The Drosophila hairy RNA localization signal modulates the kinetics of cytoplasmic mRNA transport

The dynamic duo of microtubule polymerase Mini spindles/XMAP215 and cytoplasmic dynein is essential for maintaining Drosophila oocyte fate

In many species, only one oocyte is specified among a group of interconnected germline sister cells. In Drosophila melanogaster, 16 interconnected cells form a germline cyst, where one cell differentiates into an oocyte, while the rest become nurse cells that supply the oocyte with mRNAs, proteins, and organelles through intercellular cytoplasmic bridges named ring canals via microtubule-based transport. In this study, we find that a microtubule polymerase Mini spindles (Msps), the Drosophila homolog of XMAP215, is essential for maintenance of the oocyte specification. mRNA encoding Msps is transported and concentrated in the oocyte by dynein-dependent transport along microtubules. Translated Msps stimulates microtubule polymerization in the oocyte, causing more microtubule plus ends to grow from the oocyte through the ring canals into nurse cells, further enhancing nurse cell-to-oocyte transport by dynein. Knockdown of msps blocks the oocyte growth and causes gradual loss of oocyte determinants. Thus, the Msps-dynein duo creates a positive feedback loop, ensuring oocyte fate maintenance by promoting high microtubule polymerization activity in the oocyte, and enhancing dynein-dependent nurse cell-to-oocyte transport.

Drosophila oocyte specification is maintained by the dynamic duo of microtubule polymerase Mini spindles/XMAP215 and dynein

In many species, only one oocyte is specified among a group of interconnected germline sister cells. In Drosophila melanogaster , 16-cell interconnected cells form a germline cyst, where one cell differentiates into an oocyte, while the rest become nurse cells that supply the oocyte with mRNAs, proteins, and organelles through intercellular cytoplasmic bridges named ring canals via microtubule-based transport. In this study, we find that a microtubule polymerase Mini spindles (Msps), the Drosophila homolog of XMAP215, is essential for the oocyte fate determination. mRNA encoding Msps is concentrated in the oocyte by dynein-dependent transport along microtubules. Translated Msps stimulates microtubule polymerization in the oocyte, causing more microtubule plus ends to grow from the oocyte through the ring canals into nurse cells, further enhancing nurse cell-to-oocyte transport by dynein. Knockdown of msps blocks the oocyte growth and causes gradual loss of oocyte determinants. Thus, the Msps-dynein duo creates a positive feedback loop, enhancing dynein-dependent nurse cell-to-oocyte transport and transforming a small stochastic difference in microtubule polarity among sister cells into a clear oocyte fate determination.

Significance statement

Oocyte determination in Drosophila melanogaster provides a valuable model for studying cell fate specification. We describe the crucial role of the duo of microtubule polymerase Mini spindles (Msps) and cytoplasmic dynein in this process. We show that Msps is essential for oocyte fate determination. Msps concentration in the oocyte is achieved through dynein-dependent transport of msps mRNA along microtubules. Translated Msps stimulates microtubule polymerization in the oocyte, further enhancing nurse cell-to-oocyte transport by dynein. This creates a positive feedback loop that transforms a small stochastic difference in microtubule polarity among sister cells into a clear oocyte fate determination. Our findings provide important insights into the mechanisms of oocyte specification and have implications for understanding the development of multicellular organisms.

Translational co-regulation of a ligand and inhibitor by a conserved RNA element

In many organisms, transcriptional and post-transcriptional regulation of components of pathways or processes has been reported. However, to date, there are few reports of translational co-regulation of multiple components of a developmental signaling pathway. Here, we show that an RNA element which we previously identified as a dorsal localization element (DLE) in the 3'UTR of zebrafish nodal-related1/squint (ndr1/sqt) ligand mRNA, is shared by the related ligand nodal-related2/cyclops (ndr2/cyc) and the nodal inhibitors, lefty1 (lft1) and lefty2 mRNAs. We investigated the activity of the DLEs through functional assays in live zebrafish embryos. The lft1 DLE localizes fluorescently labeled RNA similarly to the ndr1/sqt DLE. Similar to the ndr1/sqt 3'UTR, the lft1 and lft2 3'UTRs are bound by the RNA-binding protein (RBP) and translational repressor, Y-box binding protein 1 (Ybx1), whereas deletions in the DLE abolish binding to Ybx1. Analysis of zebrafish ybx1 mutants shows that Ybx1 represses lefty1 translation in embryos. CRISPR/Cas9-mediated inactivation of human YBX1 also results in human NODAL translational de-repression, suggesting broader conservation of the DLE RNA element/Ybx1 RBP module in regulation of Nodal signaling. Our findings demonstrate translational co-regulation of components of a signaling pathway by an RNA element conserved in both sequence and structure and an RBP, revealing a 'translational regulon'.

Biological functions, regulatory mechanisms, and disease relevance of RNA localization pathways

The asymmetric subcellular distribution of RNA molecules from their sites of transcription to specific compartments of the cell is an important aspect of post-transcriptional gene regulation. This involves the interplay of intrinsic cis-regulatory elements within the RNA molecules with trans-acting RNA-binding proteins and associated factors. Together, these interactions dictate the intracellular localization route of RNAs, whose downstream impacts have wide-ranging implications in cellular physiology. In this review, we examine the mechanisms underlying RNA localization and discuss their biological significance. We also review the growing body of evidence pointing to aberrant RNA localization pathways in the development and progression of diseases.

RNA-directed activation of cytoplasmic dynein-1 in reconstituted transport RNPs

Polarised mRNA transport is a prevalent mechanism for spatial control of protein synthesis. However, the composition of transported ribonucleoprotein particles (RNPs) and the regulation of their movement are poorly understood. We have reconstituted microtubule minus end-directed transport of mRNAs using purified components. A Bicaudal-D (BicD) adaptor protein and the RNA-binding protein Egalitarian (Egl) are sufficient for long-distance mRNA transport by the dynein motor and its accessory complex dynactin, thus defining a minimal transport-competent RNP. Unexpectedly, the RNA is required for robust activation of dynein motility. We show that a cis-acting RNA localisation signal promotes the interaction of Egl with BicD, which licenses the latter protein to recruit dynein and dynactin. Our data support a model for BicD activation based on RNA-induced occupancy of two Egl-binding sites on the BicD dimer. Scaffolding of adaptor protein assemblies by cargoes is an attractive mechanism for regulating intracellular transport.

