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DDI1 proteins are conserved in eukaryotes and involved in a variety of cellular processes, including proteasomal degradation of specific proteins and DNA-protein crosslink repair. All DDI1 proteins contain ubiquitin-like (UBL) and retroviral aspartyl protease (RVP) domains, and some also contain ubiquitin-associated (UBA) domain, which mediate distinct activities of these proteins. We investigated the Plasmodium DDI1 to identify its roles during parasite development and potential as a therapeutic target. The DDI1 proteins of Plasmodium and other Apicomplexan parasites vary in domain architecture, share UBL and RVP domains, and the majority of proteins contain the UBA domain. Plasmodium DDI1 is expressed across all major life stages and is essential, as conditional depletion of DDI1 protein in P. berghei and P. falciparum drastically reduced the asexual stage parasite development. Infection of mice with DDI1 knock-down P. berghei parasites was self-limiting and protected from the subsequent infection with both homologous and heterologous parasites, indicating potential of DDI1 knock-down parasites as a whole organism vaccine. P. falciparum DDI1 (PfDDI1) is associated with chromatin and DNA- protein crosslinks, and PfDDI1 knock-down parasites showed increased DNA-protein crosslinks and susceptibility to DNA damaging chemicals, indicating an important role for DDI1 in repair of DNA-protein crosslinks. The knock-down of PfDDI1 increased susceptibility to retroviral protease inhibitors, epoxomicin and artemisinin, which suggests that simultaneous inhibition of DDI1 could potentiate antimalarial activity of these inhibitors or drugs. Hence, the essentiality, ability of DDI1 knock-down parasites to confer protective immunity and increased susceptibility to inhibitors support Plasmodium DDI1 as a dual-target therapeutic candidate.

Malaria is a vector-borne disease. It is caused by Plasmodium parasites. Plasmodium yoelii is a rodent model parasite, primarily used for studying parasite development in liver cells and vectors. To better understand parasite biology, we carried out a high-throughput-based proteomic analysis of P. yoelii. From the same mass spectrometry (MS)/MS data set, we also captured several post-translational modified peptides by following a bioinformatics analysis without any prior enrichment. Further, we carried out a proteogenomic analysis, which resulted in improvements to some of the existing gene models along with the identification of several novel genes. Analysis of proteome and post-translational modifications (PTMs) together resulted in the identification of 3124 proteins. The identified PTMs were found to be enriched in mitochondrial metabolic pathways. Subsequent bioinformatics analysis provided an insight into proteins associated with metabolic regulatory mechanisms. Among these, the tricarboxylic acid (TCA) cycle and the isoprenoid synthesis pathway are found to be essential for parasite survival and drug resistance. The proteogenomic analysis discovered 43 novel protein-coding genes. The availability of an in-depth proteomic landscape of a malaria pathogen model will likely facilitate further molecular-level investigations on pre-erythrocytic stages of malaria.