1001
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Abstract
hSMG-1 is a member of the phosphoinositide 3 kinase-like kinase (PIKK) family with established roles in nonsense-mediated decay (NMD) of mRNA containing premature termination codons and in genotoxic stress responses to DNA damage. We report here a novel role for hSMG-1 in cytoplasmic stress granule (SG) formation. Exposure of cells to stress causing agents led to the localization of hSMG-1 to SG, identified by colocalization with TIA-1, G3BP1, and eIF4G. hSMG-1 small interfering RNA and the PIKK inhibitor wortmannin prevented formation of a subset of SG, while specific inhibitors of ATM, DNA-PK(cs), or mTOR had no effect. Exposure of cells to H(2)O(2) and sodium arsenite induced (S/T)Q phosphorylation of proteins. While Upf2 and Upf1, an essential substrate for hSMG-1 in NMD, were present in SG, NMD-specific Upf1 phosphorylation was not detected in SG, indicating hSMG-1's role in SG is separate from classical NMD. Thus, SG formation appears more complex than originally envisaged and hSMG-1 plays a central role in this process.
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1002
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Santiveri CM, Mirassou Y, Rico-Lastres P, Martínez-Lumbreras S, Pérez-Cañadillas JM. Pub1p C-terminal RRM domain interacts with Tif4631p through a conserved region neighbouring the Pab1p binding site. PLoS One 2011; 6:e24481. [PMID: 21931728 PMCID: PMC3169606 DOI: 10.1371/journal.pone.0024481] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2011] [Accepted: 08/11/2011] [Indexed: 11/18/2022] Open
Abstract
Pub1p, a highly abundant poly(A)+ mRNA binding protein in Saccharomyces cerevisiae, influences the stability and translational control of many cellular transcripts, particularly under some types of environmental stresses. We have studied the structure, RNA and protein recognition modes of different Pub1p constructs by NMR spectroscopy. The structure of the C-terminal RRM domain (RRM3) shows a non-canonical N-terminal helix that packs against the canonical RRM fold in an original fashion. This structural trait is conserved in Pub1p metazoan homologues, the TIA-1 family, defining a new class of RRM-type domains that we propose to name TRRM (TIA-1 C-terminal domain-like RRM). Pub1p TRRM and the N-terminal RRM1-RRM2 tandem bind RNA with high selectivity for U-rich sequences, with TRRM showing additional preference for UA-rich ones. RNA-mediated chemical shift changes map to β-sheet and protein loops in the three RRMs. Additionally, NMR titration and biochemical in vitro cross-linking experiments determined that Pub1p TRRM interacts specifically with the N-terminal region (1-402) of yeast eIF4G1 (Tif4631p), very likely through the conserved Box1, a short sequence motif neighbouring the Pab1p binding site in Tif4631p. The interaction involves conserved residues of Pub1p TRRM, which define a protein interface that mirrors the Pab1p-Tif4631p binding mode. Neither protein nor RNA recognition involves the novel N-terminal helix, whose functional role remains unclear. By integrating these new results with the current knowledge about Pub1p, we proposed different mechanisms of Pub1p recruitment to the mRNPs and Pub1p-mediated mRNA stabilization in which the Pub1p/Tif4631p interaction would play an important role.
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Affiliation(s)
- Clara M. Santiveri
- Department of Biological Physical Chemistry, Instituto de Química-Física “Rocasolano”, CSIC, Madrid, Spain
| | - Yasmina Mirassou
- Department of Biological Physical Chemistry, Instituto de Química-Física “Rocasolano”, CSIC, Madrid, Spain
| | - Palma Rico-Lastres
- Department of Biological Physical Chemistry, Instituto de Química-Física “Rocasolano”, CSIC, Madrid, Spain
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1003
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Strong MJ, Volkening K. TDP-43 and FUS/TLS: sending a complex message about messenger RNA in amyotrophic lateral sclerosis? FEBS J 2011; 278:3569-77. [DOI: 10.1111/j.1742-4658.2011.08277.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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1004
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Sinnamon JR, Czaplinski K. mRNA trafficking and local translation: the Yin and Yang of regulating mRNA localization in neurons. Acta Biochim Biophys Sin (Shanghai) 2011; 43:663-70. [PMID: 21749992 DOI: 10.1093/abbs/gmr058] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Localized translation and the requisite trafficking of the mRNA template play significant roles in the nervous system including the establishment of dendrites and axons, axon path-finding, and synaptic plasticity. We provide a brief review on the regulation of localizing mRNA in mammalian neurons through critical post-translational modifications of the factors involved. These examples highlight the relationship between mRNA trafficking and the translational regulation of trafficked mRNAs and provide insight into how extracellular signals target these events during signal transduction.
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Affiliation(s)
- John R Sinnamon
- Program in Neuroscience, Stony Brook University, NY 11794, USA
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1005
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Krokowski D, Gaccioli F, Majumder M, Mullins MR, Yuan CL, Papadopoulou B, Merrick WC, Komar AA, Taylor D, Hatzoglou M. Characterization of hibernating ribosomes in mammalian cells. Cell Cycle 2011; 10:2691-702. [PMID: 21768774 DOI: 10.4161/cc.10.16.16844] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Protein synthesis across kingdoms involves the assembly of 70S (prokaryotes) or 80S (eukaryotes) ribosomes on the mRNAs to be translated. 70S ribosomes are protected from degradation in bacteria during stationary growth or stress conditions by forming dimers that migrate in polysome profiles as 100S complexes. Formation of ribosome dimers in Escherichia coli is mediated by proteins, namely the ribosome modulation factor (RMF), which is induced in the stationary phase of cell growth. It is reported here a similar ribosomal complex of 110S in eukaryotic cells, which forms during nutrient starvation. The dynamic nature of the 110S ribosomal complex (mammalian equivalent of the bacterial 100S) was supported by the rapid conversion into polysomes upon nutrient-refeeding via a mechanism sensitive to inhibitors of translation initiation. Several experiments were used to show that the 110S complex is a dimer of nontranslating ribosomes. Cryo-electron microscopy visualization of the 110S complex revealed that two 80S ribosomes are connected by a flexible, albeit localized, interaction. We conclude that, similarly to bacteria, rat cells contain stress-induced ribosomal dimers. The identification of ribosomal dimers in rat cells will bring new insights in our thinking of the ribosome structure and its function during the cellular response to stress conditions.
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Affiliation(s)
- Dawid Krokowski
- Department of Nutrition, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
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1006
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Meyerowitz J, Parker SJ, Vella LJ, Ng DC, Price KA, Liddell JR, Caragounis A, Li QX, Masters CL, Nonaka T, Hasegawa M, Bogoyevitch MA, Kanninen KM, Crouch PJ, White AR. C-Jun N-terminal kinase controls TDP-43 accumulation in stress granules induced by oxidative stress. Mol Neurodegener 2011; 6:57. [PMID: 21819629 PMCID: PMC3162576 DOI: 10.1186/1750-1326-6-57] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2011] [Accepted: 08/08/2011] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND TDP-43 proteinopathies are characterized by loss of nuclear TDP-43 expression and formation of C-terminal TDP-43 fragmentation and accumulation in the cytoplasm. Recent studies have shown that TDP-43 can accumulate in RNA stress granules (SGs) in response to cell stresses and this could be associated with subsequent formation of TDP-43 ubiquinated protein aggregates. However, the initial mechanisms controlling endogenous TDP-43 accumulation in SGs during chronic disease are not understood. In this study we investigated the mechanism of TDP-43 processing and accumulation in SGs in SH-SY5Y neuronal-like cells exposed to chronic oxidative stress. Cell cultures were treated overnight with the mitochondrial inhibitor paraquat and examined for TDP-43 and SG processing. RESULTS We found that mild stress induced by paraquat led to formation of TDP-43 and HuR-positive SGs, a proportion of which were ubiquitinated. The co-localization of TDP-43 with SGs could be fully prevented by inhibition of c-Jun N-terminal kinase (JNK). JNK inhibition did not prevent formation of HuR-positive SGs and did not prevent diffuse TDP-43 accumulation in the cytosol. In contrast, ERK or p38 inhibition prevented formation of both TDP-43 and HuR-positive SGs. JNK inhibition also inhibited TDP-43 SG localization in cells acutely treated with sodium arsenite and reduced the number of aggregates per cell in cultures transfected with C-terminal TDP-43 162-414 and 219-414 constructs. CONCLUSIONS Our studies are the first to demonstrate a critical role for kinase control of TDP-43 accumulation in SGs and may have important implications for development of treatments for FTD and ALS, targeting cell signal pathway control of TDP-43 aggregation.
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Affiliation(s)
- Jodi Meyerowitz
- Department of Pathology, The University of Melbourne, Victoria, 3010, Australia.
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1007
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Affiliation(s)
- Stacy L Erickson
- Division of Biology, University of California San Diego, La Jolla, CA 92093, USA
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1008
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The Ataxin-2 protein is required for microRNA function and synapse-specific long-term olfactory habituation. Proc Natl Acad Sci U S A 2011; 108:E655-62. [PMID: 21795609 DOI: 10.1073/pnas.1107198108] [Citation(s) in RCA: 121] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Local control of mRNA translation has been proposed as a mechanism for regulating synapse-specific plasticity associated with long-term memory. We show here that glomerulus-selective plasticity of Drosophila multiglomerular local interneurons observed during long-term olfactory habituation (LTH) requires the Ataxin-2 protein (Atx2) to function in uniglomerular projection neurons (PNs) postsynaptic to local interneurons (LNs). PN-selective knockdown of Atx2 selectively blocks LTH to odorants to which the PN responds and in addition selectively blocks LTH-associated structural and functional plasticity in odorant-responsive glomeruli. Atx2 has been shown previously to bind DEAD box helicases of the Me31B family, proteins associated with Argonaute (Ago) and microRNA (miRNA) function. Robust transdominant interactions of atx2 with me31B and ago1 indicate that Atx2 functions with miRNA-pathway components for LTH and associated synaptic plasticity. Further direct experiments show that Atx2 is required for miRNA-mediated repression of several translational reporters in vivo. Together, these observations (i) show that Atx2 and miRNA components regulate synapse-specific long-term plasticity in vivo; (ii) identify Atx2 as a component of the miRNA pathway; and (iii) provide insight into the biological function of Atx2 that is of potential relevance to spinocerebellar ataxia and neurodegenerative disease.
