mRNA localisation gets more complex

Organizing the oocyte: RNA localization meets phase separation

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

Bioinformatics Approaches to Gain Insights into cis-Regulatory Motifs Involved in mRNA Localization

Messenger RNA (mRNA) is a fundamental intermediate in the expression of proteins. As an integral part of this important process, protein production can be localized by the targeting of mRNA to a specific subcellular compartment. The subcellular destination of mRNA is suggested to be governed by a region of its primary sequence or secondary structure, which consequently dictates the recruitment of trans-acting factors, such as RNA-binding proteins or regulatory RNAs, to form a messenger ribonucleoprotein particle. This molecular ensemble is requisite for precise and spatiotemporal control of gene expression. In the context of RNA localization, the description of the binding preferences of an RNA-binding protein defines a motif, and one, or more, instance of a given motif is defined as a localization element (zip code). In this chapter, we first discuss the cis-regulatory motifs previously identified as mRNA localization elements. We then describe motif representation in terms of entropy and information content and offer an overview of motif databases and search algorithms. Finally, we provide an outline of the motif topology of asymmetrically localized mRNA molecules.

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 localization in bacteria

One of the most important discoveries in the field of microbiology in the last two decades is that bacterial cells have intricate subcellular organization. This understanding has emerged mainly from the depiction of spatial and temporal organization of proteins in specific domains within bacterial cells, e.g., midcell, cell poles, membrane and periplasm. Because translation of bacterial RNA molecules was considered to be strictly coupled to their synthesis, they were not thought to specifically localize to regions outside the nucleoid. However, the increasing interest in RNAs, including non-coding RNAs, encouraged researchers to explore the spatial and temporal localization of RNAs in bacteria. The recent technological improvements in the field of fluorescence microscopy allowed subcellular imaging of RNAs even in the tiny bacterial cells. It has been reported by several groups, including ours that transcripts may specifically localize in such cells. Here we review what is known about localization of RNA and of the pathways that determine RNA fate in bacteria, and discuss the possible cues and mechanisms underlying these distribution patterns.

The functions and regulatory principles of mRNA intracellular trafficking

The subcellular localization of RNA molecules is a key step in the control of gene expression that impacts a broad array of biological processes in different organisms and cell types. Like other aspects of posttranscriptional gene regulation discussed in this collection of reviews, the intracellular trafficking of mRNAs is modulated by a complex regulatory code implicating specific cis-regulatory elements, RNA-binding proteins, and cofactors that function combinatorially to dictate precise localization mechanisms. In this review, we first discuss the functional benefits of transcript localization, the regulatory principles involved, and specific molecular mechanisms that have been described for a few well-characterized mRNAs. We also overview some of the emerging genomic and imaging technologies that have provided significant insights into this layer of gene regulation. Finally, we highlight examples of human diseases where defective transcript localization has been documented.

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.

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.

Asymmetric localisation of cytokine mRNA is essential for JAK/STAT activation during cell invasiveness

The transition from immotile epithelial cells to migrating cells occurs in all organisms during normal embryonic development, as well as during tumour metastasis. During Drosophila oogenesis, border cells (BCs) are recruited and delaminate from the follicular epithelium. This process is triggered by the polar cells (PCs), which secrete the cytokine Unpaired (Upd) and activate the JAK/STAT pathway in neighbouring cells, turning them into invasive BCs. Interestingly, either a decrease or an increase in BC number alters migration, indicating that mechanisms controlling the level of JAK/STAT signalling are crucial in this process. Here, we show that PCs have a highly stable and polarised network of microtubules along which upd transcripts are asymmetrically transported in a Dynein-dependent manner. We demonstrate that in the absence of upd mRNA localisation the ligand is no longer efficiently secreted, leading to a loss of signalling strength as well as recruitment and migration defects. These findings reveal a novel post-transcriptional regulatory mechanism of JAK/STAT signalling in the control of epithelial cell invasiveness.

