1
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Yi HB, Lee S, Seo K, Kim H, Kim M, Lee HS. Cellular and Biophysical Applications of Genetic Code Expansion. Chem Rev 2024. [PMID: 38753805 DOI: 10.1021/acs.chemrev.4c00112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2024]
Abstract
Despite their diverse functions, proteins are inherently constructed from a limited set of building blocks. These compositional constraints pose significant challenges to protein research and its practical applications. Strategically manipulating the cellular protein synthesis system to incorporate novel building blocks has emerged as a critical approach for overcoming these constraints in protein research and application. In the past two decades, the field of genetic code expansion (GCE) has achieved significant advancements, enabling the integration of numerous novel functionalities into proteins across a variety of organisms. This technological evolution has paved the way for the extensive application of genetic code expansion across multiple domains, including protein imaging, the introduction of probes for protein research, analysis of protein-protein interactions, spatiotemporal control of protein function, exploration of proteome changes induced by external stimuli, and the synthesis of proteins endowed with novel functions. In this comprehensive Review, we aim to provide an overview of cellular and biophysical applications that have employed GCE technology over the past two decades.
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Affiliation(s)
- Han Bin Yi
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Seungeun Lee
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Kyungdeok Seo
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Hyeongjo Kim
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Minah Kim
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Hyun Soo Lee
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
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2
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Højgaard K, Szöllősi B, Henningsen K, Minami N, Nakanishi N, Kaadt E, Tamura M, Morris RGM, Takeuchi T, Elfving B. Novelty-induced memory consolidation is accompanied by increased Agap3 transcription: a cross-species study. Mol Brain 2023; 16:69. [PMID: 37749596 PMCID: PMC10521532 DOI: 10.1186/s13041-023-01056-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 09/18/2023] [Indexed: 09/27/2023] Open
Abstract
Novelty-induced memory consolidation is a well-established phenomenon that depends on the activation of a locus coeruleus-hippocampal circuit. It is associated with the expression of activity-dependent genes that may mediate initial or cellular memory consolidation. Several genes have been identified to date, however, to fully understand the mechanisms of memory consolidation, additional candidates must be identified. In this cross-species study, we used a contextual novelty-exploration paradigm to identify changes in gene expression in the dorsal hippocampus of both mice and rats. We found that changes in gene expression following contextual novelty varied between the two species, with 9 genes being upregulated in mice and 3 genes in rats. Comparison across species revealed that ArfGAP with a GTPase domain, an ankyrin repeat and PH domain 3 (Agap3) was the only gene being upregulated in both, suggesting a potentially conserved role for Agap3. AGAP3 is known to regulate α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA)-type glutamate receptor trafficking in the synapse, which suggests that increased transcription of Agap3 may be involved in maintaining functional plasticity. While we identified several genes affected by contextual novelty exploration, we were unable to fully reverse these changes using SCH 23390, a dopamine D1/D5 receptor antagonist. Further research on the role of AGAP3 in novelty-induced memory consolidation could lead to better understanding of this process and guide future research.
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Affiliation(s)
- Kristoffer Højgaard
- Translational Neuropsychiatry Unit, Department of Clinical medicine, Aarhus University, Aarhus N, DK8200, Denmark
- Danish Research Institute of Translational Neuroscience - DANDRITE, Nordic-EMBL Partnership for Molecular Medicine, Aarhus University, Aarhus C, DK8000, Denmark
| | - Bianka Szöllősi
- Danish Research Institute of Translational Neuroscience - DANDRITE, Nordic-EMBL Partnership for Molecular Medicine, Aarhus University, Aarhus C, DK8000, Denmark
| | - Kim Henningsen
- Danish Research Institute of Translational Neuroscience - DANDRITE, Nordic-EMBL Partnership for Molecular Medicine, Aarhus University, Aarhus C, DK8000, Denmark
| | - Natsumi Minami
- Neuroscience Research Unit, Mitsubishi Tanabe Pharma Corporation, Kanagawa, 227-0033, Japan
| | - Nobuhiro Nakanishi
- Data Science Department, Mitsubishi Tanabe Pharma Corporation, Kanagawa, 227-0033, Japan
| | - Erik Kaadt
- Translational Neuropsychiatry Unit, Department of Clinical medicine, Aarhus University, Aarhus N, DK8200, Denmark
| | - Makoto Tamura
- Neuroscience Research Unit, Mitsubishi Tanabe Pharma Corporation, Kanagawa, 227-0033, Japan
- NeuroDiscovery Lab, Mitsubishi Tanabe Pharma Holdings America Inc, Cambridge, MA, 02139, USA
| | - Richard G M Morris
- Laboratory for Cognitive Neuroscience, Edinburgh Neuroscience, The University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - Tomonori Takeuchi
- Danish Research Institute of Translational Neuroscience - DANDRITE, Nordic-EMBL Partnership for Molecular Medicine, Aarhus University, Aarhus C, DK8000, Denmark.
- Center for Proteins in Memory - PROMEMO, Department of Biomedicine, Danish National Research Foundation, Aarhus University, Aarhus C, DK8000, Denmark.
- Gftd DeSci, Gftd DAO, Tokyo, 162-0044, Japan.
| | - Betina Elfving
- Translational Neuropsychiatry Unit, Department of Clinical medicine, Aarhus University, Aarhus N, DK8200, Denmark.
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Sunna S, Bowen C, Zeng H, Rayaprolu S, Kumar P, Bagchi P, Dammer EB, Guo Q, Duong DM, Bitarafan S, Natu A, Wood L, Seyfried NT, Rangaraju S. Cellular Proteomic Profiling Using Proximity Labeling by TurboID-NES in Microglial and Neuronal Cell Lines. Mol Cell Proteomics 2023; 22:100546. [PMID: 37061046 PMCID: PMC10205547 DOI: 10.1016/j.mcpro.2023.100546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 04/05/2023] [Accepted: 04/10/2023] [Indexed: 04/17/2023] Open
Abstract
Different brain cell types play distinct roles in brain development and disease. Molecular characterization of cell-specific mechanisms using cell type-specific approaches at the protein (proteomic) level can provide biological and therapeutic insights. To overcome the barriers of conventional isolation-based methods for cell type-specific proteomics, in vivo proteomic labeling with proximity-dependent biotinylation of cytosolic proteins using biotin ligase TurboID, coupled with mass spectrometry (MS) of labeled proteins, emerged as a powerful strategy for cell type-specific proteomics in the native state of cells without the need for cellular isolation. To complement in vivo proximity labeling approaches, in vitro studies are needed to ensure that cellular proteomes using the TurboID approach are representative of the whole-cell proteome and capture cellular responses to stimuli without disruption of cellular processes. To address this, we generated murine neuroblastoma (N2A) and microglial (BV2) lines stably expressing cytosolic TurboID to biotinylate the cellular proteome for downstream purification and analysis using MS. TurboID-mediated biotinylation captured 59% of BV2 and 65% of N2A proteomes under homeostatic conditions. TurboID labeled endolysosome, translation, vesicle, and signaling proteins in BV2 microglia and synaptic, neuron projection, and microtubule proteins in N2A neurons. TurboID expression and biotinylation minimally impacted homeostatic cellular proteomes of BV2 and N2A cells and did not affect lipopolysaccharide-mediated cytokine production or resting cellular respiration in BV2 cells. MS analysis of the microglial biotin-labeled proteins captured the impact of lipopolysaccharide treatment (>500 differentially abundant proteins) including increased canonical proinflammatory proteins (Il1a, Irg1, and Oasl1) and decreased anti-inflammatory proteins (Arg1 and Mgl2).
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Affiliation(s)
- Sydney Sunna
- Department of Neurology, Emory University, Atlanta Georgia, USA; Center for Neurodegenerative Diseases, Emory University, Atlanta, Georgia, USA
| | - Christine Bowen
- Department of Neurology, Emory University, Atlanta Georgia, USA; Center for Neurodegenerative Diseases, Emory University, Atlanta, Georgia, USA; Department of Biochemistry, Emory University, Atlanta, Georgia, USA
| | - Hollis Zeng
- Department of Neurology, Emory University, Atlanta Georgia, USA; Center for Neurodegenerative Diseases, Emory University, Atlanta, Georgia, USA
| | - Sruti Rayaprolu
- Department of Neurology, Emory University, Atlanta Georgia, USA; Center for Neurodegenerative Diseases, Emory University, Atlanta, Georgia, USA
| | - Prateek Kumar
- Department of Neurology, Emory University, Atlanta Georgia, USA; Center for Neurodegenerative Diseases, Emory University, Atlanta, Georgia, USA
| | - Pritha Bagchi
- Center for Neurodegenerative Diseases, Emory University, Atlanta, Georgia, USA; Department of Biochemistry, Emory University, Atlanta, Georgia, USA; Emory Integrated Proteomics Core, Emory University, Atlanta, Georgia, USA
| | - Eric B Dammer
- Center for Neurodegenerative Diseases, Emory University, Atlanta, Georgia, USA; Department of Biochemistry, Emory University, Atlanta, Georgia, USA; Emory Integrated Proteomics Core, Emory University, Atlanta, Georgia, USA
| | - Qi Guo
- Center for Neurodegenerative Diseases, Emory University, Atlanta, Georgia, USA; Department of Biochemistry, Emory University, Atlanta, Georgia, USA; Emory Integrated Proteomics Core, Emory University, Atlanta, Georgia, USA
| | - Duc M Duong
- Center for Neurodegenerative Diseases, Emory University, Atlanta, Georgia, USA; Department of Biochemistry, Emory University, Atlanta, Georgia, USA; Emory Integrated Proteomics Core, Emory University, Atlanta, Georgia, USA
| | - Sara Bitarafan
- George W. Woodruff School of Mechanical Engineering, Wallace H. Coulter Department of Biomedical Engineering, and Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Aditya Natu
- Department of Neurology, Emory University, Atlanta Georgia, USA; Center for Neurodegenerative Diseases, Emory University, Atlanta, Georgia, USA
| | - Levi Wood
- George W. Woodruff School of Mechanical Engineering, Wallace H. Coulter Department of Biomedical Engineering, and Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Nicholas T Seyfried
- Department of Neurology, Emory University, Atlanta Georgia, USA; Center for Neurodegenerative Diseases, Emory University, Atlanta, Georgia, USA; Department of Biochemistry, Emory University, Atlanta, Georgia, USA; Emory Integrated Proteomics Core, Emory University, Atlanta, Georgia, USA.
| | - Srikant Rangaraju
- Department of Neurology, Emory University, Atlanta Georgia, USA; Center for Neurodegenerative Diseases, Emory University, Atlanta, Georgia, USA.
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Zimbelman AR, Wong B, Murray CH, Wolf ME, Stefanik MT. Dopamine D1 and NMDA receptor co-regulation of protein translation in cultured nucleus accumbens neurons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.02.535293. [PMID: 37034633 PMCID: PMC10081306 DOI: 10.1101/2023.04.02.535293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
Abstract
Protein translation is essential for some forms of synaptic plasticity. We used nucleus accumbens (NAc) medium spiny neurons (MSN), co-cultured with cortical neurons to restore excitatory synapses, to examine whether dopamine modulates protein translation in NAc MSN. FUNCAT was used to measure translation in MSNs under basal conditions and after disinhibiting excitatory transmission using the GABAA receptor antagonist bicuculline (2 hr). Under basal conditions, translation was not altered by the D1-class receptor (D1R) agonist SKF81297 or the D2-class receptor (D2R) agonist quinpirole. Bicuculline alone robustly increased translation. This was reversed by quinpirole but not SKF81297. It was also reversed by co-incubation with the D1R antagonist SCH23390, but not the D2R antagonist eticlopride, suggesting dopaminergic tone at D1Rs. This was surprising because no dopamine neurons are present. An alternative explanation is that bicuculline activates translation by increasing glutamate tone at NMDA receptors (NMDAR) within D1R/NMDAR heteromers, which have been described in other cell types. Supporting this, immunocytochemistry and proximity ligation assays revealed D1/NMDAR heteromers on NAc cells both in vitro and in vivo. Further, bicuculline's effect was reversed to the same extent by SCH23390 alone, the NMDAR antagonist APV alone, or SCH23390+APV. These results suggest that: 1) excitatory synaptic transmission stimulates translation in NAc MSNs, 2) this is opposed when glutamate activates D1R/NMDAR heteromers, even in the absence of dopamine, and 3) antagonist occupation of D1Rs within the heteromers prevents their activation. Our study is the first to suggest a role for D2 receptors and D1R/NMDAR heteromers in regulating protein translation.
