Compartmentalization of the splicing machinery in plant cell nuclei

Spliceosomal protein U2B″ delays leaf senescence by enhancing splicing variant JAZ9β expression to attenuate jasmonate signaling in Arabidopsis

The regulatory framework of leaf senescence is gradually becoming clearer; however, the fine regulation of this process remains largely unknown. Here, genetic analysis revealed that U2 small nuclear ribonucleoprotein B (U2B″), a component of the spliceosome, is a negative regulator of leaf senescence. Mutation of U2B″ led to precocious leaf senescence, whereas overexpression of U2B″ extended leaf longevity. Transcriptome analysis revealed that the jasmonic acid (JA) signaling pathway was activated in the u2b″ mutant. U2B″ enhances the generation of splicing variant JASMONATE ZIM-DOMAIN 9β (JAZ9β) with an intron retention in the Jas motif, which compromises its interaction with CORONATINE INSENSITIVE1 and thus enhances the stability of JAZ9β protein. Moreover, JAZ9β could interact with MYC2 and obstruct its activity, thereby attenuating JA signaling. Correspondingly, overexpression of JAZ9β rescued the early senescence phenotype of the u2b″ mutant. Furthermore, JA treatment promoted expression of U2B″ that was found to be a direct target of MYC2. Overexpression of MYC2 in the u2b″ mutant resulted in a more pronounced premature senescence than that in wild-type plants. Collectively, our findings reveal that the spliceosomal protein U2B″ fine-tunes leaf senescence by enhancing the expression of JAZ9β and thereby attenuating JA signaling.

The Arabidopsis splicing factors, AtU2AF65, AtU2AF35, and AtSF1 shuttle between nuclei and cytoplasms

The Arabidopsis splicing factors, AtU2AF65, AtU2AF35, and AtSF1 shuttle between nuclei and cytoplasms. These proteins also move rapidly and continuously in the nuclei, and their movements are affected by ATP depletion. The U2AF65 proteins are splicing factors that interact with SF1 and U2AF35 proteins to promote U2snRNP for the recognition of the pre-mRNA 3' splice site during early spliceosome assembly. We have determined the subcellular localization and movement of these proteins' Arabidopsis homologs. It was found that Arabidopsis U2AF65 homologs, AtU2AF65a, and AtU2AF65b proteins interact with AtU2AF35a and AtU2AF35b, which are Arabidopsis U2AF35 homologs. We have examined the mobility of these proteins including AtSF1 using fluorescence recovery after photobleaching and fluorescence loss in photobleaching analyses. These proteins displayed dynamic movements in nuclei and their movements were affected by ATP depletion. We have also demonstrated that these proteins shuttle between nuclei and cytoplasms, suggesting that they may also function in cytoplasm. These results indicate that such splicing factors show very similar characteristics to their human counterparts, suggesting evolutionary conservation.

Plant snRNP Biogenesis: A Perspective from the Nucleolus and Cajal Bodies

Small nuclear ribonucleoproteins (snRNPs) are protein-RNA complexes composed of specific snRNP-associated proteins along with small nuclear RNAs (snRNAs), which are non-coding RNA molecules abundant in the nucleus. snRNPs mainly function as core components of the spliceosome, the molecular machinery for pre-mRNA splicing. Thus, snRNP biogenesis is a critical issue for plants, essential for the determination of a cell's activity through the regulation of gene expression. The complex process of snRNP biogenesis is initiated by transcription of the snRNA in the nucleus, continues in the cytoplasm, and terminates back in the nucleus. Critical steps of snRNP biogenesis, such as chemical modification of the snRNA and snRNP maturation, occur in the nucleolus and its related sub-nuclear structures, Cajal bodies. In this review, I discuss roles for the nucleolus and Cajal bodies in snRNP biogenesis, and a possible linkage between the regulation of snRNP biogenesis and plant development and environmental responses.