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1009
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Mani J, Güttinger A, Schimanski B, Heller M, Acosta-Serrano A, Pescher P, Späth G, Roditi I. Alba-domain proteins of Trypanosoma brucei are cytoplasmic RNA-binding proteins that interact with the translation machinery. PLoS One 2011; 6:e22463. [PMID: 21811616 PMCID: PMC3141063 DOI: 10.1371/journal.pone.0022463] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2011] [Accepted: 06/25/2011] [Indexed: 01/26/2023] Open
Abstract
Trypanosoma brucei and related pathogens transcribe most genes as polycistronic arrays that are subsequently processed into monocistronic mRNAs. Expression is frequently regulated post-transcriptionally by cis-acting elements in the untranslated regions (UTRs). GPEET and EP procyclins are the major surface proteins of procyclic (insect midgut) forms of T. brucei. Three regulatory elements common to the 3′ UTRs of both mRNAs regulate mRNA turnover and translation. The glycerol-responsive element (GRE) is unique to the GPEET 3′ UTR and regulates its expression independently from EP. A synthetic RNA encompassing the GRE showed robust sequence-specific interactions with cytoplasmic proteins in electromobility shift assays. This, combined with column chromatography, led to the identification of 3 Alba-domain proteins. RNAi against Alba3 caused a growth phenotype and reduced the levels of Alba1 and Alba2 proteins, indicative of interactions between family members. Tandem-affinity purification and co-immunoprecipitation verified these interactions and also identified Alba4 in sub-stoichiometric amounts. Alba proteins are cytoplasmic and are recruited to starvation granules together with poly(A) RNA. Concomitant depletion of all four Alba proteins by RNAi specifically reduced translation of a reporter transcript flanked by the GPEET 3′ UTR. Pulldown of tagged Alba proteins confirmed interactions with poly(A) binding proteins, ribosomal protein P0 and, in the case of Alba3, the cap-binding protein eIF4E4. In addition, Alba2 and Alba3 partially cosediment with polyribosomes in sucrose gradients. Alba-domain proteins seem to have exhibited great functional plasticity in the course of evolution. First identified as DNA-binding proteins in Archaea, then in association with nuclear RNase MRP/P in yeast and mammalian cells, they were recently described as components of a translationally silent complex containing stage-regulated mRNAs in Plasmodium. Our results are also consistent with stage-specific regulation of translation in trypanosomes, but most likely in the context of initiation.
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Affiliation(s)
- Jan Mani
- Institute of Cell Biology, University of Bern, Bern, Switzerland
| | | | - Bernd Schimanski
- Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Manfred Heller
- Department of Clinical Research, University of Bern, Bern, Switzerland
| | | | - Pascale Pescher
- Department of Parasitology and Mycology, G5 Virulence Parasitaire, Institut Pasteur, Paris, France
| | - Gerald Späth
- Department of Parasitology and Mycology, G5 Virulence Parasitaire, Institut Pasteur, Paris, France
| | - Isabel Roditi
- Institute of Cell Biology, University of Bern, Bern, Switzerland
- * E-mail:
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1010
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Schmitz ML, Weber A, Roxlau T, Gaestel M, Kracht M. Signal integration, crosstalk mechanisms and networks in the function of inflammatory cytokines. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2011; 1813:2165-75. [PMID: 21787809 DOI: 10.1016/j.bbamcr.2011.06.019] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Revised: 05/31/2011] [Accepted: 06/01/2011] [Indexed: 12/20/2022]
Abstract
Infection or cell damage triggers the release of pro-inflammatory cytokines such as interleukin(IL)-1α or β and tumor necrosis factor (TNF)α which are key mediators of the host immune response. Following their identification and the elucidation of central signaling pathways, recent results show a highly complex crosstalk between various cytokines and their signaling effectors. The molecular mechanisms controlling signaling thresholds, signal integration and the function of feed-forward and feedback loops are currently revealed by combining methods from biochemistry, genetics and in silico analysis. Increasing evidence is mounted that defects in information processing circuits or their components can be causative for chronic or overshooting inflammation. As progress in biosciences has always benefitted from the use of well-studied model systems, research on inflammatory cytokines may function as a paradigm to reveal general principles of signal integration, crosstalk mechanisms and signaling networks.
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Affiliation(s)
- M Lienhard Schmitz
- Institute of Biochemistry, Justus-Liebig-University Giessen, Giessen, Germany.
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1011
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Xiao L, Cui YH, Rao JN, Zou T, Liu L, Smith A, Turner DJ, Gorospe M, Wang JY. Regulation of cyclin-dependent kinase 4 translation through CUG-binding protein 1 and microRNA-222 by polyamines. Mol Biol Cell 2011; 22:3055-69. [PMID: 21737690 PMCID: PMC3164454 DOI: 10.1091/mbc.e11-01-0069] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The amino acid-derived polyamines are organic cations that are essential for growth in all mammalian cells, but their exact roles at the molecular level remain largely unknown. Here we provide evidence that polyamines promote the translation of cyclin-dependent kinase 4 (CDK4) by the action of CUG-binding protein 1 (CUGBP1) and microRNA-222 (miR-222) in intestinal epithelial cells. Both CUGBP1 and miR-222 were found to bind the CDK4 mRNA coding region and 3'-untranslated region and repressed CDK4 translation synergistically. Depletion of cellular polyamines increased cytoplasmic CUGBP1 abundance and miR-222 levels, induced their associations with the CDK4 mRNA, and inhibited CDK4 translation, whereas increasing the levels of cellular polyamines decreased CDK4 mRNA interaction with CUGBP1 and miR-222, in turn inducing CDK4 expression. Polyamine-deficient cells exhibited an increased colocalization of tagged CDK4 mRNA with processing bodies; this colocalization was abolished by silencing CUGBP1 and miR-222. Together, our findings indicate that polyamine-regulated CUGBP1 and miR-222 modulate CDK4 translation at least in part by altering the recruitment of CDK4 mRNA to processing bodies.
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Affiliation(s)
- Lan Xiao
- Cell Biology Group, Department of Surgery University of Maryland School of Medicine, Baltimore, MD 21201, USA
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1012
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Calcineurin colocalizes with P-bodies and stress granules during thermal stress in Cryptococcus neoformans. EUKARYOTIC CELL 2011; 10:1396-402. [PMID: 21724937 DOI: 10.1128/ec.05087-11] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Calcineurin is a calcium-calmodulin-activated serine/threonine-specific phosphatase that operates during cellular responses to stress and plays a prominent role in transcriptional control, whereas regulatory events beyond transcription are less well characterized. This study reveals a novel transcription-independent role of calcineurin during the temperature stress response in the human fungal pathogen Cryptococcus neoformans. The diffusely cytoplasmic calcineurin catalytic subunit Cna1 relocates to endoplasmic reticulum (ER)-associated puncta and the mother-bud neck when cells are subjected to 37°C. More than 50% of Cna1 puncta contain the P-body constituent decapping enzyme Dcp1 and the stress granule constituent poly(A)-binding protein Pub1. These results support a model in which calcineurin orchestrates thermal stress responses by associating with sites of mRNA processing.
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1013
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Abstract
Amyotrophic lateral sclerosis (ALS, also known as Lou Gehrig's disease) is a debilitating, and universally fatal, neurodegenerative disease that devastates upper and lower motor neurons. The causes of ALS are poorly understood. A central role for RNA-binding proteins and RNA metabolism in ALS has recently emerged. The RNA-binding proteins, TDP-43 and FUS, are principal components of cytoplasmic inclusions found in motor neurons of ALS patients and mutations in TDP-43 and FUS are linked to familial and sporadic ALS. Pathology and genetics also connect TDP-43 and FUS with frontotemporal lobar degeneration with ubiquitin-positive inclusions (FTLD-U). It was unknown whether mechanisms of FUS aggregation and toxicity were similar or different to those of TDP-43. To address this issue, we have employed yeast models and pure protein biochemistry to define mechanisms underlying TDP-43 and FUS aggregation and toxicity, and to identify genetic modifiers relevant for human disease. We have identified prion-like domains in FUS and TDP-43 and provide evidence that these domains are required for aggregation. Our studies have defined key similarities as well as important differences between the two proteins. Collectively, however, our findings lead us to suggest that FUS and TDP-43, though similar RNA-binding proteins, likely aggregate and confer disease phenotypes via distinct mechanisms.
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Affiliation(s)
- Aaron D Gitler
- Department of Cell and Developmental Biology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.
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1014
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The role of molecular microtubule motors and the microtubule cytoskeleton in stress granule dynamics. Int J Cell Biol 2011; 2011:939848. [PMID: 21760798 PMCID: PMC3132543 DOI: 10.1155/2011/939848] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Accepted: 04/20/2011] [Indexed: 11/18/2022] Open
Abstract
Stress granules (SGs) are cytoplasmic foci that appear in cells exposed to stress-induced translational inhibition. SGs function as a triage center, where mRNAs are sorted for storage, degradation, and translation reinitiation. The underlying mechanisms of SGs dynamics are still being characterized, although many key players have been identified. The main components of SGs are stalled 48S preinitiation complexes. To date, many other proteins have also been found to localize in SGs and are hypothesized to function in SG dynamics. Most recently, the microtubule cytoskeleton and associated motor proteins have been demonstrated to function in SG dynamics. In this paper, we will discuss current literature examining the function of microtubules and the molecular microtubule motors in SG assembly, coalescence, movement, composition, organization, and disassembly.
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1015
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Zipcode binding protein 1 regulates the development of dendritic arbors in hippocampal neurons. J Neurosci 2011; 31:5271-85. [PMID: 21471362 DOI: 10.1523/jneurosci.2387-10.2011] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The pattern of dendritic branching, together with the density of synapses and receptor composition, defines the electrical properties of a neuron. The development of the dendritic arbor and its additional stabilization are highly orchestrated at the molecular level and are guided by intrinsic mechanisms and extracellular information. Although protein translation is known to contribute to these processes, the role of its local component has not been fully explored. For local translation, mRNAs are transported to dendrites in their dormant form as ribonucleoparticles (RNPs). We hypothesized that disturbing spatial mRNA distribution via RNP targeting may result in severe underdevelopment of the dendritic arbor. Zipcode binding protein 1 (ZBP1) controls β-actin mRNA transport and translation in dendrites. We showed that proper cellular levels of ZBP1, its ability to engage in mRNA binding, and Src-dependent release of mRNA cargo from ZBP1 are vital for dendritic arbor development in cultured rat hippocampal neurons. Moreover, β-actin overexpression significantly alleviated the effects of ZBP1 knockdown. These results suggest that ZBP1-dependent dendritic mRNA transport contributes to proper dendritic branching.
