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Wingfield JL, Puthanveettil SV. Decoding the complex journeys of RNAs along neurons. Nucleic Acids Res 2025; 53:gkaf293. [PMID: 40243060 PMCID: PMC12004114 DOI: 10.1093/nar/gkaf293] [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: 12/29/2024] [Revised: 03/25/2025] [Accepted: 03/28/2025] [Indexed: 04/18/2025] Open
Abstract
Neurons are highly polarized, specialized cells that must overcome immense challenges to ensure the health and survival of the organism in which they reside. They can spread over meters and persist for decades yet communicate at sub-millisecond and millimeter scales. Thus, neurons require extreme levels of spatial-temporal control. Neurons employ molecular motors to transport coding and noncoding RNAs to distal synapses. Intracellular trafficking of RNAs enables neurons to locally regulate protein synthesis and synaptic activity. The way in which RNAs get loaded onto molecular motors and transported to their target locations, particularly following synaptic plasticity, is explored below.
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Affiliation(s)
- Jenna L Wingfield
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, United States
| | - Sathyanarayanan V Puthanveettil
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, United States
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2
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Badal KK, Sadhu A, Raveendra BL, McCracken C, Lozano‐Villada S, Shetty AC, Gillette P, Zhao Y, Stommes D, Fieber LA, Schmale MC, Mahurkar A, Hawkins RD, Puthanveettil SV. Single-neuron analysis of aging-associated changes in learning reveals impairments in transcriptional plasticity. Aging Cell 2024; 23:e14228. [PMID: 38924663 PMCID: PMC11488329 DOI: 10.1111/acel.14228] [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: 04/20/2024] [Accepted: 05/02/2024] [Indexed: 06/28/2024] Open
Abstract
The molecular mechanisms underlying age-related declines in learning and long-term memory are still not fully understood. To address this gap, our study focused on investigating the transcriptional landscape of a singularly identified motor neuron L7 in Aplysia, which is pivotal in a specific type of nonassociative learning known as sensitization of the siphon-withdraw reflex. Employing total RNAseq analysis on a single isolated L7 motor neuron after short-term or long-term sensitization (LTS) training of Aplysia at 8, 10, and 12 months (representing mature, late mature, and senescent stages), we uncovered aberrant changes in transcriptional plasticity during the aging process. Our findings specifically highlight changes in the expression of messenger RNAs (mRNAs) that encode transcription factors, translation regulators, RNA methylation participants, and contributors to cytoskeletal rearrangements during learning and long noncoding RNAs (lncRNAs). Furthermore, our comparative gene expression analysis identified distinct transcriptional alterations in two other neurons, namely the motor neuron L11 and the giant cholinergic neuron R2, whose roles in LTS are not yet fully elucidated. Taken together, our analyses underscore cell type-specific impairments in the expression of key components related to learning and memory within the transcriptome as organisms age, shedding light on the complex molecular mechanisms driving cognitive decline during aging.
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Affiliation(s)
- Kerriann K. Badal
- Department of NeuroscienceThe Herbert Wertheim UF Scripps Institute for Biomedical Innovation & TechnologyJupiterFloridaUSA
- Integrated Biology Graduate ProgramFlorida Atlantic UniversityJupiterFloridaUSA
| | - Abhishek Sadhu
- Department of NeuroscienceThe Herbert Wertheim UF Scripps Institute for Biomedical Innovation & TechnologyJupiterFloridaUSA
- Present address:
Center for Alzheimer's and Neurodegenerative Diseases, Peter O’Donnell Jr. Brain InstituteUniversity of Texas Southwestern Medical CenterDallasTexasUSA
| | - Bindu L. Raveendra
- Department of NeuroscienceThe Herbert Wertheim UF Scripps Institute for Biomedical Innovation & TechnologyJupiterFloridaUSA
| | - Carrie McCracken
- The Institute for Genome SciencesUniversity of Maryland School of MedicineBaltimoreMarylandUSA
| | - Sebastian Lozano‐Villada
- Department of NeuroscienceThe Herbert Wertheim UF Scripps Institute for Biomedical Innovation & TechnologyJupiterFloridaUSA
- Harriet L. Wilkes Honors CollegeFlorida Atlantic UniversityJupiterFloridaUSA
| | - Amol C. Shetty
- The Institute for Genome SciencesUniversity of Maryland School of MedicineBaltimoreMarylandUSA
| | - Phillip Gillette
- National Resource for AplysiaUniversity of Miami Rosenstiel School of Marine, Atmospheric, and Earth SciencesMiamiFloridaUSA
| | - Yibo Zhao
- Department of NeuroscienceThe Herbert Wertheim UF Scripps Institute for Biomedical Innovation & TechnologyJupiterFloridaUSA
| | - Dustin Stommes
- National Resource for AplysiaUniversity of Miami Rosenstiel School of Marine, Atmospheric, and Earth SciencesMiamiFloridaUSA
| | - Lynne A. Fieber
- National Resource for AplysiaUniversity of Miami Rosenstiel School of Marine, Atmospheric, and Earth SciencesMiamiFloridaUSA
| | - Michael C. Schmale