Epigenetic regulation of neuronal dendrite and dendritic spine development

Dendrites and the dendritic spines of neurons play key roles in the connectivity of the brain and have been recognized as the locus of long-term synaptic plasticity, which is correlated with learning and memory. The development of dendrites and spines in the mammalian central nervous system is a complex process that requires specific molecular events over a period of time. It has been shown that specific molecules are needed not only at the spine's point of contact, but also at a distance, providing signals that initiate a cascade of events leading to synapse formation. The specific molecules that act to signal neuronal differentiation, dendritic morphology, and synaptogenesis are tightly regulated by genetic and epigenetic programs. It has been shown that the dendritic spine structure and distribution are altered in many diseases, including many forms of mental retardation (MR), and can also be potentiated by neuronal activities and an enriched environment. Because dendritic spine pathologies are found in many types of MR, it has been proposed that an inability to form normal spines leads to the cognitive and motor deficits that are characteristic of MR. Epigenetic mechanisms, including DNA methylation, chromatin remodeling, and the noncoding RNA-mediated process, have profound regulatory roles in mammalian gene expression. The study of epigenetics focuses on cellular effects that result in a heritable pattern of gene expression without changes to genomic encoding. Despite extensive efforts to understand the molecular regulation of dendrite and spine development, epigenetic mechanisms have only recently been considered. In this review, we will focus on epigenetic mechanisms that regulate the development and maturation of dendrites and spines. We will discuss how epigenetic alterations could result in spine abnormalities that lead to MR, such as is seen in fragile X and Rett syndromes. We will also discuss both general methodology and recent technological advances in the study of neuronal dendrites and spines.

The microRNA miR-696 regulates PGC-1{alpha} in mouse skeletal muscle in response to physical activity

MicroRNAs (miRNAs) are small noncoding RNAs involved in posttranscriptional gene regulation that have been shown to be involved in growth, development, function, and stress responses of various organs. The purpose of this study was to identify the miRNA response to physical activity, which was related to functions such as nutrient metabolism, although the miRNAs involved are currently unknown. C57BL/6 mice were divided into exercise and control groups. The exercise group performed running exercise, with a gradual increase of the load over 4 wk. On the other hand, to examine the effect of muscle inactivity, the unilateral hindlimbs of other mice were fixed in a cast for 5 days. Microarray analysis for miRNA in gastrocnemius revealed that miR-696 was markedly affected by both exercise and immobilization, showing opposite responses to these two interventions. Peroxisome proliferator-activated receptor-gamma coactivator-1alpha (PGC-1alpha), which was increased by exercise and decreased by immobilization in the protein level, was predicted as a target regulated by miR-696. In cultured myocytes, intracellular miR-696 variation led to negative regulation of PGC-1alpha protein along with the expression of mRNAs for downstream genes. In addition, we found decreases in the biogenesis of mitochondria and fatty acid oxidation in miR-696-overexpressing myocytes compared with normal control myocytes. These observations demonstrate that miR-696 is a physical activity-dependent miRNA involved in the translational regulation of PGC-1alpha and skeletal muscle metabolism in mice.

A global comparison between nuclear and cytosolic transcriptomes reveals differential compartmentalization of alternative transcript isoforms

Transcriptome analyses have typically disregarded nucleocytoplasmic differences. This approach has ignored some post-transcriptional regulations and their effect on the ultimate protein expression levels. Despite a longstanding interest in the differences between the nuclear and cytosolic transcriptomes, it is only recently that data have become available to study such differences and their associated features on a genome-wide scale. Here, we compared the nuclear and cytosolic transcriptomes of HepG2 and HeLa cells. HepG2 and HeLa cells vary significantly in the differential compartmentalization of their transcript isoforms, indicating that nucleocytoplasmic compartmentalization is a cell-specific characteristic. The differential compartmentalization is manifested at the transcript isoform level instead of the gene level because alternative isoforms of one gene can display different nucleocytoplasmic distributions. The isoforms enriched in the cytosol tend to have more introns and longer introns in their pre-mRNAs. They have more functional RNA folds and unique exons in the 3′ regions. These isoforms are more conserved than the isoforms enriched in the nucleus. Surprisingly, the presence of microRNAs does not have a significant impact on the nucleocytoplasmic distribution of their target isoforms. In contrast, nonsense-mediated decay is significantly more associated with the isoforms enriched in the nucleus than those enriched in the cytosol.

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.

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.

The 5' cap of tobacco mosaic virus (TMV) is required for virion attachment to the actin/endoplasmic reticulum network during early infection

Almost nothing is known of the earliest stages of plant virus infections. To address this, we microinjected Cy3 (UTP)-labelled tobacco mosaic virus (TMV) into living tobacco trichome cells. The Cy3-virions were infectious, and the viral genome trafficked from cell to cell. However, neither the fluorescent vRNA pool nor the co-injected green fluorescent protein (GFP) left the injected trichome, indicating that the synthesis of (unlabelled) progeny viral (v)RNA is required to initiate cell-to-cell movement, and that virus movement is not accompanied by passive plasmodesmatal gating. Cy3-vRNA formed granules that became anchored to the motile cortical actin/endoplasmic reticulum (ER) network within minutes of injection. Granule movement on actin/ER was arrested by actin inhibitors indicating actin-dependent RNA movement. The 5' methylguanosine cap was shown to be required for vRNA anchoring to the actin/ER. TMV vRNA lacking the 5' cap failed to form granules and was degraded in the cytoplasm. Removal of the 3' untranslated region or replicase both inhibited replication but did not prevent granule formation and movement. Dual-labelled TMV virions in which the vRNA and the coat protein were highlighted with different fluorophores showed that both fluorescent signals were initially located on the same ER-bound granules, indicating that TMV virions may become attached to the ER prior to uncoating of the viral genome.