The conserved splicing factor SUA controls alternative splicing of the developmental regulator ABI3 in Arabidopsis

ABSCISIC ACID INSENSITIVE3 (ABI3) is a major regulator of seed maturation in Arabidopsis thaliana. We detected two ABI3 transcripts, ABI3-alpha and ABI3-beta, which encode full-length and truncated proteins, respectively. Alternative splicing of ABI3 is developmentally regulated, and the ABI3-beta transcript accumulates at the end of seed maturation. The two ABI3 transcripts differ by the presence of a cryptic intron in ABI3-alpha, which is spliced out in ABI3-beta. The suppressor of abi3-5 (sua) mutant consistently restores wild-type seed features in the frameshift mutant abi3-5 but does not suppress other abi3 mutant alleles. SUA is a conserved splicing factor, homologous to the human protein RBM5, and reduces splicing of the cryptic ABI3 intron, leading to a decrease in ABI3-beta transcript. In the abi3-5 mutant, ABI3-beta codes for a functional ABI3 protein due to frameshift restoration.

Poly(A) RNA a new component of Cajal bodies

In European larch microsporocytes, spherical structures 0.5 to 6 microm in diameter are present in which poly(A) RNA accumulates. There were one to several bodies per cell and they were often present in the vicinity of the nucleolus. No nascent transcripts were observed within them. Splicing factors of the SR family, including protein SC35, which participates in bringing the 3' and 5' sites closer in the splicing reaction, were also not observed. The absence of the above-mentioned elements within bodies containing poly(A) RNA disqualifies them as sites of synthesis and preliminary stages of primary transcript maturation. However, they contained abundant elements of the splicing machinery commonly occurring in Cajal bodies, i.e., Sm proteins or small nuclear RNA (snRNA). The molecular composition as well as the characteristic ultrastructure of bodies containing poly(A) RNA proves that these were Cajal bodies. This is the first report of such poly(A) RNA localization.

Dynamic behavior of Arabidopsis eIF4A-III, putative core protein of exon junction complex: fast relocation to nucleolus and splicing speckles under hypoxia

Here, we identify the Arabidopsis thaliana ortholog of the mammalian DEAD box helicase, eIF4A-III, the putative anchor protein of exon junction complex (EJC) on mRNA. Arabidopsis eIF4A-III interacts with an ortholog of the core EJC component, ALY/Ref, and colocalizes with other EJC components, such as Mago, Y14, and RNPS1, suggesting a similar function in EJC assembly to animal eIF4A-III. A green fluorescent protein (GFP)-eIF4A-III fusion protein showed localization to several subnuclear domains: to the nucleoplasm during normal growth and to the nucleolus and splicing speckles in response to hypoxia. Treatment with the respiratory inhibitor sodium azide produced an identical response to the hypoxia stress. Treatment with the proteasome inhibitor MG132 led to accumulation of GFP-eIF4A-III mainly in the nucleolus, suggesting that transition of eIF4A-III between subnuclear domains and/or accumulation in nuclear speckles is controlled by proteolysis-labile factors. As revealed by fluorescence recovery after photobleaching analysis, the nucleoplasmic fraction was highly mobile, while the speckles were the least mobile fractions, and the nucleolar fraction had an intermediate mobility. Sequestration of eIF4A-III into nuclear pools with different mobility is likely to reflect the transcriptional and mRNA processing state of the cell.

Role of plant RNA-binding proteins in development, stress response and genome organization

RNA-binding proteins (RBPs) in eukaryotes have crucial roles in all aspects of post-transcriptional gene regulation. They are important governors of diverse developmental processes by modulating expression of specific transcripts. The Arabidopsis (Arabidopsis thaliana) genome encodes for more than 200 different RBPs, most of which are plant specific and are therefore likely to perform plant-specific functions. Indeed, recent identification and analysis of plant RBPs clearly showed that, in addition to the important role in diverse developmental processes, they are also involved in adaptation of plants to various environmental conditions. Clearly, they act by regulating pre-mRNA splicing, polyadenylation, RNA stability and RNA export, as well as by influencing chromatin modification.

