The Puf family of RNA-binding proteins in plants: phylogeny, structural modeling, activity and subcellular localization
© Tam et al; licensee BioMed Central Ltd. 2010
Received: 31 August 2009
Accepted: 9 March 2010
Published: 9 March 2010
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.
Post-transcriptional control of gene expression functions to regulate protein synthesis in a spatial and temporal manner, and involves the activity of an extensive array of RNA-binding proteins. Throughout the lifetime of an mRNA, a dynamic association exists between mRNAs and RNA-binding proteins. These interactions are important in mediating mRNA maturation events such as splicing, capping, polyadenylation and export from the nucleus [1, 2]. RNA-binding proteins also contribute to post-transcriptional regulatory events in the cytoplasm, such as mRNA localization, mRNA stability and decay, and translation. One group of RNA-binding proteins that are important regulators of cytoplasmic post-transcriptional control is the Puf family of proteins. Puf proteins have extensive structural conservation within their RNA binding domain and regulate a range of biological processes, including developmental patterning, stem cell control, and neuron function .
The founding members of the Puf family of proteins are Pumilio in Drosophila and fem-3 binding factor (FBF) in C. elegans [4, 5]. Puf protein diversity extends across kingdoms, as mammalian, fungal, protozoan and plant homologs have been identified [6–8]. The number of Puf gene copies in each model organism is variable. For example, the Drosophila, human, yeast, and C. elegans genomes encode one, two, six and eleven Puf genes, respectively . Puf proteins are generally known to bind directly to sequence elements located within the 3' untranslated region (UTR) of their target mRNAs. Once bound, they interact with other proteins to inhibit translation or trigger mRNA decay. For instance, Drosophila Pumilio represses the translation of hunchback (hb) mRNA in early embryo development through deadenylation dependent and independent mechanisms . Pumilio binds to a pair of 32 nucleotide Nanos Response Elements (NRE1 and NRE2) located within the 3'UTR of the hunchback mRNA. Each NRE contains two core elements (Box A and Box B), each of which interacts with one Pumilio protein in a cooperative manner . This interaction provides a platform for the recruitment of Nanos (Nos) and Brain Tumor (Brat) proteins to repress the translation of hunchback mRNA in the posterior region of the embryo.
The RNA binding domain of Puf proteins (the Pumilio Homology Domain, PUM-HD) forms a crescent-shaped structure that usually contains eight imperfect tandem Puf repeats each consisting of approximately 36 amino acids [6, 7]. Each Puf repeat is organized into three α-helices, the second of which provides a binding interface with the target RNA. Within each Puf repeat, three conserved amino acid side chains are typically responsible for modular binding of the repeat to a single RNA base using hydrogen bonds, van der Waals, and base stacking interactions . Puf proteins often bind target transcripts that contain a conserved UGUR (where R represents a purine) tetranucleotide motif flanked downstream by an AU-rich sequence of four nucleotides. The modular binding of each Puf repeat to an RNA base is predictable based on the combination of specific amino acids that contact the Watson-Crick edge of the base [12–14]. This interaction, however, demonstrates considerable complexity and adaptability, as a wide range of RNA sequences are recognized by each Puf protein. For example, RNA-immunoprecipitation profiling studies have shown that individual Puf proteins can bind to hundreds of unique transcripts in vivo [15–18]. This suggests that that this family of proteins has important roles in regulating the stability and translation of numerous mRNA targets across a broad range of organisms. These and other studies have shown that Puf proteins can recognize RNA sequences that extend beyond the canonical eight nucleotide length, and can bind to non-cognate sequences [14, 19–21]. The identification of mRNA targets of individual Puf proteins has revealed that Puf proteins typically bind to subsets of mRNAs that are functionally or cytotopically related and located within macromolecular complexes. Thus, related groups of mRNAs may be coordinately regulated as 'post-transcriptional operons' or 'RNA regulons' [15, 16, 22, 23]. For example, yeast Puf3p binds to motifs located in the 3'UTR of numerous mRNAs that encode mitochondrial proteins and regulates the stability, transport and translation of these transcripts . The RNA regulon model predicts that environmental cues result in a dynamic remodeling of RNP complexes to co-regulate mRNAs in a combinatorial manner to serve various functional roles within the cell .
Plant Puf proteins have been described only briefly in the literature, in the form of limited phylogenetic analyses [9, 16, 25, 26], and recently with the identification of putative mRNA targets of Arabidopsis Puf proteins . Here, we discuss the evolutionary relationships of the complete set of Puf proteins from the dicotyledonous plant Arabidopsis thaliana (Arabidopsis) and the monocotyledonous plant Oryza sativa (rice), as well as members from a moss and algal species. We also describe three-dimensional structural modeling, and biochemical and cellular characteristics of selected members of this protein family. This work demonstrates that the plant PUM-HD adopts the typical crescent shaped structure that is characteristic of this domain in other organisms, and that it possesses sequence specific RNA binding activity in vitro. We provide evidence these plant Puf proteins are packaged into common cytoplasmic particles that presumably have an evolutionary conserved role in the post-transcriptional control of a vast array of mRNA targets.
Identification and comparative analysis of plant Puf proteins
The phylogentic tree identified several sub-families of proteins that were assigned into groups based on monophyly (Figure 1). Group I was the most extensive of all groups, and contained at least one Puf member from each of the species that were included in this analysis. This group corresponds to the 'Pumilio cluster' of proteins that was categorized previously . Group II contained plant, algal, and yeast proteins, whereas Groups III, IV, and V contained plant members only. A number of proteins are more divergent, and do not appear to belong to any of the major branches that were identified in this analysis (Figure 1). Some Arabidopsis and rice Puf genes appear to be orthologs (e.g., AtPum4 and Os02g57390, and AtPum23 and Os10g25110) as they demonstrate a high degree of sequence conservation in the PUM-HD. Additionally, two Chlamydomonas proteins (XP001703567 and XP001693949) also appear to be orthologs with plant Puf proteins. Gene expansion through tandem duplication is also evident from this analysis. AtPum 1, 2, and 3 (Group I) are clustered in one region of chromosome 2, and other tandemly located genes are also evident (i.e., AtPum 9 and 10, AtPum 13 and 14, and AtPum 18 and 19).