- National Resource for AplysiaUniversity of Miami Rosenstiel School of Marine, Atmospheric, and Earth SciencesMiamiFloridaUSA
| | - Anup Mahurkar
- The Institute for Genome SciencesUniversity of Maryland School of MedicineBaltimoreMarylandUSA
| | - Robert D. Hawkins
- Department of NeuroscienceColumbia UniversityNew YorkNew YorkUSA
- New York State Psychiatric InstituteNew YorkNew YorkUSA
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3
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Badal KK, Zhao Y, Raveendra BL, Lozano-Villada S, Miller KE, Puthanveettil SV. PKA Activity-Driven Modulation of Bidirectional Long-Distance transport of Lysosomal vesicles During Synapse Maintenance. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.28.601272. [PMID: 38979384 PMCID: PMC11230415 DOI: 10.1101/2024.06.28.601272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
The bidirectional long-distance transport of organelles is crucial for cell body-synapse communication. However, the mechanisms by which this transport is modulated for synapse formation, maintenance, and plasticity are not fully understood. Here, we demonstrate through quantitative analyses that maintaining sensory neuron-motor neuron synapses in the Aplysia gill-siphon withdrawal reflex is linked to a sustained reduction in the retrograde transport of lysosomal vesicles in sensory neurons. Interestingly, while mitochondrial transport in the anterograde direction increases within 12 hours of synapse formation, the reduction in lysosomal vesicle retrograde transport appears three days after synapse formation. Moreover, we find that formation of new synapses during learning induced by neuromodulatory neurotransmitter serotonin further reduces lysosomal vesicle transport within 24 hours, whereas mitochondrial transport increases in the anterograde direction within one hour of exposure. Pharmacological inhibition of several signaling pathways pinpoints PKA as a key regulator of retrograde transport of lysosomal vesicles during synapse maintenance. These results demonstrate that synapse formation leads to organelle-specific and direction specific enduring changes in long-distance transport, offering insights into the mechanisms underlying synapse maintenance and plasticity.
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Affiliation(s)
- Kerriann. K. Badal
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, 130 Scripps Way, Jupiter, FL 33458, USA
- Integrative Biology PhD Program, Charles E. Schmidt College of Science, Florida Atlantic University, Jupiter, FL 33458, USA
| | - Yibo. Zhao
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Bindu L Raveendra
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Sebastian Lozano-Villada
- Harriet L. Wilkes Honors College, Florida Atlantic University, 5353 Parkside Drive, Jupiter, FL 33458, USA
| | - Kyle. E. Miller
- Harriet L. Wilkes Honors College, Florida Atlantic University, 5353 Parkside Drive, Jupiter, FL 33458, USA
| | - Sathyanarayanan V. Puthanveettil
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, 130 Scripps Way, Jupiter, FL 33458, USA
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4
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Sadhu A, Badal KK, Zhao Y, Ali AA, Swarnkar S, Tsaprailis G, Crynen GC, Puthanveettil SV. Short-Term and Long-Term Sensitization Differentially Alters the Composition of an Anterograde Transport Complex in Aplysia. eNeuro 2023; 10:ENEURO.0266-22.2022. [PMID: 36549915 PMCID: PMC9829102 DOI: 10.1523/eneuro.0266-22.2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 11/09/2022] [Accepted: 11/22/2022] [Indexed: 12/24/2022] Open
Abstract
Long-term memory formation requires anterograde transport of proteins from the soma of a neuron to its distal synaptic terminals. This allows new synaptic connections to be grown and existing ones remodeled. However, we do not yet know which proteins are transported to synapses in response to activity and temporal regulation. Here, using quantitative mass spectrometry, we have profiled anterograde protein cargos of a learning-regulated molecular motor protein kinesin [Aplysia kinesin heavy chain 1 (ApKHC1)] following short-term sensitization (STS) and long-term sensitization (LTS) in Aplysia californica Our results reveal enrichment of specific proteins associated with ApKHC1 following both STS and LTS, as well as temporal changes within 1 and 3 h of LTS training. A significant number of proteins enriched in the ApKHC1 complex participate in synaptic function, and, while some are ubiquitously enriched across training conditions, a few are enriched in response to specific training. For instance, factors aiding new synapse formation, such as synaptotagmin-1, dynamin-1, and calmodulin, are differentially enriched in anterograde complexes 1 h after LTS but are depleted 3 h after LTS. Proteins including gelsolin-like protein 2 and sec23A/sec24A, which function in actin filament stabilization and vesicle transport, respectively, are enriched in cargos 3 h after LTS. These results establish that the composition of anterograde transport complexes undergo experience-dependent specific changes and illuminate dynamic changes in the communication between soma and synapse during learning.
