ORCID Profile
0000-0003-0114-7808
Current Organisation
University of Melbourne
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Research Topics
In Research Link Australia (RLA), "Research Topics" refer to ANZSRC FOR and SEO codes. These topics are either sourced from ANZSRC FOR and SEO codes listed in researchers' related grants or generated by a large language model (LLM) based on their publications.
Top 5 Research Topics
ANZSRC Field of Research (FoR)
Biochemistry and Cell Biology | Genetics | Medical Parasitology | Medical Parasitology | Genetics | Structural Biology (incl. Macromolecular Modelling) | Microbiology not elsewhere classified | Cellular Interactions (incl. Adhesion, Matrix, Cell Wall) | Gene Expression (incl. Microarray and other genome-wide approaches) | Genomics | Medical Microbiology | Cell Metabolism | Gene Expression | Genome Structure | Host-parasite interactions | Gene expression (incl. microarray and other genome-wide approaches) | Genomics and transcriptomics | Analytical Biochemistry | Cell Metabolism |
ANZSRC Socio-Economic Objective (SEO)
Expanding Knowledge in the Biological Sciences | Infectious diseases | Control of Animal Pests, Diseases and Exotic Species in Farmland, Arable Cropland and Permanent Cropland Environments | Preventive Medicine | Expanding Knowledge in the Medical and Health Sciences | Teaching and Instruction Technologies | Treatments (e.g. chemicals, antibiotics) | Expanding Knowledge in the Mathematical Sciences | Infectious Diseases | Pacific Peoples Health - Health Status and Outcomes
Related Links
Publications
An integrative bioinformatic predictor of protein sub-cellular localisation in malaria
Publisher: Springer Science and Business Media LLC
Date: 21-11-2011
Differential sub-nuclear localisation of repressive and activating histone methyl modifications in P. falciparum
Publisher: Elsevier BV
Date: 03-2009
DOI: 10.1016/J.MICINF.2008.12.010
Abstract: Post-translational histone modifications and sub-nuclear organization epigenetically influence gene regulation, especially those implicated in antigenic variation of Plasmodium falciparum. Here we screened for histone methylation modifications and determined, for the first time, their spatial nuclear localisation. Differential enrichment in sub-nuclear compartments, suggesting high local concentrations of particular methyl marks was observed. H3-K79me3 particularly, does not co-localise with already defined nuclear compartments, thus apparently defining a compartment not observed previously in other eukaryotes. Our data show the presence of discrete sub-nuclear zones enriched for histone methyl marks, pointing to the existence of specialized transcription factories and repressive regions in Plasmodium.
K13, the Cytostome, and Artemisinin Resistance
Publisher: Elsevier BV
Date: 06-2020
Antibiotic inhibition of the Plasmodium apicoplast decreases haemoglobin degradation and antagonises dihydroartemisinin action
Publisher: Cold Spring Harbor Laboratory
Date: 11-2021
DOI: 10.1101/2021.10.31.466372
Abstract: The World Health Organisation (WHO) recommends artemisinin (ART) combinations for treatment of uncomplicated Plasmodium falciparum malaria. Understanding the interaction between co-administered drugs within combination therapies is clinically important to prevent unintended consequences. The WHO guidelines recommend second line treatments that combine artesunate with tetracycline, doxycycline, or clindamycin—antibiotics that target the Plasmodium relict plastid, the apicoplast. In addition, antibiotics can be used simultaneously against other infectious diseases, leading to their inadvertent combination with ARTs. One consequence of apicoplast inhibition is a perturbation to haemoglobin uptake and trafficking—a pathway required for activation of ART derivatives. Here, we show that apicoplast-targeting antibiotics reduce the abundance of the catalyst of ART activation (free haem) in P. falciparum , likely through diminished haemoglobin digestion. We demonstrate antagonism between ART and these antibiotics, suggesting that apicoplast inhibitors reduce ART activation. These data have potential clinical implications due to the reliance on—and widespread use of—both ARTs and these antibiotics in malaria endemic regions.
The Plasmodium falciparum artemisinin resistance-associated protein Kelch 13 is required for formation of normal cytostomes
Publisher: eLife Sciences Publications, Ltd
Date: 08-08-2023
Abstract: Artemisinin (ART) is a quick-killing and effective antimalarial activated by the haem derived from haemoglobin digestion. Mutations in the parasite’s Kelch 13 (K13) protein compromise the efficacy of this drug. Recent studies indicate an undefined role for K13 in haemoglobin uptake. Here, we show that K13 is associated with the collar that constricts cytostomal invaginations required for the parasite to ingest host cytosol. Induced mislocalisation of K13 led to the formation of atypical invaginations lacking the cytostomal ring and constricted neck normally associated with cytostomes. Moreover, the levels of haemoglobin degradation products, haem and haemozoin, are decreased when K13 is inactivated. Our findings demonstrate that K13 is required for normal formation and/or stabilisation of the cytostome, and thereby the parasite’s uptake of haemoglobin. This is consistent with perturbation of K13 function leading to decreased activation of ART and consequently, reduced killing. Artemisinin-resistant parasites contain mutations in the gene encoding the Kelch 13 protein (K13). How K13 mutations result in artemisinin resistance is unclear. Here, we present evidence that normal K13 is required for the formation of the cytostome, a specialised parasite feeding apparatus used to endocytose host cell haemoglobin. Our results suggest that artemisinin resistance is due to a decrease in artemisinin activation brought about by a decrease in efficiency of haemoglobin uptake and consequently reduced production of haem.
Antigenic variation in Plasmodium falciparum is associated with movement of var loci between subnuclear locations
Publisher: Proceedings of the National Academy of Sciences
Date: 29-03-2005
Abstract: Much of the success of Plasmodium falciparum in establishing persistent infections is attributed to immune evasion through antigenic variation. This process involves periodically exchanging variants of the major surface antigen PfEMP1, a protein also responsible for parasite cytoadherence. PfEMP1 is encoded by genes of the 60-member var family, located at subtelomeric and internal chromosome loci. The active or silenced state of var genes is heritable, and its control by nonsequence information remains puzzling. Using FISH analysis, we demonstrate that both internal and subtelomeric var genes are positioned at the nuclear periphery in their repressed state. Upon activation, the same var genes are still found in the periphery, indicating that this zone can be transcriptionally competent, rather than uniformly silenced. However, activation of a var gene is linked with altered positioning at the nuclear periphery, with subtelomeric var loci exiting chromosome end clusters and being relocated to distinct nuclear sites. Serial sectioning of parasite nuclei reveals areas of both condensed and noncondensed chromatin at the nuclear periphery. Our results demonstrate that regulation of antigenic variation is associated with subnuclear position effects and point to the existence of transcriptionally permissive perinuclear zones for var genes.
3,3'-Disubstituted 5,5'-Bi(1,2,4-triazine) Derivatives with Potent in Vitro and in Vivo Antimalarial Activity.
Publisher: American Chemical Society (ACS)
Date: 04-02-2019
DOI: 10.1021/ACS.JMEDCHEM.8B01799
Abstract: A series of 3,3'-disubstituted 5,5'-bi(1,2,4-triazine) derivatives was synthesized and screened against the erythrocytic stage of Plasmodium falciparum 3D7 line. The most potent dimer, 6k, with an IC
Alternative splicing is required for stage differentiation in malaria parasites.
Publisher: Springer Science and Business Media LLC
Date: 08-2019
Targeting Protein Translation in Organelles of the Apicomplexa
Publisher: Elsevier BV
Date: 12-2016
Abstract: Antibiotics inhibiting protein translation have long been used to treat and prevent infections by apicomplexan parasites. These compounds kill parasites by inhibiting organellar translation, and most act specifically against the apicoplast, a relict plastid in apicomplexans. Drug resistance in Plasmodium and other apicomplexans dictates a need for development of novel targets. Some apicoplast inhibitors have a delayed onset of action, so they cannot replace fast-acting drugs, although they still fulfil important roles in treating and preventing infections. The plethora of bacterial-like actors in the translation machinery of parasite mitochondria and plastids presents validated targets with strong potential for selectivity. Here we discuss existing drugs that inhibit organellar translation, and explore targets that may be further exploited in antiparasitic drug design.
Organellar proteomics reveals hundreds of novel nuclear proteins in the malaria parasite Plasmodium falciparum
Publisher: Springer Science and Business Media LLC
Date: 2012
Dynamin: The endosymbiosis ring of power?
Publisher: Proceedings of the National Academy of Sciences
Date: 25-03-2003
Theileria Apicoplast as a Target for Chemotherapy
Publisher: American Society for Microbiology
Date: 03-2009
DOI: 10.1128/AAC.00126-08
Abstract: Theileria parasites cause severe bovine disease and death in a large part of the world. These apicomplexan parasites possess a relic plastid (apicoplast), whose metabolic pathways include several promising drug targets. Putative inhibitors of these targets were screened, and we identified antiproliferative compounds that merit further characterization.
