The evolutionary processes whereby free-living or symbiotic organisms made the transition to full-fledged obligate, intracellular parasites remain unclear. This is perhaps best exemplified by the case of the Apicomplexa, a group of ~5000 species that includes several major human disease-causing agents including Toxoplasma gondii, Cryptosporidium spp. and Plasmodium falciparum, the most lethal of human malaria parasites . Presumably, this transition involved the development of novel cellular differentiation pathways that enabled infection and replication within different hosts, invasion schema, cytoadhesion to host substrates and immune evasion strategies including antigenic variation.
The newly acquired lifestyle complexity might also require the acquisition of new mechanisms to control gene expression. For example, more sophisticated transcriptional regulation and epigenetic machinery would enable the evolution of complex life cycles involving multiple hosts and stages, and facilitate developmental changes accompanying the transition to parasitism. This could involve either de novo innovations or the horizontal acquisition of transcriptional and epigenetic machinery from other eukaryotes. Examples of both mechanisms of innovation have been reported. For instance, we previously described the unusual and rapid evolution of the C-terminal domain of RNA polymerase II within the Plasmodium lineage, and more specifically the expansion of this domain in parasites that infect primates . This domain is crucial for controlling many aspects of gene expression, including epigenetic mechanisms of control, and the rapid de novo evolution of host-specific modifications demonstrates how important aspects of gene expression are for parasitism.
In contrast, it is now well established that the primary class of transcription factors in apicomplexan parasites (the ApiAP2 family) was acquired through an ancient horizontal gene transfer (HGT) event . It is known that the ancestor to apicomplexans engulfed an alga, endowing it with photosynthetic abilities and enabling it to synthesize several important products, including fatty acids [4, 5]. The engulfed alga later degenerated into a relic, the apicoplast; this accompanied the loss of photosynthetic ability and the evolution of apicomplexans into obligate intracellular parasites metabolically dependent on their animal hosts. The ApiAP2 class of transcription factors was acquired horizontally from the relic alga and now contributes to controlling parasite gene expression. Similarly, protein domains involved in cytoadhesion and O-linked glycosylation appear to have been acquired through HGT, in these cases from the parasites’ hosts rather than the algal endosymbiont [6, 7]. The origin of the innate immune system in early animals, the likely hosts of newly evolved apicomplexan parasites, also dates to this evolutionary period. Thus, the hallmarks of parasitism, including nutritional dependence, invasion, and immune escape likely developed as part of the same evolutionary process during which photosynthetic ability was lost.
In the case of the Apicomplexa, therefore, two major potential sources for HGT have been established: i) transfer from an algal endosymbiont (fatty acid synthases or ApiAP2 transcription factors) [3, 8], or ii) transfer from an animal host (domains involved in cytoadhesion and O-linked glycosylation) [6, 7]. Here, we consider the putative acquisition of epigenetic machinery in the ancestor of apicomplexans with a focus on histone lysine modifiers, which are central to pathways of cellular differentiation, cell invasion and immune evasion in apicomplexan parasites.
Histone lysine methyltransferases, characterized by a SET domain, play a fundamental role in gene activation and epigenetic regulation across all eukaryotes . These domains modify histone lysine residues at Histone H3 Lysine 4, 9, 36, and Histone H4 Lysine 20. These modifications are crucial for the establishment and maintenance of epigenetic memory, including in P. falciparum, and are involved in imprinting genes involved in invasion and immune evasion [10–15]. Among these SET domain bearing modifiers, the epigenetic modifier Set8 is known to participate in mitosis and is thought to facilitate the transmission of heterochromatic marks through the cell cycle in higher eukaryotes as well as in the Apicomplexa . In recent work, Sautel et al. (2007) sampled a small set of animal sources and found strong homology to apicomplexan Set8, raising the possibility that this gene was acquired by an ancient apicomplexan ancestor from its eukaryotic host. That study, however, did not explicitly address the likelihood of HGT or, if such an event did transpire, when in the course of apicomplexan evolution it likely occurred.
An extensive examination of SET domain containing proteins (and the corresponding demethylases) found in the P. falciparum genome was reported by Cui et al. . One of these genes displays significant similarity to Set2, a chromatin modifier known to deposit methyl groups during active transcription by RNA polymerase II . This protein is present in primate malaria parasites but conspicuously missing in the closely related rodent parasites. In this work, we provide evidence for horizontal transfer of these methyltransferases. Intriguingly, the proposed transfer events occur on the branch of the phylogenetic tree on which the parasitic lifestyle of apicomplexans appears to have evolved, including the acquisition of cytoadhesion domains and their O-glycosyltransferase modifiers. The acquisition of these various capabilities were essential steps in equipping these organisms to their new host-dependent lifestyles and therefore marks a key transitional event in the evolution to parasitism in this important protozoan lineage.