RNA asymmetric distribution and daughter/mother differentiation in yeast

Opposing Roles of FACT for Euchromatin and Heterochromatin in Yeast

DNA is stored in the nucleus of a cell in a folded state; however, only the necessary genetic information is extracted from the required group of genes. The key to extracting genetic information is chromatin ambivalence. Depending on the chromosomal region, chromatin is characterized into low-density "euchromatin" and high-density "heterochromatin", with various factors being involved in its regulation. Here, we focus on chromatin regulation and gene expression by the yeast FACT complex, which functions in both euchromatin and heterochromatin. FACT is known as a histone H2A/H2B chaperone and was initially reported as an elongation factor associated with RNA polymerase II. In budding yeast, FACT activates promoter chromatin by interacting with the transcriptional activators SBF/MBF via the regulation of G1/S cell cycle genes. In fission yeast, FACT plays an important role in the formation of higher-order chromatin structures and transcriptional repression by binding to Swi6, an HP1 family protein, at heterochromatin. This FACT property, which refers to the alternate chromatin-regulation depending on the binding partner, is an interesting phenomenon. Further analysis of nucleosome regulation within heterochromatin is expected in future studies.

Walking the line: mechanisms underlying directional mRNA transport and localisation in neurons and beyond

Messenger RNA (mRNA) localisation enables a high degree of spatiotemporal control on protein synthesis, which contributes to establishing the asymmetric protein distribution required to set up and maintain cellular polarity. As such, a tight control of mRNA localisation is essential for many biological processes during development and in adulthood, such as body axes determination in Drosophila melanogaster and synaptic plasticity in neurons. The mechanisms controlling how mRNAs are localised, including diffusion and entrapment, local degradation and directed active transport, are largely conserved across evolution and have been under investigation for decades in different biological models. In this review, we will discuss the standing of the field regarding directional mRNA transport in light of the recent discovery that RNA can hitchhike on cytoplasmic organelles, such as endolysosomes, and the impact of these transport modalities on our understanding of neuronal function during development, adulthood and in neurodegeneration.

The functional organization of axonal mRNA transport and translation

Axons extend for tremendously long distances from the neuronal soma and make use of localized mRNA translation to rapidly respond to different extracellular stimuli and physiological states. The locally synthesized proteins support many different functions in both developing and mature axons, raising questions about the mechanisms by which local translation is organized to ensure the appropriate responses to specific stimuli. Publications over the past few years have uncovered new mechanisms for regulating the axonal transport and localized translation of mRNAs, with several of these pathways converging on the regulation of cohorts of functionally related mRNAs - known as RNA regulons - that drive axon growth, axon guidance, injury responses, axon survival and even axonal mitochondrial function. Recent advances point to these different regulatory pathways as organizing platforms that allow the axon's proteome to be modulated to meet its physiological needs.

Asymmetric cell division requires specific mechanisms for adjusting global transcription

Most cells divide symmetrically into two approximately identical cells. There are many examples, however, of asymmetric cell division that can generate sibling cell size differences. Whereas physical asymmetric division mechanisms and cell fate consequences have been investigated, the specific problem caused by asymmetric division at the transcription level has not yet been addressed. In symmetrically dividing cells the nascent transcription rate increases in parallel to cell volume to compensate it by keeping the actual mRNA synthesis rate constant. This cannot apply to the yeast Saccharomyces cerevisiae, where this mechanism would provoke a never-ending increasing mRNA synthesis rate in smaller daughter cells. We show here that, contrarily to other eukaryotes with symmetric division, budding yeast keeps the nascent transcription rates of its RNA polymerases constant and increases mRNA stability. This control on RNA pol II-dependent transcription rate is obtained by controlling the cellular concentration of this enzyme.

Pheromone-encoding mRNA is transported to the yeast mating projection by specific RNP granules

In response to mating pheromone, the yeast MFA2 mRNA is transported to the tip of the mating projection as an RNP granule and translated; integrity of the granules is required for normal mRNA transport and for the mating process.

