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; 124:7465-7530. [PMID: 38753805 DOI: 10.1021/acs.chemrev.4c00112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [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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Zhang Z, Luo Y, Ma Y, Zhou Y, Zhu D, Shen W, Liu J. Photocatalytic manipulation of Ca 2+ signaling for regulating cellular and animal behaviors via MOF-enabled H 2O 2 generation. SCIENCE ADVANCES 2024; 10:eadl0263. [PMID: 38640246 PMCID: PMC11029810 DOI: 10.1126/sciadv.adl0263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 03/18/2024] [Indexed: 04/21/2024]
Abstract
The in situ generation of H2O2 in cells in response to external stimulation has exceptional advantages in modulating intracellular Ca2+ dynamics, including high controllability and biological safety, but has been rarely explored. Here, we develop photocatalyst-based metal-organic frameworks (DCSA-MOFs) to modulate Ca2+ responses in cells, multicellular spheroids, and organs. By virtue of the efficient photocatalytic oxygen reduction to H2O2 without sacrificial agents, photoexcited DCSA-MOFs can rapidly trigger Ca2+ outflow from the endoplasmic reticulum with single-cell precision in a repeatable and controllable manner, enabling the propagation of intercellular Ca2+ waves (ICW) over long distances in two-dimensional and three-dimensional cell cultures. After photoexcitation, ICWs induced by DCSA-MOFs can activate neural activities in the optical tectum of tadpoles and thighs of spinal frogs, eliciting the corresponding motor behaviors. Our study offers a versatile optical nongenetic modulation technique that enables remote, repeatable, and controlled manipulation of cellular and animal behaviors.
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Affiliation(s)
- Zherui Zhang
- College of Material, Chemistry, and Chemical Engineering, Key Laboratory of Organosilicon Chemistry and Material Technology, Ministry of Education, Hangzhou Normal University, Hangzhou 311121, China
| | - Yuhao Luo
- Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang 310036, China
| | - Yuanhong Ma
- College of Material, Chemistry, and Chemical Engineering, Key Laboratory of Organosilicon Chemistry and Material Technology, Ministry of Education, Hangzhou Normal University, Hangzhou 311121, China
| | - Yaofeng Zhou
- Westlake University, Shilongshan Rd. Cloud Town, Xihu District, Hangzhou, Zhejiang, China
| | - Dingcheng Zhu
- College of Material, Chemistry, and Chemical Engineering, Key Laboratory of Organosilicon Chemistry and Material Technology, Ministry of Education, Hangzhou Normal University, Hangzhou 311121, China
| | - Wanhua Shen
- Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang 310036, China
| | - Junqiu Liu
- College of Material, Chemistry, and Chemical Engineering, Key Laboratory of Organosilicon Chemistry and Material Technology, Ministry of Education, Hangzhou Normal University, Hangzhou 311121, China
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3
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Thompson AC, Aizenman CD. Characterization of Na + currents regulating intrinsic excitability of optic tectal neurons. Life Sci Alliance 2024; 7:e202302232. [PMID: 37918964 PMCID: PMC10622587 DOI: 10.26508/lsa.202302232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 10/20/2023] [Accepted: 10/23/2023] [Indexed: 11/04/2023] Open
Abstract
Developing neurons adapt their intrinsic excitability to maintain stable output despite changing synaptic input. The mechanisms behind this process remain unclear. In this study, we examined Xenopus optic tectal neurons and found that the expressions of Nav1.1 and Nav1.6 voltage-gated Na+ channels are regulated during changes in intrinsic excitability, both during development and becsuse of changes in visual experience. Using whole-cell electrophysiology, we demonstrate the existence of distinct, fast, persistent, and resurgent Na+ currents in the tectum, and show that these Na+ currents are co-regulated with changes in Nav channel expression. Using antisense RNA to suppress the expression of specific Nav subunits, we found that up-regulation of Nav1.6 expression, but not Nav1.1, was necessary for experience-dependent increases in Na+ currents and intrinsic excitability. Furthermore, this regulation was also necessary for normal development of sensory guided behaviors. These data suggest that the regulation of Na+ currents through the modulation of Nav1.6 expression, and to a lesser extent Nav1.1, plays a crucial role in controlling the intrinsic excitability of tectal neurons and guiding normal development of the tectal circuitry.
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Affiliation(s)
- Adrian C Thompson
- https://ror.org/05gq02987 Department of Neuroscience, Brown University, Providence, RI, USA
| | - Carlos D Aizenman
- https://ror.org/05gq02987 Department of Neuroscience, Brown University, Providence, RI, USA
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4
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Gao J, Lu Y, Luo Y, Duan X, Chen P, Zhang X, Wu X, Qiu M, Shen W. β-Catenin and SOX2 Interaction Regulate Visual Experience-Dependent Cell Homeostasis in the Developing Xenopus Thalamus. Int J Mol Sci 2023; 24:13593. [PMID: 37686400 PMCID: PMC10488257 DOI: 10.3390/ijms241713593] [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: 07/31/2023] [Revised: 08/19/2023] [Accepted: 08/30/2023] [Indexed: 09/10/2023] Open
Abstract
In the vertebrate brain, sensory experience plays a crucial role in shaping thalamocortical connections for visual processing. However, it is still not clear how visual experience influences tissue homeostasis and neurogenesis in the developing thalamus. Here, we reported that the majority of SOX2-positive cells in the thalamus are differentiated neurons that receive visual inputs as early as stage 47 Xenopus. Visual deprivation (VD) for 2 days shifts the neurogenic balance toward proliferation at the expense of differentiation, which is accompanied by a reduction in nuclear-accumulated β-catenin in SOX2-positive neurons. The knockdown of β-catenin decreases the expression of SOX2 and increases the number of progenitor cells. Coimmunoprecipitation studies reveal the evolutionary conservation of strong interactions between β-catenin and SOX2. These findings indicate that β-catenin interacts with SOX2 to maintain homeostatic neurogenesis during thalamus development.
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Affiliation(s)
- Juanmei Gao
- Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China (M.Q.)
- College of Life and Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yufang Lu
- Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China (M.Q.)
| | - Yuhao Luo
- Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China (M.Q.)
| | - Xinyi Duan
- Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China (M.Q.)
| | - Peiyao Chen
- Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China (M.Q.)
| | - Xinyu Zhang
- Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China (M.Q.)
| | - Xiaohua Wu
- Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China (M.Q.)
| | - Mengsheng Qiu
- Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China (M.Q.)
- College of Life and Sciences, Zhejiang University, Hangzhou 310058, China
| | - Wanhua Shen
- Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China (M.Q.)
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5
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Pelgrom LR, Davis GM, O'Shaughnessy S, Wezenberg EJM, Van Kasteren SI, Finlay DK, Sinclair LV. QUAS-R: An SLC1A5-mediated glutamine uptake assay with single-cell resolution reveals metabolic heterogeneity with immune populations. Cell Rep 2023; 42:112828. [PMID: 37478011 DOI: 10.1016/j.celrep.2023.112828] [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: 10/26/2022] [Revised: 05/26/2023] [Accepted: 07/03/2023] [Indexed: 07/23/2023] Open
Abstract
System-level analysis of single-cell data is rapidly transforming the field of immunometabolism. Given the competitive demand for nutrients in immune microenvironments, there is a need to understand how and when immune cells access these nutrients. Here, we describe a new approach for single-cell analysis of nutrient uptake where we use in-cell biorthogonal labeling of a functionalized amino acid after transport into the cell. In this manner, the bona fide active uptake of glutamine via SLC1A5/ASCT2 could be quantified. We used this assay to interrogate the transport capacity of complex immune subpopulations, both in vitro and in vivo. Taken together, our findings provide an easy sensitive single-cell assay to assess which cells support their function via SLC1A5-mediated uptake. This is a significant addition to the single-cell metabolic toolbox required to decode the metabolic landscape of complex immune microenvironments.
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Affiliation(s)
- Leonard R Pelgrom
- Leiden Institute of Chemistry and the Institute of Chemical Immunology, Leiden University, Einsteinweg 55, 2333 CC Leiden, the Netherlands
| | - Gavin M Davis
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse Street, D02R590 Dublin, Ireland
| | - Simon O'Shaughnessy
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse Street, D02R590 Dublin, Ireland
| | - Emilie J M Wezenberg
- Leiden Institute of Chemistry and the Institute of Chemical Immunology, Leiden University, Einsteinweg 55, 2333 CC Leiden, the Netherlands
| | - Sander I Van Kasteren
- Leiden Institute of Chemistry and the Institute of Chemical Immunology, Leiden University, Einsteinweg 55, 2333 CC Leiden, the Netherlands.
| | - David K Finlay
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse Street, D02R590 Dublin, Ireland; School of Pharmacy and Pharmaceutical Sciences, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse Street, D02R590 Dublin, Ireland.
| | - Linda V Sinclair
- School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, UK.
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6
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Saleh AM, VanDyk TG, Jacobson KR, Khan SA, Calve S, Kinzer-Ursem TL. An Integrative Biology Approach to Quantify the Biodistribution of Azidohomoalanine In Vivo. Cell Mol Bioeng 2023; 16:99-115. [PMID: 37096070 PMCID: PMC10121978 DOI: 10.1007/s12195-023-00760-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 02/22/2023] [Indexed: 04/26/2023] Open
Abstract
Background Identification and quantitation of newly synthesized proteins (NSPs) are critical to understanding protein dynamics in development and disease. Probing the nascent proteome can be achieved using non-canonical amino acids (ncAAs) to selectively label the NSPs utilizing endogenous translation machinery, which can then be quantitated with mass spectrometry. We have previously demonstrated that labeling the in vivo murine proteome is feasible via injection of azidohomoalanine (Aha), an ncAA and methionine (Met) analog, without the need for Met depletion. Aha labeling can address biological questions wherein temporal protein dynamics are significant. However, accessing this temporal resolution requires a more complete understanding of Aha distribution kinetics in tissues. Results To address these gaps, we created a deterministic, compartmental model of the kinetic transport and incorporation of Aha in mice. Model results demonstrate the ability to predict Aha distribution and protein labeling in a variety of tissues and dosing paradigms. To establish the suitability of the method for in vivo studies, we investigated the impact of Aha administration on normal physiology by analyzing plasma and liver metabolomes following various Aha dosing regimens. We show that Aha administration induces minimal metabolic alterations in mice. Conclusions Our results demonstrate that we can reproducibly predict protein labeling and that the administration of this analog does not significantly alter in vivo physiology over the course of our experimental study. We expect this model to be a useful tool to guide future experiments utilizing this technique to study proteomic responses to stimuli. Supplementary Information The online version contains supplementary material available at 10.1007/s12195-023-00760-4.