Determination of protein subcellular localization in apicomplexan parasites
Publisher: Elsevier BV
Date: 12-2012
Abstract: Parasites from the phylum Apicomplexa include causative agents of serious diseases including malaria (Plasmodium spp.) and toxoplasmosis (Toxoplasma gondii). Apicomplexan parasites infect thousands of types of animal cells and send their proteins to an array of compartments within their own cell, as well as exporting proteins into and beyond their host cell. Ascertaining destinations to which in idual proteins are delivered allows researchers to better understand parasite biology and to identify potential targets for therapeutic interventions. Our toolkit for establishing subcellular locations of apicomplexan proteins is becoming more extensive and specialized, and here we review developments in this technology.
ThePlasmodiumrhoptry associated protein complex is important for parasitophorous vacuole membrane structure and intraerythrocytic parasite growth
Publisher: Hindawi Limited
Date: 08-03-2017
DOI: 10.1111/CMI.12733
Abstract: Plasmodium parasites must invade erythrocytes in order to cause the disease malaria. The invasion process involves the coordinated secretion of parasite proteins from apical organelles that include the rhoptries. The rhoptry is comprised of two compartments: the neck and the bulb. Rhoptry neck proteins are involved in host cell adhesion and formation of the tight junction that forms between the invading parasite and erythrocyte, whereas the role of rhoptry bulb proteins remains ill-defined due to the lack of functional studies. In this study, we show that the rhoptry-associated protein (RAP) complex is not required for rhoptry morphology or erythrocyte invasion. Instead, post-invasion when the parasite is bounded by a parasitophorous vacuolar membrane (PVM), the RAP complex facilitates the survival of the parasite in its new intracellular environment. Consequently, conditional knockdown of members of the RAP complex leads to altered PVM structure, delayed intra-erythrocytic growth, and reduced parasitaemias in infected mice. This study provides evidence that rhoptry bulb proteins localising to the parasite-host cell interface are not simply by-products of the invasion process but contribute to the growth of Plasmodium in vivo.
Reticulocyte-binding protein homologue 5 – An essential adhesin involved in invasion of human erythrocytes by Plasmodium falciparum
Publisher: Elsevier BV
Date: 02-2009
DOI: 10.1016/J.IJPARA.2008.10.006
Abstract: Invasion of erythrocytes is a prerequisite in the life history of the malaria parasite. Members of the reticulocyte-binding homologue family (PfRh) have been implicated in the invasion process and in some cases have been shown to act as adhesins, binding to specific receptors on the erythrocyte surface. We have identified a further, putatively essential, PfRh family member in the most virulent human malaria Plasmodium falciparum, called PfRh5, which binds to an unknown class of glycosylated receptors on the erythrocyte surface. This protein is an atypical PfRh family member, being much smaller than others and lacking a transmembrane and cytosolic region at the C-terminus. This suggests it may be part of a functional protein complex. PfRh5 localises to the rhoptries in merozoites and follows the tight junction during the process of erythrocyte invasion. Furthermore, rabbit immune serum raised against a portion of the ecto-domain, inhibits parasite invasion in vitro. We hypothesise an essential role for the PfRh5 adhesin in erythrocyte selection and commitment to invasion. Given its small size, we believe PfRh5 may prove to be a valuable candidate for inclusion in a multi-component anti-malarial vaccine.
TDR Targets: a chemogenomics resource for neglected diseases
Publisher: Oxford University Press (OUP)
Date: 23-11-2011
DOI: 10.1093/NAR/GKR1053
The AAA+ ATPase p97 as a novel parasite and tuberculosis drug target
Publisher: Elsevier BV
Date: 07-2022
Abstract: The multifunctional AAA+ ATPase p97 is an unfoldase/segregase involved in various cellular processes and present in all kingdoms of life. In mammals and yeast, p97 functions upstream of the proteasome. Interestingly, proteasome inhibitors targeting pathogenic microorganisms display efficacy in overcoming drug-resistant strains. Homologues of p97 have been found in disease-causing parasites and mycobacteria. Here, we review the current knowledge on the structure, function, and conservation of p97 in pathogens. We discuss the potential of parasite and mycobacterial p97 as a drug target against these pathogens and explore strategies in designing novel inhibitors. A successful strategy for inhibiting pathogenic p97 should lead to effectively killing the pathogen, minimising toxic and off-target effects, and providing specificity to avoid interfering with human p97.
Comparative transcriptomics of female and male gametocytes in Plasmodium berghei and the evolution of sex in alveolates
Publisher: Springer Science and Business Media LLC
Date: 18-09-2017
An FtsH Protease Is Recruited to the Mitochondrion of Plasmodium falciparum
Publisher: Public Library of Science (PLoS)
Date: 13-09-2013
Chronic arsenic exposure and microbial drug resistance
Publisher: Proceedings of the National Academy of Sciences
Date: 13-11-2013
Direct nanopore sequencing of mRNA reveals landscape of transcript isoforms in apicomplexan parasites
Publisher: Cold Spring Harbor Laboratory
Date: 17-02-2020
DOI: 10.1101/2020.02.16.946699
Abstract: Alternative splicing is a widespread phenomenon in metazoans by which single genes are able to produce multiple isoforms of the gene product. However, this has been poorly characterised in apicomplexans, a major phylum of some of the most important global parasites. Efforts have been h ered by atypical transcriptomic features, such as the high AT content of Plasmodium RNA, but also the limitations of short read sequencing in deciphering complex splicing events. In this study, we utilised the long read direct RNA sequencing platform developed by Oxford Nanopore Technologies (ONT) to survey the alternative splicing landscape of Toxoplasma gondii and Plasmodium falciparum . We find that while native RNA sequencing has a reduced throughput, it allows us to obtain full-length or near full-length transcripts with comparable quantification to Illumina sequencing. By comparing this data with available gene models, we find widespread alternative splicing, particular intron retention, in these parasites. Most of these transcripts contain premature stop codons, suggesting that in these parasites, alternative splicing represents a pathway to transcriptomic ersity, rather than expanding proteomic ersity. Moreover, alternative splicing rates are comparable between parasites, suggesting a shared splicing machinery, despite notable transcriptomic differences between the parasites. This work highlights a strategy in using long read sequencing to understand splicing events at the whole transcript level, and has implications in future interpretation of RNA-seq studies.
ThePlasmodium falciparumartemisinin resistance-associated protein Kelch 13 is required for formation of normal cytostomes
Publisher: Cold Spring Harbor Laboratory
Date: 30-03-2023
DOI: 10.1101/2023.03.30.534478
Abstract: Artemisinin (ART) is a quick-killing and effective antimalarial activated by the haem derived from haemoglobin digestion. Mutations in the parasite’s Kelch 13 (K13) protein compromise the efficacy of this drug. Recent studies indicate an undefined role for K13 in haemoglobin uptake. Here, we show that K13 is associated with the collar that constricts cytostomal invaginations required for the parasite to ingest host cytosol. Induced mislocalisation of K13 led to the formation of atypical invaginations lacking the cytostomal ring and constricted neck normally associated with cytostomes. Moreover, the levels of haemoglobin degradation products, haem and haemozoin, are decreased when K13 is inactivated. Our findings demonstrate that K13 is required for normal formation and/or stabilisation of the cytostome, and thereby the parasite’s uptake of haemoglobin. This is consistent with perturbation of K13 function leading to decreased activation of ART and consequently, reduced killing. Artemisinin-resistant parasites contain mutations in the gene encoding the Kelch 13 protein (K13). How K13 mutations result in artemisinin resistance is unclear. Here, we present evidence that normal K13 is required for the formation of the cytostome, a specialised parasite feeding apparatus used to endocytose host cell haemoglobin. Our results suggest that artemisinin resistance is due to a decrease in artemisinin activation brought about by a decrease in efficiency of haemoglobin uptake and consequently reduced production of haem.
Subcellular multitasking - Multiple destinations and roles for the Plasmodium falcilysin protease
Publisher: Wiley
Date: 21-11-2007
DOI: 10.1111/J.1365-2958.2006.05528.X
Abstract: The Plasmodium falcilysin protease is a M16-family protease that has been previously identified as a food vacuole enzyme that participates in the breakdown of haemoglobin. Plant homologues of this protease are responsible for breaking down transit peptides that have been processed in mitochondria and plastids, and in this issue of Molecular Microbiology, Ponpuak and colleagues show that falcilysin participates in degradation of transit peptides and haemoglobin in discrete subcellular organelles. The recruitment of a gene product from one cellular compartment to another is a recurring phenomenon in molecular evolutionary biology, and arises through a number of distinct mechanisms. Plasmodium accomplishes this triple act by targeting products of the single falcilysin gene to multiple compartments.