Those Arabidopsis and rice genes that were not supported by cDNA sequences (Figure 2) were analyzed more extensively in an attempt to validate their predicted ORFs. The presence of many closely related members within each of the Arabidopsis and rice Puf families allowed for sequence comparisons to provide a more confident assignment of ORFs. Notably, the ORFs of AtPum15 and AtPum17 that were listed in the database appear to have incorrectly predicted introns. In the case of AtPum15, this resulted in the merger of an ORF encoding a self-incompatibility protein with that of AtPum15. An incorrectly predicted intron in AtPum17 was likely the result of a sequencing error. This predicted intron contained sequence that was almost identical to sequence within the ORF of the intronless gene AtPum16, a close relative of AtPum17. Based on this information, the primary structure line diagrams have been modified, with the removal of the self-incompatibility ORF from AtPum15, and the intron from AtPum17 (Figure 2).
The regions of the Arabidopsis and rice Puf proteins that lie outside of the PUM-HD are variable in primary sequence and length (Figure 2, Additional file 2). These variable sequences are typically amino-terminal extensions of each protein, although carboxyl-terminal extensions of variable length are also present in several proteins. A Pfam search http://pfam.sanger.ac.uk/ of the polypeptide regions lying outside of the PUM-HD was performed in an attempt to identify significantly conserved domains that are present within the variable regions of the Arabidopsis and rice Puf proteins. AtPum23 is the only Arabidopsis or rice Puf protein that possesses Puf repeat sequences that reside outside of the conserved PUM-HD region (Figure 2). Additionally, the amino-terminal region of several related Arabidopsis and rice proteins within Group I (Figure 1) possess a motif that resembles a Nucleic Acid Binding Protein domain (NABP, pfam07990; )(Figure 2). Finally, the rice protein Os08g40830 possesses two regions in its amino terminal extension that are similar to versions of a 'domain of unknown function' (DUF, pfam04782, pfam04783)(Figure 2), a region found in some leucine zipper proteins .
AtPum transcript expression based on available public database information.
Organ/tissue with highest expression
Stimulus resulting in significant changes in transcript level
Pum 1 (At2g29200)
Hypocotyl - xylem
Nutrient - cesium
Pum 2 (At2g29190)
Hypocotyl - xylem
Heat, 2,4-dichlorophenoxyacetic acid
Pum 3 (At2g29140)
Hypocotyl - xylem
Nutrient - cesium
Pum 4 (At3g10360)
Stamen - pollen
Nematode (H. schachtii)
Pum 5 (At3g20250)
Hypocotyl - xylem
Light - extended night, Osmotic stress
Pum 6 (At4g25880)
Hypocotyl - xylem
A. tumefaciens - inoculated with cabbage leaf curl virus
Pum 7 (At1g78160)
Flower - stamen
Pum 8 (At1g22240)
Endosperm - micropylar endosperm
Exposure to unfiltered UV-B light
Pum 9 (At1g35730)
Hypocotyl - xylem
Pum 10 (At1g35750)
Hypocotyl - xylem
Exposure to unfiltered UV-B light
Pum 11 (At4g08840)
Root - lateral root
Pum 12 (At5g56510)
Seed coat - chalazal seed coat
A. tumefaciens, Nematode, Cycloheximide, Drought
Pum 13 (At5g43090)
Vegetative shoot apex
Pum 14 (At5g43110)
Endosperm - micropylar endosperm
Dark, Iron deficiency
Pum 15 (At4g08560)
Endosperm - chalazal endosperm
Nitrate deficiency, Sucrose
Pum 16 (At5g59280)
Flower - pollen
Pum 17 (At1g35850)
Mature pollen grain
Pum 18 (At5g60110)
Endosperm - peripheral endosperm
Pum 19 (At5g60180)
Young expanding leaf (Stage 4)
Pum 20 (At1g21620)
Young expanding leaf (Stage 4)
Pum 21 (At5g09610)
Senescing leaf (35 days old)
Pum 22 (At1g01410)
Pum 23 (At1g72320)
Pum 24 (At3g16810)
Root - root tip
Pum 25 (At3g24270)
Root - lateral root cap
Pum 26 (At5g64490)
Three-dimensional models of plant PUM-HDs
A homology modeling approach was used to gain insight into whether plant PUM-HDs adopt the typical crescent shaped three-dimensional structure similar to that of the PUM-HDs from human, Drosophila and yeast Puf proteins. The three-dimensional models of the AtPum2 and Os01g62650 PUM-HDs bound to BoxB of the hunchback mRNA NRE1 were constructed using the crystal structure of the PUM-HD from human Pum1 bound to the NRE1 RNA (PDB: 1M8X; ) as a template for homology modeling. This structure was determined at 2.2 Å resolution and provides the most reliable template currently available for modeling the nature of protein:RNA interactions from plant PUM-HDs. Notably, only interactions between Puf repeats 2 to 8 and the bound RNA could be modeled, since the RNA templates for the complexes determined at high resolution only included residues 1 to 9 of Box B from NRE1 (PDB: 1M8X and 1M8W; ).
