Why cells move messages: the biological functions of mRNA localization

Membrane-associated mRNAs: A Post-transcriptional Pathway for Fine-turning Gene Expression

Gene expression is a fundamental and highly regulated process involving a series of tightly coordinated steps, including transcription, post-transcriptional processing, translation, and post-translational modifications. A growing number of studies have revealed an additional layer of complexity in gene expression through the phenomenon of mRNA subcellular localization. mRNAs can be organized into membraneless subcellular structures within both the cytoplasm and the nucleus, but they can also targeted to membranes. In this review, we will summarize in particular our knowledge on localization of mRNAs to organelles, focusing on important regulators and available techniques for studying organellar localization, and significance of this localization in the broader context of gene expression regulation.

Granule regulation by phase separation during Drosophila oogenesis

Drosophila eggs are highly polarised cells that use RNA-protein complexes to regulate storage and translational control of maternal RNAs. Ribonucleoprotein granules are a class of biological condensates that form predominantly by intracellular phase separation. Despite extensive in vitro studies testing the physical principles regulating condensates, how phase separation translates to biological function remains largely unanswered. In this perspective, we discuss granules in Drosophila oogenesis as a model system for investigating the physiological role of phase separation. We review key maternal granules and their properties while highlighting ribonucleoprotein phase separation behaviours observed during development. Finally, we discuss how concepts and models from liquid-liquid phase separation could be used to test mechanisms underlying granule assembly, regulation and function in Drosophila oogenesis.

Organizing the oocyte: RNA localization meets phase separation

RNA localization is a key biological strategy for organizing the cytoplasm and generating both cellular and developmental polarity. During RNA localization, RNAs are targeted asymmetrically to specific subcellular destinations, resulting in spatially and temporally restricted gene expression through local protein synthesis. First discovered in oocytes and embryos, RNA localization is now recognized as a significant regulatory strategy for diverse RNAs, both coding and non-coding, in a wide range of cell types. Yet, the highly polarized cytoplasm of the oocyte remains a leading model to understand not only the principles and mechanisms underlying RNA localization, but also links to the formation of biomolecular condensates through phase separation. Here, we discuss both RNA localization and biomolecular condensates in oocytes with a particular focus on the oocyte of the frog, Xenopus laevis.

Spatiotemporal Organization of the E. coli Transcriptome: Translation Independence and Engagement in Regulation

RNA localization in eukaryotes is a mechanism to regulate transcripts fate. Conversely, bacterial transcripts were not assumed to be specifically localized. We previously demonstrated that E. coli mRNAs may localize to where their products localize in a translation-independent manner, thus challenging the transcription-translation coupling extent. However, the scope of RNA localization in bacteria remained unknown. Here, we report the distribution of the E. coli transcriptome between the membrane, cytoplasm, and poles by combining cell fractionation with deep-sequencing (Rloc-seq). Our results reveal asymmetric RNA distribution on a transcriptome-wide scale, significantly correlating with proteome localization and prevalence of translation-independent RNA localization. The poles are enriched with stress-related mRNAs and small RNAs, the latter becoming further enriched upon stress in an Hfq-dependent manner. Genome organization may play a role in localizing membrane protein-encoding transcripts. Our results show an unexpected level of intricacy in bacterial transcriptome organization and highlight the poles as hubs for regulation.

Modeling and Preventing Progressive Hearing Loss in Usher Syndrome III

Usher syndrome type III (USH3) characterized by progressive loss of vision and hearing is caused by mutations in the clarin-1 gene (CLRN1). Clrn1 knockout (KO) mice develop hair cell defects by postnatal day 2 (P2) and are deaf by P21-P25. Early onset profound hearing loss in KO mice and lack of information about the cochlear cell type that requires Clrn1 expression pose challenges to therapeutic investigation. We generated KO mice harboring a transgene, TgAC1, consisting of Clrn1-UTR (Clrn1 cDNA including its 5' and 3' UTR) under the control of regulatory elements (Atoh1 3' enhancer/β-globin basal promoter) to direct expression of Clrn1 in hair cells during development and down regulate it postnatally. The KO-TgAC1 mice displayed delayed onset progressive hearing loss associated with deterioration of the hair bundle structure, leading to the hypothesis that hair cell expression of Clrn1 is essential for postnatal preservation of hair cell structure and hearing. Consistent with that hypothesis, perinatal transfection of hair cells in KO-TgAC1 mice with a single injection of AAV-Clrn1-UTR vector showed correlative preservation of the hair bundle structure and hearing through adult life. Further, the efficacy of AAV-Clrn1 vector was significantly attenuated, revealing the potential importance of UTR in gene therapy.

Quantitative Immunofluorescence to Measure Global Localized Translation

The mechanisms regulating mRNA translation are involved in various biological processes, such as germ line development, cell differentiation, and organogenesis, as well as in multiple diseases. Numerous publications have convincingly shown that specific mechanisms tightly regulate mRNA translation. Increased interest in the translation-induced regulation of protein expression has led to the development of novel methods to study and follow de novo protein synthesis in cellulo. However, most of these methods are complex, making them costly and often limiting the number of mRNA targets that can be studied. This manuscript proposes a method that requires only basic reagents and a confocal fluorescence imaging system to measure and visualize the changes in mRNA translation that occur in any cell line under various conditions. This method was recently used to show localized translation in the subcellular structures of adherent cells over a short period of time, thus offering the possibility of visualizing de novo translation for a short period during a variety of biological processes or of validating changes in translational activity in response to specific stimuli.

Small Luggage for a Long Journey: Transfer of Vesicle-Enclosed Small RNA in Interspecies Communication

In the evolutionary arms race, symbionts have evolved means to modulate each other's physiology, oftentimes through the dissemination of biological signals. Beyond small molecules and proteins, recent evidence shows that small RNA molecules are transferred between organisms and transmit functional RNA interference signals across biological species. However, the mechanisms through which specific RNAs involved in cross-species communication are sorted for secretion and protected from degradation in the environment remain largely enigmatic. Over the last decade, extracellular vesicles have emerged as prominent vehicles of biological signals. They can stabilize specific RNA transcripts in biological fluids and selectively deliver them to recipient cells. Here, we review examples of small RNA transfers between plants and bacterial, fungal, and animal symbionts. We also discuss the transmission of RNA interference signals from intestinal cells to populations of the gut microbiota, along with its roles in intestinal homeostasis. We suggest that extracellular vesicles may contribute to inter-species crosstalk mediated by small RNA. We review the mechanisms of RNA sorting to extracellular vesicles and evaluate their relevance in cross-species communication by discussing conservation, stability, stoichiometry, and co-occurrence of vesicles with alternative communication vehicles.