VAJ/GFA1/CLO is involved in the directional control of floral organ growth

Flowers assume variant forms of reproductive structures, a phenomenon which may be partially due to the diversity among species in the shape and size of floral organs. However, the organ size and shape of flowers usually remain constant within a species when grown under the same environmental conditions. The molecular and genetic mechanisms that control organ size and shape are largely unknown. We isolated an Arabidopsis mutant, vajra-1 (vaj-1), exhibiting defects in the regulation of floral organ size and shape. In vaj-1, alterations in the size and shape of floral organs were caused by changes in both cell size and cell number. The vaj-1 mutation also affected the number of floral organs. In vaj-1, a mutation was found in GAMETOPHYTIC FACTOR 1 (GFA1)/CLOTHO (CLO), recently shown to be required for female gametophyte development. The VAJ/GFA1/CLO gene encodes a translational elongation factor-2 (EF-2) family protein, of which the human U5-116 kD and yeast Snu114p counterparts are U5 small nuclear ribonucleoprotein (snRNP)-specific proteins. A transient expression assay using Arabidopsis protoplasts revealed that VAJ protein co-localized with SC35, a serine/arginine-rich (SR) protein involved in pre-mRNA splicing. Our results showed that VAJ/GFA1/CLO has a novel role in the directional control of floral organ growth in Arabidopsis, possibly acting through pre-mRNA splicing.

Spatiotemporal organization of pre-mRNA splicing proteins in plants

The general organization ofeukaryotic nuclei, including plant nuclei, into functional domains is now widely recognized. Conventional immunocytochemistry and visualization of proteins fused to fluorescent proteins (FP) have revealed that in plants, RNA and protein components of pre-mRNA splicing are spatially organized depending on the stage of cell cycle, development, and the cell's physiological state. Application of some of the latest microscopy techniques, which reveal biophysical properties such as diffusion and interaction properties of proteins, has begun to provide important insights into the functional organization of spliceosomal proteins in plants. Although some progress has been made in understanding the spatial and temporal organization of splicing machinery in plants, the mechanisms that regulate this organization and its functional consequences remain unresolved.

Analyses of in vivo interaction and mobility of two spliceosomal proteins using FRAP and BiFC

U1-70K, a U1 snRNP-specific protein, and serine/arginine-rich (SR) proteins are components of the spliceosome and play critical roles in both constitutive and alternative pre-mRNA splicing. However, the mobility properties of U1-70K, its in vivo interaction with SR proteins, and the mobility of the U1-70K-SR protein complex have not been studied in any system. Here, we studied the in vivo interaction of U1-70K with an SR protein (SR45) and the mobility of the U1-70K/SR protein complex using bimolecular fluorescence complementation (BiFC) and fluorescence recovery after photobleaching (FRAP). Our results show that U1-70K exchanges between speckles and the nucleoplasmic pool very rapidly and that this exchange is sensitive to ongoing transcription and phosphorylation. BiFC analyses showed that U1-70K and SR45 interacted primarily in speckles and that this interaction is mediated by the RS1 or RS2 domain of SR45. FRAP analyses showed considerably slower recovery of the SR45/U1-70K complex than either protein alone indicating that SR45/U1-70K complexes remain in the speckles for a longer duration. Furthermore, FRAP analyses with SR45/U1-70K complex in the presence of inhibitors of phosphorylation did not reveal any significant change compared to control cells, suggesting that the mobility of the complex is not affected by the status of protein phosphorylation. These results indicate that U1-70K, like SR splicing factors, moves rapidly in the nucleus ensuring its availability at various sites of splicing. Furthermore, although it appears that U1-70K moves by diffusion its mobility is regulated by phosphorylation and transcription.

A cyclin-dependent protein kinase, CDKC2, colocalizes with and modulates the distribution of spliceosomal components in Arabidopsis

Cyclin-dependent kinases (CDKs) play key regulatory roles in diverse cellular functions, including cell-cycle progression, transcription and translation. In plants, CDKs have been classified into several groups, named A through to G, but the functions of most are poorly characterized. CDKCs are known to phosphorylate the C-terminal domain (CTD) of RNA polymerase II (RNAP II), and therefore the CDKC-cyclinT (CycT) complex may have a role similar to the animal CDK9-CycT complex of the positive transcription elongation factor b (P-TEFb). However, we found that the predicted structure of the Arabidopsis CDKC2 protein is more similar to the mammalian cdc2-related kinase, CRK7, than to CDK9. CRK7 is proposed to link transcription with splicing, and CDKC2 contains all the structural features of CRK7 that make the latter distinct from CDK9. Consistent with this, we show that GFP-CDKC2 fusion proteins co-localize with spliceosomal components, that the expression of CDKC2 modifies the location of these components, and that co-localization was dependent on the transcriptional status of the cells and on CDKC2-kinase activity. We propose, therefore, that the Arabidopsis CDKC2 combines the functions of both CRK7 and CDK9, and could also couple splicing with transcription.

