Plant F-box protein evolution is determined by lineage-specific timing of major gene family expansion waves.

F-box proteins (FBPs) represent one of the largest and fastest evolving gene/protein families in the plant kingdom. The FBP superfamily can be divided in several subfamilies characterized by different C-terminal protein-protein interaction domains that recruit targets for proteasomal degradation. He...

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Autores principales:	Aura Navarro-Quezada, Nadine Schumann, Marcel Quint
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/5301e2b12ce94578b954353f42580604
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spelling	oai:doaj.org-article:5301e2b12ce94578b954353f425806042021-11-18T09:03:43ZPlant F-box protein evolution is determined by lineage-specific timing of major gene family expansion waves.1932-620310.1371/journal.pone.0068672https://doaj.org/article/5301e2b12ce94578b954353f425806042013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23904908/?tool=EBIhttps://doaj.org/toc/1932-6203F-box proteins (FBPs) represent one of the largest and fastest evolving gene/protein families in the plant kingdom. The FBP superfamily can be divided in several subfamilies characterized by different C-terminal protein-protein interaction domains that recruit targets for proteasomal degradation. Hence, a clear picture of their phylogeny and molecular evolution is of special interest for the general understanding of evolutionary histories of multi-domain and/or large protein families in plants. In an effort to further understand the molecular evolution of F-box family proteins, we asked whether the largest subfamily in Arabidopsis thaliana, which carries a C-terminal F-box associated domain (FBA proteins) shares evolutionary patterns and signatures of selection with other FBPs. To address this question, we applied phylogenetic and molecular evolution analyses in combination with the evaluation of transcriptional profiles. Based on the 2219 FBA proteins we de novo identified in 34 completely sequenced plant genomes, we compared their evolutionary patterns to a previously analyzed large subfamily carrying C-terminal kelch repeats. We found that these two large FBP subfamilies generally tend to evolve by massive waves of duplication, followed by sequence conservation of the F-box domain and sequence diversification of the target recruiting domain. We conclude that the earlier in evolutionary time a major wave of expansion occurred, the more pronounced these selection signatures are. As a consequence, when performing cross species comparisons among FBP subfamilies, significant differences will be observed in the selective signatures of protein-protein interaction domains. Depending on the species, the investigated subfamilies comprise up to 45% of the complete superfamily, indicating that other subfamilies possibly follow similar modes of evolution.Aura Navarro-QuezadaNadine SchumannMarcel QuintPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 7, p e68672 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Aura Navarro-Quezada Nadine Schumann Marcel Quint Plant F-box protein evolution is determined by lineage-specific timing of major gene family expansion waves.
description	F-box proteins (FBPs) represent one of the largest and fastest evolving gene/protein families in the plant kingdom. The FBP superfamily can be divided in several subfamilies characterized by different C-terminal protein-protein interaction domains that recruit targets for proteasomal degradation. Hence, a clear picture of their phylogeny and molecular evolution is of special interest for the general understanding of evolutionary histories of multi-domain and/or large protein families in plants. In an effort to further understand the molecular evolution of F-box family proteins, we asked whether the largest subfamily in Arabidopsis thaliana, which carries a C-terminal F-box associated domain (FBA proteins) shares evolutionary patterns and signatures of selection with other FBPs. To address this question, we applied phylogenetic and molecular evolution analyses in combination with the evaluation of transcriptional profiles. Based on the 2219 FBA proteins we de novo identified in 34 completely sequenced plant genomes, we compared their evolutionary patterns to a previously analyzed large subfamily carrying C-terminal kelch repeats. We found that these two large FBP subfamilies generally tend to evolve by massive waves of duplication, followed by sequence conservation of the F-box domain and sequence diversification of the target recruiting domain. We conclude that the earlier in evolutionary time a major wave of expansion occurred, the more pronounced these selection signatures are. As a consequence, when performing cross species comparisons among FBP subfamilies, significant differences will be observed in the selective signatures of protein-protein interaction domains. Depending on the species, the investigated subfamilies comprise up to 45% of the complete superfamily, indicating that other subfamilies possibly follow similar modes of evolution.
format	article
author	Aura Navarro-Quezada Nadine Schumann Marcel Quint
author_facet	Aura Navarro-Quezada Nadine Schumann Marcel Quint
author_sort	Aura Navarro-Quezada
title	Plant F-box protein evolution is determined by lineage-specific timing of major gene family expansion waves.
title_short	Plant F-box protein evolution is determined by lineage-specific timing of major gene family expansion waves.
title_full	Plant F-box protein evolution is determined by lineage-specific timing of major gene family expansion waves.
title_fullStr	Plant F-box protein evolution is determined by lineage-specific timing of major gene family expansion waves.
title_full_unstemmed	Plant F-box protein evolution is determined by lineage-specific timing of major gene family expansion waves.
title_sort	plant f-box protein evolution is determined by lineage-specific timing of major gene family expansion waves.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/5301e2b12ce94578b954353f42580604
work_keys_str_mv	AT auranavarroquezada plantfboxproteinevolutionisdeterminedbylineagespecifictimingofmajorgenefamilyexpansionwaves AT nadineschumann plantfboxproteinevolutionisdeterminedbylineagespecifictimingofmajorgenefamilyexpansionwaves AT marcelquint plantfboxproteinevolutionisdeterminedbylineagespecifictimingofmajorgenefamilyexpansionwaves
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Plant F-box protein evolution is determined by lineage-specific timing of major gene family expansion waves.

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