Genome analysis: RNA recognition motif (RRM) and K homology (KH) domain RNA-binding proteins from the flowering plant Arabidopsis thaliana

The circadian RNA-binding protein CHLAMY 1 represents a novel type heteromer of RNA recognition motif and lysine homology domain-containing subunits

The RNA-binding protein CHLAMY 1 from Chlamydomonas reinhardtii binds specifically to UG> or =7 repeat sequences situated in the 3' untranslated regions of several mRNAs. Its binding activity is controlled by the circadian clock. The biochemical purification and characterization of CHLAMY 1 revealed a novel type of RNA-binding protein. It includes two different subunits (named C1 and C3), whose interaction appears necessary for RNA binding. One of them (C3) belongs to the proteins of the CELF (CUG-BP-ETR-3-like factors) family and thus bears three RNA recognition motif domains. The other is composed of three lysine homology domains and a protein-protein interaction domain (WW). The subunits C1 and C3 have theoretical molecular masses of 45 and 52 kDa, respectively, and are present in nearly equal amounts during the circadian cycle. At the beginning of the subjective night, both can be found in protein complexes of 100 to 160 kDa. However, during subjective day when binding activity of CHLAMY 1 is low, the C1 subunit in addition is present in a high-molecular-mass protein complex of more than 680 kDa. These data indicate posttranslational control of the circadian binding activity of CHLAMY 1. Notably, the C3 subunit shows significant homology to the rat CUG-binding protein 2. Anti-C3 antibodies can recognize the rat homologue, which can also be found in a protein complex in this vertebrate.

Characterization of transgenic Arabidopsis plants overexpressing GR-RBP4 under high salinity, dehydration, or cold stress

A glycine-rich RNA-binding protein4 (GR-RBP4), one of the eight GR-RBP family members in Arabidopsis thaliana, was investigated for its stress-related expression, nucleic acid-binding property, and functional roles in plants subjected to various stresses including cold, high salinity, and dehydration. Real-time RT-PCR and GUS expression analyses showed that GR-RBP4 was abundantly expressed in young plants, root tips, and flowers, but weakly in mature leaves and stems, implying that GR-RBP4 is highly expressed in actively proliferating organs. The transcript level of GR-RBP4 increased markedly with cold stress, decreased significantly with salt stress, and decreased slightly with dehydration stress. In vitro nucleic acid-binding assays revealed that GR-RBP4 protein binds sequence non-specifically to RNAs and DNAs. Characterization of the transgenic Arabidopsis plants overexpressing GR-RBP4 under the control of the 35S promoter revealed that 35S::GR-RBP4 lines displayed retarded germination compared with the wild type under salt or dehydration stress. Despite the marked up-regulation of GR-RBP4 expression by cold stress, the 35S::GR-RBP4 lines did not show any noticeable changes in cold or freezing tolerance compared with wild-type plants. These results indicate that GR-RBP4 contributes differently to altered germination and seedling growth of Arabidopsis plants under various stress conditions.

Random sheared fosmid library as a new genomic tool to accelerate complete finishing of rice (Oryza sativa spp. Nipponbare) genome sequence: sequencing of gap-specific fosmid clones uncovers new euchromatic portions of the genome

The International Rice Genome Sequencing Project has recently announced the high-quality finished sequence that covers nearly 95% of the japonica rice genome representing 370 Mbp. Nevertheless, the current physical map of japonica rice contains 62 physical gaps corresponding to approximately 5% of the genome, that have not been identified/represented in the comprehensive array of publicly available BAC, PAC and other genomic library resources. Without finishing these gaps, it is impossible to identify the complete complement of genes encoded by rice genome and will also leave us ignorant of some 5% of the genome and its unknown functions. In this article, we report the construction and characterization of a tenfold redundant, 40 kbp insert fosmid library generated by random mechanical shearing. We demonstrated its utility in refining the physical map of rice by identifying and in silico mapping 22 gap-specific fosmid clones with particular emphasis on chromosomes 1, 2, 6, 7, 8, 9 and 10. Further sequencing of 12 of the gap-specific fosmid clones uncovered unique rice genome sequence that was not previously reported in the finished IRGSP sequence and emphasizes the need to complete finishing of the rice genome.

RNA immunoprecipitation and microarray analysis show a chloroplast Pentatricopeptide repeat protein to be associated with the 5' region of mRNAs whose translation it activates

Plant nuclear genomes encode hundreds of predicted organellar RNA binding proteins, few of which have been connected with their physiological RNA substrates and functions. In fact, among the largest family of putative RNA binding proteins in plants, the pentatricopeptide repeat (PPR) family, no physiologically relevant RNA ligands have been firmly established. We used the chloroplast-splicing factor CAF1 to demonstrate the fidelity of a microarray-based method for identifying RNAs associated with specific proteins in chloroplast extract. We then used the same method to identify RNAs associated with the maize (Zea mays) PPR protein CRP1. Two mRNAs whose translation is CRP1-dependent were strongly and specifically enriched in CRP1 coimmunoprecipitations. These interactions establish CRP1 as a translational regulator by showing that the translation defects in crp1 mutants are a direct consequence of the absence of CRP1. Additional experiments localized these interactions to the 5' untranslated regions and suggested a possible CRP1 interaction motif. These results enhance understanding of the PPR protein family by showing that a PPR protein influences gene expression through association with specific mRNAs in vivo, suggesting an unusual mode of RNA binding for PPR proteins, and highlighting the possibility that translational regulation may be a particularly common function of PPR proteins. Analogous methods should have broad application for the study of native RNA-protein interactions in both mitochondria and chloroplasts.

