Multiple plant RNA binding proteins identified by PCR: expression of cDNAs encoding RNA binding proteins targeted to chloroplasts in Nicotiana plumbaginifolia

Toward a systems view on RNA-binding proteins and associated RNAs in plants: Guilt by association

RNA-binding proteins (RBPs) have a broad impact on most biochemical, physiological, and developmental processes in a plant's life. RBPs engage in an on-off relationship with their RNA partners, accompanying virtually every stage in RNA processing and function. While the function of a plethora of RBPs in plant development and stress responses has been described, we are lacking a systems-level understanding of components in RNA-based regulation. Novel techniques have substantially enlarged the compendium of proteins with experimental evidence for binding to RNAs in the cell, the RNA-binding proteome. Furthermore, ribonomics methods have been adapted for use in plants to profile the in vivo binding repertoire of RBPs genome-wide. Here, we discuss how recent technological achievements have provided novel insights into the mode of action of plant RBPs at a genome-wide scale. Furthermore, we touch upon two emerging topics, the connection of RBPs to phase separation in the cell and to extracellular RNAs. Finally, we define open questions to be addressed to move toward an integrated understanding of RBP function.

Regulated nuclear targeting of cauliflower mosaic virus

The mature cauliflower mosaic virus (CaMV) capsid protein (CP), if expressed in the absence of other viral proteins, is transported into the plant cell nucleus by the action of a nuclear localization signal (NLS) close to the N terminus. In contrast, virus particles do not enter the nucleus, but dock at the nuclear membrane, a process inhibited by anti-NLS antibodies or by GTP gamma S, and apparently mediated by interaction of CP with host importin alpha. The very acidic N-terminal extension of the viral CP precursor inhibits nuclear targeting of the protein and hence the precursor is localized in the cytoplasm. We hypothesize that this provides a control mechanism which ensures that the CP precursor is used for virus assembly in the cytoplasm and that only mature virus particles reach the nuclear pore.

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

Regulation of gene expression at the post-transcriptional level is mainly achieved by proteins containing well-defined sequence motifs involved in RNA binding. The most widely spread motifs are the RNA recognition motif (RRM) and the K homology (KH) domain. In this article, we survey the complete Arabidopsis thaliana genome for proteins containing RRM and KH RNA-binding domains. The Arabidopsis genome encodes 196 RRM-containing proteins, a more complex set than found in Caenorhabditis elegans and Drosophila melanogaster. In addition, the Arabidopsis genome contains 26 KH domain proteins. Most of the Arabidopsis RRM-containing proteins can be classified into structural and/or functional groups, based on similarity with either known metazoan or Arabidopsis proteins. Approximately 50% of Arabidopsis RRM-containing proteins do not have obvious homologues in metazoa, and for most of those that are predicted to be orthologues of metazoan proteins, no experimental data exist to confirm this. Additionally, the function of most Arabidopsis RRM proteins and of all KH proteins is unknown. Based on the data presented here, it is evident that among all eukaryotes, only those RNA-binding proteins that are involved in the most essential processes of post-transcriptional gene regulation are preserved in structure and, most probably, in function. However, the higher complexity of RNA-binding proteins in Arabidopsis, as evident in groups of SR splicing factors and poly(A)-binding proteins, may account for the observed differences in mRNA maturation between plants and metazoa. This survey provides a first systematic analysis of plant RNA-binding proteins, which may serve as a basis for functional characterisation of this important protein group in plants.

Cloning and expression of a nuclear encoded plastid specific 33 kDa ribonucleoprotein gene (33RNP) from pea that is light stimulated