Arabidopsis BIRD Zinc Finger Proteins Jointly Stabilize Tissue Boundaries by Confining the Cell Fate Regulator SHORT-ROOT and Contributing to Fate Specification

Plant cells cannot rearrange their positions; therefore, sharp tissue boundaries must be accurately programmed. Movement of the cell fate regulator SHORT-ROOT from the stele to the ground tissue has been associated with transferring positional information across tissue boundaries. The zinc finger BIRD protein JACKDAW has been shown to constrain SHORT-ROOT movement to a single layer, and other BIRD family proteins were postulated to counteract JACKDAW's role in restricting SHORT-ROOT action range. Here, we report that regulation of SHORT-ROOT movement requires additional BIRD proteins whose action is critical for the establishment and maintenance of the boundary between stele and ground tissue. We show that BIRD proteins act in concert and not in opposition. The exploitation of asymmetric redundancies allows the separation of two BIRD functions: constraining SHORT-ROOT spread through nuclear retention and transcriptional regulation of key downstream SHORT-ROOT targets, including SCARECROW and CYCLIND6. Our data indicate that BIRD proteins promote formative divisions and tissue specification in the Arabidopsis thaliana root meristem ground tissue by tethering and regulating transcriptional competence of SHORT-ROOT complexes. As a result, a tissue boundary is not "locked in" after initial patterning like in many animal systems, but possesses considerable developmental plasticity due to continuous reliance on mobile transcription factors.

The compartmentalized vessel: The bacterial cell as a model for subcellular organization (a tale of two studies)

The traditional view of bacterial cells as non-compartmentalized, which is based on the lack of membrane-engulfed organelles, is currently being reassessed. Many studies in recent years led to the realization that bacteria have an intricate internal organization that is vital for various cellular processes. Specifically, various machineries were shown to localize to the poles of rod-shaped bacteria. We have recently shown that the control center of the PTS system, which governs carbon uptake and metabolism, localizes to the poles of E. coli cells. Notably, the machinery that controls bacterial taxis along chemical gradients (chemotaxis) has a similar localization pattern. The fact that the two systems need to communicate in order to generate an optimal metabolic response suggests that their similar spatial organization is not a coincidence. Rather, due to their special characteristics, the poles may function as hubs for signaling systems to allow for efficient crosstalk between different pathways in order to improve coordination of their actions.The regulatory mechanisms that underlie the spatial and temporal organization of microbial cells are largely unknown. Thus far, these mechanisms were believed to rely on embedded features of the localized proteins. In another study, we have recently shown that mRNAs are capable of migrating to particular domains in the bacterial cell where their protein products are required. In contrast to the view that transcription and translation are coupled in bacteria, localization of bacterial transcripts may occur in a translation-independent manner. Hence, it seems that the mechanistic basis for separating transcription and translation is more primitive than assumed up until now. We propose that bacteria synthesize proteins either by a transcription-translation coupled mechanism or by transporting mRNAs away from the transcription apparatus. Obviously, eukaryotic cells rely on the latter mechanism. Hence, the capacity of prokaryotic cells to adopt the division between transcription and translation was a crucial step in the evolution of nucleus-containing cells from the prokaryotic origin. Summarily, the line that separates cells with nucleus and cells without is fading, leading to the realization that bacteria are suitable model organisms for studying universal mechanisms that underlie spatial regulation of cellular processes.

Control of cell migration through mRNA localization and local translation

Cell migration plays an important role in many normal and pathological functions such as development, wound healing, immune defense, and tumor metastasis. Polarized migrating cells exhibit asymmetric distribution of many cytoskeletal proteins, which is believed to be critical for establishing and maintaining cell polarity and directional cell migration. To target these proteins to the site of function, cells use a variety of mechanisms such as protein transport and messenger RNA (mRNA) localization-mediated local protein synthesis. In contrast to the former which is intensively investigated and relatively well understood, the latter has been understudied and relatively poorly understood. However, recent advances in the study of mRNA localization and local translation have demonstrated that mRNA localization and local translation are specific and effective ways for protein localization and are crucial for embryo development, neuronal function, and many other cellular processes. There are excellent reviews on mRNA localization, transport, and translation during development and other cellular processes. This review will focus on mRNA localization-mediated local protein biogenesis and its impact on somatic cell migration.

Phylogenetic comparison of oskar mRNA localization signals

As a way to spatially control the expression of genes within cells, RNA localization is being recognized as an important process by which proteins are restricted to specific subcellular domains, which occurs in more diverse types of tissue than previously considered. Although many localized RNAs have been identified, information on cis-acting elements of localization is still limited. As transcripts of oskar (osk) are known to localize to the posterior pole of oocytes, we computationally analyzed a conserved sequence among eight Drosophila species and tested its role as a localization element. Dimerization of osk mRNA did not occur when the motif was deleted, but this did not affect assembly of osk mRNA-containing ribonucleoprotein (RNP) complexes. Without the motif, however, large RNP complex particles accumulated in nurse cells, and only a small fraction of these RNP complexes was transported into oocytes and properly localized to the posterior pole. Therefore, this motif may be required for the early transport of osk mRNA into oocytes. Also, as dimerization of osk mRNA does not seem to be a prerequisite for the assembly of RNP complexes, a dimerization-independent mechanism may also serve to localize osk mRNA to the posterior pole.

