Questioning the Ubiquity of Neofunctionalization
Gene duplication provides much of the raw material from which functional diversity evolves. Two evolutionary mechanisms have been proposed that generate functional diversity: neofunctionalization, the de novo acquisition of function by one duplicate, and subfunctionalization, the partitioning of anc...
Autores principales: | , |
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Formato: | Texto |
Lenguaje: | English |
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Public Library of Science
2009
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2597716/ https://www.ncbi.nlm.nih.gov/pubmed/19119408 http://dx.doi.org/10.1371/journal.pcbi.1000252 |
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author | Gibson, Todd A. Goldberg, Debra S. |
author_facet | Gibson, Todd A. Goldberg, Debra S. |
author_sort | Gibson, Todd A. |
collection | PubMed |
description | Gene duplication provides much of the raw material from which functional diversity evolves. Two evolutionary mechanisms have been proposed that generate functional diversity: neofunctionalization, the de novo acquisition of function by one duplicate, and subfunctionalization, the partitioning of ancestral functions between gene duplicates. With protein interactions as a surrogate for protein functions, evidence of prodigious neofunctionalization and subfunctionalization has been identified in analyses of empirical protein interactions and evolutionary models of protein interactions. However, we have identified three phenomena that have contributed to neofunctionalization being erroneously identified as a significant factor in protein interaction network evolution. First, self-interacting proteins are underreported in interaction data due to biological artifacts and design limitations in the two most common high-throughput protein interaction assays. Second, evolutionary inferences have been drawn from paralog analysis without consideration for concurrent and subsequent duplication events. Third, the theoretical model of prodigious neofunctionalization is unable to reproduce empirical network clustering and relies on untenable parameter requirements. In light of these findings, we believe that protein interaction evolution is more persuasively characterized by subfunctionalization and self-interactions. |
format | Text |
id | pubmed-2597716 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2009 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-25977162009-01-02 Questioning the Ubiquity of Neofunctionalization Gibson, Todd A. Goldberg, Debra S. PLoS Comput Biol Research Article Gene duplication provides much of the raw material from which functional diversity evolves. Two evolutionary mechanisms have been proposed that generate functional diversity: neofunctionalization, the de novo acquisition of function by one duplicate, and subfunctionalization, the partitioning of ancestral functions between gene duplicates. With protein interactions as a surrogate for protein functions, evidence of prodigious neofunctionalization and subfunctionalization has been identified in analyses of empirical protein interactions and evolutionary models of protein interactions. However, we have identified three phenomena that have contributed to neofunctionalization being erroneously identified as a significant factor in protein interaction network evolution. First, self-interacting proteins are underreported in interaction data due to biological artifacts and design limitations in the two most common high-throughput protein interaction assays. Second, evolutionary inferences have been drawn from paralog analysis without consideration for concurrent and subsequent duplication events. Third, the theoretical model of prodigious neofunctionalization is unable to reproduce empirical network clustering and relies on untenable parameter requirements. In light of these findings, we believe that protein interaction evolution is more persuasively characterized by subfunctionalization and self-interactions. Public Library of Science 2009-01-02 /pmc/articles/PMC2597716/ /pubmed/19119408 http://dx.doi.org/10.1371/journal.pcbi.1000252 Text en Gibson et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited. |
spellingShingle | Research Article Gibson, Todd A. Goldberg, Debra S. Questioning the Ubiquity of Neofunctionalization |
title | Questioning the Ubiquity of Neofunctionalization |
title_full | Questioning the Ubiquity of Neofunctionalization |
title_fullStr | Questioning the Ubiquity of Neofunctionalization |
title_full_unstemmed | Questioning the Ubiquity of Neofunctionalization |
title_short | Questioning the Ubiquity of Neofunctionalization |
title_sort | questioning the ubiquity of neofunctionalization |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2597716/ https://www.ncbi.nlm.nih.gov/pubmed/19119408 http://dx.doi.org/10.1371/journal.pcbi.1000252 |
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