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First published online March 30, 2007
doi: 10.1242/10.1242/jcs.03429
Commentary |
1 Department of Oral Biology, University of Florida, Gainesville, FL 32610, USA
2 Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, T2N 4N1, Canada
3 Division of Rheumatology and Clinical Immunology, Department of Medicine, and Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL 32610, USA
* Author for correspondence (e-mail: echan{at}ufl.edu)
Accepted 21 February 2007
| Summary |
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Key words: GW bodies, P-bodies, RNA interference, mRNA degradation, microRNA, short-interfering RNA
| Introduction |
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RNAi is a post-transcriptional silencing mechanism in which small double-stranded RNA molecules induce sequence-specific degradation and/or translational repression of homologous mRNAs (for reviews, see Filipowicz et al., 2005
; Meister and Tuschl, 2004
; Rana, 2007
; Sen and Blau, 2006
; Valencia-Sanchez et al., 2006
). The discovery that RNAi effector proteins (Jakymiw et al., 2005
; Liu et al., 2005a
; Liu et al., 2005b
; Sen and Blau, 2005
) and small RNAs localize to GWBs (Jakymiw et al., 2005
; Pauley et al., 2006
; Pillai et al., 2005
), and that GWB assembly appears to be required for the proper functioning of the RNAi pathway (Jakymiw et al., 2005
; Liu et al., 2005a
; Meister et al., 2005
), suggests that these foci are specifically involved in short-interfering RNA (siRNA)- and microRNA (miRNA)-mediated mRNA degradation and/or translational repression
.
GWBs are enriched in mRNA decay factors and pools of stored messenger ribonucleoproteins (mRNPs) (Bruno and Wilkinson, 2006
; Sheth and Parker, 2006
). Moreover, they are dynamic structures, whose size and number appear to depend on specific intracellular processes. For instance, GWBs vary in size and number throughout the cell cycle, the largest of which are observed in late S and G2 phase (Yang et al., 2004
). Furthermore, stress (Kedersha et al., 2005
; Teixeira et al., 2005
), cell proliferation (Yang et al., 2004
), blocking mRNA decay (Andrei et al., 2005
; Cougot et al., 2004
; Sheth and Parker, 2003
) and inhibition of translational initiation (Brengues et al., 2005
; Sheth and Parker, 2003
; Teixeira et al., 2005
) all increase the size and number of GWBs. Conversely, blocking transcription, deadenylation of mRNAs or translational elongation decreases the size and number of GWBs (Cougot et al., 2004
; Sheth and Parker, 2003
). Recent studies have highlighted the importance of these structures in the regulation of mRNA turnover and provided insights into their involvement in RNA silencing. Here, we review the current understanding of GWB function, focusing on its recent links to RNAi, and discuss the role of these cytoplasmic foci in RNA-induced silencing complex (RISC) activation. We also examine the requirements for GWB formation and disassembly and propose a working model for their genesis.
| GWBs uncovered |
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These bodies are thought to be conserved in budding yeast and mammals because both the yeast P-bodies and mammalian GWBs contain activators of decapping and decapping enzymes (Cougot et al., 2004
; Eystathioy et al., 2003
; Ingelfinger et al., 2002
; Lykke-Andersen, 2002
; Segal et al., 2006
; Sheth and Parker, 2003
; Van Dijk et al., 2002
). Note, however, that GWBs differ from yeast P-bodies in that they contain translation initiation factors and other proteins that have no yeast counterparts, such as factors involved in RNAi [e.g. GW182 and Argonaute (Ago) proteins] (Anderson and Kedersha, 2006
; Segal et al., 2006
). Furthermore, there are functional differences between GWBs and yeast P-bodies in terms of their responses to stress and cell growth (Schneider et al., 2006
). For example, P-bodies increase in size and number during growth limitation, increased cell density, and stress (Teixeira et al., 2005
), whereas GWBs increase in size and number in proliferating cells (Yang et al., 2004
) and dynamically interact with stress granules
in stressed mammalian cells (Kedersha et al., 2005
). Therefore, one needs to be cautious when generalizing about these structures because differences do exist, not only between species but even within a population of GWBs in a single mammalian cell (Fig. 1). Interestingly, a recent report similarly found that some GW/P-bodies that contain Mex-3B, a newly described class of human RNA-binding protein that localizes to GW/P-bodies, are also devoid of Dcp1 (Buchet-Poyau et al., 2007
). The function of a particular GW/P-body may therefore depend on its organization or composition.