Metabolic maps and functions of the Plasmodium falciparum apicoplast
Publisher: Springer Science and Business Media LLC
Date: 03-2004
DOI: 10.1038/NRMICRO843
Is the AT-rich DNA of malaria parasites a drug target?
Publisher: Elsevier BV
Date: 04-2022
DOI: 10.1016/J.TIPS.2022.01.003
Abstract: A recent antimalarial screen by Alder and colleagues has uncovered a natural product, PDE-I
Metabolomics-Based Screening of the Malaria Box Reveals both Novel and Established Mechanisms of Action
Publisher: American Society for Microbiology
Date: 11-2016
DOI: 10.1128/AAC.01226-16
Abstract: High-throughput phenotypic screening of chemical libraries has resulted in the identification of thousands of compounds with potent antimalarial activity, although in most cases, the mechanism(s) of action of these compounds remains unknown. Here we have investigated the mode of action of 90 antimalarial compounds derived from the Malaria Box collection using high-coverage, untargeted metabolomics analysis. Approximately half of the tested compounds induced significant metabolic perturbations in in vitro cultures of Plasmodium falciparum . In most cases, the metabolic profiles were highly correlated with known antimalarials, in particular artemisinin, the 4-aminoquinolines, or atovaquone. Select Malaria Box compounds also induced changes in intermediates in essential metabolic pathways, such as isoprenoid biosynthesis (i.e., 2-C-methyl- d -erythritol 2,4-cyclodiphosphate) and linolenic acid metabolism (i.e., traumatic acid). This study provides a comprehensive database of the metabolic perturbations induced by chemically erse inhibitors and highlights the utility of metabolomics for triaging new lead compounds and defining specific modes of action, which will assist with the development and optimization of new antimalarial drugs.
Sir2 Paralogues Cooperate to Regulate Virulence Genes and Antigenic Variation in Plasmodium falciparum
Publisher: Public Library of Science (PLoS)
Date: 14-04-2009
Functional Characterization of the m 6 A-Dependent Translational Modulator PfYTH.2 in the Human Malaria Parasite
Publisher: American Society for Microbiology
Date: 27-04-2021
Abstract: Infection with the unicellular eukaryotic pathogen Plasmodium falciparum causes malaria, a mosquito-borne disease affecting more than 200 million and killing 400,000 people each year. Underlying the asexual replication within human red blood cells is a tight regulatory network of gene expression and protein synthesis.
Nonsense-mediated decay machinery in Plasmodium falciparum is inefficient and non-essential
Publisher: American Society for Microbiology
Date: 24-08-2023
Abstract: Nonsense-mediated decay (NMD) is a conserved mRNA quality control process that eliminates transcripts bearing a premature termination codon. In addition to its role in removing erroneous transcripts, NMD is involved in post-transcriptional regulation of gene expression via programmed intron retention in metazoans. The apicomplexan parasite Plasmodium falciparum shows relatively high levels of intron retention, but it is unclear whether these variant transcripts are functional targets of NMD. In this study, we use CRISPR-Cas9 to disrupt and epitope-tag the P. falciparum orthologs of two core NMD components: Pf UPF1 (PF3D7_1005500) and Pf UPF2 (PF3D7_0925800). We localize both Pf UPF1 and Pf UPF2 to puncta within the parasite cytoplasm and show that these proteins interact with each other and other mRNA-binding proteins. Using RNA-seq, we find that although these core NMD orthologs are expressed and interact in P. falciparum , they are not required for degradation of nonsense transcripts. Furthermore, our work suggests that the majority of intron retention in P. falciparum has no functional role and that NMD is not required for parasite growth ex vivo . In many organisms, the process of destroying nonsense transcripts is dependent on a small set of highly conserved proteins. We show that in the malaria parasite, these proteins do not impact the abundance of nonsense transcripts. Furthermore, we demonstrate efficient CRISPR-Cas9 editing of the malaria parasite using commercial Cas9 nuclease and synthetic guide RNA, streamlining genomic modifications in this genetically intractable organism.
A Type II Pathway for Fatty Acid Biosynthesis Presents Drug Targets in Plasmodium falciparum
Publisher: American Society for Microbiology
Date: 2003
DOI: 10.1128/AAC.47.1.297-301.2003
Abstract: It has long been held that the malaria parasite, Plasmodium sp., is incapable of de novo fatty acid synthesis. This view has recently been overturned with the emergence of data for the presence of a fatty acid biosynthetic pathway in the relict plastid of P. falciparum (known as the apicoplast). This pathway represents the type II pathway common to plant chloroplasts and bacteria but distinct from the type I pathway of animals including humans. Specific inhibitors of the type II pathway, thiolactomycin and triclosan, have been reported to target this Plasmodium pathway. Here we report further inhibitors of the plastid-based pathway that inhibit Plasmodium parasites. These include several analogues of thiolactomycin, two with sixfold-greater efficacy than thiolactomycin. We also report that parasites respond very rapidly to such inhibitors and that the greatest sensitivity is seen in ring-stage parasites. This study substantiates the importance of fatty acid synthesis for blood-stage parasite survival and shows that this pathway provides scope for the development of novel antimalarial drugs.
Trafficking and assembly of the cytoadherence complex in Plasmodium falciparum-infected human erythrocytes
Publisher: Wiley
Date: 15-10-2001
The epigenetic control of antigenic variation in Plasmodium falciparum
Publisher: Elsevier BV
Date: 08-2005
DOI: 10.1016/J.MIB.2005.06.007
Abstract: Much of what is known about antigenic variation in the human malaria parasite Plasmodium falciparum has been established by the study of phenotypic changes at the surface of parasitized red blood cells. Although this has contributed to our fundamental understanding of immune escape, nothing conclusive has been elucidated about the molecular mechanisms that determine activation and silencing of members of the antigenic variation var gene family. Recent findings indicate that reversible chromatin modifications and perinuclear gene movement are epigenetic factors that define the silent and active states of telomere-adjacent var genes.
Membrane transporters in the relict plastid of malaria parasites
Publisher: Proceedings of the National Academy of Sciences
Date: 20-06-2006
Abstract: Malaria parasites contain a nonphotosynthetic plastid homologous to chloroplasts of plants. The parasite plastid synthesizes fatty acids, heme, iron sulfur clusters and isoprenoid precursors and is indispensable, making it an attractive target for antiparasite drugs. How parasite plastid biosynthetic pathways are fuelled in the absence of photosynthetic capture of energy and carbon was not clear. Here, we describe a pair of parasite transporter proteins, PfiTPT and PfoTPT, that are homologues of plant chloroplast innermost membrane transporters responsible for moving phosphorylated C3, C5, and C6 compounds across the plant chloroplast envelope. PfiTPT is shown to be localized in the innermost membrane of the parasite plastid courtesy of a cleavable N-terminal targeting sequence. PfoTPT lacks such a targeting sequence, but is shown to localize in the outermost parasite plastid membrane with its termini projecting into the cytosol. We have identified these membrane proteins in the parasite plastid and determined membrane orientation for PfoTPT. PfiTPT and PfoTPT are proposed to act in tandem to transport phosphorylated C3 compounds from the parasite cytosol into the plastid. Thus, the transporters could shunt glycolytic derivatives of glucose scavenged from the host into the plastid providing carbon, reducing equivalents and ATP to power the organelle.
Telomeric Heterochromatin Propagation and Histone Acetylation Control Mutually Exclusive Expression of Antigenic Variation Genes in Malaria Parasites
Publisher: Elsevier BV
Date: 04-2005
DOI: 10.1016/J.CELL.2005.01.037
Abstract: Malaria parasites use antigenic variation to avoid immune clearance and increase the duration of infection in the human host. Variation at the surface of P. falciparum-infected erythrocytes is mediated by the differential control of a family of surface antigens encoded by var genes. Switching of var gene expression occurs in situ, mostly from telomere-associated loci, without detectable DNA alterations, suggesting that it is controlled by chromatin structure. We have identified chromatin modifications at telomeres that spread far into telomere-proximal regions, including var gene loci (>50 kb). One type of modification is mediated by a protein homologous to yeast Sir2 called PfSir2, which forms a chromosomal gradient of heterochromatin structure and histone hypoacetylation. Upon activation of a specific telomere-associated var gene, PfSir2 is removed from the promoter region and acetylation of histone occurs. Our data demonstrate that mutually exclusive transcription of var genes is linked to the dynamic remodeling of chromatin.