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Affiliation(s)
- Alexa R. Zimbelman
- Department of Psychology and Neuroscience, North Central College, Naperville, IL 60540
| | - Benjamin Wong
- Department of Psychology and Neuroscience, North Central College, Naperville, IL 60540
| | - Conor H. Murray
- Department of Neuroscience, The Chicago Medical School at Rosalind Franklin University of Medicine and Science, North Chicago, IL, 60064
- Present address: Department of Psychiatry and Behavioral Neuroscience, University of Chicago, Chicago, IL
| | - Marina E. Wolf
- Department of Neuroscience, The Chicago Medical School at Rosalind Franklin University of Medicine and Science, North Chicago, IL, 60064
- These authors contributed equally
- Present address: Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR 97212
| | - Michael T. Stefanik
- Department of Psychology and Neuroscience, North Central College, Naperville, IL 60540
- Department of Neuroscience, The Chicago Medical School at Rosalind Franklin University of Medicine and Science, North Chicago, IL, 60064
- These authors contributed equally
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5
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Elder MK, Erdjument-Bromage H, Oliveira MM, Mamcarz M, Neubert TA, Klann E. Age-dependent shift in the de novo proteome accompanies pathogenesis in an Alzheimer's disease mouse model. Commun Biol 2021; 4:823. [PMID: 34193971 PMCID: PMC8245541 DOI: 10.1038/s42003-021-02324-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 06/02/2021] [Indexed: 12/13/2022] Open
Abstract
Alzheimer's disease (AD) is an age-related neurodegenerative disorder associated with memory loss, but the AD-associated neuropathological changes begin years before memory impairments. Investigation of the early molecular abnormalities in AD might offer innovative opportunities to target memory impairment prior to onset. Decreased protein synthesis plays a fundamental role in AD, yet the consequences of this dysregulation for cellular function remain unknown. We hypothesize that alterations in the de novo proteome drive early metabolic alterations in the hippocampus that persist throughout AD progression. Using a combinatorial amino acid tagging approach to selectively label and enrich newly synthesized proteins, we found that the de novo proteome is disturbed in young APP/PS1 mice prior to symptom onset, affecting the synthesis of multiple components of the synaptic, lysosomal, and mitochondrial pathways. Furthermore, the synthesis of large clusters of ribosomal subunits were affected throughout development. Our data suggest that large-scale changes in protein synthesis could underlie cellular dysfunction in AD.
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Affiliation(s)
- Megan K Elder
- Center for Neural Science, New York University, New York, NY, USA
| | - Hediye Erdjument-Bromage
- Department of Cell Biology, New York University Grossman School of Medicine, New York, NY, USA
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York University Grossman School of Medicine, New York, NY, USA
| | | | - Maggie Mamcarz
- Center for Neural Science, New York University, New York, NY, USA
| | - Thomas A Neubert
- Department of Cell Biology, New York University Grossman School of Medicine, New York, NY, USA
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York University Grossman School of Medicine, New York, NY, USA
| | - Eric Klann
- Center for Neural Science, New York University, New York, NY, USA.
- NYU Neuroscience Institute, New York University Grossman School of Medicine, New York, NY, USA.
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6
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Minati L, Firrito C, Del Piano A, Peretti A, Sidoli S, Peroni D, Belli R, Gandolfi F, Romanel A, Bernabo P, Zasso J, Quattrone A, Guella G, Lauria F, Viero G, Clamer M. One-shot analysis of translated mammalian lncRNAs with AHARIBO. eLife 2021; 10:59303. [PMID: 33594971 PMCID: PMC7932693 DOI: 10.7554/elife.59303] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 02/16/2021] [Indexed: 12/12/2022] Open
Abstract
A vast portion of the mammalian genome is transcribed as long non-coding RNAs (lncRNAs) acting in the cytoplasm with largely unknown functions. Surprisingly, lncRNAs have been shown to interact with ribosomes, encode peptides, or act as ribosome sponges. These functions still remain mostly undetected and understudied owing to the lack of efficient tools for genome-wide simultaneous identification of ribosome-associated and peptide-producing lncRNAs. Here, we present AHA-mediated RIBOsome isolation (AHARIBO), a method for the detection of lncRNAs either untranslated, but associated with ribosomes, or encoding small peptides. Using AHARIBO in mouse embryonic stem cells during neuronal differentiation, we isolated ribosome-protected RNA fragments, translated RNAs, and corresponding de novo synthesized peptides. Besides identifying mRNAs under active translation and associated ribosomes, we found and distinguished lncRNAs acting as ribosome sponges or encoding micropeptides, laying the ground for a better functional understanding of hundreds of lncRNAs.
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Affiliation(s)
| | | | | | | | - Simone Sidoli
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, United States
| | - Daniele Peroni
- Mass Spectrometry Facility, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Romina Belli
- Mass Spectrometry Facility, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Francesco Gandolfi
- Laboratory of Bioinformatics and Computational Genomics, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Alessandro Romanel
- Laboratory of Bioinformatics and Computational Genomics, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | | | - Jacopo Zasso
- Laboratory of Translational Genomics, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Alessandro Quattrone
- Laboratory of Translational Genomics, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | | | - Fabio Lauria
- Institute of Biophysics, CNR Unit at Trento, Trento, Italy
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Minehart JA, Speer CM. A Picture Worth a Thousand Molecules-Integrative Technologies for Mapping Subcellular Molecular Organization and Plasticity in Developing Circuits. Front Synaptic Neurosci 2021; 12:615059. [PMID: 33469427 PMCID: PMC7813761 DOI: 10.3389/fnsyn.2020.615059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 12/07/2020] [Indexed: 12/23/2022] Open
Abstract
A key challenge in developmental neuroscience is identifying the local regulatory mechanisms that control neurite and synaptic refinement over large brain volumes. Innovative molecular techniques and high-resolution imaging tools are beginning to reshape our view of how local protein translation in subcellular compartments drives axonal, dendritic, and synaptic development and plasticity. Here we review recent progress in three areas of neurite and synaptic study in situ-compartment-specific transcriptomics/translatomics, targeted proteomics, and super-resolution imaging analysis of synaptic organization and development. We discuss synergies between sequencing and imaging techniques for the discovery and validation of local molecular signaling mechanisms regulating synaptic development, plasticity, and maintenance in circuits.
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Affiliation(s)
| | - Colenso M. Speer
- Department of Biology, University of Maryland, College Park, MD, United States
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Ross AB, Langer JD, Jovanovic M. Proteome Turnover in the Spotlight: Approaches, Applications, and Perspectives. Mol Cell Proteomics 2020; 20:100016. [PMID: 33556866 PMCID: PMC7950106 DOI: 10.1074/mcp.r120.002190] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 11/25/2020] [Accepted: 11/30/2020] [Indexed: 01/17/2023] Open
Abstract
In all cells, proteins are continuously synthesized and degraded to maintain protein homeostasis and modify gene expression levels in response to stimuli. Collectively, the processes of protein synthesis and degradation are referred to as protein turnover. At a steady state, protein turnover is constant to maintain protein homeostasis, but in dynamic responses, proteins change their rates of synthesis and degradation to adjust their proteomes to internal or external stimuli. Thus, probing the kinetics and dynamics of protein turnover lends insight into how cells regulate essential processes such as growth, differentiation, and stress response. Here, we outline historical and current approaches to measuring the kinetics of protein turnover on a proteome-wide scale in both steady-state and dynamic systems, with an emphasis on metabolic tracing using stable isotope-labeled amino acids. We highlight important considerations for designing proteome turnover experiments, key biological findings regarding the conserved principles of proteome turnover regulation, and future perspectives for both technological and biological investigation.
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Affiliation(s)
- Alison Barbara Ross
- Department of Biological Sciences, Columbia University, New York, New York, USA
| | - Julian David Langer
- Proteomics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany; Proteomics, Max Planck Institute for Brain Research, Frankfurt am Main, Germany.
| | - Marko Jovanovic
- Department of Biological Sciences, Columbia University, New York, New York, USA.
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Klein ME, Younts TJ, Cobo CF, Buxbaum AR, Aow J, Erdjument-Bromage H, Richard S, Malinow R, Neubert TA, Singer RH, Castillo PE, Jordan BA. Sam68 Enables Metabotropic Glutamate Receptor-Dependent LTD in Distal Dendritic Regions of CA1 Hippocampal Neurons. Cell Rep 2020; 29:1789-1799.e6. [PMID: 31722197 PMCID: PMC6871770 DOI: 10.1016/j.celrep.2019.10.030] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 08/15/2019] [Accepted: 10/08/2019] [Indexed: 12/13/2022] Open
Abstract
The transport and translation of dendritic mRNAs by RNA-binding proteins (RBPs) allows for spatially restricted gene expression in neuronal processes. Although local translation in neuronal dendrites is now well documented, there is little evidence for corresponding effects on local synaptic function. Here, we report that the RBP Sam68 promotes the localization and translation of Arc mRNA preferentially in distal dendrites of rodent hippocampal CA1 pyramidal neurons. Consistent with Arc function in translation-dependent synaptic plasticity, we find that Sam68 knockout (KO) mice display impaired metabotropic glutamate-receptor-dependent long-term depression (mGluR-LTD) and impaired structural plasticity exclusively at distal Schaffer-collateral synapses. Moreover, by using quantitative proteomics, we find that the Sam68 interactome contains numerous regulators of mRNA translation and synaptic function. This work identifies an important player in Arc expression, provides a general framework for Sam68 regulation of protein synthesis, and uncovers a mechanism that enables the precise spatiotemporal expression of long-term plasticity throughout neurons.
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Affiliation(s)
- Matthew E Klein
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA
| | - Thomas J Younts
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA
| | - Carmen Freire Cobo
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA
| | - Adina R Buxbaum
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA; Center for Neural Circuits and Behavior, Department of Neuroscience and Section for Neurobiology, Division of Biology, University of California at San Diego, San Diego, CA 92093, USA
| | - Jonathan Aow
- Center for Neural Circuits and Behavior, Department of Neuroscience and Section for Neurobiology, Division of Biology, University of California at San Diego, San Diego, CA 92093, USA
| | - Hediye Erdjument-Bromage
- Department of Cell Biology and Kimmel Center for Biology and Medicine, Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY 10016, USA
| | - Stéphane Richard
- Segal Cancer Center, Lady Davis Institute for Medical Research and Departments of Oncology and Medicine, McGill University, Montréal, QC H3T 1E2, Canada
| | - Roberto Malinow
- Center for Neural Circuits and Behavior, Department of Neuroscience and Section for Neurobiology, Division of Biology, University of California at San Diego, San Diego, CA 92093, USA
| | - Thomas A Neubert
- Department of Cell Biology and Kimmel Center for Biology and Medicine, Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY 10016, USA
| | - Robert H Singer
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA; Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA; Janelia Research Campus of the Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Pablo E Castillo
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA
| | - Bryen A Jordan
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA; Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA.
