Identification and phylogenetic analysis of RNA binding domain abundant in apicomplexans or RAP proteins

Identification of domains in Plasmodium falciparum proteins of unknown function using DALI search on AlphaFold predictions

Plasmodium falciparum, the causative agent of malaria, poses a significant global health challenge, yet much of its biology remains elusive. A third of the genes in the P. falciparum genome lack annotations regarding their function, impeding our understanding of the parasite's biology. In this study, we employ structure predictions and the DALI search algorithm to analyse proteins encoded by uncharacterized genes in the reference strain 3D7 of P. falciparum. By comparing AlphaFold predictions to experimentally determined protein structures in the Protein Data Bank, we found similarities to known domains in 353 proteins of unknown function, shedding light on their potential functions. The lowest-scoring 5% of similarities were additionally validated using the size-independent TM-align algorithm, confirming the detected similarities in 88% of the cases. Notably, in over 70 P. falciparum proteins the presence of domains resembling heptatricopeptide repeats, which are typically involvement in RNA binding and processing, was detected. This suggests this family, which is important in transcription in mitochondria and apicoplasts, is much larger in Plasmodium parasites than previously thought. The results of this domain search provide a resource to the malaria research community that is expected to inform and enable experimental studies.

How RNases Shape Mitochondrial Transcriptomes

Mitochondria are the power houses of eukaryote cells. These endosymbiotic organelles of prokaryote origin are considered as semi-autonomous since they have retained a genome and fully functional gene expression mechanisms. These pathways are particularly interesting because they combine features inherited from the bacterial ancestor of mitochondria with characteristics that appeared during eukaryote evolution. RNA biology is thus particularly diverse in mitochondria. It involves an unexpectedly vast array of factors, some of which being universal to all mitochondria and others being specific from specific eukaryote clades. Among them, ribonucleases are particularly prominent. They play pivotal functions such as the maturation of transcript ends, RNA degradation and surveillance functions that are required to attain the pool of mature RNAs required to synthesize essential mitochondrial proteins such as respiratory chain proteins. Beyond these functions, mitochondrial ribonucleases are also involved in the maintenance and replication of mitochondrial DNA, and even possibly in the biogenesis of mitochondrial ribosomes. The diversity of mitochondrial RNases is reviewed here, showing for instance how in some cases a bacterial-type enzyme was kept in some eukaryotes, while in other clades, eukaryote specific enzymes were recruited for the same function.

Functional genomics of RAP proteins and their role in mitoribosome regulation in Plasmodium falciparum

The RAP (RNA-binding domain abundant in Apicomplexans) protein family has been identified in various organisms. Despite expansion of this protein family in apicomplexan parasites, their main biological functions remain unknown. In this study, we use inducible knockdown studies in the human malaria parasite, Plasmodium falciparum, to show that two RAP proteins, PF3D7_0105200 (PfRAP01) and PF3D7_1470600 (PfRAP21), are essential for parasite survival and localize to the mitochondrion. Using transcriptomics, metabolomics, and proteomics profiling experiments, we further demonstrate that these RAP proteins are involved in mitochondrial RNA metabolism. Using high-throughput sequencing of RNA isolated by crosslinking immunoprecipitation (eCLIP-seq), we validate that PfRAP01 and PfRAP21 are true RNA-binding proteins and interact specifically with mitochondrial rRNAs. Finally, mitochondrial enrichment experiments followed by deep sequencing of small RNAs demonstrate that PfRAP21 controls mitochondrial rRNA expression. Collectively, our results establish the role of these RAP proteins in mitoribosome activity and contribute to further understanding this protein family in malaria parasites.

Pas de Trois: An Overview of Penta-, Tetra-, and Octo-Tricopeptide Repeat Proteins From Chlamydomonas reinhardtii and Their Role in Chloroplast Gene Expression

Penta-, Tetra-, and Octo-tricopeptide repeat (PPR, TPR, and OPR) proteins are nucleus-encoded proteins composed of tandem repeats of 35, 34, and 38-40 amino acids, respectively. They form helix-turn-helix structures that interact with mRNA or other proteins and participate in RNA stabilization, processing, maturation, and act as translation enhancers of chloroplast and mitochondrial mRNAs. These helical repeat proteins are unevenly present in plants and algae. While PPR proteins are more abundant in plants than in algae, OPR proteins are more abundant in algae. In Arabidopsis, maize, and rice there have been 450, 661, and 477 PPR proteins identified, respectively, which contrasts with only 14 PPR proteins identified in Chlamydomonas reinhardtii. Likewise, more than 120 OPR proteins members have been predicted from the nuclear genome of C. reinhardtii and only one has been identified in Arabidopsis thaliana. Due to their abundance in land plants, PPR proteins have been largely characterized making it possible to elucidate their RNA-binding code. This has even allowed researchers to generate engineered PPR proteins with defined affinity to a particular target, which has served as the basis to develop tools for gene expression in biotechnological applications. However, fine elucidation of the helical repeat proteins code in Chlamydomonas is a pending task. In this review, we summarize the current knowledge on the role PPR, TPR, and OPR proteins play in chloroplast gene expression in the green algae C. reinhardtii, pointing to relevant similarities and differences with their counterparts in plants. We also recapitulate on how these proteins have been engineered and shown to serve as mRNA regulatory factors for biotechnological applications in plants and how this could be used as a starting point for applications in algae.