Nuclear export dynamics of RNA-protein complexes

The dynamic pathway of nuclear RNA in eukaryotes

The passage of mRNA molecules from the site of synthesis, through the nucleoplasm and the nuclear pore, en route to the cytoplasm, might appear straightforward. Nonetheless, several decades of detailed examination of this pathway, from high resolution electron microscopy in fixed specimens, through the development of immuno-detection techniques and fluorescence toolkits, to the current era of live-cell imaging, show this to be an eventful journey. In addition to mRNAs, several species of noncoding RNAs travel and function in the nucleus, some being retained within throughout their lifetime. This review will highlight the nucleoplasmic paths taken by mRNAs and noncoding RNAs in eukaryotic cells with special focus on live-cell data and in concurrence with the biophysical nature of the nucleus.

Torsin mediates primary envelopment of large ribonucleoprotein granules at the nuclear envelope

A previously unrecognized mechanism through which large ribonucleoprotein (megaRNP) granules exit the nucleus is by budding through the nuclear envelope (NE). This mechanism is akin to the nuclear egress of herpes-type viruses and is essential for proper synapse development. However, the molecular machinery required to remodel the NE during this process is unknown. Here, we identify Torsin, an AAA-ATPase that in humans is linked to dystonia, as a major mediator of primary megaRNP envelopment during NE budding. In torsin mutants, megaRNPs accumulate within the perinuclear space, and the messenger RNAs contained within fail to reach synaptic sites, preventing normal synaptic protein synthesis and thus proper synaptic bouton development. These studies begin to establish the cellular machinery underlying the exit of megaRNPs via budding, offer an explanation for the "nuclear blebbing" phenotype found in dystonia models, and provide an important link between Torsin and the synaptic phenotypes observed in dystonia.

Functional architecture of the nuclear pore complex

The nuclear pore complex (NPC) is the sole gateway between the nucleus and the cytoplasm. NPCs fuse the inner and outer nuclear membranes to form aqueous translocation channels that allow the free diffusion of small molecules and ions, as well as receptor-mediated transport of large macromolecules. The NPC regulates nucleocytoplasmic transport of macromolecules, utilizing soluble receptors that identify and present cargo to the NPC, in a highly selective manner to maintain cellular functions. The NPC is composed of multiple copies of approximately 30 different proteins, termed nucleoporins, which assemble to form one of the largest multiprotein assemblies in the cell. In this review, we address structural and functional aspects of this fundamental cellular machinery.

Jumping over the fence: RNA nuclear export revisited

The nuclear envelope forms a cocoon that surrounds the cellular genome keeping it out of harm’s way and can be utilized by the cell as a means of functionally regulating chromatin structure and gene expression. At the same time, this double-layered membrane system constitutes a formidable obstacle to the unimpeded flow of genetic information between the genome and the rest of the cell. The nuclear pore has been long considered the sole passageway between nucleus and cytoplasm. A new report¹ challenges this view and proposes a novel mechanism by which RNA transcripts destined for localized translation in highly polarized cell types, cross both inner and outer nuclear envelope membranes and reach the cytoplasm without utilizing the nuclear pore route.

How networks change with time

Motivation: Biological networks change in response to genetic and environmental cues. Changes are reflected in the abundances of biomolecules, the composition of protein complexes and other descriptors of the biological state. Methods to infer the dynamic state of a cell would have great value for understanding how cells change over time to accomplish biological goals.

Results: A new method predicts the dynamic state of protein complexes in a cell, with protein expression inferred from transcription profile time courses and protein complexes inferred by joint analysis of protein co-expression and protein–protein interaction maps. Two algorithmic advances are presented: a new method, DHAC (Dynamical Hierarchical Agglomerative Clustering), for clustering time-evolving networks; and a companion method, MATCH-EM, for matching corresponding clusters across time points. With link prediction as an objective assessment metric, DHAC provides a substantial advance over existing clustering methods. An application to the yeast metabolic cycle demonstrates how waves of gene expression correspond to individual protein complexes. Our results suggest regulatory mechanisms for assembling the mitochondrial ribosome and illustrate dynamic changes in the components of the nuclear pore.