AtPum2 PUM-HD binds with specificity to the hunchback NRE1
EMSA titration experiments were conducted to determine the binding affinity of the AtPum2 PUM-HD to the wildtype and mutant NRE1. The AtPum2 PUM-HD bound to wildtype NRE with an apparent dissociation constant of 10.6 nM (Figure 7B, 7C). This value is >10-fold higher than was observed for Drosophila Pumilio PUM-HD binding to the NRE1 (Kd~0.5 nM; ), but within the range observed for other Puf protein interactions with their cognate RNAs [21, 28]. The binding affinity of the protein to the mutant NRE1 was significantly lower than to wildtype RNA (Figure 7D). Although a protein-mutant NRE1 complex was apparent at an AtPum2 PUM-HD concentration of 62.5 nM, the interaction remained weak at a protein concentration of 2000 nM, as seen by the diffuse nature of the shifted band. However, only a small amount of free RNA was present in the 1000 nM and 2000 nM samples, indicating that the low affinity binding of the AtPum-HD to the RNA resulted in a dissociation of the complex during electrophoresis. Thus, the instability of the complex did not allow for an accurate determination of the dissociation constant. However, based on the amount of free RNA in each lane, the dissociation constant value for the protein bound to mutant NRE1 appears in the range of 250 to 500 nM.
Arabidopsis Puf proteins typically localize to dynamic, punctate cytoplasmic structures
To determine whether the various AtPum proteins were segregated into distinct cytoplasmic particles, several pairs of AtPum-fluorescent protein fusions (AtPum7-GFP:AtPum18-RFP, AtPum9-GFP:AtPum18-RFP, AtPum12-GFP:AtPum18-RFP, AtPum14-GFP:AtPum18-RFP, AtPum10-GFP:AtPum8-RFP) were co-expressed in epidermal cells. Each pair of co-expressed AtPum fusion proteins co-localized within the same cytoplasmic particles (data not shown). However, there was a frequent concentration bias of either GFP or RFP fluorescence in co-localizing particles, indicating that AtPum proteins were not necessarily represented in equimolar concentrations within each particle.
The Arabidopsis and rice Puf gene families are extensive, consisting of a greater number of members than any other model species studied to date . Considering the size of the Arabidopsis and rice genomes (Arabidopsis, 125 Mb, 26751 genes; rice, 389 Mb, 42,000 genes; [37–39]), Puf genes are over-represented in the plant genome when compared to other species. Whole genome duplications may have contributed to the large number of plant Puf genes. The ancestral Arabidopsis genome was duplicated three times in the past 150-200 million years , and the rice genome, along with that of other monocots, has probably experienced at least one duplication event . In addition to whole-genome duplications, Puf gene expansion likely increased as a result of single gene duplications in both Arabidopsis and rice, as demonstrated by the presence of tandem gene copies (Figure 1). The presence of plant, algal and yeast sequences in the two main branches of the phylogenetic tree (Groups I and II, Figure 1) indicates that the PUM-HD of these proteins has remained relatively conserved in these species. Branches containing Arabidopsis sequences only (Groups III and IV) suggests that independent radiation of Puf proteins has occurred in this species, in a similar fashion to a large group of Puf proteins in Caenorhabditis elegans . The maintenance of duplicated plant Puf genes may be related to the sessile lifestyle of plants and their ability to adapt to challenging environmental conditions. If plant Puf proteins function in mRNA decay and translational repression as they do in other organisms, they could function to regulate the stability or translation of their target mRNAs in response to environmental stimuli in a rapid and coordinated manner. Indeed, microarray profiling revealed extensive changes in AtPum transcript expression patterns in response to various external stimuli (Table 1).
Homology modeling of AtPum2, AtPum13 and Os01g62650 PUM-HDs predicted that these domains adopt the characteristic crescent shaped structure that is common to PUM-HDs (Figure 5, 6). The identity of the amino acids at positions 12, 13 and 16 in each of the AtPum2 and Os01g62650 Puf repeats are identical to those in the Drosophila Pumilio and human Pum1 proteins, and provide conserved interactions with their corresponding RNA bases in the NRE1 sequence (Figure 5; [6, 12]). The predicted interaction between the AtPum2 PUM-HD and the NRE1 was confirmed by EMSA assays (Figure 7). The UGU core target sequence appears necessary for binding the AtPum2 PUM-HD, as demonstrated by the reduced affinity of AtPum2 to an NRE that contained a point mutation in this core sequence (Figure 7). This result is consistent with a recent study that utilized a three-hybrid assay to determine binding interactions . The predictable association between amino acids within each Puf repeat and their bound nucleotide was revealed previously for human Pum1, where substitution of specific amino acid side chains demonstrated that an RNA recognition code exists for this protein [13, 14]. However, Puf proteins appear able to interact with RNA binding sites that vary substantially in sequence outside of their UGU core. For instance, human Pum1 binds hundreds of mRNA targets in vivo [17, 18], as do Puf proteins from Drosophila, C. elegans and yeast [15, 16, 28, 42]. These subsets of mRNAs are typically related in function or in their subcellular localization pattern [15, 16, 18, 24]. In addition to binding to RNA targets with sequence variability, the PUM-HD of several Puf proteins can accommodate binding targets that are greater than eight nucleotides in length by flipping out spacer nucleotides [19–21, 43]. Evidence is emerging that individual plant Puf proteins also bind to a range of mRNA targets .
Many of the plant Puf proteins have considerable variability in the amino acids at position 12, 13 and 16 in their PUM-HD that are predicted to be involved in molecular interactions with RNA bases (Figure 4, Additional file 1). Several of these variable triplet amino acids are found in Puf proteins identified in other organisms [16, 28], however, many are unique to plants. Should these variable Puf proteins indeed possess RNA binding activity, the amino acid sequence variability could provide another level of specificity for Puf mRNA targets in plant cells. The triplet amino acids in the Puf repeats of AtPum13 differ from those in AtPum2 in six of the eight Puf repeats (Figure 4), and modeling of AtPum13 indicated that the NRE1 is not an ideal target for this protein, based on the predicted absence of stacking interactions (Figure 6). The observation that several of the Arabidopsis and rice proteins have fewer than 8 recognizable Puf repeats might also provide a mechanism for variable RNA target specificity. Yeast Puf proteins that possess only six Puf repeats function as RNA-binding proteins that function in post-transcriptional control of gene expression [8, 15]. Whether the plant Puf proteins that possess only two, three or four repeats are bona fide RNA-binding proteins or function in some other cellular capacity, remains to be determined. It is possible that one or more of these proteins are encoded by pseudogenes and are not functional. However, transcriptional array data indicates that these genes are actively transcribed in Arabidopsis (Table 1), providing support for their expression and activity.
