Systematic analysis of insertions and deletions specific to nematode proteins and their proposed functional and evolutionary relevance

Wang, Zhengyuan and Martin, John and Abubucker, Sahar and Yin, Yong and Gasser, Robin B. and Mitreva, Makedonka (2009) Systematic analysis of insertions and deletions specific to nematode proteins and their proposed functional and evolutionary relevance. BMC Evolutionary Biology, 9 (23). pp. 1-14.

[thumbnail of Systematic analysis of insertions.pdf]
Systematic analysis of insertions.pdf

Download (1MB) | Preview


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.

Item Type: Article
Subjects: Medical and Health Sciences > Basic medicine
Divisions: Faculty of Medical Science
Depositing User: Mirjana Kocaleva
Date Deposited: 30 Nov 2012 14:14
Last Modified: 30 Nov 2012 14:14

Actions (login required)

View Item View Item