Availability: All source code and data are available under the Boost Software License as supplementary material, at www.baderzone.org, and at sourceforge.net/projects/dhacdist

Contact: joel.bader@jhu.edu

Supplementary information:Supplementary data are available at Bioinformatics online.

Detecting Pyronin Y labeled RNA transcripts in live cell microenvironments by phasor-FLIM analysis

Pyronin Y is an environment-sensitive probe which labels all double-stranded RNA in live cells. Methods to determine which RNA species Pyronin Y may be labeling are limited due to the lack of studies aimed at determining whether this probe has different spectroscopic properties when bound to specific transcripts. A major issue is that transcripts are difficult to isolate and study individually. We detected transcripts directly in their biological environment allowing us to identify RNA species on the basis of their location in the cell. We show that the phasor approach to lifetime analysis has the sensitivity to determine at least six different RNA species in live fibroblast cells. The detected lifetime differences were consistent among cells. To our knowledge this is the first application of a spectroscopic technique aimed at identifying Pyronin Y labeled RNA subtypes in living cells.

Nuclear pore complex composition: a new regulator of tissue-specific and developmental functions

Nuclear pore complexes (NPCs) are multiprotein aqueous channels that penetrate the nuclear envelope connecting the nucleus and the cytoplasm. NPCs consist of multiple copies of roughly 30 different proteins known as nucleoporins (NUPs). Due to their essential role in controlling nucleocytoplasmic transport, NPCs have traditionally been considered as structures of ubiquitous composition. The overall structure of the NPC is indeed conserved in all cells, but new evidence suggests that the protein composition of NPCs varies among cell types and tissues. Moreover, mutations in various nucleoporins result in tissue-specific diseases. These findings point towards a heterogeneity in NPC composition and function. This unexpected heterogeneity suggests that cells use a combination of different nucleoporins to assemble NPCs with distinct properties and specialized functions.

A single molecule view on Dbp5 and mRNA at the nuclear pore

Numerous molecular details of intracellular mRNA processing have been revealed in recent years. However, the export process of single native mRNA molecules, the actual translocation through the nuclear pore complex (NPC), could not yet be examined in vivo. The problem is observing mRNA molecules without interfering with their native behavior. We used a protein-based labeling approach to visualize single native mRNPs in live salivary gland cells of Chironomus tentans, an iconic system used for decades to study the mRNA life cycle. Recombinant hrp36, the C. tentans homolog of mammalian hnRNP A1, was fluorescence labeled and microinjected into living cells, where it was integrated into nascent mRNPs. Intranuclear trajectories of single mRNPs, including their NPC passage, were observed with high space and time resolution employing a custom-built light sheet fluorescence microscope. We analyzed the kinetics and dynamics of mRNP export and started to study its mechanism and regulation by measuring the turnover-kinetics of single Dbp5 at the NPC.

High-resolution three-dimensional mapping of mRNA export through the nuclear pore

The flow of genetic information is regulated by selective nucleocytoplasmic transport of messenger RNA:protein complexes (mRNPs) through the nuclear pore complexes (NPCs) of eukaryotic cells. However, the three-dimensional (3D) pathway taken by mRNPs as they transit through the NPC, and the kinetics and selectivity of transport, remain obscure. Here we employ single-molecule fluorescence microscopy with an unprecedented spatiotemporal accuracy of 8 nm and 2 ms to provide new insights into the mechanism of nuclear mRNP export in live human cells. We find that mRNPs exiting the nucleus are decelerated and selected at the centre of the NPC, and adopt a fast-slow-fast diffusion pattern during their brief, ~12 ms, interaction with the NPC. A 3D reconstruction of the export route indicates that mRNPs primarily interact with the periphery on the nucleoplasmic side and in the centre of the NPC, without entering the central axial conduit utilized for passive diffusion of small molecules, and eventually dissociate on the cytoplasmic side.