Additional regions that were identified within Puf proteins could play a role in determining RNA target specificity. A histidine side chain in Puf repeat 8' from human PUM1 is involved in stacking interactions with the uracil base bound to Puf repeat 8 . Repeat 8' is present in most plant PUM-HDs (Figure 2), and the modeled AtPum2 structure indicates that this conserved histidine does indeed provide a stacking interaction with the corresponding RNA base (Figure 5). The NABP domain located in the amino terminal region of several Arabidopsis and rice Puf proteins, and the additional Puf repeats in the AtPum23 amino terminal region (Figure 2), could also enhance specificity of RNA targets by binding to regions of the transcript that lie outside of the PUM-HD binding site. The recruitment of other factors might also enhance the RNA binding specificity of the Pum-HD. The convex surface of repeats 7, 8 and 8' in the Drosophila PUM-HD interacts with its co-factors Nanos and Brat, and this interaction involves an extended loop that lies between repeats 7 and 8 [6, 33]. A conserved extended loop in the AtPum2 PUM-HD indicates that a similar interaction might also occur (Figure 5), although homologs of Nanos and Brat have not been identified in plants. Interestingly, the model of the AtPum13 PUM-HD structure reveals potential loops between Puf repeats 2 and 3, and repeats 3 and 4 (Figure 6). These loops also present potential binding surfaces for regulatory proteins.
Most of the AtPuf proteins that were expressed in epidermal cells as fluorescent protein fusions were localized to dynamic, punctate structures in the cytoplasm (Figure 8). The prevalence of predicted NES sequences in these proteins, and the observed nuclear accumulation of many of these after treatment with LMB indicates that nucleocytoplasmic shuttling is a common feature of these proteins. The enrichment of AtPum23 and AtPum24 fluorescent protein fusions within nucleoli provides another association of Puf proteins with the nucleus (Figure 8H, 8I). Nucleoli are traditionally known to be involved in the transcription and processing of ribosomal RNA and ribosome subunit biogenesis, and in the assembly of RNPs . More recently, the discovery that numerous mRNAs, the exon-junction complex of proteins, RNA-binding proteins, and other proteins localize to nucleoli in plant cells supports a role for the nucleolus in mRNA processing, silencing, surveillance and export [44, 45]. Additionally, a search of the human nucleolar database http://www.lamondlab.com/NOPdb3.0/ identified a human Pumilio-domain containing protein. As well, yeast Puf6p, an Ash1 mRNA-binding protein, is a nuclear shuttling protein that is enriched in the nucleolus [46, 47], as is mammalian Staufen, another protein involved in cytoplasmic mRNA localization . Thus, the nuclear associations of AtPum proteins suggest that these proteins are components of a preassembly complex that is involved in RNA decay, translational control or cytoplasmic transport of specific groups of mRNAs.
The Puf family of RNA-binding proteins in Arabidopsis and rice contain a greater number of members than in any other model species studied thus far. The modeled three-dimensional structure of three plant PUM-HDs is conserved, however, the identity of the amino acids that are predicted to contact RNA bases demonstrates considerable variability throughout this family of proteins. EMSA and subcellular localization studies indicate that these proteins are nucleocytoplasmic shuttling proteins that bind to RNA in a sequence specific manner. The large number of plant Puf protein family members suggests that these proteins are key in regulating the stability and translation of a significant number of mRNAs in the cell. Important future studies include the identification of target mRNAs for individual plant Puf proteins, determination of co-crystal structures of divergent Puf proteins with their cognate RNAs, and identification of the components of Puf protein-containing particles.
Bioinformatic analysis of plant Puf genes
Basic Local Alignment Search Tool (BLAST) analyses were performed to identify Arabidopsis and rice genes that encode regions of the conserved PUM-HD. The amino acid sequence of the Drosophila PUM-HD (residues 1093 to 1427)  was queried against Arabidopsis (http://www.ncbi.nlm.nih.gov/genome/seq/BlastGen/BlastGen.cgi?taxid=3702; http://rarge.gsc.riken.jp/; http://www.tigr.org/tdb/e2k1/osa1/) rice http://rice.plantbiology.msu.edu/index.shtml, moss (Physcomitrella patens, http://www.cosmoss.org/), and Chlamydomonas reinhardtii http://www.chlamy.org/ sequence databases using BLASTp and tBLASTn programs.
Multiple sequence alignments of Arabidopsis and rice PUM-HDs were generated using ClustalX, and then manually refined in BioEdit (version 5.0.9; ). Ambiguously aligned sites were removed from the alignment, leaving 341 amino acids that were used in the phylogenetic analysis. Three types of analyses were performed; Bayesian inference, and two methods in the maximum likelihood framework (PhyML, RAxML). The Bayesian analysis was performed using MrBayes (v3.1.2) for 20,000,000 generations with trees sampled every 1000 generations [50, 51]. The mixed model approach was implemented with MrBayes. This allowed new models to be proposed in the course of the analysis, with multiple models potentially contributing to the posterior distribution of trees. Maximum likelihood trees were estimated using the programs PhyML  and RAxML . Model selection was guided by the Akaike Information Criterion as implemented in ProtTest . In addition, 500 bootstrap replicates were performed using both PhyML and RAxML to assess statistical significance of the groups.
The sequences of the PUM-HD from AtPum2 (At2g29190, amino acids 616-952), AtPum13 (At5g43090, amino acids 252 to 527), and Os01g62650 (amino acids 707-1043) were aligned against the sequence of the PUM-HD from human PUM1 (Hs.281707, amino acids 828-1178, Protein database ID: 1M8X). Homology models were generated by Modeller 9v2  using as a template the crystal structure of the PUM-HD from human Pum1 in a complex with a 14-mer RNA sequence from the NRE1-14 of the Drosophila hunchback mRNA (PDB code 1M8X, . The homology models were refined with CNS 1.1  and the quality of geometric parameters was assessed with PROCHECK . All backbone torsion angles were within allowed regions of the Ramachandran plot, and more than 90% of the residues were in the energetically most favored regions. Figures were prepared using PyMOL software (DeLano Scientific).
