Toxoplasma gondii expressed sequence tags: insight into tachyzoite gene expression

Alternative Splicing in Apicomplexan Parasites

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.

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. Recent approaches are now providing more wide-ranging surveys of the extent of alternative splicing; some indicate that alternative splicing is less widespread than in other model eukaryotes, whereas others suggest levels comparable to those of previously studied groups. In many cases, apicomplexan alternative splicing events appear not to generate multiple alternative proteins but instead produce aberrant or noncoding transcripts. Nonetheless, appropriate regulation of alternative splicing is clearly essential in Plasmodium and Toxoplasma parasites, suggesting a biological role for at least some of the alternative splicing observed. Several studies have now disrupted conserved regulators of alternative splicing and demonstrated lethal effects in apicomplexans. This minireview discusses methods to accurately determine the extent of alternative splicing in Apicomplexa and discuss potential biological roles for this conserved process in a phylum of parasites with compact genomes.

TgCDPK3 regulates calcium-dependent egress of Toxoplasma gondii from host cells

The phylum Apicomplexa comprises a group of obligate intracellular parasites of broad medical and agricultural significance, including Toxoplasma gondii and the malaria-causing Plasmodium spp. Key to their parasitic lifestyle is the need to egress from an infected cell, actively move through tissue, and reinvade another cell, thus perpetuating infection. Ca(2+)-mediated signaling events modulate key steps required for host cell egress, invasion and motility, including secretion of microneme organelles and activation of the force-generating actomyosin-based motor. Here we show that a plant-like Calcium-Dependent Protein Kinase (CDPK) in T. gondii, TgCDPK3, which localizes to the inner side of the plasma membrane, is not essential to the parasite but is required for optimal in vitro growth. We demonstrate that TgCDPK3, the orthologue of Plasmodium PfCDPK1, regulates Ca(2+) ionophore- and DTT-induced host cell egress, but not motility or invasion. Furthermore, we show that targeting to the inner side of the plasma membrane by dual acylation is required for its activity. Interestingly, TgCDPK3 regulates microneme secretion when parasites are intracellular but not extracellular. Indeed, the requirement for TgCDPK3 is most likely determined by the high K(+) concentration of the host cell. Our results therefore suggest that TgCDPK3's role differs from that previously hypothesized, and rather support a model where this kinase plays a role in rapidly responding to Ca(2+) signaling in specific ionic environments to upregulate multiple processes required for gliding motility.

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.

Neospora caninum--how close are we to development of an efficacious vaccine that prevents abortion in cattle?

Neospora caninum is a protozoan parasite that causes abortion in cattle around the world. Although the clinical signs of disease in both dogs and cattle have now been recognised for over 20years, treatment and control options are still limited, despite the availability of a commercial vaccine in some countries of the world. The case for an efficacious vaccine has not been convincingly waged by farmers, veterinarians and other members of the agricultural and rural communities. In recent times, however, economic modelling has been used to estimate the industry losses due to Neospora-associated abortion, providing, in turn, the business case for forms of control for this parasite, including the development of vaccines. In this review, we document progress in all areas of the vaccine development pipeline, including live, killed and recombinant forms and the animal models available for vaccine evaluation. In addition, we summarise the main outcomes on the economics of Neospora control and suggest that the current boom in the global dairy industry increases the specific need for a vaccine against N. caninum-associated abortion.

A transient forward-targeting element for microneme-regulated secretion in Toxoplasma gondii

BACKGROUND INFORMATION

Accurate sorting of proteins to the three types of secretory granules in Toxoplasma gondii is crucial for successful cell invasion by this obligate intracellular parasite. As in other eukaryotic systems, propeptide sequences are a common yet poorly understood feature of proteins destined for regulated secretion, which for Toxoplasma occurs through two distinct invasion organelles, rhoptries and micronemes. Microneme discharge during parasite apical attachment plays a pivotal role in cell invasion by delivering adhesive proteins for host receptor engagement.

RESULTS

We show here that the small micronemal proprotein MIC5 (microneme protein-5) undergoes proteolytic maturation at a site beyond the Golgi, and only the processed form of MIC5 is secreted via the micronemes. Proper cleavage of the MIC5 propeptide relies on an arginine residue in the P1' position, although P1' mutants are still cleaved to a lesser extent at an alternative site downstream of the primary site. Nonetheless, this aberrantly cleaved species still correctly traffics to the micronemes, indicating that correct cleavage is not necessary for micronemal targeting. In contrast, a deletion mutant lacking the propeptide was retained within the secretory system, principally in the ER (endoplasmic reticulum). The MIC5 propeptide also supported correct trafficking when exchanged for the M2AP propeptide, which was recently shown to also be required for micronemal trafficking of the TgMIC2 (T. gondii MIC2)-M2AP complex [Harper, Huynh, Coppens, Parussini, Moreno and Carruthers (2006) Mol. Biol. Cell 17, 4551-4563].

CONCLUSION

Our results illuminate common and unique features of micronemal propeptides in their role as trafficking facilitators.