A gene-networked gel matrix-supported lipid bilayer as a synthetic nucleus system

A spheroidal transgene-networked gel matrix was designed as a synthetic nucleus system. It was spheroidically manufactured using both advanced lithography and DNA nanotechnology. Stable Aqueorea coerulescens green fluorescent protein (AcGFP)-encoding gene cross-networks have been optimized in various parameters: the number of gene-networked gel (G-net-gel) spheroids, the concentration of a AcGFP plasmid in the scaffold, and the molar ratio between the X-DNA building blocks and the gene. It was then assessed that 800 units of the gene networked gel matrix at a 4000:1 molar ratio of X-DNA blocks and AcGFP gene components accomplished 20-fold enhanced in vitro protein expression efficiency for 36 h. Furthermore, once with lipid capping, it reproduced the natural nucleus system, demonstrating the 2-fold increased levels of messenger RNAs (mRNAs) relative to solution phase vectors.

Dbp5 - from nuclear export to translation

The DEAD-box RNA helicase Dbp5 is an essential and conserved mRNA export factor which functions in the ATP dependent remodeling of RNA/protein complexes. As such it displaces mRNA bound proteins at the cytoplasmic site of the nuclear pore complex. For the regulation of its RNA-dependent ATPase activity during late steps of nuclear transport, Dbp5 requires the nucleoporin Nup159 and its cofactors Gle1 and IP6. In addition to its role in mRNA export, a second important function of Dbp5 was identified in translation termination, where it acts together with eRF1 once the translation machinery has reached the stop codon. Similar to mRNA export, this function also requires Gle1-IP6, however, the counterpart of Nup159 is still missing. Potential other functions of the nucleo-cytoplasmic protein Dbp5 are discussed as well as its substrate specificity and details in its regulatory cycle that are based on recent biochemical and structural characterization. This article is part of a Special Issue entitled: The Biology of RNA helicases - Modulation for life.

Regulation of mammalian cell differentiation by long non-coding RNAs

Differentiation of specialized cell types from stem and progenitor cells is tightly regulated at several levels, both during development and during somatic tissue homeostasis. Many long non-coding RNAs have been recognized as an additional layer of regulation in the specification of cellular identities; these non-coding species can modulate gene-expression programmes in various biological contexts through diverse mechanisms at the transcriptional, translational or messenger RNA stability levels. Here, we summarize findings that implicate long non-coding RNAs in the control of mammalian cell differentiation. We focus on several representative differentiation systems and discuss how specific long non-coding RNAs contribute to the regulation of mammalian development.

The new nucleoporin: regulator of transcriptional repression and beyond

Transcriptional regulation is a complex process that requires the integrated action of many multi-protein complexes. The way in which a living cell coordinates the action of these complexes in time and space is still poorly understood. Recent work has shown that nuclear pores, well known for their role in 3′ processing and export of transcripts, also participate in the control of transcriptional initiation. We have recently begun to explore how nuclear pores interface with the well-described machinery that regulates initiation. This work led to the discovery that specific nucleoporins are required for binding of the repressor protein Mig1 to its site in target promoters. Nuclear pores are therefore involved in repressing, as well as activating, transcription. Here we discuss in detail the main models explaining our result and consider what each implies about the roles that nuclear pores play in the regulation of gene expression.