In our cells, tiny molecular motors transport the components necessary for life’s biological processes from one location to another. They do so by loading their cargo, and burning up chemical fuel to carry it along pathways made of filaments. For example, one such motor, called dynein, can move molecules of messenger RNA (mRNA) to specific locations within the cell. There, the mRNA will be used as a template to create proteins, which will operate at exactly the right place.

Transporting mRNA in this way is critical in processes such as embryonic development and the formation of memories; yet, this mechanism is still poorly understood. Previous work suggested that the mRNA is simply a passenger of the dynein motor, but McClintock et al. asked if this is really the case. Instead, could mRNA regulate its own sorting by controlling the activity of dynein?

Studying mRNA trafficking within the complex molecular environment of a cell is challenging, so mRNA transporting machinery was recreated in the laboratory. Only the proteins necessary to build a working system were included in the experiments. In addition to the filaments, the components included dynein and a complex of proteins known as dynactin, which allows the motor to move together with a protein called BICD2. A protein named Egalitarian was used to link the mRNA to BICD2.

By filming fluorescently labelled proteins and mRNAs, McClintock et al. discovered that mRNA strongly promotes the movement of the dynein motor. A structured section in the mRNA acts as a docking area for two copies of Egalitarian. This activates BICD2, which then binds to dynein and dynactin, thereby completing the transport machinery. According to these results, the mRNA directs the assembly of the system that will carry it within the cell.

Viruses such as HIV and herpesvirus hijack dynein motors to have their genetic information moved around a cell in order to propagate infection. Understanding precisely how mRNA is transported may help to develop new strategies to fight these viruses.

A heterogeneous tRNA granule structure exhibiting rapid, bi-directional neuritic transport

mRNA translation is regulated by diverse mechanisms that converge at the initiation and elongation steps to determine the rate, profile, and localization of proteins synthesized. A consistently relevant feature of these mechanisms is the spatial re-distribution of translation machinery, a process of particular importance in neural cells. This process has, however, been largely overlooked with respect to its potential role in regulating the local concentration of cytoplasmic tRNAs, even as a multitude of data suggest that spatial regulation of the tRNA pool may help explain the remarkably high rates of peptide elongation. Here, we report that Cy3/Cy5-labeled bulk tRNAs transfected into neural cells distribute into granule-like structures - "tRNA granules" - that exhibit dynamic mixing of tRNAs between granules and rapid, bi-directional vectorial movement within neurites. Imaging of endogenous tRNA_gly and tRNA_lys by fluorescent in situ hybridization revealed a similar granular distribution of tRNAs in somata and neurites; this distribution was highly overlapping with granules imaged by introduction of exogenous Cy5-tRNA_thr and Cy3-tRNA_val. A subset of tRNA granules located in the cell body, neurite branch points and growth cones displayed fluorescence resonance energy transfer (FRET) between Cy3 and Cy5-labeled tRNAs indicative of translation, and co-localization with elongation machinery. A population of smaller, rapidly trafficked granules in neurites lacked FRET and showed poor colocalization with translation initiation and elongation factors, suggesting that they are a translationally inactive tRNA transport particle. Our data suggest that tRNAs are packaged into granules that are rapidly transported to loci where translation is needed, where they may greatly increase the local concentration of tRNAs in support of efficient elongation. The potential implications of this newly described structure for channeling of elongation, local translation, and diseases associated with altered tRNA levels or function are discussed.

Multiple cis-acting signals, some weak by necessity, collectively direct robust transport of oskar mRNA to the oocyte

Localization of mRNAs can involve multiple steps, each with its own cis-acting localization signals and transport factors. How is the transition between different steps orchestrated? We show that the initial step in localization of Drosophila oskar mRNA - transport from nurse cells to the oocyte - relies on multiple cis-acting signals. Some of these are binding sites for the translational control factor Bruno, suggesting that Bruno plays an additional role in mRNA transport. Although transport of oskar mRNA is essential and robust, the localization activity of individual transport signals is weak. Notably, increasing the strength of individual transport signals, or adding a strong transport signal, disrupts the later stages of oskar mRNA localization. We propose that the oskar transport signals are weak by necessity; their weakness facilitates transfer of the oskar mRNA from the oocyte transport machinery to the machinery for posterior localization.

RNA localization: Making its way to the center stage

Cells are highly organized entities that rely on intricate addressing mechanisms to sort their constituent molecules to precise subcellular locations. These processes are crucial for cells to maintain their proper organization and carry out specialized functions in the body, consequently genetic perturbations that clog up these addressing systems can contribute to disease aetiology. The trafficking of RNA molecules represents an important layer in the control of cellular organization, a process that is both highly prevalent and for which features of the regulatory machineries have been deeply conserved evolutionarily. RNA localization is commonly driven by trans-regulatory factors, including RNA binding proteins at the core, which recognize specific cis-acting zipcode elements within the RNA transcripts. Here, we first review the functions and biological benefits of intracellular RNA trafficking, from the perspective of both coding and non-coding RNAs. Next, we discuss the molecular mechanisms that modulate this localization, emphasizing the diverse features of the cis- and trans-regulators involved, while also highlighting emerging technologies and resources that will prove instrumental in deciphering RNA targeting pathways. We then discuss recent findings that reveal how co-transcriptional regulatory mechanisms operating in the nucleus can dictate the downstream cytoplasmic localization of RNAs. Finally, we survey the growing number of human diseases in which RNA trafficking pathways are impacted, including spinal muscular atrophy, Alzheimer's disease, fragile X syndrome and myotonic dystrophy. Such examples highlight the need to further dissect RNA localization mechanisms, which could ultimately pave the way for the development of RNA-oriented diagnostic and therapeutic strategies. This article is part of a Special Issue entitled "Biochemistry of Synthetic Biology - Recent Developments" Guest Editor: Dr. Ilka Heinemann and Dr. Patrick O'Donoghue.