Firing of transcription and compartmentalization of splicing factors in tomato radicle nuclei during germination(1)

BACKGROUND INFORMATION

Germination is a well-characterized process in which embryo cells of seeds experience a programmed transition from quiescence to proliferation. For this reason they constitute a very good system to analyse nuclear evolution from a dehydrated practically inactive state until the steady state of proliferation. We analysed the temporal and spatial organization of transcription and splicing factors in nuclei of tomato radicle cells during germination. To address this issue we performed in situ immunodetection of several markers of these processes: the Z-DNA stretches forming behind the active RNA polymerases, the splicing proteins U2B'' and Sm, and the trimethyl guanosin cap of small nuclear RNA. The concomitant structural changes of the different nuclear compartments were studied in meristematic nuclei by electron microscopy and high-resolution cytochemistry for DNA and ribonucleoproteins.

RESULTS

In quiescent cells practically no Z-DNA stretches were detected and splicing components localized mainly to one or two Cajal bodies associated to the nucleolus. In early germination, a massive de-condensation of chromatin and nucleolar Z-DNA conformation stretches were first detected, followed by the relocation of scarce splicing components to the small interchromatin spaces. Nucleoplasmic Z-DNA stretches were not detected until 4 h of imbibition and were accompanied by an important increase of splicing components in this nuclear domain. Soon after the post-germination stage, transcription and splicing topology and nuclear organization in meristematic nuclei resemble those in steady state growing tomato roots.

CONCLUSIONS

Our results demonstrate that, in tomato, dormant nuclei splicing factors are stored in nucleolar Cajal bodies. In early germination, RNA polymerase I transcription is first activated, whereas mRNA transcription is fired later and is accompanied by a massive de-condensation of chromatin and accumulation of splicing factors in the interchromatin domains. Nucleoplasmic Cajal bodies appear later in germination.

Differential expression of alternatively spliced mRNAs of Arabidopsis SR protein homologs, atSR30 and atSR45a, in response to environmental stress

Serine/arginine-rich (SR) proteins are associated with either the regulation or the execution of both constitutive splicing and the selection of alternative splice sites in animals and plants. We demonstrated the molecular characterization of a homolog of SR protein, atSR45a, in Arabidopsis plants. Six types of mRNA variants (atSR45a-1a-e and atSR45a-2) were generated by the alternative selection of transcriptional initiation sites and the alternative splicing of introns in atSR45a pre-mRNA. The atSR45a-1a and -2 proteins, presumed mature forms, were located in the nucleus and interacted with U1-70K, suggesting that these proteins function as a splicing factor in Arabidopsis. The levels of the transcripts atSR45a and atSR30, SF2/ASF-like SR proteins, were increased by various types of stress, such as high-light irradiation and salinity. Furthermore, the splicing patterns of atSR45a and atSR30 pre-mRNA themselves were altered under these stressful conditions. In particular, the expression of atSR45a-1a, atSR45a-2, atSR30 mRNA1 and atSR30 mRNA3 was greatly increased by high-light irradiation. These results indicate that the regulation of transcription and alternative splicing of atSR45a and atSR30 is responsive to various stressful conditions.

Topology of splicing and snRNP biogenesis in dinoflagellate nuclei

BACKGROUND INFORMATION

Dinoflagellates are protists that are hypothesized to have experienced a secondary loss of histones. Amongst eukaryotes, they are unique in lacking these proteins. To date, information on the mechanisms involving remodelling, transcription and splicing of their chromatin is limited. Dinoflagellate genes lack TATA boxes and downstream polyadenylation sites and particular linear arrangements. They have an alpha-amanitin-sensitive RNA polymerase, specific transcription factors and regulators, and both transcriptional and post-transcriptional regulation of gene expression. Dinoflagellates produce either polycistronic or discrete mRNAs, and have conserved snRNAs (small nuclear RNAs), indicating that their genes are spliced.