Anisakis simplex: analysis of expressed sequence tags (ESTs) of third-stage larva

This study analyzed the expressed sequence tags (ESTs) of the third-stage larvae of Anisakis simplex, in an attempt to gain further insight into its genomic expression patterns. An A. simplex cDNA library was constructed using the Uni-ZAP XR expression vector. A total of 493 clones (insert DNA>400 bp) were sequenced out of 580 clones selected randomly from a cDNA library of the A. simplex third-stage larva. After BLAST search analyses, 154 (31.2%) ESTs were found to have very low similarity, or no match at all to any of the proteins and gene sequences in the published databases. Most matched clones (98 clones, 20.0%) were determined to be highly homologous with the genes or proteins of Caenorhabditis elegans. Ten (2.0%) ESTs matched the genes isolated from humans, and 21 (4.3%) ESTs matched with the previously reported A. simplex genes or proteins. Eighty-nine clones (18.0%) matched a total of 14 genera and 17 species of human parasites. These 339 ESTs identified could be grouped into 13 categories: allergens or antigens (4.1%), growth- and cell division-related proteins (3.2%), heat shock proteins or molecular chaperones (1.8%), membrane proteins (5.6%), metabolism-associated proteins (24.2%), mitochondrial proteins (9.4%), nuclear proteins (2.4%), proteases and protease inhibitors (3.5%), signal transduction proteins (2.4%), structural proteins (7.4%), transcription and translation machinery-associated proteins (20.1%), transporters and receptor proteins (3.8%), and other protein types (12.1%). The genetic information of Anisakis determined in this study might prove to be quite helpful in elucidating the pathogenetic mechanisms of anisakidosis, and might be useful in the development of therapeutic reagents specific to anisakidosis.

Common inheritance of chromosome Ia associated with clonal expansion of Toxoplasma gondii

Toxoplasma gondii is a globally distributed protozoan parasite that can infect virtually all warm-blooded animals and humans. Despite the existence of a sexual phase in the life cycle, T. gondii has an unusual population structure dominated by three clonal lineages that predominate in North America and Europe, (Types I, II, and III). These lineages were founded by common ancestors approximately10,000 yr ago. The recent origin and widespread distribution of the clonal lineages is attributed to the circumvention of the sexual cycle by a new mode of transmission-asexual transmission between intermediate hosts. Asexual transmission appears to be multigenic and although the specific genes mediating this trait are unknown, it is predicted that all members of the clonal lineages should share the same alleles. Genetic mapping studies suggested that chromosome Ia was unusually monomorphic compared with the rest of the genome. To investigate this further, we sequenced chromosome Ia and chromosome Ib in the Type I strain, RH, and the Type II strain, ME49. Comparative genome analyses of the two chromosomal sequences revealed that the same copy of chromosome Ia was inherited in each lineage, whereas chromosome Ib maintained the same high frequency of between-strain polymorphism as the rest of the genome. Sampling of chromosome Ia sequence in seven additional representative strains from the three clonal lineages supports a monomorphic inheritance, which is unique within the genome. Taken together, our observations implicate a specific combination of alleles on chromosome Ia in the recent origin and widespread success of the clonal lineages of T. gondii.

Gene discovery in Plasmodium vivax through sequencing of ESTs from mixed blood stages

Despite the significance of Plasmodium vivax as the most widespread human malaria parasite and a major public health problem, gene expression in this parasite is poorly understood. To accelerate gene discovery and facilitate the annotation phase of the P. vivax genome project, we have undertaken a transcriptome approach to study gene expression in the mixed blood stages of a P. vivax field isolate. Using a cDNA library constructed from purified blood stages, we have obtained single-pass sequences for approximately 21,500 expressed sequence tags (ESTs), the largest number of transcript tags obtained so far for this species. Cluster analysis revealed that the library is highly redundant, resulting in 5407 clusters. Clustered ESTs were searched against public protein databases for functional annotation, and more than one-third showed a significant match, the majority of these to Plasmodium falciparum proteins. The most abundant clusters were to genes encoding ribosomal proteins and proteins involved in metabolism, consistent with the predominance of trophozoites in the field isolate sample. In spite of the scarcity of other parasite stages in the field isolate, we could identify genes that are expressed in rings, schizonts and gametocytes. This study should facilitate our understanding of the gene expression in P. vivax asexual stages and provide valuable data for gene prediction and annotation of the P. vivax genome sequence.

Receptor for retrograde transport in the apicomplexan parasite Toxoplasma gondii

Toxoplasma gondii and its apicomplexan relatives (such as Plasmodium falciparum, which causes malaria) are obligate intracellular parasites that rely on sequential protein release from specialized secretory organelles for invasion and multiplication within host cells. Because of the importance of these unusual membrane trafficking pathways for drug development and comparative cell biology, characterizing them is essential. In particular, it is unclear what role retrieval mechanisms play in parasite membrane trafficking or where they operate. Previously, we showed that T. gondii's beta-COP (TgBetaCOP; a subunit of coatomer protein complex I, COPI) and retrieval reporters localize exclusively to the zone between the parasite endoplasmic reticulum (ER) and Golgi apparatus. This suggested the existence of an HDEL receptor in T. gondii. We have now identified, cloned, and sequenced this receptor, TgERD2. TgERD2 localizes in a Golgi or ER pattern suggestive of the HDEL retrieval reporter (K. M. Hager, B. Striepen, L. G. Tilney, and D. S. Roos, J. Cell Sci. 112:2631-2638, 1999). A functional assay reveals that TgERD2 is able to complement the Saccharomyces cerevisiae ERD2 null mutant. Retrieval studies reveal that stable expression of a fluorescent exogenous retrieval ligand results in a dispersal of betaCOP signal throughout the cytoplasm and, surprisingly, results in betaCOP staining of the vacuolar space of the parasite. In contrast, stable expression of TgERD2GFP does not appear to disturb betaCOP staining. In addition to TgERD2, Toxoplasma contains two more divergent ERD2 relatives. Phylogenetic analysis reveals that these proteins belong to a previously unrecognized ERD2 subfamily common to plants and alveolate organisms and as such could represent mediators of parasite-specific retrieval functions. No evidence of class 2 ERD2 proteins was found in metazoan organisms or fungi.