PCR was used to amplify the coding regions of several Arabidopsis Puf genes. Full-length complimentary (cDNA) or genomic DNA was used as a template for PCR. Full-length cDNA clones were obtained from RIKEN and the Arabidopsis Biological Resource Center (ABRC). For recombinant protein expression, the coding region of repeats 1' through 8' of the AtPum2 PUM-HD (amino acids 614 to 963) was amplified by PCR using oligonucleotide primers 5'CGAGGAGGATCCTTTGGATCTTCAATGCTTGAAG3' and 5'CGAGGAGGATCCGGCCATGTTGTAGAGTTCAGTTC3'. The PCR product was cloned into the BamHI and SalI sites of pGEX-6P-1 (GE Healthcare).
Construction of expression vectors for AtPum subcellular localization analysis was performed using recombination or ligation based cloning of full-length AtPum coding regions into various expression vectors. Oligonucleotide primers were designed to encode the full-length AtPum protein. The PCR primers used were: AAGATGGATGAGTTTCGTGAAG and CTTCTTCAATAGATTCCTCGAGAAA (AtPum7); CACCATGATGAGAGGTGAATTTGG and ATTCTTCAAGAGATTTCGTG (AtPum8); CACCATGGGTTTTGGAGGTTTTAATG and CTTCTTCAAGATGGTCTTG (AtPum9); TGCATGGAGATTTTTAACTTCGGAC and CTTCTTCAAGATGGTCTTGGAGAAAATC (AtPum10); GAGATGGATCAGAGAAGAGGAAATG and CTTCTTCGAGCTAAGTGCGGAGAGG (AtPum12); ACCATGGACAAGAATTTTCGTG and GATATTGAGTTTCTCCAGAACTTTG (AtPum14); CACCATGGCAGTCGCTGATAATCCC and GCAACGAAGCCTAATGAGTCCAAG (AtPum18); CACCATGGTTTCTGTTGGTTCTAAATCAT and AATTCTCATTTTATTTGAATGCCGA (AtPum23); CACCATGTCTTCCAAAGGTCTGAAACCTC and TTCAGGTTTCTTGGTTGCTGAGATC (AtPum24). For recombination cloning, PCR amplified products were inserted into the pDONR221 or pENTR/D-TOPO Gateway entry vectors (Invitrogen), which were then recombined with pB7FWG2 or p2GWF7 GFP fusion destination vectors (Functional Genomics Unit, Department of Plant Systems Biology, VIB-Ghent University). Ligation cloning of PCR products into the BglII and XbaI sites of pRTL2ΔNS/RFP  was performed for RFP fusion constructs. The expression vectors used the cauliflower mosaic virus (CaMV) 35S promoter to drive transcription, and either the 35S or nopaline synthase terminator sequences. The nucleotide sequence was confirmed in each expression construct by standard sequencing techniques (Quintara Biosciences, Berkeley, CA)
Electrophoretic mobility shift assays (EMSA)
The AtPum2 PUM-HD coding sequence in pGEX-6P-1 was expressed in E. coli strain BL21(DE3) as a fusion to the carboxyl-terminus of glutathione S-transferase (GST). Bacterial cultures were grown overnight at 37°C, diluted 1 in 100 in fresh media and grown at 37°C to an OD600 value of 0.6. IPTG (0.2 mM) was added and the cultures were incubated at 37°C for 3 hours. The recombinant protein was purified using a glutathione affinity matrix (Stratagene), and reconstituted in binding buffer (10 mM HEPES pH 7.4, 1 mM EDTA, 50 mM KCl, 1 mM DTT, 0.01% BSA, 0.01% Tween 20). Synthetic RNAs (Dharmacon) were radiolabelled using 32P-γ-ATP (3000 Ci/mmol, Perkin Elmer) and T4 polynucleotide kinase (Fermentas). Labelled RNAs were purified from free nucleotides by gel filtration chromatography (NucTrap, Stratagene). Binding reactions (30 μL volume in binding buffer) contained 200 pM of labelled RNA and varying concentrations of protein, with or without cold competitor RNA. Reactions were incubated at room temperature for one hour, and run on a 6% non-denaturing acrylamide gel (Mini Protean II, BioRad) at 100 V for 45 minutes at 4°C. Gels were dried, exposed to a storage phosphor screen for 6-12 hours, and the screens scanned using a phosphorimager (Molecular Imager FX, BioRad). Densitometry was performed using Quantity One software (version 4.5.1, BioRad), and the data was analyzed using Prism 3 software (GraphPad). To determine the fraction of protein that was bound to RNA (fraction bound, Bf), the relative pixel intensity in the bound complex band was divided by the sum of the pixel intensities in the bound complex band plus the free RNA band.
Transient expression in leaf epidermal cells and microscopic analysis
GFP and RFP fusions proteins were expressed in fava bean (Vicia faba) and onion (Allium cepa) epidermal cells layers using the particle bombardment technique (PDS-1000, BioRad) . After bombardment, leaves were incubated overnight in the dark. Epidermal cell layers were peeled from the leaves, mounted on microscope slides in distilled water, and covered with a coverglass. For drug treatments, onion epidermal cell layers were floated on a Murashige and Skoog (MS) medium containing either leptomycin B (190 ng/mL, Sigma) and latrunculin B (1 nM, BIOMOL International). Negative control peels were floated on MS medium containing an appropriate volume of the drug solvent only. Epidermal cell layers were observed through FITC or rhodamine filter sets using a Plan Fluotar 40x objective lens or a Plan Apo 63x oil immersion objective lens attached to an epifluorescence microscope (DMR, Leica). Images were captured using a cooled CCD camera (Retiga 1350 EX; QImaging). Velocity software (Version 4.3.1, Improvision) was used for capturing images and image series compilation. Adobe Photoshop software (Version 8.0, Adobe Systems Inc.) was used for image modification and assembly.