Association of messenger RNAs with large complexes such as processing bodies (PBs) plays a pivotal role in regulating their translation and decay. Little is known about other possible functions of these assemblies. Exposure of haploid yeast cells, carrying mating type “a,” to “α pheromone” stimulates polarized growth resulting in a “shmoo” projection; it also induces synthesis of “a pheromone,” encoded by MFA2. In this paper, we show that, in response to α pheromone, MFA2 mRNA is assembled with two types of granules; both contain some canonical PB proteins, yet they differ in size, localization, motility, and sensitivity to cycloheximide. Remarkably, one type is involved in mRNA transport to the tip of the shmoo, whereas the other—in local translation in the shmoo. Normal assembly of these granules is critical for their movement, localization, and for mating. Thus, MFA2 mRNAs are transported to the shmoo tip, in complex with PB-like particles, where they are locally translated.

Specific interaction of KIF11 with ZBP1 regulates the transport of β-actin mRNA and cell motility

ZBP1-modulated localization of β-actin mRNA enables a cell to establish polarity and structural asymmetry. Although the mechanism of β-actin mRNA localization has been well established, the underlying mechanism of how a specific molecular motor contributes to the transport of the ZBP1 (also known as IGF2BP1) complex in non-neuronal cells remains elusive. In this study, we report the isolation and identification of KIF11, a microtubule motor, which physically interacts with ZBP1 and is a component of β-actin messenger ribonucleoprotein particles (mRNPs). We show that KIF11 colocalizes with the β-actin mRNA, and the ability of KIF11 to transport β-actin mRNA is dependent on ZBP1. We characterize the corresponding regions of ZBP1 and KIF11 that mediate the interaction of the two proteins in vitro and in vivo. Disruption of the in vivo interaction of KIF11 with ZBP1 delocalizes β-actin mRNA and affects cell migration. Our study reveals a molecular mechanism by which a particular microtubule motor mediates the transport of an mRNP through direct interaction with an mRNA-binding protein.

The yeast actin cytoskeleton

The actin cytoskeleton is a complex network of dynamic polymers, which plays an important role in various fundamental cellular processes, including maintenance of cell shape, polarity, cell division, cell migration, endocytosis, vesicular trafficking, and mechanosensation. Precise spatiotemporal assembly and disassembly of actin structures is regulated by the coordinated activity of about 100 highly conserved accessory proteins, which nucleate, elongate, cross-link, and sever actin filaments. Both in vivo studies in a wide range of organisms from yeast to metazoans and in vitro studies of purified proteins have helped shape the current understanding of actin dynamics and function. Molecular genetics, genome-wide functional analysis, sophisticated real-time imaging, and ultrastructural studies in concert with biochemical analysis have made yeast an attractive model to understand the actin cytoskeleton, its molecular dynamics, and physiological function. Studies of the yeast actin cytoskeleton have contributed substantially in defining the universal mechanism regulating actin assembly and disassembly in eukaryotes. Here, we review some of the important insights generated by the study of actin cytoskeleton in two important yeast models the budding yeast Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe.

Mitotic exit and separation of mother and daughter cells

Productive cell proliferation involves efficient and accurate splitting of the dividing cell into two separate entities. This orderly process reflects coordination of diverse cytological events by regulatory systems that drive the cell from mitosis into G1. In the budding yeast Saccharomyces cerevisiae, separation of mother and daughter cells involves coordinated actomyosin ring contraction and septum synthesis, followed by septum destruction. These events occur in precise and rapid sequence once chromosomes are segregated and are linked with spindle organization and mitotic progress by intricate cell cycle control machinery. Additionally, critical paarts of the mother/daughter separation process are asymmetric, reflecting a form of fate specification that occurs in every cell division. This chapter describes central events of budding yeast cell separation, as well as the control pathways that integrate them and link them with the cell cycle.

Organelle segregation during mitosis: lessons from asymmetrically dividing cells

Studies on cell division traditionally focus on the mechanisms of chromosome segregation and cytokinesis, yet we know comparatively little about how organelles segregate. Analysis of organelle partitioning in asymmetrically dividing cells has provided insights into the mechanisms through which cells control organelle distribution. Interestingly, these studies have revealed that segregation mechanisms frequently link organelle distribution to organelle growth and formation. Furthermore, in many cases, cells use organelles, such as the endoplasmic reticulum and P granules, as vectors for the segregation of information. Together, these emerging data suggest that the coordination between organelle growth, division, and segregation plays an important role in the control of cell fate inheritance, cellular aging, and rejuvenation, i.e., the resetting of age in immortal lineages.