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1016
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Jackowiak P, Nowacka M, Strozycki PM, Figlerowicz M. RNA degradome--its biogenesis and functions. Nucleic Acids Res 2011; 39:7361-70. [PMID: 21653558 PMCID: PMC3177198 DOI: 10.1093/nar/gkr450] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
RNA degradation is among the most fundamental processes that occur in living cells. The continuous decay of RNA molecules is associated not only with nucleotide turnover, but also with transcript maturation and quality control. The efficiency of RNA decay is ensured by a broad spectrum of both specific and non-specific ribonucleases. Some of these ribonucleases participate mainly in processing primary transcripts and in RNA quality control. Others preferentially digest mature, functional RNAs to yield a variety of molecules that together constitute the RNA degradome. Recently, it has become increasingly clear that the composition of the cellular RNA degradome can be modulated by numerous endogenous and exogenous factors (e.g. by stress). In addition, instead of being hydrolyzed to single nucleotides, some intermediates of RNA degradation can accumulate and function as signalling molecules or participate in mechanisms that control gene expression. Thus, RNA degradation appears to be not only a process that contributes to the maintenance of cellular homeostasis but also an underestimated source of regulatory molecules.
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Affiliation(s)
- Paulina Jackowiak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań and Institute of Computing Science, Poznan University of Technology, Piotrowo 3A, 60-965 Poznań, Poland
| | - Martyna Nowacka
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań and Institute of Computing Science, Poznan University of Technology, Piotrowo 3A, 60-965 Poznań, Poland
| | - Pawel M. Strozycki
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań and Institute of Computing Science, Poznan University of Technology, Piotrowo 3A, 60-965 Poznań, Poland
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań and Institute of Computing Science, Poznan University of Technology, Piotrowo 3A, 60-965 Poznań, Poland
- *To whom correspondence should be addressed. Tel: 48 61 8528503; Fax: 48 61 8520532;
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1017
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p21(WAF1/CIP1) upregulation through the stress granule-associated protein CUGBP1 confers resistance to bortezomib-mediated apoptosis. PLoS One 2011; 6:e20254. [PMID: 21637851 PMCID: PMC3102688 DOI: 10.1371/journal.pone.0020254] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Accepted: 04/28/2011] [Indexed: 12/24/2022] Open
Abstract
Background p21WAF1/CIP1 is a well known cyclin-dependent kinase inhibitor induced by various stress stimuli. Depending on the stress applied, p21 upregulation can either promote apoptosis or prevent against apoptotic injury. The stress-mediated induction of p21 involves not only its transcriptional activation but also its posttranscriptional regulation, mainly through stabilization of p21 mRNA levels. We have previously reported that the proteasome inhibitor MG132 induces the stabilization of p21 mRNA, which correlates with the formation of cytoplasmic RNA stress granules. The mechanism underlying p21 mRNA stabilization, however, remains unknown. Methodology/Principal Findings We identified the stress granules component CUGBP1 as a factor required for p21 mRNA stabilization following treatment with bortezomib ( = PS-341/Velcade). This peptide boronate inhibitor of the 26S proteasome is very efficient for the treatment of myelomas and other hematological tumors. However, solid tumors are sometimes refractory to bortezomib treatment. We found that depleting CUGBP1 in cancer cells prevents bortezomib-mediated p21 upregulation. FISH experiments combined to mRNA stability assays show that this effect is largely due to a mistargeting of p21 mRNA in stress granules leading to its degradation. Altering the expression of p21 itself, either by depleting CUGBP1 or p21, promotes bortezomib-mediated apoptosis. Conclusions/Significance We propose that one key mechanism by which apoptosis is inhibited upon treatment with chemotherapeutic drugs might involve upregulation of the p21 protein through CUGBP1.
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1018
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Legros S, Boxus M, Gatot JS, Van Lint C, Kruys V, Kettmann R, Twizere JC, Dequiedt F. The HTLV-1 Tax protein inhibits formation of stress granules by interacting with histone deacetylase 6. Oncogene 2011; 30:4050-62. [PMID: 21532619 DOI: 10.1038/onc.2011.120] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Human T cell leukemia virus type-1 (HTLV-1) is the causative agent of a fatal adult T-cell leukemia. Through deregulation of multiple cellular signaling pathways the viral Tax protein has a pivotal role in T-cell transformation. In response to stressful stimuli, cells mount a cellular stress response to limit the damage that environmental forces inflict on DNA or proteins. During stress response, cells postpone the translation of most cellular mRNAs, which are gathered into cytoplasmic mRNA-silencing foci called stress granules (SGs) and allocate their available resources towards the production of dedicated stress-management proteins. Here we demonstrate that Tax controls the formation of SGs and interferes with the cellular stress response pathway. In agreement with previous reports, we observed that Tax relocates from the nucleus to the cytoplasm in response to environmental stress. We found that the presence of Tax in the cytoplasm of stressed cells prevents the formation of SGs and counteracts the shutoff of specific host proteins. Unexpectedly, nuclear localization of Tax promotes spontaneous aggregation of SGs, even in the absence of stress. Mutant analysis revealed that the SG inhibitory capacity of Tax is independent of its transcriptional abilities but relies on its interaction with histone deacetylase 6, a critical component of SGs. Importantly, the stress-protective effect of Tax was also observed in the context of HTLV-1 infected cells, which were shown to be less prone to form SGs and undergo apoptosis under arsenite exposure. These observations identify Tax as the first virally encoded inhibitory component of SGs and unravel a new strategy developed by HTLV-1 to deregulate normal cell processes. We postulate that inhibition of the stress response pathway by Tax would favor cell survival under stressful conditions and may have an important role in HTLV-1-induced cellular transformation.
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Affiliation(s)
- S Legros
- Center for Molecular and Cellular Biology, Gembloux Agro-Bio Tech, University of Liège (ULg), Gembloux, Belgium
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1019
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Hurto RL, Hopper AK. P-body components, Dhh1 and Pat1, are involved in tRNA nuclear-cytoplasmic dynamics. RNA (NEW YORK, N.Y.) 2011; 17:912-924. [PMID: 21398402 PMCID: PMC3078740 DOI: 10.1261/rna.2558511] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2010] [Accepted: 02/06/2011] [Indexed: 05/29/2023]
Abstract
The nuclear-cytoplasmic distribution of tRNA depends on the balance between tRNA nuclear export/re-export and retrograde tRNA nuclear import in Saccharomyces cerevisiae. The distribution of tRNA is sensitive to nutrient availability as cells deprived of various nutrients exhibit tRNA nuclear accumulation. Starvation induces numerous events that result in translational repression and P-body formation. This study investigated the possible coordination of these responses with tRNA nuclear-cytoplasmic distribution. Dhh1 and Pat1 function in parallel to promote translation repression and P-body formation in response to starvation. Loss of both, Dhh1 and Pat1, results in a failure to repress translation and to induce P-body formation in response to glucose starvation. This study reports that nutrient deprived dhh1 pat1 cells also fail to accumulate tRNA within nuclei. Conversely, inhibition of translation initiation and induction of P-body formation by overproduction of Dhh1 or Pat1 cause tRNA nuclear accumulation in nutrient-replete conditions. Also, loss of the mRNA decapping activator, Lsm1, causes tRNA nuclear accumulation. However, the coordination between P-body formation, translation repression, and tRNA distribution is limited to the early part of the P-body formation/translation repression pathway as loss of mRNA decapping or 5' to 3' degradation does not influence tRNA nuclear-cytoplasmic dynamics. The data provide the first link between P-body formation/translation initiation and tRNA nuclear-cytoplasmic dynamics. The current model is that Dhh1 and Pat1 function in parallel to promote starvation-induced tRNA nuclear accumulation.
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Affiliation(s)
- Rebecca L Hurto
- Department of Molecular Genetics, The Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, USA
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1020
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Sun Z, Diaz Z, Fang X, Hart MP, Chesi A, Shorter J, Gitler AD. Molecular determinants and genetic modifiers of aggregation and toxicity for the ALS disease protein FUS/TLS. PLoS Biol 2011; 9:e1000614. [PMID: 21541367 PMCID: PMC3082519 DOI: 10.1371/journal.pbio.1000614] [Citation(s) in RCA: 357] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2010] [Accepted: 03/17/2011] [Indexed: 12/12/2022] Open
Abstract
TDP-43 and FUS are RNA-binding proteins that form cytoplasmic inclusions in some forms of amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). Moreover, mutations in TDP-43 and FUS are linked to ALS and FTLD. However, it is unknown whether TDP-43 and FUS aggregate and cause toxicity by similar mechanisms. Here, we exploit a yeast model and purified FUS to elucidate mechanisms of FUS aggregation and toxicity. Like TDP-43, FUS must aggregate in the cytoplasm and bind RNA to confer toxicity in yeast. These cytoplasmic FUS aggregates partition to stress granule compartments just as they do in ALS patients. Importantly, in isolation, FUS spontaneously forms pore-like oligomers and filamentous structures reminiscent of FUS inclusions in ALS patients. FUS aggregation and toxicity requires a prion-like domain, but unlike TDP-43, additional determinants within a RGG domain are critical for FUS aggregation and toxicity. In further distinction to TDP-43, ALS-linked FUS mutations do not promote aggregation. Finally, genome-wide screens uncovered stress granule assembly and RNA metabolism genes that modify FUS toxicity but not TDP-43 toxicity. Our findings suggest that TDP-43 and FUS, though similar RNA-binding proteins, aggregate and confer disease phenotypes via distinct mechanisms. These differences will likely have important therapeutic implications.