Association of the yeast RNA-binding protein She2p with the tubular endoplasmic reticulum depends on membrane curvature

Localization of mRNAs contributes to the generation and maintenance of cellular asymmetry in a wide range of organisms. In Saccharomyces cerevisiae, the so-called locasome complex with its core components Myo4p, She2p, and She3p localizes more than 30 mRNAs to the yeast bud tip. A significant fraction of these mRNAs encodes membrane or secreted proteins. Their localization requires, besides the locasome, a functional segregation apparatus of the cortical endoplasmic reticulum (ER), including the machinery that is involved in the movement of ER tubules into the bud. Colocalization of RNA-containing particles with these tubules suggests a coordinated transport of localized mRNAs and the cortical ER to the bud. Association of localized mRNAs to the ER requires the presence of the locasome component She2p. Here we report that She2p is not only an RNA-binding protein but can specifically bind to ER-derived membranes in a membrane curvature-dependent manner in vitro. Although it does not contain any known curvature recognizing motifs, the protein shows a binding preference for liposomes with a diameter resembling that of yeast ER tubules. In addition, membrane binding depends on tetramerization of She2p. In an in vivo membrane-tethering assay, She2p can target a viral peptide GFP fusion protein to the cortical ER, indicating that a fraction of She2p associates with the ER in vivo. Combining RNA- and membrane-binding features makes She2p an ideal coordinator of ER tubule and mRNA cotransport.

Immediate translation of Formin DIAPH1 mRNA after its exiting the nucleus is required for its perinuclear localization in fibroblasts

DIAPH1 is a formin protein which promotes actin polymerization, stabilizes microtubules and consequently is involved in cytoskeleton dynamics, cell migration and differentiation. In contrast to the relatively well-understood signaling cascades that regulate DIAPH1 activity, its spatial regulation of biogenesis is not understood. A recent report showed that synthesis of DIAPH1 is confined in the perinuclear ER compartment through translation-dependent mRNA targeting. However, the underlying mechanism of DIAPH1 local synthesis is yet to be elucidated. Here, we provide evidence to demonstrate that the 5'-cap-mediated immediate translation of DIAPH1 mRNA upon exiting nucleus is required for localizing the mRNA in the perinuclear ER compartment. This is supported by data: 1) Delayed translation of DIAPH1 mRNA resulted in loss of perinuclear localization of the mRNA; 2) Once delocalized, DIAPH1 mRNA could not be retargeted to the perinuclear region; and 3) The translation of DIAPH1 mRNA is 5'-cap dependent. These results provide new insights into the novel mechanism of DIAPH1 local synthesis. In addition, these findings have led to the development of new approaches for manipulating DIAPH1 mRNA localization and local protein synthesis in cells for functional studies. Furthermore, a correlation of DIAPH1 mRNA and DIAPH1 protein localization has been demonstrated using a new method to quantify the intracellular distribution of protein.

Protein targeting to subcellular organelles via MRNA localization

Cells have complex membranous organelles for the compartmentalization and the regulation of most intracellular processes. Organelle biogenesis and maintenance requires newly synthesized proteins, each of which needs to go from the ribosome translating its mRNA to the correct membrane for insertion or transclocation to an a organellar subcompartment. Decades of research have revealed how proteins are targeted to the correct organelle and translocated across one or more organelle membranes ro the compartment where they function. The paradigm examples involve interactions between a peptide sequence in the protein, localization factors, and various membrane embedded translocation machineries. Membrane translocation is either cotranslational or posttranslational depending on the protein and target organelle. Meanwhile research in embryos, neurons and yeast revealed an alternative targeting mechanism in which the mRNA is localized and only then translated to synthesize the protein in the correct location. In these cases, the targeting information is coded by the cis-acting sequences in the mRNA ("Zipcodes") that interact with localization factors and, in many cases, are transported by the molecular motors on the cytoskeletal filaments. Recently, evidence has been found for this "mRNA based" mechanism in organelle protein targeting to endoplasmic reticulum, mitochondria, and the photosynthetic membranes within chloroplasts. Here we review known and potential roles of mRNA localization in protein targeting to and within organelles. This article is part of a Special Issue entitled: Protein Import and Quality Control in Mitochondria and Plastids.

Molecular insights into intracellular RNA localization

Localization of mRNAs to specific destinations within a cell or an embryo is important for local control of protein synthesis. mRNA localization is well known to function in very large and polarized cells such as neurons, and to facilitate embryonic patterning during early development. However, recent genome-wide studies have revealed that mRNA localization is more widely utilized than previously thought to control gene expression. Not only can transcripts be localized asymmetrically within the cytoplasm, they are often also localized to symmetrically distributed organelles. Recent genetic, cytological, and biochemical studies have begun to provide molecular insight into how cells select RNAs for transport, move them to specific destinations, and control their translation. This chapter will summarize recent insights into the mechanisms and function of RNA localization with a specific emphasis on molecular insights into each step in the mRNA localization process.

Localization of a subset of yeast mRNAs depends on inheritance of endoplasmic reticulum

Localization of messenger RNA (mRNAs) contributes to generation and maintenance of cellular asymmetry, embryonic development and neuronal function. The She1-3 protein machinery in Saccharomyces cerevisiae localizes >30 mRNAs to the bud tip, including 13 mRNAs encoding membrane or secreted proteins. Ribonucleoprotein (RNP) particles can co-localize with tubular endoplasmic reticulum (ER) structures that form the initial elements for segregation of cortical ER (cER), suggesting a coordination of mRNA localization and cER distribution. By investigating localization of MS2-tagged mRNAs in yeast defective at various stages of cER segregation, we demonstrate that proper cER segregation is required for localization of only a subset of mRNAs. These mRNAs include WSC2, IST2, EAR1 and SRL1 that encode membrane or ER associated proteins and are expressed during S and G2 phases of the cell cycle when tubular ER movement into the bud occurs. Translation of WSC2 is not required for localization, ruling out co-translational targeting of this mRNA. Localization of ASH1 mRNA is independent of cER segregation, which is consistent with the expression pattern of ASH1 at late mitosis. Our findings indicate the presence of two different pathways to localize mRNAs to the yeast bud.

Identification of 3'UTR sequence elements and a teloplasm localization motif sufficient for the localization of Hro-twist mRNA to the zygotic animal and vegetal poles

The early localization of mRNA transcripts is critical in sorting cell fate determinants in the developing embryo. In the glossiphoniid leech, Helobdella robusta, maternal mRNAs, such as Hro-twist, localize to the zygotic teloplasm. Ten seven nucleotide repeat elements (AAUAAUA) called ARE2 and a predicted secondary structural motif, called teloplasm localization motif (TLM), are present in the 3'UTR of Hro-twist mRNA. We used site-directed mutagenesis, deletions, and microinjection of labeled, exogenous transcripts to determine if ARE2 elements, and the TLM, play a role in Hro-twist mRNA localization. Deleting the poly-A tail and the cytoplasmic polyadenylation element (CPE) had no effect on Hro-twist mRNA localization. Site-directed mutagenesis of nucleotides that altered ARE2 element sequences or the TLM suggest that the ARE2 elements and the TLM are important for Hro-twist mRNA localization to the teloplasm of pre-cleavage zygotes. Hro-Twist protein expression data suggest that the localization of Hro-twist transcripts in zygotes and stage two embryos is not involved in ensuring mesoderm specification, as Hro-Twist protein is expressed uniformly in most cells before gastrulation. Our data may support a shared molecular mechanism for leech transcripts that localize to the teloplasm.

