101
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PKA-dependent phosphorylation of ribosomal protein S6 does not correlate with translation efficiency in striatonigral and striatopallidal medium-sized spiny neurons. J Neurosci 2015; 35:4113-30. [PMID: 25762659 DOI: 10.1523/jneurosci.3288-14.2015] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Ribosomal protein S6 (rpS6), a component of the 40S ribosomal subunit, is phosphorylated on several residues in response to numerous stimuli. Although commonly used as a marker for neuronal activity, its upstream mechanisms of regulation are poorly studied and its role in protein synthesis remains largely debated. Here, we demonstrate that the psychostimulant d-amphetamine (d-amph) markedly increases rpS6 phosphorylation at Ser235/236 sites in both crude and synaptoneurosomal preparations of the mouse striatum. This effect occurs selectively in D1R-expressing medium-sized spiny neurons (MSNs) and requires the cAMP/PKA/DARPP-32/PP-1 cascade, whereas it is independent of mTORC1/p70S6K, PKC, and ERK signaling. By developing a novel assay to label nascent peptidic chains, we show that the rpS6 phosphorylation induced in striatonigral MSNs by d-amph, as well as in striatopallidal MSNs by the antipsychotic haloperidol or in both subtypes by papaverine, is not correlated with the translation of global or 5' terminal oligopyrimidine tract mRNAs. Together, these results provide novel mechanistic insights into the in vivo regulation of the post-translational modification of rpS6 in the striatum and point out the lack of a relationship between PKA-dependent rpS6 phosphorylation and translation efficiency.
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102
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Sosanya NM, Cacheaux LP, Workman ER, Niere F, Perrone-Bizzozero NI, Raab-Graham KF. Mammalian Target of Rapamycin (mTOR) Tagging Promotes Dendritic Branch Variability through the Capture of Ca2+/Calmodulin-dependent Protein Kinase II α (CaMKIIα) mRNAs by the RNA-binding Protein HuD. J Biol Chem 2015; 290:16357-71. [PMID: 25944900 DOI: 10.1074/jbc.m114.599399] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Indexed: 02/05/2023] Open
Abstract
The fate of a memory, whether stored or forgotten, is determined by the ability of an active or tagged synapse to undergo changes in synaptic efficacy requiring protein synthesis of plasticity-related proteins. A synapse can be tagged, but without the "capture" of plasticity-related proteins, it will not undergo long lasting forms of plasticity (synaptic tagging and capture hypothesis). What the "tag" is and how plasticity-related proteins are captured at tagged synapses are unknown. Ca(2+)/calmodulin-dependent protein kinase II α (CaMKIIα) is critical in learning and memory and is synthesized locally in neuronal dendrites. The mechanistic (mammalian) target of rapamycin (mTOR) is a protein kinase that increases CaMKIIα protein expression; however, the mechanism and site of dendritic expression are unknown. Herein, we show that mTOR activity mediates the branch-specific expression of CaMKIIα, favoring one secondary, daughter branch over the other in a single neuron. mTOR inhibition decreased the dendritic levels of CaMKIIα protein and mRNA by shortening its poly(A) tail. Overexpression of the RNA-stabilizing protein HuD increased CaMKIIα protein levels and preserved its selective expression in one daughter branch over the other when mTOR was inhibited. Unexpectedly, deleting the third RNA recognition motif of HuD, the domain that binds the poly(A) tail, eliminated the branch-specific expression of CaMKIIα when mTOR was active. These results provide a model for one molecular mechanism that may underlie the synaptic tagging and capture hypothesis where mTOR is the tag, preventing deadenylation of CaMKIIα mRNA, whereas HuD captures and promotes its expression in a branch-specific manner.