The evolutionarily conserved TOUGH protein is required for proper development of Arabidopsis thaliana

In this study, we characterize the evolutionarily conserved TOUGH (TGH) protein as a novel regulator required for Arabidopsis thaliana development. We initially identified TGH as a yeast two-hybrid system interactor of the transcription initiation factor TATA-box binding protein 2. TGH has apparent orthologs in all eukaryotic model organisms with the exception of the budding yeast Saccharomyces cerevisiae. TGH contains domains with strong similarity to G-patch and SWAP domains, protein domains that are characteristic of RNA binding and processing proteins. Furthermore, TGH colocalizes with the splicing regulator SRp34 to subnuclear particles. We therefore propose that TGH plays a role in RNA binding or processing. Arabidopsis tgh mutants display developmental defects, including reduced plant height, polycotyly, and reduced vascularization. We found TGH expression to be increased in the amp1-1 mutant, which is similar to tgh mutants with respect to polycotyly and defects in vascular development. Interestingly, we observed a strong genetic interaction between TGH and AMP1 in that tgh-1 amp1-1 double mutants are extremely dwarfed and severely affected in plant development in general and vascular development in particular when compared with the single mutants.

Expression patterns of TEL genes in Poaceae suggest a conserved association with cell differentiation

Poaceae species present a conserved distichous phyllotaxy (leaf position along the stem) and share common properties with respect to leaf initiation. The goal of this work was to determine if these common traits imply common genes. Therefore, homologues of the maize TERMINAL EAR1 gene in Poaceae were studied. This gene encodes an RNA-binding motif (RRM) protein, that is suggested to regulate leaf initiation. Using degenerate primers, one unique tel (terminal ear1-like) gene from seven Poaceae members, covering almost all the phylogenetic tree of the family, was identified by PCR. These genes present a very high degree of similarity, a much conserved exon-intron structure, and the three RRMs and TEL characteristic motifs. The evolution of tel sequences in Poaceae strongly correlates with the known phylogenetic tree of this family. RT-PCR gene expression analyses show conserved tel expression in the shoot apex in all species, suggesting functional orthology between these genes. In addition, in situ hybridization experiments with specific antisense probes show tel transcript accumulation in all differentiating cells of the leaf, from the recruitment of leaf founder cells to leaf margins cells. Tel expression is not restricted to initiating leaves as it is also found in pro-vascular tissues, root meristems, and immature inflorescences. Therefore, these results suggest that TEL is not only associated with leaf initiation but more generally with cell differentiation in Poaceae.

Cold-inducible zinc finger-containing glycine-rich RNA-binding protein contributes to the enhancement of freezing tolerance in Arabidopsis thaliana

Glycine-rich RNA-binding proteins (GR-RBPs) have been implicated to play roles in post-transcriptional regulation of gene expression in plants under various stress conditions, but the functional roles of GR-RBPs under stress conditions remain to be verified. Here, we examine the biological roles of a GR-RBP, designated atRZ-1a, in Arabidopsis thaliana under stress conditions. atRZ-1a was expressed ubiquitously in various Arabidopsis organs including stems, roots, leaves, flowers, and siliques. The transcript level of atRZ-1a increased markedly by cold stress, whereas its expression was marginally downregulated by drought stress or abscisic acid treatment. Germination and seedling growth of the loss-of-function mutants were retarded remarkably compared with those of the wild type under cold stress. In contrast, the transgenic Arabidopsis plants that overexpress atRZ-1a displayed earlier germination and better seedling growth than the wild type under cold stress. Moreover, the atRZ-1a-overexpressing transgenic Arabidopsis plants were more freezing tolerant than the wild-type plants. Heterologous expression of atRZ-1a in Escherichia coli demonstrated that the E. coli cells expressing atRZ-1a displayed much higher growth rate than the non-transformed cells after cold shock. These results provide evidence that atRZ-1a affects seed germination and seedling growth under low temperature and plays a role in the enhancement of freezing tolerance in Arabidopsis plants.

New insights into the complex and coordinated transcriptional regulation networks underlying rice seed development through cDNA chip-based analysis

Transcription factors (TFs) are major, crucial factors for developmental control. To elucidate the effects of TFs on rice seed development, we generated a cDNA chip containing 325 rice cDNA clones, which are from flowering stage and encode known or putative TFs belonging to 12 different families, and used this chip for expression profiling at 8 continuous seed developmental stages. The results showed that in comparison to their expression in mature leaves, a total of 135 TF genes were preferentially transcribed in seeds. Cluster analysis based on the temporal expression patterns grouped them into 12 types, each of which contained members of various families showing common unique expression patterns. The results provide insights into possible key roles for members of several TF families during seed development. In addition, the expression patterns of these genes were examined in vegetative tissues including roots, seedlings and stems, as well as in 2-week-old seedlings following the application of plant hormones or abiotic stresses. The results showed that many of the seed-preferential TFs were also involved in hormone and/or abiotic stress effects, suggesting the potential existence of uncharacterized transcriptional networks, or cross talk between hormone and abiotic stress signaling and seed development. Furthermore, analysis on the cis-elements locating in promoter region of seed preferential TF genes suggested that Dof proteins play essential roles in hierarchical regulation of gene expressions during rice seed development, which, taken together, provided informative clues for elucidation of the molecular mechanisms of transcriptional regulation and signaling networks in the complex developmental processes of rice seeds.

RNA processing and Arabidopsis flowering time control

Plants control their flowering time in order to ensure that they reproduce under favourable conditions. The components involved in this complex process have been identified using a molecular genetic approach in Arabidopsis and classified into genetically separable pathways. The autonomous pathway controls the level of mRNA encoding a floral repressor, FLC, and comprises three RNA-binding proteins, FCA, FPA and FLK. FCA interacts with the 3'-end RNA-processing factor FY to autoregulate its own expression post-transcriptionally and to control FLC. Other components of the autonomous pathway, FVE and FLD, regulate FLC epigenetically. This combination of epigenetic and post-transcriptional control gives precision to the control of FLC expression and flowering time.

A plethora of plant serine/arginine-rich proteins: redundancy or evolution of novel gene functions?

Precursor-mRNA (pre-mRNA) processing is an important step in gene expression and its regulation leads to the expansion of the gene product repertoire. SR (serine-arginine)-rich proteins are key players in intron recognition and spliceosome assembly and significantly contribute to the alternative splicing process. Due to several duplication events, at least 19 SR proteins are present in the Arabidopsis genome, which is almost twice as many as in humans. They fall into seven different subfamilies, three of them homologous with metazoan splicing factors, whereas the other four seem to be specific for plants. The current results show that most of the duplicated genes have different spatiotemporal expression patterns indicating functional diversification. Interestingly, most of the SR protein genes are alternatively spliced and in some cases this process was shown to be under developmental and/or environmental control. This might greatly influence gene expression of target genes as also exemplified by ectopic expression studies of particular SR proteins.