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Affiliation(s)
- Abhishek Sadhu
- Department of Neuroscience, UF Scripps Biomedical Research, University of Florida, Jupiter, Florida 33458
| | - Kerriann K Badal
- Department of Neuroscience, UF Scripps Biomedical Research, University of Florida, Jupiter, Florida 33458
- Integrated Biology Graduate Program, Florida Atlantic University, Jupiter, Florida 33458
| | - Yibo Zhao
- Department of Neuroscience, UF Scripps Biomedical Research, University of Florida, Jupiter, Florida 33458
| | - Adia A Ali
- Department of Neuroscience, UF Scripps Biomedical Research, University of Florida, Jupiter, Florida 33458
| | - Supriya Swarnkar
- Department of Neuroscience, UF Scripps Biomedical Research, University of Florida, Jupiter, Florida 33458
| | - George Tsaprailis
- Proteomics Core, UF Scripps Biomedical Research, University of Florida, Jupiter, Florida 33458
| | - Gogce C Crynen
- Bioinformatics Core, UF Scripps Biomedical Research, University of Florida, Jupiter, Florida 33458
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5
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Badal KK, Puthanveettil SV. Axonal transport deficits in neuropsychiatric disorders. Mol Cell Neurosci 2022; 123:103786. [PMID: 36252719 DOI: 10.1016/j.mcn.2022.103786] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 10/02/2022] [Accepted: 10/11/2022] [Indexed: 11/06/2022] Open
Abstract
Axonal transport is a major cellular process that mediates bidirectional signaling between the soma and synapse, enabling both intracellular and intercellular communications. Cellular materials, such as proteins, RNAs, and organelles, are transported by molecular motor proteins along cytoskeletal highways in a highly regulated manner. Several studies have demonstrated that axonal transport is central to normal neuronal function, plasticity, and memory storage. Importantly, disruptions in axonal transport result in neuronal dysfunction and are associated with several neurodegenerative disorders. However, we do not know much about axonal transport deficits in neuropsychiatric disorders. Here, we briefly discuss our current understanding of the role of axonal transport in schizophrenia, bipolar and autism.
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Affiliation(s)
- Kerriann K Badal
- Department of Neuroscience, UF Scripps Biomedical Research, University of Florida, 130 Scripps Way, Jupiter, FL 33458, USA; Integrative Biology PhD Program, Charles E. Schmidt College of Science, Florida Atlantic University, Jupiter, FL 33458, USA
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6
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Fan R, Lai KO. Understanding how kinesin motor proteins regulate postsynaptic function in neuron. FEBS J 2021; 289:2128-2144. [PMID: 34796656 DOI: 10.1111/febs.16285] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 11/08/2021] [Accepted: 11/17/2021] [Indexed: 01/07/2023]
Abstract
The Kinesin superfamily proteins (KIFs) are major molecular motors that transport diverse set of cargoes along microtubules to both the axon and dendrite of a neuron. Much of our knowledge about kinesin function is obtained from studies on axonal transport. Emerging evidence reveals how specific kinesin motor proteins carry cargoes to dendrites, including proteins, mRNAs and organelles that are crucial for synapse development and plasticity. In this review, we will summarize the major kinesin motors and their associated cargoes that have been characterized to regulate postsynaptic function in neuron. We will also discuss how specific kinesins are selectively involved in the development of excitatory and inhibitory postsynaptic compartments, their regulation by post-translational modifications (PTM), as well as their roles beyond conventional transport carrier.
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Affiliation(s)
- Ruolin Fan
- Max Planck Florida Institute for Neuroscience, Jupiter, FL, USA
| | - Kwok-On Lai
- Department of Neuroscience, City University of Hong Kong, Hong Kong, China
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7
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Swarnkar S, Avchalumov Y, Espadas I, Grinman E, Liu XA, Raveendra BL, Zucca A, Mediouni S, Sadhu A, Valente S, Page D, Miller K, Puthanveettil SV. Molecular motor protein KIF5C mediates structural plasticity and long-term memory by constraining local translation. Cell Rep 2021; 36:109369. [PMID: 34260917 PMCID: PMC8319835 DOI: 10.1016/j.celrep.2021.109369] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 02/16/2021] [Accepted: 06/18/2021] [Indexed: 12/20/2022] Open
Abstract
Synaptic structural plasticity, key to long-term memory storage, requires translation of localized RNAs delivered by long-distance transport from the neuronal cell body. Mechanisms and regulation of this system remain elusive. Here, we explore the roles of KIF5C and KIF3A, two members of kinesin superfamily of molecular motors (Kifs), and find that loss of function of either kinesin decreases dendritic arborization and spine density whereas gain of function of KIF5C enhances it. KIF5C function is a rate-determining component of local translation and is associated with ∼650 RNAs, including EIF3G, a regulator of translation initiation, and plasticity-associated RNAs. Loss of function of KIF5C in dorsal hippocampal CA1 neurons constrains both spatial and contextual fear memory, whereas gain of function specifically enhances spatial memory and extinction of contextual fear. KIF5C-mediated long-distance transport of local translation substrates proves a key mechanism underlying structural plasticity and memory.