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Affiliation(s)
- Natasha M Sosanya
- From the Center for Learning and Memory, Department of Neuroscience, Institute for Cell Biology, and United States Army Institute of Surgical Research, Joint Base San Antonio-Fort Sam, Houston, Texas 78234, and
| | - Luisa P Cacheaux
- From the Center for Learning and Memory, Department of Neuroscience
| | - Emily R Workman
- From the Center for Learning and Memory, Department of Neuroscience, Institute for Neuroscience, University of Texas, Austin, Texas 78712
| | - Farr Niere
- From the Center for Learning and Memory, Department of Neuroscience
| | - Nora I Perrone-Bizzozero
- Department of Neurosciences, Psychiatry and Behavioral Sciences, University of New Mexico Health Sciences Center, Albuquerque, New Mexico 87131
| | - Kimberly F Raab-Graham
- From the Center for Learning and Memory, Department of Neuroscience, Institute for Cell Biology, and Institute for Neuroscience, University of Texas, Austin, Texas 78712,
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103
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Singh G, Pratt G, Yeo GW, Moore MJ. The Clothes Make the mRNA: Past and Present Trends in mRNP Fashion. Annu Rev Biochem 2015; 84:325-54. [PMID: 25784054 DOI: 10.1146/annurev-biochem-080111-092106] [Citation(s) in RCA: 272] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Throughout their lifetimes, messenger RNAs (mRNAs) associate with proteins to form ribonucleoproteins (mRNPs). Since the discovery of the first mRNP component more than 40 years ago, what is known as the mRNA interactome now comprises >1,000 proteins. These proteins bind mRNAs in myriad ways with varying affinities and stoichiometries, with many assembling onto nascent RNAs in a highly ordered process during transcription and precursor mRNA (pre-mRNA) processing. The nonrandom distribution of major mRNP proteins observed in transcriptome-wide studies leads us to propose that mRNPs are organized into three major domains loosely corresponding to 5' untranslated regions (UTRs), open reading frames, and 3' UTRs. Moving from the nucleus to the cytoplasm, mRNPs undergo extensive remodeling as they are first acted upon by the nuclear pore complex and then by the ribosome. When not being actively translated, cytoplasmic mRNPs can assemble into large multi-mRNP assemblies or be permanently disassembled and degraded. In this review, we aim to give the reader a thorough understanding of past and current eukaryotic mRNP research.
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Affiliation(s)
- Guramrit Singh
- Department of Molecular Genetics, Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210;
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104
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KIS, a kinase associated with microtubule regulators, enhances translation of AMPA receptors and stimulates dendritic spine remodeling. J Neurosci 2015; 34:13988-97. [PMID: 25319695 DOI: 10.1523/jneurosci.1573-14.2014] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Local regulation of protein synthesis allows a neuron to rapidly alter the proteome in response to synaptic signals, an essential mechanism in synaptic plasticity that is altered in many neurological diseases. Synthesis of many synaptic proteins is under local control and much of this regulation occurs through structures termed RNA granules. KIS is a protein kinase that associates with stathmin, a modulator of the tubulin cytoskeleton. Furthermore, KIS is found in RNA granules and stimulates translation driven by the β-actin 3'UTR in neurites. Here we explore the physiological and molecular mechanisms underlying the action of KIS on hippocampal synaptic plasticity in mice. KIS downregulation compromises spine development, alters actin dynamics, and reduces postsynaptic responsiveness. The absence of KIS results in a significant decrease of protein levels of PSD-95, a postsynaptic scaffolding protein, and the AMPAR subunits GluR1 and GluR2 in a CPEB3-dependent manner. Underlying its role in spine maturation, KIS is able to suppress the spine developmental defects caused by CPEB3 overexpression. Moreover, either by direct or indirect mechanisms, KIS counteracts the inhibitory activity of CPEB3 on the GluR2 3'UTR at both mRNA translation and polyadenylation levels. Our study provides insights into the mechanisms that mediate dendritic spine morphogenesis and functional synaptic maturation, and suggests KIS as a link regulating spine cytoskeleton and postsynaptic activity in memory formation.
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105
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Luchelli L, Thomas MG, Boccaccio GL. Synaptic control of mRNA translation by reversible assembly of XRN1 bodies. J Cell Sci 2015; 128:1542-54. [DOI: 10.1242/jcs.163295] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 02/13/2015] [Indexed: 12/14/2022] Open
Abstract
Repression of mRNA translation is linked to the formation of specific cytosolic foci such as Stress Granules (SGs) and Processing Bodies (PBs), which store or degrade mRNAs. In neurons, synaptic activity regulates translation at the postsynapse and this is important for plasticity. NMDA receptor stimulation downregulates translation and we speculate that this is linked to the formation of unknown mRNA-silencing foci. Here we show that the 5′-3′ exoribonuclease XRN1 forms discrete clusters associated to the postsynapse that are different from PBs or SGs, and we named them Synaptic XRN1-bodies (SX-bodies). Using primary neurons, we found that the SX-bodies respond to synapse stimulation and that their formation correlates inversely with the local translation rate. SX-bodies enlarge in size and number upon NMDA stimulation, and metabotropic glutamate receptor activation provokes SX-body dissolution, along with increased translation. The response is specific and the previously described Smaug1-foci and FMRP granules show a different response. Finally, XRN1 knockdown impairs the translational repression triggered by NMDA. Collectively, these observations support a role for the SX-bodies in the reversible masking and silencing of mRNAs at the synapse.