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Affiliation(s)
- Aya M. Saleh
- Weldon School of Biomedical Engineering, Purdue University, 206 S. Martin Jischke Dr, West Lafayette, IN 47906 USA
| | - Tyler G. VanDyk
- Weldon School of Biomedical Engineering, Purdue University, 206 S. Martin Jischke Dr, West Lafayette, IN 47906 USA
| | - Kathryn R. Jacobson
- Purdue University Interdisciplinary Life Science Program, 155 S. Grant Street, West Lafayette, IN 47907 USA
| | - Shaheryar A. Khan
- Weldon School of Biomedical Engineering, Purdue University, 206 S. Martin Jischke Dr, West Lafayette, IN 47906 USA
| | - Sarah Calve
- Weldon School of Biomedical Engineering, Purdue University, 206 S. Martin Jischke Dr, West Lafayette, IN 47906 USA
- Purdue University Interdisciplinary Life Science Program, 155 S. Grant Street, West Lafayette, IN 47907 USA
- Paul M. Rady Department of Mechanical Engineering, University of Colorado – Boulder, 1111 Engineering Center, 427 UCB, Boulder, CO 80309 USA
| | - Tamara L. Kinzer-Ursem
- Weldon School of Biomedical Engineering, Purdue University, 206 S. Martin Jischke Dr, West Lafayette, IN 47906 USA
- Purdue University Interdisciplinary Life Science Program, 155 S. Grant Street, West Lafayette, IN 47907 USA
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7
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Neuronal membrane proteasomes regulate neuronal circuit activity in vivo and are required for learning-induced behavioral plasticity. Proc Natl Acad Sci U S A 2023; 120:e2216537120. [PMID: 36630455 PMCID: PMC9934054 DOI: 10.1073/pnas.2216537120] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Protein degradation is critical for brain function through processes that remain incompletely understood. Here, we investigated the in vivo function of the 20S neuronal membrane proteasome (NMP) in the brain of Xenopus laevis tadpoles. With biochemistry, immunohistochemistry, and electron microscopy, we demonstrated that NMPs are conserved in the tadpole brain and preferentially degrade neuronal activity-induced newly synthesized proteins in vivo. Using in vivo calcium imaging in the optic tectum, we showed that acute NMP inhibition rapidly increased spontaneous neuronal activity, resulting in hypersynchronization across tectal neurons. At the circuit level, inhibiting NMPs abolished learning-dependent improvement in visuomotor behavior in live animals and caused a significant deterioration in basal behavioral performance following visual training with enhanced visual experience. Our data provide in vivo characterization of NMP functions in the vertebrate nervous system and suggest that NMP-mediated degradation of activity-induced nascent proteins may serve as a homeostatic modulatory mechanism in neurons that is critical for regulating neuronal activity and experience-dependent circuit plasticity.
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8
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Bruno JR, Udoh UG, Landen JG, Osborn PO, Asher CJ, Hunt JE, Pratt KG. A circadian-dependent preference for light displayed by Xenopus tadpoles is modulated by serotonin. iScience 2022; 25:105375. [PMCID: PMC9636060 DOI: 10.1016/j.isci.2022.105375] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 09/10/2022] [Accepted: 10/13/2022] [Indexed: 11/06/2022] Open
Affiliation(s)
- John R. Bruno
- Department of Zoology and Physiology, University of Wyoming, Laramie, WY, USA
| | - Uwemedimo G. Udoh
- Department of Zoology and Physiology, University of Wyoming, Laramie, WY, USA
- Program in Neuroscience, University of Wyoming, Laramie, WY, USA
| | - Jason G. Landen
- Department of Zoology and Physiology, University of Wyoming, Laramie, WY, USA
| | - Paige O. Osborn
- Department of Zoology and Physiology, University of Wyoming, Laramie, WY, USA
| | - Carson J. Asher
- Department of Zoology and Physiology, University of Wyoming, Laramie, WY, USA
| | - Jasper E. Hunt
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Kara G. Pratt
- Department of Zoology and Physiology, University of Wyoming, Laramie, WY, USA
- Program in Neuroscience, University of Wyoming, Laramie, WY, USA
- Corresponding author
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9
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Gao J, Luo Y, Lu Y, Wu X, Chen P, Zhang X, Han L, Qiu M, Shen W. Epigenetic regulation of GABAergic differentiation in the developing brain. Front Cell Neurosci 2022; 16:988732. [PMID: 36212693 PMCID: PMC9539098 DOI: 10.3389/fncel.2022.988732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 08/18/2022] [Indexed: 11/13/2022] Open
Abstract
In the vertebrate brain, GABAergic cell development and neurotransmission are important for the establishment of neural circuits. Various intrinsic and extrinsic factors have been identified to affect GABAergic neurogenesis. However, little is known about the epigenetic control of GABAergic differentiation in the developing brain. Here, we report that the number of GABAergic neurons dynamically changes during the early tectal development in the Xenopus brain. The percentage of GABAergic neurons is relatively unchanged during the early stages from stage 40 to 46 but significantly decreased from stage 46 to 48 tadpoles. Interestingly, the histone acetylation of H3K9 is developmentally decreased from stage 42 to 48 (about 3.5 days). Chronic application of valproate acid (VPA), a broad-spectrum histone deacetylase (HDAC) inhibitor, at stage 46 for 48 h increases the acetylation of H3K9 and the number of GABAergic cells in the optic tectum. VPA treatment also reduces apoptotic cells. Electrophysiological recordings show that a VPA induces an increase in the frequency of mIPSCs and no changes in the amplitude. Behavioral studies reveal that VPA decreases swimming activity and visually guided avoidance behavior. These findings extend our understanding of histone modification in the GABAergic differentiation and neurotransmission during early brain development.
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Affiliation(s)
- Juanmei Gao
- College of Life Sciences, Zhejiang University, Hangzhou, China
- Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Yuhao Luo
- Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Yufang Lu
- Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Xiaohua Wu
- Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Peiyao Chen
- Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Xinyu Zhang
- Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Lu Han
- Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Mengsheng Qiu
- College of Life Sciences, Zhejiang University, Hangzhou, China
- Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- *Correspondence: Mengsheng Qiu,
| | - Wanhua Shen
- Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- Wanhua Shen,
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10
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Shah SH, Schiapparelli LM, Yokota S, Ma Y, Xia X, Shankar S, Saturday S, Nahmou M, Sun C, Yates J, Cline HT, Goldberg JL. Quantitative BONCAT Allows Identification of Newly Synthesized Proteins after Optic Nerve Injury. J Neurosci 2022; 42:4042-4052. [PMID: 35396330 PMCID: PMC9097770 DOI: 10.1523/jneurosci.3100-20.2022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 02/22/2022] [Accepted: 03/24/2022] [Indexed: 11/21/2022] Open
Abstract
Retinal ganglion cells (RGCs) die after optic nerve trauma or in degenerative disease. However, acute changes in protein expression that may regulate RGC response to injury are not fully understood, and detailed methods to quantify new protein synthesis have not been tested. Here, we develop and apply a new in vivo quantitative measure of newly synthesized proteins to examine changes occurring in the retina after optic nerve injury. Azidohomoalanine, a noncanonical amino acid, was injected intravitreally into the eyes of rodents of either sex with or without optic nerve injury. Isotope variants of biotin-alkyne were used for quantitative BONCAT (QBONCAT) mass spectrometry, allowing identification of protein synthesis and transport rate changes in more than 1000 proteins at 1 or 5 d after optic nerve injury. In vitro screening showed several newly synthesized proteins regulate axon outgrowth in primary neurons in vitro This novel approach to targeted quantification of newly synthesized proteins after injury uncovers a dynamic translational response within broader proteostasis regulation and enhances our understanding of the cellular response to injury.SIGNIFICANCE STATEMENT Optic nerve injury results in death and degeneration of retinal ganglion cells and their axons. The specific cellular response to injury, including changes in new protein synthesis, is obscured by existing proteins and protein degradation. In this study, we introduce QBONCAT to isolate and quantify acute protein synthesis and subsequent transport between cellular compartments. We identify novel candidate protein effectors of the regenerative response and uncover their regulation of axon growth in vitro, validating the utility of QBONCAT for the discovery of novel regulatory and therapeutic candidates after optic nerve injury.
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Affiliation(s)
- Sahil H Shah
- Mary M. and Sash A. Spencer Center for Vision Research, Byers Eye Institute, Stanford University, Palo Alto, California 94303
- Neuroscience Department and Dorris Neuroscience Center, Scripps Research, La Jolla, California 92093
- Neurosciences Graduate Program and Medical Scientist Training Program, University of California, San Diego, La Jolla, California 92093
| | - Lucio M Schiapparelli
- Neuroscience Department and Dorris Neuroscience Center, Scripps Research, La Jolla, California 92093
- Department of Cell Biology, Duke University Medical School, Durham, North Carolina, 27708
| | - Satoshi Yokota
- Mary M. and Sash A. Spencer Center for Vision Research, Byers Eye Institute, Stanford University, Palo Alto, California 94303
| | - Yuanhui Ma
- Department of Molecular Medicine, Scripps Research, La Jolla, California 92093
| | - Xin Xia
- Mary M. and Sash A. Spencer Center for Vision Research, Byers Eye Institute, Stanford University, Palo Alto, California 94303
| | - Sahana Shankar
- Mary M. and Sash A. Spencer Center for Vision Research, Byers Eye Institute, Stanford University, Palo Alto, California 94303
| | - Sarah Saturday
- Neuroscience Department and Dorris Neuroscience Center, Scripps Research, La Jolla, California 92093
| | - Michael Nahmou
- Mary M. and Sash A. Spencer Center for Vision Research, Byers Eye Institute, Stanford University, Palo Alto, California 94303
| | - Catalina Sun
- Mary M. and Sash A. Spencer Center for Vision Research, Byers Eye Institute, Stanford University, Palo Alto, California 94303
| | - John Yates
- Department of Molecular Medicine, Scripps Research, La Jolla, California 92093
| | - Hollis T Cline
- Neuroscience Department and Dorris Neuroscience Center, Scripps Research, La Jolla, California 92093
| | - Jeffrey L Goldberg
- Mary M. and Sash A. Spencer Center for Vision Research, Byers Eye Institute, Stanford University, Palo Alto, California 94303
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11
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Andrews B, Murphy AE, Stofella M, Maslen S, Almeida-Souza L, Skehel JM, Skene NG, Sobott F, Frank RAW. Multidimensional dynamics of the proteome in the neurodegenerative and aging mammalian brain. Mol Cell Proteomics 2021; 21:100192. [PMID: 34979241 PMCID: PMC8816717 DOI: 10.1016/j.mcpro.2021.100192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 12/03/2021] [Accepted: 12/29/2021] [Indexed: 11/18/2022] Open
Abstract
The amount of any given protein in the brain is determined by the rates of its synthesis and destruction, which are regulated by different cellular mechanisms. Here, we combine metabolic labeling in live mice with global proteomic profiling to simultaneously quantify both the flux and amount of proteins in mouse models of neurodegeneration. In multiple models, protein turnover increases were associated with increasing pathology. This method distinguishes changes in protein expression mediated by synthesis from those mediated by degradation. In the AppNL-F knockin mouse model of Alzheimer’s disease, increased turnover resulted from imbalances in both synthesis and degradation, converging on proteins associated with synaptic vesicle recycling (Dnm1, Cltc, Rims1) and mitochondria (Fis1, Ndufv1). In contrast to disease models, aging in wild-type mice caused a widespread decrease in protein recycling associated with a decrease in autophagic flux. Overall, this simple multidimensional approach enables a comprehensive mapping of proteome dynamics and identifies affected proteins in mouse models of disease and other live animal test settings. Multidimensional proteomic screen to detect imbalances in mouse models of disease. Increased proteome turnover in multiple symptomatic neurodegeneration mouse models. Healthy aging is associated with a global decrease in protein turnover.