An intracellular transmission control protocol: assembly and transport of ribonucleoprotein complexes

Initially assumed to be a special feature of highly polarized eukaryotic cells, recent evidence suggests that mRNA localization coupled with local translation is a widespread strategy for spatial restriction of protein synthesis within cells. Genome-wide analyses and live imaging approaches have shed new light on the prevalence and the mechanistic details of this phenomenon. Here we review some of the recent findings that have emerged from research from the RNA localization field, from the birth of mRNAs in the nucleus, to their delivery at specific sites within the cytoplasm.

Nucleocytoplasmic shuttling of Ssd1 defines the destiny of its bound mRNAs

Mechanisms that control mRNA metabolism are critical for cell function, development and stress response. The Saccharomyces cerevisiae mRNA-binding protein Ssd1 has been implicated in mRNA processing, ageing, stress response and maintenance of cell integrity. Ssd1 is a substrate of the LATS/NDR tumour suppressor orthologue Cbk1 kinase. Previous data indicate that Ssd1 localizes to the cytoplasm; however, biochemical interactions suggest that Ssd1 at least transiently localizes to the nucleus. We therefore explored whether nuclear localization is important for Ssd1 cytoplasmic functions. We identified a functional NLS in the N-terminal domain of Ssd1. An Ssd1-derived NLS-GFP fusion protein and several C-terminally truncated Ssd1 proteins, which presumably lack nuclear export sequences, accumulate in the nucleus. Alanine substitution of the Ssd1 NLS prevents Ssd1 nuclear entry, mRNA binding and disrupts Srl1 mRNA localization. Moreover, Ssd1-NLS mutations abolish Ssd1 toxicity in the absence of Cbk1 phosphorylation and cause Ssd1 to localize prominently to cytoplasmic puncta. These data indicate that nuclear shuttling is critical for Ssd1 mRNA binding and Ssd1-mRNA localization in the cytoplasm. Collectively these data support the model that Ssd1 functions analogously to hnRNPs, which bind mRNA co-transcriptionally, are exported to the cytoplasm and target mRNAs to sites of localized translation and P-bodies.

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.

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.

She3p possesses a novel activity required for ASH1 mRNA localization in Saccharomyces cerevisiae

Intracellular and intercellular polarity requires that specific proteins be sorted to discreet locations within and between cells. One mechanism for sorting proteins is through RNA localization. In Saccharomyces cerevisiae, ASH1 mRNA localizes to the distal tip of the bud, resulting in the asymmetric sorting of the transcriptional repressor Ash1p. ASH1 mRNA localization requires four cis-acting localization elements and the trans-acting factors Myo4p, She3p, and She2p. Myo4p is a type V myosin motor that functions to directly transport ASH1 mRNA to the bud. She2p is an RNA-binding protein that directly interacts with the ASH1 mRNA cis-acting elements. Currently, the role for She3p in ASH1 mRNA localization is as an adaptor protein, since it can simultaneously associate with Myo4p and She2p. Here, we present data for two novel mutants of She3p, S348E and the double mutant S343E S361E, that are defective for ASH1 mRNA localization, and yet both of these mutants retain the ability to associate with Myo4p and She2p. These observations suggest that She3p possesses a novel activity required for ASH1 mRNA localization, and our data imply that this function is related to the ability of She3p to associate with ASH1 mRNA. Interestingly, we determined that She3p is phosphorylated, and global mass spectrometry approaches have determined that Ser 343, 348, and 361 are sites of phosphorylation, suggesting that the novel function for She3p could be negatively regulated by phosphorylation. The present study reveals that the current accepted model for ASH1 mRNA localization does not fully account for the function of She3p in ASH1 mRNA localization.

Nuclear shuttling of She2p couples ASH1 mRNA localization to its translational repression by recruiting Loc1p and Puf6p

The transport and localization of mRNAs results in the asymmetric synthesis of specific proteins. In yeast, the nucleocytoplasmic shuttling protein She2 binds the ASH1 mRNA and targets it for localization at the bud tip by recruiting the She3p-Myo4p complex. Although the cytoplasmic role of She2p in mRNA localization is well characterized, its nuclear function is still unclear. Here, we show that She2p contains a nonclassical nuclear localization signal (NLS) that is essential for its nuclear import via the importin alpha Srp1p. Exclusion of She2p from the nucleus by mutagenesis of its NLS leads to defective ASH1 mRNA localization and Ash1p sorting. Interestingly, these phenotypes mimic knockouts of LOC1 and PUF6, which encode for nuclear RNA-binding proteins that bind the ASH1 mRNA and control its translation. We find that She2p interacts with both Loc1p and Puf6p and that excluding She2p from the nucleus decreases this interaction. Absence of nuclear She2p disrupts the binding of Loc1p and Puf6p to the ASH1 mRNA, suggesting that nuclear import of She2p is necessary to recruit both factors to the ASH1 transcript. This study reveals that a direct coupling between localization and translation regulation factors in the nucleus is required for proper cytoplasmic localization of mRNAs.