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Affiliation(s)
- Zhihui Sun
- Department of Cell and Developmental Biology, The University of
Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of
America
| | - Zamia Diaz
- Department of Biochemistry and Biophysics, The University of Pennsylvania
School of Medicine, Philadelphia, Pennsylvania, United States of
America
| | - Xiaodong Fang
- Department of Cell and Developmental Biology, The University of
Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of
America
| | - Michael P. Hart
- Department of Cell and Developmental Biology, The University of
Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of
America
| | - Alessandra Chesi
- Department of Cell and Developmental Biology, The University of
Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of
America
| | - James Shorter
- Department of Biochemistry and Biophysics, The University of Pennsylvania
School of Medicine, Philadelphia, Pennsylvania, United States of
America
- * E-mail: (ADG); (JS)
| | - Aaron D. Gitler
- Department of Cell and Developmental Biology, The University of
Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of
America
- * E-mail: (ADG); (JS)
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1021
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Lachke SA, Alkuraya FS, Kneeland SC, Ohn T, Aboukhalil A, Howell GR, Saadi I, Cavallesco R, Yue Y, Tsai ACH, Nair KS, Cosma MI, Smith RS, Hodges E, Alfadhli SM, Al-Hajeri A, Shamseldin HE, Behbehani A, Hannon GJ, Bulyk ML, Drack AV, Anderson PJ, John SWM, Maas RL. Mutations in the RNA granule component TDRD7 cause cataract and glaucoma. Science 2011; 331:1571-6. [PMID: 21436445 DOI: 10.1126/science.1195970] [Citation(s) in RCA: 155] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The precise transcriptional regulation of gene expression is essential for vertebrate development, but the role of posttranscriptional regulatory mechanisms is less clear. Cytoplasmic RNA granules (RGs) function in the posttranscriptional control of gene expression, but the extent of RG involvement in organogenesis is unknown. We describe two human cases of pediatric cataract with loss-of-function mutations in TDRD7 and demonstrate that Tdrd7 nullizygosity in mouse causes cataracts, as well as glaucoma and an arrest in spermatogenesis. TDRD7 is a Tudor domain RNA binding protein that is expressed in lens fiber cells in distinct TDRD7-RGs that interact with STAU1-ribonucleoproteins (RNPs). TDRD7 coimmunoprecipitates with specific lens messenger RNAs (mRNAs) and is required for the posttranscriptional control of mRNAs that are critical to normal lens development and to RG function. These findings demonstrate a role for RGs in vertebrate organogenesis.
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Affiliation(s)
- Salil A Lachke
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
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1022
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Kryndushkin D, Wickner RB, Shewmaker F. FUS/TLS forms cytoplasmic aggregates, inhibits cell growth and interacts with TDP-43 in a yeast model of amyotrophic lateral sclerosis. Protein Cell 2011; 2:223-36. [PMID: 21452073 DOI: 10.1007/s13238-011-1525-0] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Accepted: 03/06/2011] [Indexed: 12/12/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal disease characterized by the premature loss of motor neurons. While the underlying cellular mechanisms of neuron degeneration are unknown, the cytoplasmic aggregation of several proteins is associated with sporadic and familial forms of the disease. Both wild-type and mutant forms of the RNA-binding proteins FUS and TDP-43 accumulate in cytoplasmic inclusions in the neurons of ALS patients. It is not known if these so-called proteinopathies are due to a loss of function or a gain of toxicity resulting from the formation of cytoplasmic aggregates. Here we present a model of FUS toxicity using the yeast Saccharomyces cerevisiae in which toxicity is associated with greater expression and accumulation of FUS in cytoplasmic aggregates. We find that FUS and TDP-43 have a high propensity for co-aggregation, unlike the aggregation patterns of several other aggregation-prone proteins. Moreover, the biophysical properties of FUS aggregates in yeast are distinctly different from many amyloidogenic proteins, suggesting they are not composed of amyloid.
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Affiliation(s)
- Dmitry Kryndushkin
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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1023
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Eulalio A, Fröhlich KS, Mano M, Giacca M, Vogel J. A candidate approach implicates the secreted Salmonella effector protein SpvB in P-body disassembly. PLoS One 2011; 6:e17296. [PMID: 21390246 PMCID: PMC3046968 DOI: 10.1371/journal.pone.0017296] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2010] [Accepted: 01/28/2011] [Indexed: 01/11/2023] Open
Abstract
P-bodies are dynamic aggregates of RNA and proteins involved in several post-transcriptional regulation processes. P-bodies have been shown to play important roles in regulating viral infection, whereas their interplay with bacterial pathogens, specifically intracellular bacteria that extensively manipulate host cell pathways, remains unknown. Here, we report that Salmonella infection induces P-body disassembly in a cell type-specific manner, and independently of previously characterized pathways such as inhibition of host cell RNA synthesis or microRNA-mediated gene silencing. We show that the Salmonella-induced P-body disassembly depends on the activation of the SPI-2 encoded type 3 secretion system, and that the secreted effector protein SpvB plays a major role in this process. P-body disruption is also induced by the related pathogen, Shigella flexneri, arguing that this might be a new mechanism by which intracellular bacterial pathogens subvert host cell function.
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Affiliation(s)
- Ana Eulalio
- RNA Biology Group, Max Planck Institute for Infection Biology, Berlin, Germany
- * E-mail: (JV); (AE)
| | - Kathrin S. Fröhlich
- Institute of Molecular Infection Biology, Würzburg University, Würzburg, Germany
| | - Miguel Mano
- Molecular Medicine Laboratory, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Mauro Giacca
- Molecular Medicine Laboratory, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Jörg Vogel
- RNA Biology Group, Max Planck Institute for Infection Biology, Berlin, Germany
- Institute of Molecular Infection Biology, Würzburg University, Würzburg, Germany
- * E-mail: (JV); (AE)
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1024
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Xie W, Denman RB. Protein methylation and stress granules: posttranslational remodeler or innocent bystander? Mol Biol Int 2011; 2011:137459. [PMID: 22091395 PMCID: PMC3196864 DOI: 10.4061/2011/137459] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2010] [Accepted: 01/10/2011] [Indexed: 01/06/2023] Open
Abstract
Stress granules contain a large number of post-translationally modified proteins, and studies have shown that these modifications serve as recruitment tags for specific proteins and even control the assembly and disassembly of the granules themselves. Work originating from our laboratory has focused on the role protein methylation plays in stress granule composition and function. We have demonstrated that both asymmetrically and symmetrically dimethylated proteins are core constituents of stress granules, and we have endeavored to understand when and how this occurs. Here we seek to integrate this data into a framework consisting of the currently known post-translational modifications affecting stress granules to produce a model of stress granule dynamics that, in turn, may serve as a benchmark for understanding and predicting how post-translational modifications regulate other granule types.
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Affiliation(s)
- Wen Xie
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Medical College of Cornell University, New York, NY 1065, USA
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1025
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Kato K, Yamamoto Y, Izawa S. Severe ethanol stress induces assembly of stress granules in Saccharomyces cerevisiae. Yeast 2011; 28:339-47. [PMID: 21341306 DOI: 10.1002/yea.1842] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2010] [Accepted: 12/29/2010] [Indexed: 12/18/2022] Open
Abstract
Stress granules (SGs) and processing bodies (P bodies) are cytoplasmic domains and play a role in the control of translation and mRNA turnover in mammalian cells subjected to environmental stress. Recent studies have revealed that SGs also form in the budding yeast Saccharomyces cerevisiae in response to glucose depletion and robust heat shock. However, information about the types of stress that cause budding yeast SGs is quite limited. Here we demonstrate that severe ethanol stress generates budding yeast SGs in a manner independent of the phosphorylation of eIF2α. The concentration that generated budding yeast SGs (>10%) was higher than that causing P bodies (>6%), and P bodies were assembled prior to SGs. As well as mammalian SGs, the assembly of budding yeast SGs under ethanol stress was blocked by cycloheximide. On the other hand, the budding yeast SGs caused by ethanol stress contained eIF3c but not eIF3a and eIF3b, although the eIF3 complex is a core constituent of mammalian SGs. Moreover, null mutants (pbp1Δ, pub1Δ and tif4632Δ) with a strong reduction in SG formation did not resume proliferation after the elimination of ethanol stress, indicating that the formation of budding yeast SGs might play a role in sufficient recovery from ethanol stress.
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Affiliation(s)
- Kenta Kato
- Laboratory of Microbial Technology, Graduate School of Science and Technology, Kyoto Institute of Technology, Matsugasaki, Kyoto, Japan
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1026
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Red1 promotes the elimination of meiosis-specific mRNAs in vegetatively growing fission yeast. EMBO J 2011; 30:1027-39. [PMID: 21317872 DOI: 10.1038/emboj.2011.32] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2010] [Accepted: 01/21/2011] [Indexed: 01/01/2023] Open
Abstract
Meiosis-specific mRNAs are transcribed in vegetative fission yeast, and these meiotic mRNAs are selectively removed from mitotic cells to suppress meiosis. This RNA elimination system requires degradation signal sequences called determinant of selective removal (DSR), an RNA-binding protein Mmi1, polyadenylation factors, and the nuclear exosome. However, the detailed mechanism by which meiotic mRNAs are selectively degraded in mitosis but not meiosis is not understood fully. Here we report that Red1, a novel protein, is essential for elimination of meiotic mRNAs from mitotic cells. A red1 deletion results in the accumulation of a large number of meiotic mRNAs in mitotic cells. Red1 interacts with Mmi1, Pla1, the canonical poly(A) polymerase, and Rrp6, a subunit of the nuclear exosome, and promotes the destabilization of DSR-containing mRNAs. Moreover, Red1 forms nuclear bodies in mitotic cells, and these foci are disassembled during meiosis. These results demonstrate that Red1 is involved in DSR-directed RNA decay to prevent ectopic expression of meiotic mRNAs in vegetative cells.
