Parasite proteomics

Proteomic analysis of Neobenedenia sp. and Rhabdosynochus viridisi (Monogenea, Monopisthocotylea): Insights into potential vaccine targets and diagnostic markers for finfish aquaculture

Monogeneans are parasitic flatworms that represent a significant threat to the aquaculture industry. Species like Neobenedenia melleni (Capsalidae) and Rhabdosynochus viridisi (Diplectanidae) have been identified as causing diseases in farmed fish. In the past years, molecular research on monogeneans of the subclass Monopisthocotylea has focused on the generation of genomic and transcriptomic information and the identification in silico of some protein families of veterinary interest. Proteomic analysis has been suggested as a powerful tool to investigate proteins in parasites and identify potential targets for vaccine development and diagnosis. To date, the proteomic dataset for monogeneans has been restricted to a species of the subclass Polyopisthocotylea, while in monopisthocotyleans there is no proteomic data. In this study, we present the first proteomic data on two monopisthocotylean species, Neobenedenia sp. and R. viridisi, obtained from three distinct sample types: tissue, excretory-secretory products (ESPs), and eggs. A total of 1691 and 1846 expressed proteins were identified in Neobenedenia sp. and R. viridisi, respectively. The actin family was the largest protein family, followed by the tubulin family and the heat shock protein 70 (HSP70) family. We focused mainly on ESPs because they are important to modulate the host immune system. We identified proteins of the actin, tubulin, HSP70 and HSP90 families in both tissue and ESPs, which have been recognized for their antigenic activities in parasitic flatworms. Furthermore, our study uncovered the presence of proteins within ESPs, such as annexin, calcium-binding protein, fructose bisphosphate aldolase, glutamate dehydrogenase, myoferlin, and paramyosin, that are targets for immunodiagnostic and vaccine development and hold paramount relevance in veterinary medicine. This study expands our knowledge of monogeneans and identified proteins that, in other platyhelminths are potential targets for vaccines and drug discovery.

The parasite Schistocephalus solidus secretes proteins with putative host manipulation functions

BACKGROUND

Manipulative parasites are thought to liberate molecules in their external environment, acting as manipulation factors with biological functions implicated in their host's physiological and behavioural alterations. These manipulation factors are part of a complex mixture called the secretome. While the secretomes of various parasites have been described, there is very little data for a putative manipulative parasite. It is necessary to study the molecular interaction between a manipulative parasite and its host to better understand how such alterations evolve.

METHODS

Here, we used proteomics to characterize the secretome of a model cestode with a complex life cycle based on trophic transmission. We studied Schistocephalus solidus during the life stage in which behavioural changes take place in its obligatory intermediate fish host, the threespine stickleback (Gasterosteus aculeatus). We produced a novel genome sequence and assembly of S. solidus to improve protein coding gene prediction and annotation for this parasite. We then described the whole worm's proteome and its secretome during fish host infection using LC-MS/MS.

RESULTS

A total of 2290 proteins were detected in the proteome of S. solidus, and 30 additional proteins were detected specifically in the secretome. We found that the secretome contains proteases, proteins with neural and immune functions, as well as proteins involved in cell communication. We detected receptor-type tyrosine-protein phosphatases, which were reported in other parasitic systems to be manipulation factors. We also detected 12 S. solidus-specific proteins in the secretome that may play important roles in host-parasite interactions.

CONCLUSIONS

Our results suggest that S. solidus liberates molecules with putative host manipulation functions in the host and that many of them are species-specific.

Proteomics of Gnathostomiasis: A Way Forward for Diagnosis and Treatment Development

Gnathostoma spinigerum is the most common cause of gnathostomiasis in humans. It has a complex life cycle, which requires two intermediate hosts and a definitive host, and poses a high risk for zoonosis. Definitive prognosis of gnathostomiasis relies mainly on the isolation of advanced-stage larvae (aL3), which is very challenging especially if the aL3 is sequestered in difficult-to-reach organs. There is also a lack of a confirmatory diagnostic test for gnathostomiasis. With the ongoing advancement of proteomics, a potential diagnostic approach is underway using immunoproteomics and immunodiagnostics. In addition to this, the employment of mass spectrometry could further elucidate not only understanding the biology of the parasite but also determining potential targets of prospective drugs and vaccines. This article reports the past, present, and future application of proteomics in the study of gnathostomiasis.

Analysis of Cryptosporidium spp. from clinical samples by matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry

AIM

To purify Cryptosporidium spp. oocysts from clinical stool samples and evaluate using an up-to-date mass spectrometry protocol producing high-quality reference spectra.

METHODS AND RESULTS

A refined purification protocol was developed for oocysts from stools, involving salt flotation and potassium bromide density centrifugation. Purified oocysts were prepared for matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) by formic acid extraction, and the extracts analysed using the Bruker MALDI Biotyper system. Individual spectral markers were identified by their specific mass peaks. Cryptosporidium parvum oocysts (Iowa strain) propagated in vivo, and C.  parvum (n = 2) and Cryptosporidium hominis (n = 1) oocysts from clinical stool samples produced distinct spectra that were considered specific to Cryptosporidium spp. with no evidence of contamination.

CONCLUSIONS

The production of distinct spectra demonstrated the utility of the purification method for oocysts from clinical stool samples and provided reference spectra.

SIGNIFICANCE AND IMPACT OF THE STUDY

The use of MALDI-TOF MS and other mass spectrometry techniques has been limited previously to C.  parvum oocysts propagated in vivo. Appropriate purification of oocysts can achieve sufficient biomass, enabling analysis by MALDI-TOF MS and potentially other mass spectrometry platforms, facilitating peptide and protein discovery and identification of biomarkers from a much wider range of Cryptosporidium spp. from natural infections.

