Single-target high-throughput transcription analyses reveal high levels of alternative splicing present in the FPPS/GGPPS from Plasmodium falciparum

Antimalarial drug discovery: progress and approaches

Recent antimalarial drug discovery has been a race to produce new medicines that overcome emerging drug resistance, whilst considering safety and improving dosing convenience. Discovery efforts have yielded a variety of new molecules, many with novel modes of action, and the most advanced are in late-stage clinical development. These discoveries have led to a deeper understanding of how antimalarial drugs act, the identification of a new generation of drug targets, and multiple structure-based chemistry initiatives. The limited pool of funding means it is vital to prioritize new drug candidates. They should exhibit high potency, a low propensity for resistance, a pharmacokinetic profile that favours infrequent dosing, low cost, preclinical results that demonstrate safety and tolerability in women and infants, and preferably the ability to block Plasmodium transmission to Anopheles mosquito vectors. In this Review, we describe the approaches that have been successful, progress in preclinical and clinical development, and existing challenges. We illustrate how antimalarial drug discovery can serve as a model for drug discovery in diseases of poverty.

CmWRKY41 activates CmHMGR2 and CmFPPS2 to positively regulate sesquiterpenes synthesis in Chrysanthemum morifolium

Chrysanthemum morifolium is one of the most significant multipurpose crops with ornamental, medicinal, and edible value. Terpenoids, an essentials component of volatile oils, are abundant in chrysanthemum. However, the transcriptional regulation of terpenoid biosynthesis in chrysanthemums remains unclear. In the present investigation, we identified CmWRKY41, whose expression pattern is similar to that of terpenoid content in chrysanthemum floral scent, as a candidate gene that may promote terpenoid biosynthesis in chrysanthemum. Two structural genes 3-hydroxy-3-methylglutaryl-CoA reductase 2 (CmHMGR2) and farnesyl pyrophosphate synthase 2 (CmFPPS2), play key role in terpene biosynthesis in chrysanthemum. CmWRKY41 can directly bind to the promoters of CmHMGR2 or CmFPPS2 through GTGACA or CTGACG elements and activate its expression to promote sesquiterpene biosynthesis. In summary, these results indicate that CmWRKY41 targets CmHMGR2 and CmFPPS2 to positively regulate sesquiterpene biosynthesis in chrysanthemums. This study preliminarily revealed the molecular mechanism of terpenoid biosynthesis in chrysanthemum while enriching the secondary metabolism regulatory network.

CRISPR-Cas13 in malaria parasite: Diagnosis and prospective gene function identification

Malaria caused by Plasmodium is still a serious public health problem. Genomic editing is essential to understand parasite biology, elucidate mechanical pathways, uncover gene functions, identify novel therapeutic targets, and develop clinical diagnostic tools. Recent advances have seen the development of genomic diagnostic technologies and the emergence of genetic manipulation toolbox comprising a host of several systems for editing the genome of Plasmodium at the DNA, RNA, and protein level. Genomic manipulation at the RNA level is critical as it allows for the functional characterization of several transcripts. Of notice, some developed artificial RNA genome editing tools hinge on the endogenous RNA interference system of Plasmodium. However, Plasmodium lacks a robust RNAi machinery, hampering the progress of these editing tools. CRISPR-Cas13, which belongs to the VI type of the CRISPR system, can specifically bind and cut RNA under the guidance of crRNA, with no or minimal permanent genetic scar on genes. This review summarizes CRISPR-Cas13 system from its discovery, classification, principle of action, and diagnostic platforms. Further, it discusses the application prospects of Cas13-based systems in Plasmodium and highlights its advantages and drawbacks.

Pervasive sequence-level variation in the transcriptome of Plasmodium falciparum

Single-nucleotide variations (SNVs) in RNA, arising from co- and post-transcriptional phenomena including transcription errors and RNA-editing, are well studied in a range of organisms. In the malaria parasite Plasmodium falciparum, stage-specific and non-specific gene-expression variations accompany the parasite's array of developmental and morphological phenotypes over the course of its complex life cycle. However, the extent, rate and effect of sequence-level variation in the parasite's transcriptome are unknown. Here, we report the presence of pervasive, non-specific SNVs in the P. falciparum transcriptome. SNV rates for a gene were correlated to gene length (r[Formula: see text]0.65-0.7) but not to the AT-content of that gene. Global SNV rates for the P. falciparum lines we used, and for publicly available P. vivax and P. falciparum clinical isolate datasets, were of the order of 10-3 per base, ∼10× higher than rates we calculated for bacterial datasets. These variations may reflect an intrinsic transcriptional error rate in the parasite, and RNA editing may be responsible for a subset of them. This seemingly characteristic property of the parasite may have implications for clinical outcomes and the basic biology and evolution of P. falciparum and parasite biology more broadly. We anticipate that our study will prompt further investigations into the exact sources, consequences and possible adaptive roles of these SNVs.