MicroRNAs and their diverse functions in plants

microRNAs (miRNAs) are an extensive class of newly identified small RNAs, which regulate gene expression at the post-transcriptional level by mRNA cleavage or translation inhibition. Currently, there are 3,070 miRNAs deposited in the public available miRNA database; these miRNAs were obtained from 43 plant species using both computational (comparative genomics) and experimental (direct cloning and deep sequencing) approaches. Like other signaling molecules, plant miRNAs can also be moved from one tissue to another through the vascular system. These mobile miRNAs may play an important role in plant nutrient homeostasis and response to environmental biotic and abiotic stresses. In addition, miRNAs also control a wide range of biological and metabolic processes, including developmental timing, tissue-specific development, and stem cell maintenance and differentiation. Currently, a majority of plant miRNA-related researches are purely descriptive, and provide no further detailed mechanistic insight into miRNA-mediated gene regulation and other functions. To better understand the function and regulatory mechanisms of plant miRNAs, more strategies need to be employed to investigate the functions of miRNAs and their associated signaling pathways and gene networks. Elucidating the evolutionary mechanism of miRNAs is also important. It is possible to develop a novel miRNA-based biotechnology for improving plant yield, quality and tolerance to environmental biotic and abiotic stresses besides focusing on basic genetic studies.

Assembly of mRNA-protein complexes for directional mRNA transport in eukaryotes--an overview

At all steps from transcription to translation, RNA-binding proteins play important roles in determining mRNA function. Initially it was believed that for the vast majority of transcripts the role of RNA-binding proteins is limited to general functions such as splicing and translation. However, work from recent years showed that members of this class of proteins also recognize several mRNAs via cis-acting elements for their incorporation into large motor-containing particles. These particles are transported to distant subcellular sites, where they become subsequently translated. This process, called mRNA localization, occurs along microtubules or actin filaments, and involves kinesins, dyneins, as well as myosins. Although mRNA localization has been detected in a large number of organisms from fungi to humans, the underlying molecular machineries are not well understood. In this review we will outline general principles of mRNA localization and highlight three examples, for which a comparably large body of information is available. The first example is She2p/She3p-dependent localization of ASH1 mRNA in budding yeast. It is particularly well suited to highlight the interdependence between different steps of mRNA localization. The second example is Staufen-dependent localization of oskar mRNA in the Drosophila embryo, for which the importance of nuclear events for cytoplasmic localization and translational control has been clearly demonstrated. The third example summarizes Egalitarian/Bicaudal D-dependent mRNA transport events in the oocyte and embryo of Drosophila. We will highlight general themes and differences, point to similarities in other model systems, and raise open questions that might be answered in the coming years.

Conservation of the RNA Transport Machineries and Their Coupling to Translation Control across Eukaryotes

Restriction of proteins to discrete subcellular regions is a common mechanism to establish cellular asymmetries and depends on a coordinated program of mRNA localization and translation control. Many processes from the budding of a yeast to the establishment of metazoan embryonic axes and the migration of human neurons, depend on this type of cell polarization. How factors controlling transport and translation assemble to regulate at the same time the movement and translation of transported mRNAs, and whether these mechanisms are conserved across kingdoms is not yet entirely understood. In this review we will focus on some of the best characterized examples of mRNA transport machineries, the "yeast locasome" as an example of RNA transport and translation control in unicellular eukaryotes, and on the Drosophila Bic-D/Egl/Dyn RNA localization machinery as an example of RNA transport in higher eukaryotes. This focus is motivated by the relatively advanced knowledge about the proteins that connect the localizing mRNAs to the transport motors and the many well studied proteins involved in translational control of specific transcripts that are moved by these machineries. We will also discuss whether the core of these RNA transport machineries and factors regulating mRNA localization and translation are conserved across eukaryotes.

DivIVA-mediated polar localization of ComN, a posttranscriptional regulator of Bacillus subtilis

ComN (YrzD) is a small, 98-amino-acid protein recently shown to be involved in the posttranscriptional control of the late competence comE operon in Bacillus subtilis. We show here that ComN localizes to the division site and cell poles in a DivIVA-dependent fashion. Yeast two-hybrid and glutathione S-transferase pulldown experiments showed that ComN interacts directly with DivIVA. ComN is not essential for the polar assembly of the core competence DNA uptake machinery. Nevertheless, polar localization of ComN should play some role in competence acquisition because delocalization of ComN leads to a small reduction in competence efficiency. We found that ComN promotes the accumulation of its target comE mRNA to septal and polar sites. Thus, we speculate that localized translation of ComE proteins may be required for efficient competence development. Our results underscore the versatility of DivIVA as a promoter of the differentiation of bacterial poles and demonstrate that the repertoire of polarly localized molecules in B. subtilis is broad, including a regulator of gene expression and its target mRNA. Moreover, our findings suggest that mRNA localization may play a role in the subcellular organization of bacteria.

A novel mRNA binding protein complex promotes localized plasminogen activator inhibitor-1 accumulation at the myoendothelial junction

OBJECTIVE

Plasminogen activator inhibitor-1 (PAI-1) has previously been shown to be key to the formation of myoendothelial junctions (MEJs) in normal and pathological states (eg, obesity). We therefore sought to identify the mechanism whereby PAI-1 could be selectively accumulated at the MEJ.