Genomic-scale prioritization of drug targets: the TDR Targets database
Publisher: Springer Science and Business Media LLC
Date: 17-10-2008
DOI: 10.1038/NRD2684
Non‐canonical metabolic pathways in the malaria parasite detected by isotope‐tracing metabolomics
Publisher: EMBO
Date: 04-2021
Potential epigenetic regulatory proteins localise to distinct nuclear sub-compartments in Plasmodium falciparum
Publisher: Elsevier BV
Date: 2010
DOI: 10.1016/J.IJPARA.2009.09.002
Abstract: The life cycle of the malaria parasite Plasmodium falciparum involves dramatic morphological and molecular changes required for infection of insect and mammalian hosts. Stage-specific gene expression is crucial, yet few nuclear factors, including potential epigenetic regulators, have been identified. Epigenetic mechanisms play an important role in the switched expression of members of species-specific gene families, which encode proteins exported into the cytoplasm and onto the surface of infected erythrocytes. This includes the large virulence-associated var gene family, in which monoallelic transcription of a single member and switching to other var genes leads to a display of different surface ligands with distinct antigenic and adhesive properties. Using a bio-informatic approach we identified 24 putative nuclear proteins. Tagging with sequences encoding GFP or haemagglutinin (HA) epitopes allowed for identification and localisation analysis of 12 nuclear proteins that are potential regulators of P. falciparum gene expression. These proteins specifically localise to distinct areas of the nucleus, reaching from the centre towards the nuclear envelope, giving new insights into the apicomplexan nuclear architecture. Proteins presenting a punctate distribution in the perinuclear sub-compartments are potential virulence gene regulators as silenced and active var genes reside at the nuclear periphery either clustered or in small expression sites, respectively. These analyses demonstrated an ordered compartmentalisation, indicating a complex sub-nuclear organisation that contributes to the complexity of transcriptional regulation in P. falciparum.
Reduced ribosomes of the apicoplast and mitochondrion of Plasmodium spp. and predicted interactions with antibiotics
Publisher: The Royal Society
Date: 05-2014
DOI: 10.1098/RSOB.140045
Abstract: Apicomplexan protists such as Plasmodium and Toxoplasma contain a mitochondrion and a relic plastid (apicoplast) that are sites of protein translation. Although there is emerging interest in the partitioning and function of translation factors that participate in apicoplast and mitochondrial peptide synthesis, the composition of organellar ribosomes remains to be elucidated. We carried out an analysis of the complement of core ribosomal protein subunits that are encoded by either the parasite organellar or nuclear genomes, accompanied by a survey of ribosome assembly factors for the apicoplast and mitochondrion. A cross-species comparison with other apicomplexan, algal and diatom species revealed compositional differences in apicomplexan organelle ribosomes and identified considerable reduction and ergence with ribosomes of bacteria or characterized organelle ribosomes from other organisms. We assembled structural models of sections of Plasmodium falciparum organellar ribosomes and predicted interactions with translation inhibitory antibiotics. Differences in predicted drug–ribosome interactions with some of the modelled structures suggested specificity of inhibition between the apicoplast and mitochondrion. Our results indicate that Plasmodium and Toxoplasma organellar ribosomes have a unique composition, resulting from the loss of several large and small subunit proteins accompanied by significant sequence and size ergences in parasite orthologues of ribosomal proteins.
Recycling factors for ribosome disassembly in the apicoplast and mitochondrion of P lasmodium falciparum
Publisher: Wiley
Date: 24-04-2013
DOI: 10.1111/MMI.12230
Abstract: The reduced genomes of the apicoplast and mitochondrion of the malaria parasite Plasmodium falciparum are actively translated and antibiotic-mediated translation inhibition is detrimental to parasite survival. In order to understand recycling of organellar ribosomes, a critical step in protein translation, we identified ribosome recycling factors (RRF) encoded by the parasite nuclear genome. Targeting of PfRRF1 and PfRRF2 to the apicoplast and mitochondrion respectively was established by localization of leader sequence-GFP fusions. Unlike any RRF characterized thus far, PfRRF2 formed dimers with disulphide interaction(s) and additionally localized in the cytoplasm, thus suggesting adjunct functions for the factor. PfRRF1 carries a large 108-amino-acid insertion in the functionally critical hinge region between the head and tail domains of the protein, yet complemented Escherichia coli RRF in the LJ14frr(ts) mutant and disassembled surrogate E. coli 70S ribosomes in the presence of apicoplast-targeted EF-G. Recombinant PfRRF2 bound E. coli ribosomes and could split monosomes in the presence of the relevant mitochondrial EF-G but failed to complement the LJ14frr(ts) mutant. Although proteins comprising subunits of P. falciparum organellar ribosomes are predicted to differ from bacterial and mitoribosomal counterparts, our results indicate that the essential interactions required for recycling are conserved in parasite organelles.
Delayed death in the malaria parasite Plasmodium falciparum is caused by disruption of prenylation-dependent intracellular trafficking
Publisher: Public Library of Science (PLoS)
Date: 18-07-2019
Protein translation in Plasmodium parasites
Publisher: Elsevier BV
Date: 10-2011
Abstract: The protein translation machinery of the parasite Plasmodium is the target of important anti-malarial drugs, and encompasses many promising targets for future drugs. Plasmodium parasites have three subcellular compartments that house genomes the nucleus, mitochondrion and apicoplast, and each requires its own compartmentalized transcription and translation apparatus for survival. Despite the availability of the complete genome sequence that should reveal the requisite elements for all three compartments, our understanding of the translation machineries is patchy. We review what is known about cytosolic and organellar translation in Plasmodium and discuss the molecules that have been identified through genome sequencing and post-genomic analysis. Some translation components are yet to be found in Plasmodium, whereas others appear to be shared between translationally active organelles.
Mefloquine targets the Plasmodium falciparum 80S ribosome to inhibit protein synthesis
Publisher: Springer Science and Business Media LLC
Date: 13-03-2017
A divergent nonsense-mediated decay machinery in Plasmodium falciparum is inefficient and non-essential
Publisher: Cold Spring Harbor Laboratory
Date: 14-04-2021
DOI: 10.1101/2021.04.14.439394
Abstract: Nonsense-mediated decay (NMD) is a conserved mRNA quality control process that eliminates transcripts bearing a premature termination codon. In addition to its role in removing erroneous transcripts, NMD is involved in post-transcriptional regulation of gene expression via programmed intron retention in metazoans. The apicomplexan parasite Plasmodium falciparum shows relatively high levels of intron retention, but it is unclear whether these variant transcripts are functional targets of NMD. In this study, we use CRISPR-Cas9 to disrupt and epitope-tag two core NMD components: Pf UPF1 (PF3D7_1005500) and Pf UPF2 (PF3D7_0925800). Using RNA-seq, we find that NMD in P. falciparum is highly derived and requires UPF2, but not UPF1 for transcript degradation. Furthermore, our work suggests that the majority of intron retention in P. falciparum has no functional role and that NMD is not required for parasite growth ex vivo . We localise both Pf UPF1 and Pf UPF2 to puncta within the parasite cytoplasm, which may represent processing bodies - ribonucleoparticles that are sites of cytoplasmic mRNA decay. Finally, we identify a number of mRNA-binding proteins that co-immunoprecipitate with the NMD core complex and propose a model for a ergent NMD that does not require Pf UPF1 and incorporates novel accessory proteins to elicit mRNA decay.
Phenotypic variation of Plasmodium falciparum merozoite proteins directs receptor targeting for invasion of human erythrocytes
Publisher: Wiley
Date: 03-03-2003
DOI: 10.1093/EMBOJ/CDG096
Plasmodium falciparum glucose‐6‐phosphate dehydrogenase 6‐phosphogluconolactonase is a potential drug target
Publisher: Wiley
Date: 17-08-2015
DOI: 10.1111/FEBS.13380
Abstract: The malarial parasite Plasmodium falciparum is exposed to substantial redox challenges during its complex life cycle. In intraerythrocytic parasites, haemoglobin breakdown is a major source of reactive oxygen species. Deficiencies in human glucose-6-phosphate dehydrogenase, the initial enzyme in the pentose phosphate pathway (PPP), lead to a disturbed redox equilibrium in infected erythrocytes and partial protection against severe malaria. In P. falciparum, the first two reactions of the PPP are catalysed by the bifunctional enzyme glucose-6-phosphate dehydrogenase 6-phosphogluconolactonase (PfGluPho). This enzyme differs structurally from its human counterparts and represents a potential target for drugs. In the present study we used epitope tagging of endogenous PfGluPho to verify that the enzyme localises to the parasite cytosol. Furthermore, attempted double crossover disruption of the PfGluPho gene indicates that the enzyme is essential for the growth of blood stage parasites. As a further step towards targeting PfGluPho pharmacologically, ellagic acid was characterised as a potent PfGluPho inhibitor with an IC50 of 76 nM. Interestingly, pro-oxidative drugs or treatment of the parasites with H2O2 only slightly altered PfGluPho expression or activity under the conditions tested. Furthermore, metabolic profiling suggested that pro-oxidative drugs do not significantly perturb the abundance of PPP intermediates. These data indicate that PfGluPho is essential in asexual parasites, but that the oxidative arm of the PPP is not strongly regulated in response to oxidative challenge.
