Gene phylogenies and protein-protein interactions: possible artifacts resulting from shared protein interaction partners

dc.creatorCampos, PRA
dc.creatorde Oliveira, VM
dc.creatorWagner, GP
dc.creatorStadler, PF
dc.date2004
dc.date44501
dc.date2014-11-13T18:37:07Z
dc.date2015-11-26T17:11:03Z
dc.date2014-11-13T18:37:07Z
dc.date2015-11-26T17:11:03Z
dc.date.accessioned2018-03-28T23:59:35Z
dc.date.available2018-03-28T23:59:35Z
dc.identifierJournal Of Theoretical Biology. Academic Press Ltd Elsevier Science Ltd, v. 231, n. 2, n. 197, n. 202, 2004.
dc.identifier0022-5193
dc.identifierWOS:000224438000005
dc.identifier10.1016/j.jtbi.2004.06.014
dc.identifierhttp://www.repositorio.unicamp.br/jspui/handle/REPOSIP/67844
dc.identifierhttp://www.repositorio.unicamp.br/handle/REPOSIP/67844
dc.identifierhttp://repositorio.unicamp.br/jspui/handle/REPOSIP/67844
dc.identifier.urihttp://repositorioslatinoamericanos.uchile.cl/handle/2250/1281010
dc.descriptionThe study of gene families critically depends on the correct reconstruction of gene genealogies, as for instance in the case of transcription factor genes like Hox genes and Dlx gene families. Proteins belonging to the same family are likely to share some of the same protein interaction partners and may thus face a similar selective environment. This common selective environment can induce co-evolutionary pressures and thus can give rise to correlated rates and patterns of evolution among members of a gene family. In this study, we simulate the evolution of a family of sequences which share a set of interaction partners. Depending on the amount of sequence dedicated to protein-protein interaction and the relative rate parameters of sequence evolution three outcomes are possible: if the fraction of the sequence dedicated to interaction with common co-factors is low and the time since divergence is small, the trees based on sequence information tend to be correct. If the time since gene duplication is long two possible outcomes are observed in our simulations. If the rate of evolution of the interaction partner is small compared to the rate of evolution of the focal protein family, the reconstructed trees tend towards star phylogenies. As the rate of evolution of the interaction partner approaches that of the focal protein family the reconstructed phylogenies tend to be incorrectly resolved. We conclude that the genealogies of gene families can be hard to estimate, in particular if the proteins interact with a conserved set of binding partners, as is likely the case for transcription factors. (C) 2004 Elsevier Ltd. All rights reserved.
dc.description231
dc.description2
dc.description197
dc.description202
dc.languageen
dc.publisherAcademic Press Ltd Elsevier Science Ltd
dc.publisherLondon
dc.publisherInglaterra
dc.relationJournal Of Theoretical Biology
dc.relationJ. Theor. Biol.
dc.rightsfechado
dc.rightshttp://www.elsevier.com/about/open-access/open-access-policies/article-posting-policy
dc.sourceWeb of Science
dc.subjectgene phylogeny
dc.subjecttree reconstruction
dc.subjectcorrelated substitutions
dc.subjectComparative Sequence-analysis
dc.subjectHox Proteins
dc.subjectHomeodomain Proteins
dc.subjectCorrelated Mutations
dc.subjectSecondary Structure
dc.subjectHomeobox Genes
dc.subjectRna
dc.subjectInformation
dc.subjectPrediction
dc.subjectEvolution
dc.titleGene phylogenies and protein-protein interactions: possible artifacts resulting from shared protein interaction partners
dc.typeArtículos de revistas


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