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106
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Macromolecular transport in synapse to nucleus communication. Trends Neurosci 2014; 38:108-16. [PMID: 25534890 DOI: 10.1016/j.tins.2014.12.001] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 12/01/2014] [Indexed: 12/21/2022]
Abstract
Local signaling events at synapses or axon terminals must be communicated to the nucleus to elicit transcriptional responses. The lengths of neuronal processes pose a significant challenge for such intracellular communication. This challenge is met by mechanisms ranging from rapid signals encoded in calcium waves to slower macromolecular signaling complexes carried by molecular motors. Here we summarize recent findings on macromolecular signaling from the synapse to the nucleus, in comparison to those employed in injury signaling along axons. A number of common themes emerge, including combinatorial signal encoding by post-translational mechanisms such as differential phosphorylation and proteolysis, and conserved roles for importins in coordinating signaling complexes. Neurons may integrate ionic flux with motor-transported signals as a temporal code for synaptic plasticity signaling.
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107
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Afonina ZA, Myasnikov AG, Shirokov VA, Klaholz BP, Spirin AS. Conformation transitions of eukaryotic polyribosomes during multi-round translation. Nucleic Acids Res 2014; 43:618-28. [PMID: 25520190 PMCID: PMC4288168 DOI: 10.1093/nar/gku1270] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Using sedimentation and cryo electron tomography techniques, the conformations of eukaryotic polyribosomes formed in a long-term cell-free translation system were analyzed over all the active system lifetime (20–30 translation rounds during 6–8 h in wheat germ extract at 25°C). Three distinct types of the conformations were observed: (i) circular polyribosomes, varying from ring-shaped forms to circles collapsed into double rows, (ii) linear polyribosomes, tending to acquire planar zigzag-like forms and (iii) densely packed 3D helices. At the start, during the first two rounds of translation mostly the circular (ring-shaped and double-row) polyribosomes and the linear (free-shaped and zigzag-like) polyribosomes were formed (‘juvenile phase’). The progressive loading of the polyribosomes with translating ribosomes induced the opening of the circular polyribosomes and the transformation of a major part of the linear polyribosomes into the dense 3D helices (‘transitional phase’). After 2 h from the beginning (about 8–10 rounds of translation) this compact form of polyribosomes became predominant, whereas the circular and linear polyribosome fractions together contained less than half of polysomal ribosomes (‘steady-state phase’). The latter proportions did not change for several hours. Functional tests showed a reduced translational activity in the fraction of the 3D helical polyribosomes.
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Affiliation(s)
- Zhanna A Afonina
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
| | - Alexander G Myasnikov
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Centre National de la Recherche Scientifique (CNRS) UMR 7104; Institut National de la Santé de la Recherche Médicale (INSERM) U964; Université de Strasbourg, 1 rue Laurent Fries, 67404 Illkirch, France
| | - Vladimir A Shirokov
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
| | - Bruno P Klaholz
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Centre National de la Recherche Scientifique (CNRS) UMR 7104; Institut National de la Santé de la Recherche Médicale (INSERM) U964; Université de Strasbourg, 1 rue Laurent Fries, 67404 Illkirch, France
| | - Alexander S Spirin
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
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108
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Gkogkas CG, Khoutorsky A, Cao R, Jafarnejad SM, Prager-Khoutorsky M, Giannakas N, Kaminari A, Fragkouli A, Nader K, Price TJ, Konicek BW, Graff JR, Tzinia AK, Lacaille JC, Sonenberg N. Pharmacogenetic inhibition of eIF4E-dependent Mmp9 mRNA translation reverses fragile X syndrome-like phenotypes. Cell Rep 2014; 9:1742-1755. [PMID: 25466251 PMCID: PMC4294557 DOI: 10.1016/j.celrep.2014.10.064] [Citation(s) in RCA: 145] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Revised: 09/30/2014] [Accepted: 10/24/2014] [Indexed: 01/22/2023] Open
Abstract
Fragile X syndrome (FXS) is the leading genetic cause of autism. Mutations in Fmr1 (fragile X mental retardation 1 gene) engender exaggerated translation resulting in dendritic spine dysmorphogenesis, synaptic plasticity alterations, and behavioral deficits in mice, which are reminiscent of FXS phenotypes. Using postmortem brains from FXS patients and Fmr1 knockout mice (Fmr1(-/y)), we show that phosphorylation of the mRNA 5' cap binding protein, eukaryotic initiation factor 4E (eIF4E), is elevated concomitant with increased expression of matrix metalloproteinase 9 (MMP-9) protein. Genetic or pharmacological reduction of eIF4E phosphorylation rescued core behavioral deficits, synaptic plasticity alterations, and dendritic spine morphology defects via reducing exaggerated translation of Mmp9 mRNA in Fmr1(-/y) mice, whereas MMP-9 overexpression produced several FXS-like phenotypes. These results uncover a mechanism of regulation of synaptic function by translational control of Mmp-9 in FXS, which opens the possibility of new treatment avenues for the diverse neurological and psychiatric aspects of FXS.