We report the cloning and sequencing of both cDNA and genomic DNA of a 33 kDa chloroplast ribonucleoprotein (33RNP) from pea. The analysis of the predicted amino acid sequence of the cDNA clone revealed that the encoded protein contains two RNA binding domains, including the conserved consensus ribonucleoprotein sequences CS-RNP1 and CS-RNP2, on the C-terminus half and the presence of a putative transit peptide sequence in the N-terminus region. The phylogenetic and multiple sequence alignment analysis of pea chloroplast RNP along with RNPs reported from the other plant sources revealed that the pea 33RNP is very closely related to Nicotiana sylvestris 31RNP and 28RNP and also to 31RNP and 28RNP of Arabidopsis and spinach, respectively. The pea 33RNP was expressed in Escherichia coli and purified to homogeneity. The in vitro import of precursor protein into chloroplasts confirmed that the N-terminus putative transit peptide is a bona fide transit peptide and 33RNP is localized in the chloroplast. The nucleic acid-binding properties of the recombinant protein, as revealed by South-Western analysis, showed that 33RNP has higher binding affinity for poly (U) and oligo dT than for ssDNA and dsDNA. The steady state transcript level was higher in leaves than in roots and the expression of this gene is light stimulated. Sequence analysis of the genomic clone revealed that the gene contains four exons and three introns. We have also isolated and analyzed the 5' flanking region of the pea 33RNP gene.

Participation of nuclear genes in chloroplast gene expression

The expression of the plastid genome is dependent on a large number of nucleus-encoded factors. Some of these factors have been identified through biochemical assays, and many others by genetic screens in Arabidopsis, Chlamydomonas and maize. Nucleus-encoded factors function in each step in plastid gene expression, including transcription, RNA editing, RNA splicing, RNA processing, RNA degradation, and translation. Many of the factors discovered via biochemical approaches play general roles as components of the basic gene expression machinery, whereas the majority of those identified by genetic approaches are specifically required for the expression of small subsets of chloroplast genes and are involved in post-transcriptional steps. Some of the nucleus-encoded factors may play regulatory roles and modulate chloroplast gene expression in response to developmental or environmental cues. They may also serve to couple chloroplast gene expression with the assembly of the protein products into the large complexes of the photosynthetic apparatus. The convergence of biochemical approaches with those of classical and reverse genetics, and the contributions from large scale genomic sequencing should result in rapid advances in our understanding of the regulatory interactions that govern plastid gene expression.

UBP1, a novel hnRNP-like protein that functions at multiple steps of higher plant nuclear pre-mRNA maturation

Efficient splicing of higher plant pre-mRNAs depends on AU- or U-rich sequences in introns. Moreover, AU-rich sequences present in 3'-untranslated regions (3'-UTRs) may play a role in 3' end processing of plant mRNAs. Here, we describe the cloning and characterization of a Nicotiana plumbaginifolia nuclear protein that can be cross-linked to U-rich intron and 3'-UTR sequences in vitro, and associates with nuclear poly(A)(+) RNA in vivo. The protein, UBP1, strongly enhances the splicing of otherwise inefficiently processed introns when overexpressed in protoplasts. It also increases the accumulation of reporter mRNAs that contain suboptimal introns or are intronless. The enhanced accumulation is apparently due to UBP1 interacting with the 3'-UTR and protecting mRNA from exonucleolytic degradation. The effect on mRNA accumulation but not on mRNA splicing was found to be promoter specific. The fact that these effects of UBP1 can be separated suggests that they represent two independent activities. The properties of UBP1 indicate that it is an hnRNP protein that functions at multiple steps to facilitate the nuclear maturation of plant pre-mRNAs.

Nuclear targeting of the cauliflower mosaic virus coat protein

The entry of the viral genomic DNA of cauliflower mosaic virus into the nucleus is a critical step of viral infection. We have shown by transient expression in plant protoplasts that the viral coat protein (CP), which is processed from the product of open reading frame IV, contains an N-terminal nuclear localization signal (NLS). The NLS is exposed on the surface of the virion and is thus available for interaction with a putative NLS receptor. Phosphorylation of the matured CP did not influence the nuclear localization of the protein but improved protein stability. Mutation of the NLS completely abolished viral infectivity, thus indicating its importance in the virus life cycle. The NLS seems to be regulated by the N terminus of the precapsid, which inhibits its nuclear targeting. This regulation could be important in allowing virus assembly in the cytoplasm.