Different manifestation of Echinococcus granulosus immunogenic antigens in the liver and lungs of intermediate host

Hydatidosis is one of the most important zoonotic diseases with a worldwide distribution and it seems that the survival of Echinococcus granulosus in nature for many years, is due to having different mechanisms to escape from the host immune systems. One of these efficient mechanisms is the production of various antigens and proteins by the larva of the parasite and the main purpose of this study is evaluation of manifestation of various antigens in different parts of intermediate host. The hepatic and pulmonary hydatid cysts were gathered from sheep and the antigens of different parts of the cysts (laminated layer, protoscolices and cyst fluid) were separated and analyzed by SDS-PAGE and then transferred to nitrocellulose paper and finally, Western blot analysis was evaluated the immunogenicity of proteins. The antigens of laminated layer, protoscolices and hydatid cyst fluid, in different tissues of the liver and lungs, manifest various proteins and also these antigens are immunogenically different. Also, it is found more immunogenic proteins in the laminated layer than the other parts of the cysts. The various proteins are generated by Echinococcus granulosus larva depending on the type of tissues attacked by the parasite. Increasing the chance of survival may be the main cause of manifestation various antigens in different parts of cysts and host tissues. These antigenic variations might have made diagnostic serologic test unreliable.

Immunoproteomic and mass spectrometric analysis of Eimeria acervulina antigens recognized by antisera from chickens infected with E. acervulina, E. tenella or E. necatrix

Background

Coccidiosis is caused by Eimeria spp. and can result in severe economic losses to the global poultry industry. Due to anticoccidial drug resistance rapidly developing in the parasites and drug residues in poultry products, efficacious and safe alternative coccidia control measures are needed. The objective of the present study was to identify common protective antigens which may be used as vaccine candidates in the development of subunit, multivalent, cross-protective vaccines against most of the economically important Eimeria species.

Methods

Whole sporozoite proteins of Eimeria acervulina were prepared and analyzed by 2-dimensional gel electrophoresis (2-DE) followed by western blotting using immune sera specific to E. tenella, E. acervulina, or E. necatrix. The protein spots detected by all three immune sera were then excised from the preparative gel and protein ID was performed by MALDI-TOF-MS/MS.

Results

Approximately 620 E. acervulina sporozoite protein spots were demonstrated by 2-DE with silver staining, among which 23 protein spots were recognized by immune sera specific to all three Eimeria species. The results showed that 21 putative E. acervulina proteins were identified, which include proteins with known enzymatic properties, and those which are involved in protein translation, transport and trafficking, and ribosomal biogenesis and functions. There is one protein which may be involved in transcription and one heat-shock protein. Two proteins contain predicted domains, but with no apparent functions known. There were 2 protein spots which had no detectable proteins. None of the proteins has a predicted signal peptide or a transmembrane domain; however, 6 of the 21 putative proteins were predicted to be potentially secretory through the non-classical pathway.

Conclusions

Our study identified a diverse group of antigens immunologically common to all three Eimeria species, none of which was previously characterized and tested as a vaccine candidate. Further research on immunogenicity and cross-protective potential of these individual proteins as vaccine candidates will aid the development of vaccines against the most common and pathogenic Eimeria spp.

Molecular cross-talk in a unique parasitoid manipulation strategy

Envenomation of cockroach cerebral ganglia by the parasitoid Jewel wasp, Ampulex compressa, induces specific, long-lasting behavioural changes. We hypothesized that this prolonged action results from venom-induced changes in brain neurochemistry. Here, we address this issue by first identifying molecular targets of the venom, i.e., proteins to which venom components bind and interact with to mediate altered behaviour. Our results show that venom components bind to synaptic proteins and likely interfere with both pre- and postsynaptic processes. Since behavioural changes induced by the sting are long-lasting and reversible, we hypothesized further that long-term effects of the venom must be mediated by up or down regulation of cerebral ganglia proteins. We therefore characterize changes in cerebral ganglia protein abundance of stung cockroaches at different time points after the sting by quantitative mass spectrometry. Our findings indicate that numerous proteins are differentially expressed in cerebral ganglia of stung cockroaches, many of which are involved in signal transduction, such as the Rho GTPase pathway, which is implicated in synaptic plasticity. Altogether, our data suggest that the Jewel wasp commandeers cockroach behaviour through molecular cross-talk between venom components and molecular targets in the cockroach central nervous system, leading to broad-based alteration of synaptic efficacy and behavioural changes that promote successful development of wasp progeny.

Immunoproteomic analysis of the protein repertoire of unsporulated Eimeria tenella oocysts

The apicomplexan protozoans Eimeria spp. cause coccidioses, the most common intestinal diseases in chickens. Coccidiosis is associated with significant animal welfare issues and has a high economic impact on the poultry industry. Lack of a full understanding of immunogenic molecules and their precise functions involved in the Eimeria life cycles may limit development of effective vaccines and drug therapies. In this study, immunoproteomic approaches were used to define the antigenic protein repertoire from the total proteins of unsporulated Eimeria tenella oocysts. Approximately 101 protein spots were recognized in sera from chickens infected experimentally with E. tenella. Forty-six spots of unsporulated oocysts were excised from preparative gels and identified by matrix-assisted laser desorption ionization time-of-flight MS (MALDI-TOF-MS) and MALDI-TOF/TOF-MS. For unsporulated oocysts, 13 known proteins of E. tenella and 17 homologous proteins to other apicomplexan or protozoan parasites were identified using the 'Mascot' server. The remaining proteins were searched against the E. tenella protein sequence database using the 'Mascot in-house' search engine (version 2.1) in automated mode, and 12 unknown proteins were identified. The amino acid sequences of the unknown proteins were searched using BLAST against non-redundant sequence databases (NCBI), and 9 homologous proteins in unsporulated oocyst were found homologous to proteins of other apicomplexan parasites. These findings may provide useful evidence for understanding parasite biology, pathogenesis, immunogenicity and immune evasion mechanisms of E. tenella.

Proteomic analysis of Mecistocirrus digitatus and Haemonchus contortus intestinal protein extracts and subsequent efficacy testing in a vaccine trial

BACKGROUND

Gastrointestinal nematode infections, such as Haemonchus contortus and Mecistocirrus digitatus, are ranked in the top twenty diseases affecting small-holder farmers' livestock, yet research into M. digitatus, which infects cattle and buffalo in Asia is limited. Intestine-derived native protein vaccines are effective against Haemonchus, yet the protective efficacy of intestine-derived M. digitatus proteins has yet to be determined.

