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Systematic analysis of insertions and deletions specific to nematode proteins and their proposed functional and evolutionary relevance
BACKGROUND: Amino acid insertions and deletions in proteins are considered relatively rare events, and their associations with the evolution and adaptation of organisms are not yet understood. In this study, we undertook a systematic analysis of over 214,000 polypeptides from 32 nematode species and...
Autores principales: | , , , , , |
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Formato: | Texto |
Lenguaje: | English |
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BioMed Central
2009
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2644674/ https://www.ncbi.nlm.nih.gov/pubmed/19175938 http://dx.doi.org/10.1186/1471-2148-9-23 |
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author | Wang, Zhengyuan Martin, John Abubucker, Sahar Yin, Yong Gasser, Robin B Mitreva, Makedonka |
author_facet | Wang, Zhengyuan Martin, John Abubucker, Sahar Yin, Yong Gasser, Robin B Mitreva, Makedonka |
author_sort | Wang, Zhengyuan |
collection | PubMed |
description | BACKGROUND: Amino acid insertions and deletions in proteins are considered relatively rare events, and their associations with the evolution and adaptation of organisms are not yet understood. In this study, we undertook a systematic analysis of over 214,000 polypeptides from 32 nematode species and identified insertions and deletions unique to nematode proteins in more than 1000 families and provided indirect evidence that these alterations are linked to the evolution and adaptation of nematodes. RESULTS: Amino acid alterations in sequences of nematodes were identified by comparison with homologous sequences from a wide range of eukaryotic (metzoan) organisms. This comparison revealed that the proteins inferred from transcriptomic datasets for nematodes contained more deletions than insertions, and that the deletions tended to be larger in length than insertions, indicating a decreased size of the transcriptome of nematodes compared with other organisms. The present findings showed that this reduction is more pronounced in parasitic nematodes compared with the free-living nematodes of the genus Caenorhabditis. Consistent with a requirement for conservation in proteins involved in the processing of genetic information, fewer insertions and deletions were detected in such proteins. On the other hand, more insertions and deletions were recorded for proteins inferred to be involved in the endocrine and immune systems, suggesting a link with adaptation. Similarly, proteins involved in multiple cellular pathways tended to display more deletions and insertions than those involved in a single pathway. The number of insertions and deletions shared by a range of plant parasitic nematodes were higher for proteins involved in lipid metabolism and electron transport compared with other nematodes, suggesting an association between metabolic adaptation and parasitism in plant hosts. We also identified three sizable deletions from proteins found to be specific to and shared by parasitic nematodes, which, given their uniqueness, might serve as target candidates for drug design. CONCLUSION: This study illustrates the significance of using comparative genomics approaches to identify molecular elements unique to parasitic nematodes, which have adapted to a particular host organism and mode of existence during evolution. While the focus of this study was on nematodes, the approach has applicability to a wide range of other groups of organisms. |
format | Text |
id | pubmed-2644674 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2009 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-26446742009-02-19 Systematic analysis of insertions and deletions specific to nematode proteins and their proposed functional and evolutionary relevance Wang, Zhengyuan Martin, John Abubucker, Sahar Yin, Yong Gasser, Robin B Mitreva, Makedonka BMC Evol Biol Research Article BACKGROUND: Amino acid insertions and deletions in proteins are considered relatively rare events, and their associations with the evolution and adaptation of organisms are not yet understood. In this study, we undertook a systematic analysis of over 214,000 polypeptides from 32 nematode species and identified insertions and deletions unique to nematode proteins in more than 1000 families and provided indirect evidence that these alterations are linked to the evolution and adaptation of nematodes. RESULTS: Amino acid alterations in sequences of nematodes were identified by comparison with homologous sequences from a wide range of eukaryotic (metzoan) organisms. This comparison revealed that the proteins inferred from transcriptomic datasets for nematodes contained more deletions than insertions, and that the deletions tended to be larger in length than insertions, indicating a decreased size of the transcriptome of nematodes compared with other organisms. The present findings showed that this reduction is more pronounced in parasitic nematodes compared with the free-living nematodes of the genus Caenorhabditis. Consistent with a requirement for conservation in proteins involved in the processing of genetic information, fewer insertions and deletions were detected in such proteins. On the other hand, more insertions and deletions were recorded for proteins inferred to be involved in the endocrine and immune systems, suggesting a link with adaptation. Similarly, proteins involved in multiple cellular pathways tended to display more deletions and insertions than those involved in a single pathway. The number of insertions and deletions shared by a range of plant parasitic nematodes were higher for proteins involved in lipid metabolism and electron transport compared with other nematodes, suggesting an association between metabolic adaptation and parasitism in plant hosts. We also identified three sizable deletions from proteins found to be specific to and shared by parasitic nematodes, which, given their uniqueness, might serve as target candidates for drug design. CONCLUSION: This study illustrates the significance of using comparative genomics approaches to identify molecular elements unique to parasitic nematodes, which have adapted to a particular host organism and mode of existence during evolution. While the focus of this study was on nematodes, the approach has applicability to a wide range of other groups of organisms. BioMed Central 2009-01-28 /pmc/articles/PMC2644674/ /pubmed/19175938 http://dx.doi.org/10.1186/1471-2148-9-23 Text en Copyright ©2009 Wang et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Article Wang, Zhengyuan Martin, John Abubucker, Sahar Yin, Yong Gasser, Robin B Mitreva, Makedonka Systematic analysis of insertions and deletions specific to nematode proteins and their proposed functional and evolutionary relevance |
title | Systematic analysis of insertions and deletions specific to nematode proteins and their proposed functional and evolutionary relevance |
title_full | Systematic analysis of insertions and deletions specific to nematode proteins and their proposed functional and evolutionary relevance |
title_fullStr | Systematic analysis of insertions and deletions specific to nematode proteins and their proposed functional and evolutionary relevance |
title_full_unstemmed | Systematic analysis of insertions and deletions specific to nematode proteins and their proposed functional and evolutionary relevance |
title_short | Systematic analysis of insertions and deletions specific to nematode proteins and their proposed functional and evolutionary relevance |
title_sort | systematic analysis of insertions and deletions specific to nematode proteins and their proposed functional and evolutionary relevance |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2644674/ https://www.ncbi.nlm.nih.gov/pubmed/19175938 http://dx.doi.org/10.1186/1471-2148-9-23 |
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