The apicoplast as a potential therapeutic target in and other apicomplexan parasites

Insights into the Cell Division of Neospora caninum

Neospora caninum is an apicomplexan protozoan parasite responsible for causing neosporosis in a range of animal species. It results in substantial economic losses in the livestock industry and poses significant health risks to companion and wild animals. Central to its survival and pathogenicity is the process of cell division, which remains poorly understood in this parasite. In this study, we explored the cell division of Neospora caninum using a combination of modern and classic imaging tools, emphasizing its pivotal role in perpetuating the parasite's life cycle and contributing to its ability to persist within host organisms. We described the intricacies of endodyogeny in Neospora caninum, detailing the dynamics of the cell assembly and the nuclear division by ultrastructure expansion microscopy and regular confocal microscopy. Furthermore, we explored the centrosome dynamics, the centrioles and the apicoplast through the advancement of the cell cycle. Our analysis described with unprecedented detail, the endodyogeny in this parasite. By advancing our understanding of these molecular mechanisms, we aimed to inspire innovative strategies for disease management and control, with the ultimate goal of mitigating the devastating impact of neosporosis on animal health and welfare.

Integrating LASSO Feature Selection and Soft Voting Classifier to Identify Origins of Replication Sites

Background: DNA replication plays an indispensable role in the transmission of genetic information. It is considered to be the basis of biological inheritance and the most fundamental process in all biological life. Considering that DNA replication initiates with a special location, namely the origin of replication, a better and accurate prediction of the origins of replication sites (ORIs) is essential to gain insight into the relationship with gene expression. Objective: In this study, we have developed an efficient predictor called iORI-LAVT for ORIs identification. Methods: This work focuses on extracting feature information from three aspects, including mono-nucleotide encoding, k-mer and ring-function-hydrogen-chemical properties. Subsequently, least absolute shrinkage and selection operator (LASSO) as a feature selection is applied to select the optimal features. Comparing the different combined soft voting classifiers results, the soft voting classifier based on GaussianNB and Logistic Regression is employed as the final classifier. Results: Based on 10-fold cross-validation test, the prediction accuracies of two benchmark datasets are 90.39% and 95.96%, respectively. As for the independent dataset, our method achieves high accuracy of 91.3%. Conclusion: Compared with previous predictors, iORI-LAVT outperforms the existing methods. It is believed that iORI-LAVT predictor is a promising alternative for further research on identifying ORIs.

The apicoplast of Haemoproteus columbae: A comparative study of this organelle genome in Haemosporida

Apicomplexa is a phylum of parasitic protozoa; among them are the order Haemosporida, vector-borne parasites that include those that cause malaria (genus Plasmodium). Most Apicomplexa species have a non-photosynthetic plastid or apicoplast. Given its unique metabolic pathways, this organelle is considered a target for malaria therapeutics. Regardless of its importance, there is a paucity of complete apicoplast genome data hindering comparative studies. Here, the Haemoproteus (Haemoproteus) columbae apicoplast genome (lineage HAECOL1) was obtained using next-generation sequencing. This genome was included in a comparative analysis with other plastids. This 29.8 kb circular genome shares the same structure found in Plasmodium parasites. It is A + T rich (87.7%), comparable but at the higher end of A + T content observed in Plasmodium species (85.5-87.2%). As expected, considering its high A + T content, the synonymous codon usage (RSCU) and the effective number of codons (ENc) showed a moderate codon bias. Several apicoplast genes have a phylogenetic signal. However, unlike mitochondrial genes, single-gene phylogenies have low support in haemosporidian clades that diverged recently. The H. columbae apicoplast genome suggests that the apicoplast function may be conserved across Haemosporida. This parasite could be a model to study this organelle in a non-mammalian system.

iORI-ENST: identifying origin of replication sites based on elastic net and stacking learning

DNA replication is not only the basis of biological inheritance but also the most fundamental process in all living organisms. It plays a crucial role in the cell-division cycle and gene expression regulation. Hence, the accurate identification of the origin of replication sites (ORIs) has a great meaning for further understanding the regulatory mechanism of gene expression and treating genic diseases. In this paper, a novel, feasible and powerful model, namely, iORI-ENST is designed for identifying ORIs. Firstly, we extract the different features by incorporating mono-nucleotide binary encoding and dinucleotide-based spatial autocorrelation. Subsequently, elastic net is utilized as the feature selection method to select the optimal feature set. And then stacking learning is employed to predict ORIs and non-ORIs, which contains random forest, adaboost, gradient boosting decision tree, extra trees and support vector machine. Finally, the ORI sites are identified on the benchmark datasets S1 and S2 with their accuracies of 91.41% and 95.07%, respectively. Meanwhile, an independent dataset S3 is employed to verify the validation and transferability of our model and its accuracy reaches 91.10%. Comparing with state-of-the-art methods, our model achieves more remarkable performance. The results show our model is a feasible, effective and powerful tool for identifying ORIs. The source code and datasets are available at https://github.com/YingyingYao/iORI-ENST.