Regulation of asymmetric stem cell division: spindle orientation and the centrosome

Asymmetric stem cell division, as a means of maintaining adequate numbers of stem cells, has attracted widespread attention from researchers in the stem cell biology field. Yet, the molecular and cellular mechanisms that govern asymmetric stem cell division remain poorly understood. Stem cells are not the only cell population that divides asymmetrically, and fortunately, great progress has been made in the understanding of asymmetric cell division during development, providing insight into strategies that stem cells may employ to divide asymmetrically. This review will summarize the importance of stem cell function and the role of asymmetric division in controlling stem cell behavior.

Translation of ASH1 mRNA is repressed by Puf6p-Fun12p/eIF5B interaction and released by CK2 phosphorylation

Translational repression during mRNA transport is essential for spatial restriction of protein production. In the yeast Saccharomyces cerevisae, silencing of ASH1 mRNA before it is localized to the bud cortex in late anaphase is critical for asymmetric segregation of Ash1p to the daughter cell nucleus. Puf6p, an ASH1 mRNA-binding protein, has been implicated in this process as a translational repressor, but the underlying mechanism is unknown. Here, we used yeast extract-based in vitro translation assays, which recapitulate translation and phosphorylation, to characterize the mechanism of Puf6p-mediated translational regulation. We report that Puf6p interferes with the conversion of the 48S complex to the 80S complex during initiation, and this repression by Puf6p is mediated through the general translation factor eIF5B (Fun12p in S. cerevisiae). Puf6p interacts with Fun12p via the PUF domain, and this interaction is RNA-dependent and essential for translational repression by Puf6p. This repression is relieved by phosphorylation of the N-terminal region of Puf6p mediated by protein kinase CK2 (casein kinase II). Inhibition of phosphorylation at Ser31, Ser34, and Ser35 of Puf6p increases its translational repression and results in ASH1 mRNA delocalization. Our results indicate that Puf6p suppresses the translation initiation of ASH1 mRNA via interaction with Fun12p during its transport, and this repression can be released by CK2 phosphorylation in the N-terminal region of Puf6p when the mRNA reaches the bud tip.

Translation of ASH1 mRNA is repressed by Puf6p-Fun12p/eIF5B interaction and released by CK2 phosphorylation

Translational repression during mRNA transport is essential for spatial restriction of protein production. In the yeast Saccharomyces cerevisae, silencing of ASH1 mRNA before it is localized to the bud cortex in late anaphase is critical for asymmetric segregation of Ash1p to the daughter cell nucleus. Puf6p, an ASH1 mRNA-binding protein, has been implicated in this process as a translational repressor, but the underlying mechanism is unknown. Here, we used yeast extract-based in vitro translation assays, which recapitulate translation and phosphorylation, to characterize the mechanism of Puf6p-mediated translational regulation. We report that Puf6p interferes with the conversion of the 48S complex to the 80S complex during initiation, and this repression by Puf6p is mediated through the general translation factor eIF5B (Fun12p in S. cerevisiae). Puf6p interacts with Fun12p via the PUF domain, and this interaction is RNA-dependent and essential for translational repression by Puf6p. This repression is relieved by phosphorylation of the N-terminal region of Puf6p mediated by protein kinase CK2 (casein kinase II). Inhibition of phosphorylation at Ser31, Ser34, and Ser35 of Puf6p increases its translational repression and results in ASH1 mRNA delocalization. Our results indicate that Puf6p suppresses the translation initiation of ASH1 mRNA via interaction with Fun12p during its transport, and this repression can be released by CK2 phosphorylation in the N-terminal region of Puf6p when the mRNA reaches the bud tip.