Transport of TMV movement protein particles associated with the targeting of RNA to plasmodesmata

The cell-to-cell movement of Tobacco mosaic virus through plasmodesmata (PD) requires virus-encoded movement protein (MP). The MP targets PD through the endoplasmic reticulum (ER)/actin network, whereas the intercellular movement of the viral RNA genome has been correlated with the association of the MP with mobile, microtubule-proximal particles in cells at the leading front of infection as well as the accumulation of the protein on the microtubule network during later infection stages. To understand how the associations of MP with ER and microtubules are functionally connected, we applied multiple marker three-dimensional confocal and time-lapse video microscopies to Nicotiana benthamiana cells expressing fluorescent MP, fluorescent RNA and fluorescent cellular markers. We report the reconstitution of MP-dependent RNA transport to PD in a transient assay. We show that transiently expressed MP occurs in association with small particles as observed during infection. The same MP accumulates in PD and mediates the transport of its messenger RNA transcript to the pore. In the cellular cortex, the particles occur at microtubule-proximal sites and can undergo ER-associated and latrunculin-sensitive movements between such sites. These and other observations suggest that the microtubule network performs anchorage and release functions for controlling the assembly and intracellular movement of MP-containing RNA transport particles in association with the ER.

A novel RNA-binding protein associated with cell plate formation

Building a cell plate during cytokinesis in plant cells requires the participation of a number of proteins in a multistep process. We previously identified phragmoplastin as a cell plate-specific protein involved in creating a tubulovesicular network at the cell plate. We report here the identification and characterization of a phragmoplastin-interacting protein, PHIP1, in Arabidopsis (Arabidopsis thaliana). It contains multiple functional motifs, including a lysine-rich domain, two RNA recognition motifs, and three CCHC-type zinc fingers. Polypeptides with similar motif structures were found only in plant protein databases, but not in the sequenced prokaryotic, fungal, and animal genomes, suggesting that PHIP1 represents a plant-specific RNA-binding protein. In addition to phragmoplastin, two Arabidopsis small GTP-binding proteins, Rop1 and Ran2, are also found to interact with PHIP1. The zinc fingers of PHIP1 were not required for its interaction with Rop1 and phragmoplastin, but they may participate in its binding with the Ran2 mRNA. Immunofluorescence, in situ RNA hybridization, and green fluorescent protein tagging experiments showed the association of PHIP1 with the forming cell plate during cytokinesis. Taken together, our data suggest that PHIP1 is a novel RNA-binding protein and may play a unique role in the polarized mRNA transport to the vicinity of the cell plate.

Drosophila Dynein light chain (DDLC1) binds to gurken mRNA and is required for its localization

During oogenesis in Drosophila, mRNAs encoding determinants required for the polarization of egg and embryo become localized in the oocyte in a spatially restricted manner. The TGF-alpha like signaling molecule Gurken has a central role in the polarization of both body axes and the corresponding mRNA displays a unique localization pattern, accumulating initially at the posterior and later at the anterior-dorsal of the oocyte. Correct localization of gurken RNA requires a number of cis-acting sequence elements, a complex of trans-acting proteins, of which only several have been identified, and the motor proteins Dynein and Kinesin, traveling along polarized microtubules. Here we report that the cytoplasmic Dynein-light-chain (DDLC1) which is the cargo-binding subunit of the Dynein motor protein, directly bound with high specificity and affinity to a 230-nucleotide region within the 3'UTR of gurken, making it the first Drosophila mRNA-cargo to directly bind to the DLC. Although DDLC1 lacks known RNA-binding motifs, comparison to double-stranded RNA-binding proteins suggested structural resemblance. Phenotypic analysis of ddlc1 mutants supports a role for DDLC1 in gurken RNA localization and anchoring as well as in correct positioning of the oocyte nucleus.