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| GW body function |
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NMD is a surveillance mechanism that removes aberrant mRNA transcripts containing premature termination codons. Several factors involved in NMD, including UPF1-3, SMG5 and SMG7, as well as reporter mRNAs harboring nonsense mutations have been found to localize to GW/P-bodies (Fukuhara et al., 2005
; Sheth and Parker, 2006
; Unterholzner and Izaurralde, 2004
), which links these foci and the NMD process. GWBs have also been linked to AMD, a decay process involving messages containing AREs in the 3'-untranslated region (UTR). In particular, depletion of three GWB proteins, Xrn1, LSm1 or 4E-T, has been demonstrated to inhibit AMD (Ferraiuolo et al., 2005
; Stoecklin et al., 2006
). Moreover, evidence also indicates that the ARE-binding protein TTP, which is known to destabilize ARE-containing mRNAs, localizes to GWBs (Kedersha et al., 2005
) and interacts with and activates the decapping complex (Fenger-Gron et al., 2005
; Lykke-Andersen and Wagner, 2005
). Finally, the observation that the size and number of P-bodies increases during stress in budding yeast cells (Teixeira et al., 2005
) and that GWBs can be induced to form and interact with stress granules by specific stresses in mammalian cells demonstrates their importance in SID (Kedersha et al., 2005
). However, because budding yeast cells lack stress granules, the mechanism of SID probably differs from that in higher eukaryotes.
In mammalian cells, GWBs and stress granules have been reported to be compositionally and morphologically distinct structures (Cougot et al., 2004
; Kedersha et al., 2005
); however, evidence indicates that they are functionally and spatially linked (Kedersha et al., 2005
). Interestingly, both entities share an assortment of proteins (e.g. CPEB1, Rck/p54, FAST, Xrn1, eIF4 and TTP) and a single class of reporter mRNA has been observed within both GWBs and stress granules (Kedersha et al., 2005
; Wilczynska et al., 2005
). Moreover, overexpression of TTP and CPEB1, a translational regulator, induces the fusion of stress granules and GWBs, which suggests that these proteins regulate the dynamic interaction between these two structures (Kedersha et al., 2005
; Wilczynska et al., 2005
). One model is that stress granules serve as mRNA triage sites where transcripts are sorted for storage, re-initiation of translation, or degradation, and that mRNAs targeted for decay are exported from stress granules to GWBs (Kedersha et al., 2005
). Regardless of the mechanistic differences between yeast and higher eukaryotes, it is evident that GW/P-bodies have multiple functions, the ultimate goal being mRNA decay and/or storage. It is therefore not surprising that these foci comprise multiple factors and that their specific structural composition and organization probably determines their mode of action.
RNAi
Several groups recently demonstrated a link between GWBs and RNAi (Jakymiw et al., 2005
; Liu et al., 2005a
; Liu et al., 2005b
; Pillai et al., 2005
; Sen and Blau, 2005
). In particular, the Ago family of proteins, Ago1-4, which are components of RISC, the key effector complex of RNAi, were found to be concentrated in GWBs (Jakymiw et al., 2005
; Liu et al., 2005a
; Liu et al., 2005b
; Sen and Blau, 2005
). Moreover, GWBs also appeared to be sites involved in miRNA-mediated repression of targeted mRNAs (Liu et al., 2005b
).
