PAUSED encodes the Arabidopsis exportin-t ortholog

The evolution of core proteins involved in microRNA biogenesis

BACKGROUND

MicroRNAs (miRNAs) are a recently discovered class of non-coding RNAs (ncRNAs) which play important roles in eukaryotic gene regulation. miRNA biogenesis and activation is a complex process involving multiple protein catalysts and involves the large macromolecular RNAi Silencing Complex or RISC. While phylogenetic analyses of miRNA genes have been previously published, the evolution of miRNA biogenesis itself has been little studied. In order to better understand the origin of miRNA processing in animals and plants, we determined the phyletic occurrences and evolutionary relationships of four major miRNA pathway protein components; Dicer, Argonaute, RISC RNA-binding proteins, and Exportin-5.

RESULTS

Phylogenetic analyses show that all four miRNA pathway proteins were derived from large multiple protein families. As an example, vertebrate and invertebrate Argonaute (Ago) proteins diverged from a larger family of PIWI/Argonaute proteins found throughout eukaryotes. Further gene duplications among vertebrates after the evolution of chordates from urochordates but prior to the emergence of fishes lead to the evolution of four Ago paralogues. Invertebrate RISC RNA-binding proteins R2D2 and Loquacious are related to other RNA-binding protein families such as Staufens as well as vertebrate-specific TAR (HIV trans-activator RNA) RNA-binding protein (TRBP) and protein kinase R-activating protein (PACT). Export of small RNAs from the nucleus, including miRNA, is facilitated by three closely related karyopherin-related nuclear transporters, Exportin-5, Exportin-1 and Exportin-T. While all three exportins have direct orthologues in deutrostomes, missing exportins in arthropods (Exportin-T) and nematodes (Exportin-5) are likely compensated by dual specificities of one of the other exportin paralogues.

CONCLUSION

Co-opting particular isoforms from large, diverse protein families seems to be a common theme in the evolution of miRNA biogenesis. Human miRNA biogenesis proteins have direct, orthologues in cold-blooded fishes and, in some cases, urochordates and deutrostomes. However, lineage specific expansions of Dicer in plants and invertebrates as well as Argonaute and RNA-binding proteins in vertebrates suggests that novel ncRNA regulatory mechanisms can evolve in relatively short evolutionary timeframes. The occurrence of multiple homologues to RNA-binding and Argonaute/PIWI proteins also suggests the possible existence of further pathways for additional types of ncRNAs.

A decade of surprises for tRNA nuclear-cytoplasmic dynamics

The biosynthesis of tRNA was previously thought to occur solely in the nucleus, with tRNA functioning only in the cytoplasm of eukaryotic cells. However, recent publications have reported that pre-tRNA splicing can occur in the cytoplasm, that aminoacylation can occur in the nucleus and that tRNA can travel in a retrograde direction from the cytoplasm to the nucleus. Moreover, the subcellular distribution of tRNA seems to serve unanticipated functions in diverse processes, including response to nutrient availability, DNA repair and HIV replication.

The nuclear pore comes to the fore

The nuclear pore complex is the gateway of macromolecular trafficking between the nucleus and the cytoplasm. Although its composition is well characterized in yeast and mammalian systems, little is known about the plant nuclear pore. Several recent reports describe complex whole-organism phenotypes based on mutations in plant nucleoporins. The pathways affected include plant-microbe interactions, auxin response, cold-stress tolerance and flowering-time regulation. The effects are probably based, at least in part, on changes in protein import and/or RNA export (including regulatory small RNAs). Here, we review these new findings while comparing and contrasting them with what is known about nucleoporin functions from non-plant organisms, including nucleoporin activities not linked to nucleocytoplasmic transport.

Exportin-5 orthologues are functionally divergent among species

Exportin-5, an evolutionarily conserved nuclear export factor belonging to the importin-β family of proteins, is known to play a role in the nuclear export of small noncoding RNAs such as precursors of microRNA, viral minihelix RNA and a subset of tRNAs in mammalian cells. In this study, we show that the exportin-5 orthologues from different species such as human, fruit fly and yeast exhibit diverged functions. We found that Msn5p, a yeast exportin-5 orthologue, binds double-stranded RNAs and that it prefers a shorter 22 nt, double-stranded RNA to ∼80 nt pre-miRNA, even though both of these RNAs share a similar terminal structure. Furthermore, we found that Drosophila exportin-5 binds pre-miRNAs and that amongst the exportin-5 orthologues tested, it shows the highest affinity for tRNAs. The knockdown of Drosophila exportin-5 in cultured cells decreased the amounts of tRNA as well as miRNA, whereas the knock down of human exportin-5 in cultured cells affected only miRNA but not tRNA levels. These results indicate that double-stranded RNA binding ability is an inherited functional characteristic of the exportin-5 orthologues and that Drosophila exportin-5 functions as an exporter of tRNAs as well as pre-miRNAs in the fruit fly that lacks the orthologous gene for exportin-t.