Using extreme gradient boosting to identify origin of replication in Saccharomyces cerevisiae via hybrid features

DNA replication is a fundamental task that plays a crucial role in the propagation of all living things on earth. Hence, the accurate identification of its origin could be the key to giving an insightful understanding of the regulatory mechanism of gene expression. Indeed, with the robust development of computational techniques and the abundant biological sequencing data, it has become possible for scientists to identify the origin of replication accurately and promptly. This growing concern has drawn a lot of attention among experts in this field. However, to gain better outcomes, more work is required. Therefore, this study is designed to explore the combination of state-of-the-art features and extreme gradient boosting learning system in classifying DNA sequences. Our hybrid approach is able to identify the origin of DNA replication with achieved sensitivity of 85.19%, specificity of 93.83%, accuracy of 89.51%, and MCC of 0.7931. Evidence is presented to show that our proposed method is superior to the state-of-the-art methods on the same benchmark dataset. Moreover, the research results represent a further step towards developing the prediction models for DNA replication in particular and DNA sequences in general.

Recent Advances on the Machine Learning Methods in Identifying DNA Replication Origins in Eukaryotic Genomics

The initiate site of DNA replication is called origins of replication (ORI) which is regulated by a set of regulatory proteins and plays important roles in the basic biochemical process during cell growth and division in all living organisms. Therefore, the study of ORIs is essential for understanding the cell-division cycle and gene expression regulation so that scholars can develop a new strategy against genetic diseases by using the knowledge of DNA replication. Thus, the accurate identification of ORIs will provide key clues for DNA replication research and clinical medicine. Although, the conventional experiments could provide accurate results, they are time-consuming and cost ineffective. On the contrary, bioinformatics-based methods can overcome these shortcomings. Especially, with the emergence of DNA sequences in the post-genomic era, it is highly expected to develop high throughput tools to identify ORIs based on sequence information. In this review, we will summarize the current progress in computational prediction of eukaryotic ORIs including the collection of benchmark dataset, the application of machine learning-based techniques, the results obtained by these methods, and the construction of web servers. Finally, we gave the future perspectives on ORIs prediction. The review provided readers with a whole background of ORIs prediction based on machine learning methods, which will be helpful for researchers to study DNA replication in-depth and drug therapy of genetic defect.

Characterization of a functionally active recombinant 1-deoxy-D-xylulose-5-phosphate synthase from Babesia bovis

The 1-deoxy-D-xylulose-5-phosphate synthase (DXS) enzyme has been characterized in other species, but not in the genus Babesia, which causes major losses in the livestock industries worldwide. Therefore, we isolated, cloned and expressed the wild-type B. bovis dxs cDNA in Escherichia coli and evaluated its enzymatic activity in vitro. DNA sequence analysis revealed an open reading frame of 2061 bp capable of encoding a polypeptide of 686 amino acid residues with a calculated isoelectric point of pH 6.93 and a molecular mass of 75 kDa. The expressed soluble recombinant fusion DXS protein was approximately 78 kDa, which is similar to the native enzyme identified from the parasite merozoite using anti-rDXS serum. The recombinant fusion DXS enzyme exhibited K_m values of 380 ± 46 µM and 790 ± 52 µM for D,L-glyceraldehyde 3-phosphate and pyruvate, respectively. In this work, we present the first cloning, expression and characterization of DXS enzyme from B. bovis.

Quantitative assessment of the proliferation of the protozoan parasite Perkinsus marinus using a bioluminescence assay for ATP content

Perkinsus marinus is a protozoan parasite that causes "Dermo" disease in the eastern oyster Crasssostrea virginica in coastal areas of the USA. Until now, intervention strategies against the parasite have found limited success, and Dermo still remains one of the main hurdles for the restoration of oyster populations. We adapted a commercial adenosine tri-phosphate (ATP) content-based assay to assess the in vitro proliferation of P. marinus in a 96-well plate format, and validated the method by measuring the effects of potential anti-proliferative compounds. The sensitivity (1.5-3.1 × 10(4) cells/well), linearity (R (2) = 0.983), and signal stability (60 min) support the reliability of the assay for assessing cell proliferation. Validation of the assay by culturing P. marinus in the presence of increasing concentrations of triclosan showed a dose-response profile. The IC50 value obtained was higher than that reported earlier, possibly due to the use of different viability assay methods and a different P. marinus strain. The antibiotics G418 and tetracycline and the herbicide fluridone were active against P. marinus proliferation; the IC50 of chloramphenicol, ciprofloxacin, and atrazine was relatively high suggesting either off-target effects or inability to reach the targets. The validation of the ATP-based assay, together with significant advantages of the Perkinsus culture methodology (homogeneity, reproducibility, and high cell densities), underscores the value of this assay for developing high-throughput screens for the identification of novel leader compounds against Perkinsus species, and most importantly, for the closely-related apicomplexan parasites.

Cell biology of chromerids: autotrophic relatives to apicomplexan parasites

Chromerida are algae possessing a complex plastid surrounded by four membranes. Although isolated originally from stony corals in Australia, they seem to be globally distributed. According to their molecular phylogeny, morphology, ultrastructure, structure of organellar genomes, and noncanonical pathway for tetrapyrrole synthesis, these algae are thought to be the closest known phototrophic relatives to apicomplexan parasites. Here, we summarize the current knowledge of cell biology and evolution of this novel group of algae, which contains only two formally described species, but is apparently highly diverse and virtually ubiquitous in marine environments.

