We are analyzing https://link.springer.com/article/10.1186/1471-2229-10-44.

Title:
The Puf family of RNA-binding proteins in plants: phylogeny, structural modeling, activity and subcellular localization | BMC Plant Biology
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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Keywords {🔍}

proteins, puf, atpum, figure, rna, pubmed, protein, pumhd, amino, article, arabidopsis, google, scholar, sequence, nre, plant, cas, rice, binding, repeats, acid, acids, conserved, human, genes, mrna, osg, analysis, pumhds, pumilio, structure, drosophila, domain, bound, repeat, central, file, rnabinding, predicted, localization, interactions, gene, expression, sequences, pum, models, family, region, cells, cell,

Topics {✒️}

gov/genome/seq/blastgen/blastgen org/cgi/var/nair/resonline open access article article download pdf atpum-fluorescent fusion proteins tcmago-tcy14 heterodimer complex atpum-fluorescent protein fusions bmc cell biology purified gst-atpum2 pum-hd org/tdb/e2k1/osa1/ typically amino-terminal extensions subcellular localization pattern plant pum-hd adopts post-transcriptional regulatory events rna-immunoprecipitation profiling studies rna-binding protein she2 altered rna-binding specificity pum-hd coding sequence rice pum-hds showed full-length pum-hd ash1 mrna-binding protein cytoplasmic post-transcriptional control conserved pum-hd region full-length atpum protein plant pum-hds adopt plant pum-hd bound gerber ap pum-hd binding site gst-atpum2 pum-hd subcellular localization patterns conserved rna-binding protein nucleolar marker rfp-prh75 drosophila pumilio pum-hd cold competitor rna atpum2 pum-hd concentration exon-junction complex human pum1 pum-hd fluorescent protein fusions drosophila pum-hd proteins van der waals subcellular localization studies punctate cytoplasmic pattern cell biology studies atpum2 pum-hd interaction atpum2 pum-hd bound full-length cdna clones pfam search http engineering research council cauliflower mosaic virus plant systems biology

Questions {❓}

Spassov DS, Jurecic R: The PUF family of RNA-binding proteins: does evolutionarily conserved structure equal conserved function?
Sterck L, Rombauts S, Vandepoele K, Rouze P, Peer Van de Y: How many genes are there in plants and why are they there)?

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         description: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. 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. 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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            Fluorescent Protein Fusion
            Epidermal Cell Layer
            Amino Terminal Region
            Subcellular Localization Pattern
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            Agriculture
            Tree Biology
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         Fluorescent Protein Fusion
         Epidermal Cell Layer
         Amino Terminal Region
         Subcellular Localization Pattern
         Plant Sciences
         Agriculture
         Tree Biology
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