Translation of neutrally evolving peptides provides a basis for de novo gene evolution

Accumulating evidence indicates that some protein-coding genes have originated de novo from previously non-coding genomic sequences. However, the processes underlying de novo gene birth are still enigmatic. In particular, the appearance of a new functional protein seems highly improbable unless ther...

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Detalhes bibliográficos
Autores: Ruiz-Orera, Jorge, Verdaguer-Grau, Pol, Villanueva Cañas, José Luis, 1984-, Messeguer, Xavier, Albà Soler, Mar
Formato: artículo
Estado:Versión aceptada para publicación
Fecha de publicación:2018
País:España
Recursos:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
Repositorio:Recercat. Dipósit de la Recerca de Catalunya
OAI Identifier:oai:recercat.cat:10230/36048
Acesso em linha:http://hdl.handle.net/10230/36048
http://dx.doi.org/10.1038/s41559-018-0506-6
Access Level:acceso abierto
Palavra-chave:Genoma humà
Pèptids
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spelling Translation of neutrally evolving peptides provides a basis for de novo gene evolutionRuiz-Orera, JorgeVerdaguer-Grau, PolVillanueva Cañas, José Luis, 1984-Messeguer, XavierAlbà Soler, MarGenoma humàPèptidsAccumulating evidence indicates that some protein-coding genes have originated de novo from previously non-coding genomic sequences. However, the processes underlying de novo gene birth are still enigmatic. In particular, the appearance of a new functional protein seems highly improbable unless there is already a pool of neutrally evolving peptides that are translated at significant levels and that can at some point acquire new functions. Here, we use deep ribosome-profiling sequencing data, together with proteomics and single nucleotide polymorphism information, to search for these peptides. We find hundreds of open reading frames that are translated and that show no evolutionary conservation or selective constraints. These data suggest that the translation of these neutrally evolving peptides may be facilitated by the chance occurrence of open reading frames with a favourable codon composition. We conclude that the pervasive translation of the transcriptome provides plenty of material for the evolution of new functional proteins.We are grateful for valuable discussions with many colleagues during this study. This work was funded by grants BFU2012-36820, BFU2015-65235-P and TIN2015-69175-C4-3-R from Ministerio de Economía e Innovación (Spanish Government) and co-funded by FEDER (EC). We also received funding from Agència de Gestió d’Ajuts Universitaris i de Recerca Generalitat de Catalunya (AGAUR), grant no. 2014SGR1121.Springer20182018info:eu-repo/semantics/articleinfo:eu-repo/semantics/acceptedVersionapplication/pdfapplication/pdfhttp://hdl.handle.net/10230/36048http://dx.doi.org/10.1038/s41559-018-0506-6reponame:Recercat. Dipósit de la Recerca de Catalunyainstname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)InglésNature Ecology and Evolution. 2018 May;2(5):890-6info:eu-repo/grantAgreement/ES/3PN/BFU2012-36820info:eu-repo/grantAgreement/ES/1PE/BFU2015-65235-Pinfo:eu-repo/grantAgreement/ES/1PE/TIN2015-69175-C4-3-R© Springer The final publication is available at Springer via http://dx.doi.org/10.1038/s41559-018-0506-6info:eu-repo/semantics/openAccessoai:recercat.cat:10230/360482026-05-29T05:05:01Z
dc.title.none.fl_str_mv Translation of neutrally evolving peptides provides a basis for de novo gene evolution
title Translation of neutrally evolving peptides provides a basis for de novo gene evolution
spellingShingle Translation of neutrally evolving peptides provides a basis for de novo gene evolution
Ruiz-Orera, Jorge
Genoma humà
Pèptids
title_short Translation of neutrally evolving peptides provides a basis for de novo gene evolution
title_full Translation of neutrally evolving peptides provides a basis for de novo gene evolution
title_fullStr Translation of neutrally evolving peptides provides a basis for de novo gene evolution
title_full_unstemmed Translation of neutrally evolving peptides provides a basis for de novo gene evolution
title_sort Translation of neutrally evolving peptides provides a basis for de novo gene evolution
dc.creator.none.fl_str_mv Ruiz-Orera, Jorge
Verdaguer-Grau, Pol
Villanueva Cañas, José Luis, 1984-
Messeguer, Xavier
Albà Soler, Mar
author Ruiz-Orera, Jorge
author_facet Ruiz-Orera, Jorge
Verdaguer-Grau, Pol
Villanueva Cañas, José Luis, 1984-
Messeguer, Xavier
Albà Soler, Mar
author_role author
author2 Verdaguer-Grau, Pol
Villanueva Cañas, José Luis, 1984-
Messeguer, Xavier
Albà Soler, Mar
author2_role author
author
author
author
dc.subject.none.fl_str_mv Genoma humà
Pèptids
topic Genoma humà
Pèptids
description Accumulating evidence indicates that some protein-coding genes have originated de novo from previously non-coding genomic sequences. However, the processes underlying de novo gene birth are still enigmatic. In particular, the appearance of a new functional protein seems highly improbable unless there is already a pool of neutrally evolving peptides that are translated at significant levels and that can at some point acquire new functions. Here, we use deep ribosome-profiling sequencing data, together with proteomics and single nucleotide polymorphism information, to search for these peptides. We find hundreds of open reading frames that are translated and that show no evolutionary conservation or selective constraints. These data suggest that the translation of these neutrally evolving peptides may be facilitated by the chance occurrence of open reading frames with a favourable codon composition. We conclude that the pervasive translation of the transcriptome provides plenty of material for the evolution of new functional proteins.
publishDate 2018
dc.date.none.fl_str_mv 2018
2018
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/acceptedVersion
format article
status_str acceptedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10230/36048
http://dx.doi.org/10.1038/s41559-018-0506-6
url http://hdl.handle.net/10230/36048
http://dx.doi.org/10.1038/s41559-018-0506-6
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv Nature Ecology and Evolution. 2018 May;2(5):890-6
info:eu-repo/grantAgreement/ES/3PN/BFU2012-36820
info:eu-repo/grantAgreement/ES/1PE/BFU2015-65235-P
info:eu-repo/grantAgreement/ES/1PE/TIN2015-69175-C4-3-R
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv Springer
publisher.none.fl_str_mv Springer
dc.source.none.fl_str_mv reponame:Recercat. Dipósit de la Recerca de Catalunya
instname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
instname_str Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
reponame_str Recercat. Dipósit de la Recerca de Catalunya
collection Recercat. Dipósit de la Recerca de Catalunya
repository.name.fl_str_mv
repository.mail.fl_str_mv
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