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10
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Biever A, Glock C, Tushev G, Ciirdaeva E, Dalmay T, Langer JD, Schuman EM. Monosomes actively translate synaptic mRNAs in neuronal processes. Science 2020; 367:367/6477/eaay4991. [PMID: 32001627 DOI: 10.1126/science.aay4991] [Citation(s) in RCA: 128] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 10/29/2019] [Accepted: 12/18/2019] [Indexed: 12/13/2022]
Abstract
To accommodate their complex morphology, neurons localize messenger RNAs (mRNAs) and ribosomes near synapses to produce proteins locally. However, a relative paucity of polysomes (considered the active sites of translation) detected in electron micrographs of neuronal processes has suggested a limited capacity for local protein synthesis. In this study, we used polysome profiling together with ribosome footprinting of microdissected rodent synaptic regions to reveal a surprisingly high number of dendritic and/or axonal transcripts preferentially associated with monosomes (single ribosomes). Furthermore, the neuronal monosomes were in the process of active protein synthesis. Most mRNAs showed a similar translational status in the cell bodies and neurites, but some transcripts exhibited differential ribosome occupancy in the compartments. Monosome-preferring transcripts often encoded high-abundance synaptic proteins. Thus, monosome translation contributes to the local neuronal proteome.
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Affiliation(s)
- Anne Biever
- Max Planck Institute for Brain Research, Frankfurt, Germany
| | - Caspar Glock
- Max Planck Institute for Brain Research, Frankfurt, Germany
| | - Georgi Tushev
- Max Planck Institute for Brain Research, Frankfurt, Germany
| | | | - Tamas Dalmay
- Max Planck Institute for Brain Research, Frankfurt, Germany
| | - Julian D Langer
- Max Planck Institute for Brain Research, Frankfurt, Germany.,Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Erin M Schuman
- Max Planck Institute for Brain Research, Frankfurt, Germany.
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11
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Roy R, Shiina N, Wang DO. More dynamic, more quantitative, unexpectedly intricate: Advanced understanding on synaptic RNA localization in learning and memory. Neurobiol Learn Mem 2019; 168:107149. [PMID: 31881355 DOI: 10.1016/j.nlm.2019.107149] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 10/25/2019] [Accepted: 12/23/2019] [Indexed: 01/13/2023]
Abstract
Synaptic signaling exhibits great diversity, complexity, and plasticity which necessitates maintenance and rapid modification of a local proteome. One solution neurons actively exploit to meet such demands is the strategic deposition of mRNAs encoding proteins for both basal and experience-driven activities into ribonucleoprotein complexes at the synapse. Transcripts localized in this manner can be rapidly accessed for translation in response to a diverse range of stimuli in a temporal- and spatially-restricted manner. Here we review recent findings on localized RNAs and RNA binding proteins in the context of learning and memory, as revealed by cutting-edge in-vitro and in-vivo technologies capable of yielding quantitative and dynamic information. The new technologies include proteomic and transcriptomic analyses, high-resolution multiplexed RNA imaging, single-molecule RNA tracking in living neurons, animal models and human neuron cell models. Among many recent advances in the field, RNA chemical modification has emerged as one of the new regulatory layers of gene expression at synapse that is complex and yet largely unexplored. These exciting new discoveries have enhanced our understanding of the modulation mechanisms of synaptic gene expression and their roles in cognition.
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Affiliation(s)
- Rohini Roy
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Kyoto, Japan; Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Nobuyuki Shiina
- Laboratory of Neuronal Cell Biology, National Institute for Basic Biology, Okazaki, Japan; Department of Basic Biology, SOKENDAI, Okazaki, Japan; Exploratory Research Center on Life and Living Systems, Okazaki, Japan.
| | - Dan Ohtan Wang
- Wuya College of Innovation, Shenyang Pharmaceutical University, Liaoning, China; Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Kyoto, Japan; The Keihanshin Consortium for Fostering the Next Generation of Global Leaders in Research (K-CONNEX), Kyoto University, Kyoto, Japan.
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12
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Koren SA, Gillett DA, D'Alton SV, Hamm MJ, Abisambra JF. Proteomic Techniques to Examine Neuronal Translational Dynamics. Int J Mol Sci 2019; 20:ijms20143524. [PMID: 31323794 PMCID: PMC6678648 DOI: 10.3390/ijms20143524] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 07/08/2019] [Accepted: 07/15/2019] [Indexed: 01/30/2023] Open
Abstract
Impairments in translation have been increasingly implicated in the pathogenesis and progression of multiple neurodegenerative diseases. Assessing the spatiotemporal dynamics of translation in the context of disease is a major challenge. Recent developments in proteomic analyses have enabled the resolution of nascent peptides in a short timescale on the order of minutes. In addition, a quantitative analysis of translation has progressed in vivo, showing remarkable potential for coupling these techniques with cognitive and behavioral outcomes. Here, we review these modern approaches to measure changes in translation and ribosomal function with a specific focus on current applications in the mammalian brain and in the study of neurodegenerative diseases.
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Affiliation(s)
- Shon A Koren
- Department of Neuroscience and Center for Translational Research in Neurodegenerative Disease, University of Florida, Gainesville, FL 32601, USA
| | - Drew A Gillett
- Department of Neuroscience and Center for Translational Research in Neurodegenerative Disease, University of Florida, Gainesville, FL 32601, USA
| | - Simon V D'Alton
- Department of Neuroscience and Center for Translational Research in Neurodegenerative Disease, University of Florida, Gainesville, FL 32601, USA
| | - Matthew J Hamm
- Department of Neuroscience and Center for Translational Research in Neurodegenerative Disease, University of Florida, Gainesville, FL 32601, USA
| | - Jose F Abisambra
- Department of Neuroscience and Center for Translational Research in Neurodegenerative Disease, University of Florida, Gainesville, FL 32601, USA.
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13
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Song H, Li H, Guo S, Pan Y, Fu Y, Zhou Z, Li Z, Wen X, Sun X, He B, Gu H, Zhao Q, Wang C, An P, Luo S, Hu Y, Xie X, Lu B. Targeting Gpr52 lowers mutant HTT levels and rescues Huntington's disease-associated phenotypes. Brain 2019; 141:1782-1798. [PMID: 29608652 PMCID: PMC5972579 DOI: 10.1093/brain/awy081] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 02/03/2018] [Indexed: 01/30/2023] Open
Abstract
See Huang and Gitler (doi:10.1093/brain/awy112) for a scientific commentary on this article. Lowering the levels of disease-causing proteins is an attractive treatment strategy for neurodegenerative disorders, among which Huntington’s disease is an appealing disease for testing this strategy because of its monogenetic nature. Huntington’s disease is mainly caused by cytotoxicity of the mutant HTT protein with an expanded polyglutamine repeat tract. Lowering the soluble mutant HTT may reduce its downstream toxicity and provide potential treatment for Huntington’s disease. This is hard to achieve by small-molecule compound drugs because of a lack of effective targets. Here we demonstrate Gpr52, an orphan G protein-coupled receptor, as a potential Huntington’s disease drug target. Knocking-out Gpr52 significantly reduces mutant HTT levels in the striatum and rescues Huntington’s disease-associated behavioural phenotypes in a knock-in Huntington’s disease mouse model expressing endogenous mutant Htt. Importantly, a novel Gpr52 antagonist E7 reduces mutant HTT levels and rescues Huntington’s disease-associated phenotypes in cellular and mouse models. Our study provides an entry point for Huntington’s disease drug discovery by targeting Gpr52.
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Affiliation(s)
- Haikun Song
- Neurology Department at Huashan Hospital, State Key Laboratory of Medical Neurobiology, School of Life Sciences, Fudan University, Shanghai, China
| | - Hexuan Li
- Neurology Department at Huashan Hospital, State Key Laboratory of Medical Neurobiology, School of Life Sciences, Fudan University, Shanghai, China
| | - Shimeng Guo
- CAS Key Laboratory of Receptor Research, National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yuyin Pan
- Neurology Department at Huashan Hospital, State Key Laboratory of Medical Neurobiology, School of Life Sciences, Fudan University, Shanghai, China
| | - Yuhua Fu
- Neurology Department at Huashan Hospital, State Key Laboratory of Medical Neurobiology, School of Life Sciences, Fudan University, Shanghai, China
| | - Zijian Zhou
- Neurology Department at Huashan Hospital, State Key Laboratory of Medical Neurobiology, School of Life Sciences, Fudan University, Shanghai, China
| | - Zhaoyang Li
- Neurology Department at Huashan Hospital, State Key Laboratory of Medical Neurobiology, School of Life Sciences, Fudan University, Shanghai, China
| | - Xue Wen
- Neurology Department at Huashan Hospital, State Key Laboratory of Medical Neurobiology, School of Life Sciences, Fudan University, Shanghai, China
| | - Xiaoli Sun
- Neurology Department at Huashan Hospital, State Key Laboratory of Medical Neurobiology, School of Life Sciences, Fudan University, Shanghai, China
| | - Bingqing He
- CAS Key Laboratory of Receptor Research, National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Haifeng Gu
- CAS Key Laboratory of Receptor Research, National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Quan Zhao
- Neurology Department at Huashan Hospital, State Key Laboratory of Medical Neurobiology, School of Life Sciences, Fudan University, Shanghai, China
| | - Cen Wang
- Neurology Department at Huashan Hospital, State Key Laboratory of Medical Neurobiology, School of Life Sciences, Fudan University, Shanghai, China
| | - Ping An
- Neurology Department at Huashan Hospital, State Key Laboratory of Medical Neurobiology, School of Life Sciences, Fudan University, Shanghai, China
| | - Shouqing Luo
- Peninsula Schools of Medicine and Dentistry, Institute of Translational and Stratified Medicine, University of Plymouth, Research Way, Plymouth, UK
| | - Youhong Hu
- CAS Key Laboratory of Receptor Research, National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Xin Xie
- CAS Key Laboratory of Receptor Research, National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Boxun Lu
- Neurology Department at Huashan Hospital, State Key Laboratory of Medical Neurobiology, School of Life Sciences, Fudan University, Shanghai, China
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14
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Madan JS, Gupta K, Chattarji S, Bhattacharya A. Hippocampal and amygdalar cell-specific translation is similar soon after stress but diverge over time. Hippocampus 2019; 28:441-452. [PMID: 29626848 DOI: 10.1002/hipo.22845] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 03/16/2018] [Accepted: 03/26/2018] [Indexed: 01/16/2023]
Abstract
Stress is known to cause contrasting patterns of morphological and physiological plasticity in the hippocampus and amygdala. An obligatory cellular process underlying such neural changes is de novo translation and alterations in protein expression. Yet the nature of the translational response to stress in neurons remains largely unexplored. Even less is known about how glia are affected. Using a click-chemistry-based method to label the de novo proteome in live brain slices, we monitored translation in neurons and astrocytes of the basolateral amygdala (BLA) and dorsal hippocampal area CA3 (dCA3) in rats at different time-points after a single 2-hr exposure to immobilization stress. We observed enhancements in neuronal translation in both brain regions 1 hour after stress. This initial increase persisted in the BLA up to 10 days afterwards. In contrast, dCA3 neuronal translation gradually decreased to below control levels 10 days later. Translation profiles of dCA3 astrocytes followed timelines similar to neurons, but in BLA astrocytes translation peaked 1 day later and remained elevated 10 days later. Together our results demonstrate that stress causes an immediate upregulation of protein synthesis in both amygdalar and hippocampal neurons and astrocytes. However, these two areas eventually exhibit opposite temporal profiles of protein expression well after the end of stress. These findings identify new metrics of stress-induced plasticity at the level of cell-type specific proteomic landscape that may provide important insights into the molecular basis of the divergent temporal effects of stress across brain regions and biological scales.