Ol-insm1b, a SNAG family transcription factor involved in cell cycle arrest during medaka development

Through whole-mount in situ hybridisation screen on medaka (Oryzias latipes) brain, Ol-insm1b, a member of the Insm1/Mlt1 subfamily of SNAG-domain containing genes, has been isolated. It is strongly expressed during neurogenesis and pancreas organogenesis, with a pattern that suggests a role in cell cycle exit. Here, we describe Ol-insm1b expression pattern throughout development and in adult brain, and we report on its functional characterisation. Our data point to a previously unravelled role for Ol-insm1b as a down-regulator of cell proliferation during development, as it slows down the cycle without triggering apoptosis. Clonal analysis demonstrates that this effect is cell-autonomous, and, through molecular dissection studies, we demonstrate that it is likely to be non-transcriptional, albeit mediated by zinc-finger domains. Additionally, we report that Ol-insm1b mRNA, when injected in one cell of two-cell stage embryos, exhibits a surprising behaviour: it does not spread uniformly amongst daughter cells but remains cytoplasmically localised in the progeny of the injected blastomere. Our experiments suggest that Insm1 is a negative regulator of cell proliferation, possibly through mechanisms that do not involve modulation of transcription.

RNA localization signals: deciphering the message with bioinformatics

mRNA localization is an important posttranscriptional method of targeting proteins to their site of function. The sorting of transcripts to their correct intracellular destination is achieved by a number of mechanisms, including selective degradation or transport by molecular motors along the cytoskeleton. In all cases, this involves mRNA localization signals, or so called zip codes, being recognized by trans-acting cellular factors. In a few cases, primary sequence motifs for RNA localization can be identified, but in general, localization signals operate at the level of secondary (2D) and tertiary (3D) structure. This inevitably means that searching for localization signal motifs is a complex task requiring specialist knowledge of bioinformatics. Furthermore, the publications describing these searching methods tend to be aimed at the bioinformatics community. In this review, we have surveyed the major tools for folding, comparing, and searching potential mRNA localization signals in transcripts or across genomes. Our aim is to provide an overview for biologists, who lack specialist computer and bioinformatics training, of the major RNA bioinformatics tools that are available. The examples provided are focused on mRNA localization signals and RNA stem-loop structures, however, these tools can be applied to the study of any RNA signals.

Testosterone increases lactate transport, monocarboxylate transporter (MCT) 1 and MCT4 in rat skeletal muscle

We have examined the effects of administration of testosterone for 7 days on monocarboxylate transporter (MCT) 1 and MCT4 mRNAs and proteins in seven metabolically heterogeneous rat hindlimb muscles and in the heart. In addition, we also examined the effects of testosterone treatment on plasmalemmal MCT1 and MCT4, and lactate transport into giant sarcolemmal vesicles prepared from red and white hindlimb muscles and the heart. Testosterone did not alter MCT1 or MCT4 mRNA, except in the plantaris muscle. Testosterone increased MCT1 (20%-77%, P < 0.05) and MCT4 protein (29%-110%, P< 0.05) in five out of seven muscles examined. In contrast, in the heart MCT1 protein was not increased (P> 0.05), and MCT 4 mRNA and protein were not detected. There was no correlation between the testosterone-induced increments in MCT1 and MCT4 proteins. Muscle fibre composition was not associated with testosterone-induced increments in MCT1 protein. In contrast, there was a strong positive relationship between the testosterone-induced increments in MCT4 protein and the fast-twitch fibre composition of rat muscles. Lactate transport into giant sarcolemmal vesicles was increased in red (23%, P< 0.05) and white muscles (21%, P< 0.05), and in the heart (58%, P< 0.05) of testosterone-treated animals (P< 0.05). However, plasmalemmal MCT1 protein (red, +40%, P< 0.05; white, +39%, P< 0.05) and plasmalemmal MCT4 protein (red, +25%, P< 0.05; white, +48%, P< 0.05) were increased only in skeletal muscle. In the heart, plasmalemmal MCT1 protein was reduced (-20%, P< 0.05). In conclusion, these studies have shown that testosterone induces an increase in both MCT1 and MCT4 proteins and their plasmalemmal content in skeletal muscle. However, the testosterone-induced effect was tissue-specific, as MCT1 protein expression was not altered in the heart. In the heart, the testosterone-induced increase in lactate transport cannot be explained by changes in plasmalemmal MCT1 content, but in skeletal muscle the increase in the rate of lactate transport was associated with increases in plasmalemmal MCT1 and MCT4.