In addition, we and others demonstrated that hAgo2, the catalytic engine of RNA silencing, associates with several components of GWBs, including GW182 (Jakymiw et al., 2005
; Liu et al., 2005a
; Liu et al., 2005b
). Moreover, depletion of GW182, which disrupts GWBs (Yang et al., 2004
), perturbs both siRNA- and miRNA-mediated repression (Jakymiw et al., 2005
; Liu et al., 2005a
). Dominant interfering GW182 and hAgo2 mutants also disrupt GWB formation and similarly inhibit RNA silencing (Jakymiw et al., 2005
). The impairment in RNAi appears to depend on blocking the localization of hAgo2 to GWBs (Jakymiw et al., 2005
). Indeed, hAgo2 constructs containing point mutations that prevent siRNA binding and localization to GWBs do not repress target reporter mRNA, despite being tethered to the target (Liu et al., 2005a
). Additional evidence for the involvement of GW182 and GWB in RNAi comes from studies of the Drosophila melanogaster ortholog and Caenorhabditis elegans functional analog (Ding et al., 2005
; Rehwinkel et al., 2005
; Schneider et al., 2006
). In particular, studies in Drosophila indicate that GW182 interacts with Ago1 and promotes degradation of a subset of miRNA-mediated-decay mRNA targets (Behm-Ansmant et al., 2006
). GW182 may thus function as a molecular scaffold that bridges components of the miRNA pathway with mRNA decay enzymes (Behm-Ansmant et al., 2006
).
A point of contention is whether GW182 and GWBs are important for both slicer-dependent mechanisms (i.e. siRNA-mediated RNAi) and miRNA-mediated repression or only the latter. Work from our laboratory has demonstrated that transfected fluorophore-labeled siRNAs associate with GW182 protein complexes and localize to GWBs and that GW182 and GWBs play an important role in slicer-mediated functions (Jakymiw et al., 2005
). Moreover, Liu et al. found that suppression of GW182 similarly impairs, albeit not as effectively, the ability of an siRNA to silence its target by mRNA cleavage (Liu et al., 2005a
). In addition, silencing of the GWB protein TNRC6B, a GW182 paralog, inhibits cleavage of an mRNA reporter gene containing a target site perfectly complementary to an endogenous miRNA (Meister et al., 2005
). TNRC6B thus appears to be important for slicer-dependent mechanisms and subsequent mRNA degradation.
Other work has indicated a greater role for GW182 and GWBs in miRNA-mediated translational repression by demonstrating, using various reporter systems, that depletion of GW182 impairs miRNA function (Chu and Rana, 2006
; Liu et al., 2005a
; Rehwinkel et al., 2005
). Furthermore, depletion of GW182 has also been demonstrated to result in alterations of mRNA expression profiles very similar to those seen in cells depleted of the Drosophila miRNA effector Ago1 and not the siRNA effector Ago2, which suggests that GW182 functions in the miRNA pathway (Behm-Ansmant et al., 2006
). Whether the above disparities are because of the use of different reporter systems (i.e. exogenously introduced versus endogenous reporter systems), species variations or GW182 redundancy (three paralogs have been identified in humans) will require further study. Interestingly, in the study implicating GW182 in slicer-mediated function, we used siRNAs with a fluorophore conjugated to the 5'-end of the guide strand (Jakymiw et al., 2005
). The fluorophore might therefore have interfered with the siRNA activity, making it behave more like an miRNA by producing imperfect base-pairing between siRNA and target. Regardless, the studies collectively demonstrate a role for GW182 and GWBs in RNAi. More work will be needed to determine whether GWBs represent converging sites for siRISC and/or miRISC.
MiRNAs have similarly been identified within GWBs and demonstrated to associate with GW182 protein complexes (Pauley et al., 2006
; Pillai et al., 2005
). The identification of siRNA and/or miRNA within GWBs suggests that RISC activation, activity and/or recycling may occur within GWBs. Are GWBs sites of RISC activation and activity? Evidence supporting this possibility includes the observation that Ago2, a known GWB component, is directly involved in passenger-strand cleavage of double-stranded siRNAs during RISC assembly (Matranga et al., 2005
; Rand et al., 2005
). Also, following transient transfection of HeLa cells with a fluorophore-labeled passenger-strand siRNA duplex that has no endogenous mRNA target, the siRNA localizes to GWBs similarly to a fluorophore-labeled-guide-strand siRNA duplex that has an endogenous mRNA target (Jakymiw et al., 2005
). This suggests that the passenger strand and the guide strand localize to GWBs independently of the mRNA target and that passenger-strand cleavage and incorporation of the antisense-strand into RISC may occur within GWBs. Docking of siRNA/miRNA duplexes into RISC and its subsequent activation could therefore be early events in GWB formation. Interestingly, in fission yeast cells, a Dicer ortholog localizes to structures resembling GWBs (Carmichael et al., 2006
), which suggests that GWB formation may take place even before RISC activation.