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1027
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Thomas MG, Loschi M, Desbats MA, Boccaccio GL. RNA granules: the good, the bad and the ugly. Cell Signal 2011; 23:324-34. [PMID: 20813183 PMCID: PMC3001194 DOI: 10.1016/j.cellsig.2010.08.011] [Citation(s) in RCA: 180] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2010] [Accepted: 08/20/2010] [Indexed: 12/13/2022]
Abstract
Processing bodies (PBs) and Stress Granules (SGs) are the founding members of a new class of RNA granules, known as mRNA silencing foci, as they harbour transcripts circumstantially excluded from the translationally active pool. PBs and SGs are able to release mRNAs thus allowing their translation. PBs are constitutive, but respond to stimuli that affect mRNA translation and decay, whereas SGs are specifically induced upon cellular stress, which triggers a global translational silencing by several pathways, including phosphorylation of the key translation initiation factor eIF2alpha, and tRNA cleavage among others. PBs and SGs with different compositions may coexist in a single cell. These macromolecular aggregates are highly conserved through evolution, from unicellular organisms to vertebrate neurons. Their dynamics is regulated by several signaling pathways, and depends on microfilaments and microtubules, and the cognate molecular motors myosin, dynein, and kinesin. SGs share features with aggresomes and related aggregates of unfolded proteins frequently present in neurodegenerative diseases, and may play a role in the pathology. Virus infections may induce or impair SG formation. Besides being important for mRNA regulation upon stress, SGs modulate the signaling balancing apoptosis and cell survival. Finally, the formation of Nuclear Stress Bodies (nSBs), which share components with SGs, and the assembly of additional cytosolic aggregates containing RNA -the UV granules and the Ire1 foci-, all of them induced by specific cell damage factors, contribute to cell survival.
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Key Words
- atxn2, ataxin-2
- bicd, bicaudal d
- cbp, creb binding protein
- cpeb, cytoplasmic polyadenylation element binding protein
- dhc, dynein heavy chain
- dic, dynein intermediate chain
- fak, focal adhesion kinase
- fus/tls/hnrnp p2, fused in sarcoma
- g3bp, ras-gap sh3 domain binding protein
- gcn2, general control nonderepressible-2
- grb7, growth factor receptor-bound protein 7
- hap, hnrnp a1 interacting protein
- hdac6, histone deacetylase 6
- hri, heme-regulated inhibitor
- hsf, heat shock transcription factor
- khc, kinesin heavy chain
- klc, kinesin light chain
- mln51, metastatic lymph node 51
- nmd, nonsense mediated decay
- nsbs, nuclear stress bodies
- ogfod1, 2–14 oxoglutarate and fe(ii)-dependent oxygenase domain containing 1
- pb, processing body
- perk, pancreatic endoplasmic reticulum eif2alpha kinase
- pkr/eif2ak2, double stranded rna-dependent protein kinase
- pp1, protein phosphatase 1
- prp, prion protein
- rbp, rna binding protein
- rnp, ribonucleoparticle
- sam68, src associated in mitosis 68 kda
- member of star, signal transducer and activator of rna
- sca, spinocerebellar ataxia
- sg, stress granule
- sma, spinal muscular atrophy
- fmrp, fragile x mental retardation protein
- smn, survival of motor neuron
- tdp43, tar dna-binding protein 43
- traf2, tnf receptor associated factor 2
- uvgs, uv rna granules
- processing body
- stress granule
- kinesin
- dynein
- bicaudal d
- aggresome
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Affiliation(s)
- María Gabriela Thomas
- Instituto Leloir, Av. Patricias Argentinas 435, C1405 BWE Buenos Aires, Argentina
- CONICET, Buenos Aires, Argentina
| | - Mariela Loschi
- Instituto Leloir, Av. Patricias Argentinas 435, C1405 BWE Buenos Aires, Argentina
- CONICET, Buenos Aires, Argentina
| | - María Andrea Desbats
- Instituto Leloir, Av. Patricias Argentinas 435, C1405 BWE Buenos Aires, Argentina
| | - Graciela Lidia Boccaccio
- Instituto Leloir, Av. Patricias Argentinas 435, C1405 BWE Buenos Aires, Argentina
- CONICET, Buenos Aires, Argentina
- University of Buenos Aires
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1028
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Khong A, Jan E. Modulation of stress granules and P bodies during dicistrovirus infection. J Virol 2011; 85:1439-51. [PMID: 21106737 PMCID: PMC3028890 DOI: 10.1128/jvi.02220-10] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2010] [Accepted: 11/16/2010] [Indexed: 11/20/2022] Open
Abstract
Stress granules (SGs) are dynamic cytosolic aggregates composed of ribonucleoproteins that are induced during cellular stress when protein synthesis is inhibited. The function of SGs is poorly understood, but they are thought to be sites for reorganizing mRNA and protein. Several viruses can modulate SG formation, suggesting that SGs have an impact on virus infection. In this study, we have investigated the relationship of SG formation in Drosophila S2 cells infected by cricket paralysis virus (CrPV), a member of the Dicistroviridae family. Despite a rapid shutoff of host translation during CrPV infection, several hallmark SG markers such as the Drosophila TIA-1 and G3BP (RasGAP-SH3-binding protein) homologs, Rox8 and Rin, respectively, do not aggregate in CrPV-infected cells, even when challenged with potent SG inducers such as heat shock, oxidative stress, and pateamine A treatment. Furthermore, we demonstrate that a subset of P body markers become moderately dispersed at late times of infection. In contrast, as shown by fluorescent in situ hybridization, poly(A)(+) RNA granules still form at late times of infection. These poly(A)(+) RNA granules do not contain viral RNA nor do they colocalize with P body markers. Finally, our results demonstrate that the CrPV viral 3C protease is sequestered to SGs under cellular stress but not during virus infection. In summary, we propose that dicistrovirus infection leads to the selective inhibition of distinct SGs so that viral proteins are available for viral processing.
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Affiliation(s)
- Anthony Khong
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver BC V6T 1Z3, Canada
| | - Eric Jan
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver BC V6T 1Z3, Canada
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1029
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Yang R, Gaidamakov SA, Xie J, Lee J, Martino L, Kozlov G, Crawford AK, Russo AN, Conte MR, Gehring K, Maraia RJ. La-related protein 4 binds poly(A), interacts with the poly(A)-binding protein MLLE domain via a variant PAM2w motif, and can promote mRNA stability. Mol Cell Biol 2011; 31:542-56. [PMID: 21098120 PMCID: PMC3028612 DOI: 10.1128/mcb.01162-10] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2010] [Revised: 11/05/2010] [Accepted: 11/12/2010] [Indexed: 12/19/2022] Open
Abstract
The conserved RNA binding protein La recognizes UUU-3'OH on its small nuclear RNA ligands and stabilizes them against 3'-end-mediated decay. We report that newly described La-related protein 4 (LARP4) is a factor that can bind poly(A) RNA and interact with poly(A) binding protein (PABP). Yeast two-hybrid analysis and reciprocal immunoprecipitations (IPs) from HeLa cells revealed that LARP4 interacts with RACK1, a 40S ribosome- and mRNA-associated protein. LARP4 cosediments with 40S ribosome subunits and polyribosomes, and its knockdown decreases translation. Mutagenesis of the RNA binding or PABP interaction motifs decrease LARP4 association with polysomes. Several translation and mRNA metabolism-related proteins use a PAM2 sequence containing a critical invariant phenylalanine to make direct contact with the MLLE domain of PABP, and their competition for the MLLE is thought to regulate mRNA homeostasis. Unlike all ∼150 previously analyzed PAM2 sequences, LARP4 contains a variant PAM2 (PAM2w) with tryptophan in place of the phenylalanine. Binding and nuclear magnetic resonance (NMR) studies have shown that a peptide representing LARP4 PAM2w interacts with the MLLE of PABP within the affinity range measured for other PAM2 motif peptides. A cocrystal of PABC bound to LARP4 PAM2w shows tryptophan in the pocket in PABC-MLLE otherwise occupied by phenylalanine. We present evidence that LARP4 expression stimulates luciferase reporter activity by promoting mRNA stability, as shown by mRNA decay analysis of luciferase and cellular mRNAs. We propose that LARP4 activity is integrated with other PAM2 protein activities by PABP as part of mRNA homeostasis.
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Affiliation(s)
- Ruiqing Yang
- Intramural Research Program on Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom, Department of Biochemistry, McGill University, Montreal, QC, Canada, Commissioned Corps, U.S. Public Health Service, Washington, DC
| | - Sergei A. Gaidamakov
- Intramural Research Program on Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom, Department of Biochemistry, McGill University, Montreal, QC, Canada, Commissioned Corps, U.S. Public Health Service, Washington, DC
| | - Jingwei Xie
- Intramural Research Program on Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom, Department of Biochemistry, McGill University, Montreal, QC, Canada, Commissioned Corps, U.S. Public Health Service, Washington, DC
| | - Joowon Lee
- Intramural Research Program on Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom, Department of Biochemistry, McGill University, Montreal, QC, Canada, Commissioned Corps, U.S. Public Health Service, Washington, DC
| | - Luigi Martino
- Intramural Research Program on Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom, Department of Biochemistry, McGill University, Montreal, QC, Canada, Commissioned Corps, U.S. Public Health Service, Washington, DC
| | - Guennadi Kozlov
- Intramural Research Program on Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom, Department of Biochemistry, McGill University, Montreal, QC, Canada, Commissioned Corps, U.S. Public Health Service, Washington, DC
| | - Amanda K. Crawford
- Intramural Research Program on Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom, Department of Biochemistry, McGill University, Montreal, QC, Canada, Commissioned Corps, U.S. Public Health Service, Washington, DC
| | - Amy N. Russo
- Intramural Research Program on Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom, Department of Biochemistry, McGill University, Montreal, QC, Canada, Commissioned Corps, U.S. Public Health Service, Washington, DC
| | - Maria R. Conte
- Intramural Research Program on Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom, Department of Biochemistry, McGill University, Montreal, QC, Canada, Commissioned Corps, U.S. Public Health Service, Washington, DC
| | - Kalle Gehring
- Intramural Research Program on Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom, Department of Biochemistry, McGill University, Montreal, QC, Canada, Commissioned Corps, U.S. Public Health Service, Washington, DC
| | - Richard J. Maraia
- Intramural Research Program on Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom, Department of Biochemistry, McGill University, Montreal, QC, Canada, Commissioned Corps, U.S. Public Health Service, Washington, DC
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1030
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Functional interaction between type III-secreted protein IncA of Chlamydophila psittaci and human G3BP1. PLoS One 2011; 6:e16692. [PMID: 21304914 PMCID: PMC3031633 DOI: 10.1371/journal.pone.0016692] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2010] [Accepted: 01/11/2011] [Indexed: 11/19/2022] Open
Abstract
Chlamydophila (Cp.) psittaci, the causative agent of psittacosis in birds and humans, is the most important zoonotic pathogen of the family Chlamydiaceae. These obligate intracellular bacteria are distinguished by a unique biphasic developmental cycle, which includes proliferation in a membrane-bound compartment termed inclusion. All Chlamydiaceae spp. possess a coding capacity for core components of a Type III secretion apparatus, which mediates specific delivery of anti-host effector proteins either into the chlamydial inclusion membrane or into the cytoplasm of target eukaryotic cells. Here we describe the interaction between Type III-secreted protein IncA of Cp. psittaci and host protein G3BP1 in a yeast two-hybrid system. In GST-pull down and co-immunoprecipitation experiments both in vitro and in vivo interaction between full-length IncA and G3BP1 were shown. Using fluorescence microscopy, the localization of G3BP1 near the inclusion membrane of Cp. psittaci-infected Hep-2 cells was demonstrated. Notably, infection of Hep-2 cells with Cp. psittaci and overexpression of IncA in HEK293 cells led to a decrease in c-Myc protein concentration. This effect could be ascribed to the interaction between IncA and G3BP1 since overexpression of an IncA mutant construct disabled to interact with G3BP1 failed to reduce c-Myc concentration. We hypothesize that lowering the host cell c-Myc protein concentration may be part of a strategy employed by Cp. psittaci to avoid apoptosis and scale down host cell proliferation.