Fatty acid transport and FAT/CD36 are increased in red but not in white skeletal muscle of ZDF rats

An increased rate of fatty acid transport into skeletal muscle has been has been linked to the accumulation of intramuscular lipids and insulin resistance, and red muscles are more susceptible than white muscles in developing fatty acid-mediated insulin resistance. Therefore, we examined in Zucker diabetic fatty (ZDF) rats, relative to lean rats, 1) whether rates of fatty acid transport and transporters (FAT/CD36 and FABPpm) were upregulated in skeletal muscle during the transition from insulin resistance (week 6) to type 2 diabetes (weeks 12 and 24), 2) whether such changes occurred primarily in red skeletal muscle, and 3) whether changes in FAT/CD36 and GLUT4 were correlated. In red muscles of ZDF compared with lean rats, the rates of fatty acid transport were upregulated (+66%) early in life (week 6). Compared with the increase in fatty acid transport in lean red muscle from weeks 12-24 (+57%), the increase in fatty acid transport rate in ZDF red muscle was 50% greater during this same period. In contrast, no differences in fatty acid transport rates were observed in the white muscles of lean and ZDF rats at any time (weeks 6-24). In red muscle only, there was an inverse relationship between FAT/CD36 and GLUT4 protein expression as well as their plasmalemmal content. These studies have shown that, 1) before the onset of diabetes, as well as during diabetes, fatty acid transport and FAT/CD36 expression and plasmalemmal content are upregulated in ZDF rats, but importantly, 2) these changes occurred only in red, not white, muscles of ZDF rats.

Tissue-Specific and Fatty Acid Transporter-Specific Changes in Heart and Soleus Muscle Over a 1-yr Period

Rates of fatty acid oxidation increase rapidly in both rat heart and skeletal muscle in the early postnatal period. Therefore, we examined in heart and soleus muscle, (a) whether there were rapid changes in fatty acid transporter (FAT/CD36, FABPpm) mRNA and protein expression early in life (days 10 -36) and thereafter (days 84, 160, 365), and (b) whether the rates of fatty acid transport and the plasmalemmal content of FAT/CD36 and FABPpm were altered. Protein expression was altered rapidly from day 10-36 in both heart (FAT/CD36 only, +21%, P < 0.05)) and soleus muscle (FAT/CD36 + 100%, P < 0.05; FABPpm -20%, P < 0.05), with no further changes thereafter (P < 0.05). Rates of fatty acid transport (day 10 vs day 160) were increased in heart (+33%, P < 0.05) and muscle (+85%, P < 0.05), and were associated with concomitant increases in plasmalemmal FABPpm (+44%, P < 0.05) and FAT/CD36 (+16%, P < 0.05) in the heart, and only plasmalemmal FAT/CD36 in muscle (+90%, P < 0.05). Therefore, known changes in the rates of fatty acid oxidation in heart and muscle early in life appear to be accompanied by a concurrent upregulation in the rates of fatty acid transport and the expression of FAT/CD36 in heart and muscle, as well as an increase in plasmalemmal FAT/CD36 and FABPpm in the heart, and only plasmalemmal FAT/CD36 in soleus muscle. We speculate that the rapid upregulation of fatty acid transport rates in heart and muscle are needed to support the increased rates of fatty oxidation that have been previously observed in these tissues.

What is the biological significance of BDNF mRNA targeting in the dendrites? Clues from epilepsy and cortical development

The neurotrophin brain-derived neurotrophic factor (BDNF) is a regulatory factor of several, partially contrasting, aspects of the biology of neural cells, including survival, growth, differentiation, and cell death. Regulation of the local availability of BDNF at distinct subcellular domains such as the cell soma, dendrites, axons, and spines appears to be the key to conferring spatial and temporal specificity of the different effects elicited by this neurotrophin. This article reviews recent findings in the context of epileptogenesis and visual cortex maturation that showed that different BDNF messenger RNA (mRNA) transcripts are localized at different subcellular locations in hippocampal and cortical neurons. It also reviews findings demonstrating that strong depolarizing stimuli, both in vitro and in vivo, elicit accumulation of BDNF mRNA and protein in the distal dendrites through a signaling pathway involving the activation of the N-methyl-D-aspartate and tyrosine kinase B receptors and an intracellular increase in Ca2+ concentration. Finally, this article proposes that the regulation of the delivery of BDNF mRNA and protein to the different subcellular domains--particularly the dendritic compartment--may represent a fundamental aspect of the processes of cellular and synaptic morphological rearrangements underlying epileptogenesis and postnatal development of the visual cortex.