METHODOLOGY/PRINCIPAL FINDINGS

A simplified protein extraction protocol (A) is described and compared to an established method (B) for protein extraction from H. contortus. Proteomic analysis of the H. contortus and M. digitatus protein extracts identified putative vaccine antigens including aminopeptidases (H11), zinc metallopeptidases, glutamate dehydrogenase, and apical gut membrane polyproteins. A vaccine trial compared the ability of the M. digitatus extract and two different H. contortus extracts to protect sheep against H. contortus challenge. Both Haemonchus fractions (A and B) were highly effective, reducing cumulative Faecal Egg Counts (FEC) by 99.19% and 99.89% and total worm burdens by 87.28% and 93.64% respectively, compared to the unvaccinated controls. There was no effect on H. contortus worm burdens following vaccination with the M. digitatus extract and the 28.2% reduction in cumulative FEC was not statistically significant. However, FEC were consistently lower in the M. digitatus extract vaccinates compared to the un-vaccinated controls from 25 days post-infection.

CONCLUSIONS/SIGNIFICANCE

Similar, antigenically cross-reactive proteins are found in H. contortus and M. digitatus; this is the first step towards developing a multivalent native vaccine against Haemonchus species and M. digitatus. The simplified protein extraction method could form the basis for a locally produced vaccine against H. contortus and, possibly M. digitatus, in regions where effective cold chains for vaccine distribution are limited. The application of such a vaccine in these regions would reduce the need for anthelmintic treatment and the resultant selection for anthelmintic resistant parasites.

Proteomic characterization of the hemolymph of Octopus vulgaris infected by the protozoan parasite Aggregata octopiana

The immune system of cephalopods is poorly known to date. The lack of genomic information makes difficult to understand vital processes like immune defense mechanisms and their interaction with pathogens at molecular level. The common octopus Octopus vulgaris has a high economic relevance and potential for aquaculture. However, disease outbreaks provoke serious reductions in production with potentially severe economic losses. In this study, a proteomic approach is used to analyze the immune response of O. vulgaris against the coccidia Aggregata octopiana, a gastrointestinal parasite which impairs the cephalopod nutritional status. The hemocytes and plasma proteomes were compared by 2-DE between sick and healthy octopus. The identities of 12 differentially expressed spots and other 27 spots without significant alteration from hemocytes, and 5 spots from plasma, were determined by mass spectrometry analysis aided by a six reading-frame translation of an octopus hemocyte RNA-seq database and also public databases. Principal component analysis pointed to 7 proteins from hemocytes as the major contributors to the overall difference between levels of infection and so could be considered as potential biomarkers. Particularly, filamin, fascin and peroxiredoxin are highlighted because of their implication in octopus immune defense activity. From the octopus plasma, hemocyanin was identified. This work represents a first step forward in order to characterize the protein profile of O. vulgaris hemolymph, providing important information for subsequent studies of the octopus immune system at molecular level and also to the understanding of the basis of octopus tolerance-resistance to A. octopiana.

BIOLOGICAL SIGNIFICANCE

The immune system of cephalopods is poorly known to date. The lack of genomic information makes difficult to understand vital processes like immune defense mechanisms and their interaction with pathogens at molecular level. The study herein presented is focused to the comprehension of the octopus immune defense against a parasite infection. Particularly, it is centered in the host-parasite relationship developed between the octopus and the protozoan A. octopiana, which induces severe gastrointestinal injuries in octopus that produce a malabsorption syndrome. The common octopus is a commercially important species with a high potential for aquaculture in semi-open systems, and this pathology reduces the condition of the octopus populations on-growing in open-water systems resulting in important economical loses. This is the first proteomic approach developed on this host-parasite relationship, and therefore, the contribution of this work goes from i) ecological, since this particular relationship is tending to be established as a model of host-parasite interaction in natural populations; ii) evolutionary, due to the characterization of immune molecules that could contribute to understand the functioning of the immune defense in these highly evolved mollusks; and iii) to economical view. The results of this study provide an overview of the octopus hemolymph proteome. Furthermore, proteins influenced by the level of infection and implicated in the octopus cellular response are also showed. Consequently, a set of biomarkers for disease resistance is suggested for further research that could be valuable for the improvement of the octopus culture, taken into account their high economical value, the declining of landings and the need for the diversification of reared species in order to ensure the growth of the aquaculture activity. Although cephalopods are model species for biomedical studies and possess potential in aquaculture, their genomes have not been sequenced yet, which limits the application of genomic data to research important biological processes. Similarly, the octopus proteome, like other non-model organisms, is poorly represented in public databases. Most of the proteins were identified from an octopus' hemocyte RNA-seq database that we have performed, which will be the object of another manuscript in preparation. Therefore, the need to increase molecular data from non-model organisms is herein highlighted. Particularly, here is encouraged to expand the knowledge of the genomic of cephalopods in order to increase successful protein identifications. This article is part of a Special Issue entitled: Proteomics of non-model organisms.

Anthelmintic metabolism in parasitic helminths: proteomic insights

Anthelmintics are the cornerstone of parasitic helminth control. Surprisingly, understanding of the biochemical pathways used by parasitic helminths to detoxify anthelmintics is fragmented, despite the increasing global threat of anthelmintic resistance within the ruminant and equine industries. Reductionist biochemistry has likely over-estimated the enzymatic role of glutathione transferases in anthelmintic metabolism and neglected the potential role of the cytochrome P-450 superfamily (CYPs). Proteomic technologies offers the opportunity to support genomics, reverse genetics and pharmacokinetics, and provide an integrated insight into both the cellular mechanisms underpinning response to anthelmintics and also the identification of biomarker panels for monitoring the development of anthelmintic resistance. To date, there have been limited attempts to include proteomics in anthelmintic metabolism studies. Optimisations of membrane, post-translational modification and interaction proteomic technologies in helminths are needed to especially study Phase I CYPs and Phase III ABC transporter pumps for anthelmintics and their metabolites.

