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...

Descripción completa

Detalles Bibliográficos
Autores principales: Gibson, Todd A., Goldberg, Debra S.
Formato: Texto
Lenguaje:English
Publicado: Public Library of Science 2009
Materias:
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
_version_ 1782161891513073664
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
work_keys_str_mv AT gibsontodda questioningtheubiquityofneofunctionalization
AT goldbergdebras questioningtheubiquityofneofunctionalization