A review of the infection, genetics, and evolution of Neospora caninum: from the past to the present

This paper is a review of current knowledge on Neospora caninum in the context of other apicomplexan parasites and with an emphasis on: life cycle, disease, epidemiology, immunity, control and treatment, evolution, genomes, and biological databases and web resources. N. caninum is an obligate, intracellular, coccidian, protozoan parasite of the phylum Apicomplexa. Infection can cause the clinical disease neosporosis, which most notably is associated with abortion in cattle. These abortions are a major root cause of economic loss to both the dairy and beef industries worldwide. N. caninum has been detected in every country in which a study has been specifically conducted to detect this parasite in cattle. The major mode of transmission in cattle is transplacental (or vertical) transmission and several elements of the N. caninum life cycle are yet to be studied in detail. The outcome of an infection is inextricably linked to the precise timing of the infection coupled with the status of the immune system of the dam and foetus. There is no community consensus as to whether it is the dam's pro-inflammatory cytotoxic response to tachyzoites that kills the foetus or the tachyzoites themselves. From economic analysis the most cost-effective approach to control neosporosis is a vaccine. The perfect vaccine would protect against both infection and the clinical disease, and this implies a vaccine is needed that can induce a non-foetopathic cell mediated immunity response. Researchers are beginning to capitalise on the vast potential of -omics data (e.g. genomes, transcriptomes, and proteomes) to further our understanding of pathogens but especially to identify vaccine and drug targets. The recent publication of a genome for N. caninum offers vast opportunities in these areas.

Babesia: a world emerging

Babesia are tick-transmitted hemoprotozooans that infect mammals and birds, and which are acknowledged for their major impact on farm and pet animal health and associated economic costs worldwide. Additionally, Babesia infections of wildlife can be fatal if associated with stressful management practices; and human babesiosis, also transmitted by blood transfusion, is an increasing public-health concern. Due to the huge diversity of species reported to serve as Babesia hosts, all vertebrates might be potential carriers, as long as they are adequate hosts for Babesia-vector ticks. We here provide a comprehensive overview of the most relevant Babesia species, and a discussion of the classical taxonomic criteria. Babesia, Cytauxzoon and Theileria parasites are closely related and collectively referred to as piroplasmids. A possible scenario for the history of piroplasmids is presented in the context of recent findings, and its implications for future research avenues are outlined. Phylogenetic trees of all available 18S rRNA and hsp70 genes were generated, based on which we present a thoroughly revised molecular classification, comprising five monophyletic Babesia lineages, one Cytauxzoon clade, and one Theileria clade. Updated 18S rRNA and beta-tubulin gene trees of the B. microti isolates agree with those previously reported. To reconcile estimates of the origin of piroplasmids and ticks (~300 Ma, respectively), and mammalian radiation (60 Ma), we hypothesize that the dixenous piroplasmid life cycle evolved with the origin of ticks. Thus, the observed time gap between tick origin and mammalian radiation indicates the existence of hitherto unknown piroplasmid lineages and/or species in extant vertebrate taxa, including reptiles and possibly amphibians. The development and current status of the molecular taxonomy of Babesia, with emphasis on human-infecting species, is discussed. Finally, recent results from population genetic studies of Babesia parasites, and their implications for the development of pathogenicity, drug resistance and vaccines, are summarized.

Nucleotide correlation based measure for identifying origin of replication in genomic sequences

Computational prediction of the origin of replication is a challenging problem and of immense interest to biologists. Several methods have been proposed for identifying the replicon site for various classes of organisms. However, these methods have limited applicability since the replication mechanism is different in different organisms. We propose a correlation measure and show that it is correctly able to predict the origin of replication in most of the bacterial genomes. When applied to Methanocaldococcus jannaschii, Plasmodium falciparum apicoplast and Nicotiana tabacum plastid, this correlation based method is able to correctly predict the origin of replication whereas the generally used GC skew measure fails. Thus, this correlation based measure is a novel and promising tool for predicting the origin of replication in a wide class of organisms. This could have important implications in not only gaining a deeper understanding of the replication machinery in higher organisms, but also for drug discovery.

A Toxoplasma gondii mutant highlights the importance of translational regulation in the apicoplast during animal infection

Toxoplasma gondii is an obligate intracellular parasite of all warm-blooded animals. We previously described a forward genetic screen to identify T. gondii mutants defective in the establishment of a chronic infection. One of the mutants isolated was disrupted in the 3' untranslated region (3'UTR) of an orthologue of bacterial translation elongation factor G (EFG). The mutant does not have a growth defect in tissue culture. Genetic complementation of this mutant with the genomic locus of TgEFG restores virulence in an acute infection mouse model. Epitope tagged TgEFG localized to the apicoplast, via a non-canonical targeting signal, where it functions as an elongation factor for translation in the apicoplast. Comparisons of TgEFG expression constructs with wild-type or mutant 3'UTRs showed that a wild-type 3'UTR is necessary for translation of TgEFG. In tissue culture, the TgEFG transcript is equally abundant in wild-type and mutant parasites; however, during an animal infection, the TgEFG transcript is increased more than threefold in the mutant. These results highlight that in tissue culture, translation in the apicoplast can be diminished, but during an animal infection, translation in the apicoplast must be fully functional.

The search for the missing link: a relic plastid in Perkinsus?

