Laboratory maintenance of rodent malaria parasites.

We provide a series of protocols that have been used for the cyclic transmission of rodent malaria parasites in the laboratory. This is now possible both in vivo and in vitro. We focus on the least "resource intensive" and generic methods that we find applicable to any parasite-host combination. Nonetheless, we recognize that the ability to construct transgenic "reporter" parasites/hosts now permits the use of elegant analytical and imaging technologies both in vitro, ex vivo, and in vivo in specific instances. The descriptions given illustrate methods routinely used for the maintenance of P. berghei; where critical, we note important differences when transmitting other parasite species.

Assessing transmission blockade in Plasmodium spp.

Here we describe a series of methods that can be used to assess the activities of "vaccines," drugs, and genetically modified vectors, for their abilities to inhibit transmission of Plasmodium from its vertebrate to its mosquito hosts. The selection of method to be used is determined by the purpose of the experiment, which can include the determination of the site/time of activity, and/or the potential reduction in transmission achieved.

The rhoptry proteome of Eimeria tenella sporozoites.

Proteins derived from the rhoptry secretory organelles are crucial for the invasion and survival of apicomplexan parasites within host cells. The rhoptries are club-shaped organelles that contain two distinct subpopulations of proteins that localise to separate compartments of the organelle. Proteins from the neck region (rhoptry neck proteins, RON) are secreted early in invasion and a subset of these is critical for the formation and function of the moving junction between parasite and host membranes. Proteins from the bulb compartment (rhoptry protein, ROP) are released later, into the nascent parasitophorous vacuole where they have a role in modifying the vacuolar environment, and into the host cell where they act as key determinants of virulence through their ability to interact with host cell signalling pathways, causing an array of downstream effects. In this paper we present the results of an extensive proteomics analysis of the rhoptry organelles from the coccidian parasite, Eimeria tenella, which is a highly pathogenic parasite of the domestic chicken causing severe caecal coccidiosis. Several different classes of rhoptry protein have been identified. First are the RON proteins that have varying degrees of similarity to proteins of Toxoplasma gondii and Neospora caninum. For some RON families, E. tenella expresses more than one gene product and many of the individual RON proteins are differentially expressed between the sporozoite and merozoite developmental stages. The E. tenella sporozoite rhoptry expresses only a limited repertoire of proteins with homology to known ROP proteins from other coccidia, including just two secreted ROP kinases, both of which appear to be equipped for catalytic activity. Finally, a large number of hitherto undescribed proteins that map to the sporozoite rhoptry are identified, many of which have orthologous proteins encoded within the genomes of T. gondii and N. caninum.

Proteomic comparison of four Eimeria tenella life-cycle stages: unsporulated oocyst, sporulated oocyst, sporozoite and second-generation merozoite.

We report the proteomes of four life-cycle stages of the Apicomplexan parasite Eimeria tenella. A total of 1868 proteins were identified, with 630, 699, 845 and 1532 found in early oocysts (unsporulated), late oocysts (sporulated), sporozoites and second-generation merozoites, respectively. A multidimensional protein identification technology shotgun approach identified 812 sporozoites, 1528 merozoites and all of the oocyst proteins, whereas 2-D gel proteomics identified 230 sporozoites and 98 merozoite proteins. Comparing the invasive stages, we find moving junction components RON2 in both, whereas AMA-1 and RON4 are found only in merozoites and AMA-2 and RON5 are only found in sporozoites, suggesting stage-specific moving junction proteins. During early oocyst to sporozoite development, refractile body and most "glideosome" proteins are found throughout, whereas microneme and most rhoptry proteins are only found after sporulation. Quantitative analysis indicates glycolysis and gluconeogenesis are the most abundant metabolic groups detected in all stages. The mannitol cycle "off shoot" of glycolysis was not detected in merozoites but was well represented in the other stages. However, in merozoites we find more protein associated with oxidative phosphorylation, suggesting a metabolic shift mobilising greater energy production. We find a greater abundance of protein linked to transcription, protein synthesis and cell cycle in merozoites than in sporozoites, which may be residual protein from the preceding massive replication during schizogony.

Characterisation of Plasmodium invasive organelles; an ookinete microneme proteome.