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Affiliation(s)
- Jesvin S Madan
- National Centre for Biological Sciences, Tata Institute for Fundamental Research, Bangalore, 560065, India
| | - Kanika Gupta
- National Centre for Biological Sciences, Tata Institute for Fundamental Research, Bangalore, 560065, India
| | - Sumantra Chattarji
- National Centre for Biological Sciences, Tata Institute for Fundamental Research, Bangalore, 560065, India.,Centre for Brain Development and Repair, Institute for Stem Cell Biology and Regenerative Medicine, Bangalore, 560065, India.,Center for Integrative Physiology, Deanery of Biomedical Sciences, University of Edinburgh, Hugh Robson Building, George Square, Edinburgh, EH89XD, United Kingdom
| | - Aditi Bhattacharya
- Centre for Brain Development and Repair, Institute for Stem Cell Biology and Regenerative Medicine, Bangalore, 560065, India
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15
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Biever A, Donlin-Asp PG, Schuman EM. Local translation in neuronal processes. Curr Opin Neurobiol 2019; 57:141-148. [PMID: 30861464 DOI: 10.1016/j.conb.2019.02.008] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 02/07/2019] [Indexed: 12/19/2022]
Abstract
Neurons exhibit a unique degree of spatial compartmentalization and are able to maintain and remodel their proteomes independently from the cell body. While much effort has been devoted to understanding the capacity and role for local protein synthesis in dendrites and spines, local mRNA translation in mature axons, projecting over distances up to a meter, has received much less attention. Also, little is known about the spatio-temporal dynamics of axonal and dendritic gene expression as function of mRNA abundance, protein synthesis and degradation. Here, we summarize key recent findings that have shaped our knowledge of the precise location of local protein production and discuss unique strategies used by neurons to shape presynaptic and postsynaptic proteomes.
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Affiliation(s)
- Anne Biever
- Max Planck Institute for Brain Research, Frankfurt am Main, Germany
| | | | - Erin M Schuman
- Max Planck Institute for Brain Research, Frankfurt am Main, Germany.
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16
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J AJ, M I, A G, S A G, S SR, P SL, M A, N R K, K G, N A. Biomimetic strategies to design metallic proteins for detoxification of hazardous heavy metal. JOURNAL OF HAZARDOUS MATERIALS 2018; 358:92-100. [PMID: 29990822 DOI: 10.1016/j.jhazmat.2018.06.057] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 06/24/2018] [Accepted: 06/25/2018] [Indexed: 06/08/2023]
Abstract
Discharge of hazardous heavy metals in to the environment poses a serious threat to the ecosystem owing to its non-degradability and indestructability. Physical and chemical techniques for the removal of heavy metals from industrial effluent is expensive and causes secondary pollution. On the other hand, biological processes using microorganisms play a vital role due to their large surface area to volume ratio, which increases the interactions with metal ions present in the environment. Here, we developed a third generation biological tool for the removal of heavy metal (copper) from the effluent through the biosynthesis of intracellular and surface displayed metallic proteins with novel metal co-ordination chemistry. We evaluated the cell viability for maximum heavy metal adsorption and metal tolerance of synthesized congener metallic proteins. Finally, to eliminate the cost associated with incorporation of metal binding aminoacid, we have introduced a genetic circuit in order to evolve a novel magnetotactic bacterium. The bioreactor studies of the consortia of metallic protein expressing cells immobilized on functionalized granular activated carbon revealed that 97% of copper was adsorbed from the industrial effluent. It is evident that the use of congener metallic proteins will be a futuristic approach for the treatment of wastewater facilitating environmental detoxification.
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Affiliation(s)
- Asuma Janeena J
- Department of Biochemistry and Biotechnology, Council of Scientific and Industrial Research (CSIR)-Central Leather Research Institute (CLRI), Chennai, India; Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh, India
| | - Ilamaran M
- Department of Biochemistry and Biotechnology, Council of Scientific and Industrial Research (CSIR)-Central Leather Research Institute (CLRI), Chennai, India
| | - George A
- Department of Biochemistry and Biotechnology, Council of Scientific and Industrial Research (CSIR)-Central Leather Research Institute (CLRI), Chennai, India
| | - George S A
- Department of Biochemistry and Biotechnology, Council of Scientific and Industrial Research (CSIR)-Central Leather Research Institute (CLRI), Chennai, India
| | - Sriram Raghavan S
- Department of Crystallography and Biophysics, Madras University, Chennai, India
| | - Surya Lakshmi P
- Department of Biochemistry and Biotechnology, Council of Scientific and Industrial Research (CSIR)-Central Leather Research Institute (CLRI), Chennai, India
| | - Aarthy M
- CSIR-National Environmental Engineering Research Institute (NEERI), Chennai Zonal Laboratory, Chennai, India
| | - Kamini N R
- Department of Biochemistry and Biotechnology, Council of Scientific and Industrial Research (CSIR)-Central Leather Research Institute (CLRI), Chennai, India
| | - Gunasekaran K
- Department of Crystallography and Biophysics, Madras University, Chennai, India
| | - Ayyadurai N
- Department of Biochemistry and Biotechnology, Council of Scientific and Industrial Research (CSIR)-Central Leather Research Institute (CLRI), Chennai, India.
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17
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Ma Y, Yates JR. Proteomics and pulse azidohomoalanine labeling of newly synthesized proteins: what are the potential applications? Expert Rev Proteomics 2018; 15:545-554. [PMID: 30005169 PMCID: PMC6329588 DOI: 10.1080/14789450.2018.1500902] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
INTRODUCTION Measuring the immediate changes in cells that arise from changing environmental conditions is crucial to understanding the underlying mechanisms involved. These changes can be measured with metabolic stable isotope fully labeled proteomes, but requires looking for changes in the midst of a large background. In addition, labeling efficiency can be an issue in primary and fully differentiated cells. Area covered: Azidohomoalanine (AHA), an analog of methionine, can be accepted by cellular translational machinery and incorporated into newly synthesized proteins (NSPs). AHA-NSPs can be coupled to biotin via CuAAC-mediated click-chemistry and enriched using avidin-based affinity purification. Thus, AHA-containing proteins or peptides can be enriched and efficiently separated from the whole proteome. In this review, we describe the development of mass spectrometry (MS) based AHA strategies and discuss their potential to measure proteins involved in immune response, secretome, gut microbiome, and proteostasis as well as their potential for clinical uses. Expert commentary: AHA strategies have been used to identify synthesis activity and to compare two biological conditions in various biological model organisms. In combination with instrument development, improved sample preparation and fractionation strategies, MS-based AHA strategies have the potential for broad application, and the methods should translate into clinical use.
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Affiliation(s)
- Yuanhui Ma
- a Departments of Molecular Medicine and Neurobiology , The Scripps Research Institute , La Jolla , CA , USA
| | - John R Yates
- a Departments of Molecular Medicine and Neurobiology , The Scripps Research Institute , La Jolla , CA , USA
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18
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Proteomic approaches beyond expression profiling and PTM analysis. Anal Bioanal Chem 2018; 410:4051-4060. [PMID: 29637251 DOI: 10.1007/s00216-018-1021-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 02/22/2018] [Accepted: 03/12/2018] [Indexed: 12/15/2022]
Abstract
Essentially, all cellular functions are executed by proteins. Different physiological and pathological conditions dynamically control various properties of proteins, including expression levels, post-translational modifications (PTMs), protein-protein interactions, enzymatic activity, etc. Thus far, the vast majority of proteomic efforts have been focused on quantitative profiling of protein abundance/expression and their PTMs. In this article, we review some recent exciting progress in the development of proteomic approaches to examine protein functions from perspectives other than expression levels and PTMs. Specifically, we discuss advancements in proximity-based labeling, analysis of protein termini and newly synthesized proteins, and activity-based protein profiling.
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19
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Abstract
Koppel & Fainzilber review translatomics and proteomics methods for studying protein synthesis at subcellular resolution.
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Affiliation(s)
- Indrek Koppel
- Department of Biomolecular Sciences
- Weizmann Institute of Science
- 76100 Rehovot
- Israel
| | - Mike Fainzilber
- Department of Biomolecular Sciences
- Weizmann Institute of Science
- 76100 Rehovot
- Israel
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20
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Estell C, Stamatidou E, El-Messeiry S, Hamilton A. In situ imaging of mitochondrial translation shows weak correlation with nucleoid DNA intensity and no suppression during mitosis. J Cell Sci 2017; 130:4193-4199. [PMID: 29122981 DOI: 10.1242/jcs.206714] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 11/01/2017] [Indexed: 11/20/2022] Open
Abstract
Although mitochondrial translation produces only 13 proteins, we show here how this process can be visualised and detected in situ by fluorescence microscopy with a simple, rapid and inexpensive procedure using non-canonical amino acid labelling and click chemistry. This allows visualisation of the translational output in different mitochondria within a cell, their position within that cell and a comparison of mitochondrial translation between cells. The most highly translationally active mitochondria were closest to the nucleus but were also found at the distal end of long cellular projections. There were substantial differences in translation between adjacent mitochondria and this did not readily correlate with apparent mitochondrial genome content. Mitochondrial translation was unchanged during mitosis when cytoplasmic translation was suppressed. This method will serve both fundamental cell biology and clinically orientated studies, in which mitochondrial function is a key parameter.
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Affiliation(s)
| | | | - Sarah El-Messeiry
- School of Medicine, Dentistry and Nursing, Glasgow University, Glasgow G12 8QQ, UK.,Department of Genetics, Faculty of Agriculture, Alexandria University, Alexandria, Egypt
| | - Andrew Hamilton
- School of Medicine, Dentistry and Nursing, Glasgow University, Glasgow G12 8QQ, UK
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21
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Locus Coeruleus and Dopamine-Dependent Memory Consolidation. Neural Plast 2017; 2017:8602690. [PMID: 29123927 PMCID: PMC5662828 DOI: 10.1155/2017/8602690] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Revised: 06/06/2017] [Accepted: 06/18/2017] [Indexed: 12/12/2022] Open
Abstract
Most everyday memories including many episodic-like memories that we may form automatically in the hippocampus (HPC) are forgotten, while some of them are retained for a long time by a memory stabilization process, called initial memory consolidation. Specifically, the retention of everyday memory is enhanced, in humans and animals, when something novel happens shortly before or after the time of encoding. Converging evidence has indicated that dopamine (DA) signaling via D1/D5 receptors in HPC is required for persistence of synaptic plasticity and memory, thereby playing an important role in the novelty-associated memory enhancement. In this review paper, we aim to provide an overview of the key findings related to D1/D5 receptor-dependent persistence of synaptic plasticity and memory in HPC, especially focusing on the emerging evidence for a role of the locus coeruleus (LC) in DA-dependent memory consolidation. We then refer to candidate brain areas and circuits that might be responsible for detection and transmission of the environmental novelty signal and molecular and anatomical evidence for the LC-DA system. We also discuss molecular mechanisms that might mediate the environmental novelty-associated memory enhancement, including plasticity-related proteins that are involved in initial memory consolidation processes in HPC.
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22
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Nascent Proteome Remodeling following Homeostatic Scaling at Hippocampal Synapses. Neuron 2017; 92:358-371. [PMID: 27764671 PMCID: PMC5078608 DOI: 10.1016/j.neuron.2016.09.058] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 09/16/2016] [Accepted: 09/27/2016] [Indexed: 12/16/2022]
Abstract
Homeostatic scaling adjusts the strength of synaptic connections up or down in response to large changes in input. To identify the landscape of proteomic changes that contribute to opposing forms of homeostatic plasticity, we examined the plasticity-induced changes in the newly synthesized proteome. Cultured rat hippocampal neurons underwent homeostatic up-scaling or down-scaling. We used BONCAT (bio-orthogonal non-canonical amino acid tagging) to metabolically label, capture, and identify newly synthesized proteins, detecting and analyzing 5,940 newly synthesized proteins using mass spectrometry and label-free quantitation. Neither up- nor down-scaling produced changes in the number of different proteins translated. Rather, up- and down-scaling elicited opposing translational regulation of several molecular pathways, producing targeted adjustments in the proteome. We discovered ∼300 differentially regulated proteins involved in neurite outgrowth, axon guidance, filopodia assembly, excitatory synapses, and glutamate receptor complexes. We also identified differentially regulated proteins that are associated with multiple diseases, including schizophrenia, epilepsy, and Parkinson's disease.