Perkinsus marinus (Phylum Perkinsozoa) is a protozoan parasite that has devastated natural and farmed oyster populations in the USA, significantly affecting the shellfish industry and the estuarine environment. The other two genera in the phylum, Parvilucifera and Rastrimonas, are parasites of microeukaryotes. The Perkinsozoa occupies a key position at the base of the dinoflagellate branch, close to its divergence from the Apicomplexa, a clade that includes parasitic protista, many harbouring a relic plastid. Thus, as a taxon that has also evolved toward parasitism, the Perkinsozoa has attracted the attention of biologists interested in the evolution of this organelle, both in its ultrastructure and the conservation, loss or transfer of its genes. A review of the recent literature reveals mounting evidence in support of the presence of a relic plastid in P. marinus, including the presence of multimembrane structures, characteristic metabolic pathways and proteins with a bipartite N-terminal extension. Further, these findings raise intriguing questions regarding the potential functions and unique adaptation of the putative plastid and/or plastid genes in the Perkinsozoa. In this review we analyse the above-mentioned evidence and evaluate the potential future directions and expected benefits of addressing such questions. Given the rapidly expanding molecular/genetic resources and methodological toolbox for Perkinsus spp., these organisms should complement the currently established models for investigating plastid evolution within the Chromalveolata.

The Alveolate Perkinsus marinus: biological insights from EST gene discovery

Background

Perkinsus marinus, a protozoan parasite of the eastern oyster Crassostrea virginica, has devastated natural and farmed oyster populations along the Atlantic and Gulf coasts of the United States. It is classified as a member of the Perkinsozoa, a recently established phylum considered close to the ancestor of ciliates, dinoflagellates, and apicomplexans, and a key taxon for understanding unique adaptations (e.g. parasitism) within the Alveolata. Despite intense parasite pressure, no disease-resistant oysters have been identified and no effective therapies have been developed to date.

Results

To gain insight into the biological basis of the parasite's virulence and pathogenesis mechanisms, and to identify genes encoding potential targets for intervention, we generated >31,000 5' expressed sequence tags (ESTs) derived from four trophozoite libraries generated from two P. marinus strains. Trimming and clustering of the sequence tags yielded 7,863 unique sequences, some of which carry a spliced leader. Similarity searches revealed that 55% of these had hits in protein sequence databases, of which 1,729 had their best hit with proteins from the chromalveolates (E-value ≤ 1e-5). Some sequences are similar to those proven to be targets for effective intervention in other protozoan parasites, and include not only proteases, antioxidant enzymes, and heat shock proteins, but also those associated with relict plastids, such as acetyl-CoA carboxylase and methyl erythrithol phosphate pathway components, and those involved in glycan assembly, protein folding/secretion, and parasite-host interactions.

Conclusions

Our transcriptome analysis of P. marinus, the first for any member of the Perkinsozoa, contributes new insight into its biology and taxonomic position. It provides a very informative, albeit preliminary, glimpse into the expression of genes encoding functionally relevant proteins as potential targets for chemotherapy, and evidence for the presence of a relict plastid. Further, although P. marinus sequences display significant similarity to those from both apicomplexans and dinoflagellates, the presence of trans-spliced transcripts confirms the previously established affinities with the latter. The EST analysis reported herein, together with the recently completed sequence of the P. marinus genome and the development of transfection methodology, should result in improved intervention strategies against dermo disease.

The malaria parasite Plasmodium falciparum: cell biological peculiarities and nutritional consequences

Apicomplexan parasites obligatorily invade and multiply within eukaryotic cells. Phylogenetically, they are related to a group of algae which, during their evolution, have acquired a secondary endosymbiont. This organelle, which in the parasite is called the apicoplast, is highly reduced compared to the endosymbionts of algae, but still contains many plant-specific biosynthetic pathways. The malaria parasite Plasmodium falciparum infects mammalian erythrocytes which are devoid of intracellular compartments and which largely lack biosynthetic pathways. Despite the limited resources of nutrition, the parasite grows and generates up to 32 merozoites which are the infectious stages of the complex life cycle. A large part of the intra-erythrocytic development takes place in the so-called parasitophorous vacuole, a compartment which forms an interface between the parasite and the cytoplasm of the host cell. In the course of parasite growth, the host cell undergoes dramatic alterations which on one hand contribute directly to the symptoms of severe malaria and which, on the other hand, are also required for parasite survival. Some of these alterations facilitate the acquisition of nutrients from the extracellular environment which are not provided by the host cell. Here, we describe the cell biologically unique interactions between an intracellular eukaryotic pathogen and its metabolically highly reduced host cell. We further discuss current models to explain the appearance of pathogen-induced novel physiological properties in a host cell which has lost its genetic programme.