Proteomic profiling and protein identification by MALDI-TOF mass spectrometry in unsequenced parasitic nematodes

Lack of genomic sequence data and the relatively high cost of tandem mass spectrometry have hampered proteomic investigations into helminths, such as resolving the mechanism underpinning globally reported anthelmintic resistance. Whilst detailed mechanisms of resistance remain unknown for the majority of drug-parasite interactions, gene mutations and changes in gene and protein expression are proposed key aspects of resistance. Comparative proteomic analysis of drug-resistant and -susceptible nematodes may reveal protein profiles reflecting drug-related phenotypes. Using the gastro-intestinal nematode, Haemonchus contortus as case study, we report the application of freely available expressed sequence tag (EST) datasets to support proteomic studies in unsequenced nematodes. EST datasets were translated to theoretical protein sequences to generate a searchable database. In conjunction with matrix-assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI-TOF-MS), Peptide Mass Fingerprint (PMF) searching of databases enabled a cost-effective protein identification strategy. The effectiveness of this approach was verified in comparison with MS/MS de novo sequencing with searching of the same EST protein database and subsequent searches of the NCBInr protein database using the Basic Local Alignment Search Tool (BLAST) to provide protein annotation. Of 100 proteins from 2-DE gel spots, 62 were identified by MALDI-TOF-MS and PMF searching of the EST database. Twenty randomly selected spots were analysed by electrospray MS/MS and MASCOT Ion Searches of the same database. The resulting sequences were subjected to BLAST searches of the NCBI protein database to provide annotation of the proteins and confirm concordance in protein identity from both approaches. Further confirmation of protein identifications from the MS/MS data were obtained by de novo sequencing of peptides, followed by FASTS algorithm searches of the EST putative protein database. This study demonstrates the cost-effective use of available EST databases and inexpensive, accessible MALDI-TOF MS in conjunction with PMF for reliable protein identification in unsequenced organisms.

Our wormy world genomics, proteomics and transcriptomics in East and southeast Asia

Helminths are the cause of some of the major infectious diseases of humanity in what is still a "wormy" world. There is, in East and Southeast Asia, a high prevalence of several helminthiases which occur primarily in rural, impoverished areas of low-income and developing countries throughout the tropics and subtropics. Subsequent to various parasite genome projects that commenced in the early 1990s, under the aegis of the World Health Organization (WHO), the draft genomes of three major helminth species (Schistosoma japonicum, S. mansoni and Brugia malayi) have been sequenced, and many other helminth parasites have now been targeted for intensive genomics investigation. The continuing release of genome sequences has catalyzed the emergence of transcriptomics, proteomics and related "-omics" analyses of helminth parasites, which provide unprecedented approaches to understanding their biology that will result in new clues for the development of novel control interventions. In this review, we present a summary of current approaches employed in helminth "-omics" studies and review recent advances in helminth genomics and post-genomics in the Southeast Asian setting.

Echinococcus multilocularis: Proteomic analysis of the protoscoleces by two-dimensional electrophoresis and mass spectrometry

Echinococcus multilocularis is an important parasite that causes human alveolar echinococcosis. Identification and characterization of the proteins encoded by E. multilocularis metacestode might help to understand the complexity of the parasites and their interactions with the host, and to identify new candidates for immunodiagnosis and vaccine development. Here we present a proteomic analysis of E. multilocularis protoscolex (PSC) proteins. The proteins were resolved by 2-DE (pH range 3.5-10), followed by MALDI-TOF MS analysis. Fourteen known Echinococcus proteins were identified, including cytoskeletal proteins, heat shock proteins, metabolic enzymes, 14-3-3 protein, antigen P-29 and calreticulin. To construct a systematic reference map of the immunogenic proteins from E. multilocularis PSC, immunoblot analysis of PSC 2-DE maps was performed. Over 50 proteins spots were detected on immunoblots as antigens and 15 of them were defined. The results showed that cytoskeletal proteins and heat shock proteins were immunodominant antigens in alveolar echinococcosis.

Proteomic approaches for discovery of new targets for vaccine and therapeutics against visceral leishmaniasis

Visceral leishmaniasis (VL) is the most devastating type caused by Leishmania donovani, Leishmania infantum, and Leishmania chagasi. The therapeutic mainstay is still based on the antiquated pentavalent antimonial against which resistance is now increasing. Unfortunately, due to the digenetic life cycle of parasite, there is significant antigenic diversity. There is an urgent need to develop novel drug/vaccine targets against VL for which the primary goal should be to identify and characterize the structural and functional proteins. Proteomics, being widely employed in the study of Leishmania seems to be a suitable strategy as the availability of annotated sequenced genome of Leishmania major has opened the door for dissection of both protein expression/regulation and function. Advances in clinical proteomic technologies have enable to enhance our mechanistic understanding of virulence/pathogenicity/host-pathogen interactions, drug resistance thereby defining novel therapeutic/vaccine targets. Expression proteomics exploits the differential expression of leishmanial proteins as biomarkers for application towards early diagnosis. Further using immunoproteomics efforts were also focused on evaluating responses to define parasite T-cell epitopes as vaccine/diagnostic targets. This review has highlighted some of the relevant developments in the rapidly emerging field of leishmanial proteomics and focus on its future applications in drug and vaccine discovery against VL.

Do distantly related parasites rely on the same proximate factors to alter the behaviour of their hosts?

Phylogenetically unrelated parasites often increase the chances of their transmission by inducing similar phenotypic changes in their hosts. However, it is not known whether these convergent strategies rely on the same biochemical precursors. In this paper, we explored such aspects by studying two gammarid species (Gammarus insensibilis and Gammarus pulex; Crustacea: Amphipoda: Gammaridae) serving as intermediate hosts in the life cycle of two distantly related parasites: the trematode, Microphallus papillorobustus and the acanthocephalan, Polymorphus minutus. Both these parasite species are known to manipulate the behaviour of their amphipod hosts, bringing them towards the water surface, where they are preferentially eaten by aquatic birds (definitive hosts). By studying and comparing the brains of infected G. insensibilis and G. pulex with proteomics tools, we have elucidated some of the proximate causes involved in the parasite-induced alterations of host behaviour for each system. Protein identifications suggest that altered physiological compartments in hosts can be similar (e.g. immunoneural connexions) or different (e.g. vision process), and hence specific to the host-parasite association considered. Moreover, proteins required to alter the same physiological compartment can be specific or conversely common in both systems, illustrating in the latter case a molecular convergence in the proximate mechanisms of manipulation.