The role of mRNA and protein sorting in seed storage protein synthesis, transport, and deposition

Rice synthesizes and accumulates high levels of 2 distinct classes of seed storage proteins and sorts them to separate intracellular compartments, making it an ideal model system for studying the mechanisms of storage protein synthesis, transport, and deposition. In rice, RNA localization dictates the initial site of storage protein synthesis on specific subdomains of the cortical endoplasmic reticulum (ER), and there is a direct relation between the RNA localization site and the final destination of the encoded protein within the endomembrane system. Current data support the existence of 3 parallel RNA localization pathways leading from the nucleus to the actively synthesizing cortical ER. Additional pathways may exist for the synthesis of cytoplasmic and nuclear-encoded proteins targeted to organelles, the latter located in a stratified arrangement in developing endosperm cells. The study of rice mutants, which accumulate unprocessed glutelin precursors, indicates that these multiple pathways prevent nonproductive interactions between different classes of storage proteins that would otherwise disrupt protein sorting. Indeed, it appears that the prevention of disruptive interactions between different classes of storage proteins plays a key role in their biosynthesis in rice. In addition to highlighting the unique features of the plant endomembrane system and describing the relation between RNA and protein localization, this minireview will attempt to address a number of questions raised by recent studies on these processes.

Temporal fluctuation of nuclear pore complex localization by single diffusing mRNP complexes

There is now compelling evidence that messenger ribonucleoprotein (mRNP) complexes after the release from the transcription/processing sites execute essentially unhindered Brownian movements in the nucleoplasm and target nuclear pore complexes (NPCs) by chance encounter. For the majority of genes expressed in eukaryotic cells, only single/few transcript copies are generated, which reinforces the stochastic nature of NPC localization. In this paper, I analyse the NPC localization by freely diffusing single mRNPs and discuss the implications for the temporal progression of gene expression and consecutive processes associated with the gene products. To this end, a walk-and-capture model is considered, assuming a spherical nuclear compartment with a partially absorbing boundary. Perfect absorption and perfect reflection mark the extreme outcomes. For this model, the closed-form analytic solution of the first-passage time probability density function (FPT p.d.f.), the mean passage time and variance have been obtained. The FPT p.d.f. enables to calculate the probability that single mRNPs localize the nuclear boundary and dock to NPCs within certain time windows. For freely moving mRNP complexes in osteosarcoma cell nuclei, a mean apparent diffusion coefficient (D) of 0.04 microm2 s(-1) (range 0.01-0.09 microm2 s(-1)) has been reported. Assuming a nuclear radius of 8 microm and D=0.04 microm2 s(-1), the position-averaged minimum mean passage time <tau(r0)>min for the considered model is 1.8 min, which presupposes perfect absorption of the mRNP complex at the first encounter with the nuclear boundary. In this case, the probability of capture in the time interval (0, <tau(r0)>min) is 0.67. In smaller sized yeast cell nuclei with a radius of 0.8 mum and D=0.04 microm2 s(-1), single diffusing mRNPs would localize an NPC within tens of seconds, rather than minutes.

Inverse relationship between PGC-1alpha protein expression and triacylglycerol accumulation in rodent skeletal muscle

PGC-1alpha is a key regulator of tissue metabolism, including skeletal muscle. Because it has been shown that PGC-1alpha alters the capacity for lipid metabolism, it is possible that PGC-1alpha expression is regulated by the intramuscular lipid milieu. Therefore, we have examined the relationship between PGC-1alpha protein expression and the intramuscular fatty acid accumulation in hindlimb muscles of animals in which the capacity for fatty acid accumulation in muscle is increased (Zucker obese rat) or reduced [FAT/CD36 null (KO) mice]. Rates of palmitate incorporation into triacylglycerols were determined in perfused red (RG) and white gastrocnemius (WG) muscles of lean and obese Zucker rats and in perfused RG and WG muscles of FAT/CD36 KO and wild-type (WT) mice. In obese Zucker rats, the rate of palmitate incorporation into triacylglycerol depots in RG and WG muscles were 28 and 24% greater than in lean rats (P < 0.05). In FAT/CD36 KO mice, the rates of palmitate incorporation into triacylglycerol depots were lower in RG (-50%) and WG muscle (-24%) compared with the respective muscles in WT mice (P < 0.05). In the obese animals, PGC-1alpha protein content was reduced in both RG (-13%) and WG muscles (-15%) (P < 0.05). In FAT/CD36 KO mice, PGC-1alpha protein content was upregulated in both RG (+32%, P < 0.05) and WG muscles (+50%, P < 0.05). In conclusion, from studies in these two animal models, it appears that PGC-1alpha protein expression is inversely related to components of intramuscular lipid metabolism, because 1) PGC-1alpha protein expression is downregulated when triacylglycerol synthesis rates, an index of intramuscular lipid metabolism, are increased, and 2) PGC-1alpha protein expression is upregulated when triacylglycerol synthesis rates are reduced. Therefore, we speculate that the intramuscular lipid sensing may be involved in regulating the protein expression of PGC-1alpha in skeletal muscle.