The Toxoplasma gondii plastid replication and repair enzyme complex, PREX

A plastid-like organelle, the apicoplast, is essential to the majority of medically and veterinary important apicomplexan protozoa including Toxoplasma gondii and Plasmodium. The apicoplast contains multiple copies of a 35 kb genome, the replication of which is dependent upon nuclear-encoded proteins that are imported into the organelle. In P. falciparum an unusual multi-functional gene, pfprex, was previously identified and inferred to encode a protein with DNA primase, DNA helicase and DNA polymerase activities. Herein, we report the presence of a prex orthologue in T. gondii. The protein is predicted to have a bi-partite apicoplast targeting sequence similar to that demonstrated on the PfPREX polypeptide, capable of delivering marker proteins to the apicoplast. Unlike the P. falciparum gene that is devoid of introns, the T. gondii prex gene carries 19 introns, which are spliced to produce a contiguous mRNA. Bacterial expression of the polymerase domain reveals the protein to be active. Consistent with the reported absence of a plastid in Cryptosporidium species, in silico analysis of their genomes failed to demonstrate an orthologue of prex. These studies indicate that prex is conserved across the plastid-bearing apicomplexans and may play an important role in the replication of the plastid genome.

Sequential processing of the Toxoplasma apicoplast membrane protein FtsH1 in topologically distinct domains during intracellular trafficking

FtsH proteins are hexameric transmembrane proteases found in chloroplasts, mitochondria and bacteria. In the protozoan Toxoplasma gondii, FtsH1 is localized to membranes of the apicoplast, a relict chloroplast present in many apicomplexan parasites. We have shown that although T. gondii FtsH1 lacks the typical bipartite targeting presequence seen on apicoplast luminal proteins, it is targeted to the apicoplast via the endoplasmic reticulum. In this report, we show that FtsH1 undergoes processing events to remove both the N- and C-termini, which are topologically separated by the membrane in which FtsH1 is embedded. Pulse-chase analysis showed that N-terminal cleavage precedes C-terminal cleavage. Unlike the processing of the N-terminal transit peptide of luminal proteins, which occurs in the apicoplast, analysis of ER-retained mutants showed that N-terminal processing of FtsH1 occurs in the endoplasmic reticulum. Two of four FtsH1 mutants bearing internal epitope tags accumulated in structures peripheral to the apicoplast, implying that FtsH1 trafficking is highly sensitive to changes in protein structure. These mutant proteins did not undergo C-terminal processing, suggesting that this processing step occurs after localization to the plastid. Mutation of the peptidase active site demonstrated that neither processing event occurs in cis. These data support a model in which multiple proteases act at different points of the trafficking pathway to form mature FtsH1, making its processing more complex than other FtsHs and unique among apicoplast proteins described thus far.

Disruption of a mitochondrial MutS DNA repair enzyme homologue confers drug resistance in the parasite Toxoplasma gondii

MutS homologues (MSHs) are critical components of the eukaryotic mismatch repair machinery. In addition to repairing mismatched DNA, mismatch repair enzymes are known in higher eukaryotes to directly signal cell cycle arrest and apoptosis in response to DNA-damaging agents. Accordingly, mammalian cells lacking certain MSHs are resistant to chemotherapeutic drugs. Interestingly, we have discovered that the disruption of TgMSH-1, an MSH in the pathogenic parasite, Toxoplasma gondii, confers drug resistance. Through a genetic selection for T. gondii mutants resistant to the antiparasitic drug monensin, we have isolated a strain that is resistant not only to monensin but also to salinomycin and the alkylating agent, methylnitrosourea. We have shown that this phenotype is due to the disruption of TgMSH-1 as the multidrug-resistance phenotype is complemented by a wild-type copy of TgMSH-1 and is recapitulated by a directed disruption of this gene in a wild-type strain. We have also shown that, unlike previously described MSHs involved in signalling, TgMSH-1 localizes to the parasite mitochondrion. These results provide the first example of a mitochondrial MSH that is involved in drug sensitivity and implicate the induction of mitochondrial stress as a mode of action of the widely used drug, monensin.

Nuclear gyrB encodes a functional subunit of the Plasmodium falciparum gyrase that is involved in apicoplast DNA replication

The DNA replication machinery of the Plasmodium falciparum apicoplast is a validated drug target. Nuclear-encoded gyrase subunits are predicted to play a critical role in maintaining DNA topology during the D-loop/bi-directional ori replication process of the parasite. We show the presence of P. falciparum gyrase subunits in parasite lysates by using antibodies generated against recombinant gyrase A and B. The ATPase activity of PfGyrB was inhibited by novobiocin that also caused parasite death in culture. Reduction of apicoplast/nuclear DNA ratio in the presence of novobiocin indicated that the drug targets apicoplast DNA replication. Molecular modeling of gyrase A and B subunits revealed extensive fold conservation with the Escherichia coli counterparts as well as the presence of a long disordered loop adjacent to the ATPase domain of PfGyrB. Our results have implications for development of PfGyrB as a drug target against malaria.

Integration and mining of malaria molecular, functional and pharmacological data: how far are we from a chemogenomic knowledge space?

The organization and mining of malaria genomic and post-genomic data is important to significantly increase the knowledge of the biology of its causative agents, and is motivated, on a longer term, by the necessity to predict and characterize new biological targets and new drugs. Biological targets are sought in a biological space designed from the genomic data from Plasmodium falciparum, but using also the millions of genomic data from other species. Drug candidates are sought in a chemical space containing the millions of small molecules stored in public and private chemolibraries. Data management should, therefore, be as reliable and versatile as possible. In this context, five aspects of the organization and mining of malaria genomic and post-genomic data were examined: 1) the comparison of protein sequences including compositionally atypical malaria sequences, 2) the high throughput reconstruction of molecular phylogenies, 3) the representation of biological processes, particularly metabolic pathways, 4) the versatile methods to integrate genomic data, biological representations and functional profiling obtained from X-omic experiments after drug treatments and 5) the determination and prediction of protein structures and their molecular docking with drug candidate structures. Recent progress towards a grid-enabled chemogenomic knowledge space is discussed.