Effect of piperazine (diethylenediamine) on the moulting, proteome expression and pyrophosphatase activity of Ascaris suum lung-stage larvae

Piperazine (diethylenediamine) is an anthelmintic widely used against animal and bird ascariasis. In this study, we show that treatment with piperazine blocks Ascaris suum larval moulting and development processes and affects larval proteome expression profiles. A. suum lung-stage L3 (LL3) obtained from an infected rabbit's lungs were cultured in RPMI medium in the presence of increasing concentrations of piperazine sulfate (Pzes). Our results showed that Pzes potently inhibited moulting of A. suum LL3 in a dose-dependent manner and that moulting was completely blocked (100%) at 50mM concentrations. We then examined the changes in A. suum LL3 proteome expression patterns following Pzes exposure using two-dimensional (2D) electrophoresis. Pzes exposure inhibited expression of at least 16 major protein spots in unmoulted LL3 out of more than 200 visible protein spots resolved on 2D gels prepared from moulted larvae (i.e., lung-stage L4). Pzes exposure also inhibited expression of 13 immunogenic protein spots in unmoulted LL3. More importantly, Pzes exposure inhibited activity of a moulting-specific enzyme, inorganic pyrophosphatase of A. suum (AsPPase), by 26%. Expression of native AsPPase was also reduced following Pzes exposure as detected by immunoblotting and immunofluorescent staining. Transmission electron microscopy showed that Pzes interfered with growth and ecdysis of the cuticle and caused damage to gut tissues of the larvae. Our results suggest that A. suum LL3 may become a suitable model to screening new-class anthelmintics with antimoulting functions and that A. suum LL3-Pzes may serve as a useful tool for identification of moulting-specific potential proteins in Ascaris roundworms.

The pitfalls of proteomics experiments without the correct use of bioinformatics tools

The elucidation of the entire genomic sequence of various organisms, from viruses to complex metazoans, most recently man, is undoubtedly the greatest triumph of molecular biology since the discovery of the DNA double helix. Over the past two decades, the focus of molecular biology has gradually moved from genomes to proteomes, the intention being to discover the functions of the genes themselves. The postgenomic era stimulated the development of new techniques (e.g. 2-DE and MS) and bioinformatics tools to identify the functions, reactions, interactions and location of the gene products in tissues and/or cells of living organisms. Both 2-DE and MS have been very successfully employed to identify proteins involved in biological phenomena (e.g. immunity, cancer, host-parasite interactions, etc.), although recently, several papers have emphasised the pitfalls of 2-DE experiments, especially in relation to experimental design, poor statistical treatment and the high rate of 'false positive' results with regard to protein identification. In the light of these perceived problems, we review the advantages and misuses of bioinformatics tools - from realisation of 2-DE gels to the identification of candidate protein spots - and suggest some useful avenues to improve the quality of 2-DE experiments. In addition, we present key steps which, in our view, need to be to taken into consideration during such analyses. Lastly, we present novel biological entities named 'interactomes', and the bioinformatics tools developed to analyse the large protein-protein interaction networks they form, along with several new perspectives of the field.

Identification of proteins in excretory/secretory extracts of Echinostoma friedi (Trematoda) from chronic and acute infections

In the present study, we describe the investigation of Echinostoma friedi excretory/secretory products using a proteomic approach combined with the use of heterologous antibodies. We have identified 18 protein spots corresponding to ten proteins, including cytoskeletal proteins like actin, tropomyosin, and paramyosin; glycolytic enzymes like enolase, glyceraldehyde 3P dehydrogenase, and aldolase; detoxifying enzymes like GSTs; and stress proteins like heat shock protein (Hsp) 70. Among these proteins, both actin and, to a lesser extent, Hsp70, exhibited differential expression patterns between chronic and acute infections in the Echinostoma-rodent model, suggesting that these proteins may play a role in the survival within the host.

Proteomic analysis of the eukaryotic parasite Encephalitozoon cuniculi (microsporidia): a reference map for proteins expressed in late sporogonial stages

The microsporidian Encephalitozoon cuniculi is a unicellular obligate intracellular parasite considered as an emerging opportunistic human pathogen. The differentiation phase of its life cycle leads to the formation of stress-resistant spores. The E. cuniculi genome (2.9 Mbp) having been sequenced, we undertook a descriptive proteomic study of a spore-rich cell population isolated from culture supernatants. A combination of 2-DE and 2-DE-free techniques was applied to whole-cell protein extracts. Protein identification was performed using an automated MALDI-TOF-MS platform and a nanoLC-MS/MS instrument. A reference 2-DE map of about 350 major spots with multiple isoforms was obtained, and for the first time in microsporidia, a large set of unique proteins (177) including proteins with unknown function in a proportion of 25.6% was identified. The data are mainly discussed with reference to secretion and spore structural features, energy and carbohydrate metabolism, cell cycle control and parasite survival in the environment.

Fluoride exposure inhibits protein expression and enzyme activity in the lung-stage larvae ofAscaris suum

Sodium fluoride (NaF) is an anion that has been previously shown to block the moulting process ofAscaris suumlarvae. This study describes moulting and development-specific protein expression profiles ofA. suumlung-stage L3 (AsLL3) following NaF exposure. AsLL3s cultured in the presence or absence of NaF were prepared for protein analysis using two-dimensional (2D) electrophoresis. NaF exposure inhibited at least 22 proteins in AsLL3 compared with moulted larvae (i.e. AsLL4). A further comparison of AsLL4 with those of pre-cultured AsLL3 and NaF-exposed AsLL3 revealed 8 stage-specifically and 4 over-expressed proteins. Immunoblot analysis revealed an inhibition by NaF of 19 immunoreactive proteins. Enzyme assay and immunochemical data showed an inhibition of the moulting-specific inorganic pyrophosphatase activity by 41% and a decreased expression in NaF-treated larvae, indicating its significance in the moulting process. A protein spot associated with NaF inhibition was isolated and identified by peptide mass spectrometry and bioinformatics approaches to be a member of 3–hydroxyacyl–CoA dehydrogenase/short-chain dehydrogenase enzyme families. These results have implications for the identification of proteins specific to the moulting process as potential chemotherapeutic targets.