Control of tissue size and development by a regulatory element in the yorkie 3'UTR

Regulation of the Hippo pathway via phosphorylation of Yorkie (Yki), the Drosophila homolog of human Yes-associated protein 1, is conserved from Drosophila to humans. Overexpression of a non-phosphorylatable form of Yki induces severe overgrowth in adult fly eyes. Here, we show that yki mRNA associates with microsomal fractions and forms foci that partially colocalize to processing bodies in the vicinity of endoplasmic reticulum. This localization is dependent on a stem-loop (SL) structure in the 3' untranslated region of yki. Surprisingly, expression of SL deleted yki in eye imaginal discs also results in severe overgrowth phenotypes. When the structure of the SL is disrupted, Yki protein levels increase without a significant effect on RNA levels. When the SL is completely removed, protein levels drastically increase, but in this case, due to increased RNA stability. In the latter case, we show that the increased RNA accumulation is due to removal of a putative miR-8 seed sequence in the SL. These data demonstrate the function of two novel regulatory mechanisms, both controlled by the yki SL element, that are essential for proper Hippo pathway mediated growth regulation.

The mRNA transportome of the BicD/Egl transport machinery

mRNA (mRNA) transport focuses the expression of encoded proteins to specific regions within cells providing them with the means to assume specific functions and even identities. BicD and the mRNA binding protein Egl interact with the microtubule motor dynein to localize mRNAs in Drosophila. Because relatively few mRNA cargos were known, we isolated and identified Egl::GFP associated mRNAs. The top candidates were validated by qPCR, in situ hybridization and genetically by showing that their localization requires BicD. In young embryos these Egl target mRNAs are preferentially localized apically, between the plasma membrane and the blastoderm nuclei, but also in the pole plasm at the posterior pole. Egl targets expressed in the ovary were mostly enriched in the oocyte and some were apically localized in follicle cells. The identification of a large group of novel mRNAs associated with BicD/Egl points to several novel developmental and physiological functions of this dynein dependent localization machinery. The verified dataset also allowed us to develop a tool that predicts conserved A'-form-like stem loops that serve as localization elements in 3′UTRs.

Comparative Proteomic Analysis of Buffalo Oocytes Matured in vitro Using iTRAQ Technique

To investigate the protein profiling of buffalo oocytes at the germinal vesicle (GV) stage and metaphase II (MII) stage, an iTRAQ-based strategy was applied. A total of 3,763 proteins were identified, which representing the largest buffalo oocytes proteome dataset to date. Among these proteins identified, 173 proteins were differentially expressed in GV oocytes and competent MII oocytes, and 146 proteins were differentially abundant in competent and incompetent matured oocytes. Functional and KEGG pathway analysis revealed that the up-regulated proteins in competent MII oocytes were related to chromosome segregation, microtubule-based process, protein transport, oxidation reduction, ribosome, and oxidative phosphorylation, etc., in comparison with GV and incompetent MII oocytes. This is the first proteomic report on buffalo oocytes from different maturation stages and developmental competent status. These data will provide valuable information for understanding the molecular mechanism underlying buffalo oocyte maturation, and these proteins may potentially act as markers to predict developmental competence of buffalo oocyte during in vitro maturation.

ECHO-liveFISH: in vivo RNA labeling reveals dynamic regulation of nuclear RNA foci in living tissues

Elucidating the dynamic organization of nuclear RNA foci is important for understanding and manipulating these functional sites of gene expression in both physiological and pathological states. However, such studies have been difficult to establish in vivo as a result of the absence of suitable RNA imaging methods. Here, we describe a high-resolution fluorescence RNA imaging method, ECHO-liveFISH, to label endogenous nuclear RNA in living mice and chicks. Upon in vivo electroporation, exciton-controlled sequence-specific oligonucleotide probes revealed focally concentrated endogenous 28S rRNA and U3 snoRNA at nucleoli and poly(A) RNA at nuclear speckles. Time-lapse imaging reveals steady-state stability of these RNA foci and dynamic dissipation of 28S rRNA concentrations upon polymerase I inhibition in native brain tissue. Confirming the validity of this technique in a physiological context, the in vivo RNA labeling did not interfere with the function of target RNA nor cause noticeable cytotoxicity or perturbation of cellular behavior.

Staufen targets coracle mRNA to Drosophila neuromuscular junctions and regulates GluRIIA synaptic accumulation and bouton number

The post-synaptic translation of localised mRNAs has been postulated to underlie several forms of plasticity at vertebrate synapses, but the mechanisms that target mRNAs to these postsynaptic sites are not well understood. Here we show that the evolutionary conserved dsRNA binding protein, Staufen, localises to the postsynaptic side of the Drosophila neuromuscular junction (NMJ), where it is required for the localisation of coracle mRNA and protein. Staufen plays a well-characterised role in the localisation of oskar mRNA to the oocyte posterior, where Staufen dsRNA-binding domain 5 is specifically required for its translation. Removal of Staufen dsRNA-binding domain 5, disrupts the postsynaptic accumulation of Coracle protein without affecting the localisation of cora mRNA, suggesting that Staufen similarly regulates Coracle translation. Tropomyosin II, which functions with Staufen in oskar mRNA localisation, is also required for coracle mRNA localisation, suggesting that similar mechanisms target mRNAs to the NMJ and the oocyte posterior. Coracle, the orthologue of vertebrate band 4.1, functions in the anchoring of the glutamate receptor IIA subunit (GluRIIA) at the synapse. Consistent with this, staufen mutant larvae show reduced accumulation of GluRIIA at synapses. The NMJs of staufen mutant larvae have also a reduced number of synaptic boutons. Altogether, this suggests that this novel Staufen-dependent mRNA localisation and local translation pathway may play a role in the developmentally regulated growth of the NMJ.

The influence of dynein processivity control, MAPs, and microtubule ends on directional movement of a localising mRNA

Many cellular constituents travel along microtubules in association with multiple copies of motor proteins. How the activity of these motors is regulated during cargo sorting is poorly understood. In this study, we address this issue using a novel in vitro assay for the motility of localising Drosophila mRNAs bound to native dynein-dynactin complexes. High precision tracking reveals that individual RNPs within a population undergo either diffusive, or highly processive, minus end-directed movements along microtubules. RNA localisation signals stimulate the processive movements, with regulation of dynein-dynactin’s activity rather than its total copy number per RNP, responsible for this effect. Our data support a novel mechanism for multi-motor translocation based on the regulation of dynein processivity by discrete cargo-associated features. Studying the in vitro responses of RNPs to microtubule-associated proteins (MAPs) and microtubule ends provides insights into how an RNA population could navigate the cytoskeletal network and become anchored at its destination in cells.

