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Reassessing Domain Architecture Evolution of Metazoan Proteins: Major Impact of Errors Caused by Confusing Paralogs and Epaktologs
Genes 2011, 2(3), 578-598; doi:10.3390/genes2030578
Article

Reassessing Domain Architecture Evolution of Metazoan Proteins: The Contribution of Different Evolutionary Mechanisms

 and *
Received: 30 June 2011; in revised form: 13 July 2011 / Accepted: 2 August 2011 / Published: 5 August 2011
(This article belongs to the Special Issue Evolution and Structure of Proteins and Proteomes)
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Abstract: In the accompanying papers we have shown that sequence errors of public databases and confusion of paralogs and epaktologs (proteins that are related only through the independent acquisition of the same domain types) significantly distort the picture that emerges from comparison of the domain architecture (DA) of multidomain Metazoan proteins since they introduce a strong bias in favor of terminal over internal DA change. The issue of whether terminal or internal DA changes occur with greater probability has very important implications for the DA evolution of multidomain proteins since gene fusion can add domains only at terminal positions, whereas domain-shuffling is capable of inserting domains both at internal and terminal positions. As a corollary, overestimation of terminal DA changes may be misinterpreted as evidence for a dominant role of gene fusion in DA evolution. In this manuscript we show that in several recent studies of DA evolution of Metazoa the authors used databases that are significantly contaminated with incomplete, abnormal and mispredicted sequences (e.g., UniProtKB/TrEMBL, EnsEMBL) and/or the authors failed to separate paralogs and epaktologs, explaining why these studies concluded that the major mechanism for gains of new domains in metazoan proteins is gene fusion. In contrast with the latter conclusion, our studies on high quality orthologous and paralogous Swiss-Prot sequences confirm that shuffling of mobile domains had a major role in the evolution of multidomain proteins of Metazoa and especially those formed in early vertebrates.
Keywords: epaktologs; evolution of domain architecture; exon-shuffling; gene fusion; gene prediction error; mobility of domains; promiscuity of domains; versatility of domains epaktologs; evolution of domain architecture; exon-shuffling; gene fusion; gene prediction error; mobility of domains; promiscuity of domains; versatility of domains
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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MDPI and ACS Style

Nagy, A.; Patthy, L. Reassessing Domain Architecture Evolution of Metazoan Proteins: The Contribution of Different Evolutionary Mechanisms. Genes 2011, 2, 578-598.

AMA Style

Nagy A, Patthy L. Reassessing Domain Architecture Evolution of Metazoan Proteins: The Contribution of Different Evolutionary Mechanisms. Genes. 2011; 2(3):578-598.

Chicago/Turabian Style

Nagy, Alinda; Patthy, Laszlo. 2011. "Reassessing Domain Architecture Evolution of Metazoan Proteins: The Contribution of Different Evolutionary Mechanisms." Genes 2, no. 3: 578-598.


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