The apicoplast of Plasmodium falciparum is translationally active

Apicoplast, the plastid-like organelle of apicomplexan parasites, has generated interest as a putative drug target. Although transcripts for genes encoded by the 35 kb circular plastid DNA have been detected, the actual presence of their protein products has only been postulated. We provide evidence for translation of the tufA gene encoded by the Plasmodium falciparum apicoplast genome. Translation elongation factor Tu (EF-Tu), the product of tufA, was localized within the organelle. TufA was found to express maximally in the trophozoite stage of the intraerythrocytic cycle. Additionally, the drug thiostrepton that has a binding site in apicoplast LSU rRNA, reduced P. falciparum apicoplast EF-Tu levels thus strengthening the view that translation in the apicoplast is the site of action of this drug.

Development of antiparasitic drugs in the 21st century

Prospects for discovering new antiparasitic drugs for veterinary medicine in the coming century will be determined by economic, social and scientific factors. Consolidation in the pharmaceutical industry in general, and the animal health industry in particular, changes the business conditions in which drug discovery for veterinary medicine occurs. Social pressures on traditional animal agriculture and companion animal ownership have shifted the interest of animal companies primarily to pet medicine. Antiparasitic drug discovery is more than ever targeted to the most lucrative market segments, but the excellence of available drugs, and the apparent lack of resistance in important parasites, reduces industrial motivation to invest in parasitology. Veterinary parasitologists in academia will still have the chance to interact with their industrial counterparts in the traditional ways of supporting drug discovery and development. Nonetheless, there are many new opportunities to expand the research horizons of veterinary parasitology to strengthen the case for retaining a significant presence in the animal health industry.

Phospholipids in parasitic protozoa

Parasitic protozoa are surrounded by membrane structures that have a different lipid and protein composition relative to membranes of the host. The parasite membranes are essential structurally and also for parasite specific processes, like host cell invasion, nutrient acquisition or protection against the host immune system. Furthermore, intracellular parasites can modulate membranes of their host, and trafficking of membrane components occurs between host membranes and those of the intracellular parasite. Phospholipids are major membrane components and, although many parasites scavenge these phospholipids from their host, most parasites also synthesise phospholipids de novo, or modify a large part of the scavenged phospholipids. It was recently shown that some parasites like Plasmodium have unique phospholipid metabolic pathways. This review will focus on new developments in research on phospholipid metabolism of parasitic protozoa in relation to parasite-specific membrane structures and function, as well as on several targets for interference with the parasite phospholipid metabolism with a view to developing new anti-parasitic drugs.

Replication of the Plasmodium falciparum apicoplast DNA initiates within the inverted repeat region

The 35kb apicoplast genomes (plDNA) of Plasmodium falciparum and Toxoplasma gondii share close sequence similarity but differ in their in vivo topologies. Although sequence analysis of tandem repeats of T. gondii plDNA has suggested the presence of replication initiation sites within the inverted repeat region, the replication origins (ori) of the P. falciparum circular plDNA have not been identified. Using 5' end-labelled nascent DNA as probe, we demonstrate that the ori of P. falciparum plDNA is localised within the inverted repeat region. Our results also indicate the presence of two initiation sites within each inverted repeat segment of the circular plDNA of P. falciparum suggestive of a four D-loop/bi-directional ori mechanism of DNA replication.

Structure of 2C-methyl-d-erythritol-2,4-cyclodiphosphate synthase involved in mevalonate-independent biosynthesis of isoprenoids

Isoprenoids are biosynthesized from isopentenyl diphosphate and the isomeric dimethylallyl diphosphate via the mevalonate pathway or a mevalonate-independent pathway that was identified during the last decade. The non-mevalonate pathway is present in many bacteria, some algae and in certain protozoa such as the malaria parasite Plasmodium falciparum and in the plastids of higher plants, but not in mammals and archaea. Therefore, these enzymes have been recognised as promising drug targets. We report the crystal structure of Escherichia coli 2C- methyl-d-erythritol-2,4-cyclodiphosphate synthase (IspF), which converts 4-diphosphocytidyl-2C-methyl-d-erythritol 2-phosphate into 2C-methyl-d-erythritol 2,4-cyclodiphosphate and CMP in a Mg-dependent reaction. The protein forms homotrimers that tightly bind one zinc ion per subunit at the active site, which helps to position the substrate for direct attack of the 2-phosphate group on the beta-phosphate.

