801
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Strong MJ. The evidence for altered RNA metabolism in amyotrophic lateral sclerosis (ALS). J Neurol Sci 2009; 288:1-12. [PMID: 19840884 DOI: 10.1016/j.jns.2009.09.029] [Citation(s) in RCA: 132] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2009] [Revised: 08/27/2009] [Accepted: 09/25/2009] [Indexed: 12/11/2022]
Abstract
In this review, the role of aberrant RNA metabolism in ALS is examined, including the evidence that a majority of the genetic mutations observed in familial ALS (including mutations in TDP-43, FUS/TLS, SOD1, angiogenin (ANG) and senataxin (SETX)) can impact directly on either gene transcription, pre-mRNA splicing, ribonucleoprotein complex formation, transport, RNA translation or degradation. The evidence that perturbed expression or function of RNA binding proteins is causally related to the selective suppression of the low molecular weight subunit protein (NFL) steady state mRNA levels in degenerating motor neurons in ALS is examined. The discovery that mtSOD1, TDP-43 and 14-3-3 proteins, all of which form cytosolic aggregates in ALS, can each modulate the stability of NFL mRNA, suggests that a fundamental alteration in the interaction of mRNA species with key trans-acting binding factors has occurred in ALS. These observations lead directly to the hypothesis that ALS can be viewed as a disorder of RNA metabolism, thus providing a novel pathway for the development of molecular pharmacotherapies.
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Affiliation(s)
- Michael J Strong
- Molecular Brain Research Group, Robarts Research Institute, London, Ontario, Canada.
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802
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Loschi M, Leishman CC, Berardone N, Boccaccio GL. Dynein and kinesin regulate stress-granule and P-body dynamics. J Cell Sci 2009; 122:3973-82. [PMID: 19825938 DOI: 10.1242/jcs.051383] [Citation(s) in RCA: 134] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Stress granules (SGs) and P-bodies (PBs) are related cytoplasmic structures harboring silenced mRNAs. SGs assemble transiently upon cellular stress, whereas PBs are constitutive and are further induced by stress. Both foci are highly dynamic, with messenger ribonucleoproteins (mRNPs) and proteins rapidly shuttling in and out. Here, we show that impairment of retrograde transport by knockdown of mammalian dynein heavy chain 1 (DHC1) or bicaudal D1 (BicD1) inhibits SG formation and PB growth upon stress, without affecting protein-synthesis blockage. Conversely, impairment of anterograde transport by knockdown of kinesin-1 heavy chain (KIF5B) or kinesin light chain 1 (KLC1) delayed SG dissolution. Strikingly, SG dissolution is not required to restore translation. Simultaneous knockdown of dynein and kinesin reverted the effect of single knockdowns on both SGs and PBs, suggesting that a balance between opposing movements driven by these molecular motors governs foci formation and dissolution. Finally, we found that regulation of SG dynamics by dynein and kinesin is conserved in Drosophila.
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Affiliation(s)
- Mariela Loschi
- Instituto Leloir, Avenida Patricias Argentinas 435, C1405BWE-Buenos Aires, Argentina
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803
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Mauxion F, Chen CYA, Séraphin B, Shyu AB. BTG/TOB factors impact deadenylases. Trends Biochem Sci 2009; 34:640-7. [PMID: 19828319 DOI: 10.1016/j.tibs.2009.07.008] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2009] [Revised: 07/19/2009] [Accepted: 07/21/2009] [Indexed: 10/20/2022]
Abstract
BTG/TOB factors are a family of antiproliferative proteins whose expression is altered in numerous cancers. They have been implicated in cell differentiation, development and apoptosis. Although proposed to affect transcriptional regulation, these factors interact with CAF1, a subunit of the main eukaryotic deadenylase, and with poly(A)-binding-proteins, strongly suggesting a role in post-transcriptional regulation of gene expression. The recent determination of the structures of BTG2, TOB1 N-terminal domain (TOB1N138) and TOB1N138-CAF1 complexes support a role for BTG/TOB proteins in mRNA deadenylation, a function corroborated by recently published functional characterizations. We highlight molecular mechanisms by which BTG/TOB proteins influence deadenylation and discuss the need for a better understanding of BTG/TOB physiological functions.
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Affiliation(s)
- Fabienne Mauxion
- Equipe Labellisée La Ligue, Centre de Génétique Moléculaire, CNRS FRE3144, Gif-sur-Yvette, France
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804
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Larson DR, Singer RH, Zenklusen D. A single molecule view of gene expression. Trends Cell Biol 2009; 19:630-7. [PMID: 19819144 DOI: 10.1016/j.tcb.2009.08.008] [Citation(s) in RCA: 145] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2009] [Revised: 08/21/2009] [Accepted: 08/25/2009] [Indexed: 10/20/2022]
Abstract
Analyzing the expression of single genes in single cells appears minimalistic in comparison to gene expression studies based on more global approaches. However, stimulated by advances in imaging technologies, single-cell studies have become an essential tool in understanding the rules that govern gene expression. This quantitative view of single-cell gene expression is based on counting mRNAs in single cells, monitoring transcription in real time, and visualizing single proteins. Parallel advances in mathematical models based on stochastic, discrete descriptions of biochemical processes have provided crucial insights into the underlying cellular mechanisms that control expression. The view that has emerged is rooted in a probabilistic understanding of cellular processes that quantitatively explains both the mean and the variation observed in gene-expression patterns among single cells. Thus, the close coupling between imaging and mathematical theory has established single-cell analysis as an essential branch of systems biology.
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Affiliation(s)
- Daniel R Larson
- Department of Anatomy and Structural Biology and The Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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805
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Volkening K, Leystra-Lantz C, Yang W, Jaffee H, Strong MJ. Tar DNA binding protein of 43 kDa (TDP-43), 14-3-3 proteins and copper/zinc superoxide dismutase (SOD1) interact to modulate NFL mRNA stability. Implications for altered RNA processing in amyotrophic lateral sclerosis (ALS). Brain Res 2009; 1305:168-82. [PMID: 19815002 DOI: 10.1016/j.brainres.2009.09.105] [Citation(s) in RCA: 172] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2009] [Revised: 09/28/2009] [Accepted: 09/29/2009] [Indexed: 10/20/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurological disease characterized by progressive motor neuron degeneration in association with neurofilament (NF) aggregate formation. This process is accompanied by an alteration in the stoichiometry of NF subunit protein expression such that the steady state levels of the low molecular weight NF (NFL) mRNA levels are selectively suppressed. We have previously shown that each of TDP-43, 14-3-3 and mutant SOD1 can function as NFL mRNA 3'UTR binding proteins that directly affect the stability of NFL transcripts. In this study, we demonstrate that the interaction of TDP-43 with the NFL mRNA 3' UTR involves ribonucleotide (UG) motifs present on stem loops of the 3'UTR as well as the RRM1 and RRM2 motifs of TDP-43. Ex vivo, TDP-43, 14-3-3 and SOD1 proteins interact to modulate NFL mRNA stability, although in vivo, only TDP-43 and either mutant or wild-type SOD1 co-localize in ALS motor neurons. TDP-43 was observed to co-localize to RNA transport granules (Staufen immunoreactive) in both control and ALS spinal motor neurons. In contrast, both stress granules (TIA-1 immunoreactive) and processing bodies (P-bodies; XRN-1 immunoreactive) were more prevalent in ALS motor neurons than in controls and demonstrated strong co-localization with TDP-43. Using RNA-IP-PCR, we further demonstrate that NFL mRNA is preferentially sequestered to both stress granules and P-bodies in ALS. These data suggest that NFL mRNA processing is fundamentally altered in ALS spinal motor neurons to favour compartmentalization within both stress granules and P-bodies, and that TDP-43 plays a fundamental role in this process.
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Affiliation(s)
- Kathryn Volkening
- Molecular Brain Research Group, Robarts Research Institute, 100 Perth Drive, London, Ontario, Canada N6A 5K8
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806
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Mata J. Genome-wide mapping of myosin protein-RNA networks suggests the existence of specialized protein production sites. FASEB J 2009; 24:479-84. [PMID: 19805578 DOI: 10.1096/fj.09-140335] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Motor proteins can organize posttranscriptional processes by transporting ribonucleoprotein complexes to specific locations. To investigate a possible role of myosin proteins in gene expression control, I have identified mRNAs associated with five myosin heavy chains in the fission yeast Schizosaccharomyces pombe, by purifying the proteins and identifying bound transcripts using DNA microarrays. Each myosin coimmunoprecipitated with 5-13 different mRNAs (approximately 0.1-0.2% of all genes), including those encoding four different myosin heavy chains. Moreover, one of the myosins (Myo1) interacted with mRNAs encoding components of the cortical actin cytoskeleton. These interactions were not observed in control immunoprecipitates. A myosin-specific chaperone (Rng3) that interacts cotranslationally with myosin mRNAs was essential for the association between myosin proteins and transcripts but not between Myo1 and other mRNAs. Finally, proteins encoded by the Myo1-associated mRNAs immunoprecipitated each other's transcripts, but not myosin mRNAs. These interactions suggest the existence of two distinct myosin-containing ribonucleoprotein complexes: those containing myosin mRNAs and those associated with Myo1. They are distinguished by their mRNA composition, requirement for the Rng3 chaperone and the presence of nonmyosin cytoskeletal proteins. I propose that these complexes represent specialized sites for the production of myosin proteins and the assembly of cytoskeletal components, respectively.
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Affiliation(s)
- Juan Mata
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK.