Construction and characterization of recombinant single-chain variable fragment antibodies against Toxoplasma gondii MIC2 protein

The protozoan parasite Toxoplasma gondii produces a family of microneme proteins that are thought to play diverse roles in aiding the parasite's intracellular existence. Among these, TgMIC2 has a putative function in parasite adhesion to the host cell to initiate the invasion process. The invasion process may be localized and inhibited by monoclonal antibodies against the protein(s) involved. Here we report on the construction of a phage-displayed single-chain variable fragment (scFv) library from mice immunized with whole T. gondii parasites. The library was subsequently panned against recombinant TgMIC2 (rpTgMIC2) and 2 different groups of antibody clones were obtained, based on fingerprinting and sequencing data. The expressed recombinant scFv antibody was able to recognize rpTgMIC2 in a Western blot detection experiment. These results show that the phage display technology allows quick and effective production of monoclonal antibodies against parasite antigens. By panning the scFv-displayed library, we should be able to obtain a plethora of multi-functional scFv antibodies towards T. gondii proteins.

A conserved 19-kDa Eimeria tenella antigen is a profilin-like protein

A wide range of recombinant proteins from Eimeria species have been reported to offer some degree of protection against infection and disease, but the specific biological function of these proteins is largely unknown. Previous studies have demonstrated a 19-kDa protein of unknown function designated SZ-1 in sporozoites and merozoites of Eimeria acervulina that can be used to confer partial protection against coccidiosis. Reverse transcriptase-polymerase chain reaction indicated that the gene for SZ-1 is expressed by all the asexual stages of Eimeria tenella. Rabbit antisera to recombinant SZ-1 recognized an approximately 19-kDa protein from extracts of E. tenella sporozoites, merozoites, sporulated oocysts, and oocysts in various stages of sporulation. Immunofluorescence antibody staining indicated specific staining of E. tenella sporozoites and merozoites. Staining was most intense in the cytoplasm of the posterior end of the parasite. The primary amino acid sequence of the gene for E. tenella SZ-1 deduced from the E. tenella genome indicated a conserved domain for the actin-regulatory protein profilin. A conserved binding site for poly-L-proline (PLP), characteristic of profilin was also observed. SZ-1 was separated from soluble extract of E. tenella proteins by affinity chromatography using a PLP ligand, confirming the ability of SZ-1 to bind PLP. SZ-1 also partially inhibited the polymerization of actin. The current results are consistent with the classification of SZ-1 as a profilin-related protein.

Fluorescent protein tagging in Toxoplasma gondii: identification of a novel inner membrane complex component conserved among Apicomplexa

Toxoplasma gondii is an obligate intracellular parasite, and its sub-cellular organization shows clear adaptations to this life-style. In addition to organelles shared among all eukaryotes, the organism possesses a number of specialized compartments with important roles in host cell invasion and intra-cellular survival. These unique aspects of the parasite's biology are also reflected in its genome. The ongoing genome sequencing efforts for T. gondii and related apicomplexans predict a high proportion of genes unique to the phylum, which lack homologs in other model organisms. Knowing the sub-cellular localization of these gene products will be an important first step towards their functional characterization. We used a library approach wherein parasite genomic DNA was fused to the yellow fluorescent protein (YFP) gene. Parasites transformed with this library were screened by flow cytometry and fluorescence microscopy. Clones tagged in a wide variety of sub-cellular compartments (nucleus, mitochondria, ER, dense granules (secreted), spliceosome, plasma membrane, apicoplast, inner membrane complex) were isolated and confirmed using compartment specific markers. Clones with tags in parasite-specific localizations were subjected to insert rescue and phenotypic verification using an in vitro recombination system. Among the genes identified is a novel inner membrane complex gene (IMC3) conserved among Apicomplexa.

Gene discovery in the apicomplexa as revealed by EST sequencing and assembly of a comparative gene database

Large-scale EST sequencing projects for several important parasites within the phylum Apicomplexa were undertaken for the purpose of gene discovery. Included were several parasites of medical importance (Plasmodium falciparum, Toxoplasma gondii) and others of veterinary importance (Eimeria tenella, Sarcocystis neurona, and Neospora caninum). A total of 55192 ESTs, deposited into dbEST/GenBank, were included in the analyses. The resulting sequences have been clustered into nonredundant gene assemblies and deposited into a relational database that supports a variety of sequence and text searches. This database has been used to compare the gene assemblies using BLAST similarity comparisons to the public protein databases to identify putative genes. Of these new entries, approximately 15%-20% represent putative homologs with a conservative cutoff of p < 10(-9), thus identifying many conserved genes that are likely to share common functions with other well-studied organisms. Gene assemblies were also used to identify strain polymorphisms, examine stage-specific expression, and identify gene families. An interesting class of genes that are confined to members of this phylum and not shared by plants, animals, or fungi, was identified. These genes likely mediate the novel biological features of members of the Apicomplexa and hence offer great potential for biological investigation and as possible therapeutic targets.

Cyclin-dependent kinase TPK2 is a critical cell cycle regulator in Toxoplasma gondii

The Apicomplexan parasite Toxoplasma gondii replicates by endodyogeny, an unusual form of binary fission. We tested the role of TPK2, a homologue of the CDC2 cyclin-dependent kinases, in cell cycle regulation. TPK2 tagged with HA epitope (TPK2-HA-wt) was expressed in mammalian cells as confirmed by Western blot analysis using HA tag and PSTAIRE antibodies. TPK2-HA-wt phosphorylated a peptide from Histone H1, proving that TPK2 is a functional kinase. TPK2-HA-wt coimmunoprecipitated with mammalian cyclins A, B1, D3 and E. Despite being a functional kinase, TPK2 did not rescue Schizosaccharomyces pombe cdc2 and Saccharomyces cerevisiae cdc28 mutant strains. Overexpression of a dominant-negative mutant of TPK2 (TPK2-HA-dn) in T. gondii tachyzoites arrested replication. FACS analysis of tachyzoites expressing TPK2-HA-dn revealed an increase in the fraction of cells in S-phase when compared with TPK2-HA-wt transfected parasites. Expression of TPK2-HA-wt did not arrest tachyzoite replication. No discernable G2 cell cycle block was evident suggesting that cell cycle checkpoints differ in T. gondii from most other eukaryotic cells. These data suggest that TPK2 executes an essential function in T. gondii cell cycle and is likely to be the T. gondii CDC2 orthologue.