METHODS AND RESULTS

We identified PAI-1 protein enrichment at the MEJ in obese mice and in response to tumor necrosis factor (TNF-α) with a vascular cell coculture. However, PAI-1 mRNA was also found at the MEJ and transfection with a PAI-1-GFP with TNF-α did not demonstrate trafficking of the protein to the MEJ. We therefore hypothesized the PAI-1 mRNA was being locally translated and identified serpine binding protein-1, which stabilizes PAI-1 mRNA, as being enriched in obese mice and after treatment with TNF-α, whereas Staufen, which degrades PAI-1 mRNA, was absent in obese mice and after TNF-α application. We identified nicotinamide phosphoribosyl transferase as a serpine binding protein-1 binding partner with a functional τ-like microtubule binding domain. Application of peptides against the microtubule binding domain significantly decreased the number of MEJs and the amount of PAI-1 at the MEJ.

CONCLUSIONS

We conclude that PAI-1 can be locally translated at the MEJ as a result of a unique mRNA binding protein complex.

Control of cytoplasmic mRNA localization

mRNA localization is a mechanism used by various organisms to control the spatial and temporal production of proteins. This process is a highly regulated event that requires multiple cis- and trans-acting elements that mediate the accurate localization of target mRNAs. The intrinsic nature of localization elements, together with their interaction with different RNA-binding proteins, establishes control mechanisms that can oversee the transcript from its birth in the nucleus to its specific final destination. In this review, we aim to summarize the different mechanisms of mRNA localization, with a particular focus on the various control mechanisms that affect the localization of mRNAs in the cytoplasm.

Polarizing animal cells via mRNA localization in oogenesis and early development

The localization of mRNAs in developing animal cells is essential for establishing cellular polarity and setting up the body plan for subsequent development. Cellular and molecular mechanisms by which maternal mRNAs are localized during oogenesis have been extensively studied in Drosophila and Xenopus. In contrast, evidence for mechanisms used in the localization of mRNAs encoded by developmentally important genes has also been accumulating in several other organisms. This offers the opportunity to unravel the fundamental mechanisms of mRNA localization shared among many species, as well as unique mechanisms specifically acquired or retained by animals based on their developmental needs. In addition to maternal mRNAs, the localization of zygotically expressed mRNAs in the cells of cleaving embryos is also important for early development. In this review, mRNA localization dynamics in the oocytes/eggs of Drosophila and Xenopus are first summarized, and evidence for localized mRNAs in the oocytes/eggs and cleaving embryos of other organisms is then presented.

Fungal development of the plant pathogen Ustilago maydis

The maize pathogen Ustilago maydis has to undergo various morphological transitions for the completion of its sexual life cycle. For example, haploid cells respond to pheromone by forming conjugation tubes that fuse at their tips. The resulting dikaryon grows filamentously, expanding rapidly at the apex and inserting retraction septa at the basal pole. In this review, we present progress on the underlying mechanisms regulating such defined developmental programmes. The key findings of the postgenomic era are as follows: (1) endosomes function not only during receptor recycling, but also as multifunctional transport platforms; (2) a new transcriptional master regulator for pathogenicity is part of an intricate transcriptional network; (3) determinants for uniparental mitochondrial inheritance are encoded at the a2 mating-type locus; (4) microtubule-dependent mRNA transport is important in determining the axis of polarity; and (5) a battery of fungal effectors encoded in gene clusters is crucial for plant infection. Importantly, most processes are tightly controlled at the transcriptional, post-transcriptional and post-translational levels, resulting in a complex regulatory network. This intricate system is crucial for the timing of the correct order of developmental phases. Thus, new insights from all layers of regulation have substantially advanced our understanding of fungal development.

The RNA-binding protein Rrm4 is essential for efficient secretion of endochitinase Cts1

Long-distance transport of mRNAs is crucial in determining spatio-temporal gene expression in eukaryotes. The RNA-binding protein Rrm4 constitutes a key component of microtubule-dependent mRNA transport in filaments of Ustilago maydis. Although a number of potential target mRNAs could be identified, cellular processes that depend on Rrm4-mediated transport remain largely unknown. Here, we used differential proteomics to show that ribosomal, mitochondrial, and cell wall-remodeling proteins, including the bacterial-type endochitinase Cts1, are differentially regulated in rrm4Δ filaments. In vivo UV crosslinking and immunoprecipitation and fluorescence in situ hybridization revealed that cts1 mRNA represents a direct target of Rrm4. Filaments of cts1Δ mutants aggregate in liquid culture suggesting an altered cell surface. In wild type cells Cts1 localizes predominantly at the growth cone, whereas it accumulates at both poles in rrm4Δ filaments. The endochitinase is secreted and associates most likely with the cell wall of filaments. Secretion is drastically impaired in filaments lacking Rrm4 or conventional kinesin Kin1 as well as in filaments with disrupted microtubules. Thus, Rrm4-mediated mRNA transport appears to be essential for efficient export of active Cts1, uncovering a novel molecular link between mRNA transport and the mechanism of secretion.

Keeping mRNPs in check during assembly and nuclear export

The cell nucleus is an intricate organelle that coordinates multiple activities that are associated with DNA replication and gene expression. In all eukaryotes, it stores the genetic information and the machineries that control the production of mature and export-competent messenger ribonucleoproteins (mRNPs), a multistep process that is regulated in a spatial and temporal manner. Recent studies suggest that post-translational modifications play a part in coordinating the co-transcriptional assembly, remodelling and export of mRNP complexes through nuclear pores, adding a new level of regulation to the process of gene expression.

Pabp binds to the osk 3'UTR and specifically contributes to osk mRNA stability and oocyte accumulation

RNA localization is tightly coordinated with RNA stability and translation control. Bicaudal-D (Bic-D), Egalitarian (Egl), microtubules and their motors are part of a Drosophila transport machinery that localizes mRNAs to specific cellular regions during oogenesis and embryogenesis. We identified the Poly(A)-binding protein (Pabp) as a protein that forms an RNA-dependent complex with Bic-D in embryos and ovaries. pabp also interacts genetically with Bic-D and, similar to Bic-D, pabp is essential in the germline for oocyte growth and accumulation of osk mRNA in the oocyte. In the absence of pabp, reduced stability of osk mRNA and possibly also defects in osk mRNA transport prevent normal oocyte localization of osk mRNA. pabp also interacts genetically with osk and lack of one copy of pabp(+) causes osk to become haploinsufficient. Moreover, pointing to a poly(A)-independent role, Pabp binds to A-rich sequences (ARS) in the osk 3'UTR and these turned out to be required in vivo for osk function during early oogenesis. This effect of pabp on osk mRNA is specific for this RNA and other tested mRNAs localizing to the oocyte are less and more indirectly affected by the lack of pabp.