Secretion of microneme proteins is essential to Plasmodium invasion but the molecular composition of these secretory organelles remains poorly defined. Here, we describe the first Plasmodium microneme proteome. Purification of micronemes by subcellular fractionation from cultured ookinetes was confirmed by enrichment of known micronemal proteins and electron microscopy. Quantitation of electron micrographs showed >14-fold microneme enrichment compared to the intact ookinete, such that micronemes comprised 85% of the identifiable organelles in the fraction. Gel LC-MS/MS of the most abundant protein constituents of the fraction identified three known micronemal proteins chitinase, CTRP, SOAP, together with protein disulphide isomerase (PDI) and HSP70. Highly sensitive MudPIT shotgun proteomics described a total of 345 proteins in the fraction. M1 aminopeptidase and PDI, the former a recognised target of drug development, were both shown to have a micronemal location by IFA. We further identified numerous proteins with established vesicle trafficking and signaling functions consistent with micronemes being part of a regulated secretory pathway. Previously uncharacterised proteins comprise the largest functional group of the microneme proteome and will include secreted proteins important to invasion.

Plasmodium male development gene-1 (mdv-1) is important for female sexual development and identifies a polarised plasma membrane during zygote development.

Successful development of Plasmodium sexual stages is essential for parasite survival, but the genes involved are poorly understood. We 'knocked out' the male development gene-1 (mdv-1) locus in Plasmodium berghei and found it to be important in female gametocyte activation. Indirect immunofluorescence assays show MDV-1 has a punctate cytoplasmic distribution in gametocytes. After activation of both females and males, MDV-1 is more peripherally located but in males exclusively it becomes concentrated in a few large foci. In vitro ookinete conversion assays that test the ability of activated female gametocytes to develop into retort stage ookinetes, suggests a complicit role for MDV-1, with the knock-out parasite producing 86% reduction in ookinetes. The retort stage ookinete develops from the zygote by increasing growth of an apical protrusion and MDV-1 locates at the 'leading' extracellular apical pole of this protrusion. In the fully developed ookinete MDV-1 is localised to the posterior pole. In vivo, the knock-out parasites demonstrate a phenotype in which there is a 90% reduction of parasite transmission to oocysts in mosquitoes.

The proteome of Toxoplasma gondii: integration with the genome provides novel insights into gene expression and annotation.

BACKGROUND: Although the genomes of many of the most important human and animal pathogens have now been sequenced, our understanding of the actual proteins expressed by these genomes and how well they predict protein sequence and expression is still deficient. We have used three complementary approaches (two-dimensional electrophoresis, gel-liquid chromatography linked tandem mass spectrometry and MudPIT) to analyze the proteome of Toxoplasma gondii, a parasite of medical and veterinary significance, and have developed a public repository for these data within ToxoDB, making for the first time proteomics data an integral part of this key genome resource. RESULTS: The draft genome for Toxoplasma predicts around 8,000 genes with varying degrees of confidence. Our data demonstrate how proteomics can inform these predictions and help discover new genes. We have identified nearly one-third (2,252) of all the predicted proteins, with 2,477 intron-spanning peptides providing supporting evidence for correct splice site annotation. Functional predictions for each protein and key pathways were determined from the proteome. Importantly, we show evidence for many proteins that match alternative gene models, or previously unpredicted genes. For example, approximately 15% of peptides matched more convincingly to alternative gene models. We also compared our data with existing transcriptional data in which we highlight apparent discrepancies between gene transcription and protein expression. CONCLUSION: Our data demonstrate the importance of protein data in expression profiling experiments and highlight the necessity of integrating proteomic with genomic data so that iterative refinements of both annotation and expression models are possible.

Determining the protein repertoire of Cryptosporidium parvum sporozoites.

The genome of the intracellular parasite Cryptosporidium parvum has recently been sequenced, but protein expression data for the invasive stages of this important zoonotic gastrointestinal pathogen are limited. In this paper a comprehensive analysis of the expressed protein repertoire of an excysted oocyst/sporozoite preparation of C. parvum is presented. Three independent proteome platforms were employed which yielded more than 4800 individual protein identifications representing 1237 nonredundant proteins, corresponding to approximately 30% of the predicted proteome. Peptide data were mapped to the corresponding locations on the C. parvum genome and a publicly accessible interface for proteome data was developed for data-mining and visualisation at CryptoDB (http://cryptodb.org). These data provide a timely and valuable resource for improved annotation of the genome, verification of predicted hypothetical proteins and identification of proteins not predicted by current gene models. The data indicated the expression of proteins likely to be important to the invasion and intracellular establishment of the parasite, including surface proteins, constituents of the remnant mitochondrion and apical organelles. Comparison of the expressed proteome with existing transcriptional data indicated only a weak correlation. For approximately half the proteome there was limited functional and structural information, highlighting the limitations in the current understanding of Cryptosporidium biology.

Identification of a very large Rab GTPase family in the parasitic protozoan Trichomonas vaginalis.