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Affiliation(s)
- Byron Andrews
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Alan E Murphy
- UK Dementia Research Institute, Department of Brain Sciences, Imperial College London, W12 0BZ, UK
| | - Michele Stofella
- Astbury Centre of Molecular Structural Biology, Faculty of Biological Sciences, University of Leeds, LS2 9JT, UK
| | - Sarah Maslen
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Leonardo Almeida-Souza
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK; Helsinki Institute of Life Science - HiLIFE, Institute of Biotechnology and Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 5, 00790, Helsinki, Finland
| | - J Mark Skehel
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Nathan G Skene
- UK Dementia Research Institute, Department of Brain Sciences, Imperial College London, W12 0BZ, UK
| | - Frank Sobott
- Astbury Centre of Molecular Structural Biology, Faculty of Biological Sciences, University of Leeds, LS2 9JT, UK
| | - René A W Frank
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK; Astbury Centre of Molecular Structural Biology, Faculty of Biological Sciences, University of Leeds, LS2 9JT, UK.
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12
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van Bergen W, Heck AJR, Baggelaar MP. Recent advancements in mass spectrometry-based tools to investigate newly synthesized proteins. Curr Opin Chem Biol 2021; 66:102074. [PMID: 34364788 PMCID: PMC9548413 DOI: 10.1016/j.cbpa.2021.07.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 06/28/2021] [Accepted: 07/03/2021] [Indexed: 02/08/2023]
Abstract
Tight regulation of protein translation drives the proteome to undergo changes under influence of extracellular or intracellular signals. Despite mass spectrometry–based proteomics being an excellent method to study differences in protein abundance in complex proteomes, analyzing minute or rapid changes in protein synthesis and abundance remains challenging. Therefore, several dedicated techniques to directly detect and quantify newly synthesized proteins have been developed, notably puromycin-based, bio-orthogonal noncanonical amino acid tagging–based, and stable isotope labeling by amino acids in cell culture–based methods, combined with mass spectrometry. These techniques have enabled the investigation of perturbations, stress, or stimuli on protein synthesis. Improvements of these methods are still necessary to overcome various remaining limitations. Recent improvements include enhanced enrichment approaches and combinations with various stable isotope labeling techniques, which allow for more accurate analysis and comparison between conditions on shorter timeframes and in more challenging systems. Here, we aim to review the current state in this field.
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Affiliation(s)
- Wouter van Bergen
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, Utrecht, 3584 CH, the Netherlands; Netherlands Proteomics Center, Padualaan 8, Utrecht, 3584 CH, the Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, Utrecht, 3584 CH, the Netherlands; Netherlands Proteomics Center, Padualaan 8, Utrecht, 3584 CH, the Netherlands
| | - Marc P Baggelaar
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, Utrecht, 3584 CH, the Netherlands; Netherlands Proteomics Center, Padualaan 8, Utrecht, 3584 CH, the Netherlands.
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13
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Faulkner RL, Wall NR, Callaway EM, Cline HT. Application of Recombinant Rabies Virus to Xenopus Tadpole Brain. eNeuro 2021; 8:ENEURO.0477-20.2021. [PMID: 34099488 PMCID: PMC8260272 DOI: 10.1523/eneuro.0477-20.2021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 05/13/2021] [Accepted: 05/31/2021] [Indexed: 12/25/2022] Open
Abstract
The Xenopus laevis experimental system has provided significant insight into the development and plasticity of neural circuits. Xenopus neuroscience research would be enhanced by additional tools to study neural circuit structure and function. Rabies viruses are powerful tools to label and manipulate neural circuits and have been widely used to study mesoscale connectomics. Whether rabies virus can be used to transduce neurons and express transgenes in Xenopus has not been systematically investigated. Glycoprotein-deleted rabies virus transduces neurons at the axon terminal and retrogradely labels their cell bodies. We show that glycoprotein-deleted rabies virus infects local and projection neurons in the Xenopus tadpole when directly injected into brain tissue. Pseudotyping glycoprotein-deleted rabies with EnvA restricts infection to cells with exogenous expression of the EnvA receptor, TVA. EnvA pseudotyped virus specifically infects tadpole neurons with promoter-driven expression of TVA, demonstrating its utility to label targeted neuronal populations. Neuronal cell types are defined by a combination of features including anatomical location, expression of genetic markers, axon projection sites, morphology, and physiological properties. We show that driving TVA expression in one hemisphere and injecting EnvA pseudotyped virus into the contralateral hemisphere, retrogradely labels neurons defined by cell body location and axon projection site. Using this approach, rabies can be used to identify cell types in Xenopus brain and simultaneously to express transgenes which enable monitoring or manipulation of neuronal activity. This makes rabies a valuable tool to study the structure and function of neural circuits in Xenopus.Significance StatementStudies in Xenopus have contributed a great deal to our understanding of brain circuit development and plasticity, regeneration, and hormonal regulation of behavior and metamorphosis. Here, we show that recombinant rabies virus transduces neurons in the Xenopus tadpole, enlarging the toolbox that can be applied to studying Xenopus brain. Rabies can be used for retrograde labeling and expression of a broad range of transgenes including fluorescent proteins for anatomical tracing and studying neuronal morphology, voltage or calcium indicators to visualize neuronal activity, and photo- or chemosensitive channels to control neuronal activity. The versatility of these tools enables diverse experiments to analyze and manipulate Xenopus brain structure and function, including mesoscale connectivity.
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Affiliation(s)
- Regina L Faulkner
- Neuroscience Department and The Dorris Neuroscience Center, The Scripps Research Institute, La Jolla CA
| | | | | | - Hollis T Cline
- Neuroscience Department and The Dorris Neuroscience Center, The Scripps Research Institute, La Jolla CA
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14
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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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15
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Gao J, Shen W. Xenopus in revealing developmental toxicity and modeling human diseases. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 268:115809. [PMID: 33096388 DOI: 10.1016/j.envpol.2020.115809] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 10/01/2020] [Accepted: 10/09/2020] [Indexed: 06/11/2023]
Abstract
The Xenopus model offers many advantages for investigation of the molecular, cellular, and behavioral mechanisms underlying embryo development. Moreover, Xenopus oocytes and embryos have been extensively used to study developmental toxicity and human diseases in response to various environmental chemicals. This review first summarizes recent advances in using Xenopus as a vertebrate model to study distinct types of tissue/organ development following exposure to environmental toxicants, chemical reagents, and pharmaceutical drugs. Then, the successful use of Xenopus as a model for diseases, including fetal alcohol spectrum disorders, autism, epilepsy, and cardiovascular disease, is reviewed. The potential application of Xenopus in genetic and chemical screening to protect against embryo deficits induced by chemical toxicants and related diseases is also discussed.
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Affiliation(s)
- Juanmei Gao
- Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, 311121, China; College of Life and Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Wanhua Shen
- Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, 311121, China.
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16
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Camargo de Lima J, Floriani MA, Debarba JA, Paludo GP, Monteiro KM, Moura H, Barr JR, Zaha A, Ferreira HB. Dynamics of protein synthesis in the initial steps of strobilation in the model cestode parasite Mesocestoides corti (syn. vogae). J Proteomics 2020; 228:103939. [PMID: 32798775 PMCID: PMC10491476 DOI: 10.1016/j.jprot.2020.103939] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 08/05/2020] [Accepted: 08/10/2020] [Indexed: 01/24/2023]
Abstract
Mesocestoides corti (syn. vogae) is a useful model for developmental studies of platyhelminth parasites of the Cestoda class, such as Taenia spp. or Echinococcus spp. It has been used in studies to characterize cestode strobilation, i.e. the development of larvae into adult worms. So far, little is known about the initial molecular events involved in cestode strobilation and, therefore, we carried out a study to characterize newly synthesized (NS) proteins upon strobilation induction. An approach based on bioorthogonal noncanonical amino acid tagging and mass spectrometry was used to label, isolate, identify, and quantify NS proteins in the initial steps of M. corti strobilation. Overall, 121 NS proteins were detected exclusively after induction of strobilation, including proteins related to development pathways, such as insulin and notch signaling. Metabolic changes that take place in the transition from the larval stage to adult worm were noted in special NS protein subsets related to developmental processes, such as focal adhesion, cell leading edge, and maintenance of location. The data shed light on mechanisms underlying early steps of cestode strobilation and enabled identification of possible developmental markers. We also consider the use of developmental responsive proteins as potential drug targets for developing novel anthelmintics. BIOLOGICAL SIGNIFICANCE: Larval cestodiases are life-threatening parasitic diseases that affect both man and domestic animals worldwide. Cestode parasites present complex life cycles, in which they undergo major morphological and physiological changes in the transition from one life-stage to the next. One of these transitions occurs during cestode strobilation, when the mostly undifferentiated and non-segmented larval or pre-adult form develops into a fully segmented and sexually differentiated (strobilated) adult worm. Although the proteomes of bona fide larvae and strobialted adults have been previously characterized for a few cestode species, little is still known about the dynamic of protein synthesis during the early steps of cestode strobilation. Now, the assessment of newly synthesized (NS) proteins within the first 48 h of strobilation the model cestode M. corti allowed to shed light on molecular mechanisms that are triggered by strobilation induction. The functional analyses of this repertoire of over a hundred NS proteins pointed out to changes in metabolism and activation of classical developmental signaling pathways in early strobilation. Many of the identified NS proteins may become valuable cestode developmental markers and their involvement in vital processes make them also good candidate targets for novel anthelmintic drugs.