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807
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Lin JC, Tarn WY. RNA-binding motif protein 4 translocates to cytoplasmic granules and suppresses translation via argonaute2 during muscle cell differentiation. J Biol Chem 2009; 284:34658-65. [PMID: 19801630 DOI: 10.1074/jbc.m109.032946] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The RNA-binding motif protein 4 (RBM4) plays multiple roles in mRNA metabolism, including translation control. RBM4 suppresses cap-dependent translation but activates internal ribosome entry site-mediated translation. Because of its high expression level in muscle and heart, we investigated the function of RBM4 in myoblast cells. Here, we demonstrate that RBM4 is phosphorylated and translocates to the cytoplasm in mouse C2C12 cells upon cell differentiation. Notably, RBM4 is transiently deposited into cytoplasmic granules containing microtubule assembly factors as well as poly(A)(+) RNAs. Moreover, RBM4 colocalizes with the components of micro-ribonucleoproteins, including the Argonaute2 (Ago2) protein, during muscle cell differentiation. RBM4 interacts directly with Ago2 and may recruit Ago2 to suppress translation of target mRNAs. Furthermore, RBM4 selectively associates with muscle cell-specific microRNAs and potentiates their translation repression activity by promoting micro-ribonucleoprotein association with target mRNAs. Altogether, our results suggest that RBM4 translocates to the cytoplasm and participates in translation suppression during muscle cell differentiation.
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Affiliation(s)
- Jung-Chun Lin
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
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808
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Russell JH, Keiler KC. Subcellular localization of a bacterial regulatory RNA. Proc Natl Acad Sci U S A 2009; 106:16405-9. [PMID: 19805312 PMCID: PMC2752561 DOI: 10.1073/pnas.0904904106] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2009] [Indexed: 01/22/2023] Open
Abstract
Eukaryotes and bacteria regulate the activity of some proteins by localizing them to discrete subcellular structures, and eukaryotes localize some RNAs for the same purpose. To explore whether bacteria also spatially regulate RNAs, the localization of tmRNA was determined using fluorescence in situ hybridization. tmRNA is a small regulatory RNA that is ubiquitous in bacteria and that interacts with translating ribosomes in a reaction known as trans-translation. In Caulobacter crescentus, tmRNA was localized in a cell-cycle-dependent manner. In G(1)-phase cells, tmRNA was found in regularly spaced foci indicative of a helix-like structure. After initiation of DNA replication, most of the tmRNA was degraded, and the remaining molecules were spread throughout the cytoplasm. Immunofluorescence assays showed that SmpB, a protein that binds tightly to tmRNA, was colocalized with tmRNA in the helix-like pattern. RNase R, the nuclease that degrades tmRNA, was localized in a helix-like pattern that was separate from the SmpB-tmRNA complex. These results suggest a model in which tmRNA-SmpB is localized to sequester tmRNA from RNase R, and localization might also regulate tmRNA-SmpB interactions with ribosomes.
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Affiliation(s)
- Jay H. Russell
- The Pennsylvania State University, Department of Biochemistry and Molecular Biology, 401 Althouse Lab, University Park, PA 16802
| | - Kenneth C. Keiler
- The Pennsylvania State University, Department of Biochemistry and Molecular Biology, 401 Althouse Lab, University Park, PA 16802
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809
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St Laurent G, Savva YA, Reenan R. Enhancing non-coding RNA information content with ADAR editing. Neurosci Lett 2009; 466:89-98. [PMID: 19751800 DOI: 10.1016/j.neulet.2009.09.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2009] [Revised: 09/02/2009] [Accepted: 09/05/2009] [Indexed: 10/20/2022]
Abstract
The depth and complexity of the non-coding transcriptome in nervous system tissues provides a rich substrate for adenosine de-amination acting on RNA (ADAR). Non-coding RNAs (ncRNAs) serve diverse regulatory and computational functions, coupling signal flow from the environment to evolutionarily coded analog and digital information elements within the transcriptome. We present a perspective of ADARs interaction with the non-coding transcriptome as a computational matrix, enhancing the information processing power of the cell, adding flexibility, rapid response, and fine tuning to critical pathways. Dramatic increases in ADAR activity during stress response and inflammation result in powerful information processing events that change the functional state of the cell. This review examines the pathways and mechanisms of ADAR interaction with the non-coding transcriptome, and their functional consequences for information processing in nervous system tissues.
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Affiliation(s)
- Georges St Laurent
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI 02912, USA
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810
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Hu W, Sweet TJ, Chamnongpol S, Baker KE, Coller J. Co-translational mRNA decay in Saccharomyces cerevisiae. Nature 2009; 461:225-9. [PMID: 19701183 PMCID: PMC2745705 DOI: 10.1038/nature08265] [Citation(s) in RCA: 257] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2009] [Accepted: 07/06/2009] [Indexed: 11/26/2022]
Abstract
The rates of RNA decay and transcription determine the steady-state levels of all messenger RNA and both can be subject to regulation. Although the details of transcriptional regulation are becoming increasingly understood, the mechanism(s) controlling mRNA decay remain unclear. In yeast, a major pathway of mRNA decay begins with deadenylation followed by decapping and 5'-3' exonuclease digestion. Importantly, it is hypothesized that ribosomes must be removed from mRNA before transcripts are destroyed. Contrary to this prediction, here we show that decay takes place while mRNAs are associated with actively translating ribosomes. The data indicate that dissociation of ribosomes from mRNA is not a prerequisite for decay and we suggest that the 5'-3' polarity of mRNA degradation has evolved to ensure that the last translocating ribosome can complete translation.
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Affiliation(s)
- Wenqian Hu
- Center for RNA Molecular Biology, Case Western Reserve University, Cleveland, OH 44106 USA
| | - Thomas J. Sweet
- Center for RNA Molecular Biology, Case Western Reserve University, Cleveland, OH 44106 USA
| | | | - Kristian E. Baker
- Center for RNA Molecular Biology, Case Western Reserve University, Cleveland, OH 44106 USA
| | - Jeff Coller
- Center for RNA Molecular Biology, Case Western Reserve University, Cleveland, OH 44106 USA
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811
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Chang WL, Tarn WY. A role for transportin in deposition of TTP to cytoplasmic RNA granules and mRNA decay. Nucleic Acids Res 2009; 37:6600-12. [PMID: 19729507 PMCID: PMC2770677 DOI: 10.1093/nar/gkp717] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Importin-β family members, which shuttle between the nucleus and the cytoplasm, are essential for nucleocytoplasmic transport of macromolecules. We attempted to explore whether importin-β family proteins change their cellular localization in response to environmental change. In this report, we show that transportin (TRN) was minimally detected in cytoplasmic processing bodies (P-bodies) under normal cell conditions but largely translocated to stress granules (SGs) in stressed cells. Fluorescence recovery after photobleaching analysis indicated that TRN moves rapidly in and out of cytoplasmic granules. Depletion of TRN greatly enhanced P-body formation but did not affect the number or size of SGs, suggesting that TRN or its cargo(es) participates in cellular function of P-bodies. Accordingly, TRN associated with tristetraprolin (TTP) and its AU-rich element (ARE)-containing mRNA substrates. Depletion of TRN increased the number of P-bodies and stabilized ARE-containing mRNAs, as observed with knockdown of the 5′–3′ exonuclease Xrn1. Moreover, depletion of TRN retained TTP in P-bodies and meanwhile reduced the fraction of mobile TTP to SGs. Therefore, our data together suggest that TRN plays a role in trafficking of TTP between the cytoplasmic granules and whereby modulates the stability of ARE-containing mRNAs.
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Affiliation(s)
- Wei-Lun Chang
- Graduate Institute of Life Sciences, National Defense Medical Center and Institute of Biomedical Sciences, Academia Sinica, Nankang, Taipei 11529, Taiwan
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812
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Aslam A, Mittal S, Koch F, Andrau JC, Winkler GS. The Ccr4-NOT deadenylase subunits CNOT7 and CNOT8 have overlapping roles and modulate cell proliferation. Mol Biol Cell 2009; 20:3840-50. [PMID: 19605561 PMCID: PMC2735483 DOI: 10.1091/mbc.e09-02-0146] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2009] [Revised: 06/16/2009] [Accepted: 07/06/2009] [Indexed: 12/13/2022] Open
Abstract
Accurate gene expression requires the precise control of mRNA levels, which are determined by the relative rates of nuclear (pre-)mRNA synthesis and processing, and cytoplasmic mRNA turnover. A key step in mRNA degradation is the removal of the poly(A) tail, which involves several deadenylases including components of the Ccr4-Not complex. Here, we focused on the role of the human paralogues CNOT7 (hCaf1/Caf1a) and CNOT8 (hPop2/Caf1b/Calif), which possess deadenylase activity mediated by DEDD nuclease domains. We show that efficient proliferation requires both subunits, although combined knockdown of CNOT7 and CNOT8 further reduces cell proliferation indicating partial redundancy between these proteins. Interestingly, the function of CNOT7 in cell proliferation partly depends on its catalytic activity. On the other hand, the interaction between CNOT7 and BTG2, a member of the antiproliferative BTG/Tob family involved in transcription and mRNA decay appears less important for proliferation of MCF7 cells, suggesting that CNOT7 does not function solely in conjunction with BTG2. Further analysis of gene expression profiles of CNOT7 and/or CNOT8 knockdown cells underscores the partial redundancy between these subunits and suggests that regulation of several genes, including repression of the antiproliferative genes MSMB and PMP22, by the Ccr4-Not complex contributes to cell proliferation.
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Affiliation(s)
- Akhmed Aslam
- *The School of Pharmacy, Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom; and
| | - Saloni Mittal
- *The School of Pharmacy, Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom; and
| | - Frederic Koch
- Centre d'Immunologie de Marseille-Luminy, Université Aix-Marseille, CNRS UMR6102, Institut National de la Santé et de la Recherche Médicale U631, 13288 Marseille, France
| | - Jean-Christophe Andrau
- Centre d'Immunologie de Marseille-Luminy, Université Aix-Marseille, CNRS UMR6102, Institut National de la Santé et de la Recherche Médicale U631, 13288 Marseille, France
| | - G. Sebastiaan Winkler
- *The School of Pharmacy, Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom; and
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813
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Masuda K, Abdelmohsen K, Gorospe M. RNA-binding proteins implicated in the hypoxic response. J Cell Mol Med 2009; 13:2759-69. [PMID: 19583805 PMCID: PMC2832090 DOI: 10.1111/j.1582-4934.2009.00842.x] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2009] [Accepted: 06/25/2009] [Indexed: 12/01/2022] Open
Abstract
In cells responding to low oxygen levels, gene expression patterns are strongly influenced by post-transcriptional processes. RNA-binding proteins (RBPs) are pivotal regulators of gene expression in response to numerous stresses, including hypoxia. Here, we review the RBPs that modulate mRNA turnover and translation in response to hypoxic challenge. The RBPs HuR (human antigen R) and PTB (polypyrimidine tract-binding protein) associate with mRNAs encoding hypoxia-response proteins such as HIF-1alpha and VEGF mRNAs, enhance their expression after hypoxia and play a major role in establishing hypoxic gene expression patterns. Additional RBPs such as iron-response element-binding proteins (IRPs), cytoplasmic polyadenylation-element-binding proteins (CPEBs) and several heterogeneous nuclear ribonucleoproteins (hnRNPs) also bind to hypoxia-regulated transcripts and modulate the levels of the encoded proteins. We discuss the efficient regulation of hypoxic gene expression by RBPs and the mounting interest in targeting hypoxia-regulatory RBPs in diseases with aberrant hypoxic responses.