Nuclear transport receptor binding avidity triggers a self-healing collapse transition in FG-nucleoporin molecular brushes

Conformational changes at supramolecular interfaces are fundamentally coupled to binding activity, yet it remains a challenge to probe this relationship directly. Within the nuclear pore complex, this underlies how transport receptors known as karyopherins proceed through a tethered layer of intrinsically disordered nucleoporin domains containing Phe-Gly (FG)-rich repeats (FG domains) that otherwise hinder passive transport. Here, we use nonspecific proteins (i.e., BSA) as innate molecular probes to explore FG domain conformational changes by surface plasmon resonance. This mathematically diminishes the surface plasmon resonance refractive index constraint, thereby providing the means to acquire and correlate height changes in a surface-tethered FG domain layer to Kap binding affinities in situ with respect to their relative spatial arrangements. Stepwise measurements show that FG domain collapse is caused by karyopherin β1 (Kapβ1) binding at low concentrations, but this gradually transitions into a reextension at higher Kapβ1 concentrations. This ability to self-heal is intimately coupled to Kapβ1-FG binding avidity that promotes the maximal incorporation of Kapβ1 into the FG domain layer. Further increasing Kapβ1 to physiological concentrations leads to a "pileup" of Kapβ1 molecules that bind weakly to unoccupied FG repeats at the top of the layer. Therefore, binding avidity does not hinder fast transport per se. Revealing the biophysical basis underlying the form-function relationship of Kapβ1-FG domain behavior results in a convergent picture in which transport and mechanistic aspects of nuclear pore complex functionality are reconciled.

A spatial physiological model for p53 intracellular dynamics

In this paper we design and analyse a physiologically based model representing the accumulation of protein p53 in the nucleus after triggering of ATM by DNA damage. The p53 protein is known to have a central role in the response of the cell to cytotoxic or radiotoxic insults resulting in DNA damage. A reasonable requirement for a model describing intracellular signalling pathways is taking into account the basic feature of eukaryotic cells: the distinction between nucleus and cytoplasm. Our aim is to show, on a simple reaction network describing p53 dynamics, how this basic distinction provides a framework which is able to yield expected oscillatory dynamics without introducing either positive feedbacks or delays in the reactions. Furthermore we prove that oscillations appear only if some spatial constraints are respected, e.g. if the diffusion coefficients correspond to known biological values. Finally we analyse how the spatial features of a cell influence the dynamic response of the p53 network to DNA damage, pointing out that the protein oscillatory dynamics is indeed a response that is robust towards changes with respect to cellular environments. Even if we change the cell shape or its volume or better its ribosomal distribution, we observe that DNA damage yields sustained oscillations of p53.

A two-piece derivative of a group I intron RNA as a platform for designing self-assembling RNA templates to promote Peptide ligation

Multicomponent RNA-peptide complexes are attractive from the viewpoint of artificial design of functional biomacromolecular systems. We have developed self-folding and self-assembling RNAs that serve as templates to assist chemical ligation between two reactive peptides with RNA-binding capabilities. The design principle of previous templates, however, can be applied only to limited classes of RNA-binding peptides. In this study, we employed a two-piece derivative of a group I intron RNA from the Tetrahymena large subunit ribosomal RNA (LSU rRNA) as a platform for new template RNAs. In this group I intron-based self-assembling platform, modules for the recognition of substrate peptides can be installed independently from modules holding the platform structure. The new self-assembling platform allows us to expand the repertoire of substrate peptides in template RNA design.

Intracellular single molecule microscopy reveals two kinetically distinct pathways for microRNA assembly

MicroRNAs (miRNAs) associate with components of the RNA-induced silencing complex (RISC) to assemble on mRNA targets and regulate protein expression in higher eukaryotes. Here we describe a method for the intracellular single-molecule, high-resolution localization and counting (iSHiRLoC) of miRNAs. Microinjected, singly fluorophore-labelled, functional miRNAs were tracked within diffusing particles, a majority of which contained single such miRNA molecules. Mobility and mRNA-dependent assembly changes suggest the existence of two kinetically distinct pathways for miRNA assembly, revealing the dynamic nature of this important gene regulatory pathway. iSHiRLOC achieves an unprecedented resolution in the visualization of functional miRNAs, paving the way to understanding RNA silencing through single-molecule systems biology.