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Affiliation(s)
- Jeferson Camargo de Lima
- Programa de Pós-Graduação em Biologia Molecular e Celular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Brazil; Laboratório de Genômica Estrutural e Funcional, Centro de Biotecnologia, UFRGS, Porto Alegre, RS, Brazil
| | - Maiara Anschau Floriani
- Laboratório de Genômica Estrutural e Funcional, Centro de Biotecnologia, UFRGS, Porto Alegre, RS, Brazil
| | - João Antônio Debarba
- Programa de Pós-Graduação em Biologia Molecular e Celular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Brazil; Laboratório de Biologia Molecular de Cestódeos, Centro de Biotecnologia, UFRGS, Porto Alegre, RS, Brazil
| | - Gabriela Prado Paludo
- Programa de Pós-Graduação em Biologia Molecular e Celular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Brazil; Laboratório de Genômica Estrutural e Funcional, Centro de Biotecnologia, UFRGS, Porto Alegre, RS, Brazil
| | - Karina Mariante Monteiro
- Programa de Pós-Graduação em Biologia Molecular e Celular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Brazil; Laboratório de Genômica Estrutural e Funcional, Centro de Biotecnologia, UFRGS, Porto Alegre, RS, Brazil; Laboratório de Biologia Molecular de Cestódeos, Centro de Biotecnologia, UFRGS, Porto Alegre, RS, Brazil
| | - Hercules Moura
- Biological Mass Spectrometry Laboratory, Clinical Chemistry Branch, Division of Laboratory Sciences, National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - John R Barr
- Biological Mass Spectrometry Laboratory, Clinical Chemistry Branch, Division of Laboratory Sciences, National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Arnaldo Zaha
- Programa de Pós-Graduação em Biologia Molecular e Celular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Brazil; Laboratório de Biologia Molecular de Cestódeos, Centro de Biotecnologia, UFRGS, Porto Alegre, RS, Brazil
| | - Henrique Bunselmeyer Ferreira
- Programa de Pós-Graduação em Biologia Molecular e Celular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Brazil; Laboratório de Genômica Estrutural e Funcional, Centro de Biotecnologia, UFRGS, Porto Alegre, RS, Brazil; Laboratório de Biologia Molecular de Cestódeos, Centro de Biotecnologia, UFRGS, Porto Alegre, RS, Brazil.
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17
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McClatchy DB, Martínez-Bartolomé S, Gao Y, Lavallée-Adam M, Yates JR. Quantitative analysis of global protein stability rates in tissues. Sci Rep 2020; 10:15983. [PMID: 32994440 PMCID: PMC7524747 DOI: 10.1038/s41598-020-72410-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 08/28/2020] [Indexed: 02/06/2023] Open
Abstract
Protein degradation is an essential mechanism for maintaining proteostasis in response to internal and external perturbations. Disruption of this process is implicated in many human diseases. We present a new technique, QUAD (Quantification of Azidohomoalanine Degradation), to analyze the global degradation rates in tissues using a non-canonical amino acid and mass spectrometry. QUAD analysis reveals that protein stability varied within tissues, but discernible trends in the data suggest that cellular environment is a major factor dictating stability. Within a tissue, different organelles and protein functions were enriched with different stability patterns. QUAD analysis demonstrated that protein stability is enhanced with age in the brain but not in the liver. Overall, QUAD allows the first global quantitation of protein stability rates in tissues, which will allow new insights and hypotheses in basic and translational research.
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Affiliation(s)
- Daniel B McClatchy
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | | | - Yu Gao
- College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
| | - Mathieu Lavallée-Adam
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
- Department of Biochemistry, Microbiology and Immunology and Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada
| | - John R Yates
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA.
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18
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Hunt JE, Bruno JR, Pratt KG. An Innate Color Preference Displayed by Xenopus Tadpoles Is Persistent and Requires the Tegmentum. Front Behav Neurosci 2020; 14:71. [PMID: 32477078 PMCID: PMC7235192 DOI: 10.3389/fnbeh.2020.00071] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 04/20/2020] [Indexed: 11/26/2022] Open
Abstract
Many animals, especially those that develop externally, are equipped with innate color preferences that promote survival. For example, Xenopus tadpoles are known to phototax most robustly towards mid-spectrum (“green”) wavelengths of light while avoiding shorter (“blue”) wavelengths. The innate preference to phototax towards green likely promotes survival by guiding the tadpoles to green aquatic plants—their source of both food and safety. Here, we characterize the dynamics and circuitry that give rise to this intriguing hard-wired behavior. Using a novel open-field experimental paradigm we found that free-swimming tadpoles indeed spend most of their time in the green portion of the test dish, whether green is pitted against white (brighter than green) or black (darker than green). This preference was modest yet incredibly persistent over time, which, according to the shell game model of predator-prey interactions, minimizes being found by the predator. Furthermore, we found that this innate preference for the color green was experience-independent, and manifested mainly via profoundly slower swimming speeds while in the green region of the test dish. Ablation experiments showed that, at the circuit level, the color-guided swimming behavior requires the tegmentum, but not the optic tectum (OT). Lastly, we determined that exposing tadpoles to the selective serotonin reuptake inhibitor (SSRI) trazodone switched the tadpoles’ preference from color-based to luminance-based, implicating two distinct visual circuits in the tadpole, one that is associated with color-driven behaviors, another associated with luminance-driven behaviors.
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Affiliation(s)
- Jasper Elan Hunt
- Department of Zoology and Physiology and Program in Neuroscience, University of Wyoming, Laramie, WY, United States.,Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - John Rudolph Bruno
- Department of Zoology and Physiology and Program in Neuroscience, University of Wyoming, Laramie, WY, United States
| | - Kara Geo Pratt
- Department of Zoology and Physiology and Program in Neuroscience, University of Wyoming, Laramie, WY, United States
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19
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ZHAN FL, GAO SY, XIE YD, ZHANG JM, LI Y, LIU N. Applications of Click Chemistry Reaction for Proteomics Analysis. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2020. [DOI: 10.1016/s1872-2040(20)60007-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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20
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d-Glucuronolactone attenuates para-xylene-induced defects in neuronal development and plasticity in Xenopus tectum in vivo. Toxicology 2020; 430:152341. [DOI: 10.1016/j.tox.2019.152341] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 11/05/2019] [Accepted: 12/02/2019] [Indexed: 01/17/2023]
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21
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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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22
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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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23
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Saleh AM, Wilding KM, Calve S, Bundy BC, Kinzer-Ursem TL. Non-canonical amino acid labeling in proteomics and biotechnology. J Biol Eng 2019; 13:43. [PMID: 31139251 PMCID: PMC6529998 DOI: 10.1186/s13036-019-0166-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 04/11/2019] [Indexed: 02/03/2023] Open
Abstract
Metabolic labeling of proteins with non-canonical amino acids (ncAAs) provides unique bioorthogonal chemical groups during de novo synthesis by taking advantage of both endogenous and heterologous protein synthesis machineries. Labeled proteins can then be selectively conjugated to fluorophores, affinity reagents, peptides, polymers, nanoparticles or surfaces for a wide variety of downstream applications in proteomics and biotechnology. In this review, we focus on techniques in which proteins are residue- and site-specifically labeled with ncAAs containing bioorthogonal handles. These ncAA-labeled proteins are: readily enriched from cells and tissues for identification via mass spectrometry-based proteomic analysis; selectively purified for downstream biotechnology applications; or labeled with fluorophores for in situ analysis. To facilitate the wider use of these techniques, we provide decision trees to help guide the design of future experiments. It is expected that the use of ncAA labeling will continue to expand into new application areas where spatial and temporal analysis of proteome dynamics and engineering new chemistries and new function into proteins are desired.
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Affiliation(s)
- Aya M. Saleh
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN USA
| | - Kristen M. Wilding
- Department of Chemical Engineering, Brigham Young University, Provo, UT USA
| | - Sarah Calve
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN USA
| | - Bradley C. Bundy
- Department of Chemical Engineering, Brigham Young University, Provo, UT USA
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24
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Gambrill AC, Faulkner RL, McKeown CR, Cline HT. Enhanced visual experience rehabilitates the injured brain in Xenopus tadpoles in an NMDAR-dependent manner. J Neurophysiol 2018; 121:306-320. [PMID: 30517041 DOI: 10.1152/jn.00664.2018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Traumatic brain injuries introduce functional and structural circuit deficits that must be repaired for an organism to regain function. We developed an injury model in which Xenopus laevis tadpoles are given a penetrating stab wound that damages the optic tectal circuit and impairs visuomotor behavior. In tadpoles, as in other systems, injury induces neurogenesis. The newly generated neurons are thought to integrate into the existing circuit; however, whether they integrate via the same mechanisms that govern normal neuronal maturation during development is not understood. Development of the functional visuomotor circuit in Xenopus is driven by sensory activity. We hypothesized that enhanced visual experience would improve recovery from injury by facilitating integration of newly generated neurons into the tectal circuit. We labeled newly generated neurons in the injured tectum by green fluorescent protein expression and examined their circuit integration using electrophysiology and in vivo imaging. Providing animals with brief bouts of enhanced visual experience starting 24 h after injury increased synaptogenesis and circuit integration of new neurons and facilitated behavioral recovery. To investigate mechanisms of neuronal integration and behavioral recovery after injury, we interfered with N-methyl-d-aspartate (NMDA) receptor function. Ifenprodil, which blocks GluN2B-containing NMDA receptors, impaired dendritic arbor elaboration. GluN2B blockade inhibited functional integration of neurons generated in response to injury and prevented behavioral recovery. Furthermore, tectal GluN2B knockdown blocked the beneficial effects of enhanced visual experience on functional plasticity and behavioral recovery. We conclude that visual experience-mediated rehabilitation of the injured tectal circuit occurs by GluN2B-containing NMDA receptor-dependent integration of newly generated neurons. NEW & NOTEWORTHY Recovery from brain injury is difficult in most systems. The study of regenerative animal models that are capable of injury repair can provide insight into cellular and circuit mechanisms underlying repair. Using Xenopus tadpoles, we show enhanced sensory experience rehabilitates the injured visual circuit and that this experience-dependent recovery depends on N-methyl-d-aspartate receptor function. Understanding the mechanisms of rehabilitation in this system may facilitate recovery in brain regions and systems where repair is currently impossible.