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23
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Rangaraju V, Tom Dieck S, Schuman EM. Local translation in neuronal compartments: how local is local? EMBO Rep 2017; 18:693-711. [PMID: 28404606 DOI: 10.15252/embr.201744045] [Citation(s) in RCA: 110] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 03/15/2017] [Accepted: 03/15/2017] [Indexed: 12/18/2022] Open
Abstract
Efficient neuronal function depends on the continued modulation of the local neuronal proteome. Local protein synthesis plays a central role in tuning the neuronal proteome at specific neuronal regions. Various aspects of translation such as the localization of translational machinery, spatial spread of the newly translated proteins, and their site of action are carried out in specialized neuronal subcompartments to result in a localized functional outcome. In this review, we focus on the various aspects of these local translation compartments such as size, biochemical and organelle composition, structural boundaries, and temporal dynamics. We also discuss the apparent absence of definitive components of translation in these local compartments and the emerging state-of-the-art tools that could help dissecting these conundrums in greater detail in the future.
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Affiliation(s)
- Vidhya Rangaraju
- Max Planck Institute for Brain Research, Frankfurt am Main, Germany
| | | | - Erin M Schuman
- Max Planck Institute for Brain Research, Frankfurt am Main, Germany
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24
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Schreiner D, Savas JN, Herzog E, Brose N, de Wit J. Synapse biology in the 'circuit-age'-paths toward molecular connectomics. Curr Opin Neurobiol 2017; 42:102-110. [PMID: 28033531 PMCID: PMC5316339 DOI: 10.1016/j.conb.2016.12.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 12/07/2016] [Accepted: 12/08/2016] [Indexed: 11/23/2022]
Abstract
The neural connectome is a critical determinant of brain function. Circuits of precisely wired neurons, and the features of transmission at the synapses connecting them, are thought to dictate information processing in the brain. While recent technological advances now allow to define the anatomical and functional neural connectome at unprecedented resolution, the elucidation of the molecular mechanisms that establish the precise patterns of connectivity and the functional characteristics of synapses has remained challenging. Here, we describe the power and limitations of genetic approaches in the analysis of mechanisms that control synaptic connectivity and function, and discuss how recent methodological developments in proteomics might be used to elucidate the molecular synaptic connectome that is at the basis of the neural connectome.
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Affiliation(s)
- Dietmar Schreiner
- Biozentrum, University of Basel, Klingelbergstraße 50-70, 4056 Basel, Switzerland; Institute of Neuroanatomy and Cell Biology, Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany
| | - Jeffrey N Savas
- Department of Neurology, Northwestern University, Feinberg School of Medicine, 303 East Chicago Avenue, Chicago, IL 60611, USA
| | - Etienne Herzog
- Univ. Bordeaux, IINS, UMR 5297, F-33000 Bordeaux, France; CNRS, IINS, UMR 5297, F-33000 Bordeaux, France
| | - Nils Brose
- Department of Molecular Neurobiology, Max Planck Institute of Experimental Medicine, Hermann-Rein-Straße 3, 37075 Göttingen, Germany
| | - Joris de Wit
- VIB Center for Brain and Disease Research, Herestraat 49, 3000 Leuven, Belgium; Department of Neurosciences, KU Leuven, Herestraat 49, 3000 Leuven, Belgium.
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25
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Dieterich DC, Kreutz MR. Proteomics of the Synapse--A Quantitative Approach to Neuronal Plasticity. Mol Cell Proteomics 2016; 15:368-81. [PMID: 26307175 PMCID: PMC4739661 DOI: 10.1074/mcp.r115.051482] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 07/29/2015] [Indexed: 11/06/2022] Open
Abstract
The advances in mass spectrometry based proteomics in the past 15 years have contributed to a deeper appreciation of protein networks and the composition of functional synaptic protein complexes. However, research on protein dynamics underlying core mechanisms of synaptic plasticity in brain lag far behind. In this review, we provide a synopsis on proteomic research addressing various aspects of synaptic function. We discuss the major topics in the study of protein dynamics of the chemical synapse and the limitations of current methodology. We highlight recent developments and the future importance of multidimensional proteomics and metabolic labeling. Finally, emphasis is given on the conceptual framework of modern proteomics and its current shortcomings in the quest to gain a deeper understanding of synaptic plasticity.
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Affiliation(s)
- Daniela C Dieterich
- From the ‡Institute for Pharmacology and Toxicology, Otto-von-Guericke University Magdeburg, Germany; Research Group Neuralomics, Leibniz Institute for Neurobiology Magdeburg, Germany; ¶Center for Behavioral Brain Sciences (CBBS), Magdeburg, Germany.
| | - Michael R Kreutz
- §RG Neuroplasticity, Leibniz Institute for Neurobiology, Magdeburg, Germany; ¶Center for Behavioral Brain Sciences (CBBS), Magdeburg, Germany.
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26
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27
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Müller A, Stellmacher A, Freitag CE, Landgraf P, Dieterich DC. Monitoring Astrocytic Proteome Dynamics by Cell Type-Specific Protein Labeling. PLoS One 2015; 10:e0145451. [PMID: 26690742 PMCID: PMC4686566 DOI: 10.1371/journal.pone.0145451] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 12/03/2015] [Indexed: 01/13/2023] Open
Abstract
The ability of the nervous system to undergo long-term plasticity is based on changes in cellular and synaptic proteomes. While many studies have explored dynamic alterations in neuronal proteomes during plasticity, there has been less attention paid to the astrocytic counterpart. Indeed, progress in identifying cell type-specific proteomes is limited owing to technical difficulties. Here, we present a cell type-specific metabolic tagging technique for a mammalian coculture model based on the bioorthogonal amino acid azidonorleucine and the mutated Mus musculus methionyl-tRNA synthetaseL274G enabling azidonorleucine introduction into de novo synthesized proteins. Azidonorleucine incorporation resulted in cell type-specific protein labeling and retained neuronal or astrocytic cell viability. Furthermore, we were able to label astrocytic de novo synthesized proteins and identified both Connexin-43 and 60S ribosomal protein L10a upregulated upon treatment with Brain-derived neurotrophic factor in astrocytes of a neuron-glia coculture. Taken together, we demonstrate the successful dissociation of astrocytic from neuronal proteomes by cell type-specific metabolic labeling offering new possibilities for the analyses of cell type-specific proteome dynamics.
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Affiliation(s)
- Anke Müller
- Neural Plasticity and Communication, Institute for Pharmacology and Toxicology, Otto–von–Guericke–University Magdeburg, Magdeburg, Germany
| | - Anne Stellmacher
- Neural Plasticity and Communication, Institute for Pharmacology and Toxicology, Otto–von–Guericke–University Magdeburg, Magdeburg, Germany
| | - Christine E. Freitag
- Research Group Neuralomics, Leibniz Institute for Neurobiology, Magdeburg, Germany
| | - Peter Landgraf
- Neural Plasticity and Communication, Institute for Pharmacology and Toxicology, Otto–von–Guericke–University Magdeburg, Magdeburg, Germany
| | - Daniela C. Dieterich
- Neural Plasticity and Communication, Institute for Pharmacology and Toxicology, Otto–von–Guericke–University Magdeburg, Magdeburg, Germany
- Research Group Neuralomics, Leibniz Institute for Neurobiology, Magdeburg, Germany
- Center for Behavioral Brain Sciences, Magdeburg, Germany
- * E-mail:
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28
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McClatchy DB, Ma Y, Liu C, Stein BD, Martínez-Bartolomé S, Vasquez D, Hellberg K, Shaw RJ, Yates JR. Pulsed Azidohomoalanine Labeling in Mammals (PALM) Detects Changes in Liver-Specific LKB1 Knockout Mice. J Proteome Res 2015; 14:4815-22. [PMID: 26445171 PMCID: PMC4642245 DOI: 10.1021/acs.jproteome.5b00653] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Quantification
of proteomes by mass spectrometry has proven to
be useful to study human pathology recapitulated in cellular or animal
models of disease. Enriching and quantifying newly synthesized proteins
(NSPs) at set time points by mass spectrometry has the potential to
identify important early regulatory or expression changes associated
with disease states or perturbations. NSP can be enriched from proteomes
by employing pulsed introduction of the noncanonical amino acid, azidohomoalanine
(AHA). We demonstrate that pulsed introduction of AHA in the feed
of mice can label and identify NSP from multiple tissues. Furthermore,
we quantitate differences in new protein expression resulting from
CRE-LOX initiated knockout of LKB1 in mouse livers. Overall, the PALM
strategy allows for the first time in vivo labeling of mouse tissues
to differentiate protein synthesis rates at discrete time points.
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Affiliation(s)
- Daniel B McClatchy
- Department of Chemical Physiology and Molecular and Cellular Molecular Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Yuanhui Ma
- Department of Chemical Physiology and Molecular and Cellular Molecular Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Chao Liu
- Key Lab of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences , No. 6 Kexueyuan South Road, Beijing 100190, China
| | - Benjamin D Stein
- Department of Chemical Physiology and Molecular and Cellular Molecular Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Salvador Martínez-Bartolomé
- Department of Chemical Physiology and Molecular and Cellular Molecular Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | | | | | | | - John R Yates
- Department of Chemical Physiology and Molecular and Cellular Molecular Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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29
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BONLAC: A combinatorial proteomic technique to measure stimulus-induced translational profiles in brain slices. Neuropharmacology 2015. [PMID: 26205778 DOI: 10.1016/j.neuropharm.2015.07.017] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Stimulus-triggered protein synthesis is critical for brain health and function. However, due to technical hurdles, de novo neuronal translation is predominantly studied in cultured cells, whereas electrophysiological and circuit analyses often are performed in brain slices. The different properties of these two experimental systems create an information gap about stimulus-induced alterations in the expression of new proteins in mature circuits. To address this, we adapted two existing techniques, BONCAT and SILAC, to a combined proteomic technique, BONLAC, for use in acute adult hippocampal slices. Using BDNF-induced protein synthesis as a proof of concept, we found alterations in expression of proteins involved in neurotransmission, trafficking, and cation binding that differed from those found in a similar screen in cultured neurons. Our results indicate important differences between cultured neurons and slices, and suggest that BONLAC could be used to dissect proteomic changes underlying synaptic events in adult circuits. This article is part of the Special Issue entitled 'Synaptopathy--from Biology to Therapy'.
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30
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Erdmann I, Marter K, Kobler O, Niehues S, Abele J, Müller A, Bussmann J, Storkebaum E, Ziv T, Thomas U, Dieterich DC. Cell-selective labelling of proteomes in Drosophila melanogaster. Nat Commun 2015; 6:7521. [PMID: 26138272 PMCID: PMC4507001 DOI: 10.1038/ncomms8521] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 05/16/2015] [Indexed: 01/06/2023] Open
Abstract
The specification and adaptability of cells rely on changes in protein composition. Nonetheless, uncovering proteome dynamics with cell-type-specific resolution remains challenging. Here we introduce a strategy for cell-specific analysis of newly synthesized proteomes by combining targeted expression of a mutated methionyl-tRNA synthetase (MetRS) with bioorthogonal or fluorescent non-canonical amino-acid-tagging techniques (BONCAT or FUNCAT). Substituting leucine by glycine within the MetRS-binding pocket (MetRSLtoG) enables incorporation of the non-canonical amino acid azidonorleucine (ANL) instead of methionine during translation. Newly synthesized proteins can thus be labelled by coupling the azide group of ANL to alkyne-bearing tags through ‘click chemistry'. To test these methods for applicability in vivo, we expressed MetRSLtoG cell specifically in Drosophila. FUNCAT and BONCAT reveal ANL incorporation into proteins selectively in cells expressing the mutated enzyme. Cell-type-specific FUNCAT and BONCAT, thus, constitute eligible techniques to study protein synthesis-dependent processes in complex and behaving organisms. Mutated tRNA synthetases can incorporate non-canonical amino acids into proteins. Erdmann et al. exploit this property to metabolically label newly synthesized proteins in selected cell types in Drosophila, and demonstrate their detection using proteomics (BONCAT) and fluorescence imaging (FUNCAT).