Critical role for isoprenoids in apicoplast biogenesis by malaria parasites

Isopentenyl pyrophosphate (IPP) is an essential metabolic output of the apicoplast organelle in Plasmodium falciparum malaria parasites and is required for prenylation-dependent vesicular trafficking and other cellular processes. We have elucidated a critical and previously uncharacterized role for IPP in apicoplast biogenesis. Inhibiting IPP synthesis blocks apicoplast elongation and inheritance by daughter merozoites, and apicoplast biogenesis is rescued by exogenous IPP and polyprenols. Knockout of the only known isoprenoid-dependent apicoplast pathway, tRNA prenylation by MiaA, has no effect on blood-stage parasites and thus cannot explain apicoplast reliance on IPP. However, we have localized an annotated polyprenyl synthase (PPS) to the apicoplast. PPS knockdown is lethal to parasites, rescued by IPP and long- (C₅₀) but not short-chain (≤C₂₀) prenyl alcohols, and blocks apicoplast biogenesis, thus explaining apicoplast dependence on isoprenoid synthesis. We hypothesize that PPS synthesizes long-chain polyprenols critical for apicoplast membrane fluidity and biogenesis. This work critically expands the paradigm for isoprenoid utilization in malaria parasites and identifies a novel essential branch of apicoplast metabolism suitable for therapeutic targeting.

Contribution of Transcriptome to Elucidate the Biology of Plasmodium spp

In the present review, we discuss some of the new technologies that have been applied to elucidate how Plasmodium spp escape from the immune system and subvert the host physiology to orchestrate the regulation of its biological pathways. Our manuscript describes how techniques such as microarray approaches, RNA-Seq and single-cell RNA sequencing have contributed to the discovery of transcripts and changed the concept of gene expression regulation in closely related malaria parasite species. Moreover, the text highlights the contributions of high-throughput RNA sequencing for the current knowledge of malaria parasite biology, physiology, vaccine target and the revelation of new players in parasite signaling.

MalDA, Accelerating Malaria Drug Discovery

The Malaria Drug Accelerator (MalDA) is a consortium of 15 leading scientific laboratories. The aim of MalDA is to improve and accelerate the early antimalarial drug discovery process by identifying new, essential, druggable targets. In addition, it seeks to produce early lead inhibitors that may be advanced into drug candidates suitable for preclinical development and subsequent clinical testing in humans. By sharing resources, including expertise, knowledge, materials, and reagents, the consortium strives to eliminate the structural barriers often encountered in the drug discovery process. Here we discuss the mission of the consortium and its scientific achievements, including the identification of new chemically and biologically validated targets, as well as future scientific directions.

Species diversity and genome evolution of the pathogenic protozoan parasite, Neospora caninum

Neospora caninum is a cyst-forming coccidian parasite of veterinary and economical significance, affecting dairy and beef cattle industries on a global scale. Comparative studies suggest that N. caninum consists of a globally dispersed, diverse population of lineages, distinguished by their geographical origin, broad host range, and phenotypic features. This viewpoint is however changing. While intraspecies diversity, and more specifically pathogenic variability, has been experimentally demonstrated in a myriad of studies, the underlying contributors and sources responsible for such diversity have remained nebulous. However, recent large-scale sequence and bioinformatics studies have aided in revealing intrinsic genetic differences distinguishing isolates of this species, that await further characterisation as causative links to virulence and pathogenicity. Furthermore, progress on N. caninum research as a non-model organism is hindered by a lack of robust, annotated genomic, transcriptomic, and proteomic data for the species, especially compared to other thoroughly studied Apicomplexa such as Toxoplasma gondii and Plasmodium species. This review explores the current body of knowledge on intra-species diversity within N. caninum. This includes the contribution of sequence variants in both coding and non-coding regions, the presence of genome polymorphic hotspots, and the identification of non-synonymous mutations. The implications of such diversity on important parasite phenotypes such as pathogenicity and population structure are also discussed. Lastly, the identification of potential virulence factors from both in-silico and next generation sequencing studies is examined, offering new insights into potential avenues for future research on neosporosis.

Contribution of introns to the species diversity associated with the apicomplexan parasite, Neospora caninum

Neospora caninum is an intracellular parasite considered a leading cause of bovine reproduction failure worldwide, and a serious neurological disease of canines. Transplacental transmission in intermediate hosts is considered the most efficient means of transmission, which strictly involves asexual reproduction. Nonetheless, extensive genetic diversity has been reported within the species. What is yet to be elucidated are the major drivers of such diversity, and their impact on important parasite phenotypes such as virulence. Instead of protein-encoding sequences, genome and transcriptome data were used to investigate SNPs in introns between two distinct N. caninum isolates, with reported differences in pathogenicity. Variant analysis identified 840 and 501 SNPs within intergenic regions and introns, respectively, distinctly concentrated on chromosomes VI and XI, whereas the rest of the genome was monomorphic in comparison. Gene ontologies for SNP-dense intron-containing genes included ATP binding, transmembrane transport, protein kinase activity, and transcription and translation processes. This study shows that variation in non-coding DNA is contributing to N. caninum intraspecies genetic diversity, and potentially influencing and contributing to important parasite mechanisms. Finally, we present an assembled and annotated N. caninum apicoplast genome and show that this essential organelle is highly conserved between the two isolates, and related Coccidia.