Novel vacuoles in Toxoplasma
Publisher: Wiley
Date: 10-02-2010
A serine-arginine-rich (SR) splicing factor modulates alternative splicing of over a thousand genes in Toxoplasma gondii
Publisher: Oxford University Press (OUP)
Date: 13-04-2015
DOI: 10.1093/NAR/GKV311
Investigation of the Plasmodium falciparum Food Vacuole through Inducible Expression of the Chloroquine Resistance Transporter (PfCRT)
Publisher: Public Library of Science (PLoS)
Date: 13-06-2012
Artemisinin kills malaria parasites by damaging proteins and inhibiting the proteasome
Publisher: Springer Science and Business Media LLC
Date: 18-09-2018
DOI: 10.1038/S41467-018-06221-1
Abstract: Artemisinin and its derivatives (collectively referred to as ARTs) rapidly reduce the parasite burden in Plasmodium falciparum infections, and antimalarial control is highly dependent on ART combination therapies (ACTs). Decreased sensitivity to ARTs is emerging, making it critically important to understand the mechanism of action of ARTs. Here we demonstrate that dihydroartemisinin (DHA), the clinically relevant ART, kills parasites via a two-pronged mechanism, causing protein damage, and compromising parasite proteasome function. The consequent accumulation of proteasome substrates, i.e., unfolded/damaged and polyubiquitinated proteins, activates the ER stress response and underpins DHA-mediated killing. Specific inhibitors of the proteasome cause a similar build-up of polyubiquitinated proteins, leading to parasite killing. Blocking protein synthesis with a translation inhibitor or inhibiting the ubiquitin-activating enzyme, E1, reduces the level of damaged, polyubiquitinated proteins, alleviates the stress response, and dramatically antagonizes DHA activity.
Transcriptome analysis of antigenic variation in Plasmodium falciparum--var silencing is not dependent on antisense RNA.
Publisher: Springer Science and Business Media LLC
Date: 2005
Aminoacyl-tRNA synthetases as drug targets in eukaryotic parasites
Publisher: Elsevier BV
Date: 04-2014
AMPK β subunits display isoform specific affinities for carbohydrates
Publisher: Wiley
Date: 14-07-2010
DOI: 10.1016/J.FEBSLET.2010.07.015
Abstract: AMP-activated protein kinase (AMPK) is a heterotrimer of catalytic (alpha) and regulatory (beta and gamma) subunits with at least two isoforms for each subunit. AMPK beta1 is widely expressed whilst AMPK beta2 is highly expressed in muscle and both beta isoforms contain a mid-molecule carbohydrate-binding module (beta-CBM). Here we show that beta2-CBM has evolved to contain a Thr insertion and increased affinity for glycogen mimetics with a preference for oligosaccharides containing a single alpha-1,6 branched residue. Deletion of Thr-101 reduces affinity for single alpha-1,6 branched oligosaccharides by 3-fold, while insertion of this residue into the equivalent position in the beta1-CBM sequence increases affinity by 3-fold, confirming the functional importance of this residue.
Plasmodium sexual differentiation: how to make a female
Publisher: Wiley
Date: 18-07-2019
DOI: 10.1111/MMI.14340
Abstract: Sexual development is integral to the transmission of Plasmodium parasites between vertebrates and mosquitos. Recent years have seen great advances in understanding the gene expression that underlies commitment of asexual parasites to differentiate into sexual gametocyte stages, then how they mature and form gametes once inside a mosquito. Less well understood is how parasites differentially control development to become males or females. Plasmodium parasites are haploid at the time of sexual differentiation, but a clonal haploid line can produce both male and female gametocytes, so they presumably lack the sex-determining alleles present in some other eukaryotes. Though the molecular switch to initiate male or female development remains hidden, recent studies reveal regulatory proteins needed for the sex-specific maturation of male and female gametocytes. Yuda and collaborators report the characterization of a transcription factor necessary for female gametocyte maturation. With renewed attention on malaria elimination, sex has been an increasing focus because transmission-blocking strategies are likely to be an important component of elimination efforts.
Interaction of apicoplast-encoded elongation factor (EF) EF-Tu with nuclear-encoded EF-Ts mediates translation in the Plasmodium falciparum plastid
Publisher: Elsevier BV
Date: 03-2011
DOI: 10.1016/J.IJPARA.2010.11.003
Abstract: Protein translation in the plastid (apicoplast) of Plasmodium spp. is of immense interest as a target for potential anti-malarial drugs. However, the molecular data on apicoplast translation needed for optimisation and development of novel inhibitors is lacking. We report characterisation of two key translation elongation factors in Plasmodium falciparum, apicoplast-encoded elongation factor PfEF-Tu and nuclear-encoded PfEF-Ts. Recombinant PfEF-Tu hydrolysed GTP and interacted with its presumed nuclear-encoded partner PfEF-Ts. The EF-Tu inhibitor kirromycin affected PfEF-Tu activity in vitro, indicating that apicoplast EF-Tu is indeed the target of this drug. The predicted PfEF-Ts leader sequence targeted GFP to the apicoplast, confirming that PfEF-Ts functions in this organelle. Recombinant PfEF-Ts mediated nucleotide exchange on PfEF-Tu and homology modeling of the PfEF-Tu:PfEF-Ts complex revealed PfEF-Ts-induced structural alterations that would expedite GDP release from PfEF-Tu. Our results establish functional interaction between two apicoplast translation factors encoded by genes residing in different cellular compartments and highlight the significance of their sequence/structural differences from bacterial elongation factors in relation to inhibitor activity. These data provide an experimental system to study the effects of novel inhibitors targeting PfEF-Tu and PfEF-Tu.PfEF-Ts interaction. Our finding that apicoplast EF-Tu possesses chaperone-related disulphide reductase activity also provides a rationale for retention of the tufA gene on the plastid genome.
Direct nanopore sequencing of mrna reveals landscape of transcript isoforms in apicomplexan parasites
Publisher: American Society for Microbiology
Date: 27-04-2021
DOI: 10.1128/MSYSTEMS.01081-20
Abstract: We have used a novel nanopore sequencing technology to directly analyze parasite transcriptomes. The very long reads of this technology reveal the full-length genes of the parasites that cause malaria and toxoplasmosis. Gene transcripts must be processed in a process called splicing before they can be translated to protein. Our analysis reveals that these parasites very frequently only partially process their gene products, in a manner that departs dramatically from their human hosts.
Independent Translocation of Two Micronemal Proteins in Developing Plasmodium falciparum Merozoites
Publisher: American Society for Microbiology
Date: 10-2002
DOI: 10.1128/IAI.70.10.5751-5758.2002
Abstract: Apical membrane antigen 1 of Plasmodium falciparum (PfAMA1) contains an N-terminal propeptide that is removed prior to the translocation of the mature protein onto the merozoite surface. We localized unprocessed PfAMA1 to the microneme organelles of the intraerythrocytic schizont. The results have suggested that the processed form of PfAMA1 translocates from the microneme compartment independently of another microneme protein, EBA175, which is also involved in the invasion of human erythrocytes.
Artemisinin Action and Resistance in Plasmodium falciparum
Publisher: Elsevier BV
Date: 09-2016
Drug target prediction and prioritization: using orthology to predict essentiality in parasite genomes
Publisher: Springer Science and Business Media LLC
Date: 03-04-2010
Abstract: New drug targets are urgently needed for parasites of socio-economic importance. Genes that are essential for parasite survival are highly desirable targets, but information on these genes is lacking, as gene knockouts or knockdowns are difficult to perform in many species of parasites. We examined the applicability of large-scale essentiality information from four model eukaryotes, Caenorhabditis elegans, Drosophila melanogaster, Mus musculus and Saccharomyces cerevisiae , to discover essential genes in each of their genomes. Parasite genes that lack orthologues in their host are desirable as selective targets, so we also examined prediction of essential genes within this subset. Cross-species analyses showed that the evolutionary conservation of genes and the presence of essential orthologues are each strong predictors of essentiality in eukaryotes. Absence of paralogues was also found to be a general predictor of increased relative essentiality. By combining several orthology and essentiality criteria one can select gene sets with up to a five-fold enrichment in essential genes compared with a random selection. We show how quantitative application of such criteria can be used to predict a ranked list of potential drug targets from Ancylostoma caninum and Haemonchus contortus - two blood-feeding strongylid nematodes, for which there are presently limited sequence data but no functional genomic tools. The present study demonstrates the utility of using orthology information from multiple, erse eukaryotes to predict essential genes. The data also emphasize the challenge of identifying essential genes among those in a parasite that are absent from its host.