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Affiliation(s)
- Ines Erdmann
- 1] Research Group Neuronal Plasticity and Communication, Institute for Pharmacology and Toxicology, Otto-von-Guericke-University Magdeburg, Magdeburg 39120, Germany [2] Research Group Neuralomics, Leibniz Institute for Neurobiology, Magdeburg 39118, Germany
| | - Kathrin Marter
- 1] Research Group Neuronal Plasticity and Communication, Institute for Pharmacology and Toxicology, Otto-von-Guericke-University Magdeburg, Magdeburg 39120, Germany [2] Research Group Neuralomics, Leibniz Institute for Neurobiology, Magdeburg 39118, Germany
| | - Oliver Kobler
- Department of Neurochemistry and Molecular Biology, Leibniz Institute for Neurobiology, Magdeburg 39118, Germany
| | - Sven Niehues
- 1] Molecular Neurogenetics Laboratory, Max Planck Institute for Molecular Biomedicine, Münster 48149, Germany [2] Faculty of Medicine, University of Münster, Münster 48149, Germany
| | - Julia Abele
- 1] Research Group Neuronal Plasticity and Communication, Institute for Pharmacology and Toxicology, Otto-von-Guericke-University Magdeburg, Magdeburg 39120, Germany [2] Research Group Neuralomics, Leibniz Institute for Neurobiology, Magdeburg 39118, Germany
| | - Anke Müller
- 1] Research Group Neuronal Plasticity and Communication, Institute for Pharmacology and Toxicology, Otto-von-Guericke-University Magdeburg, Magdeburg 39120, Germany [2] Research Group Neuralomics, Leibniz Institute for Neurobiology, Magdeburg 39118, Germany
| | - Julia Bussmann
- 1] Molecular Neurogenetics Laboratory, Max Planck Institute for Molecular Biomedicine, Münster 48149, Germany [2] Faculty of Medicine, University of Münster, Münster 48149, Germany
| | - Erik Storkebaum
- 1] Molecular Neurogenetics Laboratory, Max Planck Institute for Molecular Biomedicine, Münster 48149, Germany [2] Faculty of Medicine, University of Münster, Münster 48149, Germany
| | - Tamar Ziv
- Smoler Proteomics Center, Faculty of Biology, Technion, Haifa 32000, Israel
| | - Ulrich Thomas
- Department of Neurochemistry and Molecular Biology, Leibniz Institute for Neurobiology, Magdeburg 39118, Germany
| | - Daniela C Dieterich
- 1] Research Group Neuronal Plasticity and Communication, Institute for Pharmacology and Toxicology, Otto-von-Guericke-University Magdeburg, Magdeburg 39120, Germany [2] Research Group Neuralomics, Leibniz Institute for Neurobiology, Magdeburg 39118, Germany [3] Center for Behavioral Brain Sciences, Magdeburg 39118, Germany
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31
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Walkinshaw E, Gai Y, Farkas C, Richter D, Nicholas E, Keleman K, Davis RL. Identification of genes that promote or inhibit olfactory memory formation in Drosophila. Genetics 2015; 199:1173-82. [PMID: 25644700 PMCID: PMC4391555 DOI: 10.1534/genetics.114.173575] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 01/28/2015] [Indexed: 11/18/2022] Open
Abstract
Genetic screens in Drosophila melanogaster and other organisms have been pursued to filter the genome for genetic functions important for memory formation. Such screens have employed primarily chemical or transposon-mediated mutagenesis and have identified numerous mutants including classical memory mutants, dunce and rutabaga. Here, we report the results of a large screen using panneuronal RNAi expression to identify additional genes critical for memory formation. We identified >500 genes that compromise memory when inhibited (low hits), either by disrupting the development and normal function of the adult animal or by participating in the neurophysiological mechanisms underlying memory formation. We also identified >40 genes that enhance memory when inhibited (high hits). The dunce gene was identified as one of the low hits and further experiments were performed to map the effects of the dunce RNAi to the α/β and γ mushroom body neurons. Additional behavioral experiments suggest that dunce knockdown in the mushroom body neurons impairs memory without significantly affecting acquisition. We also characterized one high hit, sickie, to show that RNAi knockdown of this gene enhances memory through effects in dopaminergic neurons without apparent effects on acquisition. These studies further our understanding of two genes involved in memory formation, provide a valuable list of genes that impair memory that may be important for understanding the neurophysiology of memory or neurodevelopmental disorders, and offer a new resource of memory suppressor genes that will aid in understanding restraint mechanisms employed by the brain to optimize resources.
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Affiliation(s)
- Erica Walkinshaw
- Department of Neuroscience, The Scripps Research Institute Florida, Jupiter, Florida 33458
| | - Yunchao Gai
- Department of Neuroscience, The Scripps Research Institute Florida, Jupiter, Florida 33458
| | - Caitlin Farkas
- Department of Neuroscience, The Scripps Research Institute Florida, Jupiter, Florida 33458
| | - Daniel Richter
- Department of Neuroscience, The Scripps Research Institute Florida, Jupiter, Florida 33458
| | - Eric Nicholas
- Department of Neuroscience, The Scripps Research Institute Florida, Jupiter, Florida 33458
| | | | - Ronald L Davis
- Department of Neuroscience, The Scripps Research Institute Florida, Jupiter, Florida 33458
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32
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Reichenbach N, Herrmann U, Kähne T, Schicknick H, Pielot R, Naumann M, Dieterich DC, Gundelfinger ED, Smalla KH, Tischmeyer W. Differential effects of dopamine signalling on long-term memory formation and consolidation in rodent brain. Proteome Sci 2015; 13:13. [PMID: 25852303 PMCID: PMC4387680 DOI: 10.1186/s12953-015-0069-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 02/25/2015] [Indexed: 12/01/2022] Open
Abstract
Background Using auditory discrimination learning in gerbils, we have previously shown that activation of auditory-cortical D1/D5 dopamine receptors facilitates mTOR-mediated, protein synthesis-dependent mechanisms of memory consolidation and anterograde memory formation. To understand molecular mechanisms of this facilitatory effect, we tested the impact of local pharmacological activation of different D1/D5 dopamine receptor signalling modes in the auditory cortex. To this end, protein patterns in soluble and synaptic protein-enriched fractions from cortical, hippocampal and striatal brain regions of ligand- and vehicle-treated gerbils were analysed by 2D gel electrophoresis and mass spectrometry 24 h after intervention. Results After auditory-cortical injection of SKF38393 – a D1/D5 dopamine receptor-selective agonist reported to activate the downstream effectors adenylyl cyclase and phospholipase C – prominent proteomic alterations compared to vehicle-treated controls appeared in the auditory cortex, striatum, and hippocampus, whereas only minor changes were detectable in the frontal cortex. In contrast, auditory-cortical injection of SKF83959 – a D1/D5 agonist reported to preferentially stimulate phospholipase C – induced pronounced changes in the frontal cortex. At the molecular level, we detected altered regulation of cytoskeletal and scaffolding proteins, changes in proteins with functions in energy metabolism, local protein synthesis, and synaptic signalling. Interestingly, abundance and/or subcellular localisation of the predominantly presynaptic protein α-synuclein displayed dopaminergic regulation. To assess the role of α-synuclein for dopaminergic mechanisms of memory modulation, we tested the impact of post-conditioning systemic pharmacological activation of different D1/D5 dopamine receptor signalling modes on auditory discrimination learning in α-synuclein-mutant mice. In C57BL/6JOlaHsd mice, bearing a spontaneous deletion of the α-synuclein-encoding gene, but not in the related substrains C57BL/6JCrl and C57BL/6JRccHsd, adenylyl cyclase-mediated signalling affected acquisition rates over future learning episodes, whereas phospholipase C-mediated signalling affected final memory performance. Conclusions Dopamine signalling modes via D1/D5 receptors in the auditory cortex differentially impact protein profiles related to rearrangement of cytomatrices, energy metabolism, and synaptic neurotransmission in cortical, hippocampal, and basal brain structures. Altered dopamine neurotransmission in α-synuclein-deficient mice revealed that distinct D1/D5 receptor signalling modes may control different aspects of memory consolidation. Electronic supplementary material The online version of this article (doi:10.1186/s12953-015-0069-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nicole Reichenbach
- Special Lab Molecular Biological Techniques, Leibniz Institute for Neurobiology, Magdeburg, 39118 Germany ; Present address: Research Group Neurovascular Diseases, German Center for Neurodegenerative Diseases (DZNE), Ludwig-Erhard-Allee 2, Bonn, 53175 Germany
| | - Ulrike Herrmann
- Special Lab Molecular Biological Techniques, Leibniz Institute for Neurobiology, Magdeburg, 39118 Germany ; Present address: Division of Cellular Neurobiology, Zoological Institute, TU Braunschweig, Braunschweig, 38106 Germany
| | - Thilo Kähne
- Institute of Experimental Internal Medicine, Medical School, Otto von Guericke University, Magdeburg, 39120 Germany
| | - Horst Schicknick
- Special Lab Molecular Biological Techniques, Leibniz Institute for Neurobiology, Magdeburg, 39118 Germany
| | - Rainer Pielot
- Department Neurochemistry and Molecular Biology, Leibniz Institute for Neurobiology, Magdeburg, 39118 Germany
| | - Michael Naumann
- Institute of Experimental Internal Medicine, Medical School, Otto von Guericke University, Magdeburg, 39120 Germany
| | - Daniela C Dieterich
- Research Group Neuralomics, Leibniz Institute for Neurobiology, Magdeburg, 39118 Germany ; Institute for Pharmacology and Toxicology, Medical Faculty, Otto-von-Guericke-University Magdeburg, Magdeburg, 39120 Germany ; Center for Behavioral Brain Sciences, Magdeburg, 39106 Germany
| | - Eckart D Gundelfinger
- Department Neurochemistry and Molecular Biology, Leibniz Institute for Neurobiology, Magdeburg, 39118 Germany ; Center for Behavioral Brain Sciences, Magdeburg, 39106 Germany ; Molecular Neurobiology, Medical Faculty, Otto-von-Guericke-University Magdeburg, Magdeburg, 39120 Germany
| | - Karl-Heinz Smalla
- Special Lab Molecular Biological Techniques, Leibniz Institute for Neurobiology, Magdeburg, 39118 Germany ; Center for Behavioral Brain Sciences, Magdeburg, 39106 Germany
| | - Wolfgang Tischmeyer
- Special Lab Molecular Biological Techniques, Leibniz Institute for Neurobiology, Magdeburg, 39118 Germany ; Center for Behavioral Brain Sciences, Magdeburg, 39106 Germany
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33
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Rosenberg T, Gal-Ben-Ari S, Dieterich DC, Kreutz MR, Ziv NE, Gundelfinger ED, Rosenblum K. The roles of protein expression in synaptic plasticity and memory consolidation. Front Mol Neurosci 2014; 7:86. [PMID: 25429258 PMCID: PMC4228929 DOI: 10.3389/fnmol.2014.00086] [Citation(s) in RCA: 103] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2014] [Accepted: 10/24/2014] [Indexed: 01/07/2023] Open
Abstract
The amount and availability of proteins are regulated by their synthesis, degradation, and transport. These processes can specifically, locally, and temporally regulate a protein or a population of proteins, thus affecting numerous biological processes in health and disease states. Accordingly, malfunction in the processes of protein turnover and localization underlies different neuronal diseases. However, as early as a century ago, it was recognized that there is a specific need for normal macromolecular synthesis in a specific fragment of the learning process, memory consolidation, which takes place minutes to hours following acquisition. Memory consolidation is the process by which fragile short-term memory is converted into stable long-term memory. It is accepted today that synaptic plasticity is a cellular mechanism of learning and memory processes. Interestingly, similar molecular mechanisms subserve both memory and synaptic plasticity consolidation. In this review, we survey the current view on the connection between memory consolidation processes and proteostasis, i.e., maintaining the protein contents at the neuron and the synapse. In addition, we describe the technical obstacles and possible new methods to determine neuronal proteostasis of synaptic function and better explain the process of memory and synaptic plasticity consolidation.
