Elucidation of DNA Repair Function of PfBlm and Potentiation of Artemisinin Action by a Small-Molecule Inhibitor of RecQ Helicase

Plasmodium Topoisomerase VIB and Spo11 Constitute Functional Type IIB Topoisomerase in Malaria Parasite: Its Possible Role in Mitochondrial DNA Segregation

The human malaria parasite undergoes a noncanonical cell division, namely, endoreduplication, where several rounds of nuclear, mitochondrial, and apicoplast replication occur without cytoplasmic division. Despite its importance in Plasmodium biology, the topoisomerases essential for decatenation of replicated chromosome during endoreduplication remain elusive. We hypothesize that the topoisomerase VI complex, containing Plasmodium falciparum topiosomerase VIB (PfTopoVIB) and catalytic P. falciparum Spo11 (PfSpo11), might be involved in the segregation of the Plasmodium mitochondrial genome. Here, we demonstrate that the putative PfSpo11 is the functional ortholog of yeast Spo11 that can complement the sporulation defects of the yeast Δspo11 strain, and the catalytic mutant Pfspo11Y65F cannot complement such defects. PfTopoVIB and PfSpo11 display a distinct expression pattern compared to the other type II topoisomerases of Plasmodium and are induced specifically at the late schizont stage of the parasite, when the mitochondrial genome segregation occurs. Furthermore, PfTopoVIB and PfSpo11 are physically associated with each other at the late schizont stage, and both subunits are localized in the mitochondria. Using PfTopoVIB- and PfSpo11-specific antibodies, we immunoprecipitated the chromatin of tightly synchronous early, mid-, and late schizont stage-specific parasites and found that both the subunits are associated with the mitochondrial genome during the late schizont stage of the parasite. Furthermore, PfTopoVIB inhibitor radicicol and atovaquone show synergistic interaction. Accordingly, atovaquone-mediated disruption of mitochondrial membrane potential reduces the import and recruitment of both subunits of PfTopoVI to mitochondrial DNA (mtDNA) in a dose-dependent manner. The structural differences between PfTopoVIB and human TopoVIB-like protein could be exploited for development of a novel antimalarial agent. IMPORTANCE This study demonstrates a likely role of topoisomerase VI in the mitochondrial genome segregation of Plasmodium falciparum during endoreduplication. We show that PfTopoVIB and PfSpo11 remain associated and form the functional holoenzyme within the parasite. The spatiotemporal expression of both subunits of PfTopoVI correlates well with their recruitment to the mitochondrial DNA at the late schizont stage of the parasite. Additionally, the synergistic interaction between PfTopoVI inhibitor and the disruptor of mitochondrial membrane potential, atovaquone, supports that topoisomerase VI is the mitochondrial topoisomerase of the malaria parasite. We propose that topoisomerase VI may act as a novel target against malaria.

Heat Shock Protein 90 Regulates the Activity of Histone Deacetylase Sir2 in Plasmodium falciparum

Sir2 protein of Plasmodium falciparum has been implicated to play crucial roles in the silencing of subtelomeric var genes and rRNA. It is also involved in telomere length maintenance. Epigenetic regulation of PfSIR2 transcription occurs through a direct participation of the molecular chaperon PfHsp90, wherein PfHsp90 acts as a transcriptional repressor. However, whether the chaperonic activity of PfHsp90 is essential for the maturation and stability of PfSir2A protein has not yet been explored. Here, we show that PfSir2A protein is a direct client of PfHsp90. We demonstrate that PfHsp90 physically interacts with PfSir2A, and the inhibition of PfHsp90 activity via chemical inhibitors, such as 17-AAG or Radicicol, results in the depletion of PfSir2A protein, and consequently its histone deacetylase activity. Thus, derepression of var genes and ribosomal silencing were observed under PfHsp90 inactivation. This finding that PfHsp90 provides stability to PfSir2A protein, in addition to the previous finding that PfHsp90 downregulates PfSIR2A transcription and subsequently cellular abundance, uncovers the multifaceted roles of PfHsp90 in regulating PfSir2 abundance and activity. Given the importance of PfSir2 protein in Plasmodium biology, it is reasonable to propose that the PfHsp90-PfSir2 axis can be exploited as a novel druggable target.

IMPORTANCE Malaria continues to severely impact the global public health not only due to the mortality and morbidity associated with it, but also because of the huge burden on the world economy it imparts. Despite the intensive vaccine-research and drug-development programs, there is not a single effective vaccine suitable for all age groups, and there is no drug on the market against which resistance is not developed. Thus, there is an urgent need to develop novel intervention strategies by identifying the crucial targets from Plasmodium biology. Here, we uncover that the molecular chaperone PfHsp90 regulates the abundance and activity of the histone-deacetylase PfSir2, a prominent regulator of Plasmodium epigenome. Given that PfSir2 controls both virulence and multiplicity of the parasite, and that PfHsp90 is an essential chaperone involved in diverse cellular processes, our findings argue that the PfHsp90-PfSir2 axis could be targeted to curb malaria.

