Transcriptional changes in Plasmodium falciparum upon conditional knock down of mitochondrial ribosomal proteins RSM22 and L23

The mitochondrion of malaria parasites is an attractive antimalarial drug target, which require mitoribosomes to translate genes encoded in the mitochondrial (mt) DNA. Plasmodium mitoribosomes are composed of highly fragmented ribosomal RNA (rRNA) encoded in the mtDNA. All mitoribosomal proteins (MRPs) and other assembly factors are encoded in the nuclear genome. Here, we have studied one small subunit (SSU) MRP, RSM22 (Pf3D7_1027200) and one large subunit (LSU) MRP, L23 (Pf3D7_1239100) in Plasmodium falciparum. We show that both proteins localize to the mitochondrion and are essential for parasite survival. However, the parasites survive conditional knock down (KD) of PfRSM22 for two days longer than PfMRPL23 KD. RNA sequencing revealed transcriptomic changes of the nuclear and mitochondrial genomes upon KD of these MRPs. In the early phase following KD, while most mt rRNAs and transcripts of putative MRPs were downregulated in the absence of PfRSM22, several mt rRNAs and MRPs were upregulated after KD of PfMRPL23. At the late time points of KD, loss of PfRSM22 and PfMRPL23 caused defects in many essential metabolic pathways, leading to parasite death. There was a significant overlap among the mitochondrial related transcripts downregulated in the late phase of PfRSM22 and PfMRPL23 KDs. We have also identified a list of mitochondrial proteins of unknown function that are likely Plasmodium MRPs based on their structural similarity to known MRPs as well as their expression profiles in KD parasites.