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Affiliation(s)
- Kiyoshi Masuda
- Laboratory of Cellular and Molecular Biology, National Institute on Aging-Intramural Research Program, National Institutes of HealthBaltimore, MD, USA
| | - Kotb Abdelmohsen
- Laboratory of Cellular and Molecular Biology, National Institute on Aging-Intramural Research Program, National Institutes of HealthBaltimore, MD, USA
| | - Myriam Gorospe
- Laboratory of Cellular and Molecular Biology, National Institute on Aging-Intramural Research Program, National Institutes of HealthBaltimore, MD, USA
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814
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Schoenberg DR, Maquat LE. Re-capping the message. Trends Biochem Sci 2009; 34:435-42. [PMID: 19729311 PMCID: PMC2743798 DOI: 10.1016/j.tibs.2009.05.003] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2009] [Revised: 05/13/2009] [Accepted: 05/13/2009] [Indexed: 10/20/2022]
Abstract
The 5'-cap structure that typifies all polymerase II-transcribed RNAs plays important roles in pre-mRNA processing and mRNA export, translation and quality control. Removal of the cap is a regulated process that is considered to be the first irreversible step in mRNA decay. An emerging view challenges this idea: mRNAs have been identified in mammalian cells that lack sequences from their 5' ends but nevertheless appear to be modified with a cap or cap-like structure. Furthermore, a cytoplasmic form of capping enzyme was recently identified that, together with a novel kinase, generates capped ends from cleaved RNAs. These and other findings provide evidence for re-capping and its possible functions.
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Affiliation(s)
- Daniel R Schoenberg
- Department of Molecular and Cellular Biochemistry and Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA.
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815
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816
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Anderson P, Kedersha N. RNA granules: post-transcriptional and epigenetic modulators of gene expression. Nat Rev Mol Cell Biol 2009; 10:430-6. [PMID: 19461665 DOI: 10.1038/nrm2694] [Citation(s) in RCA: 692] [Impact Index Per Article: 43.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The composition of cytoplasmic messenger ribonucleoproteins (mRNPs) is determined by their nuclear and cytoplasmic histories and reflects past functions and future fates. The protein components of selected mRNP complexes promote their assembly into microscopically visible cytoplasmic RNA granules, including stress granules, processing bodies and germ cell (or polar) granules. We propose that RNA granules can be both a cause and a consequence of altered mRNA translation, decay or editing. In this capacity, RNA granules serve as key modulators of post-transcriptional and epigenetic gene expression.
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Affiliation(s)
- Paul Anderson
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA.
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817
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van Gemert AMC, van der Laan AMA, Pilgram GSK, Fradkin LG, Noordermeer JN, Tanke HJ, Jost CR. In vivo monitoring of mRNA movement in Drosophila body wall muscle cells reveals the presence of myofiber domains. PLoS One 2009; 4:e6663. [PMID: 19684860 PMCID: PMC2722729 DOI: 10.1371/journal.pone.0006663] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2009] [Accepted: 07/06/2009] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND In skeletal muscle each muscle cell, commonly called myofiber, is actually a large syncytium containing numerous nuclei. Experiments in fixed myofibers show that mRNAs remain localized around the nuclei in which they are produced. METHODOLOGY/PRINCIPAL FINDINGS In this study we generated transgenic flies that allowed us to investigate the movement of mRNAs in body wall myofibers of living Drosophila embryos. We determined the dynamic properties of GFP-tagged mRNAs using in vivo confocal imaging and photobleaching techniques and found that the GFP-tagged mRNAs are not free to move throughout myofibers. The restricted movement indicated that body wall myofibers consist of three domains. The exchange of mRNAs between the domains is relatively slow, but the GFP-tagged mRNAs move rapidly within these domains. One domain is located at the centre of the cell and is surrounded by nuclei while the other two domains are located at either end of the fiber. To move between these domains mRNAs have to travel past centrally located nuclei. CONCLUSIONS/SIGNIFICANCE These data suggest that the domains made visible in our experiments result from prolonged interactions with as yet undefined structures close to the nuclei that prevent GFP-tagged mRNAs from rapidly moving between the domains. This could be of significant importance for the treatment of myopathies using regenerative cell-based therapies.
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Affiliation(s)
- Alice M. C. van Gemert
- Laboratory of Gene Expression and Imaging, Department of Molecular Cell Biology, Leiden University Medical C, Leiden, The Netherlands
| | - Annelies M. A. van der Laan
- Laboratory of Gene Expression and Imaging, Department of Molecular Cell Biology, Leiden University Medical C, Leiden, The Netherlands
| | - Gonneke S. K. Pilgram
- Laboratory of Developmental Neurobiology, Department of Molecular Cell Biology, Leiden University Medical C, Leiden, The Netherlands
| | - Lee G. Fradkin
- Laboratory of Developmental Neurobiology, Department of Molecular Cell Biology, Leiden University Medical C, Leiden, The Netherlands
| | - Jasprina N. Noordermeer
- Laboratory of Developmental Neurobiology, Department of Molecular Cell Biology, Leiden University Medical C, Leiden, The Netherlands
| | - Hans J. Tanke
- Laboratory of Gene Expression and Imaging, Department of Molecular Cell Biology, Leiden University Medical C, Leiden, The Netherlands
| | - Carolina R. Jost
- Laboratory of Gene Expression and Imaging, Department of Molecular Cell Biology, Leiden University Medical C, Leiden, The Netherlands
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818
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Lim AK, Tao L, Kai T. piRNAs mediate posttranscriptional retroelement silencing and localization to pi-bodies in the Drosophila germline. ACTA ACUST UNITED AC 2009; 186:333-42. [PMID: 19651888 PMCID: PMC2728408 DOI: 10.1083/jcb.200904063] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Nuage, a well-conserved perinuclear organelle found in germline cells, is thought to mediate retroelement repression in Drosophila melanogaster by regulating the production of Piwi-interacting RNAs (piRNAs). In this study, we present evidence that the nuage-piRNA pathway components can be found in cytoplasmic foci that also contain retroelement transcripts, antisense piRNAs, and proteins involved in messenger RNA (mRNA) degradation. These mRNA degradation proteins, decapping protein 1/2 (DCP1/2), Me31B (maternal expression at 31B), and pacman (PCM), are normally thought of as components of processing bodies. In spindle-E (spn-E) and aubergine (aub) mutants that lack piRNA production, piRNA pathway proteins no longer overlap the mRNA degradation proteins. Concomitantly, spn-E and aub mutant ovaries show an accumulation of full-length retroelement transcripts and prolonged stabilization of HeT-A mRNA, supporting the role of piRNAs in mediating posttranscriptional retroelement silencing. HeT-A mRNA is derepressed in mRNA degradation mutants twin, dcp1, and ski3, indicating that these enzymes also aid in removing full-length transcripts and/or decay intermediates.
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Affiliation(s)
- Ai Khim Lim
- Temasek Life Sciences Laboratory, The National University of Singapore, 117604 Singapore
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819
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Lee L, Davies SE, Liu JL. The spinal muscular atrophy protein SMN affects Drosophila germline nuclear organization through the U body-P body pathway. Dev Biol 2009; 332:142-55. [PMID: 19464282 DOI: 10.1016/j.ydbio.2009.05.553] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2008] [Revised: 05/15/2009] [Accepted: 05/15/2009] [Indexed: 11/19/2022]
Abstract
Survival motor neuron protein (SMN) is the determining factor for the human neurodegenerative disease spinal muscular atrophy (SMA). SMN is critical for small nuclear ribonucleoprotein (snRNP) assembly. Using Drosophila oogenesis as a model system, we show that mutations in smn cause abnormal nuclear organization in nurse cells and oocytes. Germline and mitotic clonal analysis reveals that both nurse cells and oocytes require SMN to maintain normal organization of nuclear compartments including chromosomes, nucleoli, Cajal bodies and histone locus bodies. We previously found that SMN-containing U bodies invariably associate with P bodies (Liu, J. L., and Gall, J. G. (2007). U bodies are cytoplasmic structures that contain uridine-rich small nuclear ribonucleoproteins and associate with P bodies. Proc. Natl. Acad. Sci. U. S. A. 104, 11655-11659.). Multiple lines of evidence implicate SMN in the regulation of germline nuclear organization through the connection of U bodies and P bodies. Firstly, smn germline clones phenocopy mutations for two P body components, Cup and Ovarian tumour (Otu). Secondly, P body mutations disrupt SMN distribution and the organization of U bodies. Finally, mutations in smn disrupt the function and organization of U bodies and P bodies. Taken together, our results suggest that SMN is required for the functional integrity of the U body-P body pathway, which in turn is important for maintaining proper nuclear architecture.