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Affiliation(s)
- Tali Rosenberg
- Sagol Department of Neurobiology, University of Haifa Haifa, Israel
| | | | - Daniela C Dieterich
- Institute for Pharmacology and Toxicology, Otto-von-Guericke University Magdeburg, Germany ; Research Group Neuralomics, Leibniz Institute for Neurobiology Magdeburg, Germany ; Center for Behavioral Brain Sciences Magdeburg, Germany
| | - Michael R Kreutz
- Research Group Neuroplasticity, Leibniz Institute for Neurobiology Magdeburg, Germany
| | - Noam E Ziv
- Network Biology Research Laboratories and Faculty of Medicine, Technion - Israel Institute of Technology Haifa, Israel
| | - Eckart D Gundelfinger
- Department of Neurochemistry and Molecular Biology, Leibniz Institute for Neurobiology Magdeburg, Germany ; Center for Behavioral Brain Sciences Magdeburg, Germany ; Medical School, Otto von Guericke University Magdeburg, Germany
| | - Kobi Rosenblum
- Sagol Department of Neurobiology, University of Haifa Haifa, Israel ; Center for Gene Manipulation in the Brain, University of Haifa Haifa, Israel
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34
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Zhang G, Bowling H, Hom N, Kirshenbaum K, Klann E, Chao MV, Neubert TA. In-depth quantitative proteomic analysis of de novo protein synthesis induced by brain-derived neurotrophic factor. J Proteome Res 2014; 13:5707-14. [PMID: 25271054 PMCID: PMC4261974 DOI: 10.1021/pr5006982] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
![]()
Measuring the synthesis of new proteins
in the context of a much
greater number of pre-existing proteins can be difficult. To overcome
this obstacle, bioorthogonal noncanonical amino acid tagging (BONCAT)
can be combined with stable isotope labeling by amino acid in cell
culture (SILAC) for comparative proteomic analysis of de novo protein
synthesis (BONLAC). In the present study, we show that alkyne resin-based
isolation of l-azidohomoalanine (AHA)-labeled proteins using
azide/alkyne cycloaddition minimizes contamination from pre-existing
proteins. Using this approach, we isolated and identified 7414 BONCAT-labeled
proteins. The nascent proteome isolated by BONCAT was very similar
to the steady-state proteome, although transcription factors were
highly enriched by BONCAT. About 30% of the methionine residues were
replaced by AHA in our BONCAT samples, which allowed for identification
of methionine-containing peptides. There was no bias against low-methionine
proteins by BONCAT at the proteome level. When we applied the BONLAC
approach to screen for brain-derived neurotrophic factor (BDNF)-induced
protein synthesis, 53 proteins were found to be significantly changed
2 h after BDNF stimulation. Our study demonstrated that the newly
synthesized proteome, even after a short period of stimulation, can
be efficiently isolated by BONCAT and analyzed to a depth that is
similar to that of the steady-state proteome.
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Affiliation(s)
- Guoan Zhang
- Department of Biochemistry and Molecular Pharmacology, ‡Departments of Cell Biology, Physiology, and Neuroscience and Psychiatry, Kimmel Center for Biology and Medicine at the Skirball Institute, New York University School of Medicine , New York, New York 10016, United States
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35
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Schiapparelli LM, McClatchy DB, Liu HH, Sharma P, Yates JR, Cline HT. Direct detection of biotinylated proteins by mass spectrometry. J Proteome Res 2014; 13:3966-78. [PMID: 25117199 PMCID: PMC4156236 DOI: 10.1021/pr5002862] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Mass spectrometric strategies to identify protein subpopulations involved in specific biological functions rely on covalently tagging biotin to proteins using various chemical modification methods. The biotin tag is primarily used for enrichment of the targeted subpopulation for subsequent mass spectrometry (MS) analysis. A limitation of these strategies is that MS analysis does not easily discriminate unlabeled contaminants from the labeled protein subpopulation under study. To solve this problem, we developed a flexible method that only relies on direct MS detection of biotin-tagged proteins called "Direct Detection of Biotin-containing Tags" (DiDBiT). Compared with conventional targeted proteomic strategies, DiDBiT improves direct detection of biotinylated proteins ∼200 fold. We show that DiDBiT is applicable to several protein labeling protocols in cell culture and in vivo using cell permeable NHS-biotin and incorporation of the noncanonical amino acid, azidohomoalanine (AHA), into newly synthesized proteins, followed by click chemistry tagging with biotin. We demonstrate that DiDBiT improves the direct detection of biotin-tagged newly synthesized peptides more than 20-fold compared to conventional methods. With the increased sensitivity afforded by DiDBiT, we demonstrate the MS detection of newly synthesized proteins labeled in vivo in the rodent nervous system with unprecedented temporal resolution as short as 3 h.
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Affiliation(s)
- Lucio Matias Schiapparelli
- The Dorris Neuroscience Center, Department of Molecular and Cellular Neuroscience, ‡Department of Chemical Physiology, and §Kellogg School of Science and Technology, The Scripps Research Institute , La Jolla, California 92037, United States
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36
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Genetic code expansion and bioorthogonal labelling enables cell specific proteomics in an animal. Curr Opin Chem Biol 2014; 21:154-60. [DOI: 10.1016/j.cbpa.2014.07.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 07/02/2014] [Accepted: 07/04/2014] [Indexed: 11/20/2022]
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37
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Breker M, Schuldiner M. The emergence of proteome-wide technologies: systematic analysis of proteins comes of age. Nat Rev Mol Cell Biol 2014; 15:453-64. [PMID: 24938631 DOI: 10.1038/nrm3821] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
During the lifetime of a cell proteins can change their localization, alter their abundance and undergo modifications, all of which cannot be assayed by tracking mRNAs alone. Methods to study proteomes directly are coming of age, thereby opening new perspectives on the role of post-translational regulation in stabilizing the cellular milieu. Proteomics has undergone a revolution, and novel technologies for the systematic analysis of proteins have emerged. These methods can expand our ability to acquire information from single proteins to proteomes, from static to dynamic measures and from the population level to the level of single cells. Such approaches promise that proteomes will soon be studied at a similar level of dynamic resolution as has been the norm for transcriptomes.
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Affiliation(s)
- Michal Breker
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
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38
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Lang K, Chin JW. Cellular incorporation of unnatural amino acids and bioorthogonal labeling of proteins. Chem Rev 2014; 114:4764-806. [PMID: 24655057 DOI: 10.1021/cr400355w] [Citation(s) in RCA: 775] [Impact Index Per Article: 77.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Kathrin Lang
- Medical Research Council Laboratory of Molecular Biology , Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
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39
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Bagert JD, Xie YJ, Sweredoski MJ, Qi Y, Hess S, Schuman EM, Tirrell DA. Quantitative, time-resolved proteomic analysis by combining bioorthogonal noncanonical amino acid tagging and pulsed stable isotope labeling by amino acids in cell culture. Mol Cell Proteomics 2014; 13:1352-8. [PMID: 24563536 DOI: 10.1074/mcp.m113.031914] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
An approach to proteomic analysis that combines bioorthogonal noncanonical amino acid tagging (BONCAT) and pulsed stable isotope labeling with amino acids in cell culture (pSILAC) provides accurate quantitative information about rates of cellular protein synthesis on time scales of minutes. The method is capable of quantifying 1400 proteins produced by HeLa cells during a 30 min interval, a time scale that is inaccessible to isotope labeling techniques alone. Potential artifacts in protein quantification can be reduced to insignificant levels by limiting the extent of noncanonical amino acid tagging. We find no evidence for artifacts in protein identification in experiments that combine the BONCAT and pSILAC methods.
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Affiliation(s)
- John D Bagert
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California
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40
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Shen W, Liu HH, Schiapparelli L, McClatchy D, He HY, Yates JR, Cline HT. Acute synthesis of CPEB is required for plasticity of visual avoidance behavior in Xenopus. Cell Rep 2014; 6:737-47. [PMID: 24529705 DOI: 10.1016/j.celrep.2014.01.024] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Revised: 12/30/2013] [Accepted: 01/15/2014] [Indexed: 12/16/2022] Open
Abstract
Neural plasticity requires protein synthesis, but the identity of newly synthesized proteins generated in response to plasticity-inducing stimuli remains unclear. We used in vivo bio-orthogonal noncanonical amino acid tagging (BONCAT) with the methionine analog azidohomoalanine (AHA) combined with the multidimensional protein identification technique (MudPIT) to identify proteins that are synthesized in the tadpole brain over 24 hr. We induced conditioning-dependent plasticity of visual avoidance behavior, which required N-methyl-D-aspartate (NMDA) and Ca(2+)-permeable α-Amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors, αCaMKII, and rapid protein synthesis. Combining BONCAT with western blots revealed that proteins including αCaMKII, MEK1, CPEB, and GAD65 are synthesized during conditioning. Acute synthesis of CPEB during conditioning is required for behavioral plasticity as well as conditioning-induced synaptic and structural plasticity in the tectal circuit. We outline a signaling pathway that regulates protein-synthesis-dependent behavioral plasticity in intact animals, identify newly synthesized proteins induced by visual experience, and demonstrate a requirement for acute synthesis of CPEB in plasticity.
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Affiliation(s)
- Wanhua Shen
- Key Lab of Organ Development and Regeneration of Zhejiang Province, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang 310036, China; The Dorris Neuroscience Center, Department of Molecular and Cellular Neuroscience, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Han-Hsuan Liu
- The Dorris Neuroscience Center, Department of Molecular and Cellular Neuroscience, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA; Kellogg School of Science and Technology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Lucio Schiapparelli
- The Dorris Neuroscience Center, Department of Molecular and Cellular Neuroscience, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Daniel McClatchy
- Department of Chemical Physiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Hai-Yan He
- The Dorris Neuroscience Center, Department of Molecular and Cellular Neuroscience, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - John R Yates
- Department of Chemical Physiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Hollis T Cline
- The Dorris Neuroscience Center, Department of Molecular and Cellular Neuroscience, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA; Department of Chemical Physiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA; Kellogg School of Science and Technology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
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41
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Bowling H, Zhang G, Bhattacharya A, Pérez-Cuesta LM, Deinhardt K, Hoeffer CA, Neubert TA, Gan WB, Klann E, Chao MV. Antipsychotics activate mTORC1-dependent translation to enhance neuronal morphological complexity. Sci Signal 2014; 7:ra4. [PMID: 24425786 PMCID: PMC4063438 DOI: 10.1126/scisignal.2004331] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Although antipsychotic drugs can reduce psychotic behavior within a few hours, full efficacy is not achieved for several weeks, implying that there may be rapid, short-term changes in neuronal function, which are consolidated into long-lasting changes. We showed that the antipsychotic drug haloperidol, a dopamine receptor type 2 (D₂R) antagonist, stimulated the kinase Akt to activate the mRNA translation pathway mediated by the mammalian target of rapamycin complex 1 (mTORC1). In primary striatal D₂R-positive neurons, haloperidol-mediated activation of mTORC1 resulted in increased phosphorylation of ribosomal protein S6 (S6) and eukaryotic translation initiation factor 4E-binding protein (4E-BP). Proteomic mass spectrometry revealed marked changes in the pattern of protein synthesis after acute exposure of cultured striatal neurons to haloperidol, including increased abundance of cytoskeletal proteins and proteins associated with translation machinery. These proteomic changes coincided with increased morphological complexity of neurons that was diminished by inhibition of downstream effectors of mTORC1, suggesting that mTORC1-dependent translation enhances neuronal complexity in response to haloperidol. In vivo, we observed rapid morphological changes with a concomitant increase in the abundance of cytoskeletal proteins in cortical neurons of haloperidol-injected mice. These results suggest a mechanism for both the acute and long-term actions of antipsychotics.