Dual targeting of aminoacyl-tRNA synthetases to the apicoplast and cytosol in Plasmodium falciparum
Publisher: Elsevier BV
Date: 02-2012
DOI: 10.1016/J.IJPARA.2011.11.008
Abstract: The causative agent of malaria, Plasmodium, possesses three translationally active compartments: the cytosol, the mitochondrion and a relic plastid called the apicoplast. Aminoacyl-tRNA synthetases to charge tRNA are thus required for all three compartments. However, the Plasmodiumfalciparum genome encodes too few tRNA synthetases to supply a unique enzyme for each amino acid in all three compartments. We have investigated the subcellular localisation of three tRNA synthetases (AlaRS, GlyRS and ThrRS), which occur only once in the nuclear genome, and we show that each of these enzymes is dually localised to the P. falciparum cytosol and the apicoplast. No mitochondrial fraction is apparent for these three enzymes, which suggests that the Plasmodium mitochondrion lacks at least these three tRNA synthetases. The unique Plasmodium ThrRS is the presumed target of the antimalarial compound borrelidin. Borrelidin kills P. falciparum parasites quickly without the delayed death effect typical of apicoplast translation inhibitors and without an observable effect on apicoplast morphology. By contrast, mupirocin, an inhibitor of the apicoplast IleRS, kills with a delayed death effect that inhibits apicoplast growth and ision. Because inhibition of dual targeted tRNA synthetases should arrest translation in all compartments of the parasite, these enzymes deserve further investigation as potential targets for antimalarial drug development.
Evolution of malaria parasite plastid targeting sequences
Publisher: Proceedings of the National Academy of Sciences
Date: 25-03-2008
Abstract: The transfer of genes from an endosymbiont to its host typically requires acquisition of targeting signals by the gene product to ensure its return to the endosymbiont for function. Many hundreds of plastid-derived genes must have acquired transit peptides for successful relocation to the nucleus. Here, we explore potential evolutionary origins of plastid transit peptides in the malaria parasite Plasmodium falciparum . We show that exons of the P. falciparum genome could serve as transit peptides after exon shuffling. We further demonstrate that numerous randomized peptides and even whimsical sequences based on English words can also function as transit peptides in vivo . Thus, facile acquisition of transit peptides from existing sequence likely expedited endosymbiont integration through intracellular gene transfer.
Deciphering apicoplast targeting signals – feature extraction from nuclear-encoded precursors of Plasmodium falciparum apicoplast proteins
Publisher: Elsevier BV
Date: 12-2001
DOI: 10.1016/S0378-1119(01)00776-4
Abstract: The malaria causing protozoan Plasmodium falciparum contains a vestigal, non-photosynthetic plastid, the apicoplast. Numerous proteins encoded by nuclear genes are targeted to the apicoplast courtesy of N-terminal extensions. With the impending sequence completion of an entire genome of the malaria parasite, it is important to have software tools in place for prediction of subcellular locations for all proteins. Apicoplast targeting signals are bipartite containing a signal peptide and a transit peptide. Nuclear-encoded apicoplast protein precursors were analyzed for characteristic features by statistical methods, principal component analysis, self-organizing maps, and supervised neural networks. The transit peptide contains a net positive charge and is rich in asparagine, lysine, and isoleucine residues. A novel prediction system (PATS, predict apicoplast-targeted sequences) was developed based on various sequence features, yielding a Matthews correlation coefficient of 0.91 (97% correct predictions) in a 40-fold cross-validation study. This system predicted 22% apicoplast proteins of the 205 potential proteins on P. falciparum chromosome 2, and 21% of 243 chromosome 3 proteins. A combination of the PATS results with a signal peptide prediction yields 15% potentially nuclear-encoded apicoplast proteins on chromosomes 2 and 3. The prediction tool will advance P. falciparum genome analysis, and it might help to identify apicoplast proteins as drug targets for the development of novel anti-malaria agents.
The apicoplast as an antimalarial drug target
Publisher: Elsevier BV
Date: 06-2001
Abstract: Resistance to commonly used malaria drugs is spreading and new drugs are required urgently. The recent identification of a relict chloroplast (apicoplast) in malaria and related parasites offers numerous new targets for drug therapy using well-characterized compounds. The apicoplast contains a range of metabolic pathways and housekeeping processes that differ radically to those of the host thereby presenting ideal strategies for drug therapy. Indeed, many compounds targeting these plastid pathways are antimalarial and have favourable profiles based on extensive knowledge from their use as antibacterials.
Malaria Parasite Signal Peptide Peptidase is an ER-Resident Protease Required for Growth but not for Invasion
Publisher: Wiley
Date: 23-08-2012
DOI: 10.1111/J.1600-0854.2012.01402.X
Abstract: The establishment of parasite infection within the human erythrocyte is an essential stage in the development of malaria disease. As such, significant interest has focused on the mechanics that underpin invasion and on characterization of parasite molecules involved. Previous evidence has implicated a presenilin-like signal peptide peptidase (SPP) from the most virulent human malaria parasite, Plasmodium falciparum, in the process of invasion where it has been proposed to function in the cleavage of the erythrocyte cytoskeletal protein Band 3. The role of a traditionally endoplasmic reticulum (ER) protease in the process of red blood cell invasion is unexpected. Here, using a combination of molecular, cellular and chemical approaches we provide evidence that PfSPP is, instead, a bona fide ER-resident peptidase that remains intracellular throughout the invasion process. Furthermore, SPP-specific drug inhibition has no effect on erythrocyte invasion whilst having low micromolar potency against intra-erythrocytic development. Contrary to previous reports, these results show that PfSPP plays no role in erythrocyte invasion. Nonetheless, PfSPP clearly represents a potential chemotherapeutic target to block parasite growth, supporting ongoing efforts to develop antimalarial-targeting protein maturation and trafficking during intra-erythrocytic development.
Evolutionary pressures on apicoplast transit peptides
Publisher: Oxford University Press (OUP)
Date: 11-08-2004
Chromosome-level genome of Schistosoma haematobium underpins genome-wide explorations of molecular variation.
Publisher: Public Library of Science (PLoS)
Date: 15-02-2022
DOI: 10.1371/JOURNAL.PPAT.1010288
Abstract: Urogenital schistosomiasis is caused by the blood fluke Schistosoma haematobium and is one of the most neglected tropical diseases worldwide, afflicting 100 million people. It is characterised by granulomata, fibrosis and calcification in urogenital tissues, and can lead to increased susceptibility to HIV/AIDS and squamous cell carcinoma of the bladder. To complement available treatment programs and break the transmission of disease, sound knowledge and understanding of the biology and ecology of S . haematobium is required. Hybridisation/introgression events and molecular variation among members of the S . haematobium -group might effect important biological and/or disease traits as well as the morbidity of disease and the effectiveness of control programs including mass drug administration. Here we report the first chromosome-contiguous genome for a well-defined laboratory line of this blood fluke. An exploration of this genome using transcriptomic data for all key developmental stages allowed us to refine gene models (including non-coding elements) and annotations, discover ‘new’ genes and transcription profiles for these stages, likely linked to development and/or pathogenesis. Molecular variation within S . haematobium among some geographical locations in Africa revealed unique genomic ‘signatures’ that matched species other than S . haematobium , indicating the occurrence of introgression events. The present reference genome (designated Shae.V3) and the findings from this study solidly underpin future functional genomic and molecular investigations of S . haematobium and accelerate systematic, large-scale population genomics investigations, with a focus on improved and sustained control of urogenital schistosomiasis.
Metabolic Dysregulation Induced inPlasmodium falciparumby Dihydroartemisinin and Other Front-Line Antimalarial Drugs
Publisher: Oxford University Press (OUP)
Date: 06-07-2014
Abstract: Detailed information on the mode of action of antimalarial drugs can be used to improve existing drugs, identify new drug targets, and understand the basis of drug resistance. In this study we describe the use of a time-resolved, mass spectrometry (MS)-based metabolite profiling approach to map the metabolic perturbations induced by a panel of clinical antimalarial drugs and inhibitors on Plasmodium falciparum asexual blood stages. Drug-induced changes in metabolite levels in P. falciparum-infected erythrocytes were monitored over time using gas chromatography-MS and liquid chromatography-MS and changes in specific metabolic fluxes confirmed by nonstationary [(13)C]-glucose labeling. Dihydroartemisinin (DHA) was found to disrupt hemoglobin catabolism within 1 hour of exposure, resulting in a transient decrease in hemoglobin-derived peptides. Unexpectedly, it also disrupted pyrimidine biosynthesis, resulting in increased [(13)C]-glucose flux toward malate production, potentially explaining the susceptibility of P. falciparum to DHA during early blood-stage development. Unique metabolic signatures were also found for atovaquone, chloroquine, proguanil, cycloguanil and methylene blue. We also show that this approach can be used to identify the mode of action of novel antimalarials, such as the compound Torin 2, which inhibits hemoglobin catabolism.