In vivo visualization of RNA using the U1A-based tagged RNA system

mRNA transport is a widely used method to achieve the asymmetric distribution of proteins within a cell or organism. In order to understand how RNA is transported, it is essential to utilize a system that can readily detect RNA movement in live cells. The tagged RNA system has recently emerged as a feasible non-invasive solution for such purpose. In this chapter, we describe in detail the U1A-based tagged RNA system. This system coexpresses U1Ap-GFP with the RNA of interest tagged with U1A aptamers, and has been proven to effectively track RNA in vivo. In addition, we provide further applications of the system for ribonucleoprotein complex purification by TAP-tagging the U1Ap-GFP construct.

An essential nuclear protein in trypanosomes is a component of mRNA transcription/export pathway

In eukaryotic cells, different RNA species are exported from the nucleus via specialized pathways. The mRNA export machinery is highly integrated with mRNA processing, and includes a different set of nuclear transport adaptors as well as other mRNA binding proteins, RNA helicases, and NPC-associated proteins. The protozoan parasite Trypanosoma cruzi is the causative agent of Chagas disease, a widespread and neglected human disease which is endemic to Latin America. Gene expression in Trypanosoma has unique characteristics, such as constitutive polycistronic transcription of protein-encoding genes and mRNA processing by trans-splicing. In general, post-transcriptional events are the major points for regulation of gene expression in these parasites. However, the export pathway of mRNA from the nucleus is poorly understood. The present study investigated the function of TcSub2, which is a highly conserved protein ortholog to Sub2/ UAP56, a component of the Transcription/Export (TREX) multiprotein complex connecting transcription with mRNA export in yeast/human. Similar to its orthologs, TcSub2 is a nuclear protein, localized in dispersed foci all over the nuclei —except the fibrillar center of nucleolus— and at the interface between dense and non-dense chromatin areas, proposing the association of TcSub2 with transcription/processing sites. These findings were analyzed further by BrUTP incorporation assays and confirmed that TcSub2 is physically associated with active RNA polymerase II (RNA pol II), but not RNA polymerase I (RNA pol I) or Spliced Leader (SL) transcription, demonstrating participation particularly in nuclear mRNA metabolism in T. cruzi. The double knockout of the TcSub2 gene is lethal in T. cruzi, suggesting it has an essential function. Alternatively, RNA interference assays were performed in Trypanosoma brucei. It allowed demonstrating that besides being an essential protein, its knockdown causes mRNA accumulation in the nucleus and decrease of translation levels, reinforcing that Trypanosoma-Sub2 (Tryp-Sub2) is a component of mRNA transcription/export pathway in trypanosomes.

Nuage morphogenesis becomes more complex: two translocation pathways and two forms of nuage coexist in Drosophila germline syncytia

We have developed a simple and reliable method of preserving antigen immunoreactivity with concomitant excellent retention of the cell ultrastructure. Using this method, we have been able to follow the origin and developmental stages of nuage accumulations within the nurse cell/oocyte syncytium in the ovary of the fruit fly, Drosophila melanogaster, at the ultrastructural level. We have found two morphologically and biochemically distinct forms of nuage material in the nurse cell cytoplasm: translocating accumulations of nuage containing the Vasa protein, termed sponge bodies and stationary polymorphic accumulations of nuage enriched in Argonaute and Survival of motor neuron proteins. Immunogold labeling combined with confocal fluorescent and ultrastructural analyses have revealed that the Vasa-containing nuage accumulations remain closely associated with the cisternae of the endoplasmic reticulum throughout their lifetimes. The migration mechanism of the Vasa-positive nuage appears distinct from the microtubule-dependent translocation of oskar ribonucleoprotein complexes. We postulate that these two distinct nuage translocation pathways converge in the formation of the polar granules within the polar/germ plasm of the oocyte posterior pole. We also provide morphological and immunocytochemical evidence that these polymorphic nuage accumulations correspond to the recently described cytoplasmic domains termed U body-P body complexes.

Asymmetric cell division in land plants and algae: the driving force for differentiation

Asymmetric cell division generates two cells with different fates and has an important role in plant development. It produces distinct cell types and new organs, and maintains stem cell niches. To handle the constraints of having immobile cells, plants possess numerous unique features to obtain asymmetry, such as specific regulators of intrinsic polarity. Although several components have not yet been identified, new findings, together with knowledge from different developmental systems, now allow us to take an important step towards a mechanistic overview of asymmetric cell division in plants and algae. Strikingly, several key regulators are used for different developmental processes, and common mechanisms can be recognized.

An RNA-zipcode-independent mechanism that localizes Dia1 mRNA to the perinuclear ER through interactions between Dia1 nascent peptide and Rho-GTP

Signal-peptide-mediated ER localization of mRNAs encoding for membrane and secreted proteins, and RNA-zipcode-mediated intracellular targeting of mRNAs encoding for cytosolic proteins are two well-known mechanisms for mRNA localization. Here, we report a previously unidentified mechanism by which mRNA encoding for Dia1, a cytosolic protein without the signal peptide, is localized to the perinuclear ER in an RNA-zipcode-independent manner in fibroblasts. Dia1 mRNA localization is also independent of the actin and microtubule cytoskeleton but requires translation and the association of Dia1 nascent peptide with the ribosome-mRNA complex. Sequence mapping suggests that interactions of the GTPase binding domain of Dia1 peptide with active Rho are important for Dia1 mRNA localization. This mechanism can override the β-actin RNA zipcode and redirect β-actin mRNA to the perinuclear region, providing a new way to manipulate intracellular mRNA localization.

Isolation of mRNAs encoding peroxisomal proteins from yeast using a combined cell fractionation and affinity purification procedure

Targeted mRNA localization to distinct subcellular sites occurs throughout the eukaryotes and presumably allows for the localized translation of proteins near their site of function. Specific mRNAs have been localized in cells using a variety of reliable methods, such as fluorescence in situ hybridization with labeled RNA probes, mRNA tagging using RNA aptamers and fluorescent proteins that recognize these aptamers, and quenched fluorescent RNA probes that become activated upon binding to mRNAs. However, fluorescence-based RNA localization studies can be strengthened when coupled with cell fractionation and membrane isolation techniques in order to identify mRNAs associated with specific organelles or other subcellular structures. Here we describe a novel method to isolate mRNAs associated with peroxisomes in the yeast, Saccharomyces cerevisiae. This method employs a combination of density gradient centrifugation and affinity purification to yield a highly enriched peroxisome fraction suitable for RNA isolation and reverse transcription-polymerase chain reaction detection of mRNAs bound to peroxisome membranes. The method is presented for the analysis of peroxisome-associated mRNAs; however it is applicable to studies on other subcellular compartments.