RESULTS

Five representative dinoflagellate species (Amphidinium carterae, Akashiwo sanguinea, Alexandrium lusitanicum, Alexandrium fundyense and Prorocentrum micans), which show diversity in their DNA content, nuclear organization and taxonomic position, were investigated. The nuclear distribution and ultrastructural organization of splicing and snRNP (small nuclear ribonucleoprotein) biogenesis were determined by fluorescent and electron microscopy immunolabelling with Y12 sera [recognizing the sDMA (symmetrical dimethylarginine) domain of Sm and other nuclear proteins], anti-p105-PANA [proliferation-associated nuclear antigen; a marker of IGs (interchromatin granules)] and anti-DNA antibodies. In parallel, ultrastructural analysis, including cytochemical staining for RNA, phosphorylated proteins and DNA, was carried out. Splicing factors were distributed in a diffuse perichromosomal layer containing perichromatin granules and fibrils that co-localized with the decondensed peripheral DNA loops, but not with the main chromosome body. Interchromosomal domains with IGs and Cajal-like bodies were also detected.

CONCLUSIONS

Dinoflagellates are rather dissimilar to other eukaryotes in their genomes, their mechanisms of gene expression and their chromosome ultrastructure. However, they share common splicing nuclear domains and snRNP biogenesis with that of other eukaryotes.

Biochemical and cellular characterization of the plant ortholog of PYM, a protein that interacts with the exon junction complex core proteins Mago and Y14

The exon junction complex (EJC) plays an important role in post-transcriptional control of gene expression. Mago nashi (Mago) and Y14 are core EJC proteins that operate as a functional unit in animal cells, and the Mago-Y14 heterodimer interacts with other EJC core and peripheral proteins. Little is known about the biochemical and cellular characteristics of the EJC and its orthologs in plants. Here, we demonstrate that Arabidopsis Mago and Y14 form a ternary complex with PYM, an RNA-binding protein that was previously shown to interact with the Mago-Y14 heterodimer in Drosophila. Fluorescence microscopy indicated that Arabidopsis Mago and Y14 are localized primarily in the nucleus, whereas PYM is mostly cytoplasmic. In vitro pull-down assays using recombinant proteins showed that the amino-terminal region of the Arabidopsis PYM interacts with the Mago-Y14 heterodimer, a similar observation to that previously reported for the animal versions of these proteins. However, we demonstrated also that Arabidopsis PYM has the ability to interact with monomeric Mago and monomeric Y14. Immunoprecipitation and tandem affinity purification from whole cell extracts detected a subtle interaction between the Arabidopsis Mago-Y14 heterodimer and PYM in flowers, indicating that the ternary complex is not abundant in plant cells. The regions of the polypeptide responsible for nuclear import and export were defined using protein truncations and site-directed mutagenesis. This study identifies unique characteristics of Arabidopsis Mago, Y14 and PYM compared to those observed in animal cells. These are predicted to have important functional implications associated with post-transcriptional regulation of gene expression in plant cells.

Alternative splicing of pre-messenger RNAs in plants in the genomic era

Primary transcripts (precursor-mRNAs) with introns can undergo alternative splicing to produce multiple transcripts from a single gene by differential use of splice sites, thereby increasing the transcriptome and proteome complexity within and between cells and tissues. Alternative splicing in plants is largely an unexplored area of gene expression, as this phenomenon used to be considered rare. However, recent genome-wide computational analyses have revealed that alternative splicing in flowering plants is far more prevalent than previously thought. Interestingly, pre-mRNAs of many spliceosomal proteins, especially serine/arginine-rich (SR) proteins, are extensively alternatively spliced. Furthermore, stresses have a dramatic effect on alternative splicing of pre-mRNAs including those that encode many spliceosomal proteins. Although the mechanisms that regulate alternative splicing in plants are largely unknown, several reports strongly suggest a key role for SR proteins in spliceosome assembly and regulated splicing. Recent studies suggest that alternative splicing in plants is an important posttranscriptional regulatory mechanism in modulating gene expression and eventually plant form and function.