Chloroplast RNA-binding and pentatricopeptide repeat proteins

Chloroplast gene expression is mainly regulated at the post-transcriptional level by numerous nuclear-encoded RNA-binding protein factors. In the present study, we focus on two RNA-binding proteins: cpRNP (chloroplast ribonucleoprotein) and PPR (pentatricopeptide repeat) protein. These are suggested to be major contributors to chloroplast RNA metabolism. Tobacco cpRNPs are composed of five different proteins containing two RNA-recognition motifs and an acidic N-terminal domain. The cpRNPs are abundant proteins and form heterogeneous complexes with most ribosome-free mRNAs and the precursors of tRNAs in the stroma. The complexes could function as platforms for various RNA-processing events in chloroplasts. It has been demonstrated that cpRNPs contribute to RNA stabilization, 3'-end formation and editing. The PPR proteins occur as a superfamily only in the higher plant species. They are predicted to be involved in RNA/DNA metabolism in chloroplasts or mitochondria. Nuclear-encoded HCF152 is a chloroplast-localized protein that usually has 12 PPR motifs. The null mutant of Arabidopsis, hcf152, is impaired in the 5'-end processing and splicing of petB transcripts. HCF152 binds the petB exon-intron junctions with high affinity. The number of PPR motifs controls its affinity and specificity for RNA. It has been suggested that each of the highly variable PPR proteins is a gene-specific regulator of plant organellar RNA metabolism.

Vertebrate 2xRBD hnRNP proteins: a comparative analysis of genome, mRNA and protein sequences

hnRNP proteins are involved in many cell functions, primarily in pre-mRNA processing. We report here a comparative analysis of the genes of the 2xRBD members of the hnRNP family and of their expression products. Starting from the seven well characterized hnRNP members of human and murine origin (A0, A1, A2/B1, A3, AB, D and DL) and the three MuSashI-like proteins with related RBD tandems (MSI1, MSI2 and DAZAP1), we identified through BLAST search 12 homologous genes in the genome of Danio rerio and 10 in the genome of Takifugu rubripes, which can be divided into three subgroups, each with its highly conserved exon/intron structure, matching perfectly the exon/intron structures found in human and mouse genes. An exception is the gene of hnRNP A0, which is intronless consistently in all the four species. The analysis has been supported also at the level of cDNA and EST databases and extended in this respect to other vertebrate species, namely chicken, Xenopus laevis and Silurana tropicalis. PHYLIP 3.62 package (SEQBOOT, PROTDIST/DNADIST, NEIGHBOR, CONSENSE) was used for all the proteins and their CDSs and human RBDs I and II to infer relevant aspects of the phylogenesis of these proteins. Some clues to the evolution of introns in these genes have come from the analysis of their distribution in homologous genes of other eukaryotes, namely Ciona, Drosophila, Caenorhabditis, Saccharomyces and Arabidopsis.

The ASRG database: identification and survey of Arabidopsis thaliana genes involved in pre-mRNA splicing

The database of Arabidopsis splicing related genes includes classification of genes encoding snRNAs and other splicing related proteins, together with information on gene structure, alternative splicing, gene duplications and phylogenetic relationships.

A total of 74 small nuclear RNA (snRNA) genes and 395 genes encoding splicing-related proteins were identified in the Arabidopsis genome by sequence comparison and motif searches, including the previously elusive U4atac snRNA gene. Most of the genes have not been studied experimentally. Classification of these genes and detailed information on gene structure, alternative splicing, gene duplications and phylogenetic relationships are made accessible as a comprehensive database of Arabidopsis Splicing Related Genes (ASRG) on our website.

Intron retention is a major phenomenon in alternative splicing in Arabidopsis

Alternative splicing (AS) combines different transcript splice junctions that result in transcripts with shuffled exons, alternative 5' or 3' splicing sites, retained introns and different transcript termini. In this way, multiple mRNA species and proteins can be created from a single gene expanding the potential informational content of eukaryotic genomes. Search algorithms of AS forms in a variety of Arabidopsis databases showed they contained an unusually high fraction of retained introns (above 30%), compared with 10% that was reported for humans. The preponderance of retained introns (65%) were either part of open reading frames, present in the UTR region or present as the last intron in the transcript, indicating that their occurrence would not participate in non-sense-mediated decay. Interestingly, the functional distribution of the transcripts with retained introns is skewed towards stress and external/internal stimuli-related functions. A sampling of the alternative transcripts with retained introns were confirmed by RT-PCR and were shown to co-purify with polyribosomes, indicating their nuclear export. Thus, retained introns are a prominent feature of AS in Arabidopsis and as such may play a regulatory function.

ASF/SF2-like maize pre-mRNA splicing factors affect splice site utilization and their transcripts are alternatively spliced

Three ASF/SF2-like alternative splicing genes from maize were identified, cloned, and analyzed. Each of these genes (zmSRp30, zmSRp31, and zmSRp32) contains two RNA binding domains, a signature sequence SWQDLKD, and a characteristic serine/ariginine-rich domain. There is a strong structural similarity to the human ASF/SF2 splicing factor and to the Arabidopsis atSRp34/p30 proteins. Similar to ASF/SF2-like genes in other organisms, the maize pre-mRNA messages are alternatively spliced. They are differentially expressed in maize tissues with relatively uniform levels of zmSRp30 and zmSRp31 messages being observed throughout the plant, while zmSRp32 messages preferentially accumulated in the meristematic regions. Overexpression of zmSRp32 in maize cells leads to the enhanced selection of weak 5' intron splice sites during the processing of pre-mRNA molecules. Overexpression of the zmSRp31 or zmSRp32 gene affects regulation of wheat dwarf virus rep gene pre-mRNA splicing, presumably by interacting with the weak 5' splice site, CCGU. Our results suggest that the described genes are functional homologues of the human ASF/SF2 alternative splicing factor and they indicate a diversity of the ASF/SF2-like alternative splicing factors in monocot plant cells.