Rab proteins are pivotal components of the membrane trafficking machinery in all eukaryotes. Distinct Rab proteins locate to specific endomembrane compartments and genomic studies suggest that Rab gene diversity correlates with endomembrane system complexity; for example unicellular organisms generally possess 5-20 Rab family members and the size of the repertoire increases to 25-60 in multicellular systems. Here we report 65 open reading frames from the unicellular protozoan Trichomonas vaginalis that encode distinct Rab proteins (TvRabs), indicating a family with complexity that rivals Homo sapiens in number. The detection of gene transcripts for the majority of these genes and conservation of functional motifs strongly suggests that TvRabs retain functionality and likely roles in membrane trafficking. The T. vaginalis Rab family includes orthologues of the conserved subfamilies, Rab1, Rab5, Rab6, Rab7 and Rab11, but the majority of TvRabs are not represented by orthologues in other systems and includes six novel T. vaginalis specific Rab subfamilies (A-F). The extreme size of the T. vaginalis Rab family, the presence of novel subfamilies plus the divergent nature of many TvRab sequences suggest both the presence of a highly complex endomembrane system within Trichomonas and potentially novel Rab functionality. A family of more than 65 Rab genes in a unicellular genome is unexpected, but may be a requirement for progression though an amoeboid life-cycle phase as both Dictyostelium discoideum and Entamoeba histolytica share with T. vaginalis both an amoeboid life cycle stage and very large Rab gene families.

Characterisation of blood coagulation factor XI T475I.

PCR-SSCP and DNA sequence analysis of a factor XI (FXI) deficient patient (FXI:C 39 U/dL; FXI:Ag 27 U/dL) identified a C to T transition in exon 12 of the FXI gene (F11 c.1521C>T) that predicts the substitution of Thr475 by Ile (FXI T475I) within the serine protease domain of FXI. This mutation destroys a consensus sequence for N-linked glycosylation, N473-Y-T475, known to be utilized in vivo. The FXIT475I variant was generated by site-directed mutagenesis, together with other variants that could help explain the phenotype, and recombinant FXI variants were expressed in Chinese hamster ovary cells. FXI:Ag expression was analysed by Western blot analysis, ELISA and immunocytochemical staining. Wild-type FXI:Ag was secreted at high levels, however the mutant (FXI T475I) was secreted very poorly. Substitution of Thr475 by Ala, Pro, Lys or Arg (all of which abolish the glycosylation consensus sequence) also severely reduced the level of secreted FXI:Ag suggesting that glycosylation at Asn473 is required for folding or secretion. Concordant with this hypothesis the conservative substitution of Thr475 by Ser (which preserves the glycosylation consensus sequence) had no effect on FXI secretion. Thr/Ser475 is highly conserved in serine protease domains but the glycosylation site (Asn473) is not. Surprisingly, substitution of Asn473 by Ala (which removes the N-linked glycosylation site) had no effect on the levels of FXI:Ag secreted. In conclusion, although the FXI-T475I mutation destroys an N-linked glycosylation consensus sequence, the cause of failure to secrete FXI is not the loss of a glycosylation site but rather a direct effect of the substitution of this highly conserved residue.

Molecular evolution of the vertebrate blood coagulation network.

In mammalian blood coagulation 5 proteases, factor VII (FVII), factor IX (FIX), factor X (FX), protein C (PC) and prothrombin act with two cofactors factor V and factor VIII to control the generation of fibrin. Biochemical evidence and molecular cloning data have previously indicated that blood coagulation involving tissue factor, prothrombin and fibrinogen is present in all vertebrates. Using degenerate RT-PCR we have isolated and characterized novel cDNAs with sequence identity to the blood coagulation serine proteases and cofactors from chicken and the puffer fish (Fugu rubripes). Sequence alignments, phylogenetic and comparative sequence analysis all support the existence of the Gla-EGF1-EGF2-SP domain serine proteases FVII, FIX, FX, PC and the A1-A2-B-A3-C1-C2 domain protein cofactors FV and FVIII in these species. These results strongly suggest that the blood coagulation network is present in all jawed vertebrates and evolved before the divergence of tetrapods and teleosts over 430 million years ago; and that vertebrate blood coagulation may have benefited from two rounds of gene or whole genome duplication. Sequences identified in Fugu coding for additional FVII-like, FIX-like and PC-like sequences support the possibility of further tandem and large-scale duplications in teleosts. Comparative sequence analyses of amino acid residues in the active site region suggest these additional sequences have evolved new and as yet unknown functions.