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Affiliation(s)
- Supriya Swarnkar
- Department of Neuroscience, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Yosef Avchalumov
- Department of Neuroscience, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Isabel Espadas
- Department of Neuroscience, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Eddie Grinman
- Department of Neuroscience, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Xin-An Liu
- Department of Neuroscience, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Bindu L Raveendra
- Department of Neuroscience, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Aya Zucca
- Department of Neuroscience, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Sonia Mediouni
- Department of Immunology and Microbiology, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Abhishek Sadhu
- Department of Neuroscience, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Susana Valente
- Department of Immunology and Microbiology, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Damon Page
- Department of Neuroscience, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Kyle Miller
- Department of Integrative Biology, Michigan State University, East Lansing, MI, USA
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8
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A unified resource and configurable model of the synapse proteome and its role in disease. Sci Rep 2021; 11:9967. [PMID: 33976238 PMCID: PMC8113277 DOI: 10.1038/s41598-021-88945-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 04/15/2021] [Indexed: 02/03/2023] Open
Abstract
Genes encoding synaptic proteins are highly associated with neuronal disorders many of which show clinical co-morbidity. We integrated 58 published synaptic proteomic datasets that describe over 8000 proteins and combined them with direct protein-protein interactions and functional metadata to build a network resource that reveals the shared and unique protein components that underpin multiple disorders. All the data are provided in a flexible and accessible format to encourage custom use.
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9
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Joseph NF, Swarnkar S, Puthanveettil SV. Double Duty: Mitotic Kinesins and Their Post-Mitotic Functions in Neurons. Cells 2021; 10:cells10010136. [PMID: 33445569 PMCID: PMC7827351 DOI: 10.3390/cells10010136] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 01/06/2021] [Accepted: 01/06/2021] [Indexed: 01/23/2023] Open
Abstract
Neurons, regarded as post-mitotic cells, are characterized by their extensive dendritic and axonal arborization. This unique architecture imposes challenges to how to supply materials required at distal neuronal components. Kinesins are molecular motor proteins that mediate the active delivery of cellular materials along the microtubule cytoskeleton for facilitating the local biochemical and structural changes at the synapse. Recent studies have made intriguing observations that some kinesins that function during neuronal mitosis also have a critical role in post-mitotic neurons. However, we know very little about the function and regulation of such kinesins. Here, we summarize the known cellular and biochemical functions of mitotic kinesins in post-mitotic neurons.
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Affiliation(s)
- Nadine F. Joseph
- The Skaggs Graduate School of Chemical and Biological Sciences, Scripps Research Institute, La Jolla, CA 92037, USA;
- Department of Neuroscience, The Scripps Research Institute, Jupiter, FL 33458, USA;
| | - Supriya Swarnkar
- Department of Neuroscience, The Scripps Research Institute, Jupiter, FL 33458, USA;
| | - Sathyanarayanan V Puthanveettil
- Department of Neuroscience, The Scripps Research Institute, Jupiter, FL 33458, USA;
- Correspondence: ; Tel.: +1-561-228-3504; Fax: +1-568-228-2249
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Gulyássy P, Puska G, Györffy BA, Todorov-Völgyi K, Juhász G, Drahos L, Kékesi KA. Proteomic comparison of different synaptosome preparation procedures. Amino Acids 2020; 52:1529-1543. [PMID: 33211194 PMCID: PMC7695668 DOI: 10.1007/s00726-020-02912-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 11/05/2020] [Indexed: 01/10/2023]
Abstract
Synaptosomes are frequently used research objects in neurobiology studies focusing on synaptic transmission as they mimic several aspects of the physiological synaptic functions. They contain the whole apparatus for neurotransmission, the presynaptic nerve ending with synaptic vesicles, synaptic mitochondria and often a segment of the postsynaptic membrane along with the postsynaptic density is attached to its outer surface. As being artificial functional organelles, synaptosomes are viable for several hours, retain their activity, membrane potential, and capable to store, release, and reuptake neurotransmitters. Synaptosomes are ideal subjects for proteomic analysis. The recently available separation and protein detection techniques can cope with the reduced complexity of the organelle and enable the simultaneous qualitative and quantitative analysis of thousands of proteins shaping the structural and functional characteristics of the synapse. Synaptosomes are formed during the homogenization of nervous tissue in the isoosmotic milieu and can be isolated from the homogenate by various approaches. Each enrichment method has its own benefits and drawbacks and there is not a single method that is optimal for all research purposes. For a proper proteomic experiment, it is desirable to preserve the native synaptic structure during the isolation procedure and keep the degree of contamination from other organelles or cell types as low as possible. In this article, we examined five synaptosome isolation methods from a proteomic point of view by the means of electron microscopy, Western blot, and liquid chromatography-mass spectrometry to compare their efficiency in the isolation of synaptosomes and depletion of contaminating subcellular structures. In our study, the different isolation procedures led to a largely overlapping pool of proteins with a fairly similar distribution of presynaptic, active zone, synaptic vesicle, and postsynaptic proteins; however, discrete differences were noticeable in individual postsynaptic proteins and in the number of identified transmembrane proteins. Much pronounced variance was observed in the degree of contamination with mitochondrial and glial structures. Therefore, we suggest that in selecting the appropriate isolation method for any neuroproteomics experiment carried out on synaptosomes, the degree and sort/source of contamination should be considered as a primary aspect.