Regulation of flowering time in Arabidopsis by K homology domain proteins

The transition from vegetative growth to reproductive development in Arabidopsis is regulated by multiple floral induction pathways, including the photoperiodic, the autonomous, the vernalization, and the hormonal pathways. These pathways converge to regulate the expression of a small set of genes critical for floral initiation and different signal transduction pathways can interact to govern the time to flower. One important regulator of floral initiation is the MADS-box transcription factor FLC, which acts as a negative regulator of flowering in response to both endogenous and environmental signals. In this report, we describe a study of the flowering-time gene, FLK [flowering locus K homology (KH) domain] that encodes a putative RNA-binding protein with three KH domains. The flk mutations cause delayed flowering without a significant effect on the photoperiodic or vernalization responses. FLK functions primarily as a repressor of FLC expression, although it also modestly affects expression of genes associated with the photoperiodic pathway. In addition to FLK, the expression of two other KH domain genes are modestly affected by the flk mutation, suggesting a possible involvement of more than one KH domain protein in the regulation of flowering time in Arabidopsis.

Interactions of Arabidopsis RS domain containing cyclophilins with SR proteins and U1 and U11 small nuclear ribonucleoprotein-specific proteins suggest their involvement in pre-mRNA Splicing

Ser/Arg (SR)-rich proteins are important splicing factors in both general and alternative splicing. By binding to specific sequences on pre-mRNA and interacting with other splicing factors via their RS domain they mediate different intraspliceosomal contacts, thereby helping in splice site selection and spliceosome assembly. While characterizing new members of this protein family in Arabidopsis, we have identified two proteins, termed CypRS64 and CypRS92, consisting of an N-terminal peptidyl-prolyl cis/trans isomerase domain and a C-terminal domain with many SR/SP dipeptides. Cyclophilins possess a peptidyl-prolyl cis/trans isomerase activity and are implicated in protein folding, assembly, and transport. CypRS64 interacts in vivo and in vitro with a subset of Arabidopsis SR proteins, including SRp30 and SRp34/SR1, two homologs of mammalian SF2/ASF, known to be important for 5' splice site recognition. In addition, both cyclophilins interact with U1-70K and U11-35K, which in turn are binding partners of SRp34/SR1. CypRS64 is a nucleoplasmic protein, but in most cells expressing CypRS64-GFP fusion it was also found in one to six round nuclear bodies. However, co-expression of CypRS64 with its binding partners resulted in re-localization of CypRS64 from the nuclear bodies to nuclear speckles, indicating functional interactions. These findings together with the observation that binding of SRp34/SR1 to CypRS64 is phosphorylation-dependent indicate an involvement of CypRS64 in nuclear pre-mRNA splicing, possibly by regulating phosphorylation/dephosphorylation of SR proteins and other spliceosomal components. Alternatively, binding of CypRS64 to proteins important for 5' splice site recognition suggests its involvement in the dynamics of spliceosome assembly.

The multifunctional plant viral suppressor of gene silencing P19 interacts with itself and an RNA binding host protein

Tomato bushy stunt virus (TBSV) is an RNA plant virus encoding a protein of approximately 19 kDa (P19) that is involved in various activities important for pathogenicity, including virus transport and suppression of gene silencing. In this study, we provide evidence in vivo and in vitro that P19 specifically interacts with itself to predominantly form dimers, and with a novel host protein, Hin19. Hin19 has a high degree of similarity with a class of RNA-binding proteins of which many are involved in RNA processing. The binding of P19 to itself and to Hin19 both depend on a structurally important central region of P19 that was previously shown critical for its biological function in plants. Our findings provide evidence for a model in which virus spread through suppression of defense-related gene silencing involves the formation of a complex that includes P19 dimers and a newly identified host RNA-binding protein.

Use of fluorescent protein tags to study nuclear organization of the spliceosomal machinery in transiently transformed living plant cells

Although early studies suggested that little compartmentalization exists within the nucleus, more recent studies on metazoan systems have identified a still increasing number of specific subnuclear compartments. Some of these compartments are dynamic structures; indeed, protein and RNA-protein components can cycle between different domains. This is particularly evident for RNA processing components. In plants, lack of tools has hampered studies on nuclear compartmentalization and dynamics of RNA processing components. Here, we show that transient expression of fluorescent protein fusions of U1 and U2 small nuclear ribonucleoprotein particle (snRNP)-specific proteins U1-70K, U2B", and U2A ', nucleolar proteins Nop10 and PRH75, and serine-arginine-rich proteins in plant protoplasts results in their correct localization. Furthermore, snRNP-specific proteins also were correctly assembled into mature snRNPs. This system allowed a systematic analysis of the cellular localization of Arabidopsis serine-arginine-rich proteins, which, like their animal counterparts, localize to speckles but not to nucleoli and Cajal bodies. Finally, markers for three different nuclear compartments, namely, nucleoli, Cajal bodies, and speckles, have been established and were shown to be applicable for colocalization studies in living plant protoplasts. Thus, transient expression of proteins tagged with four different fluorescent proteins is a suitable system for studying the nuclear organization of spliceosomal proteins in living plant cells and should therefore allow studies of their dynamics as well.

The splicing factor U2AF small subunit is functionally conserved between fission yeast and humans

The small subunit of U2AF, which functions in 3' splice site recognition, is more highly conserved than its heterodimeric partner yet is less thoroughly investigated. Remarkably, we find that the small subunit of Schizosaccharomyces pombe U2AF (U2AF(SM)) can be replaced in vivo by its human counterpart, demonstrating that the conservation extends to function. Precursor mRNAs accumulate in S. pombe following U2AF(SM) depletion in a time frame consistent with a role in splicing. A comprehensive mutational analysis reveals that all three conserved domains are required for viability. Notably, however, a tryptophan in the pseudo-RNA recognition motif implicated in a key contact with the large subunit by crystallographic data is dispensable whereas amino acids implicated in RNA recognition are critical. Mutagenesis of the two zinc-binding domains demonstrates that they are neither equivalent nor redundant. Finally, two- and three-hybrid analyses indicate that mutations with effects on large-subunit interactions are rare whereas virtually all alleles tested diminished RNA binding by the heterodimer. In addition to demonstrating extraordinary conservation of U2AF small-subunit function, these results provide new insights into the roles of individual domains and residues.

