Epigenetic Regulation of Multigene Families Mediates Virulence in Plasmodium falciparum Malaria

The clinical symptoms of malaria are caused by the asexual replication of Plasmodium parasites within host erythrocytes. The virulence of P. falciparum can be attributed to its relatively unrestricted ability to invade host erythrocytes and to the cytoadherence of mature parasites within host capillaries. Both of these virulence processes are mediated by selective expression within multigene families. These unique expression patterns are best explained by epigenetic phenomena. This work represents a multi-faceted study of epigenetic regulation of virulence genes in Plasmodium falciparum. We study in detail the regulatory scheme that allows PfRh4, a member of a variantly expressed invasion gene family, to alternate between heritable active and silent states. We find that, in addition to localized changes in associated histone modifications, the silencing of PfRh4 involves the relocalization of the gene from an active to a repressive zone in the nuclear periphery. By placing a drug-selectable marker within the PfRh4 locus, we further demonstrate that PfRh4 regulation involves distinct sequence- and position-dependent mechanisms. We have also adapted a bacterial Dam methylase as a tool to assay in vivo chromatin accessibility in P. falciparum, and used it to demonstrate the facultative nature of heterochromatin at the PfRh4 locus. Our study extends to the chromatin-associated proteins that propagate and maintain epigenetic signals. We categorize two putative histone deacetylase proteins as class II HDACs by their strong homologies to yeast Hda1. We deem them PfHda1 and PfHda2. PfHda2 is of special interest because it localizes to the nuclear periphery and is expressed during the replicative stages of the asexual lifecycle. An inducible knockdown of this seemingly essential protein links it to the regulation of both the var and EBA families of virulence genes. in vitro parasite growth also relies on PfHda2 for efficient progression. In total, we demonstrate that the invasion gene PfRh4 shares a fundamental regulatory scheme with the var family of cytoadherence-linked genes, and at the same time, that vars share PfHda2-dependent mechanisms of regulation with a different invasion gene family, the EBAs. Though biologically distinct, the regulation of invasion- and cytoadherence-associated genes is not as different as previously thought.