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1031
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Motta-Mena LB, Partch CL, Gardner KH. The three Rs of transcription: recruit, retain, and recycle. Mol Cell 2011; 40:855-8. [PMID: 21172650 DOI: 10.1016/j.molcel.2010.12.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The dynamic protein interactions required for transcription are functionally important yet poorly understood; in this issue of Molecular Cell, Zobeck et al. (2010) resolve the sequential recruitment and selective recycling of transcription factors at an actively transcribing locus in Drosophila.
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Affiliation(s)
- Laura B Motta-Mena
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-8816, USA
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1032
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Cohnen A, Bielig H, Hollenberg CP, Hu Z, Ramezani-Rad M. The yeast ubiquitin-like domain protein Mdy2 is required for microtubule-directed nuclear migration and localizes to cytoplasmic granules in response to heat stress. Cytoskeleton (Hoboken) 2011; 67:635-49. [PMID: 20722039 DOI: 10.1002/cm.20477] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
MDY2 encodes a ubiquitin-like (UBL)-domain protein necessary for efficient mating in Saccharomyces cerevisiae. Unlike most UBL proteins, Mdy2 is apparently not subject to C-terminal processing and is localized predominantly in the nucleus. Deletion of MDY2 is associated with a five- to seven-fold reduction in mating efficiency, mainly due to defects in nuclear migration and karyogamy at the prezygotic stage. Here, we looked for two potential interacting partners of Mdy2, investigated the function of Mdy2 in nuclear movement, determined the increased heat sensitivity defects of mdy2Δ mutants, and inspected localization of Mdy2. Coprecipitation studies show that Mdy2 associates with α-tubulin and with the microtubule (MT)-associated dynactin subunit p150(Glued)/Nip100. nip100Δ mutants exhibit no defects in nuclear migration or in MT length or orientation during shmooing growth. Deletion of MDY2 display small nuclear migration phenotype during vegetative growth and seems to exacerbate the defects in mitotic nuclear migration seen in the nip100Δ strain. Deletion of MDY2 increased heat sensitivity of the cells and these strains accumulate mitotic nuclear migration defects and shortened MTs under these conditions. GFP-Mdy2 proteins which are localized predominantly in the nucleus at permissive temperature are localized to cytoplasmic foci during heat shock. Colocalization studies revealed that heat stress-induced enrichment of Mdy2 in cytoplasmic foci merged mainly with stress granules marker Pab1. During glucose deprivation a minority of Mdy2 foci overlapped with P-bodies marker Dcp2, while most Mdy2 foci and Pab1 foci overlap. Accordingly, we propose that Mdy2 plays a critical role in the MT-dependent processes of karyogamy and stress response.
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Affiliation(s)
- André Cohnen
- Institute for Microbiology, Heinrich-Heine University, Düsseldorf, Germany
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1033
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Komar AA, Hatzoglou M. Cellular IRES-mediated translation: the war of ITAFs in pathophysiological states. Cell Cycle 2011; 10:229-40. [PMID: 21220943 DOI: 10.4161/cc.10.2.14472] [Citation(s) in RCA: 297] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Translation of cellular mRNAs via initiation at Internal Ribosome Entry Sites (IRESs) has received increased attention during recent years due to its emerging significance for many physiological and pathological stress conditions in eukaryotic cells. Expression of genes bearing IRES elements in their mRNAs is controlled by multiple molecular mechanisms, with IRES-mediated translation favored under conditions when cap-dependent translation is compromised. In this review, we discuss recent advances in the field and future directions that may bring us closer to understanding the complex mechanisms that guide cellular IRES-mediated expression. We present examples in which the competitive action of IRES-transacting factors (ITAFs) plays a pivotal role in IRES-mediated translation and thereby controls cell-fate decisions leading to either pro-survival stress adaptation or cell death.
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Affiliation(s)
- Anton A Komar
- Center for Gene Regulation in Health and Disease, Department of Biological, Geological and Environmental Sciences, Cleveland State University, Cleveland, OH, USA.
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1034
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Fawal M, Jean-Jean O, Vanzo N, Morello D. Novel mRNA-containing cytoplasmic granules in ALK-transformed cells. Mol Biol Cell 2011; 22:726-35. [PMID: 21233286 PMCID: PMC3057698 DOI: 10.1091/mbc.e10-07-0569] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
In mammalian cells, nontranslating messenger RNAs (mRNAs) are concentrated in different cytoplasmic foci, such as processing bodies (PBs) and stress granules (SGs), where they are either degraded or stored. In the present study, we have thoroughly characterized cytoplasmic foci, hereafter called AGs for ALK granules that form in transformed cells expressing the constitutively active anaplastic lymphoma kinase (ALK). AGs contain polyadenylated mRNAs and a unique combination of several RNA binding proteins that so far has not been described in mammalian foci, including AUF1, HuR, and the poly (A(+)) binding protein PABP. AGs shelter neither components of the mRNA degradation machinery present in PBs nor known markers of SGs, such as translation initiation factors or TIA/TIAR, showing that they are distinct from PBs or SGs. AGs and PBs, however, both move on microtubules with similar dynamics and frequently establish close contacts. In addition, in conditions in which mRNA metabolism is perturbed, AGs concentrate PB components with the noticeable exception of the 5' to 3' exonuclease XRN1. Altogether, we show that AGs constitute novel mRNA-containing cytoplasmic foci and we propose that they could protect translatable mRNAs from degradation, contributing thus to ALK-mediated oncogenicity.
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Affiliation(s)
- Mohamad Fawal
- CNRS-UMR 5547, IFR 109, Université Paul Sabatier, 31062 Toulouse, France
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1035
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Pothof J, van Gent DC. Spatiotemporal aspects of MicroRNA-mediated gene regulation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2011; 722:75-85. [PMID: 21915783 DOI: 10.1007/978-1-4614-0332-6_5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
MicroRNA-mediated modulation of translation has been recently discovered as a new dimension in gene expression regulation. In this chapter we review how this regulation operates in time between the fast protein modification and degradation steps on the one hand and the slow transcriptional reprogramming associated with more stable changes in gene expression patterns on the other hand. We also discuss the additional layer of complexity associated with spatial redistribution of the RNA silencing machinery in subcellular structures. Various stress conditions induce both a transient change in microRNA expression within the first few hours after exposure and a redistribution of the RNA silencing machinery from P-bodies to Stress Granules, which differ in their function and protein content. Insight into the spatiotemporal aspects of the microRNA response will be indispensable for a full understanding of this level of gene regulation.
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Affiliation(s)
- Joris Pothof
- Department of Genetics, Erasmus MC, University Medical Center, Netherlands.
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1036
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Aly ASI, Lindner SE, MacKellar DC, Peng X, Kappe SHI. SAP1 is a critical post-transcriptional regulator of infectivity in malaria parasite sporozoite stages. Mol Microbiol 2010; 79:929-39. [PMID: 21299648 DOI: 10.1111/j.1365-2958.2010.07497.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Plasmodium salivary gland sporozoites upregulate expression of a unique subset of genes, collectively called the UIS (upregulated in infectious sporozoites). Many UIS were shown to be essential for early liver stage development, although little is known about their regulation. We previously identified a conserved sporozoite-specific protein, SAP1, which has an essential role in Plasmodium liver infection. Targeted deletion of SAP1 in Plasmodium yoelii caused the depletion of a number of selectively tested UIS transcripts in sporozoites, resulting in a complete early liver stage arrest. Here, we use a global gene expression survey to more comprehensively identify transcripts that are affected by SAP1 deletion. We find an effect upon both the transcript abundance of UIS genes, as well as of select genes previously not grouped as UIS. Importantly, we show that the lack of SAP1 causes the specific degradation of these transcripts. Collectively, our data suggest that SAP1 is involved in a selective post-transcriptional mechanism to regulate the abundance of transcripts critical to the infectivity of sporozoites. Although Pysap1(-) sporozoites are depleted of many of these important transcripts, they confer long-lasting sterile protection against wild-type sporozoite challenge in mice. SAP1 is therefore an appealing candidate locus for attenuation of Plasmodium falciparum.