Multiple forms of the U2 small nuclear ribonucleoprotein auxiliary factor U2AF subunits expressed in higher plants

Requirements for intron recognition during pre-mRNA splicing in plants differ from those in vertebrates and yeast. Plant introns contain neither conserved branch points nor distinct 3' splice site-proximal polypyrimidine tracts characteristic of the yeast and vertebrate introns, respectively. However, they are strongly enriched in U residues throughout the intron, property essential for splicing. To understand the roles of different sequence elements in splicing, we are characterizing proteins involved in intron recognition in plants. In this work we show that Nicotiana plumbaginifolia, a dicotyledonous plant, contains two genes encoding different homologs of the large 50-65-kDa subunit of the polypyrimidine tract binding factor U2AF, characterized previously in animals and Schizosaccharomyces pombe. Both plant U2AF65 isoforms, referred to as NpU2AF65a and NpU2AF65b, support splicing of an adenovirus pre-mRNA in HeLa cell nuclear extracts depleted of the endogenous U2AF factor. Both proteins interact with RNA fragments containing plant introns and show affinity for poly(U) and, to a lesser extend, poly(C) and poly(G). The branch point or the 3' splice site regions do not contribute significantly to intron recognition by NpU2AF65. The existence of multiple isoforms of U2AF may be quite general in plants because two genes expressing U2AF65 have been identified in Arabidopsis, and different isoforms of the U2AF small subunit are expressed in rice.

Characterization of an AGAMOUS homologue from the conifer black spruce (Picea mariana) that produces floral homeotic conversions when expressed in Arabidopsis

Advances in elucidating the molecular processes controlling flower initiation and development have provided unique opportunities to investigate the developmental genetics of non-flowering plants. In addition to providing insights into the evolutionary aspects of seed plants, identification of genes regulating reproductive organ development in gymnosperms could help determine the level of homology with current models of flower induction and floral organ identity. Based upon this, we have searched for putative developmental regulators in conifers with amino acid sequence homology to MADS-box genes. PCR cloning using degenerate primers targeted to the MADS-box domain revealed the presence of over 27 MADS-box genes within black spruce (Picea mariana), including several with extensive homology to either AP1 or AGAMOUS, both known to regulate flower development in Arabidopsis. This indicates that like angiosperms, conifers contain a large and diverse MADS-box gene family that probably includes regulators of reproductive organ development. Confirmation of this was provided by the characterization of an AGAMOUS-like cDNA clone called SAG1, whose conservation of intron position and tissue-specific expression within reproductive organs indicate that it is a homologue of AGAMOUS. Functional homology with AGAMOUS was demonstrated by the ability of SAG1 to produce homeotic conversions of sepals to carpels and petals to stamens when ectopically expressed in transgenic Arabidopsis. This suggests that some of the genetic pathways controlling flower and cone development are homologous, and antedate the 300-million-year-old divergence of angiosperms and gymnosperms.

Characterization of protein-binding to the spinach chloroplast psbA mRNA 5' untranslated region

RNA-binding proteins play a major role in regulating mRNA metabolism in chloroplasts. In this work we characterized two proteins, of 43 and 47 kDa, which bind to the spinach psbA mRNA 5' untranslated region (psbA encoding the D1 protein of photosystem II). The 43 kDa protein, which is present in the stroma and in membranes, co-sediments with a complex of 68S. It was purified, and the N-terminal sequence was determined. Upon homology search it was identified as the chloroplast homologue of the Escherichia coli ribosomal protein S1. The 47 kDa protein, which, in contrast with the 43 kDa protein, sediments with a small sedimentation coefficient, is only detected in the stromal fraction. It is soluble in an uncomplexed form. By deletion analysis, an element within the psbA mRNA 5' untranslated region was identified that is necessary but not sufficient for binding of stromal proteins. The 'central protein binding element' ranges from nucleotide -49 to -9 of the psbA mRNA 5' untranslated region. It comprises the Shine-Dalgarno-like GGAG motif and, 7 nucleotides upstream, an endonucleolytic cleavage site involved in psbA mRNA degradation in vitro . The mechanistic impacts of this region in relation to RNA-binding proteins are discussed.