A protease inhibitor associated with the surface of Toxoplasma gondii

Toxoplasma gondii has a broad host-range including man and a variety of warm-blooded animals. The ability to infect and survive in this wide spectrum of hosts suggests highly evolved mechanisms to handle the harsh environments encountered. Here we show that extracellular tachyzoites are resistant to milligram levels of trypsin and describe the presence of an inhibitor of trypsin associated with the surface of T. gondii, TgTI. TgTI has an estimated molecular mass of 37000 dalton and is encoded by the TgTI-gene which is found at low abundance as an expressed sequence tag (EST) in both the bradyzoite and tachyzoite stages. The inhibitory binding region was found to be in the N-terminus of TgTI where aminoacid-alignment to earlier described protease inhibitors demonstrates 75% similarity. In functional analysis, recombinant TgTI-protein inhibits the activity of trypsin approximately 10 times more efficiently than an inhibitor isolated from soybean. In contrast to other known trypsin inhibitors, TgTI also possesses a predicted membrane-binding region. Polyclonal antibodies raised against recombinant TgTI bind to the surface of the tachyzoite stage as seen both by immunofluorescence and immunoprecipitation of surface labelled parasite proteins. The high survival rate of the parasite in the upper gastrointestinal tract may be enhanced by the presence of the TgTI-molecule.

Exploring the transcriptome of the malaria sporozoite stage

Most studies of gene expression in Plasmodium have been concerned with asexual and/or sexual erythrocytic stages. Identification and cloning of genes expressed in the preerythrocytic stages lag far behind. We have constructed a high quality cDNA library of the Plasmodium sporozoite stage by using the rodent malaria parasite P. yoelii, an important model for malaria vaccine development. The technical obstacles associated with limited amounts of RNA material were overcome by PCR-amplifying the transcriptome before cloning. Contamination with mosquito RNA was negligible. Generation of 1,972 expressed sequence tags (EST) resulted in a total of 1,547 unique sequences, allowing insight into sporozoite gene expression. The circumsporozoite protein (CS) and the sporozoite surface protein 2 (SSP2) are well represented in the data set. A BLASTX search with all tags of the nonredundant protein database gave only 161 unique significant matches (P(N) < or = 10(-4)), whereas 1,386 of the unique sequences represented novel sporozoite-expressed genes. We identified ESTs for three proteins that may be involved in host cell invasion and documented their expression in sporozoites. These data should facilitate our understanding of the preerythrocytic Plasmodium life cycle stages and the development of preerythrocytic vaccines.

TgM2AP participates in Toxoplasma gondii invasion of host cells and is tightly associated with the adhesive protein TgMIC2

Like other members of the medically important phylum Apicomplexa, Toxoplasma gondii is an obligate intracellular parasite that secretes several classes of proteins involved in the active invasion of target host cells. Proteins in apical secretory organelles known as micronemes have been strongly implicated in parasite attachment to host cells. TgMIC2 is a microneme protein with multiple adhesive domains that bind target cells and is mobilized onto the parasite surface during parasite attachment. Here, we describe a novel parasite protein, TgM2AP, which is physically associated with TgMIC2. TgM2AP complexes with TgMIC2 within 15 min of synthesis and remains associated with TgMIC2 in the micronemes, on the parasite surface during invasion and in the culture medium after release from the parasite plasma membrane. TgM2AP is proteolytically processed initially when its propeptide is removed during transit through the golgi and later while it occupies the parasite surface after discharge from the micronemes. We show that TgM2AP is a member of a protein family expressed by coccidian parasites including Neospora caninum and Eimeria tenella. This phylogenic conservation and association with a key adhesive protein suggest that TgM2AP is a fundamental component of the T. gondii invasion machinery.

Expressed sequence tags (ESTs) analysis of Acanthamoeba healyi

Randomly selected 435 clones from Acanthamoeba healyi cDNA library were sequenced and a total of 387 expressed sequence tags (ESTs) had been generated. Based on the results of BLAST search, 130 clones (34.4%) were identified as the genes encoding surface proteins, enzymes for DNA, energy production or other metabolism, kinases and phosphatases, protease, proteins for signal transduction, structural and cytoskeletal proteins, cell cycle related proteins, transcription factors, transcription and translational machineries, and transporter proteins. Most of the genes (88.5%) are newly identified in the genus Acanthamoeba. Although 15 clones matched the genes of Acanthamoeba located in the public databases, twelve clones were actin gene which was the most frequently expressed gene in this study. These ESTs of Acanthamoeba would give valuable information to study the organism as a model system for biological investigations such as cytoskeleton or cell movement, signal transduction, transcriptional and translational regulations. These results would also provide clues to elucidate factors for pathogenesis in human granulomatous amoebic encephalitis or keratitis by Acanthamoeba.

