Integrative proteomics and bioinformatic prediction enable a high-confidence apicoplast proteome in malaria parasites

Abstract

Malaria parasites (Plasmodium spp.) and related apicomplexan pathogens contain a nonphotosynthetic plastid called the apicoplast. Derived from an unusual secondary eukaryote–eukaryote endosymbiosis, the apicoplast is a fascinating organelle whose function and biogenesis rely on a complex amalgamation of bacterial and algal pathways. Because these pathways are distinct from the human host, the apicoplast is an excellent source of novel antimalarial targets. Despite its biomedical importance and evolutionary significance, the absence of a reliable apicoplast proteome has limited most studies to the handful of pathways identified by homology to bacteria or primary chloroplasts, precluding our ability to study the most novel apicoplast pathways. Here, we combine proximity biotinylation-based proteomics (BioID) and a new machine learning algorithm to generate a high-confidence apicoplast proteome consisting of 346 proteins. Critically, the high accuracy of this proteome significantly outperforms previous prediction-based methods and extends beyond other BioID studies of unique parasite compartments. Half of identified proteins have unknown function, and 77% are predicted to be important for normal blood-stage growth. We validate the apicoplast localization of a subset of novel proteins and show that an ATP-binding cassette protein ABCF1 is essential for blood-stage survival and plays a previously unknown role in apicoplast biogenesis. These findings indicate critical organellar functions for newly discovered apicoplast proteins. The apicoplast proteome will be an important resource for elucidating unique pathways derived from secondary endosymbiosis and prioritizing antimalarial drug targets.

Plasmodium falciparum Apn1 homolog is a mitochondrial base excision repair protein with restricted enzymatic functions

“…Interestingly, there is only one DNA ligase in the entire P. falciparum genome. Pf DNA‐ligase 1 has been functionally characterized , has a positive prediction for apicoplast targeting and is detected in the apicoplast proteome .…”

Protein ubiquitylation is essential for the schizont to merozoite transition in Plasmodium falciparum blood-stage development

“…In contrast, only five of the exported proteins ubiquitylated only in merozoites contain a PEXEL/HT motif, but 25 of them have a signal peptide. It is possible that this group includes proteins targeted to the apicoplast [44], which has its own ubiquitylation machinery [9], although most of the proteins are not present in the recently described apicoplast proteome [45]. The three exported proteins detected as ubiquitylated only in rings are likely inserted by the invading parasite (but they were not detected in the merozoite ubiquitome).…”

Lipoic acid biosynthesis is essential forPlasmodium falciparumtransmission and influences redox response and carbon metabolism of parasite asexual blood stages

“…The Plasmodium orthologue of ATrx2 ( Pf ATrx2; PF3D7_0529100) is likely essential too (Bushell et al, 2017; Zhang et al, 2018). Many other potential redox-active proteins are predicted to be localised in the apicoplast (Boucher et al, 2018), but their roles are uncharacterized.…”