DOI:http://dx.doi.org/10.7554/eLife.01596.001

For a cell to do its job, the different components inside it need to be moved to different locations. This is achieved by an elaborate cellular transport system. To move a component to where it needs to be, motor proteins bind to it, often with the assistance of other ‘accessory’ proteins. This cargo-motor complex then moves along a network of tracks within the cell. Viruses also exploit this transport system in order to be trafficked to specific parts of the cell during their life cycles.

Many cargos are moved along microtubule tracks. Multiple microtubule motor proteins often attach to the same cargo, but it is unclear how they work together during transport. Previous studies have attempted to address this issue by attaching motor proteins to artificial cargoes, such as synthetic beads. However, these experiments did not include some of the accessory proteins that are thought to play a role during transport within the living cell.

Soundararajan and Bullock have now examined how complexes containing multiple motors bound to accessory proteins move molecules of messenger RNA to specific sites within cells. By visualising fruit fly mRNA moving along microtubules attached to a glass surface, the transport process can be studied in detail. It appears that the complexes travel using one of two methods: they either diffuse along the microtubules, which they can do in either direction, or they power themselves along the microtubules, which they can only do in one direction. Although previous experiments with artificial cargos suggested that the number of motors in the complex determines the likelihood of one-way traffic, it appears that one or more accessory proteins are actually in control during mRNA transport.

Soundararajan and Bullock also documented how the mRNA-motor complexes react to roadblocks and dead-ends on the microtubule highway. Rather than letting go of the microtubule upon such an encounter, the complexes can reverse back down the track. This behaviour may help them to find a new route to their destination.

DOI:http://dx.doi.org/10.7554/eLife.01596.002

A stem-loop structure directs oskar mRNA to microtubule minus ends

mRNA transport coupled with translational control underlies the intracellular localization of many proteins in eukaryotic cells. This is exemplified in Drosophila, where oskar mRNA transport and translation at the posterior pole of the oocyte direct posterior patterning of the embryo. oskar localization is a multistep process. Within the oocyte, a spliced oskar localization element (SOLE) targets oskar mRNA for plus end-directed transport by kinesin-1 to the posterior pole. However, the signals mediating the initial minus end-directed, dynein-dependent transport of the mRNA from nurse cells into the oocyte have remained unknown. Here, we show that a 67-nt stem-loop in the oskar 3' UTR promotes oskar mRNA delivery to the developing oocyte and that it shares functional features with the fs(1)K10 oocyte localization signal. Thus, two independent cis-acting signals, the oocyte entry signal (OES) and the SOLE, mediate sequential dynein- and kinesin-dependent phases of oskar mRNA transport during oogenesis. The OES also promotes apical localization of injected RNAs in blastoderm stage embryos, another dynein-mediated process. Similarly, when ectopically expressed in polarized cells of the follicular epithelium or salivary glands, reporter RNAs bearing the oskar OES are apically enriched, demonstrating that this element promotes mRNA localization independently of cell type. Our work sheds new light on how oskar mRNA is trafficked during oogenesis and the RNA features that mediate minus end-directed transport.

Lissencephaly-1 promotes the recruitment of dynein and dynactin to transported mRNAs

Lissencephaly-1 promotes the interaction of dynein with dynactin and facilitates motor complex association with mRNA cargos.

Microtubule-based transport mediates the sorting and dispersal of many cellular components and pathogens. However, the mechanisms by which motor complexes are recruited to and regulated on different cargos remain poorly understood. Here we describe a large-scale biochemical screen for novel factors associated with RNA localization signals mediating minus end–directed mRNA transport during Drosophila development. We identified the protein Lissencephaly-1 (Lis1) and found that minus-end travel distances of localizing transcripts are dramatically reduced in lis1 mutant embryos. Surprisingly, given its well-documented role in regulating dynein mechanochemistry, we uncovered an important requirement for Lis1 in promoting the recruitment of dynein and its accessory complex dynactin to RNA localization complexes. Furthermore, we provide evidence that Lis1 levels regulate the overall association of dynein with dynactin. Our data therefore reveal a critical role for Lis1 within the mRNA localization machinery and suggest a model in which Lis1 facilitates motor complex association with cargos by promoting the interaction of dynein with dynactin.

Protein targeting via mRNA in bacteria

Proteins of all living organisms must reach their subcellular destination to sustain the cell structure and function. The proteins are transported to one of the cellular compartments, inserted into the membrane, or secreted across the membrane to the extracellular milieu. Cells have developed various mechanisms to transport proteins across membranes, among them localized translation. Evidence for targeting of Messenger RNA for the sake of translation of their respective protein products at specific subcellular sites in many eukaryotic model organisms have been accumulating in recent years. Cis-acting RNA localizing elements, termed RNA zip-codes, which are embedded within the mRNA sequence, are recognized by RNA-binding proteins, which in turn interact with motor proteins, thus coordinating the intracellular transport of the mRNA transcripts. Despite the rareness of conventional organelles, first and foremost a nucleus, pieces of evidence for mRNA localization to specific subcellular domains, where their protein products function, have also been obtained for prokaryotes. Although the underlying mechanisms for transcript localization in bacteria are yet to be unraveled, it is now obvious that intracellular localization of mRNA is a common mechanism to spatially localize proteins in both eukaryotes and prokaryotes. This article is part of a Special Issue entitled: Protein trafficking and secretion in bacteria. Guest Editors: Anastassios Economou and Ross Dalbey.

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.

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.

Spatial regulation of translation through RNA localization

RNA localization is a mechanism to post-transcriptionally regulate gene expression. Eukaryotic organisms ranging from fungi to mammals localize mRNAs to spatially restrict synthesis of specific proteins to distinct regions of the cytoplasm. In this review, we provide a general summary of RNA localization pathways in Saccharomyces cerevisiae, Xenopus, Drosophila and mammalian neurons.