Motor-driven motility of fungal nuclear pores organizes chromosomes and fosters nucleocytoplasmic transport

Exchange between the nucleus and the cytoplasm is controlled by nuclear pore complexes (NPCs). In animals, NPCs are anchored by the nuclear lamina, which ensures their even distribution and proper organization of chromosomes. Fungi do not possess a lamina and how they arrange their chromosomes and NPCs is unknown. Here, we show that motor-driven motility of NPCs organizes the fungal nucleus. In Ustilago maydis, Aspergillus nidulans, and Saccharomyces cerevisiae fluorescently labeled NPCs showed ATP-dependent movements at ~1.0 µm/s. In S. cerevisiae and U. maydis, NPC motility prevented NPCs from clustering. In budding yeast, NPC motility required F-actin, whereas in U. maydis, microtubules, kinesin-1, and dynein drove pore movements. In the latter, pore clustering resulted in chromatin organization defects and led to a significant reduction in both import and export of GFP reporter proteins. This suggests that fungi constantly rearrange their NPCs and corresponding chromosomes to ensure efficient nuclear transport and thereby overcome the need for a structural lamina.

RNP export by nuclear envelope budding

Nuclear export of mRNAs is thought to occur exclusively through nuclear pore complexes. In this issue of Cell, Speese et al. identify an alternate pathway for mRNA export in muscle cells where ribonucleoprotein complexes involved in forming neuromuscular junctions transit the nuclear envelope by fusing with and budding through the nuclear membrane.

Nuclear export of single native mRNA molecules observed by light sheet fluorescence microscopy

Nuclear export of mRNA is a key transport process in eukaryotic cells. To investigate it, we labeled native mRNP particles in living Chironomus tentans salivary gland cells with fluorescent hrp36, the hnRNP A1 homolog, and the nuclear envelope by fluorescent NTF2. Using light sheet microscopy, we traced single native mRNA particles across the nuclear envelope. The particles were observed to often probe nuclear pore complexes (NPC) at their nuclear face, and in only 25% of the cases yielded actual export. The complete export process took between 65 ms up to several seconds. A rate-limiting step was observed, which could be assigned to the nuclear basket of the pore and might correspond to a repositioning and unfolding of mRNPs before the actual translocation. Analysis of single fluorescent Dbp5 molecules, the RNA helicase essential for mRNA export, revealed that Dbp5 most often approached the cytoplasmic face of the NPC, and exhibited a binding duration of approximately 55 ms. Our results have allowed a refinement of the current models for mRNA export.

Structural basis for polyadenosine-RNA binding by Nab2 Zn fingers and its function in mRNA nuclear export

Polyadenylation regulation and efficient nuclear export of mature mRNPs both require the polyadenosine-RNA-binding protein, Nab2, which contains seven CCCH Zn fingers. We describe here the solution structure of fingers 5-7, which are necessary and sufficient for high-affinity polyadenosine-RNA binding, and identify key residues involved. These Zn fingers form a single structural unit. Structural coherence is lost in the RNA-binding compromised Nab2-C437S mutant, which also suppresses the rat8-2 allele of RNA helicase Dbp5. Structure-guided Nab2 variants indicate that dbp5(rat8-2) suppression is more closely linked to hyperadenylation and suppression of mutant alleles of the nuclear RNA export adaptor, Yra1, than to affinity for polyadenosine-RNA. These results indicate that, in addition to modulating polyA tail length, Nab2 has an unanticipated function associated with generating export-competent mRNPs, and that changes within fingers 5-7 lead to suboptimal assembly of mRNP export complexes that are more easily disassembled by Dbp5 upon reaching the cytoplasm.

DAG1, no gene for RNA regulation?