Analysis of the expressed genome of the lone star tick, Amblyomma americanum (Acari: Ixodidae) using an expressed sequence tag approach

An expressed sequence tag (EST) approach was used to study the genome of two developmental stages of the lone star tick, Amblyomma americanum. cDNA libraries were constructed from the larval and adult stages of A. americanum. In total, 1942 ESTs were sequenced (1462 adult ESTs and 480 larval ESTs) and analyzed using bioinformatic programs. Contig assembly using the CAPII program revealed 11% and 15% redundancy of sequences in the larval and adult ESTs, respectively. Of the 1942 ESTs, 1738 sequences were considered quality sequences and of these, 771 or approximately 44.4% of the sequences were putatively identified based on amino acid identity using the protein Basic Local Alignment Search Tool (BLAST) algorithm. Putatively identified sequences were classified according to their predicted gene function. In total, 967 sequences, or 55.6% of the quality sequences, had limited or no protein similarity to previously identified gene products. Sequences lacking protein homology were analyzed using an automated sequence annotation system for predicted protein characteristics such as open reading frames, signal peptides, protein motifs, and transmembrane regions. In this paper we describe the sequencing of the largest number of ESTs obtained from an arachnid species to date and the subsequent detailed analysis of these sequences.

Initiation of a Sarcocystis neurona expressed sequence tag (EST) sequencing project: a preliminary report

To accelerate genetic and molecular characterization of Sarcocystis neurona, the primary causative agent of equine protozoal myeloencephalitis (EPM), a sequencing project has been initiated that will generate approximately 7000-8000 expressed sequence tags (ESTs) from this apicomplexan parasite. Poly(A)(+) RNA was isolated from culture-derived S. neurona merozoites, and a cDNA library was constructed in a unidirectional lambda phage cloning vector. Sixty phage clones were randomly picked from the library, and the cDNA inserts were amplified from these clones using the T3 and T7 primers that flank the multi-cloning site of the lambda vector. This analysis demonstrated that 100% (60/60) of the clones selected from this library contained recombinant cDNA inserts ranging in size from 0.4 to 4.0 kilobases (kb) with an average size of 1.23kb. Single-pass sequencing from the 5' end of the 60 amplified cDNAs produced high-quality nucleotide sequence from 53 of the clones. Comparison of these ESTs to the current gene databases revealed significant matches for 10 of the ESTs, six of which are similar to sequences from other Apicomplexa (i.e., Toxoplasma gondii). Importantly, none of the ESTs were of obvious mammalian origin, thus indicating that the cDNAs in this library were derived primarily from parasite mRNA and not from mRNA of the bovine turbinate host cells. Collectively, these data indicate that the described cDNA library will provide an excellent substrate for generating a portion of the ESTs that are planned from S. neurona. This sequencing project will greatly hasten gene discovery for this protozoan pathogen thereby enhancing efforts towards the development of improved diagnostics, treatments, and preventatives for EPM. In addition, the S. neurona ESTs will represent a significant contribution to the extensive database of sequences from the Apicomplexa. Comparative analyses of these apicomplexan sequences will likely offer a multitude of important information about the biology and evolutionary history of this phylogenetic grouping of parasites.

The toxoplasma micronemal protein MIC4 is an adhesin composed of six conserved apple domains

The initial stage of invasion by apicomplexan parasites involves the exocytosis of the micronemes-containing molecules that contribute to host cell attachment and penetration. MIC4 was previously described as a protein secreted by Toxoplasma gondii tachyzoites upon stimulation of micronemes exocytosis. We have microsequenced the mature protein, purified after discharge from micronemes and cloned the corresponding gene. The deduced amino acid sequence of MIC4 predicts a 61-kDa protein that contains 6 conserved apple domains. Apple domains are composed of six spacely conserved cysteine residues which form disulfide bridges and are also present in micronemal proteins from two closely related apicomplexan parasites, Sarcocystis muris and Eimeria species, and several mammalian serum proteins, including kallikrein. Here we show that MIC4 localizes in the micronemes of all the invasive forms of T. gondii, tachyzoites, bradyzoites, sporozoites, and merozoites. The protein is proteolytically processed both at the N and the C terminus only upon release from the organelle. MIC4 binds efficiently to host cells, and the adhesive motif maps in the most C-terminal apple domain.

Molecular characterization of TgMIC5, a proteolytically processed antigen secreted from the micronemes of Toxoplasma gondii

During invasion of host cells, Toxoplasma gondii discharges the contents of small, apically located secretory organelles called micronemes. Micronemal proteins are known to be necessary for both parasite motility and invasion of host cells. To further define the contents of Toxoplasma micronemes, we used cell fractionation and secretion-modulating drugs to identify six novel, putative micronemal proteins. In this paper we describe preliminary characterization of one of these novel proteins, TgMIC5. Molecular cloning and DNA sequence analysis of the TgMIC5 cDNA and gene revealed that it encodes a previously identified immunodominant antigen called H4. TgMIC5 also possesses a consensus sequence unique to members of the parvulin family of peptidyl-prolyl cis-trans isomerases (PPIases). TgMIC5 is expressed as a preproprotein, which is proteolytically processed to a proprotein by signal peptidase before being further processed to a mature protein of 22 kDa. Using a combination of protein secretion experiments, immunofluorescence and immunoelectron microscopy, we demonstrated that TgMIC2 is stored in the micronemes of T. gondii tachyzoites before it is secreted into the surrounding medium. Based on its homology with parvulin-like PPIases, TgMIC5 may assist in the folding of other micronemal proteins that function in invasion of host cells by T. gondii tachyzoites.

