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Domain architecture conservation in orthologs

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Item Type:Article
Title:Domain architecture conservation in orthologs
Creators Name:Forslund, K. and Pekkari, I. and Sonnhammer, E.L.L.
Abstract:Background: As orthologous proteins are expected to retain function more often than other homologs, they are often used for functional annotation transfer between species. However, ortholog identification methods do not take into account changes in domain architecture, which are likely to modify a protein's function. By domain architecture we refer to the sequential arrangement of domains along a protein sequence.To assess the level of domain architecture conservation among orthologs, we carried out a large-scale study of such events between human and 40 other species spanning the entire evolutionary range. We designed a score to measure domain architecture similarity and used it to analyze differences in domain architecture conservation between orthologs and paralogs relative to the conservation of primary sequence. We also statistically characterized the extents of different types of domain swapping events across pairs of orthologs and paralogs. Results: The analysis shows that orthologs exhibit greater domain architecture conservation than paralogous homologs, even when differences in average sequence divergence are compensated for, for homologs that have diverged beyond a certain threshold. We interpret this as an indication of a stronger selective pressure on orthologs than paralogs to retain the domain architecture required for the proteins to perform a specific function. In general, orthologs as well as the closest paralogous homologs have very similar domain architectures, even at large evolutionary separation.The most common domain architecture changes observed in both ortholog and paralog pairs involved insertion/deletion of new domains, while domain shuffling and segment duplication/deletion were very infrequent. Conclusions: On the whole, our results support the hypothesis that function conservation between orthologs demands higher domain architecture conservation than other types of homologs, relative to primary sequence conservation. This supports the notion that orthologs are functionally more similar than other types of homologs at the same evolutionary distance.
Keywords:Amino Acid Sequence, Conserved Sequence, Molecular Evolution, Proteins, Tertiary Protein Structure, Animals
Source:BMC Bioinformatics
ISSN:1471-2105
Publisher:BioMed Central (U.K.)
Volume:12
Page Range:326
Date:5 August 2011
Official Publication:https://doi.org/10.1186/1471-2105-12-326
PubMed:View item in PubMed

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