DAG1 encodes for a precursor protein that liberates the two subunits featured by the dystroglycan (DG) adhesion complex that are involved in an increasing number of cellular functions in a wide variety of cells and tissues. Aside from the proteolytic events producing the α and β subunits, especially the former undergoes extensive "post-production" modifications taking place within the ER/Golgi where its core protein is both N- and O-decorated with sugars. These post-translational events, that are mainly orchestrated by a plethora of certified, or putative, glycosyltransferases, prelude to the excocytosis-mediated trafficking and targeting of the DG complex to the plasma membrane. Extensive genetic and biochemical evidences have been accumulated so far on α-DG glycosylation, while little is know on possible regulatory events underlying the chromatine activation, transcription or post-transcription (splicing and escape from the nucleus) of DAG1 or of its mRNA. A scenario is envisaged in which cells would use a sort of preferential, and scarcely regulated, route for DAG1 activation, that would imply fast mRNA transcription, maturation and export to the cytosol, and would prelude to the multiple time-consuming enzymatic post-translational activities needed for its glycosylation. Such a provocative view might be helpful to trigger future work aiming at disclosing the complete molecular mechanisms underlying DAG1 activation and at improving our knowledge of any pre-translational step that is involved in dystroglycan regulation.

Structural features of transversal barrier in central channel of nuclear pore complex

The most important entity of the selective behavior of the nuclear pore complex (NPC) is considered to be the matter called "barrier," "meshwork" or "sieve." This part of NPC has not been well elucidated by using electron microscopy methods to date. In the present study, we demonstrated the presence of a coherent transversal barrier in the central channel of NPC, using high resolution transmission electron microscopy. It was found that the barrier is located in the middle of the central channel, i.e. at the level where the outer and inner nuclear membranes fuse. The thickness of this layer is evidently different in various NPCs and usually varies between 20 and 30 nm and its diameter is approximately 40 nm. The cytoplasmic and nuclear surfaces of the barrier are roughly parallel and plane. Moreover we suggest that the barrier may not be interrupted by any channel(s), at least not with a diameter above 10 nm. Further various appearances of the central channel with different particles were observed, presumably cargos and karyopherins captured in transit. A different type of central channel barrier with lipid bilayer membrane-like appearance is also discussed.

Structural organization of the nuclear pore permeability barrier

The efficiency of gene therapy in non-dividing cells is particularly poor due to restricted nuclear delivery rates of exogenously applied macromolecules across the nuclear pore complexes (NPCs). Therefore, improved intranuclear delivery of transgenes requires an ability to modulate the barrier function of the NPC. Despite a large body of experimental evidence accumulated to date, the contribution of individual NPC proteins (nucleoporins) to the formation of the NPC permeability barrier as well as their structural organization within the NPC remains under debate. In the present study, we revisit the view on the spatial arrangement of the Phe-Gly rich domains (FG-domains) of a subset of nucleoporins known as FG-nucleoporins. They are generally believed to be the key constituents of the NPC permeability barrier. Comparison of the binding pattern of a transport receptor importin β fragment, that binds specifically to FG-domains, with the binding pattern of wheat germ agglutinin that binds elsewhere in the NPC, reveals that FG-domains tend to cluster in the very center of the NPC. Furthermore, a controlled sequential release of the barrier-forming nucleoporins results in a gradual breakdown of the NPC permeability barrier. The breakdown is initiated by a dissociation of Nup62 from the NPC. This is accompanied by an increased passive diffusion of small molecules across the NPC. Subsequent dissociation of Nup98 and possibly other nucleoporins results in a collapse of the barrier for larger molecules. We therefore conclude that FG-nucleoporins do not contribute equally to the maintenance of the NPC permeability barrier exclusion limit. This implies that a controlled release of nucleoporins that contribute most to the formation and maintenance of the NPC barrier can facilitate access of therapeutic macromolecules into the nucleus.

To the pore and through the pore: a story of mRNA export kinetics

The evolutionary 'decision' to store genetic information away from the place of protein synthesis, in a separate compartment, has forced eukaryotic cells to establish a system to transport mRNAs from the nucleus to the cytoplasm for translation. To ensure export to be fast and efficient, cells have evolved a complex molecular interplay that is tightly regulated. Over the last few decades, many of the individual players in this process have been described, starting with the composition of the nuclear pore complex to proteins that modulate co-transcriptional events required to prepare an mRNP for export to the cytoplasm. How the interplay between all the factors and processes results in the efficient and selective export of mRNAs from the nucleus and how the export process itself is executed within cells, however, is still not fully understood. Recent advances in using proteomic and single molecule microscopy approaches have provided important insights into the process and its kinetics. This review summarizes these recent advances and how they led to the current view on how cells orchestrate the export of mRNAs. This article is part of a Special Issue entitled: Nuclear Transport and RNA Processing.

