Cargando…

Analysis of functional redundancies within the Arabidopsis TCP transcription factor family

Analyses of the functions of TEOSINTE-LIKE1, CYCLOIDEA, and PROLIFERATING CELL FACTOR1 (TCP) transcription factors have been hampered by functional redundancy between its individual members. In general, putative functionally redundant genes are predicted based on sequence similarity and confirmed by...

Descripción completa

Detalles Bibliográficos
Autores principales: Danisman, Selahattin, van Dijk, Aalt D. J., Bimbo, Andrea, van der Wal, Froukje, Hennig, Lars, de Folter, Stefan, Angenent, Gerco C., Immink, Richard G. H.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3871820/
https://www.ncbi.nlm.nih.gov/pubmed/24129704
http://dx.doi.org/10.1093/jxb/ert337
_version_ 1782296883997179904
author Danisman, Selahattin
van Dijk, Aalt D. J.
Bimbo, Andrea
van der Wal, Froukje
Hennig, Lars
de Folter, Stefan
Angenent, Gerco C.
Immink, Richard G. H.
author_facet Danisman, Selahattin
van Dijk, Aalt D. J.
Bimbo, Andrea
van der Wal, Froukje
Hennig, Lars
de Folter, Stefan
Angenent, Gerco C.
Immink, Richard G. H.
author_sort Danisman, Selahattin
collection PubMed
description Analyses of the functions of TEOSINTE-LIKE1, CYCLOIDEA, and PROLIFERATING CELL FACTOR1 (TCP) transcription factors have been hampered by functional redundancy between its individual members. In general, putative functionally redundant genes are predicted based on sequence similarity and confirmed by genetic analysis. In the TCP family, however, identification is impeded by relatively low overall sequence similarity. In a search for functionally redundant TCP pairs that control Arabidopsis leaf development, this work performed an integrative bioinformatics analysis, combining protein sequence similarities, gene expression data, and results of pair-wise protein–protein interaction studies for the 24 members of the Arabidopsis TCP transcription factor family. For this, the work completed any lacking gene expression and protein–protein interaction data experimentally and then performed a comprehensive prediction of potential functional redundant TCP pairs. Subsequently, redundant functions could be confirmed for selected predicted TCP pairs by genetic and molecular analyses. It is demonstrated that the previously uncharacterized class I TCP19 gene plays a role in the control of leaf senescence in a redundant fashion with TCP20. Altogether, this work shows the power of combining classical genetic and molecular approaches with bioinformatics predictions to unravel functional redundancies in the TCP transcription factor family.
format Online
Article
Text
id pubmed-3871820
institution National Center for Biotechnology Information
language English
publishDate 2013
publisher Oxford University Press
record_format MEDLINE/PubMed
spelling pubmed-38718202013-12-26 Analysis of functional redundancies within the Arabidopsis TCP transcription factor family Danisman, Selahattin van Dijk, Aalt D. J. Bimbo, Andrea van der Wal, Froukje Hennig, Lars de Folter, Stefan Angenent, Gerco C. Immink, Richard G. H. J Exp Bot Research Paper Analyses of the functions of TEOSINTE-LIKE1, CYCLOIDEA, and PROLIFERATING CELL FACTOR1 (TCP) transcription factors have been hampered by functional redundancy between its individual members. In general, putative functionally redundant genes are predicted based on sequence similarity and confirmed by genetic analysis. In the TCP family, however, identification is impeded by relatively low overall sequence similarity. In a search for functionally redundant TCP pairs that control Arabidopsis leaf development, this work performed an integrative bioinformatics analysis, combining protein sequence similarities, gene expression data, and results of pair-wise protein–protein interaction studies for the 24 members of the Arabidopsis TCP transcription factor family. For this, the work completed any lacking gene expression and protein–protein interaction data experimentally and then performed a comprehensive prediction of potential functional redundant TCP pairs. Subsequently, redundant functions could be confirmed for selected predicted TCP pairs by genetic and molecular analyses. It is demonstrated that the previously uncharacterized class I TCP19 gene plays a role in the control of leaf senescence in a redundant fashion with TCP20. Altogether, this work shows the power of combining classical genetic and molecular approaches with bioinformatics predictions to unravel functional redundancies in the TCP transcription factor family. Oxford University Press 2013-12 2013-10-15 /pmc/articles/PMC3871820/ /pubmed/24129704 http://dx.doi.org/10.1093/jxb/ert337 Text en © The Author 2013. Published by Oxford University Press on behalf of the Society for Experimental Biology. http://creativecommons.org/licenses/by/3.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Paper
Danisman, Selahattin
van Dijk, Aalt D. J.
Bimbo, Andrea
van der Wal, Froukje
Hennig, Lars
de Folter, Stefan
Angenent, Gerco C.
Immink, Richard G. H.
Analysis of functional redundancies within the Arabidopsis TCP transcription factor family
title Analysis of functional redundancies within the Arabidopsis TCP transcription factor family
title_full Analysis of functional redundancies within the Arabidopsis TCP transcription factor family
title_fullStr Analysis of functional redundancies within the Arabidopsis TCP transcription factor family
title_full_unstemmed Analysis of functional redundancies within the Arabidopsis TCP transcription factor family
title_short Analysis of functional redundancies within the Arabidopsis TCP transcription factor family
title_sort analysis of functional redundancies within the arabidopsis tcp transcription factor family
topic Research Paper
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3871820/
https://www.ncbi.nlm.nih.gov/pubmed/24129704
http://dx.doi.org/10.1093/jxb/ert337
work_keys_str_mv AT danismanselahattin analysisoffunctionalredundancieswithinthearabidopsistcptranscriptionfactorfamily
AT vandijkaaltdj analysisoffunctionalredundancieswithinthearabidopsistcptranscriptionfactorfamily
AT bimboandrea analysisoffunctionalredundancieswithinthearabidopsistcptranscriptionfactorfamily
AT vanderwalfroukje analysisoffunctionalredundancieswithinthearabidopsistcptranscriptionfactorfamily
AT henniglars analysisoffunctionalredundancieswithinthearabidopsistcptranscriptionfactorfamily
AT defolterstefan analysisoffunctionalredundancieswithinthearabidopsistcptranscriptionfactorfamily
AT angenentgercoc analysisoffunctionalredundancieswithinthearabidopsistcptranscriptionfactorfamily
AT imminkrichardgh analysisoffunctionalredundancieswithinthearabidopsistcptranscriptionfactorfamily