She3p binds to the rod of yeast myosin V and prevents it from dimerizing, forming a single-headed motor complex

Vertebrate myosin Va is a dimeric processive motor that walks on actin filaments to deliver cargo. In contrast, the two class V myosins in budding yeast, Myo2p and Myo4p, are non-processive (Reck-Peterson, S. L., Tyska, M. J., Novick, P. J., and Mooseker, M. S. (2001) J. Cell Biol. 153, 1121-1126). We previously showed that a chimera with the motor domain of Myo4p on the backbone of vertebrate myosin Va was processive, demonstrating that the Myo4p motor domain has a high duty ratio. Here we examine the properties of a chimera containing the rod and globular tail of Myo4p joined to the motor domain and neck of mouse myosin Va. Surprisingly, the adaptor protein She3p binds to the rod region of Myo4p and forms a homogeneous single-headed myosin-She3p complex, based on sedimentation equilibrium and velocity data. We propose that She3p forms a heterocoiled-coil with Myo4p and is a subunit of the motor. She3p does not affect the maximal actin-activated ATPase in solution or the velocity of movement in an ensemble in vitro motility assay. At the single molecule level, the monomeric myosin-She3p complex showed no processivity. When this construct was dimerized with a leucine zipper, short processive runs were obtained. Robust continuous movement was observed when multiple monomeric myosin-She3p motors were bound to a quantum dot "cargo." We propose that continuous transport of mRNA by Myo4p-She3p in yeast is accomplished either by multiple high duty cycle monomers or by molecules that may be dimerized by She2p, the homodimeric downstream binding partner of She3p.

Dendritic mRNA: transport, translation and function

Many cellular functions require the synthesis of a specific protein or functional cohort of proteins at a specific time and place in the cell. Local protein synthesis in neuronal dendrites is essential for understanding how neural activity patterns are transduced into persistent changes in synaptic connectivity during cortical development, memory storage and other long-term adaptive brain responses. Regional and temporal changes in protein levels are commonly coordinated by an asymmetric distribution of mRNAs. This Review attempts to integrate current knowledge of dendritic mRNA transport, storage and translation, placing particular emphasis on the coordination of regulation and function during activity-dependent synaptic plasticity in the adult mammalian brain.

mRNA trafficking in fungi

Fungal growth depends on active transport of macromolecules along the actin and/or microtubule cytoskeleton. Thereby, molecular cargo such as proteins, lipids, and mRNAs is targeted to defined subcellular regions. Active transport and localisation of mRNAs mediate localised translation so that protein synthesis occurs where protein function is required. In Saccharomyces cerevisiae, actomyosin-dependent mRNA trafficking participates in polar growth, asymmetric cell division, targeting of membrane proteins and import of mitochondrial proteins. The best-understood example is transport of ASH1 mRNA to the distal pole of the incipient daughter cell. cis-acting RNA sequences are recognised by the RNA-binding protein She2p that is connected via the adaptor She3p to the molecular motor Myo4p. Local translation at the poles of daughter cells causes Ash1p to accumulate predominantly in nuclei of daughter cells, where this transcription factor inhibits mating-type switching. Recently, it was also shown that actomyosin-dependent ASH1 mRNA transport directs tip cell-specific gene expression in filaments of the human pathogen Candida albicans. Furthermore, in the plant pathogen Ustilago maydis microtubule-dependent shuttling of the RNA-binding protein Rrm4 is essential to determine the axis of polarity in infectious filaments. Thus, mRNA trafficking appears to be universally required for polar growth of fungi.

Local activation of yeast ASH1 mRNA translation through phosphorylation of Khd1p by the casein kinase Yck1p

In S. cerevisiae, the ASH1 mRNA is localized at the bud tip of late-anaphase cells, resulting in the exclusive sorting of Ash1p to the daughter cell nucleus. While the mechanism behind the localization of this transcript has been well studied, the regulation of its translation is still poorly understood. We now report that the RNA binding protein Khd1 interacts with the ASH1 mRNA localization element E1 and with the C-terminal domain of eIF4G1 to regulate the translation of this transcript. Khd1p reduces translation initiation on the ASH1 mRNA and diminishes Ash1p leakage into the mother cell nucleus. Furthermore, we show that the casein kinase Yck1p phosphorylates Khd1p at the plasma membrane, disrupting the Khd1p-RNA complex and releasing its translational repression on the ASH1 mRNA. This study reveals how, by linking mRNA sorting and translational activation, Khd1p and Yck1p regulate the spatiotemporal expression of a cell fate determinant.

