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Needles in the EST haystack: large-scale identification and analysis of excretory-secretory (ES) proteins in parasitic nematodes using expressed sequence tags (ESTs).

Nagaraj SH, Gasser RB, Ranganathan S - PLoS Negl Trop Dis (2008)

Bottom Line: Of these 4,710 proteins, 2,490 (52.8%) had orthologues in Caenorhabditis elegans, whereas 621 (13.8%) appeared to be novel, currently having no significant match to any molecule available in public databases.We report the large-scale analysis of ES proteins inferred from EST data for a range of parasitic nematodes.This set of ES proteins provides an inventory of known and novel members of ES proteins as a foundation for studies focused on understanding the biology of parasitic nematodes and their interactions with their hosts, as well as for the development of novel drugs or vaccines for parasite intervention and control.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, New South Wales, Australia.

ABSTRACT

Background: Parasitic nematodes of humans, other animals and plants continue to impose a significant public health and economic burden worldwide, due to the diseases they cause. Promising antiparasitic drug and vaccine candidates have been discovered from excreted or secreted (ES) proteins released from the parasite and exposed to the immune system of the host. Mining the entire expressed sequence tag (EST) data available from parasitic nematodes represents an approach to discover such ES targets.

Methods and findings: In this study, we predicted, using EST2Secretome, a novel, high-throughput, computational workflow system, 4,710 ES proteins from 452,134 ESTs derived from 39 different species of nematodes, parasitic in animals (including humans) or plants. In total, 2,632, 786, and 1,292 ES proteins were predicted for animal-, human-, and plant-parasitic nematodes. Subsequently, we systematically analysed ES proteins using computational methods. Of these 4,710 proteins, 2,490 (52.8%) had orthologues in Caenorhabditis elegans, whereas 621 (13.8%) appeared to be novel, currently having no significant match to any molecule available in public databases. Of the C. elegans homologues, 267 had strong "loss-of-function" phenotypes by RNA interference (RNAi) in this nematode. We could functionally classify 1,948 (41.3%) sequences using the Gene Ontology (GO) terms, establish pathway associations for 573 (12.2%) sequences using Kyoto Encyclopaedia of Genes and Genomes (KEGG), and identify protein interaction partners for 1,774 (37.6%) molecules. We also mapped 758 (16.1%) proteins to protein domains including the nematode-specific protein family "transthyretin-like" and "chromadorea ALT," considered as vaccine candidates against filariasis in humans.

Conclusions: We report the large-scale analysis of ES proteins inferred from EST data for a range of parasitic nematodes. This set of ES proteins provides an inventory of known and novel members of ES proteins as a foundation for studies focused on understanding the biology of parasitic nematodes and their interactions with their hosts, as well as for the development of novel drugs or vaccines for parasite intervention and control.

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Related in: MedlinePlus

Comparison of ES proteins with the respective C. elegans, parasitic nematodes and host orthologues using SimiTri.Data for parasitic nematodes of A. humans, B. other animals or C. plants are presented, compared with their respective host organism. The numbers at each vertex indicate the number of ES proteins matching only the specific database. The numbers on the edges indicate the number of ES proteins matching the two databases linked by that edge. The boxed number within each triangle indicates the number of ES proteins with matches to all three datasets compared: C. elegans, parasitic nematodes and host databases.
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pntd-0000301-g004: Comparison of ES proteins with the respective C. elegans, parasitic nematodes and host orthologues using SimiTri.Data for parasitic nematodes of A. humans, B. other animals or C. plants are presented, compared with their respective host organism. The numbers at each vertex indicate the number of ES proteins matching only the specific database. The numbers on the edges indicate the number of ES proteins matching the two databases linked by that edge. The boxed number within each triangle indicates the number of ES proteins with matches to all three datasets compared: C. elegans, parasitic nematodes and host databases.