Critical roles for excretory-secretory cysteine proteases during tissue invasion of Paragonimus westermani newly excysted metacercariae

Paragonimus westermani is a trematode parasite, which causes pulmonary and/or extrapulmonary granulomatous disease in humans. Successful invasion of the host tissue is critical for the survival of this tissue-invasive parasite. The enzymatic hydrolysis of host proteins is clearly a prerequisite of this process. In this study, we have investigated the functional roles of the excretory-secretory cysteine proteases of P. westermani newly excysted metacercariae (PwNEM) in tissue invasion. The 27 and 28 kDa enzymes (PwMc27 and PwMc28) purified from PwNEM excretory-secretory products (ESP), preferentially degraded fibrillar proteins, but not globular proteins. PwMc28 significantly facilitated the invasion of PwNEM into mouse peritoneum, whereas a diffusible cysteine protease inhibitor, trans-epoxysuccinyl-L-leuciloamido-(4-guanidino) butane (E-64) inhibited this process dose-dependently. Two distinct isoforms of PwMc28 (PwMc28a and PwMc28b), which exhibited two amino acid differences in their mature domains, were identified by tandem mass spectrometry and sequence analysis. Both enzymes were localized at the tegument on the anterior border and on the oral sucker, which suggests excretion-secretion via exocytosis or via the excretory canal network. The mRNA transcripts of PwMc28a and b were expressed abundantly during the active invasion/migration through the host's tissues, suggesting their relevant function to tissue invasion/migration in the definitive host.

Identification of developmentally-regulated proteins in Leishmania panamensis by proteome profiling of promastigotes and axenic amastigotes

We have employed proteomics to identify proteins upregulated in the amastigote life-stage of Leishmaniapanamensis, using axenically-differentiated forms as models of authentic intracellular parasites. Resolution of the soluble proteomes of axenic amastigotes and promastigotes by two-dimensional electrophoresis (2DE) in the neutral pI range (5-7) revealed equivalent numbers of protein spots in both life-stages (644-682 using Coomassie Blue and 851-863 by silver staining). Although representing a relatively low proportion (8.1-10.8%) of the predicted 8000 gene products of Leishmania, these proteome maps enabled the reproducible detection of 75 differentially-regulated protein spots in amastigotes, comprising 24 spots "uniquely" expressed in this life-stage and 51 over-expressed by 1.2-5.7-fold compared to promastigotes. Of the 11 amastigote-specific spots analysed by mass spectrometry (MS), 5 yielded peptide sequences with no orthologues in Leishmania major, and the remaining 6 were identified as 7 distinct proteins (some of which were truncated isoforms) representing several functional classes: carbohydrate/energy metabolism (fructose 1,6-bisphosphate aldolase, glucose 6-phosphate dehydrogenase, pyruvate dehydrogenase), stress response (heat shock protein [HSP] 83), cell membrane/cytoskeleton (beta-tubulin), amino acid metabolism (cysteine synthase) and cell-cycle (ran-binding protein). Four additional over-expressed spots were tentatively identified as HSPs 60 and 70 and HSP 70-related proteins -1 and -4 by positional analogy with these landmark proteins in the Leishmania guyanensis proteome. Our data demonstrate the feasibility of proteomics as an approach to identify novel developmentally-regulated proteins linked to Leishmania differentiation and intracellular survival, while simultaneously pinpointing therapeutic targets. In particular, the amastigote-specific expression of cysteine synthase underlines the importance of de novo cysteine synthesis both as a potential parasite virulence factor and as a major metabolic difference from mammalian host cells.

Identification of immunodominant excretory–secretory cysteine proteases of adultParagonimus westermani by proteome analysis

Paragonimus westermani causes inflammatory lung disease in humans. The parasite excretes a host of biologically active molecules, which are thought to be involved in pathophysiological and immunological events during infection. Analyses of the 2-DE protein profiles of the excretory-secretory products (ESP) of adult P. westermani revealed approximately 147 protein spots, at least 15 of which were identified as cysteine proteases (CPs), at pHs between 4.5 and 8.5, and molecular weights (MWs) between 27 and 35 kDa. An additional three CPs (designated as PwCP-3, -8 and -11) were newly recognized by TOF/TOF MS. Their molecular biological information, which shared a high level sequence homology, was elucidated. The majority of the CPs reacted strongly with sera from paragonimiasis patients. When we observed the chronological changes in the antibody responses of the respective CPs against canine sera collected serially at 1, 3, 5, 7, 11 and 14 wk after experimental infection, these molecules exhibited a multiplicity of distinct immune recognition patterns. Our results clearly showed that P. westermani adult ESP were principally composed of excretory-secretory CPs, and that these CPs may exert effects not only on host tissue degradation and nutrient uptake, but also on the immune-regulating cells via synergistic and independent interactions.

Fractionation and identification of proteins by 2-DE and MS: towards a proteomic analysis ofPlasmodium falciparum

Since completion of genome sequencing of the malarial parasite Plasmodium falciparum, proteomic tools for the identification of parasite proteins have become particularly attractive as they allow a more thorough interpretation of these data. Recent advances in 2-D PAGE, MS, and bioinformatics have created great opportunities for mapping and characterization of protein populations. We employed these improvements in a proteomic approach for the analysis of proteins detected in two blood stages of P. falciparum, (i) in the schizont stage and (ii) in the merozoite stage. For the isolation of merozoites, we introduced a new protocol based on the preparation of clustered structures of merozoites upon treatment of cultures with the common cysteine proteinase inhibitor E64. Peptide mass fingerprints of excised and trypsinated protein spots, acquired by MALDI-TOF MS were generated to identify a variety of proteins. Moreover, prefractionation procedures were used to enrich and map low-abundance proteins in protein samples. The data demonstrate that classic proteomic analyses using 2-D PAGE are now feasible for P. falciparum and represent the first step in the direction of creating 2-D reference maps for this medically most relevant protozoon.

Model-organism genomics in veterinary parasite drug-discovery

A recent article about genomic filtering highlights exciting new opportunities for antiparasitic drug discovery resulting from major advances in genomic technologies. In this article, we discuss several approaches in which model-organism genomics and proteomics could be applied to the identification and validation of novel targets for antiparasitic drug discovery in veterinary medicine.