Molecular composition of IMP1 ribonucleoprotein granules

Localized mRNAs are transported to sites of local protein synthesis in large ribonucleoprotein (RNP) granules, but their molecular composition is incompletely understood. Insulin-like growth factor II mRNA-binding protein (IMP) zip code-binding proteins participate in mRNA localization, and in motile cells IMP-containing granules are dispersed around the nucleus and in cellular protrusions. We isolated the IMP1-containing RNP granules and found that they represent a unique RNP entity distinct from neuronal hStaufen and/or fragile X mental retardation protein granules, processing bodies, and stress granules. Granules were 100-300 nm in diameter and consisted of IMPs, 40 S ribosomal subunits, shuttling heterologous nuclear RNPs, poly(A)-binding proteins, and mRNAs. Moreover granules contained CBP80 and factors belonging to the exon junction complex and lacked eIF4E, eIF4G, and 60 S ribosomal subunits, indicating that embodied mRNAs are not translated. Granules embodied mRNAs corresponding to about 3% of the human embryonic kidney 293 mRNA transcriptome. Messenger RNAs encoding proteins participating in the secretory pathway and endoplasmic reticulum-associated quality control, as well as ubiquitin-dependent metabolism, were enriched in the granules, reinforcing the concept of RNP granules as post-transcriptional operons.

Dynamics of bidirectional transport of Arc mRNA in neuronal dendrites

The mRNA for Arc (activity-regulated cytoskeletal protein) is delivered into dendrites and localizes selectively at active synapses. Here we use a green fluorescent protein-based labeling system and confocal microscopy to define the transport kinetics of exogenously expressed mRNA from chimaeric Arc constructs (Arc/MS2 mRNA) in the dendrites of living rat neurons in culture. Arc/MS2 mRNA assembles into particles that move independently, bidirectionally, and intermittently in a fashion indicative of transport. Transport velocities range from below 6 to 65 mum/minute, which is consistent with actin-based and microtubule-based transport, respectively. In general, orthograde translocations are longer than retrograde translocations. Rapidly translocating Arc/MS2 mRNA particles sometimes reverse direction and decrease velocity just before stopping, suggesting that local signals regulate Arc mRNA targeting movements. These observations identify several phases of Arc mRNA movement that serve as potential points for regulating Arc mRNA localization.

Mitochondria-associated yeast mRNAs and the biogenesis of molecular complexes

The coherence of mitochondrial biogenesis relies on spatiotemporally coordinated associations of 800-1000 proteins mostly encoded in the nuclear genome. We report the development of new quantitative analyses to assess the role of local protein translation in the construction of molecular complexes. We used real-time PCR to determine the cellular location of 112 mRNAs involved in seven mitochondrial complexes. Five typical cases were examined by an improved FISH protocol. The proteins produced in the vicinity of mitochondria (MLR proteins) were, almost exclusively, of prokaryotic origin and are key elements of the core construction of the molecular complexes; the accessory proteins were translated on free cytoplasmic polysomes. These two classes of proteins correspond, at least as far as intermembrane space (IMS) proteins are concerned, to two different import pathways. Import of MLR proteins involves both TOM and TIM23 complexes whereas non-MLR proteins only interact with the TOM complex. Site-specific translation loci, both outside and inside mitochondria, may coordinate the construction of molecular complexes composed of both nuclearly and mitochondrially encoded subunits.

Intracellular Trafficking of RNA in Neurons

The transport of messenger RNAs (mRNAs) in neurons serves many purposes. During development, trafficking of mRNAs to both axonal and dendritic growth cones regulates neuronal growth. After synapse formation, mRNAs continue to be transported to dendrites both as a mechanism for the localization of proteins to specific compartments and as a substrate for local translational regulation of synaptic plasticity. Finally, activity-dependent mRNAs are transported quickly to dendrites after transcription. Determining how mRNAs are transported and specifically translated in these different paradigms is a major unanswered question. Addressing this question is also complicated by the presence of many other RNA processing and storage centers that may not be involved in transport but share components with the transport structures. In the present review, we will discuss several recent studies addressing mechanisms of mRNA transport in neurons, as well as proteomic characterization of mRNA transporting structures in neurons. We define two types of RNA transport structures in neurons, transport particles and RNA granules and distinguish them by the presence or absence of ribosomes. We will present a number of different molecular models for how mRNAs are repressed during transport, and how these may affect the regulation of local translation in neurons.