Endoplasmic reticulum: one continuous network compartmentalized by extrinsic cues

The endoplasmic reticulum (ER) is an extensive three-dimensional network that stretches from the inner nuclear envelope to the cell cortex with a single, continuous membrane and a single, continuous lumen. Yet the ER contains specialized regions that carry out unique functions. The question that immediately arises is how the ER can be compartmentalized if it is continuous, and the answer to this is that cellular landmarks with unique sub-cellular distributions impose non-uniformity on the ER from outside, creating structural and functional sub-domains of the ER.

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.

Dynein anchors its mRNA cargo after apical transport in the Drosophila blastoderm embryo

Molecular motors actively transport many types of cargo along the cytoskeleton in a wide range of organisms. One class of cargo is localized mRNAs, which are transported by myosin on actin filaments or by kinesin and dynein on microtubules. How the cargo is kept at its final intracellular destination and whether the motors are recycled after completion of transport are poorly understood. Here, we use a new RNA anchoring assay in living Drosophila blastoderm embryos to show that apical anchoring of mRNA after completion of dynein transport does not depend on actin or on continuous active transport by the motor. Instead, apical anchoring of RNA requires microtubules and involves dynein as a static anchor that remains with the cargo at its final destination. We propose a general principle that could also apply to other dynein cargo and to some other molecular motors, whereby cargo transport and anchoring reside in the same molecule.

The translational efficiencies of the two Leishmania infantum HSP70 mRNAs, differing in their 3'-untranslated regions, are affected by shifts in the temperature of growth through different mechanisms

Exposure of Leishmania promastigotes to the temperature of their mammalian hosts induces a typical heat-shock response. In Leishmania infantum, HSP70 is encoded by two types of genes that differ in their 3'-untranslated regions (3'-UTRs). Previously, we have shown that specific transcripts for each gene are present in promastigotes growing at normal temperature (26 degrees C), but only transcripts with 3'-UTR-type I (3'-UTRI) accumulate in a temperature-dependent manner. Here, we have investigated the translational efficiencies of both types of HSP70 transcripts at the different temperatures that the parasite encounters in the insect (26 degrees C, normal temperature) or in the mammalian host (heat-shock temperatures). Interestingly, 3'-UTRI-bearing transcripts (HSP70-I) were found associated with ribosomes in promastigotes at normal and heat-shock temperatures, whereas the HSP70-II transcripts appear to be preferentially translated at heat-shock temperatures but not at 26 degrees C. We have analyzed the function of these UTRs in the translational control by use of plasmid constructs in which the CAT reporter gene was flanked by UTRs of the HSP70 genes. Unexpectedly, it was found that CAT transcripts with 3'-UTRII bind to ribosomes at 26 degrees C, and, indeed, the CAT protein is synthesized. A valid conclusion of these experiments was that both types of 3'-UTRs are essential for translation of HSP70 mRNAs at heat shock temperatures, although the 3'-UTRII is more efficient during severe heat shock (39 degrees C). In addition, these results suggest that sequence region other than the 3'-UTR of HSP70-II gene is involved in the translational silent state of HSP70-II transcripts at 26 degrees C. Finally, a null mutant has been created by targeted disruption of both HSP70-II alleles. Remarkably, the deltaHSP70 mutant synthesizes HSP70 at a lower rate than the wild-type parasites. Overall, our data suggest that the biological function of the HSP70-II gene is to top up HSP70 levels under conditions of stress.

From mRNP trafficking to spine dysmorphogenesis: the roots of fragile X syndrome

The mental retardation protein FMRP is involved in the transport of mRNAs and their translation at synapses. Patients with fragile X syndrome, in whom FMRP is absent or mutated, show deficits in learning and memory that might reflect impairments in the translational regulation of a subset of neuronal mRNAs. The study of FMRP provides important insights into the regulation and functions of local protein synthesis in the neuronal periphery, and increases our understanding of how these functions can produce specific effects at individual synapses.