Mutation of SAD2, an importin beta-domain protein in Arabidopsis, alters abscisic acid sensitivity

A number of protein and RNA-processing mutants have been shown to affect ABA sensitivity. A new mutant, sad2-1, was isolated from a T-DNA mutagenized population of RD29A:LUC plants and shown to have increased luminescence after ABA, salt, cold or polyethylene glycol treatments. Expression of several ABA- and stress-responsive genes was higher in the mutant than in the wild type. sad2-1 also exhibited ABA hypersensitivity in seed germination and seedling growth. SAD2 was found to encode an importin beta-domain family protein likely to be involved in nuclear transport. SAD2 was expressed at a low level in all tissues examined except flowers, but SAD2 expression was not inducible by ABA or stress. Subcellular localization of GFP-tagged SAD2 showed a predominantly nuclear localization, consistent with a role for SAD2 in nuclear transport. Knockout of the closest importin beta homolog of SAD2 in Arabidopsis did not duplicate the sad2 phenotype, indicating that SAD2 plays a specific role in ABA signaling. Analysis of RD29A:LUC luminescence and ABA and stress sensitivity in double mutants of sad2-1 and sad1 or abh1-7, a newly isolated allele of ABH1 also in the RD29A:LUC background, suggested that SAD2 acts upstream of or has additive effects with these two genes. The results suggest a role for nuclear transport in ABA signal transduction, and the possible roles of SAD2 in relation to that of SAD1 and ABH1 are discussed.

The Arabidopsis SUPPRESSOR OF AUXIN RESISTANCE proteins are nucleoporins with an important role in hormone signaling and development

Nucleocytoplasmic transport of macromolecules is regulated by a large multisubunit complex called the nuclear pore complex (NPC). Although this complex is well characterized in animals and fungi, there is relatively little information on the NPC in plants. The suppressor of auxin resistance1 (sar1) and sar3 mutants were identified as suppressors of the auxin-resistant1 (axr1) mutant. Molecular characterization of these genes reveals that they encode proteins with similarity to vertebrate nucleoporins, subunits of the NPC. Furthermore, a SAR3-green fluorescent protein fusion protein localizes to the nuclear membrane, indicating that SAR1 and SAR3 are Arabidopsis thaliana nucleoporins. Plants deficient in either protein exhibit pleiotropic growth defects that are further accentuated in sar1 sar3 double mutants. Both sar1 and sar3 mutations affect the localization of the transcriptional repressor AXR3/INDOLE ACETIC ACID17, providing a likely explanation for suppression of the phenotype conferred by axr1. In addition, sar1 sar3 plants accumulate polyadenylated RNA within the nucleus, indicating that SAR1 and SAR3 are required for mRNA export. Our results demonstrate the important role of the plant NPC in hormone signaling and development.

Cellular dynamics of small RNAs

This review highlights the unexpectedly complicated nuclear egress and nuclear import of small RNAs. Although nucleus/cytoplasm trafficking was thought to be restricted to snRNAs of many, but not all, eukaryotes, recent data indicate that such traffic may be more common than previously appreciated. First, in conflict with numerous previous reports, new information indicates that Saccharomyces cerevisiae snRNAs may cycle between the nucleus and the cytoplasm. Second, recent studies also provide evidence that other small RNAs that function exclusively in the nucleus-the budding yeast telomerase RNA and possibly small nucleolar RNAs-may exit to the cytoplasm, only to return to the nucleus. Third, nucleus/cytoplasm cycling of RNAs also occurs for RNAs that function solely in the cytoplasm, as it has been discovered that cytoplasmic tRNAs of budding yeast travel "retrograde" to the nucleus and, perhaps, back again to the cytoplasm to function in protein synthesis. Fourth, there is at least one example in ciliates of small double-stranded RNAs traveling multiple cycles between the cytoplasm and distinct nuclei to direct genome structure. This report discusses data that support or argue against nucleus/cytoplasm bidirectional movement for each category of small RNA and the possible roles that such movement may serve.