Two genes encoding unique proliferating-cell-nuclear-antigens are expressed in Toxoplasma gondii

Complete cDNA sequences encoding two novel proliferating-cell-nuclear-antigens (designated TgPCNA1 and 2) were isolated from a Toxoplasma gondii tachyzoite cDNA library, and Southern analysis using cDNA probes confirmed the presence of two PCNA genes in T. gondii genomic DNA. Expressed-sequence-tags were identified in the T. gondii database that matched each TgPCNA cDNA and closely related PCNA coding regions (designated PfPCNA1 and 2) were discovered in sequence data obtained from chromosome 12 and 13 of Plasmodium falciparum. TgPCNA1 and PfPCNA1 were found to share the highest amino acid identity at 49% compared to TgPCNA2 and PfPCNA2 (37% identity) whereas intraspecies PCNAs were determined to be less similar (27-30% identity). Phylogenetic analysis suggests the two apicomplexan PCNAs are the result of a gene duplication in the common ancestor of these parasites. Antibodies specific for TgPCNA1 ( approximately 40 kDa) or TgPCNA2 ( approximately 37 kDa) detected single antigen species in tachyzoite extracts that were expressed at similar levels in isolates representative of the T. gondii Type I, II and III strains. TgPCNA1-specific cDNA probes detected multiple mRNA species on Northern blots, which when combined, were expressed 5-7 fold higher than the single species of mRNA detected by the TgPCNA2 probe. The difference in the number of mRNA species and comparative mRNA levels suggests each TgPCNA gene is independently controlled, although in light of the nearly equal levels of protein a post-transcriptional mechanism may be responsible for equalizing protein expression.

A European perspective on Neospora caninum

Since the identification of Neospora caninum in 1984 as a parasite separate from Toxoplasma gondii by Bjerkas et al., and its subsequent characterization and classification in 1988 by Dubey and co-workers, this parasite has attracted increasing attention, primarily as an important causative agent of abortion in cattle and neuromuscular disease in dogs, but also as a complementary model system to T. gondii for investigating the basic biology of intracellular parasitism. During November 11-14, 1999, the COST 820 Annual meeting (Vaccines against coccidioses) took place in Interlaken, Switzerland. Almost half of the papers presented at that meeting were on N. caninum and neosporosis, reflecting the increasing awareness of the importance of this parasite on part of the scientific community in Europe. On the occasion of the meeting, participants in this COST Action involved in Neospora research in Europe were asked to participate in this invited review in order to document the growing interest in N. caninum and the disease it causes. Thus, this paper is a unique collection of contributions provided by several European experts in the field. It is comprised of 10 reviews or original papers on different aspects of Neospora research including epidemiology, immunology, application and development of serological tools, and molecular characterisation of the parasite currently carried out throughout Europe. In addition, two distinguished invited speakers from overseas (Milton McAllister and John Ellis) provided valuable contributions. This invited review demonstrates that the COST 820 Action has brought together scientists from all over Europe and other parts of the world, and has laid the basis for many fruitful collaborations. The studies described here will contribute in assessing the relevance of neosporosis as a potential risk factor not only for animals, but also for human health.

The Toxoplasma adhesive protein MIC2 is proteolytically processed at multiple sites by two parasite-derived proteases

MIC2 is an adhesive protein that participates in host cell invasion by the obligate intracellular parasite Toxoplasma gondii. Earlier studies established that MIC2 is secreted into the culture medium by extracellular parasites and that release is coincident with proteolytic modification. Since little is known about proteolytic processing of proteins secreted by T. gondii, we undertook this study to investigate the proteolytic events that accompany secretion of MIC2. We demonstrate that the C-terminal domain of MIC2 is removed by a protease, termed MPP1, when MIC2 is released into the culture supernatant. Additionally, prior to release, a second protease, termed MPP2, trims the N terminus of MIC2, resulting in the release of heterogeneously sized species of MIC2. Although MPP1 activity was unaffected by any of the protease inhibitors tested, MPP2 activity was blocked by a subset of serine and cysteine protease inhibitors. These results establish that MIC2 is proteolytically modified at multiple sites by two distinct enzymes that probably operate on the parasite surface.

Generation of expressed sequence tags as physical landmarks in the genome of Trypanosoma brucei

Previous molecular genetic studies on the African trypanosome have focused on only a few genes and gene products, the majority of which are concerned with surface antigenic variation; consequently, an insignificant number of the genes of this organism have been characterized to date. In order to: (1) identify new genes and analyze their expression profile, (2) generate expressed sequence tags (ESTs) for derivation of a physical map of the trypanosome genome, and (3) make available the partial sequence information and the corresponding clones for general biomedical research on the parasite, we have performed single-pass sequencing of random, directionally cloned cDNAs from a bloodstream form Trypanosoma brucei rhodesiense library. Analysis of 2128 such ESTs sequenced so far in this study showed significant similarities [BLASTX P(n)-value < 10(-4), and a match > 10 amino acid residues] with proteins whose genes have been described in diverse organisms including man, rodents, kinetoplastids, yeasts and plants. A number of the ESTs encode homologues of proteins involved in various functions including signal reception and transduction, cell division, gene regulation, DNA repair and replication, general metabolism, and structural integrity. Although some of these genes may have been expected to be present in the African trypanosomes, the majority of them had not previously been described in these organisms. A large proportion, 768 individual ESTs (36%, representing 385 different transcripts), had a significant homology with genes described in organisms other than the African trypanosomes; however, 15% of the ESTs were from genes already described in trypanosomes. Among the ESTs analysed were 462 distinct known genes, only 77 of which have been described in T. brucei. Approximately 52% of the ESTs did not show any significant homology with the sequences in any of the public domain databases.

Toxoplasma gondii: ESTs and gene discovery

Partial cDNA sequences or Expressed Sequence Tags (ESTs) have proven to be an economical way to gain information about expressed genes in a variety of organisms. Further, ESTs can be generated for strain or developmental stage comparisons. Currently there are over 10, 000 ESTs for Toxoplasma gondii derived from RH tachyzoite, ME49 tachyzoite and ME 49 bradyzoite cDNA libraries. A set of Web pages and tools have been developed to proved easy access and rapid analysis of these data. Top Hits lists, T. gondii-specific databases/search tools and cluster analyses can be browsed or used to rapidly gain insight into the structure and potential function of genes/proteins held within the database. The previously characterized Eimeria protein Etp 100 has been used to demonstrate how it is possible to use these tools to extract and assemble information about the putative T. gondii homologue.