Molecular characterization of a 2-Cys peroxiredoxin from the human malaria parasite Plasmodium falciparum

We have identified the 2-Cys peroxiredoxin (PfPrx-1) from the human malaria parasite Plasmodium falciparum. The PfPrx-1 showed the highest identity at amino acid level to the type II Prx among the currently known six subfamilies of mammalian Prx. The sequence identity between the PfPrx-1 and the previously reported 1-Cys Prx of P. falciparum (PfPrx-2), which corresponded to mammalian type VI Prx, was 25%. This suggests that the parasite possesses two Prx subfamilies. The PfPrx-1 showed significant sequence similarities with those of 2-Cys peroxiredoxins of plants in the BLASTX search. This may reflect the consequences of a genetic transfer from an algal endosymbiont to the parasite nucleus during evolution. The recombinant PfPrx-1 protein (rPfPrx-1) was expressed as a histidine fusion protein in Escherichia coli and purified with Ni chromatography. The rPfPrx-1 existed as dimers under non-reducing conditions and dissociated into monomers in the presence of dithiothreitol. The PfPrx-1 protein also exists as a dimer in the parasites themselves. The reduction of the oxidized enzyme by the donation of electrons from E. coli thioredoxin (Trx)/Trx reductase system was demonstrated in its reaction with H(2)O(2), using the rPfPrx-1 protein. These results suggested that the PfPrx-1 can act as a terminal peroxidase of the parasite Trx system. An elevated expression of the PfPrx-1 protein seen in the trophozoite, the stage with active metabolism, suggests an association of the parasite Trx system with its intracellular redox control.

The role of molecular biology in veterinary parasitology

The tools of molecular biology are increasingly relevant to veterinary parasitology. The sequencing of the complete genomes of Caenorhabditis elegans and other helminths and protozoa is allowing great advances in studying the biology, and improving diagnosis and control of parasites. Unique DNA sequences provide very high levels of specificity for the diagnosis and identification of parasite species and strains, and PCR allows extremely high levels of sensitivity. New techniques, such as the use of uniquely designed molecular beacons and DNA microarrays will eventually allow rapid screening for specific parasite genotypes and assist in diagnostic and epidemiological studies of veterinary parasites. The ability to use genome data to clone and sequence genes which when expressed will provide antigens for vaccine screening and receptors and enzymes for mechanism-based chemotherapy screening will increase our options for parasite control. In addition, DNA vaccines can have desirable characteristics, such as sustained stimulation of the host immune system compared with protein based vaccines. One of the greatest threats to parasite control has been the development of drug resistance in parasites. Our knowledge of the basis of drug resistance and our ability to monitor its development with highly sensitive and specific DNA-based assays for 'resistance'-alleles will help maintain the effectiveness of existing antiparasitic drugs and provide hope that we can maintain control of parasitic disease outbreaks.

Anti-toxoplasma activities of 24 quinolones and fluoroquinolones in vitro: prediction of activity by molecular topology and virtual computational techniques

The apicoplast, a plastid-like organelle of Toxoplasma gondii, is thought to be a unique drug target for quinolones. In this study, we assessed the in vitro activity of quinolones against T. gondii and developed new quantitative structure-activity relationship models able to predict this activity. The anti-Toxoplasma activities of 24 quinolones were examined by means of linear discriminant analysis (LDA) using topological indices as structural descriptors. In parallel, in vitro 50% inhibitory concentrations (IC(50)s) were determined in tissue culture. A multilinear regression (MLR) analysis was then performed to establish a model capable of classifying quinolones by in vitro activity. LDA and MLR analysis were applied to virtual structures to identify the influence of each atom or substituent of the quinolone ring on anti-Toxoplasma activity. LDA predicted that 20 of the 24 quinolones would be active against T. gondii. This was confirmed in vitro for most of the quinolones. Trovafloxacin, grepafloxacin, gatifloxacin, and moxifloxacin were the quinolones most potent against T. gondii, with IC(50)s of 0.4, 2.4, 4.1, and 5.1 mg/liter, respectively. Using MLR analysis, a good correlation was found between measured and predicted IC(50)s (r(2) = 0.87, cross-validation r(2) = 0.74). MLR analysis showed that the carboxylic group at position C-3 of the quinolone ring was not essential for anti-Toxoplasma activity. In contrast, activity was totally dependent on the presence of a fluorine at position C-6 and was enhanced by the presence of a methyl group at C-5 or an azabicyclohexane at C-7. A nucleophilic substituent at C-8 was essential for the activity of gatifloxacin and moxifloxacin.

Cotrimoxazole for prenatal treatment of congenital toxoplasmosis?

Congenital toxoplasmosis is still one of the most frequent causes of fetal death. Despite a significant improvement in diagnosis, particularly in utero diagnosis, maternal treatment is only partially effective in preventing transmission to the fetus and treating fetal infection. Maternal treatment is based on drugs developed 50 years ago, which may have limited efficacy (spiramycin) or serious side-effects (pyrimethamine). Data on the use of cotrimoxazole in mouse models of toxoplasmosis and for preventing toxoplasmic encephalitis in patients suffering from AIDS have led Francis Derouin and colleagues to consider the potential of cotrimoxazole for prenatal prevention and treatment of toxoplasmic fetal death.