The Arabidopsis cyclophilin gene family

Database searching has allowed the identification of a number of previously unreported single and multidomain isoform members of the Arabidopsis cyclophilin gene family. In addition to the cyclophilin-like peptidyl-prolyl cis-trans isomerase domain, the latter contain a variety of other domains with characterized functions. Transcriptional analysis showed they are expressed throughout the plant, and different isoforms are present in all parts of the cell including the cytosol, nucleus, mitochondria, secretory pathway, and chloroplast. The abundance and diversity of cyclophilin isoforms suggests that, like their animal counterparts, plant cyclophilins are likely to be important proteins involved in a wide variety of cellular processes. As well as fulfilling the basic role of protein folding, they may also play important roles in mRNA processing, protein degradation, and signal transduction and thus may be crucial during both development and stress responsiveness.

Enod40, a short open reading frame-containing mRNA, induces cytoplasmic localization of a nuclear RNA binding protein in Medicago truncatula

In eukaryotes, diverse mRNAs containing only short open reading frames (sORF-mRNAs) are induced at specific stages of development. Their mechanisms of action may involve the RNA itself and/or sORF-encoded oligopeptides. Enod40 genes code for highly structured plant sORF-mRNAs involved in root nodule organogenesis. A novel RNA binding protein interacting with the enod40 RNA, MtRBP1 (for Medicago truncatula RNA Binding Protein 1), was identified using a yeast three-hybrid screening. Immunolocalization studies and use of a MtRBP1-DsRed2 fluorescent protein fusion showed that MtRBP1 localized to nuclear speckles in plant cells but was exported into the cytoplasm during nodule development in enod40-expressing cells. Direct involvement of the enod40 RNA in MtRBP1 relocalization into cytoplasmic granules was shown using a transient expression assay. Using a (green fluorescent protein)/MS2 bacteriophage system to tag the enod40 RNA, we detected in vivo colocalization of the enod40 RNA and MtRBP1 in these granules. This in vivo approach to monitor RNA-protein interactions allowed us to demonstrate that cytoplasmic relocalization of nuclear proteins is an RNA-mediated cellular function of a sORF-mRNA.

Tissue-specific expression and dynamic organization of SR splicing factors in Arabidopsis

The organization of the pre-mRNA splicing machinery has been extensively studied in mammalian and yeast cells and far less is known in living plant cells and different cell types of an intact organism. Here, we report on the expression, organization, and dynamics of pre-mRNA splicing factors (SR33, SR1/atSRp34, and atSRp30) under control of their endogenous promoters in Arabidopsis. Distinct tissue-specific expression patterns were observed, and differences in the distribution of these proteins within nuclei of different cell types were identified. These factors localized in a cell type-dependent speckled pattern as well as being diffusely distributed throughout the nucleoplasm. Electron microscopic analysis has revealed that these speckles correspond to interchromatin granule clusters. Time-lapse microscopy revealed that speckles move within a constrained nuclear space, and their organization is altered during the cell cycle. Fluorescence recovery after photobleaching analysis revealed a rapid exchange rate of splicing factors in nuclear speckles. The dynamic organization of plant speckles is closely related to the transcriptional activity of the cells. The organization and dynamic behavior of speckles in Arabidopsis cell nuclei provides significant insight into understanding the functional compartmentalization of the nucleus and its relationship to chromatin organization within various cell types of a single organism.

A new Arabidopsis gene, FLK, encodes an RNA binding protein with K homology motifs and regulates flowering time via FLOWERING LOCUS C

Posttranscriptional RNA metabolism plays versatile roles in the regulation of gene expression during eukaryotic growth and development. It is mediated by a group of RNA binding proteins with distinct conserved motifs. In this study, an Arabidopsis (Arabidopsis thaliana) gene, designated FLK, was identified and shown to encode a putative RNA binding protein with K homology motifs. A mutant in which FLK was inactivated by T-DNA insertion exhibited a severe late flowering phenotype both in long and short days. The late flowering phenotype was reversed by gibberellin and vernalization treatments. The FLOWERING LOCUS C (FLC) transcription was greatly upregulated, whereas those of FLOWERING LOCUS T and SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 decreased in the mutant. These observations demonstrate that FLK regulates the autonomous flowering pathway via FLC. It is now evident that a battery of different RNA binding proteins are involved in the posttranscriptional regulation of flowering time in Arabidopsis.

Diversification of genes encoding mei2 -like RNA binding proteins in plants

A predominantly plant-based family of genes encoding RNA binding proteins is defined by the presence of a highly conserved RNA binding motif first described in the mei2 gene of the fission yeast Schizosaccharomyces pombe. In silico analyses reveal nine mei2 -like genes in Arabidopsis thaliana and six in Oryza sativa. These predicted genes group into four distinct clades, based on overall sequence similarity and subfamily-specific sequence elements. In situ analysis show that Arabidopsis genes from one of these clades, TEL1 and TEL2, are specifically expressed in central zone of the shoot apical meristem and the quiescent center of the root apical meristem, suggesting that they may somehow function to maintain indeterminacy in these tissues. By contrast, members of two sister clades, AML1 through AML5, are expressed more broadly, a trend that was confirmed by Q-PCR analysis. mei2 -like transcripts with similar sequences showed similar expression patterns, suggesting functional redundancy within the four clades. Phenotypic analyses of lines that contain T-DNA insertions to individual mei2 -like genes reveal no obvious phenotypes, further suggesting redundant activities for these gene products.

Posttranscriptional control of plant development

Genetic studies have provided increasing evidence that proteins involved in all aspects of RNA metabolism, such as RNA processing, transport, stability, and translation, are required for plant development and for plants' responses to the environment. Such proteins act in floral transition, floral patterning, and signaling by abscisic acid, low temperature and circadian rhythms. Although some of these proteins belong to core RNA metabolic machineries, others may have more specialized cellular functions. Despite the limited knowledge of the underlying molecular mechanisms, posttranscriptional regulation is known to play a key role in the control of plant development.