| GW body formation and structure |
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Fig. 2 shows our working model, in which several factors, including RISC, initially interact with the target mRNA to form a specific RNP structure dependent on the type of decay or storage process that will occur (e.g. siRNA-mediated decay versus miRNA-mediated translational repression). This results in the recruitment of other protein complexes, which depend on the composition of the initial RNP; so their final composition or structural organization promotes the proper decay mechanism and/or storage of the mRNA. Such a model would explain why disruption of GWBs by depletion of other GWB components, such as LSm1 or RCK/p54, does not necessarily translate into impaired RISC activity (Chu and Rana, 2006
), whereas silencing of GW182 does (Jakymiw et al., 2005
). One possibility is that GW182 exists in a smaller RNP complex with RISC components (e.g. hAgo2) that is undetectable by fluorescence microscopy and supersedes the requirement of LSm1 and RCK/p54 for initial target recognition and endonucleolytic cleavage or translation repression. Moreover, not all silencing of GWB factors impairs formation of GWBs equivalently. Interestingly, Andrei et al. have demonstrated that silencing of RCK/p54 has a less pronounced effect on the disassembly of GWBs compared with other factors (Andrei et al., 2005
).
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The integrity of GWBs also appears to depend on RNA. Studies in yeast and mammals indicate that mRNA is an integral component of GW/P-bodies (Andrei et al., 2005
; Cougot et al., 2004
; Eystathioy et al., 2002
; Teixeira et al., 2005
). Furthermore, silencing of Drosha or its required partner protein, DGCR8, which together comprise the microprocessor complex and are responsible for processing long nuclear primary miRNA (pri-miRNA) transcripts to
70-nucleotide hairpin precursor miRNA (pre-miRNA), depletes cells of mature miRNA and causes the disappearance of GWBs (Pauley et al., 2006
). This suggests that miRNAs are required for the formation of GWBs. Although the possibility that the effect is indirect cannot be ruled out, this seems unlikely because siRNA transfected into Drosha-deficient cells can serve as a surrogate for miRNA and drive the reappearance of GWBs.
The dependence of GWBs on miRNA means that many of the functions attributed to GWBs similarly may depend on miRNAs in mammalian cells. Processes such as translational repression, mRNA decay and storage depend on miRNAs. Furthermore, miRNAs are involved in ARE-mediated degradation events (Jing et al., 2005
). All of these processes are associated with GWBs. The primary function of GWBs might therefore be to provide a microenvironment for miRNA-mRNA interactions that lead to translational inhibition and/or mRNA degradation. Whether NMD processes share this requirement for miRNAs requires further study. Nevertheless, if this hypothesis holds, a more appropriate name for these foci in mammalian cells may be miRNA-induced bodies (miRBs).