The yeast actin cytoskeleton: from cellular function to biochemical mechanism

All cells undergo rapid remodeling of their actin networks to regulate such critical processes as endocytosis, cytokinesis, cell polarity, and cell morphogenesis. These events are driven by the coordinated activities of a set of 20 to 30 highly conserved actin-associated proteins, in addition to many cell-specific actin-associated proteins and numerous upstream signaling molecules. The combined activities of these factors control with exquisite precision the spatial and temporal assembly of actin structures and ensure dynamic turnover of actin structures such that cells can rapidly alter their cytoskeletons in response to internal and external cues. One of the most exciting principles to emerge from the last decade of research on actin is that the assembly of architecturally diverse actin structures is governed by highly conserved machinery and mechanisms. With this realization, it has become apparent that pioneering efforts in budding yeast have contributed substantially to defining the universal mechanisms regulating actin dynamics in eukaryotes. In this review, we first describe the filamentous actin structures found in Saccharomyces cerevisiae (patches, cables, and rings) and their physiological functions, and then we discuss in detail the specific roles of actin-associated proteins and their biochemical mechanisms of action.

Aspergillus nidulans swoK encodes an RNA binding protein that is important for cell polarity

The Aspergillus nidulans swoK1 mutant is defective in polarity maintenance when grown at restrictive temperature (38 degrees C). Upon germination, the mutant extends a primary germ tube that swells to an enlarged, non-uniform cell with pronounced wall thickenings. The mutant is fully restored to wild-type growth when transformed with a plasmid containing the AN5802.2 ORF as designated in The Broad Institute A. nidulans sequence database. Genetic mapping places swoK in the same region of chromosome I, as that occupied by An5802.2 on the physical map. swoK is predicted to encode a protein that contains an N-terminal RRM (RNA Recognition Motif) and a highly repetitive C-terminus with numerous RD/DR and RS/SR dipeptides. We hypothesize that SwoK participates in one of the known functions of SR proteins (those that contain SR/RS repeats): mRNA maturation through the spliceosome and or transport of mRNAs out of the nucleus to sites of protein translation.

RNA localization in yeast: moving towards a mechanism

RNA localization is a widely utilized strategy employed by cells to spatially restrict protein function. In Saccharomyces cerevisiae asymmetric sorting of mRNA to the bud has been reported for at least 24 mRNAs. The mechanism by which the mRNAs are trafficked to the bud, illustrated by ASH1 mRNA, involves recognition of cis-acting localization elements present in the mRNA by the RNA-binding protein, She2p. The She2p/mRNA complex subsequently associates with the myosin motor protein, Myo4p, through an adapter, She3p. This ribonucleoprotein complex is transported to the distal tip of the bud along polarized actin cables. While the mechanism by which ASH1 mRNA is anchored at the bud tip is unknown, current data point to a role for translation in this process, and the rate of translation of Ash1p during the transport phase is regulated by the cis-acting localization elements. Subcellular sorting of mRNA in yeast is not limited to the bud; certain mRNAs corresponding to nuclear-encoded mitochondrial proteins are specifically sorted to the proximity of mitochondria. Analogous to ASH1 mRNA localization, mitochondrial sorting requires cis-acting elements present in the mRNA, though trans-acting factors involved with this process remain to be identified. This review aims to discuss mechanistic details of mRNA localization in S. cerevisiae.

She2p Is a Novel RNA Binding Protein with a Basic Helical Hairpin Motif

Selective transport of mRNAs in ribonucleoprotein particles (mRNP) ensures asymmetric distribution of information within and among eukaryotic cells. Actin-dependent transport of ASH1 mRNA in yeast represents one of the best-characterized examples of mRNP translocation. Formation of the ASH1 mRNP requires recognition of zip code elements by the RNA binding protein She2p. We determined the X-ray structure of She2p at 1.95 A resolution. She2p is a member of a previously unknown class of nucleic acid binding proteins, composed of a single globular domain with a five alpha helix bundle that forms a symmetric homodimer. After demonstrating potent, dimer-dependent RNA binding in vitro, we mapped the RNA binding surface of She2p to a basic helical hairpin in vitro and in vivo and present a mechanism for mRNA-dependent initiation of ASH1 mRNP complex assembly.

