Age-dependent evolution of the yeast protein interaction network suggests a limited role of gene duplication and divergence.

Proteins interact in complex protein-protein interaction (PPI) networks whose topological properties-such as scale-free topology, hierarchical modularity, and dissortativity-have suggested models of network evolution. Currently preferred models invoke preferential attachment or gene duplication and...

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Autores principales:	Wan Kyu Kim, Edward M Marcotte
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2008
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/a9908b02f7464b33bfeabc4bfb8276cb
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spelling	oai:doaj.org-article:a9908b02f7464b33bfeabc4bfb8276cb2021-11-25T05:41:56ZAge-dependent evolution of the yeast protein interaction network suggests a limited role of gene duplication and divergence.1553-734X1553-735810.1371/journal.pcbi.1000232https://doaj.org/article/a9908b02f7464b33bfeabc4bfb8276cb2008-11-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/19043579/?tool=EBIhttps://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358Proteins interact in complex protein-protein interaction (PPI) networks whose topological properties-such as scale-free topology, hierarchical modularity, and dissortativity-have suggested models of network evolution. Currently preferred models invoke preferential attachment or gene duplication and divergence to produce networks whose topology matches that observed for real PPIs, thus supporting these as likely models for network evolution. Here, we show that the interaction density and homodimeric frequency are highly protein age-dependent in real PPI networks in a manner which does not agree with these canonical models. In light of these results, we propose an alternative stochastic model, which adds each protein sequentially to a growing network in a manner analogous to protein crystal growth (CG) in solution. The key ideas are (1) interaction probability increases with availability of unoccupied interaction surface, thus following an anti-preferential attachment rule, (2) as a network grows, highly connected sub-networks emerge into protein modules or complexes, and (3) once a new protein is committed to a module, further connections tend to be localized within that module. The CG model produces PPI networks consistent in both topology and age distributions with real PPI networks and is well supported by the spatial arrangement of protein complexes of known 3-D structure, suggesting a plausible physical mechanism for network evolution.Wan Kyu KimEdward M MarcottePublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 4, Iss 11, p e1000232 (2008)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Wan Kyu Kim Edward M Marcotte Age-dependent evolution of the yeast protein interaction network suggests a limited role of gene duplication and divergence.
description	Proteins interact in complex protein-protein interaction (PPI) networks whose topological properties-such as scale-free topology, hierarchical modularity, and dissortativity-have suggested models of network evolution. Currently preferred models invoke preferential attachment or gene duplication and divergence to produce networks whose topology matches that observed for real PPIs, thus supporting these as likely models for network evolution. Here, we show that the interaction density and homodimeric frequency are highly protein age-dependent in real PPI networks in a manner which does not agree with these canonical models. In light of these results, we propose an alternative stochastic model, which adds each protein sequentially to a growing network in a manner analogous to protein crystal growth (CG) in solution. The key ideas are (1) interaction probability increases with availability of unoccupied interaction surface, thus following an anti-preferential attachment rule, (2) as a network grows, highly connected sub-networks emerge into protein modules or complexes, and (3) once a new protein is committed to a module, further connections tend to be localized within that module. The CG model produces PPI networks consistent in both topology and age distributions with real PPI networks and is well supported by the spatial arrangement of protein complexes of known 3-D structure, suggesting a plausible physical mechanism for network evolution.
format	article
author	Wan Kyu Kim Edward M Marcotte
author_facet	Wan Kyu Kim Edward M Marcotte
author_sort	Wan Kyu Kim
title	Age-dependent evolution of the yeast protein interaction network suggests a limited role of gene duplication and divergence.
title_short	Age-dependent evolution of the yeast protein interaction network suggests a limited role of gene duplication and divergence.
title_full	Age-dependent evolution of the yeast protein interaction network suggests a limited role of gene duplication and divergence.
title_fullStr	Age-dependent evolution of the yeast protein interaction network suggests a limited role of gene duplication and divergence.
title_full_unstemmed	Age-dependent evolution of the yeast protein interaction network suggests a limited role of gene duplication and divergence.
title_sort	age-dependent evolution of the yeast protein interaction network suggests a limited role of gene duplication and divergence.
publisher	Public Library of Science (PLoS)
publishDate	2008
url	https://doaj.org/article/a9908b02f7464b33bfeabc4bfb8276cb
work_keys_str_mv	AT wankyukim agedependentevolutionoftheyeastproteininteractionnetworksuggestsalimitedroleofgeneduplicationanddivergence AT edwardmmarcotte agedependentevolutionoftheyeastproteininteractionnetworksuggestsalimitedroleofgeneduplicationanddivergence
_version_	1718414535665123328

Age-dependent evolution of the yeast protein interaction network suggests a limited role of gene duplication and divergence.

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