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Affiliation(s)
- Heather Bowling
- Departments of Cell Biology, Physiology and Neuroscience, Psychiatry
- Department of Neuroscience and Physiology and Neuroscience, NYU Neuroscience Institute, NYU Langone Medical Center, New York, New York 10016
| | - Guoan Zhang
- Biochemistry and Molecular Pharmacology, Kimmel Center for Biology and Medicine at the Skirball Institute of Biomolecular Medicine, New York University Langone School of Medicine, New York, New York 10016
| | - Aditi Bhattacharya
- Center for Neural Science, New York University, New York, New York 10003
| | | | - Katrin Deinhardt
- Departments of Cell Biology, Physiology and Neuroscience, Psychiatry
| | - Charles A. Hoeffer
- Department of Neuroscience and Physiology and Neuroscience, NYU Neuroscience Institute, NYU Langone Medical Center, New York, New York 10016
| | - Thomas A. Neubert
- Biochemistry and Molecular Pharmacology, Kimmel Center for Biology and Medicine at the Skirball Institute of Biomolecular Medicine, New York University Langone School of Medicine, New York, New York 10016
| | - Wen-biao Gan
- Departments of Cell Biology, Physiology and Neuroscience, Psychiatry
- Department of Neuroscience and Physiology and Neuroscience, NYU Neuroscience Institute, NYU Langone Medical Center, New York, New York 10016
| | - Eric Klann
- Center for Neural Science, New York University, New York, New York 10003
| | - Moses V. Chao
- Departments of Cell Biology, Physiology and Neuroscience, Psychiatry
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42
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43
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Abstract
The elaborate morphology of neurons together with the information processing that occurs in remote dendritic and axonal compartments makes the use of decentralized cell biological machines necessary. Recent years have witnessed a revolution in our understanding of signaling in neuronal compartments and the manifold functions of a variety of RNA molecules that regulate protein translation and other cellular functions. Here we discuss the view that mRNA localization and RNA-regulated and localized translation underlie many fundamental neuronal processes and highlight key issues for future experiments.
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44
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The changing brain--insights into the mechanisms of neural and behavioral adaptation to the environment. Neuroscience 2013; 247:412-22. [PMID: 23602885 DOI: 10.1016/j.neuroscience.2013.04.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The Kavli Prize in Neuroscience was awarded for the third time in September 2012, by the Norwegian Academy of Science and Letters in Oslo. The accompanying Kavli Prize Symposium on Neuroscience, held in Bergen and Trondheim, was a showcase of excellence in neuroscience research. The common theme of the Symposium presentations was the mechanisms by which animals adapt to their environment. The symposium speakers--Michael Greenberg, Erin Schuman, Chiara Cirelli, Michael Meaney, Catherine Dulac, Hopi Hoekstra, and Stanislas Dehaene--covered topics ranging from the molecular and cellular levels to the systems level and behavior. Thus a single amino acid change in a transcriptional repressor can disrupt gene regulation through neural activity (Greenberg). Deep sequencing analysis of the neuropil transcriptome indicates that a large fraction of the synaptic proteome is synthesized in situ in axons and dendrites, permitting local regulation (Schuman). The nature of the 'reset' function that makes animals dependent of sleep is being revealed (Cirelli). Maternal behavior can cause changes in gene expression that stably modify behavior in the offspring (Meaney). Removal of a single sensory channel protein in the vomero-nasal organ can switch off male-specific and switch on female-specific innate behavior of mice in response to environmental stimulation (Dulac). Innate behaviors can be stably transmitted from parent to offspring through generations even when those behaviors cannot be expressed, as illustrated by the elaborate burrowing behavior in a rodent species, in which independent genetic regions regulate distinct modules of the burrowing pattern (Hoekstra). Finally, at the other extreme of the nature-nurture scale, functional magnetic resonance imaging (fMRI) analysis in children and adults identified a brain area specifically involved in reading (Dehaene). As the area must originally have developed for a purpose other than reading, such as shape recognition, this illustrates the use of a previously formed neural structure to tackle a new challenge.
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45
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Yuet KP, Tirrell DA. Chemical tools for temporally and spatially resolved mass spectrometry-based proteomics. Ann Biomed Eng 2013; 42:299-311. [PMID: 23943069 DOI: 10.1007/s10439-013-0878-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Accepted: 07/24/2013] [Indexed: 11/29/2022]
Abstract
Accurate measurements of the abundances, synthesis rates and degradation rates of cellular proteins are critical for understanding how cells and organisms respond to changes in their environments. Over the past two decades, there has been increasing interest in the use of mass spectrometry for proteomic analysis. In many systems, however, protein diversity as well as cell and tissue heterogeneity limit the usefulness of mass spectrometry-based proteomics. As a result, researchers have had difficulty in systematically identifying proteins expressed within specified time intervals, or low abundance proteins expressed in specific tissues or in a few cells in complex microbial systems. In this review, we present recently-developed tools and strategies that probe these two subsets of the proteome: proteins synthesized during well-defined time intervals--temporally resolved proteomics--and proteins expressed in predetermined cell types, cells or cellular compartments--spatially resolved proteomics--with a focus on chemical and biological mass spectrometry-based methodologies.
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Affiliation(s)
- Kai P Yuet
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
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46
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Hinz FI, Dieterich DC, Schuman EM. Teaching old NCATs new tricks: using non-canonical amino acid tagging to study neuronal plasticity. Curr Opin Chem Biol 2013; 17:738-46. [PMID: 23938204 DOI: 10.1016/j.cbpa.2013.07.021] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Revised: 07/15/2013] [Accepted: 07/23/2013] [Indexed: 11/26/2022]
Abstract
The non-canonical amino acid labeling techniques BONCAT (bioorthogonal non-canonical amino acid tagging) and FUNCAT (fluorescent non-canonical amino acid tagging) enable the specific identification and visualization of newly synthesized proteins. Recently, these techniques have been applied to neuronal systems to elucidate protein synthesis dynamics during plasticity, identify stimulation-induced proteomes and subproteomes and to investigate local protein synthesis in specific subcellular compartments. The next generation of tools and applications, reviewed here, includes the development of new tags, the quantitative identification of newly synthesized proteins, the application of NCAT to whole animals, and the ability to genetically restrict NCAT labeling. These techniques will enable not only improved detection but also allow new scientific questions to be tackled.
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Affiliation(s)
- F I Hinz
- Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA; Max Planck Institute for Brain Research, D-60528 Frankfurt am Main, Germany
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47
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Panja D, Bramham CR. BDNF mechanisms in late LTP formation: A synthesis and breakdown. Neuropharmacology 2013; 76 Pt C:664-76. [PMID: 23831365 DOI: 10.1016/j.neuropharm.2013.06.024] [Citation(s) in RCA: 228] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Revised: 06/21/2013] [Accepted: 06/23/2013] [Indexed: 12/12/2022]
Abstract
Unraveling the molecular mechanisms governing long-term synaptic plasticity is a key to understanding how the brain stores information in neural circuits and adapts to a changing environment. Brain-derived neurotrophic factor (BDNF) has emerged as a regulator of stable, late phase long-term potentiation (L-LTP) at excitatory glutamatergic synapses in the adult brain. However, the mechanisms by which BDNF triggers L-LTP are controversial. Here, we distill and discuss the latest advances along three main lines: 1) TrkB receptor-coupled translational control underlying dendritic protein synthesis and L-LTP, 2) Mechanisms for BDNF-induced rescue of L-LTP when protein synthesis is blocked, and 3) BDNF-TrkB regulation of actin cytoskeletal dynamics in dendritic spines. Finally, we explore the inter-relationships between BDNF-regulated mechanisms, how these mechanisms contribute to different forms of L-LTP in the hippocampus and dentate gyrus, and outline outstanding issues for future research. This article is part of the Special Issue entitled 'BDNF Regulation of Synaptic Structure, Function, and Plasticity'.
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Affiliation(s)
- Debabrata Panja
- Department of Biomedicine, University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway; KG Jebsen Centre for Research on Neuropsychiatric Disorders, University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway
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48
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Low dopamine D5 receptor density in hippocampus in an animal model of attention-deficit/hyperactivity disorder (ADHD). Neuroscience 2013; 242:11-20. [DOI: 10.1016/j.neuroscience.2013.03.036] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2012] [Revised: 03/18/2013] [Accepted: 03/19/2013] [Indexed: 11/23/2022]
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49
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Mutant methionyl-tRNA synthetase from bacteria enables site-selective N-terminal labeling of proteins expressed in mammalian cells. Proc Natl Acad Sci U S A 2013; 110:4992-7. [PMID: 23479642 DOI: 10.1073/pnas.1216375110] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Newly synthesized cellular proteins can be tagged with a variety of metabolic labels that distinguish them from preexisting proteins and allow them to be identified and tracked. Many such labels are incorporated into proteins via the endogenous cellular machinery and can be used in numerous cell types and organisms. Though broad applicability has advantages, we aimed to develop a strategy to restrict protein labeling to specified mammalian cells that express a transgene. Here we report that heterologous expression of a mutant methionyl-tRNA synthetase from Escherichia coli permits incorporation of azidonorleucine (Anl) into proteins made in mammalian (HEK293) cells. Anl is incorporated site-selectively at N-terminal positions (in competition with initiator methionines) and is not found at internal sites. Site selectivity is enabled by the fact that the bacterial synthetase aminoacylates mammalian initiator tRNA, but not elongator tRNA. N-terminally labeled proteins can be selectively conjugated to a variety of useful probes; here we demonstrate use of this system in enrichment and visualization of proteins made during various stages of the cell cycle. N-terminal incorporation of Anl may also be used to engineer modified proteins for therapeutic and other applications.
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50
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Mahdavi A, Segall-Shapiro TH, Kou S, Jindal GA, Hoff KG, Liu S, Chitsaz M, Ismagilov RF, Silberg JJ, Tirrell DA. A genetically encoded and gate for cell-targeted metabolic labeling of proteins. J Am Chem Soc 2013; 135:2979-82. [PMID: 23406315 DOI: 10.1021/ja400448f] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
We describe a genetic AND gate for cell-targeted metabolic labeling and proteomic analysis in complex cellular systems. The centerpiece of the AND gate is a bisected methionyl-tRNA synthetase (MetRS) that charges the Met surrogate azidonorleucine (Anl) to tRNA(Met). Cellular protein labeling occurs only upon activation of two different promoters that drive expression of the N- and C-terminal fragments of the bisected MetRS. Anl-labeled proteins can be tagged with fluorescent dyes or affinity reagents via either copper-catalyzed or strain-promoted azide-alkyne cycloaddition. Protein labeling is apparent within 5 min after addition of Anl to bacterial cells in which the AND gate has been activated. This method allows spatial and temporal control of proteomic labeling and identification of proteins made in specific cellular subpopulations. The approach is demonstrated by selective labeling of proteins in bacterial cells immobilized in the center of a laminar-flow microfluidic channel, where they are exposed to overlapping, opposed gradients of inducers of the N- and C-terminal MetRS fragments. The observed labeling profile is predicted accurately from the strengths of the individual input signals.
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Affiliation(s)
- Alborz Mahdavi
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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