Selective gene expression in multigene families from yeast to mammals

Exclusive gene expression, where only one member of a gene or gene cassette family is selected for expression, plays an important role in the establishment of cell identity in several biological systems. Here, we compare four such systems: mating-type switching in fission and budding yeast, where cells choose between expressing one of the two different mating-type cassettes, and immunoglobulin and odorant receptor gene expression in mammals, where the number of gene choices is substantially higher. The underlying mechanisms that establish this selective expression pattern in each system differ in almost every detail. In all four systems, once a successful gene activation event has taken place, a feedback mechanism affects the fate of the cell. In the mammalian systems, feedback is mediated by the expressed cell surface receptor to ensure monoallelic gene expression, whereas in the yeasts, the expressed gene cassette at the mating-type locus affects donor choice during the subsequent switching event.

Are genetic determinants of asymmetric stem cell division active in hematopoietic stem cells?

Stem cells have acquired a golden glow in the past few years as they represent possible tools for reversing the damage wreak on organs. These cells are found not only in major regenerative tissues, such as the epithelia, blood and testes, but also in 'static tissues', such as the nervous system and liver, where they play a central role in tissue growth and maintenance. The mechanism by which stem cells maintain populations of highly differentiated, short-lived cells seems to involve a critical balance between alternate fates: daughter cells either maintain stem cell identity or initiate differentiation. Recent studies in lower organisms have unveiled the regulatory mechanisms of asymmetric stem cell divisions. In these models, the surrounding environment likely provides key instructive signals for the cells to choose one fate over another. Our understanding now extends to the intrinsic mechanisms of cell polarity that influence asymmetrical stem cell divisions. This article focuses on the genetic determinants of asymmetric stem cell divisions in lower organisms as a model for studying the process of self-renewal of mammalian hematopoietic stem cells.

ASH1 mRNA Anchoring Requires Reorganization of the Myo4p-She3p-She2p Transport Complex

One mechanism by which cells post-transcriptionally regulate gene expression is via intercellular and intracellular sorting of mRNA. In Saccharomyces cerevisiae, the localization of ASH1 mRNA to the distal tip of budding cells results in the asymmetric sorting of Ash1p to daughter cell nuclei. Efficient localization of ASH1 mRNA depends upon the activity of four cis-acting localization elements and also upon the activity of trans-factors She2p, She3p, and Myo4p. She2p, She3p, and Myo4p have been proposed to form an ASH1 mRNA localization particle. She2p directly and specifically binds each of the four ASH1 cis-acting localization elements, whereas She3p has been hypothesized to function as an adaptor by recruiting the She2p-mRNA complex to Myo4p, a type V myosin. The Myo4p-She3p-She2p heterotrimeric protein complex has been proposed to localize mRNA to daughter cells using polarized actin cables. Here we demonstrate that whereas the predicted Myo4p-She3p-She2p heterotrimeric complex forms in vivo, it represents a relatively minor species compared with the Myo4p-She3p complex. Furthermore, contrary to a prediction of the heterotrimeric complex model for ASH1 mRNA localization, ASH1 mRNA artificially tethered to She2p is not localized. Upon closer examination, we found that mRNA tightly associated with She2p is transported to daughter cells but is not properly anchored at the bud tip. These results are consistent with a model whereby anchoring of ASH1 mRNA requires molecular remodeling of the Myo4p-She3p-She2p heterotrimeric complex, a process that is apparently altered when mRNA is artificially tethered to She2p.

A new yeast PUF family protein, Puf6p, represses ASH1 mRNA translation and is required for its localization

In yeast Saccharomyces cerevisiae, Ash1p, a protein determinant for mating-type switching, is segregated within the daughter cell nucleus to establish asymmetry of HO expression. The accumulation of Ash1p results from ASH1 mRNA that is sorted as a ribonucleoprotein particle (mRNP or locasome) to the distal tip of the bud where translation occurs. To study the mechanism regulating ASH1 mRNA translation, we isolated the ASH1 locasome and characterized the associated proteins by MALDI-TOF. One of these proteins was Puf6p, a new member of the PUF family of highly conserved RNA-binding proteins such as Pumilio in Drosophila, responsible for translational repression, usually to effect asymmetric expression. Puf6p-bound PUF consensus sequences in the 3'UTR of ASH1 mRNA and repressed the translation of ASH1 mRNA both in vivo and in vitro. In the puf6 Delta strain, asymmetric localization of both Ash1p and ASH1 mRNA were significantly reduced. We propose that Puf6p is a protein that functions in the translational control of ASH1 mRNA, and this translational inhibition is necessary before localization can proceed.