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Affiliation(s)
- Christos G Gkogkas
- Department of Biochemistry and Goodman Cancer Research Centre, McGill University, Montréal, QC H3A 1A3, Canada.
| | - Arkady Khoutorsky
- Department of Biochemistry and Goodman Cancer Research Centre, McGill University, Montréal, QC H3A 1A3, Canada
| | - Ruifeng Cao
- Department of Biochemistry and Goodman Cancer Research Centre, McGill University, Montréal, QC H3A 1A3, Canada
| | - Seyed Mehdi Jafarnejad
- Department of Biochemistry and Goodman Cancer Research Centre, McGill University, Montréal, QC H3A 1A3, Canada
| | - Masha Prager-Khoutorsky
- Center for Research in Neuroscience, McGill University, Montréal General Hospital, Montréal, QC H3G 1A4, Canada
| | - Nikolaos Giannakas
- Institute of Biosciences and Applications, National Center for Scientific Research Demokritos, Agia Paraskevi, 15310 Athens, Greece
| | - Archontia Kaminari
- Institute of Biosciences and Applications, National Center for Scientific Research Demokritos, Agia Paraskevi, 15310 Athens, Greece
| | - Apostolia Fragkouli
- Institute of Biosciences and Applications, National Center for Scientific Research Demokritos, Agia Paraskevi, 15310 Athens, Greece
| | - Karim Nader
- Department of Psychology, McGill University, Montréal, QC H3A 1B1, Canada
| | - Theodore J Price
- School of Behavioral and Brain Sciences, University of Texas at Dallas, Richardson, TX 75080, USA
| | - Bruce W Konicek
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285, USA
| | - Jeremy R Graff
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285, USA
| | - Athina K Tzinia
- Institute of Biosciences and Applications, National Center for Scientific Research Demokritos, Agia Paraskevi, 15310 Athens, Greece
| | - Jean-Claude Lacaille
- GRSNC and Department of Neurosciences, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Nahum Sonenberg
- Department of Biochemistry and Goodman Cancer Research Centre, McGill University, Montréal, QC H3A 1A3, Canada.
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109
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Fernandez-Moya SM, Bauer KE, Kiebler MA. Meet the players: local translation at the synapse. Front Mol Neurosci 2014; 7:84. [PMID: 25426019 PMCID: PMC4227489 DOI: 10.3389/fnmol.2014.00084] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 10/15/2014] [Indexed: 01/10/2023] Open
Abstract
It is widely believed that activity-dependent synaptic plasticity is the basis for learning and memory. Both processes are dependent on new protein synthesis at the synapse. Here, we describe a mechanism how dendritic mRNAs are transported and subsequently translated at activated synapses. Furthermore, we present the players involved in the regulation of local dendritic translation upon neuronal stimulation and their molecular interplay that maintain local proteome homeostasis. Any dysregulation causes several types of neurological disorders including muscular atrophies, cancers, neuropathies, neurodegenerative, and cognitive disorders.
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Affiliation(s)
| | - Karl E Bauer
- Department of Anatomy and Cell Biology, Ludwig-Maximilians-University Munich, Germany
| | - Michael A Kiebler
- Department of Anatomy and Cell Biology, Ludwig-Maximilians-University Munich, Germany
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110
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Myasnikov AG, Afonina ZA, Ménétret JF, Shirokov VA, Spirin AS, Klaholz BP. The molecular structure of the left-handed supra-molecular helix of eukaryotic polyribosomes. Nat Commun 2014; 5:5294. [PMID: 25376914 DOI: 10.1038/ncomms6294] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 09/17/2014] [Indexed: 01/07/2023] Open
Abstract
During protein synthesis, several ribosomes bind to a single messenger RNA (mRNA) forming large macromolecular assemblies called polyribosomes. Here we report the detailed molecular structure of a 100 MDa eukaryotic poly-ribosome complex derived from cryo electron tomography, sub-tomogram averaging and pseudo-atomic modelling by crystal structure fitting. The structure allowed the visualization of the three functional parts of the polysome assembly, the central core region that forms a rather compact left-handed supra-molecular helix, and the more open regions that harbour the initiation and termination sites at either ends. The helical region forms a continuous mRNA channel where the mRNA strand bridges neighbouring exit and entry sites of the ribosomes and prevents mRNA looping between ribosomes. This structure provides unprecedented insights into protein- and RNA-mediated inter-ribosome contacts that involve conserved sites through 40S subunits and long protruding RNA expansion segments, suggesting a role in stabilizing the overall polyribosomal assembly.