Cloning and Characterization of Glycine-Rich RNA-Binding Protein cDNAs in the Moss Physcomitrella patens

We isolated three cDNAs for the genes PpGRP1, PpGRP2 and PpGRP3 that encode glycine-rich RNA-binding proteins (GRPs) from Physcomitrella patens. Three full-length cDNA clones were isolated from a cDNA library prepared from poly(A)(+) RNA from 7-day-old protonemata of P. patens. They were named PpGRP1, PpGRP2 and PpGRP3, which encode putative polypeptides of 162, 178 and 155 residues, respectively. Preliminary genomic sequencing suggested that the positions of the three introns in the PpGRP3 gene are similar to those of introns in Arabidopsis GRP genes. PpGRP3 had a putative transit sequence. The PpGRP1-sGFP and PpGRP2-sGFP fusions were targeted to the cell nucleus, while PpGRP3-sGFP fusion was targeted to mitochondria. The level of these PpGRP transcripts as well as that of PpGRP proteins increased after cold treatment. Homoribopolymer RNA assay revealed that PpGRP3 protein show high affinity for poly(U) and poly(G). Results of phylogenetic analysis suggest that the nuclear and mitochondrial forms of GRP have been established early during the evolution of green plants.

Sam68, the KH domain-containing superSTAR

Sam68 is one of the most studied members of the STAR family of RNA-binding proteins since its identification over a decade ago. Since its ascension into prominence, enormous progress has been made to unmask the link between the RNA-binding properties of Sam68 and the regulation of cellular processes including signal transduction, cell cycle regulation and tumorigenesis and RNA biogenesis in general. In this review we provide a detailed description of the functional domains of Sam68 and the possible biological roles that justify its superSTAR status.

Nuclear localization and in vivo dynamics of a plant-specific serine/arginine-rich protein

Serine/arginine-rich (SR) proteins in non-plant systems are known to play important roles in both constitutive and alternative splicing of pre-messenger RNAs (pre-mRNAs). Recently, we isolated a novel SR protein (SR45), which interacts with U1 snRNP 70K protein, a key protein involved in 5' splice site recognition. SR45 is found only in plants and is unique in having two SR domains separated by an RNA recognition motif (RRM). To study the localization and dynamics of SR45, we expressed it as a fusion to green fluorescent protein (GFP) in cultured cells and transgenic Arabidopsis plants. The SR45 is localized exclusively to nuclei. In interphase nuclei, GFP-SR45 was found both in speckles and nucleoplasm. The speckles exhibited intranuclear movements and changes in morphology. Inhibition of transcription and protein phosphorylation resulted in redistribution of SR45 to bigger speckles. The change in the number and morphology of speckles caused by inhibition of transcription was blocked by an inhibitor of phosphatases. These results indicate that transcription activity of the cell and protein (de)phosphorylation regulate the intranuclear distribution of SR45.

The Need for Winter in the Switch to Flowering

Vernalization is the process whereby the floral transition is promoted through exposure of plants to long periods of cold temperature or winter. A requirement for vernalization aligns flowering with the seasons to ensure that their reproductive phase occurs in favorable conditions. The mitotic stability of vernalization, suggestive of an epigenetic mechanism, has intrigued researchers for many years. Genetic analysis of the vernalization requirement in Arabidopsis has identified key floral repressor genes, FRI and FLC. The action of these floral repressors is antagonized by vernalization and the activity of a set of genes grouped into the autonomous floral pathway. Analysis of the vernalization pathway has defined a series of epigenetic regulators crucial for "cellular-memory" of the cold signal, whereas the autonomous pathway appears to function in part through posttranscriptional mechanisms. The mechanism of the vernalization requirement, which is now being explored in a range of plant species, should uncover the evolutionary origins of this key agronomic trait.

Impacts of altered RNA metabolism on abscisic acid signaling

The plant hormone abscisic acid (ABA) regulates many essential processes in growth and development. The recent characterization of ABA-sensitivity mutations in RNA-binding proteins has led to the recognition of a functional link between post-transcriptional mRNA processing and the ABA signal transduction machinery. By influencing transcript abundance, these RNA-binding proteins may modulate ABA signaling through the alteration of mRNA processing events such as splicing, 3' processing, nuclear export, transcript stability and RNA degradation.

Ectopic expression of atRSZ33 reveals its function in splicing and causes pleiotropic changes in development

Splicing provides an additional level in the regulation of gene expression and contributes to proteome diversity. Herein, we report the functional characterization of a recently described plant-specific protein, atRSZ33, which has characteristic features of a serine/arginine-rich protein and the ability to interact with other splicing factors, implying that this protein might be involved in constitutive and/or alternative splicing. Overexpression of atRSZ33 leads to alteration of splicing patterns of atSRp30 and atSRp34/SR1, indicating that atRSZ33 is indeed a splicing factor. Moreover, atRSZ33 is a regulator of its own expression, as splicing of its pre-mRNA is changed in transgenic plants. Investigations by promoter-beta-glucuronidase (GUS) fusion and in situ hybridization revealed that atRSZ33 is expressed during embryogenesis and early stages of seedling formation, as well as in flower and root development. Ectopic expression of atRSZ33 caused pleiotropic changes in plant development resulting in increased cell expansion and changed polarization of cell elongation and division. In addition, changes in activity of an auxin-responsive promoter suggest that auxin signaling is disturbed in these transgenic plants.

Chloroplast RNA-binding proteins

Chloroplast gene expression is regulated by nucleus-encoded factors, which mainly act at the post-transcriptional level. Plastid RNA-binding proteins (RBPs) represent good candidates for mediating these functions. The picture emerging from recent analyses is that of a great number of differentially regulated RBPs, which are organized in distinct, spatially separated supramolecular complexes. This reflects the complexity of the regulatory network that underlies the intracellular communication system between the nucleus and the chloroplast.