First analysis of the proteome in two nematomorph species, Paragordius tricuspidatus (Chordodidae) and Spinochordodes tellinii (Spinochordodidae)

The proteome of most parasite species is currently unknown. Hairworms (Nematomorpha), 300 species distributed around the world, are parasitic in arthropods (mainly terrestrial species) when juveniles, but they are free-living in aquatic environments when adult. Most aspects of their systematics and biology are currently unknown. The aim of this paper was (i) to report a novel and reproducible protocol for the analysis of the proteome of hairworms using two-dimensional gel electrophoresis (2-DGE) and mass spectrometry (matrix laser desorption ionization-time of flight mass spectrometry (MALDI-TOF)) and (ii) to determine the level of proteomic divergence between two sympatric but taxonomically unrelated nematomorph species in the adult stage, Paragordius tricuspidatus Dufour (Nematomorpha, Gordiidae) and Spinochordodes tellinii Camerano (Nematomorpha, Gordiidae). In total, 689 protein spots were observed for P. tricuspidatus, 575 for S. tellinii. Only 36.2% spots were shared between the two species. Quantitative analysis of the proteins which are common to both parasite species reveals substantial differences in the pattern of protein expression. These results suggest a rapid evolutionary divergence between these two nematomorph families. Also, to test the value of our MALDI-TOF protocol, we used Actin-2 (Act-2), a protein highly conserved in the course of evolution. Peptide mass fingerprint (PMF) data obtained for Act-2 of P. tricuspidatus and S. tellinii suggest a very high homology with Act-2 of different worms species belonging to the Bilateria phylum (Annelida and Nematoda) and more specifically to Lumbricus terrestris (Annelida, Lumbricidae) and Caenorhabditis elegans (Nematoda, Rhabditidae). We discuss our results in relationship with current ideas concerning the use of proteomics in systematics.

Towards a new conceptual approach to ‘parasitoproteomics’

Many parasitologists are betting heavily on proteomic studies to explain biochemical host-parasite interactions and, thus, to contribute to disease control. However, many "parasitoproteomic" studies are performed with powerful techniques but without a conceptual approach to determine whether the host genomic responses during a parasite infection represent a nonspecific response that might be induced by any parasite or any other stress. In this article, a new conceptual approach, based on evolutionary concepts of immune responses of a host to a parasite, is suggested for parasitologists to study the host proteome reaction after parasite invasion. Also, this new conceptual approach can be used to study other host-parasite interactions such as behavioral manipulation.

Technological advances and genomics in metazoan parasites

Molecular biology has provided the means to identify parasite proteins, to define their function, patterns of expression and the means to produce them in quantity for subsequent functional analyses. Whole genome and expressed sequence tag programmes, and the parallel development of powerful bioinformatics tools, allow the execution of genome-wide between stage or species comparisons and meaningful gene-expression profiling. The latter can be undertaken with several new technologies such as DNA microarray and serial analysis of gene expression. Proteome analysis has come to the fore in recent years providing a crucial link between the gene and its protein product. RNA interference and ballistic gene transfer are exciting developments which can provide the means to precisely define the function of individual genes and, of importance in devising novel parasite control strategies, the effect that gene knockdown will have on parasite survival.

Genomics and its impact on parasitology and the potential for development of new parasite control methods

Parasitic organisms remain the scourge of the developed and underdeveloped worlds. Malaria, schistosomiasis, leishmaniasis, and trypanosomiasis, for example, still result in a large number of human deaths each year worldwide, while drug resistance among nematodes still poses a major problem to the livestock industries. Genome projects involving parasitic organisms are now abundant, and technologies for the investigations of the parasite transcriptome and proteome are well established. There is no doubt the era of the "omics" is with parasitology, and current trends in the discipline are addressing fundamental biological questions that can make best use of the new technologies, as well as the vast amount of new data being generated. Will this become the "golden age of molecular parasitology," leading to the control of parasitic diseases that have plagued mankind for hundreds of years? The primary aim of this paper is to review advances in the general area of parasite genomics, and to outline where the application of "omics" technologies can and have impacted on the development of new control methods for parasitic organisms.

Progress and new technologies for developing vaccines against gastrointestinal nematode parasites of sheep

Despite the identification of highly effective native antigens for vaccination against Haemonchus contortus, particularly 'hidden' antigens derived from the intestine of adult worms, to date similar efficacy has not been shown with recombinant antigens. In addition, progress towards identification of protective antigens from other sheep gastrointestinal (GI) nematode species is limited. Coupled with this is an incomplete understanding of the mechanism of natural immunity to GI nematodes, making selection of appropriate immunization strategies and adjuvants for evaluation of candidate 'natural' antigens problematic. The current explosion in new high-throughput technologies, arising from human studies, for analysis of the genome, transcriptome, proteome and glycome offers the opportunity to gain a better understanding of the molecular pathways underlying pathogen biology, the host immune system and the host-pathogen interaction. An overview is provided on how these technologies can be applied to parasite research and how they may aid in overcoming some of the current problems in development of commercial vaccines against GI nematode parasites.

Immunisation of channel catfish, Ictalurus punctatus, with Ichthyophthirius multifiliis immobilisation antigens elicits serotype-specific protection

Surface immobilisation antigens (i-antigens) were purified from two strains of Ichthyophthirius multifiliis (NY1 and G5) that represent different i-antigen serotypes, namely A and D, respectively. The efficacy of the purified antigens as subunit vaccines was then tested in challenge studies using parasites of the homologous or heterologous serotype. Three groups of juvenile channel catfish (70 animals per group) were immunised with i-antigens from either the G5 or NY1 isolates, or with bovine serum albumin (BSA) as a control. Proteins were injected intraperitoneally (i.p.) at a dose of 10 microg/fish with complete Freund's adjuvant on day 1, followed by a second injection in incomplete Freund's adjuvant on day 15. Fish immunised with the purified i-antigens developed high titres of serum immobilising antibodies whereas sera from BSA-injected control fish did not. Fish antisera immobilised parasites of the homologous, but not the heterologous strain, and recognised the corresponding i-antigens on Western blots run under non-reducing conditions. On day 36, each group was divided into two subgroups (n=30). One subgroup was challenged with G5 parasites, and the other was challenged with NY1 parasites. When challenged with G5 parasites, 70% of fish immunised with the G5 i-antigens survived. When challenged with NY1 parasites, 33.3% of fish immunised with the NY1 i-antigens survived. All BSA-injected control fish died, as did all fish injected with the purified antigens and challenged with the non-homologous parasite strain. Statistical analyses indicated significant differences among test and control groups with regard to the mean days to death (MDD). While the results of these studies clearly support a role for i-antigens in protection, active immunity in response to natural infection is not serotype-specific. The utility of i-antigens, as well as the existence of other potential vaccine candidates for the prevention of 'white-spot' disease, are discussed.