Theileria parva genomics reveals an atypical apicomplexan genome

The discipline of genomics is setting new paradigms in research approaches to resolving problems in human and animal health. We propose to determine the genome sequence of Theileria parva, a pathogen of cattle, using the random shotgun approach pioneered at The Institute for Genomic Research (TIGR). A number of features of the T. parva genome make it particularly suitable for this approach. The G+C content of genomic DNA is about 31%, non-coding repetitive DNA constitutes less than 1% of total DNA and a framework for the 10-12 Mbp genome is available in the form of a physical map for all four chromosomes. Minisatellite sequences are the only dispersed repetitive sequences identified so far, but they are limited in distribution to 13 of 33 SfiI fragments. Telomere and sub-telomeric non-coding sequences occupy less than 10 kbp at each chromosomal end and there are only two units encoding cytoplasmic rRNAs. Three sets of distinct multicopy sequences encoding ORFs have been identified but it is not known if these are associated with expression of parasite antigenic diversity. Protein coding genes exhibit a bias in codon usage and introns when present are unusually short. Like other apicomplexan organisms, T. parva contains two extrachromosomal DNAs, a mitochondrial DNA and a plastid DNA molecule. By annotating the genome sequence, in combination with the use of microarray technology and comparative genomics, we expect to gain significant insights into unique aspects of the biology of T. parva. We believe that the data will underpin future research to aid in the identification of targets of protective CD8+ cell mediated immune responses, and parasite molecules involved in inducing reversible host leukocyte transformation and tumour-like behaviour of transformed parasitised cells.

Impact of a plastid-bearing endocytobiont on apicomplexan genomes

Both the chromosomal and extrachromosomal components of the apicomplexan genome have been supplemented by genes from a plastid-bearing endocytobiont: probably an algal cell. The sequence of the apicomplexan plastid's vestigial genome indicates that a large number (>100) of genes of endocytobiotic origin must have transferred laterally to the host cell nucleus where they control maintenance of the plastid organelle and supply its functional components by means of post-translational protein trafficking. Should the nuclear genes prove to be less divergent phylogenetically than those left on the plastid genome, they might give better clues than we have at present to the origin of the plastid-bearing endocytobiont. Most of these nuclear genes still await discovery, but the on-going genome sequencing project will reveal the function of the organelle, as well as many "housekeeping" processes of interest on a wider front. The plastid's own protein synthetic machinery, being cyanobacterial in origin, offers conventional targets for antibiotic intervention, and this is discussed here using a structural model of elongation factor Tu. Uncovering the vital function(s) of the plastid organelle will provide new drug targets.

Targeting and subcellular localization of Toxoplasma gondii catalase. Identification of peroxisomes in an apicomplexan parasite

We sought to identify and characterize peroxisomes in the apicomplexan parasite Toxoplasma gondii. To initiate this process, we first cloned and sequenced the gene for T. gondii catalase (EC 1. 11.1.6), a marker enzyme for peroxisomes in eukaryotic cells. The gene predicts a protein of 57.2 kDa and 502 amino acids and has a strong homology to other eukaryotic catalases. A polyclonal antiserum raised against a glutathione S-transferase fusion protein recognized a single band with a molecular mass of 63 kDa by immunoblot. By immunofluorescence T. gondii catalase is present primarily in a punctate staining pattern anterior to the parasite nucleus. This compartment is distinguishable from other parasite organelles, namely micronemes, rhoptries, dense granules, and the apicoplast. Cytochemical visualization of catalase using diaminobenzidine precipitation gives a vesicular staining pattern anterior to the nucleus at the light level and round, vesicular structures with an estimated diameter of 100-300 nm by electron microscopy. T. gondii catalase has a putative C-terminal peroxisomal targeting signal in the last 3 amino acids (-AKM). Expression of T. gondii catalase in mammalian cells results in peroxisomal localization, whereas a construct lacking the targeting signal remains in the cytosol. Furthermore, addition of -AKM to the C terminus of chloramphenicol acetyltransferase is sufficient to target this protein to peroxisomes. These results provide the first evidence for peroxisomes in Apicomplexan parasites.

The genome of the malaria parasite

The genome of the human malaria parasite Plasmodium falciparum is being sequenced by an international consortium. Two of the parasite's 14 chromosomes have been completed and several other chromosomes are nearly finished. Even at this early stage of the project, analysis of the genome sequence has provided promising new leads for drug and vaccine development.

The complete nucleotide sequence of chromosome 3 of Plasmodium falciparum

Analysis of Plasmodium falciparum chromosome 3, and comparison with chromosome 2, highlights novel features of chromosome organization and gene structure. The sub-telomeric regions of chromosome 3 show a conserved order of features, including repetitive DNA sequences, members of multigene families involved in pathogenesis and antigenic variation, a number of conserved pseudogenes, and several genes of unknown function. A putative centromere has been identified that has a core region of about 2 kilobases with an extremely high (adenine + thymidine) composition and arrays of tandem repeats. We have predicted 215 protein-coding genes and two transfer RNA genes in the 1,060,106-base-pair chromosome sequence. The predicted protein-coding genes can be divided into three main classes: 52.6% are not spliced, 45.1% have a large exon with short additional 5' or 3' exons, and 2.3% have a multiple exon structure more typical of higher eukaryotes.

Biochemical peculiarities and drug targets in Cryptosporidium parvum: lessons from other coccidian parasites

There is an urgent need for effective medicines for treating human and animal cryptosporidiosis. In the absence of drugs being found using an empirical route, the structure-based approach may be the better option for discovering new chemotherapeutic agents against these diseases. With this objective, what possible drug targets are there? Here, Graham Coombs speculates on the best putative targets for chemotherapeutic attack, and reviews what is known and what can be deduced about the biochemical features of Cryptosporidium parvum, the causative agent of cryptosporidiosis, emphasizing the ways in which the parasite differs biochemically from its mammalian hosts.