Basic Local Alignment Search Tool
domain of unknown function
electrophoresis mobility shift assays
fem-3 binding factor
green fluorescent protein
nucleic acid binding protein
nuclear export signal
nuclear localization signal
Nanos response element
Open reading frame
Pumilio homology domain
red fluorescent protein
We thank Anshula Ambasta, Nam-Il Park, Kelly Rainey, and Priyana Sharma for their technical assistance, and Dave Hansen for his critical review of the manuscript. Some phylogenetic analyses were performed with the use of Westgrid, which is funded in part by the Canadian Foundation for Innovation, Alberta Innovation and Science, BC Advanced Education, and the participating research institutions. This research was funded by a Natural Sciences and Engineering Research Council (NSERC) of Canada Discovery Grant, and a University of Calgary URGC project initiation grant awarded to DGM.
- Kohler A, Hurt E: Exporting RNA from the nucleus to the cytoplasm. Nat Rev Mol Cell Biol. 2007, 8 (10): 761-773. 10.1038/nrm2255.PubMedView ArticleGoogle Scholar
- Moore MJ: From birth to death: the complex lives of eukaryotic mRNAs. Science. 2005, 309 (5740): 1514-1518. 10.1126/science.1111443.PubMedView ArticleGoogle Scholar
- Wharton RP, Aggarwal AK: mRNA regulation by Puf domain proteins. Sci STKE. 2006, 2006 (354): pe37-10.1126/stke.3542006pe37.PubMedView ArticleGoogle Scholar
- Lehmann R, Nusslein-Volhard C: Involvement of the pumilio gene in the transport of an abdominal signal in the Drosophila embryo. Nature. 1987, 329: 167-170. 10.1038/329167a0.View ArticleGoogle Scholar
- Zhang B, Gallegos M, Puoti A, Durkin E, Fields S, Kimble J, Wickens MP: A conserved RNA-binding protein that regulates sexual fates in the C. elegans hermaphrodite germ line. Nature. 1997, 390 (6659): 477-484. 10.1038/37297.PubMedView ArticleGoogle Scholar
- Edwards TA, Pyle SE, Wharton RP, Aggarwal AK: Structure of Pumilio reveals similarity between RNA and peptide binding motifs. Cell. 2001, 105 (2): 281-289. 10.1016/S0092-8674(01)00318-X.PubMedView ArticleGoogle Scholar
- Wang X, Zamore PD, Hall TM: Crystal structure of a Pumilio homology domain. Mol Cell. 2001, 7 (4): 855-865. 10.1016/S1097-2765(01)00229-5.PubMedView ArticleGoogle Scholar
- Zamore PD, Williamson JR, Lehmann R: The Pumilio protein binds RNA through a conserved domain that defines a new class of RNA-binding proteins. RNA. 1997, 3 (12): 1421-1433.PubMedPubMed CentralGoogle Scholar
- Wickens M, Bernstein DS, Kimble J, Parker R: A PUF family portrait: 3'UTR regulation as a way of life. Trends Genet. 2002, 18 (3): 150-157. 10.1016/S0168-9525(01)02616-6.PubMedView ArticleGoogle Scholar
- Chagnovich D, Lehmann R: Poly(A)-independent regulation of maternal hunchback translation in the Drosophila embryo. Proc Natl Acad Sci USA. 2001, 98 (20): 11359-11364. 10.1073/pnas.201284398.PubMedPubMed CentralView ArticleGoogle Scholar
- Gupta YK, Lee TH, Edwards TA, Escalante CR, Kadyrova LY, Wharton RP, Aggarwal AK: Co-occupancy of two Pumilio molecules on a single hunchback NRE. RNA. 2009, 15 (6): 1029-1035. 10.1261/rna.1327609.PubMedPubMed CentralView ArticleGoogle Scholar
- Wang X, McLachlan J, Zamore PD, Hall TM: Modular recognition of RNA by a human pumilio-homology domain. Cell. 2002, 110 (4): 501-512. 10.1016/S0092-8674(02)00873-5.PubMedView ArticleGoogle Scholar
- Lu G, Dolgner SJ, Hall TM: Understanding and engineering RNA sequence specificity of PUF proteins. Curr Opin Struct Biol. 2009, 19 (1): 110-115. 10.1016/j.sbi.2008.12.009.PubMedPubMed CentralView ArticleGoogle Scholar
- Cheong CG, Hall TM: Engineering RNA sequence specificity of Pumilio repeats. Proc Natl Acad Sci USA. 2006, 103 (37): 13635-13639. 10.1073/pnas.0606294103.PubMedPubMed CentralView ArticleGoogle Scholar
- Gerber AP, Herschlag D, Brown PO: Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast. PLoS Biol. 2004, 2 (3): E79-10.1371/journal.pbio.0020079.PubMedPubMed CentralView ArticleGoogle Scholar
- Gerber AP, Luschnig S, Krasnow MA, Brown PO, Herschlag D: Genome-wide identification of mRNAs associated with the translational regulator PUMILIO in Drosophila melanogaster. Proc Natl Acad Sci USA. 2006, 103 (12): 4487-4492. 10.1073/pnas.0509260103.PubMedPubMed CentralView ArticleGoogle Scholar
- Galgano A, Forrer M, Jaskiewicz L, Kanitz A, Zavolan M, Gerber AP: Comparative analysis of mRNA targets for human PUF-family proteins suggests extensive interaction with the miRNA regulatory system. PLoS ONE. 2008, 3 (9): e3164-10.1371/journal.pone.0003164.PubMedPubMed CentralView ArticleGoogle Scholar
- Morris AR, Mukherjee N, Keene JD: Ribonomic analysis of human Pum1 reveals cis-trans conservation across species despite evolution of diverse mRNA target sets. Mol Cell Biol. 2008, 28 (12): 4093-4103. 10.1128/MCB.00155-08.PubMedPubMed CentralView ArticleGoogle Scholar