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.

RNA:RNA interaction can enhance RNA localization in Drosophila oocytes

RNA localization is a key mechanism for targeting proteins to particular subcellular domains. Sequences necessary and sufficient for localization have been identified, but little is known about factors that affect its kinetics. Transcripts of gurken and the I factor, a non-LTR retrotransposon, colocalize at the nucleus in the dorso-antero corner of the Drosophila oocyte directed by localization signals, the GLS and ILS. I factor RNA localizes faster than gurken after injection into oocytes, due to a difference in the intrinsic localization ability of the GLS and ILS. The kinetics of localization of RNA containing the ILS are enhanced by the presence of a stem-loop, the A loop. This acts as an RNA:RNA interaction element in vivo and in vitro, and stimulates localization of RNA containing other localization signals. RNA:RNA interaction may be a general mechanism for modulating RNA localization and could allow an mRNA that lacks a localization signal to hitchhike on another RNA that has one.

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.

Binary function of mRNA

Since the discovery of messenger RNA (mRNA) over half a century ago, the assumption has always been that the only function of mRNA is to make a protein. However, recent studies of prokaryotic and eukaryotic organisms unexpectedly show that some mRNAs may be functionally binary and have additional structural functions that are unrelated to their translation product. These findings imply that some of the phenotypic features of cells and organisms can also be binary, that is, they depend both on the function of a protein and the independent structural function of its mRNA. In this review, we will discuss this concept within the framework of multifunctional RNA molecules and the RNA World Hypothesis.

mRNA localization: assembly of transport complexes and their incorporation into particles

Localization of mRNAs to subcellular domains can enrich proteins at sites where they function. Coordination with translational control can ensure that the encoded proteins will not appear elsewhere, an important property for factors that control cell fate or body patterning. Here I focus on two aspects of mRNA localization. One is the question of how mRNAs that undergo directed transport by a shared mechanism are bound to the transport machinery, and why localization signals from these mRNAs have very diverse sequences. The second topic concerns the role of particles, in which localized mRNAs often appear. Recent evidence highlights the importance of such assemblies, and the possibility that close association of mRNAs confers community effects and a novel form of regulation.

Identifying and searching for conserved RNA localisation signals

RNA localisation is an important mode of delivering proteins to their site of function. Cis-acting signals within the RNAs, which can be thought of as zip-codes, determine the site of localisation. There are few examples of fully characterised RNA signals, but the signals are thought to be defined through a combination of primary, secondary, and tertiary structures. In this chapter, we describe a selection of computational methods for predicting RNA secondary structure, identifying localisation signals, and searching for similar localisation signals on a genome-wide scale. The chapter is aimed at the biologist rather than presenting the details of each of the individual methods.

Selective constraints in conserved folded RNAs of drosophilid and hominid genomes

Small noncoding RNAs as well as folded RNA structures in genic regions are crucial for many cellular processes. They are involved in posttranscriptional gene regulation (microRNAs), RNA modification (small nucleolar RNAs), regulation of splicing, correct localization of proteins, and many other processes. In most cases, a distinct secondary structure of the molecule is necessary for its correct function. Hence, selection should act to retain the structure of the molecule, although the underlying sequence is allowed to vary. Here, we present the first genome-wide estimates of selective constraints in folded RNA molecules in the nuclear genomes of drosophilids and hominids. In comparison to putatively neutrally evolving sites, we observe substantially reduced rates of substitutions at paired and unpaired sites of folded molecules. We estimated evolutionary constraints to be in the ranges of (0.974,0.991) and (0.895,1.000) for paired nucleotides in drosophilids and hominids, respectively. These values are significantly higher than for constraints at nonsynonymous sites of protein-coding genes in both genera. Nonetheless, valleys of only moderately reduced fitness (s ≈ 10(-4)) are sufficient to generate the observed fraction of nucleotide changes that are removed by purifying selection. In addition, a comparison of selective coefficients between drosophilids and hominids revealed significantly higher constraints in drosophilids, which can be attributed to the difference in long-term effective population size between these two groups of species. This difference is particularly apparent at the independently evolving (unpaired) sites.

ParticleStats: open source software for the analysis of particle motility and cytoskeletal polarity

The study of dynamic cellular processes in living cells is central to biology and is particularly powerful when the motility characteristics of individual objects within cells can be determined and analysed statistically. However, commercial programs only offer a limited range of inflexible analysis modules and there are currently no open source programs for extensive analysis of particle motility. Here, we describe ParticleStats (http://www.ParticleStats.com), a web server and open source programs, which input the X,Y coordinate positions of objects in time, and output novel analyses, graphical plots and statistics for motile objects. ParticleStats comprises three separate analysis programs. First, ParticleStats:Directionality for the global analysis of polarity, for example microtubule plus end growth in Drosophila oocytes. Second, ParticleStats:Compare for the analysis of saltatory movement in terms of runs and pauses. This can be applied to chromosome segregation and molecular motor-based movements. Thirdly ParticleStats:Kymographs for the analysis of kymograph images, for example as applied to separation of chromosomes in mitosis. These analyses have provided key insights into molecular mechanisms that are not possible from qualitative analysis alone and are widely applicable to many other cell biology problems.

Dendritically localized transcripts are sorted into distinct ribonucleoprotein particles that display fast directional motility along dendrites of hippocampal neurons

Localization of mRNAs to postsynaptic sites and their subsequent translation is thought to contribute to synapse-specific plasticity. However, the direct visualization of dendritic RNA transport in living neurons remains a major challenge. Here, we analyze the transport of Alexa-labeled RNAs microinjected into mature hippocampal neurons. We show that microinjected MAP2 and CaMKIIalpha RNAs form particles that localize into dendrites as their endogenous counterparts. In contrast, nonlocalizing RNAs or truncated CaMKIIalpha, lacking the dendritic targeting element, remain in the cell body. Furthermore, our microinjection approach allowed us to identify a novel dendritically localized RNA, Septin7. Time-lapse videomicroscopy of neurons injected with CaMKIIalpha and Septin7 RNAs demonstrates fast directional movement along the dendrites of hippocampal neurons, with similar kinetics to Staufen1 ribonucleoprotein particles (RNPs). Coinjection and simultaneous visualization of two RNAs, as well as double detection of the corresponding endogenous RNAs, reveal that neuronal transcripts are differentially sorted in dendritic RNPs.