ATP, phosphorylation and transcription regulate the mobility of plant splicing factors

Serine-arginine-rich (SR) proteins, a family of spliceosomal proteins, function at multiple steps in the assembly of the spliceosome in non-plant systems. Limited studies with metazoan SR splicing factors (ASF/SF2 and SC35) indicated that their mobility is not dependent on ATP and phosphorylation. In addition, inhibition of transcription slightly increased their mobility. Here, we analyzed the mobility of SR45, a plant-specific SR protein with unique domain organization, and SR1/SRp34, a plant homolog of metazoan ASF/SF2, using fluorescence recovery after photobleaching (FRAP) and fluorescence loss in photobleaching (FLIP). Our results show that, in contrast to metazoan SR splicing factors, the movement of the plant SR proteins is dependent on ATP, phosphorylation and transcription. To understand the underlying mechanism for these observations, we carried out mobility analyses with the domain-deletion mutants of SR45 in ATP-depleted cells and in the presence of inhibitors of transcription or phosphorylation. Our results show that the sensitivity of SR45 to these inhibitors is conferred by an RNA-recognition motif (RRM) and the serine-arginine-rich (RS) domain 2. These results provide important insights into the mechanisms of plant SR protein movement and suggest fundamental differences in the regulation of the mobility of plant and animal SR splicing factors.

Arabidopsis RNA-binding protein UBA2a relocalizes into nuclear speckles in response to abscisic acid

The Arabidopsis thaliana RNA binding protein UBA2a is the closest homologue of the Vicia faba AKIP1 (56% identity). Like AKIP1, UBA2a is a constitutively-expressed nuclear protein and in response to ABA it is also reorganized within the nucleus in "speckles" suggesting a possible role of this protein in the regulation of mRNA metabolism during ABA signaling. AKIP1 interacts with, and is phosphorylated by, the upstream ABA-activated protein kinase AAPK. We have investigated if a pathway similar to that described in Vicia faba also exists in Arabidopsis. Our results showed that despite the resemblance between the corresponding Vicia and Arabidopsis proteins, it appears that the function of UBA2a is independent of OST1 phosphorylation.

Distribution of poly(A) RNA and splicing machinery elements in mature Hyacinthus orientalis L. pollen grains and pollen tubes growing in vitro

The localization of poly(A) mRNA and molecules participating in pre-mRNA splicing, i.e., small nuclear ribonucleoproteins (snRNPs) and the SC35 protein, in mature Hyacinthus orientalis L. pollen grains before anthesis and pollen tubes germinating in vitro were analyzed. The observations indicated a pattern of poly(A) mRNA distribution in mature pollen grains before anthesis which differed from that in germinating pollen grains. Directly before anthesis, poly(A) mRNA was homogeneously distributed throughout the whole cytoplasm, whereas after rehydration, it accumulated at one of the pollen poles. In the pollen tube, poly(A) mRNA was present in the cytoplasm, mainly in the areas beneath the cell membrane and the apical zone. Both before anthesis and during growth of the pollen tube, splicing snRNPs and SC35 protein were localized mainly in the area of the pollen nuclei. During anthesis and just after rehydration of the pollen grains, the pattern of labeling and the levels of the investigated antigens in the areas of the vegetative and generative nuclei were similar. During growth of the pollen tube, a change was observed in the distribution and an increase in the levels of trimethylguanosine snRNA and SC35 protein in the vegetative nucleus. Such a pattern of localization of the splicing machinery suggests resumption of transcription and/or maturation of pre-mRNA in the growing pollen tube.