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Affiliation(s)
- Abigail C Gambrill
- Department of Neuroscience, the Dorris Neuroscience Center, The Scripps Research Institute , La Jolla, California
| | - Regina L Faulkner
- Department of Neuroscience, the Dorris Neuroscience Center, The Scripps Research Institute , La Jolla, California
| | - Caroline R McKeown
- Department of Neuroscience, the Dorris Neuroscience Center, The Scripps Research Institute , La Jolla, California
| | - Hollis T Cline
- Department of Neuroscience, the Dorris Neuroscience Center, The Scripps Research Institute , La Jolla, California
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25
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Liu Z, Thakar A, Santoro SW, Pratt KG. Presenilin Regulates Retinotectal Synapse Formation through EphB2 Receptor Processing. Dev Neurobiol 2018; 78:1171-1190. [PMID: 30246932 DOI: 10.1002/dneu.22638] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 08/18/2018] [Accepted: 08/31/2018] [Indexed: 12/15/2022]
Abstract
As the catalytic component of γ-secretase, presenilin (PS) has long been studied in the context of Alzheimer's disease through cleaving the amyloid precursor protein. PS/γ-secretase, however, also cleaves a multitude of single-pass transmembrane proteins that are important during development, including Notch, the netrin receptor DCC, cadherins, drebrin-A, and the EphB2 receptor. Because transgenic PS-KO mice do not survive to birth, studies of this molecule during later embryonic or early postnatal stages of development have been carried out using cell cultures or conditional knock-out mice, respectively. As a result, the function of PS in synapse formation had not been well-addressed. Here, we study the role of PS in the developing Xenopus tadpole retinotectal circuit, an in-vivo model that allows for protein expression to be manipulated specifically during the peak of synapse formation between retinal ganglion cells and tectal neurons. We found that inhibiting PS in the postsynaptic tectal neurons impaired tadpole visual avoidance behavior. Whole cell recordings indicated weaker retinotectal synaptic transmission which was characterized by significant reductions in both NMDA receptor (NMDAR)- and AMPA receptor (AMPAR)-mediated currents. We also found that expression of the C-tail fragment of the EphB2 receptor, which is normally cleaved by PS/γ-secretase and which has been shown to upregulate NMDARs at the synapse, rescued the reduced NMDAR-mediated responses. Our data determine that normal PS function is important for proper formation and strengthening of retinotectal synapses through cleaving the EphB2 receptor.
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Affiliation(s)
- Zhenyu Liu
- Department of Zoology and Physiology and Program in Neuroscience, University of Wyoming, Laramie, Wyoming
| | - Amit Thakar
- Department of Zoology and Physiology and Program in Neuroscience, University of Wyoming, Laramie, Wyoming
| | - Stephen W Santoro
- Department of Zoology and Physiology and Program in Neuroscience, University of Wyoming, Laramie, Wyoming
| | - Kara G Pratt
- Department of Zoology and Physiology and Program in Neuroscience, University of Wyoming, Laramie, Wyoming
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He HY, Shen W, Zheng L, Guo X, Cline HT. Excitatory synaptic dysfunction cell-autonomously decreases inhibitory inputs and disrupts structural and functional plasticity. Nat Commun 2018; 9:2893. [PMID: 30042473 PMCID: PMC6057951 DOI: 10.1038/s41467-018-05125-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 06/08/2018] [Indexed: 12/23/2022] Open
Abstract
Functional circuit assembly is thought to require coordinated development of excitation and inhibition, but whether they are co-regulated cell-autonomously remains unclear. We investigate effects of decreased glutamatergic synaptic input on inhibitory synapses by expressing AMPAR subunit, GluA1 and GluA2, C-terminal peptides (GluA1CTP and GluA2CTP) in developing Xenopus tectal neurons. GluACTPs decrease excitatory synaptic inputs and cell-autonomously decreases inhibitory synaptic inputs in excitatory and inhibitory neurons. Visually evoked excitatory and inhibitory currents decrease proportionately, maintaining excitation/inhibition. GluACTPs affect dendrite structure and visual experience-dependent structural plasticity differently in excitatory and inhibitory neurons. Deficits in excitatory and inhibitory synaptic transmission and experience-dependent plasticity manifest in altered visual receptive field properties. Both visual avoidance behavior and learning-induced behavioral plasticity are impaired, suggesting that maintaining excitation/inhibition alone is insufficient to preserve circuit function. We demonstrate that excitatory synaptic dysfunction in individual neurons cell-autonomously decreases inhibitory inputs and disrupts neuronal and circuit plasticity, information processing and learning. Both inhibitory and excitatory input development are shaped by activity, but one may be dependent on the other. Here, the authors examine plasticity of inhibitory inputs in vivo, as well as behavioral consequences in tadpoles where excitatory transmission has been impaired.
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Affiliation(s)
- Hai-Yan He
- The Dorris Neuroscience Center, Department of Neuroscience, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Wanhua Shen
- Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, 310036, China.
| | - Lijun Zheng
- Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, 310036, China
| | - Xia Guo
- Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, 310036, China
| | - Hollis T Cline
- The Dorris Neuroscience Center, Department of Neuroscience, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA.
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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: 22] [Impact Index Per Article: 3.7] [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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Gambrill AC, Faulkner RL, Cline HT. Direct intertectal inputs are an integral component of the bilateral sensorimotor circuit for behavior in Xenopus tadpoles. J Neurophysiol 2018; 119:1947-1961. [PMID: 29442555 DOI: 10.1152/jn.00051.2018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The circuit controlling visually guided behavior in nonmammalian vertebrates, such as Xenopus tadpoles, includes retinal projections to the contralateral optic tectum, where visual information is processed, and tectal motor outputs projecting ipsilaterally to hindbrain and spinal cord. Tadpoles have an intertectal commissure whose function is unknown, but it might transfer information between the tectal lobes. Differences in visual experience between the two eyes have profound effects on the development and function of visual circuits in animals with binocular vision, but the effects on animals with fully crossed retinal projections are not clear. We tested the effect of monocular visual experience on the visuomotor circuit in Xenopus tadpoles. We show that cutting the intertectal commissure or providing visual experience to one eye (monocular visual experience) is sufficient to disrupt tectally mediated visual avoidance behavior. Monocular visual experience induces asymmetry in tectal circuit activity across the midline. Repeated exposure to monocular visual experience drives maturation of the stimulated retinotectal synapses, seen as increased AMPA-to-NMDA ratios, induces synaptic plasticity in intertectal synaptic connections, and induces bilaterally asymmetric changes in the tectal excitation-to-inhibition ratio (E/I). We show that unilateral expression of peptides that interfere with AMPA or GABAA receptor trafficking alters E/I in the transfected tectum and is sufficient to degrade visuomotor behavior. Our study demonstrates that monocular visual experience in animals with fully crossed visual systems produces asymmetric circuit function across the midline and degrades visuomotor behavior. The data further suggest that intertectal inputs are an integral component of a bilateral visuomotor circuit critical for behavior. NEW & NOTEWORTHY The developing optic tectum of Xenopus tadpoles represents a unique circuit in which laterally positioned eyes provide sensory input to a circuit that is transiently monocular, but which will be binocular in the animal's adulthood. We challenge the idea that the two lobes of tadpole optic tectum function independently by testing the requirement of interhemispheric communication and demonstrate that unbalanced sensory input can induce structural and functional plasticity in the tectum sufficient to disrupt function.
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Affiliation(s)
- Abigail C Gambrill
- Department of Neuroscience, Dorris Neuroscience Center, The Scripps Research Institute , La Jolla, California
| | - Regina L Faulkner
- Department of Neuroscience, Dorris Neuroscience Center, The Scripps Research Institute , La Jolla, California
| | - Hollis T Cline
- Department of Neuroscience, Dorris Neuroscience Center, The Scripps Research Institute , La Jolla, California
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Liu HH, McClatchy DB, Schiapparelli L, Shen W, Yates JR, Cline HT. Role of the visual experience-dependent nascent proteome in neuronal plasticity. eLife 2018; 7:e33420. [PMID: 29412139 PMCID: PMC5815848 DOI: 10.7554/elife.33420] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 02/05/2018] [Indexed: 01/02/2023] Open
Abstract
Experience-dependent synaptic plasticity refines brain circuits during development. To identify novel protein synthesis-dependent mechanisms contributing to experience-dependent plasticity, we conducted a quantitative proteomic screen of the nascent proteome in response to visual experience in Xenopus optic tectum using bio-orthogonal metabolic labeling (BONCAT). We identified 83 differentially synthesized candidate plasticity proteins (CPPs). The CPPs form strongly interconnected networks and are annotated to a variety of biological functions, including RNA splicing, protein translation, and chromatin remodeling. Functional analysis of select CPPs revealed the requirement for eukaryotic initiation factor three subunit A (eIF3A), fused in sarcoma (FUS), and ribosomal protein s17 (RPS17) in experience-dependent structural plasticity in tectal neurons and behavioral plasticity in tadpoles. These results demonstrate that the nascent proteome is dynamic in response to visual experience and that de novo synthesis of machinery that regulates RNA splicing and protein translation is required for experience-dependent plasticity.