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Affiliation(s)
- Alexander G Myasnikov
- 1] Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), 1 rue Laurent Fries, BP 10142, 67404 Illkirch, France [2] Centre National de la Recherche Scientifique (CNRS) UMR 7104, 67404 Illkirch, France [3] Institut National de la Santé et de la Recherche Médicale (INSERM), 67404 Illkirch, France [4] Université de Strasbourg, 67400 Strasbourg, France
| | - Zhanna A Afonina
- Institute of Protein Research, Russian Academy of Sciences, 142290 Moscow, Russia
| | - Jean-François Ménétret
- 1] Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), 1 rue Laurent Fries, BP 10142, 67404 Illkirch, France [2] Centre National de la Recherche Scientifique (CNRS) UMR 7104, 67404 Illkirch, France [3] Institut National de la Santé et de la Recherche Médicale (INSERM), 67404 Illkirch, France [4] Université de Strasbourg, 67400 Strasbourg, France
| | - Vladimir A Shirokov
- Institute of Protein Research, Russian Academy of Sciences, 142290 Moscow, Russia
| | - Alexander S Spirin
- Institute of Protein Research, Russian Academy of Sciences, 142290 Moscow, Russia
| | - Bruno P Klaholz
- 1] Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), 1 rue Laurent Fries, BP 10142, 67404 Illkirch, France [2] Centre National de la Recherche Scientifique (CNRS) UMR 7104, 67404 Illkirch, France [3] Institut National de la Santé et de la Recherche Médicale (INSERM), 67404 Illkirch, France [4] Université de Strasbourg, 67400 Strasbourg, France
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111
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Abstract
Synaptic plasticity, learning, and memory require high temporal and spatial control of gene expression. These processes are thought to rely mainly on asymmetric mRNA transport to synapses. Already in the early days of studying mRNA transport, Wilhelm and Vale proposed a multi-step process in 1993. Since then, we have gained important novel insights into how these individual steps are controlled by research performed in various cell types and organisms. Here, we present the latest view on how dendritic mRNA localization is achieved and how local translation at the synapse is regulated. In particular, we propose that the recently observed heterogeneity of RNA-protein particle assembly in neurons might be the key for how precise gene expression in the brain is achieved. In addition, we focus on latest data dealing with translational activation of translationally repressed mRNPs at a synapse that experiences learning-induced changes in its morphology and function. Together, these new findings shed new light on how precise regulatory mechanisms can lead to synaptic plasticity and memory formation.
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Affiliation(s)
- Saskia Hutten
- a Department of Anatomy and Cell Biology ; Ludwig-Maximilians-University ; Munich , Germany
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112
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Faye MD, Graber TE, Holcik M. Assessment of selective mRNA translation in mammalian cells by polysome profiling. J Vis Exp 2014:e52295. [PMID: 25407425 PMCID: PMC4353390 DOI: 10.3791/52295] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Regulation of protein synthesis represents a key control point in cellular response to stress. In particular, discreet RNA regulatory elements were shown to allow to selective translation of specific mRNAs, which typically encode for proteins required for a particular stress response. Identification of these mRNAs, as well as the characterization of regulatory mechanisms responsible for selective translation has been at the forefront of molecular biology for some time. Polysome profiling is a cornerstone method in these studies. The goal of polysome profiling is to capture mRNA translation by immobilizing actively translating ribosomes on different transcripts and separate the resulting polyribosomes by ultracentrifugation on a sucrose gradient, thus allowing for a distinction between highly translated transcripts and poorly translated ones. These can then be further characterized by traditional biochemical and molecular biology methods. Importantly, combining polysome profiling with high throughput genomic approaches allows for a large scale analysis of translational regulation.
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Affiliation(s)
- Mame Daro Faye
- Apoptosis Research Centre, Children's Hospital of Eastern Ontario Research Institute and Department of Biochemistry, Microbiology and Immunology, University of Ottawa
| | | | - Martin Holcik
- Apoptosis Research Centre, Children's Hospital of Eastern Ontario Research Institute and Department of Pediatrics, University of Ottawa;
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113
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Pimentel J, Boccaccio GL. Translation and silencing in RNA granules: a tale of sand grains. Front Mol Neurosci 2014; 7:68. [PMID: 25100944 PMCID: PMC4107967 DOI: 10.3389/fnmol.2014.00068] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Accepted: 07/05/2014] [Indexed: 01/19/2023] Open
Abstract
The transcriptome at the synapse consists of thousands of messengers encoding several cellular functions, including a significant number of receptors and ion channels and associated proteins. The concerted translational regulation of all these molecules contributes to the dynamic control of synaptic strength. Cumulative evidence supports that dendritic RNA granules and mRNA-silencing foci play an important role in translational regulation. Several relevant RBPs – FMRP; FUS/TLS; TDP-43; Staufen; Smaug; Pumilio; CPEB; HuD; ZBP1; and DDX6 among others – form granules that contain dormant mRNAs repressed by multiple pathways. Recent reports indicate that dendritic granules may contain stalled polysomes, and furthermore, active translation may occur in association with RNA granules. Here, we discuss the molecules and pathways involved in this continuum of RNA granules that contain masked mRNAs, mRNAs trapped in inactive polysomes or mRNAs engaged in translation.