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Affiliation(s)
- Lin Lee
- Medical Research Council Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, Henry Wellcome Building for Gene Function, University of Oxford, Oxford OX1 3QX, UK
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820
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Bailey-Serres J, Sorenson R, Juntawong P. Getting the message across: cytoplasmic ribonucleoprotein complexes. TRENDS IN PLANT SCIENCE 2009; 14:443-53. [PMID: 19616989 DOI: 10.1016/j.tplants.2009.05.004] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2009] [Revised: 05/29/2009] [Accepted: 05/29/2009] [Indexed: 05/20/2023]
Abstract
mRNA-ribonucleoprotein (mRNP) complexes mediate post-transcriptional control mechanisms in the cell nucleus and cytoplasm. Transcriptional control is paramount to gene expression but is followed by regulated nuclear pre-mRNA maturation and quality control processes that culminate in the export of a functional transcript to the cytoplasm. Once in the cytosol, mRNPs determine the activity of individual mRNAs through regulation of localization, translation, sequestration and turnover. Here, we review how quantitative assessment of mRNAs in distinct cytoplasmic mRNPs, such as polyribosomes (polysomes), has provided new perspectives on post-transcriptional regulation from the global to gene-specific level. In addition, we explore recent genetic and biochemical studies of cytoplasmic mRNPs that have begun to expose RNA-binding proteins in an integrated network that fine-tunes gene expression.
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Affiliation(s)
- J Bailey-Serres
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, CA 92521-0124, USA
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821
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Rao DD, Vorhies JS, Senzer N, Nemunaitis J. siRNA vs. shRNA: similarities and differences. Adv Drug Deliv Rev 2009; 61:746-59. [PMID: 19389436 DOI: 10.1016/j.addr.2009.04.004] [Citation(s) in RCA: 433] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2009] [Accepted: 04/13/2009] [Indexed: 12/11/2022]
Abstract
RNA interference (RNAi) is a natural process through which expression of a targeted gene can be knocked down with high specificity and selectivity. Using available technology and bioinformatics investigators will soon be able to identify relevant bio molecular tumor network hubs as potential key targets for knockdown approaches. Methods of mediating the RNAi effect involve small interfering RNA (siRNA), short hairpin RNA (shRNA) and bi-functional shRNA. The simplicity of siRNA manufacturing and transient nature of the effect per dose are optimally suited for certain medical disorders (i.e. viral injections). However, using the endogenous processing machinery, optimized shRNA constructs allow for high potency and sustainable effects using low copy numbers resulting in less off-target effects, particularly if embedded in a miRNA scaffold. Bi-functional design may further enhance potency and safety of RNAi-based therapeutics. Remaining challenges include tumor selective delivery vehicles and more complete evaluation of the scope and scale of off-target effects. This review will compare siRNA, shRNA and bi-functional shRNA.
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822
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Translation and replication of hepatitis C virus genomic RNA depends on ancient cellular proteins that control mRNA fates. Proc Natl Acad Sci U S A 2009; 106:13517-22. [PMID: 19628699 DOI: 10.1073/pnas.0906413106] [Citation(s) in RCA: 116] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Inevitably, viruses depend on host factors for their multiplication. Here, we show that hepatitis C virus (HCV) RNA translation and replication depends on Rck/p54, LSm1, and PatL1, which regulate the fate of cellular mRNAs from translation to degradation in the 5'-3'-deadenylation-dependent mRNA decay pathway. The requirement of these proteins for efficient HCV RNA translation was linked to the 5' and 3' untranslated regions (UTRs) of the viral genome. Furthermore, LSm1-7 complexes specifically interacted with essential cis-acting HCV RNA elements located in the UTRs. These results bridge HCV life cycle requirements and highly conserved host proteins of cellular mRNA decay. The previously described role of these proteins in the replication of 2 other positive-strand RNA viruses, the plant brome mosaic virus and the bacteriophage Qss, pinpoint a weak spot that may be exploited to generate broad-spectrum antiviral drugs.
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823
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Rao S, Dinkins RD, Hunt AG. Distinctive interactions of the Arabidopsis homolog of the 30 kD subunit of the cleavage and polyadenylation specificity factor (AtCPSF30) with other polyadenylation factor subunits. BMC Cell Biol 2009; 10:51. [PMID: 19573236 PMCID: PMC2712457 DOI: 10.1186/1471-2121-10-51] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2008] [Accepted: 07/02/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Arabidopsis ortholog of the 30 kD subunit of the mammalian Cleavage and Polyadenylation Specificity Factor (AtCPSF30) is an RNA-binding endonuclease that is associated with other Arabidopsis CPSF subunits (orthologs of the 160, 100, and 73 kD subunits of CPSF). In order to further explore the functions of AtCPSF30, the subcellular distribution of the protein was examined by over-expressing fusion proteins containing fluorescent reporters linked to different CPSF subunits. RESULTS It was found that AtCPSF30 by itself localizes, not to the nucleus, but to the cytoplasm. AtCPSF30 could be found in the nucleus when co-expressed with AtCPSF160 or AtCPSF73(I), one of the two Arabidopsis orthologs of CPSF73. This re-directing of AtCPSF30 indicates that AtCPSF30 is retained in the nucleus via interactions with either or both of these other CPSF subunits. Co-expression of AtCSPF30 with AtCPSF100 altered the location, not of AtCPSF30, but rather of AtCPSF100, with these proteins residing in the cytoplasm. Deletion of plant-specific N- or C-terminal domains of AtCPSF30 abolished various of the interactions between AtCPSF30 and other CPSF subunits, suggesting that the plant CPSF complex assembles via novel protein-protein interactions. CONCLUSION These results suggest that the nuclear CPSF complex in plants is a dynamic one, and that the interactions between AtCPSF30 and other CPSF subunits are different from those existing in other eukaryotes.
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Affiliation(s)
- Suryadevara Rao
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546-0312 USA
| | - Randy D Dinkins
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546-0312 USA
- USDA-ARS, FAPRU, Lexington, KY 40546-0091 USA
| | - Arthur G Hunt
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546-0312 USA
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824
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Kim SH, Koroleva OA, Lewandowska D, Pendle AF, Clark GP, Simpson CG, Shaw PJ, Brown JWS. Aberrant mRNA transcripts and the nonsense-mediated decay proteins UPF2 and UPF3 are enriched in the Arabidopsis nucleolus. THE PLANT CELL 2009; 21:2045-57. [PMID: 19602621 PMCID: PMC2729600 DOI: 10.1105/tpc.109.067736] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/09/2009] [Revised: 06/10/2009] [Accepted: 06/24/2009] [Indexed: 05/19/2023]
Abstract
The eukaryotic nucleolus is multifunctional and involved in the metabolism and assembly of many different RNAs and ribonucleoprotein particles as well as in cellular functions, such as cell division and transcriptional silencing in plants. We previously showed that Arabidopsis thaliana exon junction complex proteins associate with the nucleolus, suggesting a role for the nucleolus in mRNA production. Here, we report that the plant nucleolus contains mRNAs, including fully spliced, aberrantly spliced, and single exon gene transcripts. Aberrant mRNAs are much more abundant in nucleolar fractions, while fully spliced products are more abundant in nucleoplasmic fractions. The majority of the aberrant transcripts contain premature termination codons and have characteristics of nonsense-mediated decay (NMD) substrates. A direct link between NMD and the nucleolus is shown by increased levels of the same aberrant transcripts in both the nucleolus and in Up-frameshift (upf) mutants impaired in NMD. In addition, the NMD factors UPF3 and UPF2 localize to the nucleolus, suggesting that the Arabidopsis nucleolus is therefore involved in identifying aberrant mRNAs and NMD.
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Affiliation(s)
- Sang Hyon Kim
- Genetics Programme, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, Scotland, United Kingdom
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825
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Stalder L, Mühlemann O. Processing bodies are not required for mammalian nonsense-mediated mRNA decay. RNA (NEW YORK, N.Y.) 2009; 15:1265-73. [PMID: 19474145 PMCID: PMC2704072 DOI: 10.1261/rna.1672509] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2009] [Accepted: 04/22/2009] [Indexed: 05/18/2023]
Abstract
Nonsense-mediated mRNA decay (NMD) is a eukaryotic quality-control mechanism that recognizes and degrades mRNAs with premature termination codons (PTCs). In yeast, PTC-containing mRNAs are targeted to processing bodies (P-bodies), and yeast strains expressing an ATPase defective Upf1p mutant accumulate P-bodies. Here we show that in human cells, an ATPase-deficient UPF1 mutant and a fraction of UPF2 and UPF3b accumulate in cytoplasmic foci that co-localize with P-bodies. Depletion of the P-body component Ge-1, which prevents formation of microscopically detectable P-bodies, also impairs the localization of mutant UPF1, UPF2, and UPF3b in cytoplasmic foci. However, the accumulation of the ATPase-deficient UPF1 mutant in P-bodies is independent of UPF2, UPF3b, or SMG1, and the ATPase-deficient UPF1 mutant can localize into the P-bodies independent of its phosphorylation status. Most importantly, disruption of P-bodies by depletion of Ge-1 affects neither the mRNA levels of PTC-containing reporter genes nor endogenous NMD substrates. Consistent with the recently reported decapping-independent SMG6-mediated endonucleolytic decay of human nonsense mRNAs, our results imply that microscopically detectable P-bodies are not required for mammalian NMD.
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Affiliation(s)
- Lukas Stalder
- Institute of Cell Biology, University of Berne, 3012 Berne, Switzerland
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826
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Abstract
In this issue of Molecular Cell, Cole et al. (2009) provide evidence that different defects in rRNA function are recognized by distinct RNA quality control systems, and suggest that a stalled ribosome can trigger either no-go decay of the mRNA or degradation of a nonfunctional 18S rRNA.
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827
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Konecna A, Heraud JE, Schoderboeck L, Raposo AASF, Kiebler MA. What are the roles of microRNAs at the mammalian synapse? Neurosci Lett 2009; 466:63-8. [PMID: 19545603 DOI: 10.1016/j.neulet.2009.06.050] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2009] [Revised: 06/12/2009] [Accepted: 06/17/2009] [Indexed: 01/14/2023]
Abstract
The modification of neuronal connections in response to stimuli is believed to be the basis of long-term memory formation. It is currently accepted that local protein synthesis critically contributes to site-restricted modulation of individual synapses. Here, we summarize recent evidence implicating miRNAs in this process, leading to altered dendrite morphogenesis and synaptic plasticity. Second, we discuss findings in non-neuronal systems about how RNA-binding proteins can modulate miRNA-mRNA interactions, and how these mechanisms might apply to neurons. Finally, we review recent findings that P-bodies may be important sites for miRNA action at the synapse.