Bloom Helicase Along with Recombinase Rad51 Repairs the Mitochondrial Genome of the Malaria Parasite

The homologous recombination (HR) pathway has been implicated as the predominant mechanism for the repair of chromosomal DNA double-strand breaks (DSBs) of the malarial parasite. Although the extrachromosomal mitochondrial genome of this parasite experiences a greater number of DSBs due to its close proximity to the electron transport chain, nothing is known about the proteins involved in the repair of the mitochondrial genome. We investigated the involvement of nucleus-encoded HR proteins in the repair of the mitochondrial genome, as this genome does not code for any DNA repair proteins. Here, we provide evidence that the nucleus-encoded "recombinosome" of the parasite is also involved in mitochondrial genome repair. First, two crucial HR proteins, namely, Plasmodium falciparum Rad51 (PfRad51) and P. falciparum Bloom helicase (PfBlm) are located in the mitochondria. They are recruited to the mitochondrial genome at the schizont stage, a stage that is prone to DSBs due to exposure to various endogenous and physiologic DNA-damaging agents. Second, the recruitment of these two proteins to the damaged mitochondrial genome coincides with the DNA repair kinetics. Moreover, both the proteins exit the mitochondrial DNA (mtDNA) once the genome is repaired. Most importantly, the specific chemical inhibitors of PfRad51 and PfBlm block the repair of UV-induced DSBs of the mitochondrial genome. Additionally, overexpression of these two proteins resulted in a kinetically faster repair. Given the essentiality of the mitochondrial genome, blocking its repair by inhibiting the HR pathway could offer a novel strategy for curbing malaria. IMPORTANCE The impact of malaria on global public health and the world economy continues to surge despite decades of vaccine research and drug development efforts. An alarming rise in resistance toward all the commercially available antimalarial drugs and the lack of an effective malaria vaccine brings us to the urge to identify novel intervention strategies for curbing malaria. Here, we uncover the molecular mechanism behind the repair of the most deleterious form of DNA lesions on the parasitic mitochondrial genome. Given that the single-copy mitochondrion is an indispensable organelle of the malaria parasite, we propose that targeting the mitochondrial DNA repair pathways should be exploited as a potential malaria control strategy. The establishment of the parasitic homologous recombination machinery as the predominant repair mechanism of the mitochondrial DNA double-strand breaks underscores the importance of this pathway as a novel druggable target.

Synergistic Action between PfHsp90 Inhibitor and PfRad51 Inhibitor Induces Elevated DNA Damage Sensitivity in the Malaria Parasite

The DNA recombinase Rad51 from the human malaria parasite Plasmodium falciparum has emerged as a potential drug target due to its central role in the homologous recombination (HR)-mediated double-strand break (DSB) repair pathway. Inhibition of the ATPase and strand exchange activity of P. falciparum Rad51 (PfRad51) by a small-molecule inhibitor, B02 [3-(phenylmethyl)-2-[(1E)-2-(3-pyridinyl)ethenyl]-4(3H)-quinazolinone], renders the parasite more sensitive to genotoxic agents. Here, we investigated whether the inhibition of the molecular chaperone PfHsp90 potentiates the antimalarial action of B02. We found that the PfHsp90 inhibitor 17-AAG [17-(allylamino)-17-demethoxygeldanamycin] exhibits strong synergism with B02 in both drug-sensitive (strain 3D7) and multidrug-resistant (strain Dd2) P. falciparum parasites. 17-AAG causes a greater than 200-fold decrease in the half-maximal inhibitory concentration (IC50) of B02 in 3D7 parasites. Our results provide mechanistic insights into such profound synergism between 17-AAG and B02. We report that PfHsp90 physically interacts with PfRad51 and promotes the UV irradiation-induced DNA repair activity of PfRad51 by controlling its stability. We find that 17-AAG reduces PfRad51 protein levels by accelerating proteasomal degradation. Consequently, PfHsp90 inhibition renders the parasites more susceptible to the potent DNA-damaging agent methyl methanesulfonate (MMS) in a dose-dependent manner. Thus, our study provides a rationale for targeting PfHsp90 along with the recombinase PfRad51 for controlling malaria propagation.

Integration of population and functional genomics to understand mechanisms of artemisinin resistance in Plasmodium falciparum

Resistance to antimalarial drugs, and in particular to the artemisinin derivatives and their partner drugs, threatens recent progress toward regional malaria elimination and eventual global malaria eradication. Population-level studies utilizing whole-genome sequencing approaches have facilitated the identification of regions of the parasite genome associated with both clinical and in vitro drug-resistance phenotypes. However, the biological relevance of genes identified in these analyses and the establishment of a causal relationship between genotype and phenotype requires functional characterization. Here we examined data from population genomic and transcriptomic studies in the context of data generated from recent functional studies, using a new population genetic approach designed to identify potential favored mutations within the region of a selective sweep (iSAFE). We identified several genes functioning in pathways now known to be associated with artemisinin resistance that were supported in early population genomic studies, as well as potential new drug targets/pathways for further validation and consideration for treatment of artemisinin-resistant Plasmodium falciparum. In addition, we establish the utility of iSAFE in identifying positively-selected mutations in population genomic studies, potentially accelerating the time to functional validation of candidate genes.