A'-form RNA helices are required for cytoplasmic mRNA transport in Drosophila

Microtubule-based mRNA transport is widely used to restrict protein expression to specific regions in the cell, and has important roles in defining cell polarity, axis determination and for neuronal function. However, the structural basis of recognition of cis-acting mRNA localization signals by motor complexes is poorly understood. We have used NMR spectroscopy to describe the first tertiary structure of an RNA element responsible for mRNA transport. The Drosophila fs(1)K10 signal, which mediates transport by the dynein motor, forms a stem-loop with two double-stranded RNA helices adopting an unusual A′-form conformation with widened, major grooves reminiscent of those in B-form DNA. Structure determination of four mutant RNAs and extensive functional assays in Drosophila embryos indicate that the two spatially registered A′-form helices represent critical recognition sites for the transport machinery. Our study provides important insights into the basis for RNA cargo recognition and reveals a key biological function encoded by A′-form RNA conformation.

RNA localization in neurite morphogenesis and synaptic regulation: current evidence and novel approaches

It is now generally accepted that RNA localization in the central nervous system conveys important roles both during development and in the adult brain. Of special interest is protein synthesis located at the synapse, as this potentially confers selective synaptic modification and has been implicated in the establishment of memories. However, the underlying molecular events are largely unknown. In this review, we will first discuss novel findings that highlight the role of RNA localization in neurons. We will focus on the role of RNA localization in neurotrophin signaling, axon outgrowth, dendrite and dendritic spine morphogenesis as well as in synaptic plasticity. Second, we will briefly present recent work on the role of microRNAs in translational control in dendrites and its implications for learning and memory. Finally, we discuss recent approaches to visualize RNAs in living cells and their employment for studying RNA trafficking in neurons.

Rapid, nondenaturing RNA purification using weak anion-exchange fast performance liquid chromatography

We present a simple and fast method for large-scale purification of RNA oligonucleotides suitable for biochemical and structural studies. RNAs are transcribed in vitro with T7 RNA polymerase using linearized plasmid DNA templates. After addition of EDTA, the crude transcription reaction is subjected directly to weak anion-exchange chromatography using DEAE-sepharose to separate the T7 RNA polymerase, unincorporated rNTPs, small abortive transcripts, and the plasmid DNA template from the desired RNA product. The novel method does neither require tedious phenol/chloroform extraction of the T7 RNA polymerase nor denaturation of the RNA, which is desirable especially for larger RNAs. In addition, isotopically labeled rNTPs can be easily recycled from the column flow-through and oligomeric RNA aggregates can be separated from the natively folded monomeric RNA product.

Bicaudal-D and its role in cargo sorting by microtubule-based motors

Many cytoplasmic cargoes are transported along microtubules using dynein or kinesin molecular motors. As the sorting machinery of the cell needs to be tightly controlled, associated factors are employed to either recruit cargoes to motors or to regulate their activities. In the present review, we concentrate on the BicD (Bicaudal-D) protein, which has recently emerged as an essential element for transport of several important cargoes by the minus-end-directed motor cytoplasmic dynein. BicD was proposed to be a linker bridging cargo and dynein, although recent studies suggest that it may also have roles in the regulation of cargo motility. Here we summarize the current knowledge of the role that BicD plays in the transport of diverse cellular constituents. We catalogue the molecular interactions that underpin these functions and also highlight important questions to be addressed in the future.

Translational control during early development

Translational control of specific messenger RNAs, which themselves are often asymmetrically localized within the cytoplasm of a cell, underlies many events in germline development, and in embryonic axis specification. This comprehensive, but by no means exhaustive, review attempts to present a picture of the present state of knowledge about mechanisms underlying mRNA localization and translational control of specific mRNAs that are mediated by trans-acting protein factors. While RNA localization and translational control are widespread in evolution and have been studied in many experimental systems, this article will focus mainly on three particularly well-characterized systems: Drosophila, Caenorhabditis elegans, and Xenopus. In keeping with the overall theme of this volume, instances in which translational control factors have been linked to human disease states will also be discussed.

Egalitarian recruitment of localized mRNAs

Bicaudal-D (Bic-D) and Egalitarian (Egl) are required for the dynein-dependent localization of many mRNAs in Drosophila, but the mRNAs show no obvious sequence similarities, and the RNA-binding proteins that recognize them and link them to dynein are not known. In this issue of Genes & Development, Dienstbier and colleagues (pp. 1546-1558) present evidence that the elusive RNA-binding protein is Egl itself. As well as linking mRNA to dynein, they show that Egl also activates dynein motility by binding Bic-D and the dynein light chain.

Egalitarian is a selective RNA-binding protein linking mRNA localization signals to the dynein motor

Cytoplasmic sorting of mRNAs by microtubule-based transport is widespread, yet very little is known at the molecular level about how specific transcripts are linked to motor complexes. In Drosophila, minus-end-directed transport of developmentally important transcripts by the dynein motor is mediated by seemingly divergent mRNA elements. Here we provide evidence that direct recognition of these mRNA localization signals is mediated by the Egalitarian (Egl) protein. Egl and the dynein cofactor Bicaudal-D (BicD) are the only proteins from embryonic extracts that are abundantly and specifically enriched on RNA localization signals from transcripts of gurken, hairy, K10, and the I factor retrotransposon. In vitro assays show that, despite lacking a canonical RNA-binding motif, Egl directly recognizes active localization elements. We also reveal a physical interaction between Egl and a conserved domain for cargo recruitment in BicD and present data suggesting that Egl participates selectively in BicD-mediated transport of mRNA in vivo. Our work leads to the first working model for a complete connection between minus-end-directed mRNA localization signals and microtubules and reveals molecular strategies that are likely to be of general relevance for cargo transport by dynein.

A trypsin-like protease with apparent dual function in early Lepeophtheirus salmonis (Krøyer) development

BACKGROUND

Trypsin-like serine proteases are involved in a large number of processes including digestive degradation, regulation of developmental processes, yolk degradation and yolk degradome activation. Trypsin like peptidases considered to be involved in digestion have been characterized in Lepeophtheirus salmonis. During these studies a trypsin-like peptidase which differed in a number of traits were identified.