The function of circadian RNA-binding proteins and their cis-acting elements in microalgae

An endogenous clock regulates the temporal expression of genes/mRNAs that are involved in the circadian output pathway. In the bioluminescent dinoflagellate Gonyaulax polyedra circadian expression of the luciferin-binding protein (LBP) is controlled at the translational level. Thereby, a clock-controlled RNA-binding protein, called circadian controlled translational regulator (CCTR), interacts specifically with an UG-repeat, which is situated in the lbp 3' UTR. Its binding activity correlates negatively with the amount of LBP during a circadian cycle. In the green alga Chlamydomonas reinhardtii, a clock-controlled RNA-binding protein (CHLAMY 1) was identified, which represents an analog of the CCTR from the phylogenetically diverse alga G. polyedra. CHLAMY 1 binds specifically to the 3' UTRs of several mRNAs and recognizes them all via a common cis-acting element, composed of at least seven UG-repeats. The binding strength of CHLAMY 1 is strongest to mRNAs, whose products are key components of nitrogen metabolism resulting in arginine biosynthesis as well as of CO2 metabolism. Since temporal activities of processes involved in nitrogen metabolism have an opposite phase than CHLAMY 1 binding activity, the protein might repress the translation of the cognate mRNAs.

FY is an RNA 3' end-processing factor that interacts with FCA to control the Arabidopsis floral transition

The nuclear RNA binding protein, FCA, promotes Arabidopsis reproductive development. FCA contains a WW protein interaction domain that is essential for FCA function. We have identified FY as a protein partner for this domain. FY belongs to a highly conserved group of eukaryotic proteins represented in Saccharomyces cerevisiae by the RNA 3' end-processing factor, Pfs2p. FY regulates RNA 3' end processing in Arabidopsis as evidenced through its role in FCA regulation. FCA expression is autoregulated through the use of different polyadenylation sites within the FCA pre-mRNA, and the FCA/FY interaction is required for efficient selection of the promoter-proximal polyadenylation site. The FCA/FY interaction is also required for the downregulation of the floral repressor FLC. We propose that FCA controls 3' end formation of specific transcripts and that in higher eukaryotes, proteins homologous to FY may have evolved as sites of association for regulators of RNA 3' end processing.

RNA recognition motif-type RNA-binding proteins in Trypanosoma cruzi form a family involved in the interaction with specific transcripts in vivo

Trypanosomes, protozoan parasites from the order Kinetoplastida, have to deal with environmental changes during the interaction with their hosts. Trypanosoma cruzi, the causative agent of Chagas' disease, uses post-transcriptional mechanisms to regulate gene expression. However, few RNA-binding proteins involved in mRNA turnover control have been identified to date. In this work, an RNA recognition motif (RRM)-type RNA-binding protein family named T. cruzi RNA-binding protein (TcRBP) and composed of at least six members was identified. The genomic organization of four members revealed a head to tail arrangement within a region of 15 kilobase pairs. TcRBP members have a common RRM and different auxiliary domains with a high content of glycine, glutamine, and histidine residues within their N- and C-terminal regions. TcRBPs differ in their expression patterns as well as in their homoribopolymer binding interaction in vitro, although they preferentially recognize poly(U) and poly(G) RNAs. An interesting observation was the relaxed RNA-binding interactions with several trypanosome transcripts in vitro. In contrast, co-immunoprecipitation experiments of TcRBP-containing ribonucleoprotein complexes formed in vivo revealed a highly restricted binding interaction with specific RNAs. Several TcRBP-containing complexes are stage-specific and, in some cases, bear the poly(A)-binding protein TcPABP1. Altogether, these results suggest that TcRBPs might be modulated in vivo, to favor or preclude the interaction with specific transcripts in a developmentally regulated manner.

Alternative splicing modulation by a LAMMER kinase impinges on developmental and transcriptome expression

Alternative splicing is a major contributor to genome complexity, playing a significant role in various cellular functions, including signal transduction, immunity, and development. The spliceosomal machinery is responsible for the processing of nuclear RNA. Several splicing factors associated with this complex are phosphorylated by kinases that possess a conserved LAMMER motif. We demonstrate in BY-2 tobacco cells a novel role for the LAMMER motif in the maintenance of proper subnuclear localization. Furthermore, high expression of the LAMMER kinase in Arabidopsis plants modulated the alternative splicing of specific endogenous genes and resulted in abnormal plant development and a novel transcriptome profile. A prominent feature was the upregulation of genes that play a role in protein turnover, suggesting a moderating function for these gene products in the control of alternative splicing events. Together, these results demonstrate alternative splicing modulation as a result of phosphorylation activity, providing an opportunity to study its global effect on the plasticity of plant development and gene expression at the organism level.

Organization, Developmental Dynamics, and Evolution of Plastid Nucleoids

The plastid is a semiautonomous organelle essential in photosynthesis and other metabolic activities of plants and algae. Plastid DNA is organized into the nucleoid with various proteins and RNA, and the nucleoid is subject to dynamic changes during the development of plant cells. Characterization of the major DNA-binding proteins of nucleoids revealed essential differences in the two lineages of photosynthetic eukaryotes, namely nucleoids of green plants contain sulfite reductase as a major DNA-binding protein that represses the genomic activity, whereas the prokaryotic DNA-binding protein HU is abundant in plastid nucleoids of the rhodophyte lineage. In addition, current knowledge on DNA-binding proteins, as well as the replication and transcription systems of plastids, is reviewed from comparative and evolutionary points of view. A revised hypothesis on the discontinuous evolution of plastid genomic machinery is presented: despite the cyanobacterial origin of plastids, the genomic machinery of the plastid genome is fundamentally different from its counterpart in cyanobacteria.

Two RNA binding proteins, HEN4 and HUA1, act in the processing of AGAMOUS pre-mRNA in Arabidopsis thaliana

AGAMOUS, a key player in floral morphogenesis, specifies reproductive organ identities and regulates the timely termination of stem cell fates in the floral meristem. Here, we report that strains carrying mutations in three genes, HUA1, HUA2, and HUA ENHANCER4 (HEN4), exhibit floral defects similar to those in agamous mutants: reproductive-to-perianth organ transformation and loss of floral determinacy. HEN4 codes for a K homology (KH) domain-containing, putative RNA binding protein that interacts with HUA1, a CCCH zinc finger RNA binding protein in the nucleus. We show that HUA1 binds AGAMOUS pre-mRNA in vitro and that HEN4, HUA1, and HUA2 act in floral morphogenesis by specifically promoting the processing of AGAMOUS pre-mRNA. Our studies underscore the importance of RNA processing in modulating plant development.