Coordination of nuclear and chloroplast gene expression in plant cells

Plastid proteins are encoded in two genomes, one in the nucleus and the other in the organelle. The expression of genes in these two compartments in coordinated during development and in response to environmental parameters such as light. Two converging approaches reveal features of this coordination: the biochemical analysis of proteins involved in gene expression, and the genetic analysis of mutants affected in plastid function or development. Because the majority of proteins implicated in plastid gene expression are encoded in the nucleus, regulatory processes in the nucleus and in the cytoplasm control plastid gene expression, in particular during development. Many nucleus-encoded factors involved in transcriptional and posttranscriptional steps of plastid gene expression have been characterized. We are also beginning to understand whether and how certain developmental or environmental signals perceived in one compartment may be transduced to the other.

Regulation of gene expression in chloroplasts of higher plants

Chloroplasts contain their own genetic system which has a number of prokaryotic as well as some eukaryotic features. Most chloroplast genes of higher plants are organized in clusters and are cotranscribed as polycistronic pre-RNAs which are generally processes into many shorter overlapping RNA species, each of which accumulates of steady-state RNA levels. This indicates that posttranscriptional RNA processing of primary transcripts is an important step in the control of chloroplast gene expression. Chloroplast RNA processing steps include RNA cleavage/trimming, RNA splicing, ENA editing and RNA stabilization. Several chloroplast genes are interrupted by introns and therefore require processing for gene function. In tobacco chloroplasts, 18 genes contain introns, six for tRNA genes and 12 for protein-encoding genes. A number of specific proteins and RNA factors are believed to be involved in splicing and maturation of pre-RNAs in chloroplasts. Processing enzymes and RNA-binding proteins which could be involved in posttranscriptional steps have been identified in the last several years. Our current knowledge of the regulation of gene expression in chloroplasts of higher plants is overviewed and further studies on this matter are also considered.

Isolation of a novel RNA-binding protein and its association with a large ribonucleoprotein particle present in the nucleoplasm of tobacco cells

A cDNA encoding a protein with a consensus sequence-type RNA-binding domain (CS-RBD) has been isolated from a Nicotiana sylvestris cDNA library. The deduced protein (designated 'RZ-1') contains CS-RBD in its N-terminal half, arginine/aspartic acid repeats in its center and a glycine-rich-C-terminal region in which a zinc finger motif of the CCHC type is present. The corresponding gene appears to be expressed constitutively in all tobacco organs. Immunocytochemical assays revealed that RZ-1 is localized in the nucleoplasm of tobacco cultured cells. Glycerol gradient fractionation of tobacco nuclear lysates showed that RZ-1 is associated with a large ribonucleoprotein particle of around 60 S in size. Nucleic acid-binding assays indicated that RZ-1 binds preferentially to poly (G) and both the CS-RBD and glycine-rich region are necessary for its binding activity. A possible role of RZ-1 is discussed.

cDNA encoding a wheat (Triticum aestivum cv. Chinese spring) glycine-rich RNA-binding protein

A wheat cDNA encoding a glycine-rich RNA-binding protein, whGRP-1, was isolated. WhGRP-1 contains two conserved domains, the RNA-binding motif (RNP motif) combined with a series of glycine-rich imperfect repeats, characteristic of a conserved family of plant RNA-binding proteins. Northern analysis revealed that whGRP-1 mRNA accumulates to high levels in roots and to lower levels in leaves of wheat seedlings, whGRP-1 mRNA accumulation is not enhanced by exogenous abscisic acid in seedlings and accumulates to very high levels during wheat embryo development, showing a pattern different from that of the ABA-inducible wheat Em gene.

Nuclear mutants of Chlamydomonas reinhardtii defective in the biogenesis of the cytochrome b6f complex

The random integration of transforming DNA into the nuclear genome of Chlamydomonas has been employed as an insertional mutagen to generate a collection of photosynthetic mutants that display abnormal steady-state fluorescence levels and an acetate-requiring phenotype. Electron paramagnetic resonance spectroscopy was then used to identify those mutants that specifically lack a functional cytochrome b6f complex. Our analysis of RNA and protein synthesis in five of these mutants reveals four separate phenotypes. One mutant fails to accumulate transcript for cytochrome f, whilst a second displays a severely reduced accumulation of the cytochrome b6 transcript. Two other mutants appear to be affected in the insertion of the haem co-factor into cytochrome b6. The fifth mutant displays no detectable defect in the synthesis of any of the known subunits of the complex. Genetic analysis of the mutants demonstrates that in three cases, the mutant phenotype co-segregates with the introduced DNA. For the mutant affected in the accumulation of the cytochrome f transcript, we have used the introduced DNA as a tag to isolate the wild-type version of the affected gene.