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Affiliation(s)
- Ahmed S I Aly
- Seattle Biomedical Research Institute, Seattle, WA 98109, USA
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1037
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Buchan JR, Yoon JH, Parker R. Stress-specific composition, assembly and kinetics of stress granules in Saccharomyces cerevisiae. J Cell Sci 2010; 124:228-39. [PMID: 21172806 DOI: 10.1242/jcs.078444] [Citation(s) in RCA: 184] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Eukaryotic cells respond to cellular stresses by the inhibition of translation and the accumulation of mRNAs in cytoplasmic RNA-protein (ribonucleoprotein) granules termed stress granules and P-bodies. An unresolved issue is how different stresses affect formation of messenger RNP (mRNP) granules. In the present study, we examine how sodium azide (NaN(3)), which inhibits mitochondrial respiration, affects formation of mRNP granules as compared with glucose deprivation in budding yeast. We observed that NaN(3) treatment inhibits translation and triggers formation of P-bodies and stress granules. The composition of stress granules induced by NaN(3) differs from that of glucose-deprived cells by containing eukaryotic initiation factor (eIF)3, eIF4A/B, eIF5B and eIF1A proteins, and by lacking the heterogeneous nuclear RNP (hnRNP) protein Hrp1. Moreover, in contrast with glucose-deprived stress granules, NaN(3)-triggered stress granules show different assembly rules, form faster and independently from P-bodies and dock or merge with P-bodies over time. Strikingly, addition of NaN(3) and glucose deprivation in combination, regardless of the order, always results in stress granules of a glucose deprivation nature, suggesting that both granules share an mRNP remodeling pathway. These results indicate that stress granule assembly, kinetics and composition in yeast can vary in a stress-specific manner, which we suggest reflects different rate-limiting steps in a common mRNP remodeling pathway.
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Affiliation(s)
- J Ross Buchan
- Howard Hughes Medical Institute, University of Arizona, Tucson, AZ 85721, USA.
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1038
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Richter K, Haslbeck M, Buchner J. The heat shock response: life on the verge of death. Mol Cell 2010; 40:253-66. [PMID: 20965420 DOI: 10.1016/j.molcel.2010.10.006] [Citation(s) in RCA: 1276] [Impact Index Per Article: 91.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2010] [Revised: 10/03/2010] [Accepted: 10/05/2010] [Indexed: 12/16/2022]
Abstract
Organisms must survive a variety of stressful conditions, including sudden temperature increases that damage important cellular structures and interfere with essential functions. In response to heat stress, cells activate an ancient signaling pathway leading to the transient expression of heat shock or heat stress proteins (Hsps). Hsps exhibit sophisticated protection mechanisms, and the most conserved Hsps are molecular chaperones that prevent the formation of nonspecific protein aggregates and assist proteins in the acquisition of their native structures. In this Review, we summarize the concepts of the protective Hsp network.
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Affiliation(s)
- Klaus Richter
- Munich Center for Integrated Protein Science, Department Chemie Technische Universität München, 85747 Garching, Germany
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1039
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Spriggs KA, Bushell M, Willis AE. Translational regulation of gene expression during conditions of cell stress. Mol Cell 2010; 40:228-37. [PMID: 20965418 DOI: 10.1016/j.molcel.2010.09.028] [Citation(s) in RCA: 523] [Impact Index Per Article: 37.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2010] [Revised: 09/10/2010] [Accepted: 09/28/2010] [Indexed: 01/17/2023]
Abstract
A number of stresses, including nutrient stress, temperature shock, DNA damage, and hypoxia, can lead to changes in gene expression patterns caused by a general shutdown and reprogramming of protein synthesis. Each of these stress conditions results in selective recruitment of ribosomes to mRNAs whose protein products are required for responding to stress. This recruitment is regulated by elements within the 5' and 3' untranslated regions of mRNAs, including internal ribosome entry segments, upstream open reading frames, and microRNA target sites. These elements can act singly or in combination and are themselves regulated by trans-acting factors. Translational reprogramming can result in increased life span, and conversely, deregulation of these translation pathways is associated with disease including cancer and diabetes.
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Affiliation(s)
- Keith A Spriggs
- Centre for Biomolecular Sciences, School of Pharmacy, University of Nottingham, University Park, Nottingham NG7 2RD, UK
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1040
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Kishore S, Luber S, Zavolan M. Deciphering the role of RNA-binding proteins in the post-transcriptional control of gene expression. Brief Funct Genomics 2010; 9:391-404. [PMID: 21127008 DOI: 10.1093/bfgp/elq028] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Eukaryotic cells express a large variety of ribonucleic acid-(RNA)-binding proteins (RBPs) with diverse affinity and specificity towards target RNAs that play a crucial role in almost every aspect of RNA metabolism. In addition, specific domains in RBPs impart catalytic activity or mediate protein-protein interactions, making RBPs versatile regulators of gene expression. In this review, we elaborate on recent experimental and computational approaches that have increased our understanding of RNA-protein interactions and their role in cellular function. We review aspects of gene expression that are modulated post-transcriptionally by RBPs, namely the stability of polymerase II-derived mRNA transcripts and their rate of translation into proteins. We further highlight the extensive regulatory networks of RBPs that implement a combinatorial control of gene expression. Taking cues from the recent development in the field, we argue that understanding spatio-temporal RNA-protein association on a transcriptome level will provide invaluable and unexpected insights into the regulatory codes that define growth, differentiation and disease.
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1041
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Janowicz A, Michalak M, Krebs J. Stress induced subcellular distribution of ALG-2, RBM22 and hSlu7. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2010; 1813:1045-9. [PMID: 21122810 DOI: 10.1016/j.bbamcr.2010.11.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2010] [Revised: 11/15/2010] [Accepted: 11/16/2010] [Indexed: 11/30/2022]
Abstract
ALG-2 is a highly conserved calcium binding protein in the cytoplasm which belongs to the family of penta-EF hand proteins. Recently, we showed that ALG-2 is interacting with RBM22, a highly conserved spliceosomal nuclear protein (Montaville et al. Biochim. Biophys. Acta 1763, 1335, 2006; Krebs, Biochim. Biophys. Acta 1793, 979, 2009). In NIH 3T3 cells expressing both proteins a significant amount of ALG-2mRFP is translocated to the nucleus due to the interaction with RBM22-EGFP. hSlu7, another spliceosomal nuclear protein, known to interact with RBM22 in yeast, has been shown to translocate to the cytoplasm under cellular stress conditions. Here we provide evidence that the 2 spliceosomal proteins differ significantly in their subcellular distributions under stress conditions, and that RBM22 enhances the cytoplasmic translocation of hSlu7 under stress, especially a stress induced by thapsigargin. On the other hand, in NIH 3T3 cells expressing RBM22-EGFP and ALG-2-mRFP, ALG-2 remains translocated into the nucleus under both stress conditions, i.e. heat shock or treatment with thapsigargin. We could further demonstrate that these stress conditions had a different influence on the splicing pattern of XBP-1, a marker for the unfolded protein response indicating that ER stress may play a role in stress-induced translocation of spliceosomal proteins. The article is part of a Special Issue entitled: 11th European Symposium on Calcium.
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Affiliation(s)
- Aleksandra Janowicz
- Department of Biochemistry, School of Molecular and Systems Biology, University of Alberta, Edmonton, Canada
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1042
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Wei LN. The RNA superhighway: axonal RNA trafficking of kappa opioid receptor mRNA for neurite growth. Integr Biol (Camb) 2010; 3:10-6. [PMID: 21116543 DOI: 10.1039/c0ib00107d] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Neurons are highly polarized cells with extensive sub-cellular compartmentalization to accommodate diverse local needs. Information flows between the pre-synaptic (axon) and post-synaptic (dendrite) compartments, as well as between the soma and the nerve termini. It is critical that a neuron controls efficient molecular transfer/transport through its axon. But this is extremely challenging to study because of the long distance molecules must travel through axons and the apparent contextual difference in the axons' various local environments, which should not be examined in isolation. Understanding the action in neurons of drug-responsive neurotransmitter receptors such as opioid receptors has been hindered by the lack of information on the control of molecular flow between such various sub-cellular neuron compartments. Recent studies have uncovered new transport systems other than the classical vesicle transport in neurons, particularly those utilizing various granules containing certain RNAs including protein-coding mRNAs. Through integrated approaches exploiting various experimental systems, tools, and methodologies, studies have provided solid evidence for functional roles of specific RNA granules in several biological processes crucial for the survival and function of neurons. These include neurons' transport of molecules/information, stress response, and local axonal translation. By using the kappa opioid receptor (KOR) as a model, studies have also revealed a novel physiological function of KOR in mediating growth factor-stimulated neurite outgrowth during a critical period of development, which requires specific KOR mRNA untranslated sequences that direct spatially and temporally specific expression of KOR.
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Affiliation(s)
- Li-Na Wei
- Department of Pharmacology, University of Minnesota Medical School, Minneapolis, 55455, USA.
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1043
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Escape from stress granule sequestration: another way to drug resistance? Biochem Soc Trans 2010; 38:1537-42. [DOI: 10.1042/bst0381537] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Overexpression of P-glycoprotein, encoded by the MDR1 (multidrug resistance 1) gene, is often responsible for multidrug resistance and chemotherapy failure in cancer. We have demonstrated that, in leukaemic cells, P-glycoprotein expression is regulated at the translational level. More recently, we have shown that in cells overexpressing P-glycoprotein, MDR1 mRNA does not aggregate into translationally silent stress granules. Importantly, this is not unique for MDR1, since other transcripts encoding transmembrane proteins, and which are thus translated at the endoplasmic reticulum, follow the same pattern. By using a series of chimaeric transcripts, we have demonstrated that transcript localization at the endoplasmic reticulum bypasses the signals dictating stress granule sequestration. Polysome profile analyses and protein synthesis experiments indicate that, upon stress withdrawal, endoplasmic-reticulum-bound transcripts resume translation faster than those at the cytosol, which have been sequestered into stress granules. This may represent a novel mechanism by which drug-resistant cells respond quickly to stress, helping them to survive the cytotoxic effect of chemotherapeutic drugs.