A nucleoporin, Nup60p, affects the nuclear and cytoplasmic localization of ASH1 mRNA in S. cerevisiae

The biogenesis of a localization-competent mRNP begins in the nucleus. It is thought that the coordinated action of nuclear and cytoplasmic components of the localization machinery is required for the efficient export and subsequent subcellular localization of these mRNAs in the cytoplasm. Using quantitative poly(A)(+) and transcript-specific fluorescent in situ hybridization, we analyzed different nonessential nucleoporins and nuclear pore-associated proteins for their potential role in mRNA export and localization. We found that Nup60p, a nuclear pore protein located on the nucleoplasmic side of the nuclear pore complex, was required for the mRNA localization pathway. In a Δnup60 background, localized mRNAs were preferentially retained within the nucleus compared to nonlocalized transcripts. However, the export block was only partial and some transcripts could still reach the cytoplasm. Importantly, downstream processes were also affected. Localization of ASH1 and IST2 mRNAs to the bud was impaired in the Δnup60 background, suggesting that the assembly of a localization competent mRNP ("locasome") was inhibited when NUP60 was deleted. These results demonstrate transcript specificity of a nuclear mRNA retention defect and identify a specific nucleoporin as a functional component of the localization pathway in budding yeast.

A novel mRNA affinity purification technique for the identification of interacting proteins and transcripts in ribonucleoprotein complexes

Intracellular mRNA targeting and localized translation are potential determinants for protein localization. To facilitate targeting, mRNAs possess specific cis-acting sequence motifs that are recognized by trans-acting RNA-binding proteins (RBPs). While many mRNAs are trafficked, our knowledge of the RBPs involved and presence of additional transcripts within these ribonucleoprotein (RNP) complexes is limited. To facilitate the identification of RBPs and transcripts that bind to specific mRNAs, we developed RNA-binding protein purification and identification (RaPID), a novel technique that allows for the affinity purification of MS2 aptamer-tagged mRNAs and subsequent detection of bound RBPs and transcripts using mass-spectometry and RT-PCR, respectively. RaPID effectively isolated specific mRNAs from both yeast and mammalian cells, and identified known mRNA-RBP interactions (e.g., ASH1-She2; β-Actin-IMP1). By isolating tagged OXA1 mRNA using RaPID, we could identify a yeast COPI subunit (i.e., Sec27) as a candidate interacting protein. This finding was strengthened by the observation that a portion of OXA1 mRNA was delocalized in a sec27-1 temperature-sensitive mutant at restrictive temperatures. Finally, RaPID could also be used to show biochemically the coexistence of different RNA species within the same RNP complex (e.g., coprecipitation of the yeast SRO7, WSC2, SEC3, and IST2 mRNAs with ASH1 mRNA) for the first time.

Yolk nucleus--the complex assemblage of cytoskeleton and ER is a site of lipid droplet formation in spider oocytes

Oocytes (future egg cells) of various animal groups often contain complex organelle assemblages (Balbiani bodies, yolk nuclei). The molecular composition and function of Balbiani bodies, such as those found in the oocytes of Xenopus laevis, have been recently recognized. In contrast, the functional significance of more complex and highly ordered yolk nuclei has not been elucidated to date. In this report we describe the structure, cytochemical content and evolution of the yolk nucleus in the oocytes of a common spider, Clubiona sp. We show that the yolk nucleus is a spherical, rather compact and persistent cytoplasmic accumulation of several different organelles. It consists predominantly of a highly elaborate cytoskeletal scaffold of condensed filamentous actin and a dense meshwork of intermediate-sized filaments. The yolk nucleus also comprises cisterns of endoplasmic reticulum, mitochondria, lipid droplets and other organelles. Nascent lipid droplets are regularly found in the cortical regions of the yolk nucleus in association with the endoplasmic reticulum. Single lipid droplets become surrounded by filamentous cages formed by intermediate filaments. Coexistence of the forming lipid droplets with the endoplasmic reticulum in the cortical zone of the yolk nucleus and their later investment by intermediate-sized filamentous cages suggest that the yolk nucleus is the birthplace of lipid droplets.

Cotranscriptional recruitment of She2p by RNA pol II elongation factor Spt4-Spt5/DSIF promotes mRNA localization to the yeast bud

Pre-mRNA processing is coupled with transcription. It is still unclear if the transcription machinery can also directly affect the cytoplasmic fate of a transcript, such as its intracellular localization. In yeast, the RNA-binding protein She2p binds several mRNAs and targets them for localization at the bud. Here we report that She2p is recruited cotranscriptionally to the nascent bud-localized ASH1, IST2, and EAR1 mRNA. She2p interacts in vivo with the elongating forms of RNA polymerase II (pol II) via the transcription elongation factor Spt4-Spt5. Mutations in either SPT4 or SPT5 reduce the cotranscriptional recruitment of She2p on the ASH1 gene, disrupt the proper localization of ASH1 mRNA at the bud tip, and affect Ash1p sorting to the daughter cell nucleus. We propose that She2p is recruited by the RNA pol II machinery prior to its transfer to nascent bud-localized mRNAs. Indeed, She2p is present with RNA pol II on genes coding for localized or nonlocalized transcripts, but is associated with nascent mRNA only on genes coding for bud-localized transcripts. Moreover, a She2p mutant defective in RNA binding still associates with RNA pol II transcribed genes. This study uncovers a novel mechanism for the cotranscriptional assembly of mRNP complexes primed for localization in the cytoplasm.

