Evolution of transcriptional regulation and epigenetic machinery in malaria parasites

The acquisition of additional transcriptional regulatory units and epigenetic machinery facilitated the transition of ancestral apicomplexans to parasitic life cycles. The C-terminal domain (CTD) of the enzyme RNA polymerase 11 is responsible for integrating the diverse events of gene expression in eukaryotes and is indispensable for life in yeast, fruit flies and mice. The CTD is comprised of tandemly repeated Y1-S2-P3-T4-S 5-P6-S7 amino acid heptads that are highly conserved across evolutionary lineages, with all mammalian polymerases featuring 52 identical heptad repeats. We show that malaria parasites display an unprecedented plasticity within the length and composition of their CTDs. The CTD in malaria parasites that infect human and non-human primates has expanded compared to closely related parasite species that infect rodents or birds. Based on a recent report suggesting rodent parasites lack epigenetic memory at virulence genes, we hypothesized that the expanded CTD in primate parasites permitted the binding of novel primate parasite-specific transcription factors to facilitate epigenetic memory. A comparative screen of three primate and three rodent parasite genomes indicated the presence a complementary pair of histone modifiers specific to primate parasites (PfSet2, a dominant H3K36 methylase and Pflmj1, a H3K36 demethylase). Consistent with our hypothesis, in higher eukaryotes Set2 orthologs are known to bind phosphorylated CTD, deposit chromatin marks only in the process of active transcription by RNA polymerase II and bind non-coding RNA, suggesting a primary role in the maintenance of epigenetic memory. We provide with the first conclusive identification of the H3K36-triMe modification in P. falciparum across the parasite life cycle. The evolutionary history of PfSet2 and PfJmjC1, and a H4K20 methyltransferase (PfSet8) proteins and their relation to the expansion of the RNA polymerase II CTD in the genus Plasmodium is discussed. We provide the first conclusive evidence of a horizontal gene transfer of Set8 from animal hosts to the ancestral apicomplexan. This work should provide new insights on the nexus of evolutionary history of transcription units in basal eukaryotes.