Gene amplification in Leishmania tarentolae selected for resistance to sodium stibogluconate

Leishmania tarentolae promastigotes were selected step by step for resistance to sodium stibogluconate (Pentostam). Mutants resistant to antimony-containing drugs and cross-resistant to arsenite were therefore obtained. Amplification of one common locus was observed in several independent sodium stibogluconate-resistant mutants, and the locus amplified was novel. The copy number of the amplified locus was related to the level of resistance to pentavalent antimony. The gene responsible for antimony resistance was isolated by transfection and was shown to correspond to an open reading frame coding for 770 amino acids. The putative gene product did not exhibit significant homology with sequences present in data banks, and the putative role of this protein in antimony resistance is discussed.

Cloning and in vitro expression of TPK3, a Toxoplasma gondii homologue of shaggy/glycogen synthase kinase-3 kinases

As an initial effort to dissect the signaling pathways responsible for pathogenesis of Toxoplasma gondii infection, we report the cloning and in vitro functional studies of TPK3 (Toxoplasma protein kinase-3), a homologue of shaggy/glycogen synthase kinase-3 (GSK-3) kinases. The shaggy/GSK-3 family of kinases are highly conserved protein kinases that play important roles in cell fate determination, nuclear signaling and hormonal regulation. The TPK3 gene was isolated by RT-PCR with degenerate primers corresponding to highly conserved regions of serine/threonine protein kinases. The complete sequences of genomic and cDNA clones indicated the open reading frame, 1185 bp in size, is interrupted by five introns. The predicted protein sequence of TPK3 shows 54% identity to shaggy/GSK-3 over the catalytic domains. Southern analysis revealed TPK3 is a single copy locus in the Toxoplasma genome. Antisera to other GSK-3 proteins from other species recognized GST-TPK3 and a protein of the predicted size in parasites lysates. In vitro kinase assays with GST-TPK3 indicated that TPK3 autophosphorylates and phosphorylates protein phosphatase inhibitor-2 (I-2), a specific substrate of GSK-3 kinase.

The surface of Toxoplasma tachyzoites is dominated by a family of glycosylphosphatidylinositol-anchored antigens related to SAG1

Toxoplasma gondii is an Apicomplexan parasite with a complex life cycle that includes a rapidly dividing asexual stage known as the tachyzoite. The tachyzoite surface has been reported to comprise five major antigens, the most abundant of which is designated SAG1 (for surface antigen 1). At least one of the other four (SAG3) and another recently described minor antigen (SRS1 [for SAG1-related sequence 1]) have previously been shown to be structurally related to SAG1. To determine if further SAG1 homologs exist, we searched a Toxoplasma expressed sequence tag (EST) database and found numerous ESTs corresponding to at least three new genes related to SAG1. Like SAG1, these new SRS genes encode apparently glycosylphosphatidylinositol-anchored proteins that share several motifs and a set of conserved cysteine residues. This family appears to have arisen by divergence from a common ancestor under selection for the conservation of overall topology. The products of two of these new genes (SRS2 and SRS3) are shown to be expressed on the surface of Toxoplasma tachyzoites by immunofluorescence. We also identified strain-specific differences in relative expression levels. A total of 10 members of the SAG1 gene family have now been identified, which apparently include three of the five major surface antigens previously described and one antigen expressed only in bradyzoites. The function of this family may be to provide a redundant system of receptors for interaction with host cells and/or to direct the immune responses that limit acute T. gondii infections.

The surface of Toxoplasma: more and less

As for any intracellular parasite, the surface of the Apicomplexan parasite Toxoplasma gondii must fulfil many functions including a role in attachment, signalling, invasion, transport and interaction with the immune response of the host. In this review, we describe the current state of knowledge on the molecules that are found on the surface of the different developmental stages of this parasite and speculate as to how at least some of these multiple functions are fulfilled. Special emphasis is given to the growing family of surface antigens that are related to the tachyzoite-specific surface antigen 1. We conclude that the surface (of tachyzoites, at least) is both more and less complex than previously thought: there are more proteins present but their sequences suggest that the majority may share a similar overall structure typified by surface antigen 1.

Tagging genes and trapping promoters in Toxoplasma gondii by insertional mutagenesis

Plasmid vectors that incorporate sequence elements from the dehydrofolate reductase-thymidylate synthase (DHFR-TS) locus of Toxoplasma gondii integrate into the parasite genome with remarkably high frequency (>1% of transfected parasites). These vectors may-but need not-include mutant DHFR-TS alleles that confer pyrimethamine resistance to transgenic parasites. Large genomic constructs integrate at the endogenous locus by homologous recombination, but cDNA-derived sequences lacking long stretches of contiguous genomic DNA (due to intron excision) typically integrate into chromosomal DNA by nonhomologous recombination. Nonhomologous integration occurs effectively at random; and coupled with the high frequency of transformation, this allows a large fraction of the parasite genome to be tagged in a single electroporation cuvette. Genomic tagging permits insertional mutagenesis studies conceptually analogous to transposon mutagenesis in bacteria, yeast, Drosophila, etc. In theory (and, thus far, in practice), this allows identification of any gene whose inactivation is not lethal to the haploid tachyzoite form of T. gondii and for which a suitable selection or screen is available. Transformation vectors can be engineered to facilitate rescue of the tagged locus and to include a variety of reporters or selectable markers. Genetic strategies are also possible, using reporters whose function can be assayed by metabolic, visual, or immunological screens to "trap" genes that are activated (or inactivated) under various conditions of interest.