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Affiliation(s)
- Anetta Konecna
- Center for Brain Research, Medical University of Vienna, Spitalgasse 4, 1090 Vienna, Austria
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828
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Takimoto K, Wakiyama M, Yokoyama S. Mammalian GW182 contains multiple Argonaute-binding sites and functions in microRNA-mediated translational repression. RNA (NEW YORK, N.Y.) 2009; 15:1078-89. [PMID: 19398495 PMCID: PMC2685530 DOI: 10.1261/rna.1363109] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
In mammalian cells, microRNAs (miRNAs) are incorporated into miRNA-induced silencing complexes (miRISCs), which regulate protein expression post-transcriptionally through binding to 3'-untranslated regions of target mRNAs. Argonaute2 (Ago2), a key component of the miRISC, recruits GW182, a component of the processing body (GW/P-body), to the target mRNAs. To elucidate the function of GW182 in an miRNA-mediated translational repression, we analyzed Argonaute-binding sites in GW182. We found that human GW182 contains three binding sites for Ago2, within the amino-terminal glycine tryptophan (GW/WG)-repeated region that is characteristic of the GW182 family proteins. We also found that the first and second Ago2-binding site is conserved within the amino-terminal half of TNRC6B, which is a paralog of GW182. Each of the Ago-binding sites is alone sufficient to bind Ago2. Furthermore, we demonstrated that multiple Argonaute proteins were connected via the GW182 protein. A GW182 fragment containing the Ago2-binding region partially relieved let-7-mediated repression of protein synthesis in a mammalian cell-free system. Coincidentally, let-7-directed target mRNA deadenylation was delayed. Together, these results strongly suggested that the interactions of GW182 with Argonautes may induce the formation of large complexes containing miRNA target mRNAs, and may be critical for miRNA-mediated translational repression.
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Affiliation(s)
- Koji Takimoto
- Systems and Structural Biology Center, Yokohama Institute, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
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829
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Romero-Santacreu L, Moreno J, Pérez-Ortín JE, Alepuz P. Specific and global regulation of mRNA stability during osmotic stress in Saccharomyces cerevisiae. RNA (NEW YORK, N.Y.) 2009; 15:1110-20. [PMID: 19369426 PMCID: PMC2685517 DOI: 10.1261/rna.1435709] [Citation(s) in RCA: 123] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2008] [Accepted: 02/27/2009] [Indexed: 05/23/2023]
Abstract
Hyperosmotic stress yields reprogramming of gene expression in Saccharomyces cerevisiae cells. Most of this response is orchestrated by Hog1, a stress-activated, mitogen-activated protein kinase (MAPK) homologous to human p38. We investigated, on a genomic scale, the contribution of changes in transcription rates and mRNA stabilities to the modulation of mRNA amounts during the response to osmotic stress in wild-type and hog1 mutant cells. Mild osmotic shock induces a broad mRNA destabilization; however, osmo-mRNAs are up-regulated by increasing both transcription rates and mRNA half-lives. In contrast, mild or severe osmotic stress in hog1 mutants, or severe osmotic stress in wild-type cells, yields global mRNA stabilization and sequestration of mRNAs into P-bodies. After adaptation, the absence of Hog1 affects the kinetics of P-bodies disassembly and the return of mRNAs to translation. Our results indicate that regulation of mRNA turnover contributes to coordinate gene expression upon osmotic stress, and that there are both specific and global controls of mRNA stability depending on the strength of the osmotic stress.
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Affiliation(s)
- Lorena Romero-Santacreu
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universitat de València, E-46100 Burjassot, Spain
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830
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Balagopal V, Parker R. Polysomes, P bodies and stress granules: states and fates of eukaryotic mRNAs. Curr Opin Cell Biol 2009; 21:403-8. [PMID: 19394210 PMCID: PMC2740377 DOI: 10.1016/j.ceb.2009.03.005] [Citation(s) in RCA: 309] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2009] [Revised: 03/16/2009] [Accepted: 03/24/2009] [Indexed: 12/16/2022]
Abstract
The control of translation and mRNA degradation plays a key role in the regulation of eukaryotic gene expression. In the cytosol, mRNAs engaged in translation are distributed throughout the cytosol, while translationally inactive mRNAs can accumulate in P bodies, in complex with mRNA degradation and translation repression machinery, or in stress granules, which appear to be mRNAs stalled in translation initiation. Here we discuss how these different granules suggest a dynamic model for the metabolism of cytoplasmic mRNAs wherein they cycle between different mRNP states with different functional properties and subcellular locations.
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Affiliation(s)
- Vidya Balagopal
- Department of Molecular and Cellular Biology & Howard Hughes Medical Institute, University of Arizona, Tucson, Arizona, 85721-0206, USA
| | - Roy Parker
- Department of Molecular and Cellular Biology & Howard Hughes Medical Institute, University of Arizona, Tucson, Arizona, 85721-0206, USA
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831
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Abstract
The increased sensitivity of peripheral pain-sensing neurons, or nociceptors, is a major cause of the sensation of pain that follows injury. This plasticity is thought to contribute to the maintenance of chronic pain states. Although we have a broad knowledge of the factors that stimulate changes in nociceptor sensitivity, the cellular mechanisms that underlie this plasticity are still poorly understood; however, they are likely to involve changes in gene expression required for the phenotypic and functional changes seen in nociceptive neurons after injury. While the regulation of gene expression at the transcriptional level has been studied extensively, the regulation of protein synthesis, which is also a tightly controlled process, has only recently received more attention. Despite the established role of protein synthesis in the plasticity of neuronal cell bodies and dendrites, little attention has been paid to the role of translation control in mature undamaged axons. In this regard, several recent studies have demonstrated that the control of protein synthesis within the axonal compartment is crucial for the normal function and regulation of sensitivity of nociceptors. Pathways and proteins regulating this process, such as the mammalian target of rapamycin signaling cascade and the fragile X mental retardation protein, have recently been identified. We review here recent evidence for the regulation of protein synthesis within a nociceptor's axonal compartment and its contribution to this neuron's plasticity. We believe that an increased understanding of this process will lead to the identification of novel targets for the treatment of chronic pain.
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Affiliation(s)
- Theodore J Price
- The University of Arizona, School of Medicine, Department of Pharmacology, 1501 N Campbell Ave, Tucson, AZ 85724, USA.
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832
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Grousl T, Ivanov P, Frýdlová I, Vasicová P, Janda F, Vojtová J, Malínská K, Malcová I, Nováková L, Janosková D, Valásek L, Hasek J. Robust heat shock induces eIF2alpha-phosphorylation-independent assembly of stress granules containing eIF3 and 40S ribosomal subunits in budding yeast, Saccharomyces cerevisiae. J Cell Sci 2009; 122:2078-88. [PMID: 19470581 DOI: 10.1242/jcs.045104] [Citation(s) in RCA: 192] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Environmental stresses inducing translation arrest are accompanied by the deposition of translational components into stress granules (SGs) serving as mRNA triage sites. It has recently been reported that, in Saccharomyces cerevisiae, formation of SGs occurs as a result of a prolonged glucose starvation. However, these SGs did not contain eIF3, one of hallmarks of mammalian SGs. We have analyzed the effect of robust heat shock on distribution of eIF3a/Tif32p/Rpg1p and showed that it results in the formation of eIF3a accumulations containing other eIF3 subunits, known yeast SG components and small but not large ribosomal subunits and eIF2alpha/Sui2p. Interestingly, under these conditions, Dcp2p and Dhh1p P-body markers also colocalized with eIF3a. Microscopic analyses of the edc3Deltalsm4DeltaC mutant demonstrated that different scaffolding proteins are required to induce SGs upon robust heat shock as opposed to glucose deprivation. Even though eIF2alpha became phosphorylated under these stress conditions, the decrease in polysomes and formation of SGs occurred independently of phosphorylation of eIF2alpha. We conclude that under specific stress conditions, such as robust heat shock, yeast SGs do contain eIF3 and 40S ribosomes and utilize alternative routes for their assembly.
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Affiliation(s)
- Tomás Grousl
- Laboratory of Cell Reproduction, Institute of Microbiology of the AS CR, v.v.i., Prague, Czech Republic
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833
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Reijns MAM, Auchynnikava T, Beggs JD. Analysis of Lsm1p and Lsm8p domains in the cellular localization of Lsm complexes in budding yeast. FEBS J 2009; 276:3602-17. [PMID: 19490016 PMCID: PMC2776932 DOI: 10.1111/j.1742-4658.2009.07080.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
In eukaryotes, two heteroheptameric Sm-like (Lsm) complexes that differ by a single subunit localize to different cellular compartments and have distinct functions in RNA metabolism. The cytoplasmic Lsm1–7p complex promotes mRNA decapping and localizes to processing bodies, whereas the Lsm2–8p complex takes part in a variety of nuclear RNA processing events. The structural features that determine their different functions and localizations are not known. Here, we analyse a range of mutant and hybrid Lsm1 and Lsm8 proteins, shedding light on the relative importance of their various domains in determining their localization and ability to support growth. Although no single domain is either essential or sufficient for cellular localization, the Lsm1p N-terminus may act as part of a nuclear exclusion signal for Lsm1–7p, and the shorter Lsm8p N-terminus contributes to nuclear accumulation of Lsm2–8p. The C-terminal regions seem to play a secondary role in determining localization, with little or no contribution coming from the central Sm domains. The essential Lsm8 protein is remarkably resistant to mutation in terms of supporting viability, whereas Lsm1p appears more sensitive. These findings contribute to our understanding of how two very similar protein complexes can have different properties.