AtCyp59 is a multidomain cyclophilin from Arabidopsis thaliana that interacts with SR proteins and the C-terminal domain of the RNA polymerase II

AtCyp59 and its orthologs from different organisms belong to a family of modular proteins consisting of a peptidyl-prolyl cis-trans isomerase (PPIase) domain, followed by an RNA recognition motif (RRM), and a C-terminal domain enriched in charged amino acids. AtCyp59 was identified in a yeast two-hybrid screen as an interacting partner of the Arabidopsis SR protein SCL33/SR33. The interaction with SCL33/SR33 and with a majority of Arabidopsis SR proteins was confirmed by in vitro pull-down assays. Consistent with these interactions, AtCyp59 localizes to the cell nucleus, but it does not significantly colocalize with SR proteins in nuclear speckles. Rather, it shows a punctuate localization pattern resembling transcription sites. Indeed, by using yeast two-hybrid, in vitro pull-down, and immunoprecipitation assays, we found that AtCyp59 interacts with the C-terminal domain (CTD) of the largest subunit of RNA polymerase II. Ectopic expression of the tagged protein in Arabidopsis cell suspension resulted in highly reduced growth that is most probably due to reduced phosphorylation of the CTD. Together our data suggest a possible function of AtCyp59 in activities connecting transcription and pre-mRNA processing. We discuss our data in the context of a dynamic interplay between transcription and pre-mRNA processing.

Molecular characterization and phylogeny of U2AF35 homologs in plants

U2AF (U2 small nuclear ribonucleoprotein auxiliary factor) is an essential splicing factor with critical roles in recognition of the 3'-splice site. In animals, the U2AF small subunit (U2AF35) can bind to the 3'-AG intron border and promote U2 small nuclear RNP binding to the branch-point sequences of introns through interaction with the U2AF large subunit. Two copies of U2AF35-encoding genes were identified in Arabidopsis (Arabidopsis thaliana; atU2AF35a and atU2AF35b). Both are expressed in all tissues inspected, with atU2AF35a expressed at a higher level than atU2AF35b in most tissues. Differences in the expression patterns of atU2AF35a and atU2AF35b in roots were revealed by a promoter::beta-glucuronidase assay, with atU2AF35b expressed strongly in whole young roots and root tips and atU2AF35a limited to root vascular regions. Altered expression levels of atU2AF35a or atU2AF35b cause pleiotropic phenotypes (including flowering time, leaf morphology, and flower and silique shape). Novel slicing isoforms were generated from FCA pre-mRNA by splicing of noncanonical introns in plants with altered expression levels of atU2AF35. U2AF35 homologs were also identified from maize (Zea mays) and other plants with large-scale expressed sequence tag projects. A C-terminal motif (named SERE) is highly conserved in all seed plant protein homologs, suggesting it may have an important function specific to higher plants.

Identification of LOV KELCH PROTEIN2 (LKP2)-interacting factors that can recruit LKP2 to nuclear bodies

LOV KELCH PROTEIN2 (LKP2) is an F-box protein that has been postulated to function centrally, or near to the circadian clock oscillator. As a first step to determine which proteins act as substrates of LKP2, yeast two-hybrid screening was performed using LKP2 as bait, and two interaction factors, Di19 and COL1, were isolated. The transiently expressed Di19-GUS fusion protein was localized in the nucleus of Arabidopsis petiole cells. COL1 and other CO/COL family proteins could also interact with LKP1/ZTL, LKP2 or FKF1. The LKP2-binding site in CO or COL1 was near the center of each protein. The CCT motif in CO or COL1 was not sufficient for interaction with LKP2. LKP2 recognized CO with F-box and kelch repeat-containing regions, while it recognized COL1 with an LOV domain. When LKP2 was fused with cyan fluorescent proein (CFP) and transiently expressed in onion epidermal cells, CFP-LKP2 signals were localized in the nucleus and cytosol. Both yellow fluorescent protein (YFP)-CO and YFP-COL1 were located in the nucleus, forming nuclear bodies when they were transiently expressed. However, co-expression of CFP-LKP2 with YFP fused to either CO or COL1 resulted in the recruitment of CFP-LKP2 in nuclear bodies. Furthermore, the CFP-LKP2 and YFP-CO signals co-localized with signals for pU2B''-mRFP, which is a marker for Cajal bodies. These results suggest the possibility that LKP2 functions with CO/COL family proteins in the nuclear bodies.