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Affiliation(s)
- Péter Gulyássy
- MTA-TTK NAP B MS Neuroproteomics Research Group, Hungarian Academy of Sciences, Budapest, 1117, Hungary.
| | - Gina Puska
- Department of Anatomy, Cell and Development Biology, Institute of Biology, ELTE Eötvös Loránd University, Budapest, 1117, Hungary.,Department of Ecology, University of Veterinary Medicine Budapest, Budapest, 1078, Hungary.,MTA-ELTE NAP Laboratory of Molecular and Systems Neurobiology, Institute of Biology, Hungarian Academy of Sciences and ELTE Eötvös Loránd University, Budapest, 1117, Hungary
| | - Balázs A Györffy
- Laboratory of Proteomics, Institute of Biology, ELTE Eötvös Loránd University, Budapest, 1117, Hungary.,ELTE-NAP Neuroimmunology Research Group, Institute of Biology, ELTE Eötvös Loránd University, Budapest, 1117, Hungary
| | - Katalin Todorov-Völgyi
- MTA-ELTE NAP Laboratory of Molecular and Systems Neurobiology, Institute of Biology, Hungarian Academy of Sciences and ELTE Eötvös Loránd University, Budapest, 1117, Hungary.,Laboratory of Proteomics, Institute of Biology, ELTE Eötvös Loránd University, Budapest, 1117, Hungary
| | - Gábor Juhász
- MTA-TTK NAP B MS Neuroproteomics Research Group, Hungarian Academy of Sciences, Budapest, 1117, Hungary.,Laboratory of Proteomics, Institute of Biology, ELTE Eötvös Loránd University, Budapest, 1117, Hungary
| | - László Drahos
- MTA-TTK NAP B MS Neuroproteomics Research Group, Hungarian Academy of Sciences, Budapest, 1117, Hungary.,MS Proteomics Research Group, Research Centre for Natural Sciences, Budapest, 1117, Hungary
| | - Katalin Adrienna Kékesi
- Laboratory of Proteomics, Institute of Biology, ELTE Eötvös Loránd University, Budapest, 1117, Hungary.,Department of Physiology and Neurobiology, ELTE Eötvös Loránd University, Budapest, 1117, Hungary
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11
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Joseph NF, Grinman E, Swarnkar S, Puthanveettil SV. Molecular Motor KIF3B Acts as a Key Regulator of Dendritic Architecture in Cortical Neurons. Front Cell Neurosci 2020; 14:521199. [PMID: 33192305 PMCID: PMC7604319 DOI: 10.3389/fncel.2020.521199] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 09/09/2020] [Indexed: 01/08/2023] Open
Abstract
Neurons require a well-coordinated intercellular transport system to maintain their normal cellular function and morphology. The kinesin family of proteins (KIFs) fills this role by regulating the transport of a diverse array of cargos in post-mitotic cells. On the other hand, in mitotic cells, KIFs facilitate the fidelity of the cellular division machinery. Though certain mitotic KIFs function in post-mitotic neurons, little is known about them. We studied the role of a mitotic KIF (KIF3B) in neuronal architecture. We find that the RNAi mediated knockdown of KIF3B in primary cortical neurons resulted in an increase in spine density; the number of thin and mushroom spines; and dendritic branching. Consistent with the change in spine density, we observed a specific increase in the distribution of the excitatory post-synaptic protein, PSD-95 in KIF3B knockdown neurons. Interestingly, overexpression of KIF3B produced a reduction in spine density, in particular mushroom spines, and a decrease in dendritic branching. These studies suggest that KIF3B is a key determinant of cortical neuron morphology and that it functions as an inhibitory constraint on structural plasticity, further illuminating the significance of mitotic KIFs in post-mitotic neurons.
