RAP proteins regulate apicoplast noncoding RNA processing in Plasmodium falciparum

The human malaria parasite, Plasmodium falciparum, contains a non-photosynthetic and essential plastid called the apicoplast. This organelle is of major interest for its unique biology and potential as an attractive drug target. In this study, we characterize PfRAP03 and PfRAP08, two members of the RAP (RNA-binding domain abundant in apicomplexans) protein family. We generate inducible knockdown lines in P. falciparum to validate that both RAP proteins are essential for parasite survival and localize to the apicoplast. Transcriptomic analysis demonstrates that PfRAP03 and PfRAP08 depletion significantly affect apicoplast gene expression. Using enhanced crosslinking immunoprecipitation sequencing (eCLIP-seq) method, we show that apicoplast ribosomal RNAs and transfer RNAs are the targets of PfRAP03 and PfRAP08, respectively. Collectively, our results establish the role of these RAP proteins in controlling apicoplast gene expression in P. falciparum, revealing parasite-specific organellar pathways with biomedical significance.