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Molecular determinants archetypical to the phylum Nematoda.

Yin Y, Martin J, Abubucker S, Wang Z, Wyrwicz L, Rychlewski L, McCarter JP, Wilson RK, Mitreva M - BMC Genomics (2009)

Bottom Line: Nearly 1,600 of the multi-species families did not share homology to Pfam domains, including a total of 758 restricted to Nematoda.Features of these protein families were revealed through extrapolation of essential functions from observed RNAi phenotypes in C. elegans, bioinformatics-based functional annotations, identification of distant homology based on protein folds, and prediction of expression at accessible nematode surfaces.This study identified and characterized the molecular determinants that help in defining the phylum Nematoda, and therefore improved our understanding of nematode protein evolution and provided novel insights for the development of next generation parasite control strategies.

View Article: PubMed Central - HTML - PubMed

Affiliation: The Genome Center, Department of Genetics, Washington University School of Medicine, St Louis, Missouri, USA. yyin@watson.wustl.edu

ABSTRACT

Background: Nematoda diverged from other animals between 600-1,200 million years ago and has become one of the most diverse animal phyla on earth. Most nematodes are free-living animals, but many are parasites of plants and animals including humans, posing major ecological and economical challenges around the world.

Results: We investigated phylum-specific molecular characteristics in Nematoda by exploring over 214,000 polypeptides from 32 nematode species including 27 parasites. Over 50,000 nematode protein families were identified based on primary sequence, including approximately 10% with members from at least three different species. Nearly 1,600 of the multi-species families did not share homology to Pfam domains, including a total of 758 restricted to Nematoda. Majority of the 462 families that were conserved among both free-living and parasitic species contained members from multiple nematode clades, yet approximately 90% of the 296 parasite-specific families originated only from a single clade. Features of these protein families were revealed through extrapolation of essential functions from observed RNAi phenotypes in C. elegans, bioinformatics-based functional annotations, identification of distant homology based on protein folds, and prediction of expression at accessible nematode surfaces. In addition, we identified a group of nematode-restricted sequence features in energy-generating electron transfer complexes as potential targets for new chemicals with minimal or no toxicity to the host.

Conclusion: This study identified and characterized the molecular determinants that help in defining the phylum Nematoda, and therefore improved our understanding of nematode protein evolution and provided novel insights for the development of next generation parasite control strategies.

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Identification and classification of nematode-restricted protein families.
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Figure 1: Identification and classification of nematode-restricted protein families.

Mentions: Protein families were built using MCL clustering [27] with the Markov cluster algorithm (MCL), which would not suffer greatly from potential problems caused by multi-domain proteins, promiscuous domains, or fragmented sequences. In total, the 214,159 nematode coding sequences were clustered into 54,036 protein families. Protein families conserved across multiple species suggest conserved features and essential functions, therefore a total of 5,326 multi-species families (112,271 sequences), with members from at least three different nematode species, were chosen for further evaluation. Of these, 1,939 protein families (36%) did not share homology to protein family models in Pfam-A (Figure 1).


Molecular determinants archetypical to the phylum Nematoda.

Yin Y, Martin J, Abubucker S, Wang Z, Wyrwicz L, Rychlewski L, McCarter JP, Wilson RK, Mitreva M - BMC Genomics (2009)

Identification and classification of nematode-restricted protein families.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2666764&req=5

Figure 1: Identification and classification of nematode-restricted protein families.
Mentions: Protein families were built using MCL clustering [27] with the Markov cluster algorithm (MCL), which would not suffer greatly from potential problems caused by multi-domain proteins, promiscuous domains, or fragmented sequences. In total, the 214,159 nematode coding sequences were clustered into 54,036 protein families. Protein families conserved across multiple species suggest conserved features and essential functions, therefore a total of 5,326 multi-species families (112,271 sequences), with members from at least three different nematode species, were chosen for further evaluation. Of these, 1,939 protein families (36%) did not share homology to protein family models in Pfam-A (Figure 1).

Bottom Line: Nearly 1,600 of the multi-species families did not share homology to Pfam domains, including a total of 758 restricted to Nematoda.Features of these protein families were revealed through extrapolation of essential functions from observed RNAi phenotypes in C. elegans, bioinformatics-based functional annotations, identification of distant homology based on protein folds, and prediction of expression at accessible nematode surfaces.This study identified and characterized the molecular determinants that help in defining the phylum Nematoda, and therefore improved our understanding of nematode protein evolution and provided novel insights for the development of next generation parasite control strategies.

View Article: PubMed Central - HTML - PubMed

Affiliation: The Genome Center, Department of Genetics, Washington University School of Medicine, St Louis, Missouri, USA. yyin@watson.wustl.edu

ABSTRACT

Background: Nematoda diverged from other animals between 600-1,200 million years ago and has become one of the most diverse animal phyla on earth. Most nematodes are free-living animals, but many are parasites of plants and animals including humans, posing major ecological and economical challenges around the world.

Results: We investigated phylum-specific molecular characteristics in Nematoda by exploring over 214,000 polypeptides from 32 nematode species including 27 parasites. Over 50,000 nematode protein families were identified based on primary sequence, including approximately 10% with members from at least three different species. Nearly 1,600 of the multi-species families did not share homology to Pfam domains, including a total of 758 restricted to Nematoda. Majority of the 462 families that were conserved among both free-living and parasitic species contained members from multiple nematode clades, yet approximately 90% of the 296 parasite-specific families originated only from a single clade. Features of these protein families were revealed through extrapolation of essential functions from observed RNAi phenotypes in C. elegans, bioinformatics-based functional annotations, identification of distant homology based on protein folds, and prediction of expression at accessible nematode surfaces. In addition, we identified a group of nematode-restricted sequence features in energy-generating electron transfer complexes as potential targets for new chemicals with minimal or no toxicity to the host.

Conclusion: This study identified and characterized the molecular determinants that help in defining the phylum Nematoda, and therefore improved our understanding of nematode protein evolution and provided novel insights for the development of next generation parasite control strategies.

Show MeSH
Related in: MedlinePlus