Variation in the expression of a Plasmodium falciparum protein family implicated in erythrocyte invasion

The PfRH protein family of Plasmodium falciparum is implicated in erythrocyte invasion. Here we report variations in the sequence, transcription, and protein expression of four different members of this family in three parasite lines, 3D7, T996, and FCB1. There are sequence polymorphisms in PfRH1, PfRH2a, PfRH2b, and PfRH3, ranging from variations across repeat regions to a 585-bp deletion in the 3' end of PfRH2b in T996. Not all the genes are transcribed: although all members of the family are transcribed in 3D7 and T996, PfRH2a and PfRH2b are not transcribed in FCB1. The PfRH1, PfRH2a, and PfRH2b proteins are expressed in late schizonts and merozoites and are located in apical organelles and on the apical surface. However, the PfRH1 protein does not appear to be correctly targeted to the apex in 3D7 and T996. In contrast, the PfRH1 protein is present at the apical end of FCB1 merozoites, but the PfRH2a and PfRH2b proteins are undetectable. The apparent redundancy in the PfRH family of proteins at the level of gene number and sequence and the variations in transcription and protein expression may allow the parasite to use alternative invasion pathways.

Lung-stage protein profile and antigenic relationship between Ascaris lumbricoides and Ascaris suum

The protein profile and antigenic properties of lung-stage larvae of Ascaris lumbricoides and A. suum were studied using 2-dimensional electrophoresis and immunoblot analysis, respectively. The protein profiles of the 2 parasites were identical except for the presence of only 1 major protein spot specific for each. There was a complete cross-reactivity between the 2 parasites at the immunological level, and no specific antigen was recognized using specific antibody raised against the 2 parasites in rabbits.

Characterisation of global protein expression by two-dimensional electrophoresis and mass spectrometry: proteomics of Toxoplasma gondii

The development of tools for the analysis of global gene expression is vital for the optimal exploitation of the data on parasite genomes that are now being generated in abundance. Recent advances in two-dimensional electrophoresis (2-DE), mass spectrometry and bioinformatics have greatly enhanced the possibilities for mapping and characterisation of protein populations. We have employed these developments in a proteomics approach for the analysis of proteins expressed in the tachyzoite stage of Toxoplasma gondii. Over 1000 polypeptides were reproducibly separated by high-resolution 2-DE using the pH ranges 4-7 and 6-11. Further separations using narrow range gels suggest that at least 3000-4000 polypeptides should be resolvable by 2-DE using multiple single pH unit gels. Mass spectrometry was used to characterise a variety of protein spots on the 2-DE gels. Peptide mass fingerprints, acquired by matrix-assisted laser desorption/ionisation-(MALDI) mass spectrometry, enabled unambiguous protein identifications to be made where full gene sequence information was available. However, interpretation of peptide mass fingerprint data using the T. gondii expressed sequence tag (EST) database was less reliable. Peptide fragmentation data, acquired by post-source decay mass spectrometry, proved a more successful strategy for the putative identification of proteins using the T. gondii EST database and protein databases from other organisms. In some instances, several protein spots appeared to be encoded by the same gene, indicating that post-translational modification and/or alternative splicing events may be a common feature of functional gene expression in T. gondii. The data demonstrate that proteomic analyses are now viable for T. gondii and other protozoa for which there are good EST databases, even in the absence of complete genome sequence. Moreover, proteomics is of great value in interpreting and annotating EST databases.

The contribution of molecular biology to the development of vaccines against nematode and trematode parasites of domestic ruminants

Rapid developments in molecular biology have had an enormous impact on the prospects for the development of vaccines to control the major nematode and trematode infestations of livestock. Vaccine candidates are purified using conventional protein chemistry techniques but the limitations imposed by the scarcity of parasite material provide an insurmountable barrier for commercial vaccine production by this means. The ability to purify mRNA from different parasite life-cycle stages and to prepare cDNA expression libraries from it has proven central to the identification of immunogenic parasite proteins. Potentially, protective parasite antigens can now be produced in recombinant form in a variety of vectors and this represents a key breakthrough on the road to commercial vaccine production. The contribution of molecular biology to this process is discussed using several examples, particularly in vaccine development against the pathogenic abomasal nematode of sheep and goats, Haemonchus contortus, and the liver fluke of sheep and cattle, Fasciola hepatica. The difficulties of producing recombinant proteins in the correct form, with appropriate post-translational modification and conformation, are discussed as well as emerging means of antigen delivery including DNA vaccination. The opportunities offered by genome and expressed sequence tag analyses programmes for antigen targeting are discussed in association with developing microarray and proteomics technologies which offer the prospect of large scale, rapid antigen screening and identification.

Parasite genomics: current status and future prospects

The past year has brought great progress in the genome-sequencing efforts on a large number of protozoan and metazoan parasites. Whereas many of these projects are in their initial stages, at least one (for Plasmodium falciparum) is nearing completion. The information released to date has been most revealing with respect to immune evasion mechanisms.

Parasite vaccines--a reality?

Over the last decade, the anti-parasitics market has been the fastest growing sector of the overall $18 billion animal health market. While drugs for the treatment of parasites of livestock still dominate this sector and will continue to be developed or re-formulated, because of consumer demands for chemical-free food and of concerns regarding the environment and animal welfare there is a growing interest in the development of safe and effective vaccines. There is also a call for vaccines in the lucrative $3 billion-plus companion animal market. These demands for vaccines will add a greater impetus to an area that has seen tremendous success in the last 15 years. A number of anti-parasite vaccines have been developed, e.g. the recombinant 45w and EG95 oncosphere proteins against Taenia ovis and Echinococcus granulosis, respectively, and the Bm86 vaccine against Boophilus microplus. In addition, the cathepsin L vaccines against the liver fluke, Fasciola hepatica, and the H11 vaccine against Haemonchus contortus are progressing well. There are also many additional vaccine candidates for H. contortus and for other nematodes such as Ostertagia and Trichostrongylus spp. that may ultimately lead to broad-spectrum gastrointestinal worm vaccines. Live or attenuated-live vaccines are available for the control of avian coccidiosis, toxplasmosis in sheep and anaplasmosis in cattle, although molecular vaccines against protozoans are still proving elusive. The wealth of information in genomics, proteomics and immunology that has been forthcoming together will new methods of vaccine production and delivery should see many new vaccines reach the marketplace in the near future.