Alternative Splicing in Apicomplexan Parasites.
Publisher: American Society for Microbiology
Date: 26-02-2019
Abstract: Alternative splicing is a widespread, essential, and complex component of gene regulation. Apicomplexan parasites have long been recognized to produce alternatively spliced transcripts for some genes and can produce multiple protein products that are essential for parasite growth.
Decreased K13 Abundance Reduces Hemoglobin Catabolism and Proteotoxic Stress, Underpinning Artemisinin Resistance.
Publisher: Elsevier BV
Date: 11-2019
DOI: 10.1016/J.CELREP.2019.10.095
Abstract: Increased tolerance of Plasmodium falciparum to front-line artemisinin antimalarials (ARTs) is associated with mutations in Kelch13 (K13), although the precise role of K13 remains unclear. Here, we show that K13 mutations result in decreased expression of this protein, while mislocalization of K13 mimics resistance-conferring mutations, pinpointing partial loss of function of K13 as the relevant molecular event. K13-GFP is associated with ∼170 nm diameter doughnut-shaped structures at the parasite periphery, consistent with the location and dimensions of cytostomes. Moreover, the hemoglobin-peptide profile of ring-stage parasites is reduced when K13 is mislocalized. We developed a pulse-SILAC approach to quantify protein turnover and observe less disruption to protein turnover following ART exposure when K13 is mislocalized. Our findings suggest that K13 regulates digestive vacuole biogenesis and the uptake/degradation of hemoglobin and that ART resistance is mediated by a decrease in heme-dependent drug activation, less proteotoxicity, and increased survival of parasite ring stages.
Glycosylated compounds of parasitic protozoa
Publisher: Elsevier
Date: 2010
3, 2, 1, go! Cryptosporidium counts down to sex
Publisher: Public Library of Science (PLoS)
Date: 12-05-2022
A Genome-wide Chromatin-associated Nuclear Peroxiredoxin from the Malaria Parasite Plasmodium falciparum
Publisher: Elsevier BV
Date: 04-2011
Expression of P. falciparum var Genes Involves Exchange of the Histone Variant H2A.Z at the Promoter
Publisher: Public Library of Science (PLoS)
Date: 17-02-2011
Open Source Drug Discovery: Highly Potent Antimalarial Compounds Derived from the Tres Cantos Arylpyrroles
Publisher: American Chemical Society (ACS)
Date: 14-09-2016
Massively Parallel Sequencing and Analysis of the Necator americanus Transcriptome
Publisher: Public Library of Science (PLoS)
Date: 11-05-2010
Large scale production of a mammalian cell derived quadrivalent hepatitis C virus like particle vaccine.
Publisher: Elsevier BV
Date: 10-2016
DOI: 10.1016/J.JVIROMET.2016.06.012
Abstract: A method for the large-scale production of a quadrivalent mammalian cell derived hepatitis C virus-like particles (HCV VLPs) is described. The HCV core E1 and E2 coding sequences of genotype 1a, 1b, 2a or 3a were co-expressed in Huh7 cell factories using a recombinant adenoviral expression system. The structural proteins self-assembled into VLPs that were purified from Huh7 cell lysates by iodixanol ultracentrifugation and Stirred cell ultrafiltration. Electron microscopy, revealed VLPs of the different genotypes that are morphologically similar. Our results show that it is possible to produce large quantities of in idual HCV genotype VLPs with relative ease thus making this approach an alternative for the manufacture of a quadrivalent mammalian cell derived HCV VLP vaccine.
In silico prediction of antimalarial drug target candidates
Publisher: Elsevier BV
Date: 12-2012
REX1 and Pf62: Are they one and the same?
Publisher: Springer Science and Business Media LLC
Date: 05-03-2009
Identification of Attractive Drug Targets in Neglected-Disease Pathogens Using an In Silico Approach
Publisher: Public Library of Science (PLoS)
Date: 24-08-2010
Delayed Death by Plastid Inhibition in Apicomplexan Parasites
Publisher: Elsevier BV
Date: 10-2019
Abstract: The discovery of a plastid in apicomplexan parasites was hoped to be a watershed moment in the treatment of parasitic diseases as it revealed drug targets that are implicitly ergent from host molecular processes. Indeed, this organelle, known as the apicoplast, has since been a productive therapeutic target for pharmaceutical interventions against infections by Plasmodium, Toxoplasma, Babesia, and Theileria. However, some inhibitors of the apicoplast are restricted in their treatment utility because of their slow-kill kinetics, and this characteristic is called the delayed death effect. Here we review the recent genetic and pharmacological experiments that interrogate the causes of delayed death and explore the foundation of this phenomenon in Plasmodium and Toxoplasma parasites.
Integrative proteomics and bioinformatic prediction enable a high-confidence apicoplast proteome in malaria parasites
Publisher: Public Library of Science (PLoS)
Date: 13-09-2018
Properties and prediction of mitochondrial transit peptides from Plasmodium falciparum
Publisher: Elsevier BV
Date: 12-2003
DOI: 10.1016/J.MOLBIOPARA.2003.07.001
Abstract: A neural network approach for the prediction of mitochondrial transit peptides (mTPs) from the malaria-causing parasite Plasmodium falciparum is presented. Nuclear-encoded mitochondrial protein precursors of P. falciparum were analyzed by statistical methods, principal component analysis and supervised neural networks, and were compared to those of other eukaryotes. A distinct amino acid usage pattern has been found in protein encoding regions of P. falciparum: glycine, alanine, tryptophan and arginine are under-represented, whereas isoleucine, tyrosine, asparagine and lysine are over-represented compared to the SwissProt average. Similar patterns were observed in mTPs of P. falciparum. Using principal component analysis (PCA), mTPs from P. falciparum were shown to differ considerably from those of other organisms. A neural network system (PlasMit) for prediction of mTPs in P. falciparum sequences was developed, based on the relative amino acid frequency in the first 24 N-terminal amino acids, yielding a Matthews correlation coefficient of 0.74 (90% correct prediction) in a 20-fold cross-validation study. This system predicted 1177 (22%) mitochondrial genes, based on 5334 annotated genes in the P. falciparum genome. A second network with the same topology was trained to give more conservative estimate. This more stringent network yielded a Matthews correlation coefficient of 0.51 (84% correct prediction) in a 10-fold cross-validation study. It predicted 381 (7.1%) mitochondrial genes, based on 5334 annotated genes in the P. falciparum genome.
Characterization of a hepatitis C virus-like particle vaccine produced in a human hepatocyte-derived cell line
Publisher: Microbiology Society
Date: 08-2016
DOI: 10.1099/JGV.0.000493
Abstract: An effective immune response against hepatitis C virus (HCV) requires the early development of multi-specific class 1 CD8+ and class II CD4+ T-cells together with broad neutralizing antibody responses. We have produced mammalian-cell-derived HCV virus-like particles (VLPs) incorporating core, E1 and E2 of HCV genotype 1a to produce such immune responses. Here we describe the biochemical and morphological characterization of the HCV VLPs and study HCV core-specific T-cell responses to the particles. The E1 and E2 glycoproteins in HCV VLPs formed non-covalent heterodimers and together with core protein assembled into VLPs with a buoyant density of 1.22 to 1.28 g cm-3. The HCV VLPs could be immunoprecipited with anti-ApoE and anti-ApoC. On electron microscopy, the VLPs had a heterogeneous morphology and ranged in size from 40 to 80 nm. The HCV VLPs demonstrated dose-dependent binding to murine-derived dendritic cells and the entry of HCV VLPs into Huh7 cells was blocked by anti-CD81 antibody. Vaccination of BALB/c mice with HCV VLPs purified from iodixanol gradients resulted in the production of neutralizing antibody responses while vaccination of humanized MHC class I transgenic mice resulted in the prodution of HCV core-specific CD8+ T-cell responses. Furthermore, IgG purified from the sera of patients chronically infected with HCV genotypes 1a and 3a blocked the binding and entry of the HCV VLPs into Huh7 cells. These results show that our mammalian-cell-derived HCV VLPs induce humoral and HCV-specific CD8+ T-cell responses and will have important implications for the development of a preventative vaccine for HCV.