Nucleic-acid based gene therapeutics: delivery challenges and modular design of nonviral gene carriers and expression cassettes to overcome intracellular barriers for sustained targeted expression

The delivery of nucleic acid molecules into cells to alter physiological functions at the genetic level is a powerful approach to treat a wide range of inherited and acquired disorders. Biocompatible materials such as cationic polymers, lipids, and peptides are being explored as safer alternatives to viral gene carriers. However, the comparatively low efficiency of nonviral carriers currently hampers their translation into clinical settings. Controlling the size and stability of carrier/nucleic acid complexes is one of the primary hurdles as the physicochemical properties of the complexes can define the uptake pathways, which dictate intracellular routing, endosomal processing, and nucleocytoplasmic transport. In addition to nuclear import, subnuclear trafficking, posttranscriptional events, and immune responses can further limit transfection efficiency. Chemical moieties, reactive linkers or signal peptide have been conjugated to carriers to prevent aggregation, induce membrane destabilization and localize to subcellular compartments. Genetic elements can be inserted into the expression cassette to facilitate nuclear targeting, delimit expression to targeted tissue, and modulate transgene expression. The modular option afforded by both gene carriers and expression cassettes provides a two-tier multicomponent delivery system that can be optimized for targeted gene delivery in a variety of settings.

mRNA export and sumoylation-Lessons from plants

SUMO is a small ubiquitin-related protein modifier that is involved in a number of biological processes, including transcription, DNA repair, genome stability, and chromatin organization. Its potential role in mRNA biogenesis is less well investigated. The biogenesis of mRNA is closely coupled to transcription as well as mRNA nuclear export and several of the involved proteins have dual roles and appear in several complexes. Recently, SUMO-proteome analyses have discovered a number of these proteins as putative targets of SUMO regulation. In the model plant Arabidopsis thaliana, several mutants as well as environmental conditions have been identified that show a close correlation between over- and under-sumoylation of nuclear proteins and mRNA export retention. Three new plant SUMO-proteome studies add to the list of potentially sumoylated RNA-related proteins. Here, the emerging connection between SUMO and mRNA export is compared across kingdoms and its potential mechanistic role is discussed. This article is part of a Special Issue entitled: Nuclear Transport and RNA Processing.

Nuclear routing networks span between nuclear pore complexes and genomic DNA to guide nucleoplasmic trafficking of biomolecules

In health and disease, biomolecules, which are involved in gene expression, recombination, or reprogramming have to traffic through the nucleoplasm, between nuclear pore complexes (NPCs) and genomic DNA (gDNA). This trafficking is guided by the recently revealed nuclear routing networks (NRNs).In this study, we aimed to investigate, if the NRNs have established associations with the genomic DNA in situ and if the NRNs have capabilities to bind the DNA de novo. Moreover, we aimed to study further, if nucleoplasmic trafficking of the histones, rRNA, and transgenes' vectors, between the NPCs and gDNA, is guided by the NRNs.We used Xenopus laevis oocytes as the model system. We engineered the transgenes' DNA vectors equipped with the SV40 LTA nuclear localization signals (NLS) and/or HIV Rev nuclear export signals (NES). We purified histones, 5S rRNA, and gDNA. We rendered all these molecules superparamagnetic and fluorescent for detection with nuclear magnetic resonance (NMR), total reflection x-ray fluorescence (TXRF), energy dispersive x-ray spectroscopy (EDXS), and electron energy loss spectroscopy (EELS).The NRNs span between the NPCs and genomic DNA. They form firm bonds with the gDNA in situ. After complete digestion of the nucleic acids with the RNases and DNases, the newly added DNA - modified with the dNTP analogs, bonds firmly to the NRNs. Moreover, the NRNs guide the trafficking of the DNA transgenes' vectors - modified with the SV40 LTA NLS, following their import into the nuclei through the NPCs. The pathway is identical to that of histones. The NRNs also guide the trafficking of the DNA transgenes' vectors, modified with the HIV Rev NES, to the NPCs, followed by their export out of the nuclei. Ribosomal RNAs follow the same pathway.To summarize, the NRNs are the structures connecting the NPCs and the gDNA. They guide the trafficking of the biomolecules between the NPCs and the gDNA.