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Affiliation(s)
| | - Graciela L Boccaccio
- Instituto Leloir Buenos Aires, Argentina ; Instituto de Investigaciones Bioquímicas Buenos Aires - Consejo Nacional de Investigaciones Científicas y Tecnológicas Buenos Aires, Argentina ; Facultad de Ciencias Exactas y Naturales, University of Buenos Aires Buenos Aires, Argentina
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114
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Poliakov E, Koonin EV, Rogozin IB. Impairment of translation in neurons as a putative causative factor for autism. Biol Direct 2014; 9:16. [PMID: 25011470 PMCID: PMC4099083 DOI: 10.1186/1745-6150-9-16] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 07/01/2014] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND A dramatic increase in the prevalence of autism and Autistic Spectrum Disorders (ASD) has been observed over the last two decades in USA, Europe and Asia. Given the accumulating data on the possible role of translation in the etiology of ASD, we analyzed potential effects of rare synonymous substitutions associated with ASD on mRNA stability, splicing enhancers and silencers, and codon usage. PRESENTATION OF THE HYPOTHESIS We hypothesize that subtle impairment of translation, resulting in dosage imbalance of neuron-specific proteins, contributes to the etiology of ASD synergistically with environmental neurotoxins. TESTING THE HYPOTHESIS A statistically significant shift from optimal to suboptimal codons caused by rare synonymous substitutions associated with ASD was detected whereas no effect on other analyzed characteristics of transcripts was identified. This result suggests that the impact of rare codons on the translation of genes involved in neuron development, even if slight in magnitude, could contribute to the pathogenesis of ASD in the presence of an aggressive chemical background. This hypothesis could be tested by further analysis of ASD-associated mutations, direct biochemical characterization of their effects, and assessment of in vivo effects on animal models. IMPLICATIONS OF THE HYPOTHESIS It seems likely that the synergistic action of environmental hazards with genetic variations that in themselves have limited or no deleterious effects but are potentiated by the environmental factors is a general principle that underlies the alarming increase in the ASD prevalence. REVIEWERS This article was reviewed by Andrey Rzhetsky, Neil R. Smalheiser, and Shamil R. Sunyaev.
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Affiliation(s)
- Eugenia Poliakov
- Laboratory of Retinal Cell & Molecular Biology, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Igor B Rogozin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
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115
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Di Prisco GV, Huang W, Buffington SA, Hsu CC, Bonnen PE, Placzek AN, Sidrauski C, Krnjević K, Kaufman RJ, Walter P, Costa-Mattioli M. Translational control of mGluR-dependent long-term depression and object-place learning by eIF2α. Nat Neurosci 2014; 17:1073-82. [PMID: 24974795 DOI: 10.1038/nn.3754] [Citation(s) in RCA: 139] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 05/30/2014] [Indexed: 02/06/2023]
Abstract
At hippocampal synapses, activation of group I metabotropic glutamate receptors (mGluRs) induces long-term depression (LTD), which requires new protein synthesis. However, the underlying mechanism remains elusive. Here we describe the translational program that underlies mGluR-LTD and identify the translation factor eIF2α as its master effector. Genetically reducing eIF2α phosphorylation, or specifically blocking the translation controlled by eIF2α phosphorylation, prevented mGluR-LTD and the internalization of surface AMPA receptors (AMPARs). Conversely, direct phosphorylation of eIF2α, bypassing mGluR activation, triggered a sustained LTD and removal of surface AMPARs. Combining polysome profiling and RNA sequencing, we identified the mRNAs translationally upregulated during mGluR-LTD. Translation of one of these mRNAs, oligophrenin-1, mediates the LTD induced by eIF2α phosphorylation. Mice deficient in phospho-eIF2α-mediated translation are impaired in object-place learning, a behavioral task that induces hippocampal mGluR-LTD in vivo. Our findings identify a new model of mGluR-LTD, which promises to be of value in the treatment of mGluR-LTD-linked cognitive disorders.