Microtubule-dependent mRNA transport in fungi

The localization and local translation of mRNAs constitute an important mechanism to promote the correct subcellular targeting of proteins. mRNA localization is mediated by the active transport of mRNPs, large assemblies consisting of mRNAs and associated factors such as RNA-binding proteins. Molecular motors move mRNPs along the actin or microtubule cytoskeleton for short-distance or long-distance trafficking, respectively. In filamentous fungi, microtubule-based long-distance transport of vesicles, which are involved in membrane and cell wall expansion, supports efficient hyphal growth. Recently, we discovered that the microtubule-mediated transport of mRNAs is essential for the fast polar growth of infectious filaments in the corn pathogen Ustilago maydis. Combining in vivo UV cross-linking and RNA live imaging revealed that the RNA-binding protein Rrm4, which constitutes an integral part of the mRNP transport machinery, mediates the transport of distinct mRNAs encoding polarity factors, protein synthesis factors, and mitochondrial proteins. Moreover, our results indicate that microtubule-dependent mRNA transport is evolutionarily conserved from fungi to higher eukaryotes. This raises the exciting possibility of U. maydis as a model system to uncover basic concepts of long-distance mRNA transport.

Multiple Myo4 motors enhance ASH1 mRNA transport in Saccharomyces cerevisiae

In Saccharomyces cerevisiae, ASH1 mRNA is transported to the bud tip by the class V myosin Myo4. In vivo, Myo4 moves RNA in a rapid and continuous fashion, but in vitro Myo4 is a nonprocessive, monomeric motor that forms a complex with She3. To understand how nonprocessive motors generate continuous transport, we used a novel purification method to show that Myo4, She3, and the RNA-binding protein She2 are the sole major components of an active ribonucleoprotein transport unit. We demonstrate that a single localization element contains multiple copies of Myo4 and a tetramer of She2, which suggests that She2 may recruit multiple motors to an RNA. Furthermore, we show that increasing the number of Myo4-She3 molecules bound to ASH1 RNA in the absence of She2 increases the efficiency of RNA transport to the bud. Our data suggest that multiple, nonprocessive Myo4 motors can generate continuous transport of mRNA to the bud tip.

Cell signalling by microRNA165/6 directs gene dose-dependent root cell fate

A key question in developmental biology is how cells exchange positional information for proper patterning during organ development. In plant roots the radial tissue organization is highly conserved with a central vascular cylinder in which two water conducting cell types, protoxylem and metaxylem, are patterned centripetally. We show that this patterning occurs through crosstalk between the vascular cylinder and the surrounding endodermis mediated by cell-to-cell movement of a transcription factor in one direction and microRNAs in the other. SHORT ROOT, produced in the vascular cylinder, moves into the endodermis to activate SCARECROW. Together these transcription factors activate MIR165a and MIR166b. Endodermally produced microRNA165/6 then acts to degrade its target mRNAs encoding class III homeodomain-leucine zipper transcription factors in the endodermis and stele periphery. The resulting differential distribution of target mRNA in the vascular cylinder determines xylem cell types in a dosage-dependent manner.

Cell signalling by microRNA165/6 directs gene dose-dependent root cell fate

A key question in developmental biology is how cells exchange positional information for proper patterning during organ development. In plant roots the radial tissue organization is highly conserved with a central vascular cylinder in which two water conducting cell types, protoxylem and metaxylem, are patterned centripetally. We show that this patterning occurs through crosstalk between the vascular cylinder and the surrounding endodermis mediated by cell-to-cell movement of a transcription factor in one direction and microRNAs in the other. SHORT ROOT, produced in the vascular cylinder, moves into the endodermis to activate SCARECROW. Together these transcription factors activate MIR165a and MIR166b. Endodermally produced microRNA165/6 then acts to degrade its target mRNAs encoding class III homeodomain-leucine zipper transcription factors in the endodermis and stele periphery. The resulting differential distribution of target mRNA in the vascular cylinder determines xylem cell types in a dosage-dependent manner.

Ca(2+) channels on the move

The versatility of Ca(2+) as an intracellular messenger derives largely from the spatial organization of cytosolic Ca(2+) signals, most of which are generated by regulated openings of Ca(2+)-permeable channels. Most Ca(2+) channels are expressed in the plasma membrane (PM). Others, including the almost ubiquitous inositol 1,4,5-trisphosphate receptors (IP(3)R) and their relatives, the ryanodine receptors (RyR), are predominantly expressed in membranes of the sarcoplasmic or endoplasmic reticulum (ER). Targeting of these channels to appropriate destinations underpins their ability to generate spatially organized Ca(2+) signals. All Ca(2+) channels begin life in the cytosol, and the vast majority are then functionally assembled in the ER, where they may either remain or be dispatched to other membranes. Here, by means of selective examples, we review two issues related to this trafficking of Ca(2+) channels via the ER. How do cells avoid wayward activity of Ca(2+) channels in transit as they pass from the ER via other membranes to their final destination? How and why do some cells express small numbers of the archetypal intracellular Ca(2+) channels, IP(3)R and RyR, in the PM?

Localization of mRNAs coding for peroxisomal proteins in the yeast, Saccharomyces cerevisiae

Targeted mRNA trafficking and local translation may play a significant role in controlling protein localization. Here we examined for the first time the localization of all ( approximately 50) mRNAs encoding peroxisomal proteins (mPPs) involved in peroxisome biogenesis and function. By using the bacteriophage MS2-CP RNA-binding protein (RBP) fused to multiple copies of GFP, we demonstrated that >40 endogenously expressed mPPs tagged with the MS2 aptamer form fluorescent RNA granules in vivo. The use of different RFP-tagged organellar markers revealed 3 basic patterns of mPP granule localization: to peroxisomes, to the endoplasmic reticulum (ER), and nonperoxisomal. Twelve mPPs (i.e., PEX1, PEX5, PEX8, PEX11-15, DCI1, NPY1, PCS60, and POX1) had a high percentage (52%-80%) of mRNA colocalization with peroxisomes. Thirteen mPPs (i.e., AAT2, PEX6, MDH3, PEX28, etc.) showed a low percentage (30%-42%) of colocalization, and 1 mPP (PEX3) preferentially localized to the ER. The mPPs of the nonperoxisomal pattern (i.e., GPD1, PCD1, PEX7) showed <<30% colocalization. mPP association with the peroxisome or ER was verified using cell fractionation and RT-PCR analysis. A model mPP, PEX14 mRNA, was found to be in close association with peroxisomes throughout the cell cycle, with its localization depending in part on the 3'-UTR, initiation of translation, and the Puf5 RBP. The different patterns of mPP localization observed suggest that multiple mechanisms involved in mRNA localization and translation may play roles in the importation of protein into peroxisomes.