Multiscale dynamics in nucleocytoplasmic transport

The nuclear pore complex (NPC) has long been viewed as a point-like entry and exit channel between the nucleus and the cytoplasm. New data support a different view whereby the complex displays distinct spatial dynamics of variable duration ranging from milliseconds to events spanning the entire cell cycle. Discrete interaction sites outside the central channel become apparent, and transport regulation at these sites seems to be of greater importance than currently thought. Nuclear pore components are highly active outside the NPC or impact the fate of cargo transport away from the nuclear pore. The NPC is a highly dynamic, crowded environment-constantly loaded with cargo while providing selectivity based on unfolded proteins. Taken together, this comprises a new paradigm in how we view import/export dynamics and emphasizes the multiscale nature of NPC-mediated cellular transport.

The structure of the NXF2/NXT1 heterodimeric complex reveals the combined specificity and versatility of the NTF2-like fold

NXF1-like members of the NXF (nuclear export factor) family orchestrate bulk nuclear export of mRNA, while functionally distinct NXF variant proteins carry out separate substrate-specific and tissue-specific RNA regulation. Metazoan organisms possess at least one NXF1-like gene and one or more NXF variant genes. Heterodimerization of both proteins with the NXT (NTF2-related export) protein is central to NXF family function; however, given the multiplicity of NXF/NXT complexes, the specificity and mechanism of heterodimerization remain unclear. Here, we report the structural and functional analyses of the Caenorhabditis elegans NXF variant ceNXF2 bound to ceNXT1. Contacts crucial for NXF/NXT heterodimer stability and specificity, including a probable site for phosphoregulation, have been identified. The ceNXF2 NTF2 domain bears at least two nucleoporin (Nup) binding pockets necessary for the colocalization of ceNXF2/ceNXT1 at the nuclear envelope. Unexpectedly, one Nup binding pocket is formed at the heterodimer interface of the ceNXF2/ceNXT1 complex, demonstrating that NXT binding directly regulates NXF function.

Examining the requirements for nucleoporins by HIV-1

Evaluation of: Matreyek KA, Engelman A. The requirement for nucleoporin Nup153 during human immunodeficiency virus type 1 infection is determined by the viral capsid. J. Virol. 85(15), 7818–7827 (2011). A hallmark of HIV type 1 and other lentiviruses is their ability to infect and replicate in nondividing cells by commandeering host nuclear transport factors. During the early stages of infection, this is expected to permit the safe passage of viral preintegration complexes (PICs) through nuclear pores. Numerous nuclear transport factors have been identified as essential for HIV-1 infection by genome-wide small interfering RNA screens, and many of these are currently under investigation. Here, using knockdown studies, Matreyek and Engelman further characterize the importance of transportin-3 and nuclear pore complex component nucleoporin 153 for the early stages of HIV-1 infection and show that these two proteins operate synergistically. Also, as was previously observed for transportin-3, they show that the requirement of nucleoporin 153 for PIC nuclear entry is determined by the HIV-1 Capsid protein. The refinement of the list of key nuclear pore complex and transport proteins required for PIC entry, along with a better understanding of the specific mechanisms employed, will undoubtedly lead to the development of future antiretroviral therapies that will have the potential to block HIV-1 viral DNA integration.