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Affiliation(s)
- Nadine F Joseph
- The Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, La Jolla, CA, United States.,Department of Neuroscience, The Scripps Research Institute, Jupiter, FL, United States
| | - Eddie Grinman
- The Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, La Jolla, CA, United States.,Department of Neuroscience, The Scripps Research Institute, Jupiter, FL, United States
| | - Supriya Swarnkar
- Department of Neuroscience, The Scripps Research Institute, Jupiter, FL, United States
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12
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Kinesin Family of Proteins Kif11 and Kif21B Act as Inhibitory Constraints of Excitatory Synaptic Transmission Through Distinct Mechanisms. Sci Rep 2018; 8:17419. [PMID: 30479371 PMCID: PMC6258692 DOI: 10.1038/s41598-018-35634-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 11/09/2018] [Indexed: 02/03/2023] Open
Abstract
Despite our understanding of the functions of the kinesin family of motor proteins (Kifs) in neurons, their specific roles in neuronal communication are less understood. To address this, by carrying out RNAi-mediated loss of function studies, we assessed the necessity of 18 Kifs in excitatory synaptic transmission in mouse primary hippocampal neurons prepared from both sexes. Our measurements of excitatory post-synaptic currents (EPSCs) have identified 7 Kifs that were found to be not critical and 11 Kifs that are essential for synaptic transmission by impacting either frequency or amplitude or both components of EPSCs. Intriguingly we found that knockdown of mitotic Kif4A and Kif11 and post-mitotic Kif21B resulted in an increase in EPSCs suggesting that they function as inhibitory constraints on synaptic transmission. Furthermore, Kifs (11, 21B, 13B) with distinct effects on synaptic transmission are expressed in the same hippocampal neuron. Mechanistically, unlike Kif21B, Kif11 requires the activity of pre-synaptic NMDARs. In addition, we find that Kif11 knockdown enhanced dendritic arborization, synapse number, expression of synaptic vesicle proteins synaptophysin and active zone protein Piccolo. Moreover, expression of Piccolo constrained Kif11 function in synaptic transmission. Together these results suggest that neurons are able to utilize specific Kifs as tools for calibrating synaptic function. These studies bring novel insights into the biology of Kifs and functioning of neural circuits.
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13
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Common general anesthetic propofol impairs kinesin processivity. Proc Natl Acad Sci U S A 2017; 114:E4281-E4287. [PMID: 28484025 DOI: 10.1073/pnas.1701482114] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Propofol is the most widely used i.v. general anesthetic to induce and maintain anesthesia. It is now recognized that this small molecule influences ligand-gated channels, including the GABAA receptor and others. Specific propofol binding sites have been mapped using photoaffinity ligands and mutagenesis; however, their precise target interaction profiles fail to provide complete mechanistic underpinnings for the anesthetic state. These results suggest that propofol and other common anesthetics, such as etomidate and ketamine, may target additional protein networks of the CNS to contribute to the desired and undesired anesthesia end points. Some evidence for anesthetic interactions with the cytoskeleton exists, but the molecular motors have received no attention as anesthetic targets. We have recently discovered that propofol inhibits conventional kinesin-1 KIF5B and kinesin-2 KIF3AB and KIF3AC, causing a significant reduction in the distances that these processive kinesins can travel. These microtubule-based motors are highly expressed in the CNS and the major anterograde transporters of cargos, such as mitochondria, synaptic vesicle precursors, neurotransmitter receptors, cell signaling and adhesion molecules, and ciliary intraflagellar transport particles. The single-molecule results presented show that the kinesin processive stepping distance decreases 40-60% with EC50 values <100 nM propofol without an effect on velocity. The lack of a velocity effect suggests that propofol is not binding at the ATP site or allosteric sites that modulate microtubule-activated ATP turnover. Rather, we propose that a transient propofol allosteric site forms when the motor head binds to the microtubule during stepping.