Mentions: Sequence-based searches were performed to classify the ES proteins, to identify the presence or absence of putative homologues in C. elegans, and to infer nematode-specific and parasite-specific genes. For parasitic nematodes, Parkinson et al. [40],[58] suggested previously that it is beneficial to make simultaneous three-way comparisons (using SimiTri) of a specific organism or a group of organisms with homologues in C. elegans (the ‘model nematode’), other nematode species as well as the host organism. Such an analysis provides a means for the rapid identification of genes/proteins conserved between any two datasets compared (e.g., between parasitic nematodes and free-living ones, or between parasitic nematode and its host). In the present study, we systematically compared inferred ES protein data with those available in three relevant databases. For the three ES protein datasets from nematodes parasitic in humans (786 proteins), animals (2,632 proteins) or plants (1,292 proteins), we selected C. elegans and parasitic nematode databases as well as databases specific to the host organisms for comparative analysis. For instance, data for parasitic nematodes of humans were matched with those of the human host, C. elegans and parasitic nematodes from other hosts. Similarly, ES proteins predicted for nematodes parasitic in animals or plants were compared against host datasets. Protein sequences available in the following three datasets (i) C. elegans (from Wormpep [31]), (ii) parasitic nematodes (constructed locally) and (iii) respective hosts (human, other animal and plants sequences from NCBI non-redundant protein database) were processed. Three-way comparison of the parasitic nematode database with homologues in C. elegans, their principal definitive host organism (human, other animal or plant) and the database of all available parasitic nematodes, have been presented using SimiTri [40] in Figure 4. In all three datasets for parasitic nematodes, inferred ES proteins congregated with parasitic nematodes rather than with C. elegans or with the host species (lower right hand corner of each triangle, coloured in red in Figure 4). Overall, 320 (40.7%), 789 (29.7%) and 581 (44.9%) ES proteins inferred from human-, other animal- and plant-parasitic nematodes were associated exclusively with parasitic nematodes and are interpreted to be parasite-specific, based on the data currently available. Of the homologues predicted to be nematode-specific (along the side of the triangle connecting C. elegans and parasitic nematodes), 585 (74.4%), 1,511 (57.4%) and 1,034 (80.0%) of the inferred ES proteins were confined to nematodes (based on currently available datasets). Based on these comparisons, we illustrate that a significant percentage of these proteins in parasitic nematodes are either parasite- or nematode-specific and are either absent from or very divergent in sequence from molecules in their host(s). These molecules might represent candidate targets for novel anthelmintics for parasite intervention. Importantly, their apparent specificity to parasitic nematodes or different groups within the phylum Nematoda renders them as important groups of molecules for future study, particularly in relation to the roles of these molecules in the host-parasite interplay, their involvement in inducing immune responses and disease in the host.


Needles in the EST haystack: large-scale identification and analysis of excretory-secretory (ES) proteins in parasitic nematodes using expressed sequence tags (ESTs).

Nagaraj SH, Gasser RB, Ranganathan S - PLoS Negl Trop Dis (2008)

Comparison of ES proteins with the respective C. elegans, parasitic nematodes and host orthologues using SimiTri.Data for parasitic nematodes of A. humans, B. other animals or C. plants are presented, compared with their respective host organism. The numbers at each vertex indicate the number of ES proteins matching only the specific database. The numbers on the edges indicate the number of ES proteins matching the two databases linked by that edge. The boxed number within each triangle indicates the number of ES proteins with matches to all three datasets compared: C. elegans, parasitic nematodes and host databases.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2553489&req=5