- Gupta YK, Nair DT, Wharton RP, Aggarwal AK: Structures of human Pumilio with noncognate RNAs reveal molecular mechanisms for binding promiscuity. Structure. 2008, 16 (4): 549-557. 10.1016/j.str.2008.01.006.PubMedView ArticleGoogle Scholar
- Opperman L, Hook B, DeFino M, Bernstein DS, Wickens M: A single spacer nucleotide determines the specificities of two mRNA regulatory proteins. Nat Struct Mol Biol. 2005, 12 (11): 945-951.PubMedView ArticleGoogle Scholar
- Miller MT, Higgin JJ, Hall TM: Basis of altered RNA-binding specificity by PUF proteins revealed by crystal structures of yeast Puf4p. Nat Struct Mol Biol. 2008, 15 (4): 397-402. 10.1038/nsmb.1390.PubMedPubMed CentralView ArticleGoogle Scholar
- Keene JD: RNA regulons: coordination of post-transcriptional events. Nat Rev Genet. 2007, 8 (7): 533-543. 10.1038/nrg2111.PubMedView ArticleGoogle Scholar
- Keene JD, Tenenbaum SA: Eukaryotic mRNPs may represent posttranscriptional operons. Mol Cell. 2002, 9 (6): 1161-1167. 10.1016/S1097-2765(02)00559-2.PubMedView ArticleGoogle Scholar
- Saint-Georges Y, Garcia M, Delaveau T, Jourdren L, Le Crom S, Lemoine S, Tanty V, Devaux F, Jacq C: Yeast mitochondrial biogenesis: a role for the PUF RNA-binding protein Puf3p in mRNA localization. PLoS ONE. 2008, 3 (6): e2293-10.1371/journal.pone.0002293.PubMedPubMed CentralView ArticleGoogle Scholar
- Spassov DS, Jurecic R: The PUF family of RNA-binding proteins: does evolutionarily conserved structure equal conserved function?. IUBMB Life. 2003, 55 (7): 359-366. 10.1080/15216540310001603093.PubMedView ArticleGoogle Scholar
- Spassov DS, Jurecic R: Cloning and comparative sequence analysis of PUM1 and PUM2 genes, human members of the Pumilio family of RNA-binding proteins. Gene. 2002, 299 (1-2): 195-204. 10.1016/S0378-1119(02)01060-0.PubMedView ArticleGoogle Scholar
- Francischini CW, Quaggio RB: Molecular characterization of Arabidopsis thaliana PUF proteins--binding specificity and target candidates. Febs J. 2009, 276 (19): 5456-5470. 10.1111/j.1742-4658.2009.07230.x.PubMedView ArticleGoogle Scholar
- Stumpf CR, Kimble J, Wickens M: A Caenorhabditis elegans PUF protein family with distinct RNA binding specificity. Rna. 2008, 14 (8): 1550-1557. 10.1261/rna.1095908.PubMedPubMed CentralView ArticleGoogle Scholar
- Miyazaki Y, Jojima T, Ono T, Yamazaki T, Shishido K: A cDNA homologue of Schizosaccharomyces pombe cdc5(+) from the mushroom Lentinula edodes: characterization of the cDNA and its expressed product. Biochim Biophys Acta. 2004, 1680 (2): 93-102.PubMedView ArticleGoogle Scholar
- Marchler-Bauer A, Anderson JB, Chitsaz F, Derbyshire MK, DeWeese-Scott C, Fong JH, Geer LY, Geer RC, Gonzales NR, Gwadz M, He S, Hurwitz DI, Jackson JD, Ke Z, Lanczycki CJ, Liebert CA, Liu C, Lu F, Lu S, Marchler GH, Mullokandov M, Song JS, Tasneem A, Thanki N, Yamashita RA, Zhang D, Zhang N, Bryant SH: CDD: specific functional annotation with the Conserved Domain Database. Nucleic Acids Res. 2009, D205-210. 10.1093/nar/gkn845. 37 Database
- Zimmermann P, Hirsch-Hoffmann M, Hennig L, Gruissem W: GENEVESTIGATOR. Arabidopsis microarray database and analysis toolbox. Plant Physiol. 2004, 136 (1): 2621-2632. 10.1104/pp.104.046367.PubMedPubMed CentralView ArticleGoogle Scholar
- Winter D, Vinegar B, Nahal H, Ammar R, Wilson GV, Provart NJ: An "electronic fluorescent pictograph" browser for exploring and analyzing large-scale biological data sets. PLoS One. 2007, 2 (1): e718-10.1371/journal.pone.0000718.PubMedPubMed CentralView ArticleGoogle Scholar
- Edwards TA, Wilkinson BD, Wharton RP, Aggarwal AK: Model of the brain tumor-Pumilio translation repressor complex. Genes Dev. 2003, 17 (20): 2508-2513. 10.1101/gad.1119403.PubMedPubMed CentralView ArticleGoogle Scholar
- Zamore PD, Bartel DP, Lehmann R, Williamson JR: The PUMILIO-RNA interaction: a single RNA-binding domain monomer recognizes a bipartite target sequence. Biochemistry. 1999, 38 (2): 596-604. 10.1021/bi982264s.PubMedView ArticleGoogle Scholar
- Nishi K, Yoshida M, Fujiwara D, Nishikawa M, Horinouchi S, Beppu T: Leptomycin B targets a regulatory cascade of crm1, a fission yeast nuclear protein, involved in control of higher order chromosome structure and gene expression. J Biol Chem. 1994, 269 (9): 6320-6324.PubMedGoogle Scholar
- Park NI, Muench DG: Biochemical and cellular characterization of the plant ortholog of PYM, a protein that interacts with the exon junction complex core proteins Mago and Y14. Planta. 2007, 225: 625-639. 10.1007/s00425-006-0385-y.PubMedView ArticleGoogle Scholar
- Initiative TAG: Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature. 2000, 408 (6814): 796-815. 10.1038/35048692.View ArticleGoogle Scholar