The Plasmodium falciparum artemisinin resistance-associated protein Kelch 13 is required for formation of normal cytostomes
Publisher: eLife Sciences Publications, Ltd
Date: 08-08-2023
DOI: 10.7554/ELIFE.90290
Abstract: Artemisinin (ART) is a quick-killing and effective antimalarial activated by the haem derived from haemoglobin digestion. Mutations in the parasite’s Kelch 13 (K13) protein compromise the efficacy of this drug. Recent studies indicate an undefined role for K13 in haemoglobin uptake. Here, we show that K13 is associated with the collar that constricts cytostomal invaginations required for the parasite to ingest host cytosol. Induced mislocalisation of K13 led to the formation of atypical invaginations lacking the cytostomal ring and constricted neck normally associated with cytostomes. Moreover, the levels of haemoglobin degradation products, haem and haemozoin, are decreased when K13 is inactivated. Our findings demonstrate that K13 is required for normal formation and/or stabilisation of the cytostome, and thereby the parasite’s uptake of haemoglobin. This is consistent with perturbation of K13 function leading to decreased activation of ART and consequently, reduced killing. Artemisinin-resistant parasites contain mutations in the gene encoding the Kelch 13 protein (K13). How K13 mutations result in artemisinin resistance is unclear. Here, we present evidence that normal K13 is required for the formation of the cytostome, a specialised parasite feeding apparatus used to endocytose host cell haemoglobin. Our results suggest that artemisinin resistance is due to a decrease in artemisinin activation brought about by a decrease in efficiency of haemoglobin uptake and consequently reduced production of haem.
A dual-targeted aminoacyl-tRNA synthetase in Plasmodium falciparum charges cytosolic and apicoplast tRNACys
Publisher: Portland Press Ltd.
Date: 28-02-2014
DOI: 10.1042/BJ20131451
Abstract: Plasmodium parasites possess two endosymbiotic organelles: a mitochondrion and a relict plastid called the apicoplast. To accommodate the translational requirements of these organelles in addition to its cytosolic translation apparatus, the parasite must maintain a supply of charged tRNA molecules in each of these compartments. In the present study we investigate how the parasite manages these translational requirements for charged tRNACys with only a single gene for CysRS (cysteinyl-tRNA synthetase). We demonstrate that the single PfCysRS (Plasmodium falciparum CysRS) transcript is alternatively spliced, and, using a combination of endogenous and heterologous tagging experiments in both P. falciparum and Toxoplasma gondii, we show that CysRS isoforms traffic to the cytosol and apicoplast. PfCysRS can recognize and charge the eukaryotic tRNACys encoded by the Plasmodium nucleus as well as the bacterial-type tRNA encoded by the apicoplast genome, albeit with a preference for the eukaryotic type cytosolic tRNA. The results of the present study indicate that apicomplexan parasites have lost their original plastidic cysteinyl-tRNA synthetase, and have replaced it with a dual-targeted eukaryotic type CysRS that recognizes plastid and nuclear tRNACys. Inhibitors of the Plasmodium dual-targeted CysRS would potentially offer a therapy capable of the desirable immediate effects on parasite growth as well as the irreversibility of inhibitors that disrupt apicoplast inheritance.
Strange organelles - Plasmodium mitochondria lack a pyruvate dehydrogenase complex
Publisher: Wiley
Date: 25-11-2005
DOI: 10.1111/J.1365-2958.2004.04314.X
Abstract: Our understanding of the Plasmodium mitochondrion and apicoplast has been greatly assisted by the genome sequence project. Sequence data have seeded recent research showing that the apicoplast is the site of several anabolic pathways including fatty acid synthesis. The discovery of an active apicoplast pyruvate dehydrogenase complex implies this enzyme generates the acetyl-CoA needed for fatty acid synthesis. However, the absence of a corresponding mitochondrial complex suggests that energy generation in Plasmodium is considerably different from pathways described in other eukaryotes.
Integrating and Mining Helminth Genomes to Discover and Prioritize Novel Therapeutic Targets
Publisher: Wiley
Date: 18-07-2012
Dissecting Apicoplast Targeting in the Malaria Parasite Plasmodium falciparum
Publisher: American Association for the Advancement of Science (AAAS)
Date: 31-01-2003
Abstract: Transit peptides mediate protein targeting into plastids and are only poorly understood. We extracted amino acid features from transit peptides that target proteins to the relict plastid (apicoplast) of malaria parasites. Based on these amino acid characteristics, we identified 466 putative apicoplast proteins in the Plasmodium falciparum genome. Altering the specific charge characteristics in a model transit peptide by site-directed mutagenesis severely disrupted organellar targeting in vivo. Similarly, putative Hsp70 (DnaK) binding sites present in the transit peptide proved to be important for correct targeting.
Targeting and function of proteins mediating translation initiation in organelles of Plasmodium falciparum
Publisher: Wiley
Date: 16-03-2015
DOI: 10.1111/MMI.12972
Abstract: The malaria parasite Plasmodium falciparum has two translationally active organelles - the apicoplast and mitochondrion, which import nuclear-encoded translation factors to mediate protein synthesis. Initiation of translation is a complex step wherein initiation factors (IFs) act in a regulated manner to form an initiation complex. We identified putative organellar IFs and investigated the targeting, structure and function of IF1, IF2 and IF3 homologues encoded by the parasite nuclear genome. A single PfIF1 is targeted to the apicoplast. Apart from its critical ribosomal interactions, PfIF1 also exhibited nucleic-acid binding and melting activities and mediated transcription anti-termination. This suggests a prominent ancillary function for PfIF1 in destabilisation of DNA and RNA hairpin loops encountered during transcription and translation of the A+T rich apicoplast genome. Of the three putative IF2 homologues, only one (PfIF2a) was an organellar protein with mitochondrial localisation. We additionally identified an IF3 (PfIF3a) that localised exclusively to the mitochondrion and another protein, PfIF3b, that was apicoplast targeted. PfIF3a exhibited ribosome anti-association activity, and monosome splitting by PfIF3a was enhanced by ribosome recycling factor (PfRRF2) and PfEF-G(Mit). These results fill a gap in our understanding of organellar translation in Plasmodium, which is the site of action of several anti-malarial compounds.
Selective inhibition of apicoplast tryptophanyl-tRNA synthetase causes delayed death in Plasmodium falciparum
Publisher: Springer Science and Business Media LLC
Date: 09-06-2016
DOI: 10.1038/SREP27531
Abstract: The malaria parasite Plasmodium falciparum relies on efficient protein translation. An essential component of translation is the tryptophanyl-tRNA synthetase (TrpRS) that charges tRNA trp . Here we characterise two isoforms of TrpRS in Plasmodium one eukaryotic type localises to the cytosol and a bacterial type localises to the remnant plastid (apicoplast). We show that the apicoplast TrpRS aminoacylates bacterial tRNA trp while the cytosolic TrpRS charges eukaryotic tRNA trp . An inhibitor of bacterial TrpRSs, indolmycin, specifically inhibits aminoacylation by the apicoplast TrpRS in vitro , and inhibits ex vivo Plasmodium parasite growth, killing parasites with a delayed death effect characteristic of apicoplast inhibitors. Indolmycin treatment ablates apicoplast inheritance and is rescuable by addition of the apicoplast metabolite isopentenyl pyrophosphate (IPP). These data establish that inhibition of an apicoplast housekeeping enzyme leads to loss of the apicoplast and this is sufficient for delayed death. Apicoplast TrpRS is essential for protein translation and is a promising, specific antimalarial target.
PfCERLI1 is a conserved rhoptry associated protein essential for Plasmodium falciparum merozoite invasion of erythrocytes
Publisher: Springer Science and Business Media LLC
Date: 16-03-2020
DOI: 10.1038/S41467-020-15127-W
Abstract: The disease-causing blood-stage of the Plasmodium falciparum lifecycle begins with invasion of human erythrocytes by merozoites. Many vaccine candidates with key roles in binding to the erythrocyte surface and entry are secreted from the large bulb-like rhoptry organelles at the apical tip of the merozoite. Here we identify an essential role for the conserved protein P. falciparum Cytosolically Exposed Rhoptry Leaflet Interacting protein 1 (PfCERLI1) in rhoptry function. We show that PfCERLI1 localises to the cytosolic face of the rhoptry bulb membrane and knockdown of PfCERLI1 inhibits merozoite invasion. While schizogony and merozoite organelle biogenesis appear normal, biochemical techniques and semi-quantitative super-resolution microscopy show that PfCERLI1 knockdown prevents secretion of key rhoptry antigens that coordinate merozoite invasion. PfCERLI1 is a rhoptry associated protein identified to have a direct role in function of this essential merozoite invasion organelle, which has broader implications for understanding apicomplexan invasion biology.
The Novel bis-1,2,4-Triazine MIPS-0004373 Demonstrates Rapid and Potent Activity against All Blood Stages of the Malaria Parasite
Publisher: American Society for Microbiology
Date: 18-10-2021
DOI: 10.1128/AAC.00311-21
Abstract: Novel bis-1,2,4-triazine compounds with potent in vitro activity against Plasmodium falciparum parasites were recently identified. The bis-1,2,4-triazines represent a unique antimalarial pharmacophore and are proposed to act by a novel but as-yet-unknown mechanism of action.
Plasmodium falciparum Heterochromatin Protein 1 Marks Genomic Loci Linked to Phenotypic Variation of Exported Virulence Factors
Publisher: Public Library of Science (PLoS)
Date: 04-09-2009
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