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834
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Cole SE, LaRiviere FJ, Merrikh C, Moore MJ. A convergence of rRNA and mRNA quality control pathways revealed by mechanistic analysis of nonfunctional rRNA decay. Mol Cell 2009; 34:440-50. [PMID: 19481524 PMCID: PMC2712825 DOI: 10.1016/j.molcel.2009.04.017] [Citation(s) in RCA: 146] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2008] [Revised: 02/23/2009] [Accepted: 04/13/2009] [Indexed: 11/19/2022]
Abstract
Eukaryotes possess numerous quality control systems that monitor both the synthesis of RNA and the integrity of the finished products. We previously demonstrated that Saccharomyces cerevisiae possesses a quality control mechanism, nonfunctional rRNA decay (NRD), capable of detecting and eliminating translationally defective rRNAs. Here we show that NRD can be divided into two mechanistically distinct pathways: one that eliminates rRNAs with deleterious mutations in the decoding site (18S NRD) and one that eliminates rRNAs containing deleterious mutations in the peptidyl transferase center (25S NRD). 18S NRD is dependent on translation elongation and utilizes the same proteins as those participating in no-go mRNA decay (NGD). In cells that accumulate 18S NRD and NGD decay intermediates, both RNA types can be seen in P-bodies. We propose that 18S NRD and NGD are different observable outcomes of the same initiating event: a ribosome stalled inappropriately at a sense codon during translation elongation.
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MESH Headings
- Adaptor Proteins, Signal Transducing
- Animals
- Biomarkers/metabolism
- Cell Nucleus/metabolism
- Exoribonucleases/genetics
- Exoribonucleases/metabolism
- GTP-Binding Proteins/genetics
- GTP-Binding Proteins/metabolism
- HSP70 Heat-Shock Proteins/genetics
- HSP70 Heat-Shock Proteins/metabolism
- Humans
- In Situ Hybridization, Fluorescence
- Peptide Elongation Factors/genetics
- Peptide Elongation Factors/metabolism
- RNA Stability
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Ribosomal/genetics
- RNA, Ribosomal/metabolism
- RNA, Ribosomal, 18S/genetics
- RNA, Ribosomal, 18S/metabolism
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/metabolism
- Saccharomyces cerevisiae Proteins/genetics
- Saccharomyces cerevisiae Proteins/metabolism
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Affiliation(s)
- Sarah E. Cole
- Howard Hughes Medical Institute, Department of Biochemistry, Brandeis University, Waltham, MA 02454 U.S.A
| | - Fredrick J. LaRiviere
- Howard Hughes Medical Institute, Department of Biochemistry, Brandeis University, Waltham, MA 02454 U.S.A
| | - Chris Merrikh
- Howard Hughes Medical Institute, University of Massachusetts Medical School, Department of Biochemistry and Molecular Pharmacology, Worcester, MA 01605 U.S.A
| | - Melissa J. Moore
- Howard Hughes Medical Institute, Department of Biochemistry, Brandeis University, Waltham, MA 02454 U.S.A
- Howard Hughes Medical Institute, University of Massachusetts Medical School, Department of Biochemistry and Molecular Pharmacology, Worcester, MA 01605 U.S.A
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835
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Halbeisen RE, Gerber AP. Stress-dependent coordination of transcriptome and translatome in yeast. PLoS Biol 2009; 7:e1000105. [PMID: 19419242 PMCID: PMC2675909 DOI: 10.1371/journal.pbio.1000105] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2008] [Accepted: 03/23/2009] [Indexed: 01/10/2023] Open
Abstract
Cells rapidly alter gene expression in response to environmental stimuli such as nutrients, hormones, and drugs. During the imposed “remodeling” of gene expression, changes in the levels of particular mRNAs do not necessarily correlate with those of the encoded proteins, which could in part rely on the differential recruitment of mRNAs to translating ribosomes. To systematically address this issue, we have established an approach to rapidly access the translational status of each mRNA in the yeast Saccharomyces cerevisiae by affinity purification of endogenously formed ribosomes and the analysis of associated mRNAs with DNA microarrays. Using this method, we compared changes in total mRNA levels (transcriptome) with ribosome associations (translatome) after the application of different conditions of cellular stress. Severe stresses, induced by amino acid depletion or osmotic shock, stimulated highly correlated responses affecting about 15% of both total RNA levels and translatome. Many of the regulated messages code for functionally related proteins, thus reflecting logical responses to the particular stress. In contrast, mild stress provoked by addition of Calcofluor-white and menadione altered the translatome of approximately 1% of messages with only marginal effects on total mRNA, suggesting largely uncorrelated responses of transcriptome and translatome. Among these putative translationally regulated messages were most components of the mitochondrial ATPase. Increased polysome associations of corresponding messages and higher mitochondrial ATPase activities upon treatment confirmed the relevance for regulation of this macromolecular complex. Our results suggest the presence of highly sensitive translational regulatory networks that coordinate functionally related messages. These networks are preferentially activated for rapid adaptation of cells to minor environmental perturbations. Organisms respond to environmental or physiological changes by altering the amounts and activities of specific proteins that are necessary for their adaptation and survival. Importantly, protein levels can be modulated by changing either the rate of synthesis or the stability of the messenger RNA (mRNA or transcript), or the synthesis or stability of the protein itself. Scientists often measure global mRNA levels upon changing conditions to identify transcripts that are differentially regulated, and often the assumption is made that changes in transcript levels lead to corresponding changes in protein levels. Here, we systematically compared global transcript levels (transcriptome) with global alterations in the levels of ribosome association of transcripts (translatome) when yeast cells are exposed to different stresses to determine how significant the discrepancy between transcript and protein levels can be. We found that changes in the transcriptome correlate well with those in the translatome after application of harsh stresses that arrest cell growth. However, this correlation is generally lost under more mild stresses that do not affect cell growth. In this case, remodeling of gene expression is mainly executed at the translational level by modulating mRNA association with ribosomes. As one example, we show that expression for many components of the mitochondrial ATPase, the major energy production machinery in cells, is translationally but not transcriptionally activated under a specific mild stress condition. Our results therefore show that alteration of protein synthesis can be the dominant mediator of changes of gene expression during adaptation to minor changes in cellular needs. During cellular adaptation to changing growth conditions, the extent of correlation between changes in transcriptional and translational regulation varies with the severity of the stress.
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836
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Zipprich JT, Bhattacharyya S, Mathys H, Filipowicz W. Importance of the C-terminal domain of the human GW182 protein TNRC6C for translational repression. RNA (NEW YORK, N.Y.) 2009; 15:781-93. [PMID: 19304925 PMCID: PMC2673060 DOI: 10.1261/rna.1448009] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Proteins of the GW182 family play an important role in the execution of microRNA repression in metazoa. They interact directly with Argonaute proteins, components of microRNPs, and also form part of P-bodies, structures implicated in translational repression and mRNA degradation. Recent results demonstrated that Drosophila GW182 has the potential to both repress translation and accelerate mRNA deadenylation and decay. In contrast to a single GW182 protein in Drosophila, the three GW182 paralogs TNRC6A, TNRC6B, and TNRC6C are encoded in mammalian genomes. In this study, we provide evidence that TNRC6C, like TNRC6A and TNRC6B, is important for efficient miRNA repression. We further demonstrate that tethering of each of the human TNRC6 proteins to a reporter mRNA has a dramatic inhibitory effect on protein synthesis. The repression is due to a combination of effects on the mRNA level and mRNA translation. Through deletion and mutagenesis, we identified the C-terminal part of TNRC6C encompassing the RRM RNA-binding motif as a key effector domain mediating protein synthesis repression by TNRC6C.
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Affiliation(s)
- Jakob T Zipprich
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
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837
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Cheever A, Ceman S. Translation regulation of mRNAs by the fragile X family of proteins through the microRNA pathway. RNA Biol 2009; 6:175-8. [PMID: 19276651 DOI: 10.4161/rna.6.2.8196] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Small, genomically-encoded microRNAs are important factors in the regulation of mRNA translation. Although their biogenesis is relatively well-defined, it is still unclear how they are recruited to their mRNA targets. The fragile X mental retardation protein family members, FMRP, FXR1P and FXR2P are RNA binding proteins that regulate translation of their cargo mRNAs. All three proteins, in addition to the single Drosophila ortholog, dFmrp, associate physically and functionally with the microRNA pathway. In this review, we summarize what is known about the role of the fragile X family members in translation regulation, highlighting evidence for their association with the microRNA pathway. In addition, we present a new model for the effect of phosphorylation on FMRP function, where phosphorylation of FMRP inhibits Dicer binding, leading to the accumulation of precursor microRNAs and possibly a paucity of activating microRNAs.
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Affiliation(s)
- Anne Cheever
- Department of Cell and Developmental Biology, University of Illinois, Chicago, IL, USA
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838
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Schmid M, Küchler B, Eckmann CR. Two conserved regulatory cytoplasmic poly(A) polymerases, GLD-4 and GLD-2, regulate meiotic progression in C. elegans. Genes Dev 2009; 23:824-36. [PMID: 19339688 DOI: 10.1101/gad.494009] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Translational regulation is heavily employed during developmental processes to control the timely accumulation of proteins independently of gene transcription. In particular, mRNA poly(A) tail metabolism in the cytoplasm is a key determinant for balancing an mRNA's translational output and its decay rate. Noncanonical poly(A) polymerases (PAPs), such as germline development defective-2 (GLD-2), can mediate poly(A) tail extension. Little is known about the regulation and functional complexity of cytoplasmic PAPs. Here we report the discovery of Caenorhabditis elegans GLD-4, a cytoplasmic PAP present in P granules that is orthologous to Trf4/5p from budding yeast. GLD-4 enzymatic activity is enhanced by its interaction with GLS-1, a protein associated with the RNA-binding protein GLD-3. GLD-4 is predominantly expressed in germ cells, and its activity is essential for early meiotic progression of male and female gametes in the absence of GLD-2. For commitment into female meiosis, both PAPs converge on at least one common target mRNA-i.e., gld-1 mRNA-and, as a consequence, counteract the repressive action of two PUF proteins and the putative deadenylase CCR-4. Together our findings suggest that two different cytoplasmic PAPs stabilize and translationally activate several meiotic mRNAs to provide a strong fail-safe mechanism for early meiotic progression.
