80 are given for both the Coccidia and the Ciliates. The phylogenetic relationships are shown as described in reference 86 .