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Rizzo V, Touzani K, Raveendra BL, Swarnkar S, Lora J, Kadakkuzha BM, Liu XA, Zhang C, Betel D, Stackman RW, Puthanveettil SV. Encoding of contextual fear memory requires de novo proteins in the prelimbic cortex. BIOLOGICAL PSYCHIATRY: COGNITIVE NEUROSCIENCE AND NEUROIMAGING 2017; 2:158-169. [PMID: 28503670 DOI: 10.1016/j.bpsc.2016.10.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
BACKGROUND Despite our understanding of the significance of the prefrontal cortex in the consolidation of long-term memories (LTM), its role in the encoding of LTM remains elusive. Here we investigated the role of new protein synthesis in the mouse medial prefrontal cortex (mPFC) in encoding contextual fear memory. METHODS Because a change in the association of mRNAs to polyribosomes is an indicator of new protein synthesis, we assessed the changes in polyribosome-associated mRNAs in the mPFC following contextual fear conditioning (CFC) in the mouse. Differential gene expression in mPFC was identified by polyribosome profiling (n = 18). The role of new protein synthesis in mPFC was determined by focal inhibition of protein synthesis (n = 131) and by intra-prelimbic cortex manipulation (n = 56) of Homer 3, a candidate identified from polyribosome profiling. RESULTS We identified several mRNAs that are differentially and temporally recruited to polyribosomes in the mPFC following CFC. Inhibition of protein synthesis in the prelimbic (PL), but not in the anterior cingulate cortex (ACC) region of the mPFC immediately after CFC disrupted encoding of contextual fear memory. Intriguingly, inhibition of new protein synthesis in the PL 6 hours after CFC did not impair encoding. Furthermore, expression of Homer 3, an mRNA enriched in polyribosomes following CFC, in the PL constrained encoding of contextual fear memory. CONCLUSIONS Our studies identify several molecular substrates of new protein synthesis in the mPFC and establish that encoding of contextual fear memories require new protein synthesis in PL subregion of mPFC.
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Affiliation(s)
- Valerio Rizzo
- Department of Neuroscience, The Scripps Research Institute, Scripps Florida 130 Scripps Way, Jupiter, FL 33458
| | - Khalid Touzani
- Department of Neuroscience, The Scripps Research Institute, Scripps Florida 130 Scripps Way, Jupiter, FL 33458
| | - Bindu L Raveendra
- Department of Neuroscience, The Scripps Research Institute, Scripps Florida 130 Scripps Way, Jupiter, FL 33458
| | - Supriya Swarnkar
- Department of Neuroscience, The Scripps Research Institute, Scripps Florida 130 Scripps Way, Jupiter, FL 33458
| | - Joan Lora
- Department of Psychology, Center for Complex Systems & Brain Sciences, College of Science, Florida Atlantic University, Jupiter, FL 33458
| | - Beena M Kadakkuzha
- Department of Neuroscience, The Scripps Research Institute, Scripps Florida 130 Scripps Way, Jupiter, FL 33458
| | - Xin-An Liu
- Department of Neuroscience, The Scripps Research Institute, Scripps Florida 130 Scripps Way, Jupiter, FL 33458
| | - Chao Zhang
- Department of Medicine and Institute for Computational Biomedicine, Weill Cornell Medical College, New York. NY10065. USA
| | - Doron Betel
- Department of Medicine and Institute for Computational Biomedicine, Weill Cornell Medical College, New York. NY10065. USA
| | - Robert W Stackman
- Department of Psychology, Center for Complex Systems & Brain Sciences, College of Science, Florida Atlantic University, Jupiter, FL 33458
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Lee PKM, Goh WWB, Sng JCG. Network-based characterization of the synaptic proteome reveals that removal of epigenetic regulator Prmt8 restricts proteins associated with synaptic maturation. J Neurochem 2017; 140:613-628. [PMID: 27935040 DOI: 10.1111/jnc.13921] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Revised: 11/30/2016] [Accepted: 12/04/2016] [Indexed: 12/13/2022]
Abstract
The brain adapts to dynamic environmental conditions by altering its epigenetic state, thereby influencing neuronal transcriptional programs. An example of an epigenetic modification is protein methylation, catalyzed by protein arginine methyltransferases (PRMT). One member, Prmt8, is selectively expressed in the central nervous system during a crucial phase of early development, but little else is known regarding its function. We hypothesize Prmt8 plays a role in synaptic maturation during development. To evaluate this, we used a proteome-wide approach to characterize the synaptic proteome of Prmt8 knockout versus wild-type mice. Through comparative network-based analyses, proteins and functional clusters related to neurite development were identified to be differentially regulated between the two genotypes. One interesting protein that was differentially regulated was tenascin-R (TNR). Chromatin immunoprecipitation demonstrated binding of PRMT8 to the tenascin-r (Tnr) promoter. TNR, a component of perineuronal nets, preserves structural integrity of synaptic connections within neuronal networks during the development of visual-somatosensory cortices. On closer inspection, Prmt8 removal increased net formation and decreased inhibitory parvalbumin-positive (PV+) puncta on pyramidal neurons, thereby hindering the maturation of circuits. Consequently, visual acuity of the knockout mice was reduced. Our results demonstrated Prmt8's involvement in synaptic maturation and its prospect as an epigenetic modulator of developmental neuroplasticity by regulating structural elements such as the perineuronal nets.