Functional characteristics of the maize RNA-binding protein MA16

The maize RNA-binding protein MA16 is a non-ribosomal nucleolar protein widely distributed in different maize tissues. We have previously shown that the MA16 protein binds preferentially to guanosine- and uridine-rich sequences. As a step towards the identification of specific targets with which MA16 interacts within the cell, we investigated the RNA-binding affinities and several other aspects of the protein by using binding assays and immunochemistry. The MA16 protein showed a wide spectrum of RNA-binding activities with lower affinities to several RNAs that was salt and heparin-sensitive indicative of electrostatic interactions, and higher affinities to particular RNAs including rRNA and translatable mRNA sequences. Among the RNAs found associated with MA16 protein was that encoding MA16 itself. This observation raises the possibility that MA16 gene expression could be self-regulated. Immunoprecipitation studies showed that in vivo MA16 was phosphorylated and that MA16 interacts with RNAs through complex association with several proteins. These results suggest that both phosphorylation and interaction with other proteins may be involved in determining RNA-binding specificities of MA16 in the cell.

Phosphorylation of a chloroplast RNA-binding protein changes its affinity to RNA

An RNA-binding protein of 28 kDa (28RNP) was previously isolated from spinach chloroplasts and found to be required for 3' end-processing of chloroplast mRNAs. The amino acid sequence of 28RNP revealed two approximately 80 amino-acid RNA-binding domains, as well as an acidic- and glycine-rich amino terminal domain. Upon analysis of the RNA-binding properties of the 'native' 28RNP in comparison to the recombinant bacterial expressed protein, differences were detected in the affinity to some chloroplastic 3' end RNAs. It was suggested that post-translational modification can modulate the affinity of the 28RNP in the chloroplast to different RNAs. In order to determine if phosphorylation accounts for this post-translational modification, we examined if the 28RNP is a phosphoprotein and if it can serve as a substrate for protein kinases. It was found that the 28RNP was phosphorylated when intact chloroplasts were metabolically labeled with [32P] orthophosphate, and that recombinant 28RNP served as an excellent substrate in vitro for protein kinase isolated from spinach chloroplasts or recombinant alpha subunit of maize casein kinase II. The 28RNP was apparently phosphorylated at one site located in the acidic domain at the N-terminus of the protein. Site-directed mutagenesis of the serines in that region revealed that the phosphorylation of the protein was eliminated when serine number 22 from the N-terminus was changed to tryptophan. RNA-binding analysis of the phosphorylated 28RNP revealed that the affinity of the phosphorylated protein was reduced approximately 3-4-fold in comparison to the non-phosphorylated protein. Therefore, phosphorylation of the 28RNP modulates its affinity to RNA and may play a significant role in its biological function in the chloroplast.

Extreme heterogeneity of polyadenylation sites in mRNAs encoding chloroplast RNA-binding proteins in Nicotiana plumbaginifolia

We have previously characterized nuclear cDNA clones encoding two RNA binding proteins, CP-RBP30 and CP-RBP-31, which are targeted to chloroplasts in Nicotiana plumbaginifolia. In this report we describe the analysis of the 3'-untranslated regions (3'-UTRs) in 22 CP-RBP30 and 8 CP-RBP31 clones which reveals that mRNAs encoding both proteins have a very complex polyadenylation pattern. Fourteen distinct poly(A) sites were identified among CP-RBP30 clones and four sites among the CP-RBP31 clones. The authenticity of the sites was confirmed by RNase A/T1 mapping of N. plumbaginifolia RNA. CP-RBP30 provides an extreme example of the heterogeneity known to be a feature of mRNA polyadenylation in higher plants. Using PCR we have demonstrated that CP-RBP genes in N. plumbaginifolia and N. sylvestris, in addition to the previously described introns interrupting the coding region, contain an intron located in the 3' non-coding part of the gene. In the case of the CP-RBP31, we have identified one polyadenylation event occurring in this intron.