Genetic analysis in Toxoplasma: gene discovery with expressed sequence tags and rapid mapping of natural polymorphisms

Genetic analysis of the protozoan parasite Toxoplasma gondii has undergone a rapid expansion in recent years. This is due to effort in a number of laboratories that have worked on the development of molecular genetic techniques. It is also due, however, to the natural biology of this system (including a well-described sexual cycle) that makes possible genetic mapping of the F1 progeny from a cross. In this article, we present a detailed methodology for rapidly mapping natural polymorphisms between the ME49 and CEP strains for which extensive restriction fragment length polymorphism analysis has already been performed. The example we present shows that the failure to detect expression of bradyzoite-specific surface antigens in the CEP strain under conditions that promote differentiation in vitro is not a result of a general failure to express such genes; instead, it is apparently due to antigenic polymorphism in the gene products concerned. This conclusion was reached rapidly and definitively by genetic mapping, whereas molecular approaches would have taken considerably longer. We also show how the recent effort to create an extensive database of expressed sequence tags for this parasite can promote the very rapid discovery of genes that reveal much about the biology of Toxoplasma. The example presented deals with the expression of a family of closely related surface antigens in the tachyzoite stage.

Genetic and biochemical analysis of development in Toxoplasma gondii

Toxoplasma gondii has recently come under intense study as a model for intracellular parasitism because it has a number of properties that facilitate experimental manipulation. Attention is now being turned towards understanding the developmental biology of this complex parasite. The differentiation between the two asexual stages, the rapidly growing tachyzoites and the more slowly dividing, encysted bradyzoites, is of particular interest. Progression from the former to the latter is influenced by the host's immune response. This paper describes current progress on a number of research fronts, all aimed at understanding the triggers that push the tachyzoite-bradyzoite equilibrium in one or other direction and the changes that occur in gene expression (and ultimately metabolism and function). Chief among the techniques used for these studies are genetics and molecular genetics. Recent progress in these areas is described.

Parasite genome analysis. Progress in the Leishmania genome project

Genome projects have been established for 7 major groups of human parasitic infections: malaria, leishmaniasis, African trypanosomiasis, American trypanosomiasis, toxoplasmosis, schistosomiasis and filariasis. All except malaria and toxoplasmosis have come under the umbrella of the World Health Organization's Strategic Committee on Parasite Genome Analysis. The focus of this meeting of the Society was to review progress made in the Leishmania and African trypanosome genome projects. This paper introduces the genome projects and reviews briefly progress in pulsed-field gel karyotype mapping and gene identification via expressed sequence tag sequencing for the leishmaniasis genome project. The overall aim of the genome projects is to harness the latest developments in molecular genetic technology and sequence analysis for the rapid-generation of new data which may, in turn, revolutionize our approaches to the study of the biology of these organisms.

Molecular characterisation of an expressed sequence tag locus of Toxoplasma gondii encoding the micronemal protein MIC2

The expressed sequence tag (EST) dataset of Toxoplasma gondii provides a wealth of information towards gene discovery. The complete cDNA and genomic sequence of EST tgc050 locus shows that it contains five copies of the conserved thrombospondin (TSP)-like motif present in a number of molecules with adhesive properties. A conserved region implicated with the adhesive characteristic of another group of proteins including several integrins, is also present in this molecule. The protein encoded by this sequence (rc50) is strongly recognised by monoclonal antibodies to MIC2. Affinity purified anti-rc50 antisera specifically reacted with a single protein of identical molecular mass as MIC2 and exclusively labeled the micronemes of T. gondii by cryo-immunoelectron microscopy. These results demonstrate that c50 encodes for MIC2, a previously characterised microneme protein of T. gondii. The extensive sequence similarity across multiple protein domains provides evidence that the protein encoded by this locus is the homologue to the Etp100 microneme protein of Eimeria tenella.

Biodiversity, genomes, and DNA sequence databases

There are approximately 1.4 million organisms on this planet that have been described morphologically but there is no comparable coverage of biodiversity at the molecular level. Little more than 1% of the known species have been subject to any molecular scrutiny and eukaryotic genome projects have focused on a group of closely related model organisms. The past year, however, has seen an approximately 80% increase in the number of species represented in sequence databases and the completion of the sequencing of three prokaryotic genomes. Large-scale sequencing projects seem set to begin coverage of a wider range of the eukaryotic diversity, including green plants, microsporidians and diplomonads.

Unravelling the Leishmania genome

The past few years have been significant advances in our understanding of eukaryotic genomes. In the field of parasitology, this is best exemplified by the application of genome mapping techniques to the study of genome structure and function in the protozoan parasite, Leishmania. Although much is known about the organism and the diseases it causes, molecular genetics has only recently begun to play a major part in elucidating some of the unusual characteristics of this interesting parasite. Mapping of the small (35 Mb) genome and determination of the functional role of genes by the application of in vitro homologous gene targeting techniques are revealing novel avenues for the development of prophylactic measures.

Molecular genetic strategies in Toxoplasma gondii: close in on a successful invader

Toxoplasma gondii is an obligate intracellular parasite with an exceptional ability to invade, survive and replicate within nearly all nucleated cells. Upon differentiation into an encysted form (bradyzoites), the parasites escape the host immune defenses and thus persist long enough in man and other hosts to ensure maintenance of transmission. This protozoan parasite has long been known to cause severe congenital infections in humans and animals but has recently gained additional notoriety as an opportunistic pathogen associated with AIDS. Development of a DNA transfection system for T. gondii has provided a new tool for exploring molecular aspects of important processes such as invasion and differentiation. Additional strategies associated with genetic transformation have been devised and elaboration of even more desirable molecular tools is in progress.