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The Puf family of RNA-binding proteins in plants: phylogeny, structural modeling, activity and subcellular localization

BACKGROUND: Puf proteins have important roles in controlling gene expression at the post-transcriptional level by promoting RNA decay and repressing translation. The Pumilio homology domain (PUM-HD) is a conserved region within Puf proteins that binds to RNA with sequence specificity. Although Puf p...

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Autores principales: Tam, Patrick PC, Barrette-Ng, Isabelle H, Simon, Dawn M, Tam, Michael WC, Ang, Amanda L, Muench, Douglas G
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2010
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2848763/
https://www.ncbi.nlm.nih.gov/pubmed/20214804
http://dx.doi.org/10.1186/1471-2229-10-44
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author Tam, Patrick PC
Barrette-Ng, Isabelle H
Simon, Dawn M
Tam, Michael WC
Ang, Amanda L
Muench, Douglas G
author_facet Tam, Patrick PC
Barrette-Ng, Isabelle H
Simon, Dawn M
Tam, Michael WC
Ang, Amanda L
Muench, Douglas G
author_sort Tam, Patrick PC
collection PubMed
description BACKGROUND: Puf proteins have important roles in controlling gene expression at the post-transcriptional level by promoting RNA decay and repressing translation. The Pumilio homology domain (PUM-HD) is a conserved region within Puf proteins that binds to RNA with sequence specificity. Although Puf proteins have been well characterized in animal and fungal systems, little is known about the structural and functional characteristics of Puf-like proteins in plants. RESULTS: The Arabidopsis and rice genomes code for 26 and 19 Puf-like proteins, respectively, each possessing eight or fewer Puf repeats in their PUM-HD. Key amino acids in the PUM-HD of several of these proteins are conserved with those of animal and fungal homologs, whereas other plant Puf proteins demonstrate extensive variability in these amino acids. Three-dimensional modeling revealed that the predicted structure of this domain in plant Puf proteins provides a suitable surface for binding RNA. Electrophoretic gel mobility shift experiments showed that the Arabidopsis AtPum2 PUM-HD binds with high affinity to BoxB of the Drosophila Nanos Response Element I (NRE1) RNA, whereas a point mutation in the core of the NRE1 resulted in a significant reduction in binding affinity. Transient expression of several of the Arabidopsis Puf proteins as fluorescent protein fusions revealed a dynamic, punctate cytoplasmic pattern of localization for most of these proteins. The presence of predicted nuclear export signals and accumulation of AtPuf proteins in the nucleus after treatment of cells with leptomycin B demonstrated that shuttling of these proteins between the cytosol and nucleus is common among these proteins. In addition to the cytoplasmically enriched AtPum proteins, two AtPum proteins showed nuclear targeting with enrichment in the nucleolus. CONCLUSIONS: The Puf family of RNA-binding proteins in plants consists of a greater number of members than any other model species studied to date. This, along with the amino acid variability observed within their PUM-HDs, suggests that these proteins may be involved in a wide range of post-transcriptional regulatory events that are important in providing plants with the ability to respond rapidly to changes in environmental conditions and throughout development.
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spelling pubmed-28487632010-04-03 The Puf family of RNA-binding proteins in plants: phylogeny, structural modeling, activity and subcellular localization Tam, Patrick PC Barrette-Ng, Isabelle H Simon, Dawn M Tam, Michael WC Ang, Amanda L Muench, Douglas G BMC Plant Biol Research article BACKGROUND: Puf proteins have important roles in controlling gene expression at the post-transcriptional level by promoting RNA decay and repressing translation. The Pumilio homology domain (PUM-HD) is a conserved region within Puf proteins that binds to RNA with sequence specificity. Although Puf proteins have been well characterized in animal and fungal systems, little is known about the structural and functional characteristics of Puf-like proteins in plants. RESULTS: The Arabidopsis and rice genomes code for 26 and 19 Puf-like proteins, respectively, each possessing eight or fewer Puf repeats in their PUM-HD. Key amino acids in the PUM-HD of several of these proteins are conserved with those of animal and fungal homologs, whereas other plant Puf proteins demonstrate extensive variability in these amino acids. Three-dimensional modeling revealed that the predicted structure of this domain in plant Puf proteins provides a suitable surface for binding RNA. Electrophoretic gel mobility shift experiments showed that the Arabidopsis AtPum2 PUM-HD binds with high affinity to BoxB of the Drosophila Nanos Response Element I (NRE1) RNA, whereas a point mutation in the core of the NRE1 resulted in a significant reduction in binding affinity. Transient expression of several of the Arabidopsis Puf proteins as fluorescent protein fusions revealed a dynamic, punctate cytoplasmic pattern of localization for most of these proteins. The presence of predicted nuclear export signals and accumulation of AtPuf proteins in the nucleus after treatment of cells with leptomycin B demonstrated that shuttling of these proteins between the cytosol and nucleus is common among these proteins. In addition to the cytoplasmically enriched AtPum proteins, two AtPum proteins showed nuclear targeting with enrichment in the nucleolus. CONCLUSIONS: The Puf family of RNA-binding proteins in plants consists of a greater number of members than any other model species studied to date. This, along with the amino acid variability observed within their PUM-HDs, suggests that these proteins may be involved in a wide range of post-transcriptional regulatory events that are important in providing plants with the ability to respond rapidly to changes in environmental conditions and throughout development. BioMed Central 2010-03-09 /pmc/articles/PMC2848763/ /pubmed/20214804 http://dx.doi.org/10.1186/1471-2229-10-44 Text en Copyright ©2010 Tam et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research article
Tam, Patrick PC
Barrette-Ng, Isabelle H
Simon, Dawn M
Tam, Michael WC
Ang, Amanda L
Muench, Douglas G
The Puf family of RNA-binding proteins in plants: phylogeny, structural modeling, activity and subcellular localization
title The Puf family of RNA-binding proteins in plants: phylogeny, structural modeling, activity and subcellular localization
title_full The Puf family of RNA-binding proteins in plants: phylogeny, structural modeling, activity and subcellular localization
title_fullStr The Puf family of RNA-binding proteins in plants: phylogeny, structural modeling, activity and subcellular localization
title_full_unstemmed The Puf family of RNA-binding proteins in plants: phylogeny, structural modeling, activity and subcellular localization
title_short The Puf family of RNA-binding proteins in plants: phylogeny, structural modeling, activity and subcellular localization
title_sort puf family of rna-binding proteins in plants: phylogeny, structural modeling, activity and subcellular localization
topic Research article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2848763/
https://www.ncbi.nlm.nih.gov/pubmed/20214804
http://dx.doi.org/10.1186/1471-2229-10-44
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