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Affiliation(s)
- Han-Hsuan Liu
- The Dorris Neuroscience CenterThe Scripps Research InstituteLa JollaUnited States
- Department of NeuroscienceThe Scripps Research InstituteLa JollaUnited States
- Kellogg School of Science and TechnologyThe Scripps Research InstituteLa JollaUnited States
| | - Daniel B McClatchy
- Department of Molecular MedicineThe Scripps Research InstituteLa JollaUnited States
| | - Lucio Schiapparelli
- The Dorris Neuroscience CenterThe Scripps Research InstituteLa JollaUnited States
- Department of NeuroscienceThe Scripps Research InstituteLa JollaUnited States
| | - Wanhua Shen
- The Dorris Neuroscience CenterThe Scripps Research InstituteLa JollaUnited States
- Department of NeuroscienceThe Scripps Research InstituteLa JollaUnited States
- Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental SciencesHangzhou Normal UniversityHangzhouChina
| | - John R Yates
- Department of NeuroscienceThe Scripps Research InstituteLa JollaUnited States
- Department of Molecular MedicineThe Scripps Research InstituteLa JollaUnited States
| | - Hollis T Cline
- The Dorris Neuroscience CenterThe Scripps Research InstituteLa JollaUnited States
- Department of NeuroscienceThe Scripps Research InstituteLa JollaUnited States
- Kellogg School of Science and TechnologyThe Scripps Research InstituteLa JollaUnited States
- Department of Molecular MedicineThe Scripps Research InstituteLa JollaUnited States
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Thyroid Hormone Acts Locally to Increase Neurogenesis, Neuronal Differentiation, and Dendritic Arbor Elaboration in the Tadpole Visual System. J Neurosci 2017; 36:10356-10375. [PMID: 27707971 DOI: 10.1523/jneurosci.4147-15.2016] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 08/01/2016] [Indexed: 11/21/2022] Open
Abstract
Thyroid hormone (TH) regulates many cellular events underlying perinatal brain development in vertebrates. Whether and how TH regulates brain development when neural circuits are first forming is less clear. Furthermore, although the molecular mechanisms that impose spatiotemporal constraints on TH action in the brain have been described, the effects of local TH signaling are poorly understood. We determined the effects of manipulating TH signaling on development of the optic tectum in stage 46-49 Xenopus laevis tadpoles. Global TH treatment caused large-scale morphological effects in tadpoles, including changes in brain morphology and increased tectal cell proliferation. Either increasing or decreasing endogenous TH signaling in tectum, by combining targeted DIO3 knockdown and methimazole, led to corresponding changes in tectal cell proliferation. Local increases in TH, accomplished by injecting suspensions of tri-iodothyronine (T3) in coconut oil into the midbrain ventricle or into the eye, selectively increased tectal or retinal cell proliferation, respectively. In vivo time-lapse imaging demonstrated that local TH first increased tectal progenitor cell proliferation, expanding the progenitor pool, and subsequently increased neuronal differentiation. Local T3 also dramatically increased dendritic arbor growth in neurons that had already reached a growth plateau. The time-lapse data indicate that the same cells are differentially sensitive to T3 at different time points. Finally, TH increased expression of genes pertaining to proliferation and neuronal differentiation. These experiments indicate that endogenous TH locally regulates neurogenesis at developmental stages relevant to circuit assembly by affecting cell proliferation and differentiation and by acting on neurons to increase dendritic arbor elaboration. SIGNIFICANCE STATEMENT Thyroid hormone (TH) is a critical regulator of perinatal brain development in vertebrates. Abnormal TH signaling in early pregnancy is associated with significant cognitive deficits in humans; however, it is difficult to probe the function of TH in early brain development in mammals because of the inaccessibility of the fetal brain in the uterine environment and the challenge of disambiguating maternal versus fetal contributions of TH. The external development of tadpoles allows manipulation and direct observation of the molecular and cellular mechanisms underlying TH's effects on brain development in ways not possible in mammals. We find that endogenous TH locally regulates neurogenesis at developmental stages relevant to circuit assembly by affecting neural progenitor cell proliferation and differentiation and by acting on neurons to enhance dendritic arbor elaboration.
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Fragile X Mental Retardation Protein Is Required to Maintain Visual Conditioning-Induced Behavioral Plasticity by Limiting Local Protein Synthesis. J Neurosci 2017; 36:7325-39. [PMID: 27383604 DOI: 10.1523/jneurosci.4282-15.2016] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 05/28/2016] [Indexed: 12/30/2022] Open
Abstract
UNLABELLED Fragile X mental retardation protein (FMRP) is thought to regulate neuronal plasticity by limiting dendritic protein synthesis, but direct demonstration of a requirement for FMRP control of local protein synthesis during behavioral plasticity is lacking. Here we tested whether FMRP knockdown in Xenopus optic tectum affects local protein synthesis in vivo and whether FMRP knockdown affects protein synthesis-dependent visual avoidance behavioral plasticity. We tagged newly synthesized proteins by incorporation of the noncanonical amino acid azidohomoalanine and visualized them with fluorescent noncanonical amino acid tagging (FUNCAT). Visual conditioning and FMRP knockdown produce similar increases in FUNCAT in tectal neuropil. Induction of visual conditioning-dependent behavioral plasticity occurs normally in FMRP knockdown animals, but plasticity degrades over 24 h. These results indicate that FMRP affects visual conditioning-induced local protein synthesis and is required to maintain the visual conditioning-induced behavioral plasticity. SIGNIFICANCE STATEMENT Fragile X syndrome (FXS) is the most common form of inherited intellectual disability. Exaggerated dendritic protein synthesis resulting from loss of fragile X mental retardation protein (FMRP) is thought to underlie cognitive deficits in FXS, but no direct evidence has demonstrated that FMRP-regulated dendritic protein synthesis affects behavioral plasticity in intact animals. Xenopus tadpoles exhibit a visual avoidance behavior that improves with visual conditioning in a protein synthesis-dependent manner. We showed that FMRP knockdown and visual conditioning dramatically increase protein synthesis in neuronal processes. Furthermore, induction of visual conditioning-dependent behavioral plasticity occurs normally after FMRP knockdown, but performance rapidly deteriorated in the absence of FMRP. These studies show that FMRP negatively regulates local protein synthesis and is required to maintain visual conditioning-induced behavioral plasticity in vivo.
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32
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Ramberger E, Dittmar G. Tissue Specific Labeling in Proteomics. Proteomes 2017; 5:proteomes5030017. [PMID: 28718811 PMCID: PMC5620534 DOI: 10.3390/proteomes5030017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 07/13/2017] [Accepted: 07/14/2017] [Indexed: 01/08/2023] Open
Abstract
Mass spectrometry-based proteomics is a powerful tool for identifying and quantifying proteins in biological samples. While it is routinely used for the characterization of simple cell line systems, the analysis of the cell specific proteome in multicellular organisms and tissues poses a significant challenge. Isolating a subset of cells from tissues requires mechanical and biochemical separation or sorting, a process which can alter cellular signaling, and thus, the composition of the proteome. Recently, several approaches for cell selective labeling of proteins, that include bioorthogonal amino acids, biotinylating enzymes, and genetic tools, have been developed. These tools facilitate the selective labeling of proteins, their interactome, or of specific cell types within a tissue or an organism, while avoiding the difficult and contamination-prone biochemical separation of cells from the tissue. In this review, we give an overview of existing techniques and their application in cell culture models and whole animals.
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Affiliation(s)
- Evelyn Ramberger
- Mass-Spectrometry Core Unit, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany.
- Berlin School of Integrative Oncology (BSIO), Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany.
| | - Gunnar Dittmar
- Proteome and Genome Research Laboratory, Luxembourg Institute of Health, 1272 Strassen, Luxembourg.
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Ruan H, Gao J, Qi X, Tao Y, Guo X, Guo Z, Zheng L, Song Y, Liao Y, Shen W. Visual experience dependent regulation of neuronal structure and function by histone deacetylase 1 in developing Xenopus tectum in vivo. Dev Neurobiol 2017; 77:947-962. [PMID: 28033671 DOI: 10.1002/dneu.22480] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 12/13/2016] [Accepted: 12/16/2016] [Indexed: 01/28/2023]
Abstract
Histone deacetylase 1 (HDAC1) is thought to play pivotal roles in neurogenesis and neurodegeneration. However, the role of HDAC1 in neuronal growth and structural plasticity in the developing brain in vivo remains unclear. Here, we show that in the optic tectum of Xenopus laevis, HDAC1 knockdown dramatically decreased the frequency of AMPAR-mediated synaptic currents and increased the frequency of GABAAR-mediated currents, whereas HDAC1 overexpression significantly decreased the frequency of GABAAR-mediated synaptic currents. Both HDAC1 knockdown and overexpression adversely affected dendritic arbor growth and visual experience-dependent structural plasticity. Furthermore, HDAC1 knockdown decreased BDNF expression via a mechanism that involves acetylation of specific histone H4 residues at lysine K5. In particular, the deficits in dendritic growth and visually guided avoidance behavior in HDAC1-knockdown tadpoles could be rescued by acute tectal infusion of BDNF. These results establish a relationship between HDAC1 expression, histone H4 modification and BDNF signaling in the visual-experience dependent regulation of dendritic growth, structural plasticity and function in intact animals in vivo. © 2016 Wiley Periodicals, Inc. Develop Neurobiol 77: 947-962, 2017.
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Affiliation(s)
- Hangze Ruan
- Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, 310036, China
| | - Juanmei Gao
- Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, 310036, China
| | - Xianjie Qi
- Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, 310036, China
| | - Yi Tao
- Department of Neurosurgery, Nanjing Medical University Affiliated Jiangsu Cancer Hospital, Nanjing, Jiangsu, 210029, China
| | - Xia Guo
- Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, 310036, China
| | - Zhaoyi Guo
- Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, 310036, China
| | - Lijun Zheng
- Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, 310036, China
| | - Yaling Song
- Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, 310036, China
| | - Yuan Liao
- Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, 310036, China
| | - Wanhua Shen
- Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, 310036, China
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Visualizing Local Protein Synthesis and Its Modulation by FMRP and Visual Experience. J Neurosci 2016; 36:11834-11836. [PMID: 27881771 DOI: 10.1523/jneurosci.2803-16.2016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 10/11/2016] [Accepted: 10/19/2016] [Indexed: 11/21/2022] Open
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Chen YP, Bai GS, Wu MF, Chiao CC, Huang YS. Loss of CPEB3 Upregulates MEGF10 to Impair Mosaic Development of ON Starburst Amacrine Cells. Front Mol Neurosci 2016; 9:105. [PMID: 27822178 PMCID: PMC5075539 DOI: 10.3389/fnmol.2016.00105] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2016] [Accepted: 10/04/2016] [Indexed: 01/20/2023] Open
Abstract
Cytoplasmic polyadenylation element binding protein 3 (CPEB3) regulates target RNA translation in neurons. Here, we examined CPEB3 distribution and function in the mouse retina. CPEB3 is expressed in retinal neurons, including those located in the inner nuclear layer (INL) and ganglion cell layer (GCL) but not in cone and rod photoreceptors in the outer nuclear layer (ONL). A previous study found CPEB3 expressed in cholinergic starburst amacrine cells (SACs). We first examined these cells and observed aberrant SAC mosaicism in CPEB3-knockout (KO) retinas. Retinal neurons showed orderly spatial arrangements. Many individual subtypes are organized non-randomly in patterns called mosaics. Despite CPEB3 being expressed in both populations of SACs, OFF SACs in the INL and ON SACs in the GCL, aberrant mosaic regularity was observed in only ON SACs of CPEB3-KO retinas. Molecular characterization revealed that translation of multiple epidermal growth factor 10 (Megf10) RNA is suppressed by CPEB3 during the first week of postnatal development, when MEGF10 is primarily expressed in SACs and mediates homotypic repulsive interactions to define intercellular spacing of SACs. Thus, elevated MEGF10 expression in the absence of the translational repressor CPEB3 may account for the defective spatial organization of ON SACs. Our findings uncover for the first time that translational control plays a role in shaping retinal mosaic arrangement.