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1044
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Gudkova DO, Panasyuk GG, Nemazanyy IO, Filonenko VV. Novel antibodies against RCD-8 as a tool to study processing bodies. ACTA ACUST UNITED AC 2010. [DOI: 10.7124/bc.00017c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- D. O. Gudkova
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine
- Taras Shevchenko National University of Kyiv
| | - G. G. Panasyuk
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine
| | - I. O. Nemazanyy
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine
| | - V. V. Filonenko
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine
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1045
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Papoulas O, Monzo KF, Cantin GT, Ruse C, Yates JR, Ryu YH, Sisson JC. dFMRP and Caprin, translational regulators of synaptic plasticity, control the cell cycle at the Drosophila mid-blastula transition. Development 2010; 137:4201-9. [PMID: 21068064 DOI: 10.1242/dev.055046] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The molecular mechanisms driving the conserved metazoan developmental shift referred to as the mid-blastula transition (MBT) remain mysterious. Typically, cleavage divisions give way to longer asynchronous cell cycles with the acquisition of a gap phase. In Drosophila, rapid synchronous nuclear divisions must pause at the MBT to allow the formation of a cellular blastoderm through a special form of cytokinesis termed cellularization. Drosophila Fragile X mental retardation protein (dFMRP; FMR1), a transcript-specific translational regulator, is required for cellularization. The role of FMRP has been most extensively studied in the nervous system because the loss of FMRP activity in neurons causes the misexpression of specific mRNAs required for synaptic plasticity, resulting in mental retardation and autism in humans. Here, we show that in the early embryo dFMRP associates specifically with Caprin, another transcript-specific translational regulator implicated in synaptic plasticity, and with eIF4G, a key regulator of translational initiation. dFMRP and Caprin collaborate to control the cell cycle at the MBT by directly mediating the normal repression of maternal Cyclin B mRNA and the activation of zygotic frühstart mRNA. These findings identify two new targets of dFMRP regulation and implicate conserved translational regulatory mechanisms in processes as diverse as learning, memory and early embryonic development.
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Affiliation(s)
- Ophelia Papoulas
- The Section of MCD Biology and Institute for Cellular and Molecular Biology, The University of Texas at Austin, TX 78712, USA.
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1046
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Sphingolipids mediate formation of mRNA processing bodies during the heat-stress response of Saccharomyces cerevisiae. Biochem J 2010; 431:31-8. [PMID: 20629639 DOI: 10.1042/bj20100307] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Recent work, especially in the yeast Saccharomyces cerevisiae, has demonstrated that mRNA movement from active translation to cytoplasmic granules, termed mRNA'p-bodies' (processing bodies), occurs in concert with the regulation of translation during cell stress. However, the signals regulating p-body formation are poorly defined. Recent results have demonstrated a function for sphingolipids in regulating translation during heat stress, which led to the current hypothesis that p-bodies may form during heat stress in a sphingolipid-dependent manner. In the present study, we demonstrate that mild-heat-stress-induced formation of p-bodies, as determined by localization of a GFP (green fluorescent protein)-tagged Dcp2p and RFP (red fluorescent protein)-tagged Edc3p to discrete cytoplasmic foci. Sphingoid base synthesis was required for this effect, as inhibition of sphingoid base synthesis attenuated formation of these foci during heat stress. Moreover, treatment of yeast with the exogenous sphingoid bases phyto- and dihydro-sphingosine promoted formation of p-bodies in the absence of heat stress, and the lcb4/lcb5 double-deletion yeast, which accumulates high intracellular levels of sphingoid bases, had large clearly defined p-bodies under non-stress conditions. Functionally, inhibition of sphingolipid synthesis during heat stress did not prevent translation stalling, but extended translation arrest, indicating that sphingolipids mediate translation initiation. These results are consistent with the notion that p-bodies serve not only in mRNA degradation, but also for re-routing transcripts back to active translation, and that sphingolipids play a role in this facet of the heat-stress response. Together, these results demonstrate a critical and novel role for sphingolipids in mediating p-body formation during heat stress.
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1047
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Abstract
Long terminal repeat (LTR) retrotransposons are not only the ancient predecessors of retroviruses, but they constitute significant fractions of the genomes of many eukaryotic species. Studies of their structure and function are motivated by opportunities to gain insight into common functions of retroviruses and retrotransposons, diverse mechanisms of intracellular genomic mobility, and host factors that diminish or enhance retrotransposition. This review focuses on the nucleocapsid (NC) protein of a Saccharomyces cerevisiae LTR retrotransposon, the metavirus, Ty3. Retrovirus NC promotes genomic (g)RNA dimerization and packaging, tRNA primer annealing, reverse transcription strand transfers, and host protein interactions with gRNA. Studies of Ty3 NC have revealed key roles for Ty3 NC in formation of retroelement assembly sites (retrosomes), and in chaperoning primer tRNA to both dimerize and circularize Ty3 gRNA. We speculate that Ty3 NC, together with P-body and stress-granule proteins, plays a role in transitioning Ty3 RNA from translation template to gRNA, and that interactions between the acidic spacer domain of Ty3 Gag3 and the adjacent basic NC domain control condensation of the virus-like particle.
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Affiliation(s)
- Suzanne B Sandmeyer
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA USA.
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1048
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Naarmann IS, Harnisch C, Müller-Newen G, Urlaub H, Ostareck-Lederer A, Ostareck DH. DDX6 recruits translational silenced human reticulocyte 15-lipoxygenase mRNA to RNP granules. RNA (NEW YORK, N.Y.) 2010; 16:2189-204. [PMID: 20884783 PMCID: PMC2957058 DOI: 10.1261/rna.2211110] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2010] [Accepted: 08/11/2010] [Indexed: 05/29/2023]
Abstract
Erythroid precursor cells lose the capacity for mRNA synthesis due to exclusion of the nucleus during maturation. Therefore, the stability and translation of mRNAs that code for specific proteins, which function in late stages of maturation when reticulocytes become erythrocytes, are controlled tightly. Reticulocyte 15-lipoxygenase (r15-LOX) initiates the breakdown of mitochondria in mature reticulocytes. Through the temporal restriction of mRNA translation, the synthesis of r15-LOX is prevented in premature cells. The enzyme is synthesized only in mature reticulocytes, although r15-LOX mRNA is already present in erythroid precursor cells. Translation of r15-LOX mRNA is inhibited by hnRNP K and hnRNP E1, which bind to the differentiation control element (DICE) in its 3' untranslated region (3'UTR). The hnRNP K/E1-DICE complex interferes with the joining of the 60S ribosomal subunit to the 40S subunit at the AUG. We took advantage of the inducible human erythroid K562 cell system that fully recapitulates this process to identify so far unknown factors, which are critical for DICE-dependent translational regulation. Applying RNA chromatography with the DICE as bait combined with hnRNP K immunoprecipitation, we specifically purified the DEAD-box RNA helicase 6 (DDX6) that interacts with hnRNP K and hnRNP E1 in a DICE-dependent manner. Employing RNA interference and fluorescence in situ hybridization, we show that DDX6 colocalizes with endogenous human (h)r15-LOX mRNA to P-body-like RNP granules, from which 60S ribosomal subunits are excluded. Our data suggest that in premature erythroid cells translational silencing of hr15-LOX mRNA is maintained by DDX6 mediated storage in these RNP granules.
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Affiliation(s)
- Isabel S Naarmann
- Department of Intensive Care, Experimental Research Unit, University Hospital, RWTH Aachen University, 52074 Aachen, Germany
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1049
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von Roretz C, Di Marco S, Mazroui R, Gallouzi IE. Turnover of AU-rich-containing mRNAs during stress: a matter of survival. WILEY INTERDISCIPLINARY REVIEWS-RNA 2010; 2:336-47. [PMID: 21957021 DOI: 10.1002/wrna.55] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cells undergo various adaptive measures in response to stress. Among these are specific changes in the posttranscriptional regulation of various genes. In particular, the turnover of mRNA is modified to either increase or decrease the abundance of certain target messages. Some of the best-studied mRNAs that are affected by stress are those that contain adenine/uridine-rich elements (AREs) in their 3'-untranslated regions. ARE-containing mRNAs are involved in many important cellular processes and are normally labile, but in response to stress they are differentially regulated through the concerted efforts of ARE-binding proteins (AUBPs) such as HuR, AUF1, tristetraprolin, BRF1, and KSRP, along with microRNA-mediated effects. Additionally, the fate of ARE-containing mRNAs is modified by inducing their localization to stress granules or mRNA processing bodies. Coordination of these various mechanisms controls the turnover of ARE-containing mRNAs, and thereby enables proper responses to cellular stress. In this review, we discuss how AUBPs regulate their target mRNAs in response to stress, along with the involvement of cytoplasmic granules in this process.
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1050
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Wang Y, Lacroix G, Haines J, Doukhanine E, Almazan G, Richard S. The QKI-6 RNA binding protein localizes with the MBP mRNAs in stress granules of glial cells. PLoS One 2010; 5. [PMID: 20862255 PMCID: PMC2941464 DOI: 10.1371/journal.pone.0012824] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2010] [Accepted: 08/12/2010] [Indexed: 12/23/2022] Open
Abstract
Background The quaking viable (qkv) mouse has several developmental defects that result in rapid tremors in the hind limbs. The qkI gene expresses three major alternatively spliced mRNAs (5, 6 and 7 kb) that encode the QKI-5, QKI-6 and QKI-7 RNA binding proteins that differ in their C-terminal 30 amino acids. The QKI isoforms are known to regulate RNA metabolism within oligodendrocytes, however, little is known about their roles during cellular stress. Methodology/Principal Findings In this study, we report an interaction between the QKI-6 isoform and a component of the RNA induced silencing complex (RISC), argonaute 2 (Ago2). We show in glial cells that QKI-6 co-localizes with Ago2 and the myelin basic protein mRNA in cytoplasmic stress granules. Conclusions Our findings define the QKI isoforms as Ago2-interacting proteins. We also identify the QKI-6 isoform as a new component of stress granules in glial cells.
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Affiliation(s)
- Yunling Wang
- Terry Fox Molecular Oncology Group, Lady Davis Institute for Medical Research and Departments of Oncology and Medicine, Bloomfield Center for Research on Aging, McGill University, Montréal, Québec, Canada
| | - Geneviève Lacroix
- Terry Fox Molecular Oncology Group, Lady Davis Institute for Medical Research and Departments of Oncology and Medicine, Bloomfield Center for Research on Aging, McGill University, Montréal, Québec, Canada
| | - Jeffery Haines
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec, Canada
| | - Evgueni Doukhanine
- Terry Fox Molecular Oncology Group, Lady Davis Institute for Medical Research and Departments of Oncology and Medicine, Bloomfield Center for Research on Aging, McGill University, Montréal, Québec, Canada
| | - Guillermina Almazan
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec, Canada
| | - Stéphane Richard
- Terry Fox Molecular Oncology Group, Lady Davis Institute for Medical Research and Departments of Oncology and Medicine, Bloomfield Center for Research on Aging, McGill University, Montréal, Québec, Canada
- * E-mail:
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