Lateral root initiation or the birth of a new meristem

Root branching happens through the formation of new meristems out of a limited number of pericycle cells inside the parent root. As opposed to shoot branching, the study of lateral root formation has been complicated due to its internal nature, and a lot of questions remain unanswered. However, due to the availability of new molecular tools and more complete genomic data in the model species Arabidopsis, the probability to find new and crucial elements in the lateral root formation pathway has increased. Increasingly more data are supporting the idea that lateral root founder cells become specified in young root parts before differentiation is accomplished. Next, pericycle founder cells undergo anticlinal asymmetric, divisions followed by an organized cell division pattern resulting in the formation of a new organ. The whole process of cell cycle progression and stimulation of the molecular pathway towards lateral root initiation is triggered by the plant hormone auxin. In this review, we aim to give an overview on the developmental events taking place from the very early specification of founder cells in the pericycle until the first anticlinal divisions by combining the knowledge originating from classical physiology studies with new insights from genetic-molecular analyses. Based on the current knowledge derived from recent genetic and developmental studies, we propose here a hypothetical model for LRI.

A nucleoporin is required for induction of Ca2+ spiking in legume nodule development and essential for rhizobial and fungal symbiosis

Nuclear-cytoplasmic partitioning and traffic between cytoplasmic and nuclear compartments are fundamental processes in eukaryotic cells. Nuclear pore complexes mediate transport of proteins, RNAs and ribonucleoprotein particles in and out of the nucleus. Here we present positional cloning of a plant nucleoporin gene, Nup133, essential for a symbiotic signal transduction pathway shared by Rhizobium bacteria and mycorrhizal fungi. Mutation of Nup133 results in a temperature sensitive nodulation deficient phenotype and absence of mycorrhizal colonization. Root nodules developing with reduced frequency at permissive temperatures are ineffective and electron microscopy show that Rhizobium bacteria are not released from infection threads. Measurement of ion fluxes using a calcium-sensitive dye show that Nup133 is required for the Ca2+ spiking normally detectable within minutes after application of purified rhizobial Nod-factor signal molecules to root hairs. Localization of NUP133 in the nuclear envelope of root cells and root hair cells shown with enhanced yellow fluorescent protein fusion proteins suggests a novel role for NUP133 nucleoporins in a rapid nuclear-cytoplasmic communication after host-plant recognition of symbiotic microbes. Our results identify a component of an intriguing signal process requiring interaction at the cell plasma membrane and at intracellular nuclear and plastid organelle-membranes to induce a second messenger.

The control of leaf development

The formation of a leaf is a basic aspect of plant development. This review provides an overview of our present understanding of the process from initiation to the final form of the leaf. Molecular genetic and cell biology approaches have yielded significant advances in this area, adding not only to our knowledge of leaf development but also to fundamental principles in plant biology. These principles will be highlighted, as well as areas where our understanding is still incomplete, in particular the problem of coordinating the multifaceted steps involved in the generation of the leaf structure.

Nuclear processing and export of microRNAs in Arabidopsis

In mammalian cells, the nuclear export receptor, Exportin 5 (Exp5), exports pre-microRNAs (pre-miRNAs) as well as tRNAs into the cytoplasm. In this study, we examined the function of HASTY (HST), the Arabidopsis ortholog of Exp5, in the biogenesis of miRNAs and tRNAs. In contrast to mammals, we found that miRNAs exist as single-stranded 20- to 21-nt molecules in the nucleus in Arabidopsis. This observation is consistent with previous studies indicating that proteins involved in miRNA biogenesis are located in the nucleus in Arabidopsis. Although miRNAs exist in the nucleus, a majority accumulate in the cytoplasm. Interestingly, loss-of-function mutations in HST reduced the accumulation of most miRNAs but had no effect on the accumulation of tRNAs and endogenous small interfering RNAs, or on transgene silencing. In contrast, a mutation in PAUSED (PSD), the Arabidopsis ortholog of the tRNA export receptor, Exportin-t, interfered with the processing of tRNA-Tyr but did not affect the accumulation or nuclear export of miRNAs. These results demonstrate that HST and PSD do not share RNA cargos in nuclear export and strongly suggest that there are multiple nuclear export pathways for these small RNAs in Arabidopsis.