| Conclusions and perspectives |
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Our understanding of the cell biology of RNAi and its relationship to GWBs is still limited, however. During the course of writing this review, several articles were published demonstrating that a large fraction of miRNAs and Ago proteins reside in the cytoplasm (Leung et al., 2006
; Maroney et al., 2006
; Nottrott et al., 2006
), in particular on mRNAs being actively translated by polyribosomes (Maroney et al., 2006
; Nottrott et al., 2006
). Furthermore, inhibiting translation initiation or inducing stress has been shown to result in localization of miRNA and Ago to stress granules (Leung et al., 2006
). Data from these studies suggest that miRNPs first associate with and suppress actively translating mRNAs in the cytoplasm prior to completely dropping off ribosomes. Upon miRNA-mediated repression, these mRNA are then believed to be targeted to either stress granules for storage or sorted and shuttled to GWBs for decay. Given the close relationship between GWBs and stress granules, this would not be surprising; however, one needs to be cautious in interpreting the stress granule data because stress granules are generally observed only during a stress response, whereas GWBs are present continuously (Teixeira et al., 2005
). Alternatively, inhibition of actively translating polysomes on mRNAs by miRISCs might directly trigger the recruitment of RNP complexes involved in either early stages of GWB formation and/or GWB targeting. Much more work will be needed if we are to completely understand the interactions between GWBs and other mRNP structures and the significance of their heterogeneous composition.
Finally, although numerous studies have demonstrated that RNAi occurs in the cytoplasm of a cell, a growing number of reports suggest that it occurs within the nucleus as well. In particular, recent studies in human cells have implicated the RNAi effector proteins hAgo1 and hAgo2 in the post-transcriptional modulation of gene expression in the nucleus (Robb et al., 2005
) and transcriptional silencing (Janowski et al., 2006
; Kim et al., 2006
). Furthermore, transfection of siRNAs targeting small nuclear RNAs (e.g. 7SK and U6 RNA) leads to their translocation into the nucleus and silencing of the target genes (Berezhna et al., 2006
). How the cytoplasmic and nuclear RNAi pathways are interrelated and the relationship between GWBs and nuclear RNAi are currently unclear. Biochemical evidence suggests that these processes are linked by a common requirement for Ago proteins; however, immunofluorescence studies using a newly developed mouse monoclonal antibody specific for hAgo2 show no evidence of nuclear localization of this endogenous protein (Ikeda et al., 2006
), which is consistent with our earlier work using polyclonal autoimmune sera (Jakymiw et al., 2006
). Regardless, the recent findings that GWBs appear to function in siRNA/miRNA-mediated forms of post-transcriptional regulation, the apparent requirement for GWBs in Drosophila (Schneider et al., 2006
) and C. elegans (Ding et al., 2005
) development, and the knowledge that small RNAs regulate many cellular activities (Ambros, 2004
), including differentiation, stem cell division, and apoptosis, underline the importance of GWBs for many biological processes.
| Acknowledgments |
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| Footnotes |
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siRNAs are small RNAs of
21 nucleotides in length and are derived from the progressive cleavage of long, perfectly complementary double-stranded RNAs (dsRNAs) by an RNase-III-type endonuclease, Dicer. They can originate from long dsRNAs transiently introduced into cells by transfection or stably expressed hairpin-containing dsRNA precursors derived from DNA constructs. They assemble into an RNA-protein complex known as the RNA-induced silencing complex (RISC or siRISC), which includes Argonaute 2 (Ago2), a key component of RNAi that possesses endonuclease activity. RISC then targets and cleaves perfectly complementary mRNAs, generating 5' and 3' fragments, which are subsequently degraded. MiRNAs are similar in size to siRNAs but originate from hairpin-containing precursors encoded by the genome. These non-coding precursors of miRNAs have double-stranded regions with imperfect complementarity and are sequentially processed by RNase-III-type enzymes Drosha and Dicer into mature miRNAs. The mature miRNAs then assemble into an RNA-protein complex referred to as the miRNA ribonucleoprotein complex (miRNP or miRISC), which is structurally similar to RISC and contains at least one Argonaute protein. Multiple copies of miRNPs are directed to the 3'-UTR of certain mRNAs that have imperfect complementarity to the bound miRNAs. In plants, miRNAs cleave their regulated target mRNA, whereas in mammals miRNAs promote translational repression of the targeted mRNA. Until recently, this was considered the major distinction between siRISC and miRISC in mammalian cells. However, new evidence suggests that miRNAs can also regulate mRNA degradation similarly to siRNAs (Bagga et al., 2005
Stress granules are large RNP particles that store non-translating mRNAs when cells are exposed to environmental stresses, but are absent in budding yeast cells. ![]()
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