Three types of nuclear genes encoding chloroplast RNA-binding proteins (cp29, cp31 and cp33) are present in Arabidopsis thaliana: presence of cp31 in chloroplasts and its homologue in nuclei/cytoplasms

Five chloroplast RNA-binding proteins with consensus sequence-type RNA-binding domains have been isolated from tobacco chloroplasts. Here we report three nuclear genes for similar chloroplast RNA-binding proteins (cp29, cp31 and cp33) from Arabidopsis thaliana. Each of the three genes consists of four exons and three introns and their exon/intron junctions were determined by sequencing respective cDNAs. In vitro import assays showed that all three proteins are located in chloroplasts. The three genes are singly-copy each and the transcription start sites were determined to be 80/82 bp (cp29) and 76/88 bp (cp31) upstream from the translational initiation codons. Northern blot analysis revealed that the three genes are transcribed both in leaves and roots, but the transcript level in leaves is higher than in roots. Phylogenetic analysis of chloroplast RNA-binding proteins so far identified shows that these proteins can be classified into three groups. Tobacco and Arabidopsis have these three types of proteins and structural features of each group are conserved between the two plants, suggesting that they are important for chloroplast functions. Interestingly, cp31 (238 amino acids) shares the identical amino acid sequence from the 30th to the last (238th) residues (including two RNA-binding domains) with the Arabidopsis nucleolin-like ribonucleoprotein, FMV3bp [11]. FMV3bp lacks a transit-peptide and must be located in the nucleus or the cytoplasm.

RNA-binding activities of the different domains of a spinach chloroplast ribonucleoprotein

An RNA-binding protein of 28 kD (28RNP) has been previously isolated from spinach chloroplasts and was found to be required for 3' end processing of chloroplast mRNAs. The amino acid sequence of 28RNP revealed two approximately 80 amino-acid RNA-binding domains, as well as an acidic and glycine-rich amino terminal domain. Each domain by itself, as well as in combination with other domains, was expressed in bacterial cells and the polypeptides were purified to homogeneity. We have investigated the RNA-binding properties of the different structural domains using UV-crosslinking, saturation binding and competition between the different domains on RNA-binding. It was found that the acidic domain does not bind RNA, but that each of the RNA-binding domains, expressed either individually or together, do bind RNA, although with differing affinities. When either the first or second RNA-binding domain was coupled to the acidic domain, the affinity for RNA was greatly reduced. However, the acidic domain has a positive effect on the binding of the full-length protein to RNA, because the mature protein binds RNA with a better affinity than the truncated protein which lacks the acidic domain. In addition, it was found that a stretch of two or three G residues is enough to mediate binding of the 28RNP, whereas four U residues were insufficient. The implications of the RNA-binding properties of 28RNP to its possible function in the processing of chloroplast RNA is discussed.

Environmental stress-mediated differential 3' end formation of chloroplast RNA-binding protein transcripts

We report the characterization of transcripts from the halophyte, Mesembryanthemum crystallinum, encoding a protein with high homology to chloroplast RNA-binding proteins (cRBP). In this plant chloroplast-related functions are largely protected against salt stress. cRBP transcripts are derived from a single gene, Mc32crbp, although three size classes of polyadenylated mRNAs are detected. Transcription rate and steady state amounts of mRNA are developmentally regulated and light controlled with strong transcriptional activity as functional chloroplasts are established, and with lower maintenance activity thereafter. Upon salt stress, the rate of transcription decreases, although transcript levels increase. Accompanying stress, a change in the distribution of transcript size classes is observed as the longest transcript with an untranslated 3' end of 381 nucleotides increases relative to transcripts with shorter 3' ends. The long transcript is characterized by the presence of five sequence elements in the 3'-untranslated region that are present in cRBP mRNAs from a variety of plants, although not all elements are found in each mRNA. The results may indicate a mechanism by which mRNA levels of constitutively light-regulated genes may be modulated without enhanced transcription in response to environmental cues.