pntd-0000301-g004: Comparison of ES proteins with the respective C. elegans, parasitic nematodes and host orthologues using SimiTri.Data for parasitic nematodes of A. humans, B. other animals or C. plants are presented, compared with their respective host organism. The numbers at each vertex indicate the number of ES proteins matching only the specific database. The numbers on the edges indicate the number of ES proteins matching the two databases linked by that edge. The boxed number within each triangle indicates the number of ES proteins with matches to all three datasets compared: C. elegans, parasitic nematodes and host databases.
Mentions: Sequence-based searches were performed to classify the ES proteins, to identify the presence or absence of putative homologues in C. elegans, and to infer nematode-specific and parasite-specific genes. For parasitic nematodes, Parkinson et al. [40],[58] suggested previously that it is beneficial to make simultaneous three-way comparisons (using SimiTri) of a specific organism or a group of organisms with homologues in C. elegans (the ‘model nematode’), other nematode species as well as the host organism. Such an analysis provides a means for the rapid identification of genes/proteins conserved between any two datasets compared (e.g., between parasitic nematodes and free-living ones, or between parasitic nematode and its host). In the present study, we systematically compared inferred ES protein data with those available in three relevant databases. For the three ES protein datasets from nematodes parasitic in humans (786 proteins), animals (2,632 proteins) or plants (1,292 proteins), we selected C. elegans and parasitic nematode databases as well as databases specific to the host organisms for comparative analysis. For instance, data for parasitic nematodes of humans were matched with those of the human host, C. elegans and parasitic nematodes from other hosts. Similarly, ES proteins predicted for nematodes parasitic in animals or plants were compared against host datasets. Protein sequences available in the following three datasets (i) C. elegans (from Wormpep [31]), (ii) parasitic nematodes (constructed locally) and (iii) respective hosts (human, other animal and plants sequences from NCBI non-redundant protein database) were processed. Three-way comparison of the parasitic nematode database with homologues in C. elegans, their principal definitive host organism (human, other animal or plant) and the database of all available parasitic nematodes, have been presented using SimiTri [40] in Figure 4. In all three datasets for parasitic nematodes, inferred ES proteins congregated with parasitic nematodes rather than with C. elegans or with the host species (lower right hand corner of each triangle, coloured in red in Figure 4). Overall, 320 (40.7%), 789 (29.7%) and 581 (44.9%) ES proteins inferred from human-, other animal- and plant-parasitic nematodes were associated exclusively with parasitic nematodes and are interpreted to be parasite-specific, based on the data currently available. Of the homologues predicted to be nematode-specific (along the side of the triangle connecting C. elegans and parasitic nematodes), 585 (74.4%), 1,511 (57.4%) and 1,034 (80.0%) of the inferred ES proteins were confined to nematodes (based on currently available datasets). Based on these comparisons, we illustrate that a significant percentage of these proteins in parasitic nematodes are either parasite- or nematode-specific and are either absent from or very divergent in sequence from molecules in their host(s). These molecules might represent candidate targets for novel anthelmintics for parasite intervention. Importantly, their apparent specificity to parasitic nematodes or different groups within the phylum Nematoda renders them as important groups of molecules for future study, particularly in relation to the roles of these molecules in the host-parasite interplay, their involvement in inducing immune responses and disease in the host.

Bottom Line: Of these 4,710 proteins, 2,490 (52.8%) had orthologues in Caenorhabditis elegans, whereas 621 (13.8%) appeared to be novel, currently having no significant match to any molecule available in public databases.We report the large-scale analysis of ES proteins inferred from EST data for a range of parasitic nematodes.This set of ES proteins provides an inventory of known and novel members of ES proteins as a foundation for studies focused on understanding the biology of parasitic nematodes and their interactions with their hosts, as well as for the development of novel drugs or vaccines for parasite intervention and control.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, New South Wales, Australia.

ABSTRACT

Background: Parasitic nematodes of humans, other animals and plants continue to impose a significant public health and economic burden worldwide, due to the diseases they cause. Promising antiparasitic drug and vaccine candidates have been discovered from excreted or secreted (ES) proteins released from the parasite and exposed to the immune system of the host. Mining the entire expressed sequence tag (EST) data available from parasitic nematodes represents an approach to discover such ES targets.

Methods and findings: In this study, we predicted, using EST2Secretome, a novel, high-throughput, computational workflow system, 4,710 ES proteins from 452,134 ESTs derived from 39 different species of nematodes, parasitic in animals (including humans) or plants. In total, 2,632, 786, and 1,292 ES proteins were predicted for animal-, human-, and plant-parasitic nematodes. Subsequently, we systematically analysed ES proteins using computational methods. Of these 4,710 proteins, 2,490 (52.8%) had orthologues in Caenorhabditis elegans, whereas 621 (13.8%) appeared to be novel, currently having no significant match to any molecule available in public databases. Of the C. elegans homologues, 267 had strong "loss-of-function" phenotypes by RNA interference (RNAi) in this nematode. We could functionally classify 1,948 (41.3%) sequences using the Gene Ontology (GO) terms, establish pathway associations for 573 (12.2%) sequences using Kyoto Encyclopaedia of Genes and Genomes (KEGG), and identify protein interaction partners for 1,774 (37.6%) molecules. We also mapped 758 (16.1%) proteins to protein domains including the nematode-specific protein family "transthyretin-like" and "chromadorea ALT," considered as vaccine candidates against filariasis in humans.

Conclusions: We report the large-scale analysis of ES proteins inferred from EST data for a range of parasitic nematodes. This set of ES proteins provides an inventory of known and novel members of ES proteins as a foundation for studies focused on understanding the biology of parasitic nematodes and their interactions with their hosts, as well as for the development of novel drugs or vaccines for parasite intervention and control.

Show MeSH
Related in: MedlinePlus