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Affiliation(s)
- Gonzalo Viana Di Prisco
- 1] Department of Neuroscience, Baylor College of Medicine, Houston, Texas, USA. [2] Memory and Brain Research Center, Baylor College of Medicine, Houston, Texas, USA. [3]
| | - Wei Huang
- 1] Department of Neuroscience, Baylor College of Medicine, Houston, Texas, USA. [2] Memory and Brain Research Center, Baylor College of Medicine, Houston, Texas, USA. [3]
| | - Shelly A Buffington
- 1] Department of Neuroscience, Baylor College of Medicine, Houston, Texas, USA. [2] Memory and Brain Research Center, Baylor College of Medicine, Houston, Texas, USA. [3]
| | - Chih-Chun Hsu
- 1] Department of Neuroscience, Baylor College of Medicine, Houston, Texas, USA. [2] Memory and Brain Research Center, Baylor College of Medicine, Houston, Texas, USA
| | - Penelope E Bonnen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Andon N Placzek
- 1] Department of Neuroscience, Baylor College of Medicine, Houston, Texas, USA. [2] Present address: Division of Basic Medical Sciences, Mercer University School of Medicine, Macon, Georgia, USA
| | - Carmela Sidrauski
- Department of Biochemistry and Biophysics, Howard Hughes Medical Institute, University of California San Francisco, San Francisco, California, USA
| | - Krešimir Krnjević
- Department of Physiology, McGill University, Montreal, Quebec, Canada
| | - Randal J Kaufman
- Center for Neuroscience, Aging, and Stem Cell Research, Sanford-Burnham Medical Research Institute, La Jolla, California, USA
| | - Peter Walter
- Department of Biochemistry and Biophysics, Howard Hughes Medical Institute, University of California San Francisco, San Francisco, California, USA
| | - Mauro Costa-Mattioli
- 1] Department of Neuroscience, Baylor College of Medicine, Houston, Texas, USA. [2] Memory and Brain Research Center, Baylor College of Medicine, Houston, Texas, USA
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116
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Gebicke-Haerter PJ. Engram formation in psychiatric disorders. Front Neurosci 2014; 8:118. [PMID: 24904262 PMCID: PMC4036307 DOI: 10.3389/fnins.2014.00118] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Accepted: 05/02/2014] [Indexed: 01/17/2023] Open
Abstract
Environmental factors substantially influence beginning and progression of mental illness, reinforcing or reducing the consequences of genetic vulnerability. Often initiated by early traumatic events, “engrams” or memories are formed that may give rise to a slow and subtle progression of psychiatric disorders. The large delay between beginning and time of onset (diagnosis) may be explained by efficient compensatory mechanisms observed in brain metabolism that use optional pathways in highly redundant molecular interactions. To this end, research has to deal with mechanisms of learning and long-term memory formation, which involves (a) epigenetic changes, (b) altered neuronal activities, and (c) changes in neuron-glia communication. On the epigenetic level, apparently DNA-methylations are more stable than histone modifications, although both closely interact. Neuronal activities basically deliver digital information, which clearly can serve as basis for memory formation (LTP). However, research in this respect has long time neglected the importance of glia. They are more actively involved in the control of neuronal activities than thought before. They can both reinforce and inhibit neuronal activities by transducing neuronal information from frequency-encoded to amplitude and frequency-modulated calcium wave patterns spreading in the glial syncytium by use of gap junctions. In this way, they serve integrative functions. In conclusion, we are dealing with two concepts of encoding information that mutually control each other and synergize: a digital (neuronal) and a wave-like (glial) computing, forming neuron-glia functional units with inbuilt feedback loops to maintain balance of excitation and inhibition. To better understand mental illness, we have to gain more insight into the dynamics of adverse environmental impact on those cellular and molecular systems. This report summarizes existing knowledge and draws some outline about further research in molecular psychiatry.
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Affiliation(s)
- Peter J Gebicke-Haerter
- Medical Faculty Mannheim, Central Institute of Mental Health, Institute of Psychopharmacology, Heidelberg University Mannheim, Germany ; Progrs. de Farmacología y Inmunología, Facultad de Medicina, Universidad de Chile Santiago, Chile
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117
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Shelkovnikova TA, Robinson HK, Southcombe JA, Ninkina N, Buchman VL. Multistep process of FUS aggregation in the cell cytoplasm involves RNA-dependent and RNA-independent mechanisms. Hum Mol Genet 2014; 23:5211-26. [PMID: 24842888 PMCID: PMC4159159 DOI: 10.1093/hmg/ddu243] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Fused in sarcoma (FUS) is an RNA-binding protein involved in pathogenesis of several neurodegenerative diseases. Aggregation of mislocalized FUS into non-amyloid inclusions is believed to be pivotal in the development of cell dysfunction, but the mechanism of their formation is unclear. Using transient expression of a panel of deletion and chimeric FUS variants in various cultured cells, we demonstrated that FUS accumulating in the cytoplasm nucleates a novel type of RNA granules, FUS granules (FGs), that are structurally similar but not identical to physiological RNA transport granules. Formation of FGs requires FUS N-terminal prion-like domain and the ability to bind specific RNAs. Clustering of FGs coupled with further recruitment of RNA and proteins produce larger structures, FUS aggregates (FAs), that resemble but are clearly distinct from stress granules. In conditions of attenuated transcription, FAs lose RNA and dissociate into RNA-free FUS complexes that become precursors of large aggresome-like structures. We propose a model of multistep FUS aggregation involving RNA-dependent and RNA-independent stages. This model can be extrapolated to formation of pathological inclusions in human FUSopathies.