Characterization of a cDNA encoding a novel type of RNA-binding protein in tobacco: its expression and nucleic acid-binding properties

A cDNA encoding an RNA-binding protein (ribonucleoprotein or RNP) was isolated from a tobacco (Nicotiana sylvestris) cDNA library. The predicted protein (termed RGP-2) is 259 amino acids in length and consists of an N-terminal sequence of 39 amino acids, a consensus sequence type RNA-binding domain of 82 amino acids, a glycine-rich domain of 83 amino acids and an acidic C-terminal domain of 46 amino acids. It is distinct from the RGP-1 proteins previously reported, which consist of an RNA-binding domain in the N-terminal half and a glycine-rich domain in the C-terminal half. Homology searches revealed that RGP-2 is a novel consensus sequence-type RNA-binding protein. Its RNA-binding domain is structurally related to those of some chloroplast RNPs, while the amino acid composition of its glycine-rich domain (rich in glycine and asparagine) is similar to those in animal heterogeneous nuclear RNPs (hnRNP) A1 and A2/B1. The RGP-2 gene seems to be a single-copy gene, and its transcripts accumulate mainly in cultured cells and roots. A nucleic acid-binding assay using RGP-2 protein synthesized in vitro confirmed that it is an RNA-binding protein. Based on its greater affinity for total tobacco RNA than for poly(G) and poly(U), RGP-2 is suggested to bind to specific RNA sequences, probably G/U-rich regions. Quantitative analysis of the nucleic acid-binding properties of RGP-2 and RGP-1b indicates that they bind differently to nucleic acids. A possible role for RGP-2 is discussed in relation to known functions of animal hnRNP proteins.

cDNA structure, expression and nucleic acid-binding properties of three RNA-binding proteins in tobacco: occurrence of tissue-specific alternative splicing

Three cDNAs encoding RNA-binding proteins were isolated from a tobacco (Nicotiana sylvestris) cDNA library. The predicted proteins (RGP-1) are homologous to each other and consist of a consensus-sequence type RNA-binding domain of 80 amino acids in the N-terminal half and a glycine-rich domain of 61-78 amino acids in the C-terminal half. Nucleic acid-binding assay using the in vitro synthesized RGP-1 protein confirmed that it is an RNA-binding protein. Based on its strong affinity for poly(G) and poly(U), the RGP-1 proteins are suggested to bind specifically to G and/or U rich sequences. All three genes are expressed in leaves, roots, flowers and cultured cells, however, the substantial amount of pre-mRNAs are accumulated especially in roots. Sequence analysis and ribonuclease protection assay indicated that significant amounts of alternatively spliced mRNAs, which are produced by differential selection of 5' splice sites, are also present in various tissues. Tissue-specific alternative splicing was found in two of the three genes. The alternatively spliced mRNAs are also detected in polysomal fractions and are suggested to produce truncated polypeptides. A possible role of this alternative splicing is discussed.

Three new members of the RNP protein family in Xenopus

Many RNP proteins contain one or more copies of the RNA recognition motif (RRM) and are thought to be involved in cellular RNA metabolism. We have previously characterized in Xenopus a nervous system specific gene, nrp1, that is more similar to the hnRNP A/B proteins than to other known proteins (K. Richter, P. J. Good, and I. B. Dawid (1990), New Biol. 2, 556-565). PCR amplification with degenerate primers was used to identify additional cDNAs encoding two RRMs in Xenopus. Three previously uncharacterized genes were identified. Two genes encode hnRNP A/B proteins with two RRMs and a glycine-rich domain. One of these is the Xenopus homolog of the human A2/B1 gene; the other, named hnRNP A3, is similar to both the A1 and A2 hnRNP genes. The Xenopus hnRNP A1, A2 and A3 genes are expressed throughout development and in all adult tissues. Multiple protein isoforms for the hnRNP A2 gene are predicted that differ by the insertion of short peptide sequences in the glycine-rich domain. The third newly isolated gene, named xrp1, encodes a protein that is related by sequence to the nrp1 protein but is expressed ubiquitously. Despite the similarity to nuclear RNP proteins, both the nrp1 and xrp1 proteins are localized to the cytoplasm in the Xenopus oocyte. The xrp1 gene may have a function in all cells that is similar to that executed by nrp1 specifically within the nervous system.