Cohesive versus flexible evolution of functional modules in eukaryotes.

Although functionally related proteins can be reliably predicted from phylogenetic profiles, many functional modules do not seem to evolve cohesively according to case studies and systematic analyses in prokaryotes. In this study we quantify the extent of evolutionary cohesiveness of functional modu...

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Autores principales:	Like Fokkens, Berend Snel
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2009
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/6bd9b99681844826ac7e55d6827d0e92
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spelling	oai:doaj.org-article:6bd9b99681844826ac7e55d6827d0e922021-11-25T05:41:52ZCohesive versus flexible evolution of functional modules in eukaryotes.1553-734X1553-735810.1371/journal.pcbi.1000276https://doaj.org/article/6bd9b99681844826ac7e55d6827d0e922009-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/19180181/?tool=EBIhttps://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358Although functionally related proteins can be reliably predicted from phylogenetic profiles, many functional modules do not seem to evolve cohesively according to case studies and systematic analyses in prokaryotes. In this study we quantify the extent of evolutionary cohesiveness of functional modules in eukaryotes and probe the biological and methodological factors influencing our estimates. We have collected various datasets of protein complexes and pathways in Saccheromyces cerevisiae. We define orthologous groups on 34 eukaryotic genomes and measure the extent of cohesive evolution of sets of orthologous groups of which members constitute a known complex or pathway. Within this framework it appears that most functional modules evolve flexibly rather than cohesively. Even after correcting for uncertain module definitions and potentially problematic orthologous groups, only 46% of pathways and complexes evolve more cohesively than random modules. This flexibility seems partly coupled to the nature of the functional module because biochemical pathways are generally more cohesively evolving than complexes.Like FokkensBerend SnelPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 5, Iss 1, p e1000276 (2009)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Like Fokkens Berend Snel Cohesive versus flexible evolution of functional modules in eukaryotes.
description	Although functionally related proteins can be reliably predicted from phylogenetic profiles, many functional modules do not seem to evolve cohesively according to case studies and systematic analyses in prokaryotes. In this study we quantify the extent of evolutionary cohesiveness of functional modules in eukaryotes and probe the biological and methodological factors influencing our estimates. We have collected various datasets of protein complexes and pathways in Saccheromyces cerevisiae. We define orthologous groups on 34 eukaryotic genomes and measure the extent of cohesive evolution of sets of orthologous groups of which members constitute a known complex or pathway. Within this framework it appears that most functional modules evolve flexibly rather than cohesively. Even after correcting for uncertain module definitions and potentially problematic orthologous groups, only 46% of pathways and complexes evolve more cohesively than random modules. This flexibility seems partly coupled to the nature of the functional module because biochemical pathways are generally more cohesively evolving than complexes.
format	article
author	Like Fokkens Berend Snel
author_facet	Like Fokkens Berend Snel
author_sort	Like Fokkens
title	Cohesive versus flexible evolution of functional modules in eukaryotes.
title_short	Cohesive versus flexible evolution of functional modules in eukaryotes.
title_full	Cohesive versus flexible evolution of functional modules in eukaryotes.
title_fullStr	Cohesive versus flexible evolution of functional modules in eukaryotes.
title_full_unstemmed	Cohesive versus flexible evolution of functional modules in eukaryotes.
title_sort	cohesive versus flexible evolution of functional modules in eukaryotes.
publisher	Public Library of Science (PLoS)
publishDate	2009
url	https://doaj.org/article/6bd9b99681844826ac7e55d6827d0e92
work_keys_str_mv	AT likefokkens cohesiveversusflexibleevolutionoffunctionalmodulesineukaryotes AT berendsnel cohesiveversusflexibleevolutionoffunctionalmodulesineukaryotes
_version_	1718414522637615104

Cohesive versus flexible evolution of functional modules in eukaryotes.

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