Network of interactions of a novel plant-specific Arg/Ser-rich protein, atRSZ33, with atSC35-like splicing factors

Arg/Ser-rich (RS) proteins play a crucial role in splicing and are implicated in splice site selection in metazoa. In plants, intron recognition seems to differ from the one in animals due to specific factor requirements. Here we describe a new plant-specific RS-rich protein, atRSZ33, with a unique domain structure consisting of an RNA recognition motif (RRM), two zinc knuckles embedded in a basic RS region, and an acidic C-terminal domain. atRSZ33 was found to be a phosphoprotein that concentrates in nuclear speckles and is predominantly present in roots and flowers. In a yeast two-hybrid screen, atRSZ33 interacted with splicing factors atSRp34/SR1, an Arabidopsis ortholog of human SF2/ASF; atRSZp21 and atRSZp22, which are similar to the human 9G8; and three novel SC35-like splicing factors termed atSCL28, atSCL30, and atSCL33/SR33. Two further members of the SCL family, namely SCL30a and the ortholog of mammalian SC35, atSC35, were also found to interact with atRSZ33. These interactions were verified by in vitro binding assays; furthermore, the transcriptional activity of atRSZ33 was found to overlap with the ones of its interacting partners. These specific interactions coupled with the many similarities of atRSZ33 to SR proteins suggest that its main activity is in spliceosome assembly. Mapping of regions necessary for protein-protein interaction between atRSZ33 and atSCL33/SR33 revealed that both zinc knuckles together with a small part of the RS and the RRM domain are required for efficient binding. However, the interacting domain is relatively small, allowing binding of additional proteins, a feature that is consistent with the proposed role of atRSZ33 in spliceosome assembly.

Modulation of an RNA-binding protein by abscisic-acid-activated protein kinase

Protein kinases are involved in stress signalling in both plant and animal systems. The hormone abscisic acid mediates the responses of plants to stresses such as drought, salinity and cold. Abscisic-acid-activated protein kinase (AAPK -- found in guard cells, which control stomatal pores -- has been shown to regulate plasma membrane ion channels. Here we show that AAPK-interacting protein 1 (AKIP1), with sequence homology to heterogeneous nuclear RNA-binding protein A/B, is a substrate of AAPK. AAPK-dependent phosphorylation is required for the interaction of AKIP1 with messenger RNA that encodes dehydrin, a protein implicated in cell protection under stress conditions. AAPK and AKIP1 are present in the guard-cell nucleus, and in vivo treatment of such cells with abscisic acid enhances the partitioning of AKIP1 into subnuclear foci which are reminiscent of nuclear speckles. These results show that phosphorylation-regulated RNA target discrimination by heterogeneous nuclear RNA-binding proteins may be a general phenomenon in eukaryotes, and implicate a plant hormone in the regulation of protein dynamics during rapid subnuclear reorganization.

AtMRD1 and AtMRU1, two novel genes with altered mRNA levels in the methionine over-accumulating mto1-1 mutant of Arabidopsis thaliana

The mto1-1 mutant of Arabidopsis thaliana over-accumulates soluble methionine (Met) up to 40-fold higher than that in its Col-0 wild type. In order to identify genes regulated by altered Met concentrations, microarray analysis of gene expression in young rosettes and developing siliques of the mto1-1 mutant were performed. Expression of selected genes was then examined in detail in three developmental stages of the mto1-1 mutant using a combination of Northern hybridisation analysis and real-time PCR. Eight genes were identified that had altered mRNA accumulation levels in the mto1-1 mutant compared to that in wild-type plants. Three of the genes have known roles in plant development unrelated to amino acid biosynthesis. One other gene up-regulated specifically in mto1-1 rosettes shared similarity with the embryo-specific protein 3 (ATS3). Two novel genes, referred to as AtMRD1 and AtMRU1, were also identified that were expressed in a developmental manner in wild-type Col-0 and do not share sequence similarity with genes of known function. AtMRD1 was strongly down-regulated in both rosette and young silique tissues of the mto1-1 mutant. AtMRU1 was up-regulated approximately 3-fold in young mto1-1 rosettes and exhibited a developmental response to the mto1-1 mutation.

AtSWI3B, an Arabidopsis homolog of SWI3, a core subunit of yeast Swi/Snf chromatin remodeling complex, interacts with FCA, a regulator of flowering time

ATP-dependent nucleosome remodeling plays a central role in the regulation of access to chromatin DNA. Swi/Snf remodeling complexes characterized in yeast, Drosophila and mammals all contain a conserved set of core subunits composed of homologs of yeast SNF2-type DNA-dependent ATPase, SNF5 and SWI3 proteins. So far, no complete Swi/Snf-type complex has been characterized in plants. Arabidopsis contains a single SNF5-type gene, BSH, which has been shown to complement the yeast snf5 mutation. Here we describe the characterization of AtSWI3B, the smallest of the four Arabidopsis homologs of SWI3. The gene encoding AtSWI3B is expressed ubiquitously in the plant. AtSWI3B is localized to nuclei and is associated mostly with the chromatin and soluble protein fractions. When expressed in Saccharomyces cerevisiae, the cDNA encoding AtSWI3B partially complements the swi3 mutant phenotype. However, like BSH, AtSWI3B is unable to activate transcription in yeast when tethered to DNA. The analysis by yeast two-hybrid indicates that AtSWI3B is capable of forming homodimers and interacts with BSH as well as with two other members of the Arabidopsis SWI3 family: AtSWI3A and AtSWI3C. The results of phage display screen using recombinant protein, confirmed by direct yeast two-hybrid analyses, indicate that AtSWI3B interacts with FCA, a regulator of flowering time in Arabidopsis. This interaction is through the C-terminal region of FCA, located outside the conserved RNA- and protein-binding domains of this protein.