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Affiliation(s)
- Tatyana A Shelkovnikova
- School of Biosciences, Cardiff University, Museum Avenue, Cardiff CF10 3AX, UK, Institute of Physiologically Active Compounds Russian Academy of Sciences, 1 Severniy proezd, Chernogolovka 142432, Moscow Region, Russian Federation and
| | - Hannah K Robinson
- School of Biosciences, Cardiff University, Museum Avenue, Cardiff CF10 3AX, UK
| | - Joshua A Southcombe
- School of Biosciences, Cardiff University, Museum Avenue, Cardiff CF10 3AX, UK
| | - Natalia Ninkina
- School of Biosciences, Cardiff University, Museum Avenue, Cardiff CF10 3AX, UK, Institute of General Pathology and Pathophysiology of Russian Academy of Medical Science, 8 Baltijskaya str, Moscow 125315, Russian Federation
| | - Vladimir L Buchman
- School of Biosciences, Cardiff University, Museum Avenue, Cardiff CF10 3AX, UK,
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118
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Buxbaum AR, Wu B, Singer RH. Single β-actin mRNA detection in neurons reveals a mechanism for regulating its translatability. Science 2014; 343:419-22. [PMID: 24458642 DOI: 10.1126/science.1242939] [Citation(s) in RCA: 218] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The physical manifestation of learning and memory formation in the brain can be expressed by strengthening or weakening of synaptic connections through morphological changes. Local actin remodeling underlies some forms of plasticity and may be facilitated by local β-actin synthesis, but dynamic information is lacking. In this work, we use single-molecule in situ hybridization to demonstrate that dendritic β-actin messenger RNA (mRNA) and ribosomes are in a masked, neuron-specific form. Chemically induced long-term potentiation prompts transient mRNA unmasking, which depends on factors active during synaptic activity. Ribosomes and single β-actin mRNA motility increase after stimulation, indicative of release from complexes. Hence, the single-molecule assays we developed allow for the quantification of activity-induced unmasking and availability for active translation. Further, our work demonstrates that β-actin mRNA and ribosomes are in a masked state that is alleviated by stimulation.
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Affiliation(s)
- Adina R Buxbaum
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
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119
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Affiliation(s)
- Güney Akbalik
- Max Planck Institute for Brain Research, 60438 Frankfurt, Germany
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120
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Doll CA, Broadie K. Impaired activity-dependent neural circuit assembly and refinement in autism spectrum disorder genetic models. Front Cell Neurosci 2014; 8:30. [PMID: 24570656 PMCID: PMC3916725 DOI: 10.3389/fncel.2014.00030] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 01/21/2014] [Indexed: 01/23/2023] Open
Abstract
Early-use activity during circuit-specific critical periods refines brain circuitry by the coupled processes of eliminating inappropriate synapses and strengthening maintained synapses. We theorize these activity-dependent (A-D) developmental processes are specifically impaired in autism spectrum disorders (ASDs). ASD genetic models in both mouse and Drosophila have pioneered our insights into normal A-D neural circuit assembly and consolidation, and how these developmental mechanisms go awry in specific genetic conditions. The monogenic fragile X syndrome (FXS), a common cause of heritable ASD and intellectual disability, has been particularly well linked to defects in A-D critical period processes. The fragile X mental retardation protein (FMRP) is positively activity-regulated in expression and function, in turn regulates excitability and activity in a negative feedback loop, and appears to be required for the A-D remodeling of synaptic connectivity during early-use critical periods. The Drosophila FXS model has been shown to functionally conserve the roles of human FMRP in synaptogenesis, and has been centrally important in generating our current mechanistic understanding of the FXS disease state. Recent advances in Drosophila optogenetics, transgenic calcium reporters, highly-targeted transgenic drivers for individually-identified neurons, and a vastly improved connectome of the brain are now being combined to provide unparalleled opportunities to both manipulate and monitor A-D processes during critical period brain development in defined neural circuits. The field is now poised to exploit this new Drosophila transgenic toolbox for the systematic dissection of A-D mechanisms in normal versus ASD brain development, particularly utilizing the well-established Drosophila FXS disease model.
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Affiliation(s)
- Caleb A Doll
- Department of Biological Sciences, Vanderbilt University Nashville, TN, USA
| | - Kendal Broadie
- Department of Biological Sciences, Vanderbilt University Nashville, TN, USA ; Kennedy Center for Research on Human Development, Vanderbilt University Nashville, TN, USA
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