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Affiliation(s)
- Yin-Peng Chen
- Institute of Biomedical Sciences, Academia Sinica Taipei, Taiwan
| | - Geng-Shuo Bai
- Institute of Biomedical Sciences, Academia SinicaTaipei, Taiwan; Institute of Neuroscience, National Yang-Ming UniversityTaipei, Taiwan
| | - Meng-Fang Wu
- Institute of Biomedical Sciences, Academia Sinica Taipei, Taiwan
| | - Chuan-Chin Chiao
- Institute of Systems Neuroscience and Department of Life Science, National Tsing-Hua University Hsinchu, Taiwan
| | - Yi-Shuian Huang
- Institute of Biomedical Sciences, Academia SinicaTaipei, Taiwan; Institute of Neuroscience, National Yang-Ming UniversityTaipei, Taiwan
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Pratt KG, Hiramoto M, Cline HT. An Evolutionarily Conserved Mechanism for Activity-Dependent Visual Circuit Development. Front Neural Circuits 2016; 10:79. [PMID: 27818623 PMCID: PMC5073143 DOI: 10.3389/fncir.2016.00079] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 09/26/2016] [Indexed: 12/01/2022] Open
Abstract
Neural circuit development is an activity-dependent process. This activity can be spontaneous, such as the retinal waves that course across the mammalian embryonic retina, or it can be sensory-driven, such as the activation of retinal ganglion cells (RGCs) by visual stimuli. Whichever the source, neural activity provides essential instruction to the developing circuit. Indeed, experimentally altering activity has been shown to impact circuit development and function in many different ways and in many different model systems. In this review, we contemplate the idea that retinal waves in amniotes, the animals that develop either in ovo or utero (namely reptiles, birds and mammals) could be an evolutionary adaptation to life on land, and that the anamniotes, animals whose development is entirely external (namely the aquatic amphibians and fish), do not display retinal waves, most likely because they simply don’t need them. We then review what is known about the function of both retinal waves and visual stimuli on their respective downstream targets, and predict that the experience-dependent development of the tadpole visual system is a blueprint of what will be found in future studies of the effects of spontaneous retinal waves on instructing development of retinorecipient targets such as the superior colliculus (SC) and the lateral geniculate nucleus.
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Affiliation(s)
- Kara G Pratt
- Program in Neuroscience, Department of Zoology and Physiology, University of Wyoming Laramie, WY, USA
| | - Masaki Hiramoto
- Department of Molecular and Cellular Neuroscience and The Dorris Neuroscience Center, The Scripps Research Institute La Jolla, CA, USA
| | - Hollis T Cline
- Department of Molecular and Cellular Neuroscience and The Dorris Neuroscience Center, The Scripps Research Institute La Jolla, CA, USA
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Gao J, Ruan H, Qi X, Tao Y, Guo X, Shen W. HDAC3 But not HDAC2 Mediates Visual Experience-Dependent Radial Glia Proliferation in the Developing Xenopus Tectum. Front Cell Neurosci 2016; 10:221. [PMID: 27729849 PMCID: PMC5037170 DOI: 10.3389/fncel.2016.00221] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Accepted: 09/09/2016] [Indexed: 01/12/2023] Open
Abstract
Radial glial cells (RGs) are one of the important progenitor cells that can differentiate into neurons or glia to form functional neural circuits in the developing central nervous system (CNS). Histone deacetylases (HDACs) has been associated with visual activity dependent changes in BrdU-positive progenitor cells in the developing brain. We previously have shown that HDAC1 is involved in the experience-dependent proliferation of RGs. However, it is less clear whether two other members of class I HDACs, HDAC2 and HDAC3, are involved in the regulation of radial glia proliferation. Here, we reported that HDAC2 and HDAC3 expression were developmentally regulated in tectal cells, especially in the ventricular layer of the BLBP-positive RGs. Pharmacological blockade using an inhibitor of class I HDACs, MS-275, decreased the number of BrdU-positive dividing progenitor cells. Specific knockdown of HDAC3 but not HDAC2 decreased the number of BrdU- and BLBP-labeled cells, suggesting that the proliferation of radial glia was selectively mediated by HDAC3. Visual deprivation induced selective augmentation of histone H4 acetylation at lysine 16 in BLBP-positive cells. Furthermore, the visual deprivation-induced increase in BrdU-positive cells was partially blocked by HDAC3 downregulation but not by HDAC2 knockdown at stage 49 tadpoles. These data revealed a specific role of HDAC3 in experience-dependent radial glia proliferation during the development of Xenopus tectum.
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Affiliation(s)
- Juanmei Gao
- Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental Sciences, Hangzhou Normal University Hangzhou, Zhejiang, China
| | - Hangze Ruan
- Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental Sciences, Hangzhou Normal University Hangzhou, Zhejiang, China
| | - Xianjie Qi
- Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental Sciences, Hangzhou Normal University Hangzhou, Zhejiang, China
| | - Yi Tao
- Department of Neurosurgery, Nanjing Medical University and Jiangsu Cancer Hospital Nanjing, Jiangsu, China
| | - Xia Guo
- Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental Sciences, Hangzhou Normal University Hangzhou, Zhejiang, China
| | - Wanhua Shen
- Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental Sciences, Hangzhou Normal University Hangzhou, Zhejiang, China
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38
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Increased apoptosis and abnormal visual behavior by histone modifications with exposure to para-xylene in developing Xenopus. Neuroscience 2016; 331:177-85. [DOI: 10.1016/j.neuroscience.2016.06.027] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2016] [Revised: 05/30/2016] [Accepted: 06/14/2016] [Indexed: 11/23/2022]
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39
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Incorporation of non-canonical amino acids into the developing murine proteome. Sci Rep 2016; 6:32377. [PMID: 27572480 PMCID: PMC5004113 DOI: 10.1038/srep32377] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 08/09/2016] [Indexed: 12/25/2022] Open
Abstract
Analysis of the developing proteome has been complicated by a lack of tools that can be easily employed to label and identify newly synthesized proteins within complex biological mixtures. Here, we demonstrate that the methionine analogs azidohomoalanine and homopropargylglycine can be globally incorporated into the proteome of mice through facile intraperitoneal injections. These analogs contain bio-orthogonal chemical handles to which fluorescent tags can be conjugated to identify newly synthesized proteins. We show these non-canonical amino acids are incorporated into various tissues in juvenile mice and in a concentration dependent manner. Furthermore, administration of these methionine analogs to pregnant dams during a critical stage of murine development, E10.5-12.5 when many tissues are assembling, does not overtly disrupt development as assessed by proteomic analysis and normal parturition and growth of pups. This successful demonstration that non-canonical amino acids can be directly administered in vivo will enable future studies that seek to characterize the murine proteome during growth, disease and repair.
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40
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Liu Z, Hamodi AS, Pratt KG. Early development and function of the Xenopus tadpole retinotectal circuit. Curr Opin Neurobiol 2016; 41:17-23. [PMID: 27475307 DOI: 10.1016/j.conb.2016.07.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 06/28/2016] [Accepted: 07/10/2016] [Indexed: 01/14/2023]
Abstract
The retinotectal circuit is the major component of the amphibian visual system. It is comprised of the retinal ganglion cells (RGCs) in the eye, which project their axons to the optic tectum and form synapses onto postsynaptic tectal neurons. The retinotectal circuit is relatively simple, and develops quickly: Xenopus tadpoles begin displaying retinotectal-dependent visual avoidance behaviors by approximately 7-8 days post-fertilization, early larval stage. In this review we first provide a summary of the dynamic development of the retinotectal circuit, including the microcircuitry formed by local tectal-tectal connections within the tectum. Second, we discuss the basic visual avoidance behavior generated specifically by this circuit, and how this behavior is being used as an assay to test visual system function.
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Affiliation(s)
- Zhenyu Liu
- Department of Zoology and Physiology and Program in Neuroscience, University of Wyoming, Laramie, WY 82071, United States
| | - Ali S Hamodi
- Department of Zoology and Physiology and Program in Neuroscience, University of Wyoming, Laramie, WY 82071, United States
| | - Kara G Pratt
- Department of Zoology and Physiology and Program in Neuroscience, University of Wyoming, Laramie, WY 82071, United States.
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41
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Zhou A. Proteomics in stroke research: potentials of the nascent proteomics. J Investig Med 2016; 64:1236-1240. [PMID: 27430243 DOI: 10.1136/jim-2016-000186] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 06/23/2016] [Accepted: 06/27/2016] [Indexed: 01/22/2023]
Abstract
Among omics, the proteomics assumes a unique role in that it offers the effectors or actuators of a biological condition. This brief review attempts to summarize the development in a relatively new but important subdiscipline of proteomics, the so-called nascent proteomics, and its potential applications in stroke research. First, we will discuss a few examples of proteomics-led discoveries in stroke research, and challenges or unmet demands when using commonly practiced proteomics approaches. Then we will introduce nascent proteomics and its studying tools, followed by discussions on its potentials in stroke research.
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42
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Guo X, Ruan H, Li X, Qin L, Tao Y, Qi X, Gao J, Gan L, Duan S, Shen W. Subcellular Localization of Class I Histone Deacetylases in the Developing Xenopus tectum. Front Cell Neurosci 2016; 9:510. [PMID: 26793062 PMCID: PMC4709447 DOI: 10.3389/fncel.2015.00510] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 12/20/2015] [Indexed: 11/13/2022] Open
Abstract
Histone deacetylases (HDACs) are thought to localize in the nucleus to regulate gene transcription and play pivotal roles in neurogenesis, apoptosis, and plasticity. However, the subcellular distribution of class I HDACs in the developing brain remains unclear. Here, we show that HDAC1 and HDAC2 are located in both the mitochondria and the nucleus in the Xenopus laevis stage 34 tectum and are mainly restricted to the nucleus following further brain development. HDAC3 is widely present in the mitochondria, nucleus, and cytoplasm during early tectal development and is mainly distributed in the nucleus in stage 45 tectum. In contrast, HDAC8 is broadly located in the mitochondria, nucleus, and cytoplasm during tectal development. These data demonstrate that HDAC1, HDAC2, and HDAC3 are transiently localized in the mitochondria and that the subcellular distribution of class I HDACs in the Xenopus tectum is heterogeneous. Furthermore, we observed that spherical mitochondria accumulate in the cytoplasm at earlier stages, whereas elongated mitochondria are evenly distributed in the tectum at later stages. The activity of histone acetylation (H4K12) remains low in mitochondria during tectal development. Pharmacological blockades of HDACs using a broad spectrum HDAC inhibitor of Trichostatin A (TSA) or specific class I HDAC inhibitors of MS-275 and MGCD0103 decrease the number of mitochondria in the tectum at stage 34. These findings highlight a link between the subcellular distribution of class I HDACs and mitochondrial dynamics in the developing optic tectum of Xenopus laevis.