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Affiliation(s)
- Mark Schmid
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
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839
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Jaag HM, Nagy PD. Silencing of Nicotiana benthamiana Xrn4p exoribonuclease promotes tombusvirus RNA accumulation and recombination. Virology 2009; 386:344-52. [PMID: 19232421 DOI: 10.1016/j.virol.2009.01.015] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2008] [Revised: 11/08/2008] [Accepted: 01/15/2009] [Indexed: 10/21/2022]
Abstract
The cytosolic 5'-to-3' exoribonuclease Xrn1p plays a major role in recombination and degradation of Tomato bushy stunt tombusvirus (TBSV) replicon (rep)RNA in yeast, a model host (Serviene, E., Shapka, N., Cheng, C.P., Panavas, T., Phuangrat, B., Baker, J., and Nagy, P.D., 2005. Genome-wide screen identifies host genes affecting viral RNA recombination. Proc. Natl. Acad. Sci. U. S. A. 102(30), 10545-10550.). To test if the plant cytosolic 5'-to-3' exoribonuclease Xrn4p, similar to the yeast Xrn1p, could also affect TBSV recombination, in this paper, we silenced XRN4 in Nicotiana benthamiana, an experimental host. The accumulation of tombusvirus genomic RNA and repRNA increased by 50% and 220%, respectively, in XRN4-silenced N. benthamiana. We also observed up to 125-fold increase in the emergence of new recombinants and partly degraded viral RNAs in the silenced plants. Using a cell-free assay based on a yeast extract, which supports authentic replication and recombination of TBSV, we demonstrate that the purified recombinant Xrn1p efficiently inhibited the accumulation of recombinants and partly degraded viral RNAs. Altogether, the data from a plant host and cell-free system confirm a central role for the plant cytosolic 5'-to-3' exoribonuclease in TBSV replication, recombination and viral RNA degradation.
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Affiliation(s)
- Hannah M Jaag
- Department of Plant Pathology, University of Kentucky, Plant Science Building, Lexington, KY40546, USA
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840
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Execution of nonsense-mediated mRNA decay: what defines a substrate? Curr Opin Cell Biol 2009; 21:394-402. [PMID: 19359157 DOI: 10.1016/j.ceb.2009.02.007] [Citation(s) in RCA: 214] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2008] [Revised: 02/17/2009] [Accepted: 02/20/2009] [Indexed: 11/23/2022]
Abstract
The nonsense-mediated mRNA decay (NMD) pathway targets mRNAs with premature termination codons as well as a subset of normal mRNAs for rapid decay. Emerging evidence suggests that mRNAs become NMD substrates based on the composition of the mRNP downstream of the translation termination event, which either stimulates or antagonizes recruitment of the NMD machinery. The NMD mRNP subsequently undergoes several remodeling events, which involve hydrolysis of ATP by the NMD factor Upf1 and in metazoans, a phosphorylation/dephosphorylation cycle of Upf1 mediated by Smg proteins. This leads to mRNA decay following translational repression. Recent evidence suggests that in Drosophila and human cells, decay is initiated by the endonuclease Smg6.
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841
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Miller LC, Blandford V, McAdam R, Sanchez-Carbente MR, Badeaux F, DesGroseillers L, Sossin WS. Combinations of DEAD box proteins distinguish distinct types of RNA: protein complexes in neurons. Mol Cell Neurosci 2009; 40:485-95. [PMID: 19340935 DOI: 10.1016/j.mcn.2009.01.007] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Transport of mRNAs to axons and dendrites in neurons is important for growth, polarization and plasticity. Recent proteomic studies in neurons have identified a number of DEAD box proteins as components of RNA granules. Using DEAD box proteins as markers, we have defined classes of RNA:protein structures present in neurons. In particular, we demonstrate that the conjunction of DEAD box 1 and DEAD box 3 identifies a motile ribosome-containing RNA granule present in both axons and dendrites that is similar to the biochemically isolated RNA granule. Conjunction of DEAD box 1 and the novel protein CGI-99 defines a distinct complex in neurons. Attempts to define a P-body like structure with expression of DEAD box 6 and decapping enzymes suggest that this structure may be more complex in neuronal processes than in other compartments. These studies hint at a great complexity in RNA transport and storage in neuronal processes.
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Affiliation(s)
- Linda C Miller
- Department of Neurology and Neurosurgery, McGill University, Montreal Neurological Institute, BT 110, 3801 University Street, Montreal, Quebec H3A2B4, Canada
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842
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Peng Y, Murray EL, Sarkar M, Liu X, Schoenberg DR. The cytoskeleton-associated Ena/VASP proteins are unanticipated partners of the PMR1 mRNA endonuclease. RNA (NEW YORK, N.Y.) 2009; 15:576-87. [PMID: 19223443 PMCID: PMC2661838 DOI: 10.1261/rna.1206209] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The PMR1 mRNA endonuclease catalyzes the selective decay of a limited number of mRNAs. It participates in multiple complexes, including one containing c-Src, its activating kinase, and one containing its substrate mRNA. This study used tandem affinity purification (TAP) chromatography to identify proteins in HeLa cell S100 associated with the mature 60-kDa form of Xenopus PMR1 (xPMR60). Unexpectedly, this identified a number of cytoskeleton-associated proteins, most notably the Ena family proteins mammalian Enabled (Mena) and vasodilator-stimulated phosphoprotein (VASP). These are regulators of actin dynamics that distribute throughout the cytoplasm and concentrate along the leading edge of the cell. xPMR60 interacts with Mena and VASP in vivo, overexpression of Mena has no impact on mRNA decay, and Mena and VASP are recovered together with xPMR60 in each of the major complexes of PMR1-mRNA decay. In a wound-healing experiment induced expression of active xPMR60 in stably transfected cells resulted in a twofold increase in cell motility compared with uninduced cells or cells expressing inactive xPMR60 degrees . Under these conditions xPMR60 colocalizes with VASP along one edge of the cell.
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Affiliation(s)
- Yong Peng
- Department of Molecular and Cellular Biochemistry, The Ohio State University, Columbus, 43210, USA
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843
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Ma C, Liu Y, He L. MicroRNAs - powerful repression comes from small RNAs. SCIENCE IN CHINA. SERIES C, LIFE SCIENCES 2009; 52:323-30. [PMID: 19381458 PMCID: PMC3681298 DOI: 10.1007/s11427-009-0056-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/05/2009] [Accepted: 03/15/2009] [Indexed: 10/20/2022]
Abstract
microRNAs (miRNAs) encode a novel class of small, non-coding RNAs that regulate gene expression post-trancriptionally. miRNAs comprise one of the major non-coding RNA families, whose diverse biological functions and unusual capacity for gene regulation have attracted enormous interests in the RNA world. Over the past 16 years, genetic, biochemical and computational approaches have greatly shaped the growth of the field, leading to the identification of thousands of miRNA genes in nearly all metazoans. The key molecular machinery for miRNA biogenesis and silencing has been identified, yet the precise biochemical and regulatory mechanisms still remain elusive. However, recent findings have shed new light on how miRNAs are generated and how they function to repress gene expression. miRNAs provide a paradigm for endogenous small RNAs that mediate gene silencing at a genome-wide level. The gene silencing mediated by these small RNAs constitutes a major component of gene regulation during various developmental and physiological processes. The accumulating knowledge about their biogenesis and gene silencing mechanism will add a new dimension to our understanding about the complex gene regulatory networks.
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Affiliation(s)
- Cong Ma
- 535 LSA, Division of Cell and Developmental Biology, MCB Department, University of California at Berkeley, Berkeley, CA 94720-3200
| | - Yufei Liu
- 535 LSA, Division of Cell and Developmental Biology, MCB Department, University of California at Berkeley, Berkeley, CA 94720-3200
| | - Lin He
- 535 LSA, Division of Cell and Developmental Biology, MCB Department, University of California at Berkeley, Berkeley, CA 94720-3200
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844
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Nguyen Chi M, Chalmel F, Agius E, Vanzo N, Khabar KSA, Jégou B, Morello D. Temporally regulated traffic of HuR and its associated ARE-containing mRNAs from the chromatoid body to polysomes during mouse spermatogenesis. PLoS One 2009; 4:e4900. [PMID: 19333380 PMCID: PMC2659425 DOI: 10.1371/journal.pone.0004900] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2008] [Accepted: 02/07/2009] [Indexed: 12/17/2022] Open
Abstract
Background In mammals, a temporal disconnection between mRNA transcription and protein synthesis occurs during late steps of germ cell differentiation, in contrast to most somatic tissues where transcription and translation are closely linked. Indeed, during late stages of spermatogenesis, protein synthesis relies on the appropriate storage of translationally inactive mRNAs in transcriptionally silent spermatids. The factors and cellular compartments regulating mRNA storage and the timing of their translation are still poorly understood. The chromatoid body (CB), that shares components with the P. bodies found in somatic cells, has recently been proposed to be a site of mRNA processing. Here, we describe a new component of the CB, the RNA binding protein HuR, known in somatic cells to control the stability/translation of AU-rich containing mRNAs (ARE-mRNAs). Methodology/Principal Findings Using a combination of cell imagery and sucrose gradient fractionation, we show that HuR localization is highly dynamic during spermatid differentiation. First, in early round spermatids, HuR colocalizes with the Mouse Vasa Homolog, MVH, a marker of the CB. As spermatids differentiate, HuR exits the CB and concomitantly associates with polysomes. Using computational analyses, we identified two testis ARE-containing mRNAs, Brd2 and GCNF that are bound by HuR and MVH. We show that these target ARE-mRNAs follow HuR trafficking, accumulating successively in the CB, where they are translationally silent, and in polysomes during spermatid differentiation. Conclusions/Significance Our results reveal a temporal regulation of HuR trafficking together with its target mRNAs from the CB to polysomes as spermatids differentiate. They strongly suggest that through the transport of ARE-mRNAs from the CB to polysomes, HuR controls the appropriate timing of ARE-mRNA translation. HuR might represent a major post-transcriptional regulator, by promoting mRNA storage and then translation, during male germ cell differentiation.
