Cathepsin C-like protease regulates DNA replication by histone H3 N-terminal clipping in malaria parasites

Post-translational modifications (PTMs) of histone N-terminal tails are key regulators of gene expression in the human malaria parasite Plasmodium falciparum. Here, we identify developmentally controlled proteolytic clipping of the N-terminus of histone H3 at amino acid position 21 by a cathepsin C-type protease termed dipeptidyl aminopeptidase 2 (PfDPAP2) as a new PTM in intra-erythrocytic parasite stages. Conditionally knocked down PfDPAP2 abrogated histone H3 clipping and blocked intra-erythrocytic parasite DNA replication. Correspondingly, genome-wide occupancy of clipped histone H3 identified the upstream regions of several DNA replication genes as targets of the protease. Because episomally expressed clipped histone H3 showed nucleosomal incorporation at similar genomic loci as the endogenous clipped protein, this points to a novel type of nucleosome replacement mechanism in P. falciparum. The discovery of an unprecedented protease-mediated, epigenetic control mechanism of DNA replication makes PfDPAP2 a promising therapeutic target to develop anti-malarials.

组蛋白N端尾的翻译后修饰（post-translational modifications, PTMs）是人类疟疾寄生虫恶性疟原虫（Plasmodium falciparum）基因表达的关键调控因子。本研究鉴定出：由一种被命名为二肽基氨基肽酶2（PfDPAP2）的组织蛋白酶C型蛋白酶，在氨基酸位点21处对组蛋白H3的N端进行发育调控的蛋白水解剪切，这是红细胞内期疟原虫阶段的一种新型翻译后修饰。条件性敲低PfDPAP2可消除组蛋白H3的剪切过程，并阻断红细胞内期疟原虫的DNA复制。相应地，对剪切型组蛋白H3的全基因组占据分析显示，多个DNA复制基因的上游区域为该蛋白酶的作用靶点。由于游离表达的剪切型组蛋白H3可在内源剪切型蛋白的相似基因组位点上发生核小体整合，这提示恶性疟原虫中存在一种新型核小体替换机制。此次发现的这种前所未有的、由蛋白酶介导的DNA复制表观遗传调控机制，使得PfDPAP2成为开发抗疟疾药物的极具潜力的治疗靶点。