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Affiliation(s)
- Xia Guo
- Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental Sciences, Hangzhou Normal University Hangzhou, China
| | - Hangze Ruan
- Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental Sciences, Hangzhou Normal University Hangzhou, China
| | - Xia Li
- Key Laboratory of Medical Neurobiology of Ministry of Health of China, Key Laboratory of Neurobiology, Department of Neurobiology, Zhejiang University School of Medicine Hangzhou, China
| | - Liming Qin
- Key Laboratory of Medical Neurobiology of Ministry of Health of China, Key Laboratory of Neurobiology, Department of Neurobiology, Zhejiang University School of Medicine Hangzhou, China
| | - Yi Tao
- Department of Neurosurgery, First Affiliated Hospital of Nanjing Medical University Nanjing, China
| | - Xianjie Qi
- Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental Sciences, Hangzhou Normal University Hangzhou, China
| | - Juanmei Gao
- Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental Sciences, Hangzhou Normal University Hangzhou, China
| | - Lin Gan
- Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental Sciences, Hangzhou Normal University Hangzhou, China
| | - Shumin Duan
- Key Laboratory of Medical Neurobiology of Ministry of Health of China, Key Laboratory of Neurobiology, Department of Neurobiology, Zhejiang University School of Medicine Hangzhou, China
| | - Wanhua Shen
- Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental Sciences, Hangzhou Normal University Hangzhou, China
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43
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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: 56] [Impact Index Per Article: 6.2] [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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44
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Nagaoka K, Fujii K, Zhang H, Usuda K, Watanabe G, Ivshina M, Richter JD. CPEB1 mediates epithelial-to-mesenchyme transition and breast cancer metastasis. Oncogene 2015; 35:2893-901. [PMID: 26411364 PMCID: PMC4809797 DOI: 10.1038/onc.2015.350] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Revised: 07/28/2015] [Accepted: 08/17/2015] [Indexed: 01/08/2023]
Abstract
In mouse mammary epithelial cells, CPEB1 mediates the apical localization of ZO-1 mRNA, which encodes a critical tight junction component. In mice lacking CPEB1 and in cultured cells from which CPEB has been depleted, randomly distributed ZO-1 mRNA leads to the loss of cell polarity. We have investigated whether this diminution of polarity results in an epithelial-to-mesenchyme (EMT) transition and possible increased metastatic potential. Here, we show that CPEB1-depleted mammary epithelial cells alter their gene expression profile in a manner consistent with an EMT and also become motile, which are made particularly robust when cells are treated with TGF-β, an enhancer of EMT. CPEB1-depleted mammary cells become metastatic to the lung following injection into mouse fat pads while ectopically-expressed CPEB1 prevents metastasis. Surprisingly, CPEB1 depletion causes some EMT/metastasis-related mRNAs to have shorter poly(A) tails while other mRNAs to have longer poly(A) tails. Matrix metalloproteinase 9 (MMP9) mRNA, which encodes a metastasis-promoting factor, undergoes poly(A) lengthening and enhanced translation upon CPEB reduction. Moreover, in human breast cancer cells that become progressively more metastatic, CPEB1 is reduced while MMP9 becomes more abundant. These data suggest that at least in part, CPEB1 regulation of MMP9 mRNA expression mediates metastasis of breast cancer cells.
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Affiliation(s)
- K Nagaoka
- Laboratory of Veterinary Physiology, Department of Veterinary Medicine, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - K Fujii
- Laboratory of Veterinary Physiology, Department of Veterinary Medicine, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - H Zhang
- Laboratory of Veterinary Physiology, Department of Veterinary Medicine, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - K Usuda
- Laboratory of Veterinary Physiology, Department of Veterinary Medicine, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - G Watanabe
- Laboratory of Veterinary Physiology, Department of Veterinary Medicine, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - M Ivshina
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - J D Richter
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
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45
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Larance M, Lamond AI. Multidimensional proteomics for cell biology. Nat Rev Mol Cell Biol 2015; 16:269-80. [DOI: 10.1038/nrm3970] [Citation(s) in RCA: 311] [Impact Index Per Article: 34.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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46
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Bestman JE, Huang LC, Lee-Osbourne J, Cheung P, Cline HT. An in vivo screen to identify candidate neurogenic genes in the developing Xenopus visual system. Dev Biol 2015; 408:269-91. [PMID: 25818835 PMCID: PMC4584193 DOI: 10.1016/j.ydbio.2015.03.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2014] [Revised: 01/30/2015] [Accepted: 03/17/2015] [Indexed: 11/26/2022]
Abstract
Neurogenesis in the brain of Xenopus laevis continues throughout larval stages of development. We developed a 2-tier screen to identify candidate genes controlling neurogenesis in Xenopus optic tectum in vivo. First, microarray and NanoString analyses were used to identify candidate genes that were differentially expressed in Sox2-expressing neural progenitor cells or their neuronal progeny. Then an in vivo, time-lapse imaging-based screen was used to test whether morpholinos against 34 candidate genes altered neural progenitor cell proliferation or neuronal differentiation over 3 days in the optic tectum of intact Xenopus tadpoles. We co-electroporated antisense morpholino oligonucleotides against each of the candidate genes with a plasmid that drives GFP expression in Sox2-expressing neural progenitor cells and quantified the effects of morpholinos on neurogenesis. Of the 34 morpholinos tested, 24 altered neural progenitor cell proliferation or neuronal differentiation. The candidates which were tagged as differentially expressed and validated by the in vivo imaging screen include: actn1, arl9, eif3a, elk4, ephb1, fmr1-a, fxr1-1, fbxw7, fgf2, gstp1, hat1, hspa5, lsm6, mecp2, mmp9, and prkaca. Several of these candidates, including fgf2 and elk4, have known or proposed neurogenic functions, thereby validating our strategy to identify candidates. Genes with no previously demonstrated neurogenic functions, gstp1, hspa5 and lsm6, were identified from the morpholino experiments, suggesting that our screen successfully revealed unknown candidates. Genes that are associated with human disease, such as such as mecp2 and fmr1-a, were identified by our screen, providing the groundwork for using Xenopus as an experimental system to probe conserved disease mechanisms. Together the data identify candidate neurogenic regulatory genes and demonstrate that Xenopus is an effective experimental animal to identify and characterize genes that regulate neural progenitor cell proliferation and differentiation in vivo.
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Affiliation(s)
- Jennifer E Bestman
- Drug Discovery & Biomedical Sciences, The Medical University of South Carolina, Charleston, SC 29425, United States
| | - Lin-Chien Huang
- The Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, CA 92037, United States
| | - Jane Lee-Osbourne
- University of Nebraska Medical Center, Omaha, NE 68198, United States
| | - Phillip Cheung
- Dart Neuroscience, LLC, San Diego, CA 92064, United States
| | - Hollis T Cline
- The Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, CA 92037, United States.
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47
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Tao Y, Ruan H, Guo X, Li L, Shen W. HDAC1 regulates the proliferation of radial glial cells in the developing Xenopus tectum. PLoS One 2015; 10:e0120118. [PMID: 25789466 PMCID: PMC4366096 DOI: 10.1371/journal.pone.0120118] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Accepted: 02/04/2015] [Indexed: 12/01/2022] Open
Abstract
In the developing central nervous system (CNS), progenitor cells differentiate into progeny to form functional neural circuits. Radial glial cells (RGs) are a transient progenitor cell type that is present during neurogenesis. It is thought that a combination of neural trophic factors, neurotransmitters and electrical activity regulates the proliferation and differentiation of RGs. However, it is less clear how epigenetic modulation changes RG proliferation. We sought to explore the effect of histone deacetylase (HDAC) activity on the proliferation of RGs in the visual optic tectum of Xenopus laevis. We found that the number of BrdU-labeled precursor cells along the ventricular layer of the tectum decrease developmentally from stage 46 to stage 49. The co-labeling of BrdU-positive cells with brain lipid-binding protein (BLBP), a radial glia marker, showed that the majority of BrdU-labeled cells along the tectal midline are RGs. BLBP-positive cells are also developmentally decreased with the maturation of the brain. Furthermore, HDAC1 expression is developmentally down-regulated in tectal cells, especially in the ventricular layer of the tectum. Pharmacological blockade of HDACs using Trichostatin A (TSA) or Valproic acid (VPA) decreased the number of BrdU-positive, BLBP-positive and co-labeling cells. Specific knockdown of HDAC1 by a morpholino (HDAC1-MO) decreased the number of BrdU- and BLBP-labeled cells and increased the acetylation level of histone H4 at lysine 12 (H4K12). The visual deprivation-induced increase in BrdU- and BLBP-positive cells was blocked by HDAC1 knockdown at stage 49 tadpoles. These data demonstrate that HDAC1 regulates radial glia cell proliferation in the developing optical tectum of Xenopus laevis.
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Affiliation(s)
- Yi Tao
- Department of Neurosurgery, First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, Jiangsu, 210029, China
| | - Hangze Ruan
- Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Xia Guo
- Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Lixin Li
- Department of Neurosurgery, First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, Jiangsu, 210029, China
- * E-mail: (LL); (WS)
| | - Wanhua Shen
- Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, China
- * E-mail: (LL); (WS)
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48
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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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49
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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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50
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Khakhalin AS, Koren D, Gu J, Xu H, Aizenman CD. Excitation and inhibition in recurrent networks mediate collision avoidance in Xenopus tadpoles. Eur J Neurosci 2014; 40:2948-62. [PMID: 24995793 DOI: 10.1111/ejn.12664] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 04/23/2014] [Accepted: 05/28/2014] [Indexed: 01/24/2023]
Abstract
Information processing in the vertebrate brain is thought to be mediated through distributed neural networks, but it is still unclear how sensory stimuli are encoded and detected by these networks, and what role synaptic inhibition plays in this process. Here we used a collision avoidance behavior in Xenopus tadpoles as a model for stimulus discrimination and recognition. We showed that the visual system of the tadpole is selective for behaviorally relevant looming stimuli, and that the detection of these stimuli first occurs in the optic tectum. By comparing visually guided behavior, optic nerve recordings, excitatory and inhibitory synaptic currents, and the spike output of tectal neurons, we showed that collision detection in the tadpole relies on the emergent properties of distributed recurrent networks within the tectum. We found that synaptic inhibition was temporally correlated with excitation, and did not actively sculpt stimulus selectivity, but rather it regulated the amount of integration between direct inputs from the retina and recurrent inputs from the tectum. Both pharmacological suppression and enhancement of synaptic inhibition disrupted emergent selectivity for looming stimuli. Taken together these findings suggested that, by regulating the amount of network activity, inhibition plays a critical role in maintaining selective sensitivity to behaviorally-relevant visual stimuli.
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Affiliation(s)
- Arseny S Khakhalin
- Department of Neuroscience, Brown University, Box G-LN, Providence, RI, 02912, USA
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