Neuronal activity regulates the developmental expression and subcellular localization of cortical BDNF mRNA isoforms in vivo

Activity-dependent changes in BDNF expression have been implicated in developmental plasticity. Although its expression is widespread in visual cortex, developmental regulation of its different transcripts by visual experience has not been investigated. Here, we investigated the cellular expression of different BDNF transcripts in rat visual cortex during postnatal development. We found that transcripts I and II are expressed only in adults but III and IV are expressed from early postnatal stage. Total BDNF mRNA is expressed throughout the age groups. Transcripts III and IV show a differential intracellular localization, while former was detected only in cell bodies, latter is present both in cell bodies and dendritic processes. Inhibition of visual activity decreases the levels of exons, with exon IV transcript almost disappearing from dendrites. In vitro experiments also confirmed the above results, indicating activity-dependent regulation of different BDNF promoters with specific temporal and cellular patterns of expression in developing visual cortex.

Transport of Drosophila fragile X mental retardation protein-containing ribonucleoprotein granules by kinesin-1 and cytoplasmic dynein

Transport and translation of mRNA are tightly coupled to ensure strict temporal and spatial expression of nascent proteins. Fragile X mental retardation protein (FMRP) has been shown to be involved in translational regulation and is found in ribonucleoprotein (RNP) granules that travel along dendrites of neurons. In this study, GFP-tagged Drosophila homologue of FMRP (dFMR) was used to visualize RNP granule movement in Drosophila S2 cells. GFP-dFMR form granules that contain both endogenous dFMR and mRNA. Live fluorescence microscopy revealed that dFMR-containing RNP granules move bidirectionally in thin processes formed by S2 cells in the presence of cytochalasin D. Knocking down the heavy chains of either kinesin-1 (kinesin heavy chain) or cytoplasmic dynein (dynein heavy chain) by RNA interference blocks the movement of the dFMR granules. In contrast, knockdown of kinesin light chain (KLC), which is typically necessary for movement of membrane organelles by kinesin-1, had no effect on the dFMR granule translocation. In immunoprecipitation assays, dFMR associates with both kinesin heavy chain and dynein heavy chain, but not KLC. Based on these findings, we conclude that dFMR-containing RNP granules are moved by both kinesin-1 and cytoplasmic dynein and that KLC is not essential and is likely missing from RNP-transporting kinesin-1.

A systems view of mRNP biology

Gene expression occurs through a complex mRNA-protein (mRNP) system that stretches from transcription to translation. Gene expression processes are increasingly studied from global perspectives in order to understand their pathways, properties, and behaviors as a system. Here we review these beginnings of mRNP systems biology, as they have emerged from recent large-scale investigation of mRNP components, interactions, and dynamics. Such work has begun to lay the foundation for a broader, integrated view of mRNP organization in gene expression.

Exercise rapidly increases expression of the monocarboxylate transporters MCT1 and MCT4 in rat muscle

We examined the effect of a single exercise session on the protein and mRNA expression of the monocarboxylate transporters MCT1 and MCT4 in rat soleus (SOL), and red (RG) and white gastrocnemius (WG) muscles. Muscle samples were obtained at rest before 2 h of treadmill exercise (21 m min(-1), 15% grade) and immediately after exercise, as well as 5, 10 and 24 h after exercise. During the 2 h exercise bout, MCT1 proteins in RG (+60%) and WG (+56%) were increased (P < 0.05). MCT1 protein was further increased thereafter, with peak increments occurring 10 h after exercise in RG (+157%), WG (+193%) and SOL (+179%) (P < 0.05). Twenty-four hours after exercise, MCT1 protein was still up-regulated in WG (+100%) and SOL (+55%) (P < 0.05), but not in RG. MCT1 mRNA was up-regulated during exercise in RG (+53%) and WG (+98%) and remained elevated until 24 h post-exercise in RG (P < 0.05), but in WG, MCT1 mRNA decreased transiently to pre-exercise levels at 5 and 10 h after exercise, before increasing again at 24 h (+150%) (P < 0.05). MCT4 protein and mRNA were not increased in WG muscle during and after exercise (P > 0.05). In contrast, during exercise, in RG (+41%) and SOL (+98%) MCT4 protein was increased (P < 0.05). Peak increases in MCT4 protein were observed 10 h after exercise in RG (+131%) and SOL (+323%) (P < 0.05). MCT4 protein was still up-regulated 24 h after exercise (RG: +106%; SOL +225%) (P < 0.05). MCT4 mRNA in RG was not increased until 10 (+132%) and 24 h after exercise (+55%) (P < 0.05). These studies have shown that MCT1 and 4 proteins are transiently up-regulated by a single bout of exercise, involving post-transcriptional and transcriptional mechanisms. Thus, MCT1 and MCT4 belong to a class of selected metabolic genes that are very rapidly up-regulated with an exercise stimulus.