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Affiliation(s)
- Mai Nguyen Chi
- CBD, CNRS UMR5547, IFR 109, Université Paul Sabatier, Toulouse, France
| | - Frédéric Chalmel
- Inserm, U625, Rennes, France
- Université Rennes I, Campus de Beaulieu, IFR-140, GERHM, Rennes, France
| | - Eric Agius
- CBD, CNRS UMR5547, IFR 109, Université Paul Sabatier, Toulouse, France
| | - Nathalie Vanzo
- CBD, CNRS UMR5547, IFR 109, Université Paul Sabatier, Toulouse, France
| | - Khalid S. A. Khabar
- Program in Biomolecular Research, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Bernard Jégou
- Inserm, U625, Rennes, France
- Université Rennes I, Campus de Beaulieu, IFR-140, GERHM, Rennes, France
| | - Dominique Morello
- CBD, CNRS UMR5547, IFR 109, Université Paul Sabatier, Toulouse, France
- * E-mail:
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845
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Gouw JW, Pinkse MWH, Vos HR, Moshkin Y, Verrijzer CP, Heck AJR, Krijgsveld J. In vivo stable isotope labeling of fruit flies reveals post-transcriptional regulation in the maternal-to-zygotic transition. Mol Cell Proteomics 2009; 8:1566-78. [PMID: 19321433 DOI: 10.1074/mcp.m900114-mcp200] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
An important hallmark in embryonic development is characterized by the maternal-to-zygotic transition (MZT) where zygotic transcription is activated by a maternally controlled environment. Post-transcriptional and translational regulation is critical for this transition and has been investigated in considerable detail at the gene level. We used a proteomics approach using metabolic labeling of Drosophila to quantitatively assess changes in protein expression levels before and after the MZT. By combining stable isotope labeling of fruit flies in vivo with high accuracy quantitative mass spectrometry we could quantify 2,232 proteins of which about half changed in abundance during this process. We show that approximately 500 proteins increased in abundance, providing direct evidence of the identity of proteins as a product of embryonic translation. The group of down-regulated proteins is dominated by maternal factors involved in translational control of maternal and zygotic transcripts. Surprisingly a direct comparison of transcript and protein levels showed that the mRNA levels of down-regulated proteins remained relatively constant, indicating a translational control mechanism specifically targeting these proteins. In addition, we found evidence for post-translational processing of cysteine proteinase-1 (Cathepsin L), which became activated during the MZT as evidenced by the loss of its N-terminal propeptide. Poly(A)-binding protein was shown to be processed at its C-terminal tail, thereby losing one of its protein-interacting domains. Altogether this quantitative proteomics study provides a dynamic profile of known and novel proteins of maternal as well as embryonic origin. This provides insight into the production, stability, and modification of individual proteins, whereas discrepancies between transcriptional profiles and protein dynamics indicate novel control mechanisms in genome activation during early fly development.
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Affiliation(s)
- Joost W Gouw
- Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
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846
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Gregio APB, Cano VPS, Avaca JS, Valentini SR, Zanelli CF. eIF5A has a function in the elongation step of translation in yeast. Biochem Biophys Res Commun 2009; 380:785-90. [PMID: 19338753 DOI: 10.1016/j.bbrc.2009.01.148] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2009] [Accepted: 01/26/2009] [Indexed: 11/23/2022]
Abstract
The putative translation factor eIF5A is essential for cell viability and is highly conserved throughout evolution. Here, we describe genetic interactions between an eIF5A mutant and a translation initiation mutant (eIF4E) or a translation elongation mutant (eEF2). Polysome profile analysis of single and double mutants revealed that mutation in eIF5A reduces polysome run-off, contrarily to translation initiation mutants. Moreover, the polysome profile of an eIF5A mutant alone is very similar to that of a translation elongation mutant. Furthermore, depletion of eIF5A causes a significant decrease in total protein synthesis and an increase of the average ribosome transit time. Finally, we demonstrate that the formation of P bodies is inhibited in an eIF5A mutant, similarly to the effect of the translation elongation inhibitor cycloheximide. Taken together, these results not only reinforce a role for eIF5A in translation but also strongly support a function for eIF5A in the elongation step of protein synthesis.
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Affiliation(s)
- Ana P B Gregio
- Department of Biological Sciences, School of Pharmaceutical Sciences, São Paulo State University-UNESP, Faculdade de Ciências Farmacêuticas, Rodovia Araraquara-Jaú, km 01, Araraquara, SP 14801-902, Brazil
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847
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Minshall N, Kress M, Weil D, Standart N. Role of p54 RNA helicase activity and its C-terminal domain in translational repression, P-body localization and assembly. Mol Biol Cell 2009; 20:2464-72. [PMID: 19297524 DOI: 10.1091/mbc.e09-01-0035] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The RNA helicase p54 (DDX6, Dhh1, Me31B, Cgh-1, RCK) is a prototypic component of P-(rocessing) bodies in cells ranging from yeast to human. Previously, we have shown that it is also a component of the large cytoplasmic polyadenylation element-binding protein translation repressor complex in Xenopus oocytes and that when tethered to the 3' untranslated region, Xp54 represses reporter mRNA translation. Here, we examine the role of the p54 helicase activity in translational repression and in P-body formation. Mutagenesis of conserved p54 helicase motifs activates translation in the tethered function assay, reduces accumulation of p54 in P-bodies in HeLa cells, and inhibits its capacity to assemble P-bodies in p54-depleted cells. Similar results were obtained in four helicase motifs implicated in ATP binding and in coupling ATPase and RNA binding activities. This is accompanied by changes in the interaction of the mutant p54 with the oocyte repressor complex components. Surprisingly, the C-terminal D2 domain alone is sufficient for translational repression and complete accumulation in P-bodies, although it is deficient for P-body assembly. We propose a novel RNA helicase model, in which the D2 domain acts as a protein binding platform and the ATPase/helicase activity allows protein complex remodeling that dictates the balance between repressors and an activator of translation.
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Affiliation(s)
- Nicola Minshall
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
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848
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Hammell CM, Lubin I, Boag PR, Blackwell TK, Ambros V. nhl-2 Modulates microRNA activity in Caenorhabditis elegans. Cell 2009; 136:926-38. [PMID: 19269369 PMCID: PMC2670343 DOI: 10.1016/j.cell.2009.01.053] [Citation(s) in RCA: 146] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2008] [Revised: 12/19/2008] [Accepted: 01/28/2009] [Indexed: 10/21/2022]
Abstract
TRIM-NHL proteins represent a large class of metazoan proteins implicated in development and disease. We demonstrate that a C. elegans TRIM-NHL protein, NHL-2, functions as a cofactor for the microRNA-induced silencing complex (miRISC) and thereby enhances the posttranscriptional repression of several genetically verified microRNA targets, including hbl-1 and let-60/Ras (by the let-7 family of microRNAs) and cog-1 (by the lsy-6 microRNA). NHL-2 is localized to cytoplasmic P-bodies and physically associates with the P-body protein CGH-1 and the core miRISC components ALG-1/2 and AIN-1. nhl-2 and cgh-1 mutations compromise the repression of microRNA targets in vivo but do not affect microRNA biogenesis, indicating a role for an NHL-2:CGH-1 complex in the effector phase of miRISC activity. We propose that the NHL-2:CGH-1 complex functions in association with mature miRISC to modulate the efficacy of microRNA:target interactions in response to physiological and developmental signals, thereby ensuring the robustness of genetic regulatory pathways regulated by microRNAs.
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Affiliation(s)
- Christopher M. Hammell
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, ph: 508 856-6380
| | - Isabella Lubin
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, ph: 508 856-6380
| | - Peter R. Boag
- Joslin Diabetes Center, Department of Pathology, Harvard Medical School, Harvard Stem Cell Institute, One Joslin Place, Boston, MA 02215
- Department of Biochemistry and Molecular Biology, Monash University, Melbourne 3800, Australia
| | - T. Keith Blackwell
- Joslin Diabetes Center, Department of Pathology, Harvard Medical School, Harvard Stem Cell Institute, One Joslin Place, Boston, MA 02215
| | - Victor Ambros
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, ph: 508 856-6380
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849
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Abstract
Translational control in eukaryotic cells is critical for gene regulation during nutrient deprivation and stress, development and differentiation, nervous system function, aging, and disease. We describe recent advances in our understanding of the molecular structures and biochemical functions of the translation initiation machinery and summarize key strategies that mediate general or gene-specific translational control, particularly in mammalian systems.
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Affiliation(s)
- Nahum Sonenberg
- Department of Biochemistry and Goodman Cancer Centre, McGill University, Montreal, Quebec, H3G 1Y6, Canada
| | - Alan G. Hinnebusch
- Laboratory of Gene Regulation and Development, National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892, USA
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850
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Beilharz TH, Preiss T. Transcriptome-wide measurement of mRNA polyadenylation state. Methods 2009; 48:294-300. [PMID: 19233282 DOI: 10.1016/j.ymeth.2009.02.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2008] [Revised: 02/09/2009] [Accepted: 02/09/2009] [Indexed: 10/21/2022] Open
Abstract
The 3' poly(A) tail has important roles throughout the eukaryotic mRNA life cycle. A characteristic aspect of poly(A) tail function is furthermore that it can be modulated by changes in its length. This is in turn a well-recognised cellular means to regulate both, mRNA translation and stability, and a positive correlation has often been found between the efficiency of mRNA translation and the length of its poly(A) tail. Here we describe methodology to measure mRNA polyadenylation state in a transcriptome-wide manner, using separation of cellular mRNA populations on poly(U) sepharose in combination with microarray analysis of the resulting fractions. We further detail methods for bulk and mRNA-specific poly(A) tail length measurements to monitor the efficiency of initial mRNA separation and to verify candidates selected from the microarray data. Although detailed here for the study of yeast mRNAs, these methods are adaptable to the investigation of any cellular context in which poly(A) tail length control is known or suspected to operate.
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Affiliation(s)
- Traude H Beilharz
- Molecular Genetics Division, Victor Chang Cardiac Research Institute (VCCRI), Lowy Packer Building, 405 Liverpool Street, Darlinghurst (Sydney), NSW 2010, Australia.
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