- Project IRGS: The map-based sequence of the rice genome. Nature. 2005, 436 (7052): 793-800. 10.1038/nature03895.View ArticleGoogle Scholar
- Sterck L, Rombauts S, Vandepoele K, Rouze P, Peer Van de Y: How many genes are there in plants and why are they there)?. Curr Opin Plant Biol. 2007, 10 (2): 199-203. 10.1016/j.pbi.2007.01.004.PubMedView ArticleGoogle Scholar
- Bowers JE, Chapman BA, Rong J, Paterson AH: Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature. 2003, 422 (6930): 433-438. 10.1038/nature01521.PubMedView ArticleGoogle Scholar
- Paterson AH, Freeling M, Sasaki T: Grains of knowledge: genomics of model cereals. Genome Res. 2005, 15 (12): 1643-1650. 10.1101/gr.3725905.PubMedView ArticleGoogle Scholar
- Chen YR, Chu FH: Identification of proteins that interact with a TcMago-TcY14 heterodimer complex in Taiwania crytomerioides. Tree Physiol. 2008, 28 (8): 1211-1220.PubMedView ArticleGoogle Scholar
- Koh YY, Opperman L, Stumpf C, Mandan A, Keles S, Wickens M: A single C. elegans PUF protein binds RNA in multiple modes. Rna. 2009, 15 (6): 1090-1099. 10.1261/rna.1545309.PubMedPubMed CentralView ArticleGoogle Scholar
- Brown JW, Shaw PJ: The role of the plant nucleolus in pre-mRNA processing. Curr Top Microbiol Immunol. 2008, 326: 291-311. full_text.PubMedGoogle Scholar
- Pendle AF, Clark GP, Boon R, Lewandowska D, Lam YW, Andersen J, Mann M, Lamond AI, Brown JW, Shaw PJ: Proteomic analysis of the Arabidopsis nucleolus suggests novel nucleolar functions. Mol Biol Cell. 2005, 16 (1): 260-269. 10.1091/mbc.E04-09-0791.PubMedPubMed CentralView ArticleGoogle Scholar
- Gu W, Deng Y, Zenklusen D, Singer RH: A new yeast PUF family protein, Puf6p, represses ASH1 mRNA translation and is required for its localization. Genes Dev. 2004, 18 (12): 1452-1465. 10.1101/gad.1189004.PubMedPubMed CentralView ArticleGoogle Scholar
- Du TG, Jellbauer S, Muller M, Schmid M, Niessing D, Jansen RP: Nuclear transit of the RNA-binding protein She2 is required for translational control of localized ASH1 mRNA. EMBO Rep. 2008, 9 (8): 781-787. 10.1038/embor.2008.112.PubMedPubMed CentralView ArticleGoogle Scholar
- Martel C, Macchi P, Furic L, Kiebler MA, Desgroseillers L: Staufen1 is imported into the nucleolus via a bipartite nuclear localization signal and several modulatory determinants. Biochem J. 2006, 393 (Pt 1): 245-254.PubMedPubMed CentralView ArticleGoogle Scholar
- Hall T: Bioedit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser. 1999, 41: 95-98.Google Scholar
- Huelsenbeck JP, Ronquist F: MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics. 2001, 17 (8): 754-755. 10.1093/bioinformatics/17.8.754.PubMedView ArticleGoogle Scholar
- Ronquist F, Huelsenbeck JP: MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics. 2003, 19 (12): 1572-1574. 10.1093/bioinformatics/btg180.PubMedView ArticleGoogle Scholar
- Guindon S, Gascuel O: A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 2003, 52 (5): 696-704. 10.1080/10635150390235520.PubMedView ArticleGoogle Scholar
- Stamatakis A, Hoover P, Rougemont J: A rapid bootstrap algorithm for the RAxML Web servers. Syst Biol. 2008, 57 (5): 758-771. 10.1080/10635150802429642.PubMedView ArticleGoogle Scholar
- Abascal F, Zardoya R, Posada D: ProtTest: selection of best-fit models of protein evolution. Bioinformatics. 2005, 21 (9): 2104-2105. 10.1093/bioinformatics/bti263.PubMedView ArticleGoogle Scholar
- Marti-Renom MA, Stuart AC, Fiser A, Sanchez R, Melo F, Sali A: Comparative protein structure modeling of genes and genomes. Annu Rev Biophys Biomol Struct. 2000, 29: 291-325. 10.1146/annurev.biophys.29.1.291.PubMedView ArticleGoogle Scholar
- Brunger AT, Adams PD, Clore GM, DeLano WL, Gros P, Grosse-Kunstleve RW, Jiang JS, Kuszewski J, Nilges M, Pannu NS, Read RJ, Rice LM, Simonson T, Warren GL: Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr D Biol Crystallogr. 1998, 54 (Pt 5): 905-921. 10.1107/S0907444998003254.PubMedView ArticleGoogle Scholar
- Laskowski J, MacArthur M, Moss D, Thornton J: PROCHECK - a program to check the steriochemical quality of protein structures. Journal of Applied Crystallography. 1993, 26: 283-291. 10.1107/S0021889892009944.View ArticleGoogle Scholar
- McCartney AW, Greenwood JS, Fabian MR, White KA, Mullen RT: Localization of the tomato bushy stunt virus replication protein p33 reveals a peroxisome-to-endoplasmic reticulum sorting pathway. Plant Cell. 2005, 17 (12): 3513-3531. 10.1105/tpc.105.036350.PubMedPubMed CentralView ArticleGoogle Scholar
- Chuong SD, Mullen RT, Muench DG: The peroxisomal multifunctional protein interacts with cortical microtubules in plant cells. BMC Cell Biology. 2005, 6: 40-10.1186/1471-2121-6-40.PubMedPubMed CentralView ArticleGoogle Scholar
This article is published under license to BioMed Central Ltd. 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.