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Affiliation(s)
- Patrick Kia Ming Lee
- Integrative Neuroscience Program, Singapore Institute for Clinical Sciences, Agency for Science Technology and Research (A*STAR), Singapore.,Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Wilson Wen Bin Goh
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China.,Department of Computer Science, National University of Singapore, Singapore
| | - Judy Chia Ghee Sng
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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16
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Briggs CA, Chakroborty S, Stutzmann GE. Emerging pathways driving early synaptic pathology in Alzheimer's disease. Biochem Biophys Res Commun 2016; 483:988-997. [PMID: 27659710 DOI: 10.1016/j.bbrc.2016.09.088] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 09/13/2016] [Accepted: 09/17/2016] [Indexed: 11/25/2022]
Abstract
The current state of the AD research field is highly dynamic is some respects, while seemingly stagnant in others. Regarding the former, our current lack of understanding of initiating disease mechanisms, the absence of effective treatment options, and the looming escalation of AD patients is energizing new research directions including a much-needed re-focusing on early pathogenic mechanisms, validating novel targets, and investigating relevant biomarkers, among other exciting new efforts to curb disease progression and foremost, preserve memory function. With regard to the latter, the recent disappointing series of failed Phase III clinical trials targeting Aβ and APP processing, in concert with poor association between brain Aβ levels and cognitive function, have led many to call for a re-evaluation of the primacy of the amyloid cascade hypothesis. In this review, we integrate new insights into one of the earliest described signaling abnormalities in AD pathogenesis, namely intracellular Ca2+ signaling disruptions, and focus on its role in driving synaptic deficits - which is the feature that does correlate with AD-associated memory loss. Excess Ca2+release from intracellular stores such as the endoplasmic reticulum (ER) has been well-described in cellular and animal models of AD, as well as human patients, and here we expand upon recent developments in ER-localized release channels such as the IP3R and RyR, and the recent emphasis on RyR2. Consistent with ER Ca2+ mishandling in AD are recent findings implicating aspects of SOCE, such as STIM2 function, and TRPC3 and TRPC6 levels. Other Ca2+-regulated organelles important in signaling and protein handling are brought into the discussion, with new perspectives on lysosomal regulation. These early signaling abnormalities are discussed in the context of synaptic pathophysiology and disruptions in synaptic plasticity with a particular emphasis on short-term plasticity deficits. Overall, we aim to update and expand the list of early neuronal signaling abnormalities implicated in AD pathogenesis, identify specific channels and organelles involved, and link these to proximal synaptic impairments driving the memory loss in AD. This is all within the broader goal of identifying novel therapeutic targets to preserve cognitive function in AD.
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Affiliation(s)
- Clark A Briggs
- Department of Neuroscience, Rosalind Franklin University of Medicine and Science, The Chicago Medical School, North Chicago, IL 60064, USA
| | - Shreaya Chakroborty
- Department of Neuroscience, Rosalind Franklin University of Medicine and Science, The Chicago Medical School, North Chicago, IL 60064, USA
| | - Grace E Stutzmann
- Department of Neuroscience, Rosalind Franklin University of Medicine and Science, The Chicago Medical School, North Chicago, IL 60064, USA.
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Miller KE, Liu XA, Puthanveettil SV. Automated measurement of fast mitochondrial transport in neurons. Front Cell Neurosci 2015; 9:435. [PMID: 26578890 PMCID: PMC4630299 DOI: 10.3389/fncel.2015.00435] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 10/16/2015] [Indexed: 01/20/2023] Open
Abstract
There is growing recognition that fast mitochondrial transport in neurons is disrupted in multiple neurological diseases and psychiatric disorders. However, a major constraint in identifying novel therapeutics based on mitochondrial transport is that the large-scale analysis of fast transport is time consuming. Here we describe methodologies for the automated analysis of fast mitochondrial transport from data acquired using a robotic microscope. We focused on addressing questions of measurement precision, speed, reliably, workflow ease, statistical processing, and presentation. We used optical flow and particle tracking algorithms, implemented in ImageJ, to measure mitochondrial movement in primary cultured cortical and hippocampal neurons. With it, we are able to generate complete descriptions of movement profiles in an automated fashion of hundreds of thousands of mitochondria with a processing time of approximately one hour. We describe the calibration of the parameters of the tracking algorithms and demonstrate that they are capable of measuring the fast transport of a single mitochondrion. We then show that the methods are capable of reliably measuring the inhibition of fast mitochondria transport induced by the disruption of microtubules with the drug nocodazole in both hippocampal and cortical neurons. This work lays the foundation for future large-scale screens designed to identify compounds that modulate mitochondrial motility.
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Affiliation(s)
- Kyle E Miller
- Department of Integrative Biology, Michigan State University East Lansing, MI, USA
| | - Xin-An Liu
- Department of Neuroscience, The Scripps Research Institute, Scripps Florida Jupiter, FL, USA
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