RESULTS

An intronless trypsin-like serine peptidase (LsTryp10) from L., salmonis was identified and characterized. LsTryp10 mRNA is evenly distributed in the ovaries and oocytes, but is located along the ova periphery. LsTryp10 protein is deposited in the oocytes and all embryonic cells. LsTryp10 mRNA translation and concurrent degradation after fertilization was found in the embryos demonstrating that LsTryp10 protein is produced both by the embryo and maternally. The results furthermore indicate that LsTryp10 protein of maternal origin has a distribution pattern different to that of embryonic origin.

CONCLUSION

Based on present data and previous studies of peptidases in oocytes and embryos, we hypothesize that maternally deposited LsTryp10 protein is involved in regulation of the yolk degradome. The function of LsTryp10 produced by the embryonic cells remains unknown. To our knowledge a similar expression pattern has not previously been reported for any protease.

A bioinformatics search pipeline, RNA2DSearch, identifies RNA localization elements in Drosophila retrotransposons

mRNA localization is a widespread mode of delivering proteins to their site of function. The embryonic axes in Drosophila are determined in the oocyte, through Dynein-dependent transport of gurken/TGF-alpha mRNA, containing a small localization signal that assigns its destination. A signal with a similar secondary structure, but lacking significant sequence similarity, is present in the I factor retrotransposon mRNA, also transported by Dynein. It is currently unclear whether other mRNAs exist that are localized to the same site using similar signals. Moreover, searches for other genes containing similar elements have not been possible due to a lack of suitable bioinformatics methods for searches of secondary structure elements and the difficulty of experimentally testing all the possible candidates. We have developed a bioinformatics approach for searching across the genome for small RNA elements that are similar to the secondary structures of particular localization signals. We have uncovered 48 candidates, of which we were able to test 22 for their localization potential using injection assays for Dynein mediated RNA localization. We found that G2 and Jockey transposons each contain a gurken/I factor-like RNA stem-loop required for Dynein-dependent localization to the anterior and dorso-anterior corner of the oocyte. We conclude that I factor, G2, and Jockey are members of a "family" of transposable elements sharing a gurken-like mRNA localization signal and Dynein-dependent mechanism of transport. The bioinformatics pipeline we have developed will have broader utility in fields where small RNA signals play important roles.

A targeted gain-of-function screen identifies genes affecting salivary gland morphogenesis/tubulogenesis in Drosophila

During development individual cells in tissues undergo complex cell-shape changes to drive the morphogenetic movements required to form tissues. Cell shape is determined by the cytoskeleton and cell-shape changes critically depend on a tight spatial and temporal control of cytoskeletal behavior. We have used the formation of the salivary glands in the Drosophila embryo, a process of tubulogenesis, as an assay for identifying factors that impinge on cell shape and the cytoskeleton. To this end we have performed a gain-of-function screen in the salivary glands, using a collection of fly lines carrying EP-element insertions that allow the overexpression of downstream-located genes using the UAS-Gal4 system. We used a salivary-gland-specific fork head-Gal4 line to restrict expression to the salivary glands, in combination with reporters of cell shape and the cytoskeleton. We identified a number of genes known to affect salivary gland formation, confirming the effectiveness of the screen. In addition, we found many genes not implicated previously in this process, some having known functions in other tissues. We report the initial characterization of a subset of genes, including chickadee, rhomboid1, egalitarian, bitesize, and capricious, through comparison of gain- and loss-of-function phenotypes.

Atomic force microscopy reveals binding of mRNA to microtubules mediated by two major mRNP proteins YB-1 and PABP

A significant fraction of mRNAs is known to be associated in the form of mRNPs with microtubules for active transport. However, little is known about the interaction between mRNPs and microtubules and most of previous works were focused on molecular motor:microtubule interactions. Here, we have identified, via high resolution atomic force microscopy imaging, a significant binding of mRNA to microtubules mediated by two major mRNP proteins, YB-1 and PABP. This interaction with microtubules could be of critical importance for active mRNP traffic and for mRNP granule formation. A similar role may be fulfilled by other cationic mRNA partners.

A stem-loop structure in the wingless transcript defines a consensus motif for apical RNA transport

Although the subcellular localization of mRNA transcripts is a well-established mechanism for controlling protein localization, the basis for the recognition of mRNA localization elements is only now emerging. For example, although localization elements have been defined for many mRNAs that localize to apical cytoplasm in Drosophila embryos, no unifying properties have been identified within these elements. In this study, we identify and characterize an apical localization element in the 3'UTR of the Drosophila wingless mRNA. We show that this element, referred to as WLE3, is both necessary and sufficient for apical RNA transport. Full, unrestricted activity, however, requires the presence of one of several downstream potentiating elements. Comparison of WLE3 sequences within the Drosophila genus, and their predicted secondary structures, defines a highly conserved stem-loop structure. Despite these high levels of sequence and predicted structure conservation, however, mutagenesis shows significant leeway for both sequence and structure variation in the predicted stem-loop. Importantly, the features that emerge as crucial include an accessible distal helix sequence motif, which is also found in the predicted structures of other apical localization elements.

A Dynein-dependent shortcut rapidly delivers axis determination transcripts into the Drosophila oocyte

The primary axes of Drosophila are set up by the localization of transcripts within the oocyte. These mRNAs originate in the nurse cells, but how they move into the oocyte remains poorly understood. Here, we study the path and mechanism of movement of gurken RNA within the nurse cells and towards and through ring canals connecting them to the oocyte. gurken transcripts, but not control transcripts, recruit the cytoplasmic Dynein-associated co-factors Bicaudal D (BicD) and Egalitarian in the nurse cells. gurken RNA requires BicD and Dynein for its transport towards the ring canals, where it accumulates before moving into the oocyte. Our results suggest that bicoid and oskar transcripts are also delivered to the oocyte by the same mechanism, which is distinct from cytoplasmic flow. We propose that Dynein-mediated transport of specific RNAs along specialized networks of microtubules increases the efficiency of their delivery, over the flow of general cytoplasmic components, into the oocyte.