Nucleocytoplasmic Trafficking in Plant Cells

In a eukaryotic cell, the nuclear envelope (NE) separates genetic information from the environment of biosynthesis and metabolism. Transfer of macromolecules across the NE involves the nuclear pores--large multisubunit protein complexes--and machinery that facilitates rapid, directional, and selective transport. While core elements of the transport process are conserved between kingdoms, different solutions to similar problems have also evolved. Although the structure and composition of the yeast and mammalian nuclear pore have been unraveled recently, the plant nuclear pore remains largely enigmatic. Like any other process, nucleocytoplasmic transport can be regulated. Several examples from plants are discussed that promise insights into the regulation of signaling pathways. While controlling the partitioning of cellular components, the nuclear envelope also presents an obstacle to viruses and transforming agents that need access to the genome, and different mechanisms have evolved to overcome this obstacle. Finally, the recent recognition of the importance of small RNAs for gene regulation emphasizes the need to understand small RNA nuclear export and the levels of its regulation. This review attempts to wed our molecular-mechanistic understanding of nucleocytoplasmic trafficking drawn from all model systems with the intriguing examples of regulated nucleocytoplasmic partitioning in plants.

The plant nuclear envelope: new prospects for a poorly understood structure

The nuclear envelope (NE) is one of the least characterized cellular structures in plant cells. In particular, knowledge of its dynamic behaviour during the cell cycle and of its protein composition is limited. This review summarizes current views on the plant NE and highlights fundamental differences with other organisms. We also introduce the power of new technology available to investigate the NE and how this has already begun to revolutionize our knowledge of the biology of the plant NE. Contents Summary 227 I. Introduction 227 II. The membranes of the nuclear envelope 228 III. Functions of the nuclear envelope 231 IV. Proteins associated with the nuclear envelope 236 V. New tools for studying the nuclear envelope 239 VI. Conclusions and future prospects 241 Acknowledgements 242 References 242.

The Arabidopsis heterochronic gene ZIPPY is an ARGONAUTE family member

Plants progress through a temporal sequence of juvenile, adult, and reproductive phases, each marked by the expression of phase-specific traits. Here we show that loss-of-function mutations in ZIPPY (ZIP) cause the premature expression of adult vegetative traits but do not accelerate the onset of reproductive competence or flowering time. ZIP encodes ARGONAUTE7 (AGO7), one of ten members of the ARGONAUTE family in Arabidopsis. In addition to playing developmental roles, some ARGONAUTE family members are required for RNAi-like phenomena, such as posttranscriptional gene silencing. In contrast to Arabidopsis ARGONAUTE1, ZIP has no significant role in transgene silencing; its primary function is in the regulation of developmental timing.

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.

Nucleo-cytoplasmic partitioning of proteins in plants: implications for the regulation of environmental and developmental signalling

Considerable progress has been made in the past few years in characterising Arabidopsis nuclear transport receptors and in elucidating plant signal transduction pathways that employ nucleo-cytoplasmic partitioning of a member of the signal transduction chain. This review briefly introduces the major principles of nuclear transport of macromolecules across the nuclear envelope and the proteins involved, as they have been described in vertebrates and yeast. Proteins of the plant nuclear transport machinery that have been identified to date are discussed, the focus being on Importin beta-like nuclear transport receptors. Finally, the importance of nucleo-cytoplasmic partitioning as a regulatory tool for signalling is highlighted, and different plant signal transduction pathways that make use of this regulatory potential are presented.

PAUSED, a putative exportin-t, acts pleiotropically in Arabidopsis development but is dispensable for viability

Exportin-t was first identified in humans as a protein that mediates the export of tRNAs from the nucleus to the cytoplasm. Mutations in Los1p, the Saccharomyces cerevisiae exportin-t homolog, result in nuclear accumulation of tRNAs. Because no exportin-t mutants have been reported in multicellular organisms, the developmental functions of exportin-t have not been determined. Here, we report the isolation and characterization of two Arabidopsis exportin-t mutants, paused-5 and paused-6. The mutant phenotypes indicate that exportin-t acts pleiotropically in plant development. In particular, paused-5 and paused-6 result in delayed leaf formation during vegetative development. The two paused mutations also cause the transformation of reproductive organs into perianth organs in the hua1-1 hua2-1 background, which is partially defective in reproductive organ identity specification. The floral phenotypes of hua1-1 hua2-1 paused mutants resemble those of mutations in the floral homeotic gene AGAMOUS. Moreover, paused-5 enhances the mutant phenotypes of two floral meristem identity genes, LEAFY and APETALA1. The developmental defects caused by paused mutations confirm the important roles of exportin-t in gene expression in multicellular organisms. In addition, a paused null allele, paused-6, is still viable, suggesting the presence of redundant tRNA export pathway(s) in Arabidopsis.