On the use of in vivo cargo velocity as a biophysical marker

Molecular motors move many intracellular cargos along microtubules. Recently, it has been hypothesized that in vivo cargo velocity can be used to determine the number of engaged motors. We use theoretical and experimental approaches to investigate these assertions, and find that this hypothesis is inconsistent with previously described motor behavior, surveyed and re-analyzed in this paper. Studying lipid droplet motion in Drosophila embryos, we compare transport in a mutant, Delta(halo), with that in wild-type embryos. The minus-end moving cargos in the mutant appear to be driven by more motors (based on in vivo stall force observations). Periods of minus-end motion are indeed longer than in wild-type embryos but the corresponding velocities are not higher. We conclude that velocity is not a definitive read-out of the number of motors propelling a cargo.

Guidance of bidirectional motor complexes by mRNA cargoes through control of dynein number and activity

During asymmetric cytoplasmic mRNA transport, cis-acting localization signals are widely assumed to tether a specific subset of transcripts to motor complexes that have intrinsic directionality. Here we provide evidence that mRNA transcripts control their sorting by regulating the relative activities of opposing motors on microtubules. We show in Drosophila embryos that all mRNAs undergo bidirectional transport on microtubules and that cis-acting elements produce a range of polarized transcript distributions by regulating the frequency, velocity, and duration of minus-end-directed runs. Increased minus-end motility is dependent on the dosage of RNA elements and the proteins Egalitarian (Egl) and Bicaudal-D (BicD). We show that these proteins, together with the dynein motor, are recruited differentially to different RNA signals. Cytoplasmic transfer experiments reveal that, once assembled, cargo/motor complexes are insensitive to reduced cytoplasmic levels of transport proteins. Thus, the concentration of these proteins is only critical at the onset of transport. This work suggests that the architecture of RNA elements, through Egl and BicD, regulates directional transport by controlling the relative numbers of opposite polarity motors assembled. Our data raise the possibility that recruitment of different numbers of motors and regulatory proteins is a general strategy by which microtubule-based cargoes control their sorting.

An N-terminally acetylated Arf-like GTPase is localised to lysosomes and affects their motility

Small GTPases of the Arf and Rab families play key roles in the function of subcellular organelles. Each GTPase is usually found on only one compartment and, hence, they confer organelle specificity to many intracellular processes. However, there has so far been little evidence for specific GTPases present on lysosomes. Here, we report that two closely related human Arf-like GTPases, Arl8a and Arl8b (also known as Arl10b/c and Gie1/2), localise to lysosomes in mammalian cells, with the single homologue in Drosophila cells having a similar location. Conventionally, membrane binding of Arf and Arl proteins is mediated by both an N-terminal myristoyl group and an N-terminal amphipathic helix that is inserted into the lipid bilayer upon activation of the GTPase. Arl8a and Arl8b do not have N-terminal myristoylation sites, and we find that Arl8b is instead N-terminally acetylated, and an acetylated methionine is necessary for its lysosomal localization. Overexpression of Arl8a or Arl8b results in a microtubule-dependent redistribution of lysosomes towards the cell periphery. Live cell imaging shows that lysosomes move more frequently both toward and away from the cell periphery, suggesting a role for Arl8a and Arl8b as positive regulators of lysosomal transport.

BicD-dependent localization processes: from Drosophilia development to human cell biology

Many eukaryotic cells depend on proper cell polarization for their development and physiological function. The establishment of these polarities often involve the subcellular localization of a specific subset of proteins, RNAs and organelles. In Drosophila, the microtubule-dependent BicD (BicaudalD) localization machinery is involved in the proper localization of mRNA during oogenesis and embryogenesis and the proper positioning of the oocyte and photoreceptor nuclei. BicD acts together with the minus-end directed motor dynein as well as Egl and Lis-1. The finding that the mammalian homologs of BicD function in retrograde Golgi-to-ER transport has supported the view that BicD may be part of a repeatedly used and evolutionary conserved localization machinery. In this review we focus on the various processes in which BicD is involved during Drosophilian development and in mammals. In addition, we evaluate the interactions between BicD, the dynein localization machinery and associated factors.

gurken and the I factor retrotransposon RNAs share common localization signals and machinery

Drosophila gurken mRNA is localized by dynein-mediated transport to a crescent near the oocyte nucleus, thus targeting the TGFalpha signal and forming the primary embryonic axes. Here, we show that gurken and the I factor, a non-LTR retrotransposon, share a small consensus RNA stem loop of defined secondary structure, which forms a conserved signal for dynein-mediated RNA transport to the oocyte nucleus. Furthermore, gurken and the I factor compete in vivo for the same localization machinery. I factor transposition leads to its mRNA accumulating near and within the oocyte nucleus, thus causing perturbations in gurken and bicoid mRNA localization and axis specification. These observations further our understanding of the close association of transposable elements with their host and provide an explanation for how I factor transposition causes female sterility. We propose that the transposition of other elements may exploit the host's RNA transport signals and machinery.

Identification of a conserved RNA motif essential for She2p recognition and mRNA localization to the yeast bud

In Saccharomyces cerevisiae, over twenty mRNAs localize to the bud tip of daughter cells, playing roles in processes as different as mating type switching and plasma membrane targeting. The localization of these transcripts depends on interactions between a cis-acting localization element(s) or zipcodes and the RNA-binding protein She2p. While previous studies identified four different localization elements in the bud-localized ASH1 mRNA, the main determinants for She2p recognition are still unknown. To investigate the RNA-binding specificity of She2p, we isolated She2p-binding RNAs by in vivo selection from libraries of partially randomized ASH1 localization elements. The RNAs isolated contained a similar loop-stem-loop structure with a highly conserved CGA triplet in one loop and a single conserved cytosine in the other loop. Mutating these conserved nucleotides or the stem separating them resulted in the loss of She2p binding and in the delocalization of a reporter mRNA. Using this information, we identified the same RNA motif in two other known bud-localized transcripts, suggesting that this motif is conserved among bud-localized mRNAs. These results show that mRNAs with zipcodes lacking primary sequence similarity can rely on a few conserved nucleotides properly oriented in their three-dimensional structure in order to be recognized by the same localization machinery.