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Mehta K, Yentsch H, Lee J, Gao TT, Zhang K. Phosphatidylinositol 3-phosphate mediates Arc capsids secretion through the multivesicular body pathway. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.19.572392. [PMID: 38187623 PMCID: PMC10769229 DOI: 10.1101/2023.12.19.572392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Activity-regulated cytoskeleton-associated protein (Arc/Arg3.1) is an immediate early gene that plays a vital role in learning and memory. The recent discovery that Arc mediates the inter-neuronal RNA transfer implies its role in regulating neuronal functions across long distances. Arc protein has structural and functional properties similar to viral Group-specific antigen (Gag). By assembling into high-order, virus-like capsids, Arc mediates the intercellular RNA transfer. However, the exact secretion pathway through which Arc capsids maneuver cargos is unclear. Here, we identified that Arc capsids assemble and secrete through the endosomal-multivesicular body (MVB) pathway. Arc's endosomal entry is likely mediated by phosphatidylinositol-3-phosphate (PI3P). Indeed, reconstituted Arc protein preferably binds to PI3P. In mammalian cells, Arc forms puncta that colocalizes with FYVE, an endosomal PI3P marker, and competitive binding to PI3P via prolonged FYVE expression reduces the average number of Arc puncta per cell. Overexpression of MTMR1, a PI3P phosphatase, significantly reduces Arc capsid secretion. Arc capsids secrete through the endosomal-MVB axis as extracellular vesicles. Live-cell imaging shows that fluorescently labeled Arc primarily colocalizes Rab5 and CD63, early endosomal and MVB markers, respectively. Superresolution imaging resolves Arc accumulates within the intraluminal vesicles of MVB. CRISPR double knockout of RalA and RalB, crucial GTPases for MVB biogenesis and exocytosis, severely reduces Arc-mediated RNA transfer efficiency. These results suggest that, unlike the Human Immunodeficiency Virus Gag, which assembles on and bud off from the plasma membrane, Arc capsids assemble at the endocytic membranes of the endosomal-MVB pathway mediated by PI3P. Understanding Arc's secretion pathway helps gain insights into its role in intercellular cargo transfer and highlights the commonality and distinction of trafficking mechanisms between structurally resembled capsid proteins.
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Sibarov DA, Tsytsarev V, Volnova A, Vaganova AN, Alves J, Rojas L, Sanabria P, Ignashchenkova A, Savage ED, Inyushin M. Arc protein, a remnant of ancient retrovirus, forms virus-like particles, which are abundantly generated by neurons during epileptic seizures, and affects epileptic susceptibility in rodent models. Front Neurol 2023; 14:1201104. [PMID: 37483450 PMCID: PMC10361770 DOI: 10.3389/fneur.2023.1201104] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 06/02/2023] [Indexed: 07/25/2023] Open
Abstract
A product of the immediate early gene Arc (Activity-regulated cytoskeleton-associated protein or Arc protein) of retroviral ancestry resides in the genome of all tetrapods for millions of years and is expressed endogenously in neurons. It is a well-known protein, very important for synaptic plasticity and memory consolidation. Activity-dependent Arc expression concentrated in glutamatergic synapses affects the long-time synaptic strength of those excitatory synapses. Because it modulates excitatory-inhibitory balance in a neuronal network, the Arc gene itself was found to be related to the pathogenesis of epilepsy. General Arc knockout rodent models develop a susceptibility to epileptic seizures. Because of activity dependence, synaptic Arc protein synthesis also is affected by seizures. Interestingly, it was found that Arc protein in synapses of active neurons self-assemble in capsids of retrovirus-like particles, which can transfer genetic information between neurons, at least across neuronal synaptic boutons. Released Arc particles can be accumulated in astrocytes after seizures. It is still not known how capsid assembling and transmission timescale is affected by seizures. This scientific field is relatively novel and is experiencing swift transformation as it grapples with difficult concepts in light of evolving experimental findings. We summarize the emergent literature on the subject and also discuss the specific rodent models for studying Arc effects in epilepsy. We summarized both to clarify the possible role of Arc-related pseudo-viral particles in epileptic disorders, which may be helpful to researchers interested in this growing area of investigation.
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Affiliation(s)
- Dmitry A. Sibarov
- Sechenov Institute of Evolutionary Physiology and Biochemistry of the Russian Academy of Sciences, Saint Petersburg, Russia
| | - Vassiliy Tsytsarev
- Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Anna Volnova
- Institute of Translational Biomedicine, Saint Petersburg State University, Saint Petersburg, Russia
| | - Anastasia N. Vaganova
- Institute of Translational Biomedicine, Saint Petersburg State University, Saint Petersburg, Russia
| | - Janaina Alves
- School of Medicine, Universidad Central del Caribe, Bayamón, PR, United States
| | - Legier Rojas
- School of Medicine, Universidad Central del Caribe, Bayamón, PR, United States
| | - Priscila Sanabria
- School of Medicine, Universidad Central del Caribe, Bayamón, PR, United States
| | | | | | - Mikhail Inyushin
- School of Medicine, Universidad Central del Caribe, Bayamón, PR, United States
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Avallone M, Pardo J, Mergiya TF, Rájová J, Räsänen A, Davidsson M, Åkerblom M, Quintino L, Kumar D, Bramham CR, Björklund T. Visualizing Arc protein dynamics and localization in the mammalian brain using AAV-mediated in situ gene labeling. Front Mol Neurosci 2023; 16:1140785. [PMID: 37415832 PMCID: PMC10321715 DOI: 10.3389/fnmol.2023.1140785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 05/11/2023] [Indexed: 07/08/2023] Open
Abstract
The activity-regulated cytoskeleton-associated (Arc) protein is essential for synaptic plasticity and memory formation. The Arc gene, which contains remnants of a structural GAG retrotransposon sequence, produces a protein that self-assembles into capsid-like structures harboring Arc mRNA. Arc capsids, released from neurons, have been proposed as a novel intercellular mechanism for mRNA transmission. Nevertheless, evidence for intercellular transport of Arc in the mammalian brain is still lacking. To enable the tracking of Arc molecules from individual neurons in vivo, we devised an adeno-associated virus (AAV) mediated approach to tag the N-terminal of the mouse Arc protein with a fluorescent reporter using CRISPR/Cas9 homologous independent targeted integration (HITI). We show that a sequence coding for mCherry can successfully be knocked in at the 5' end of the Arc open reading frame. While nine spCas9 gene editing sites surround the Arc start codon, the accuracy of the editing was highly sequence-dependent, with only a single target resulting in an in-frame reporter integration. When inducing long-term potentiation (LTP) in the hippocampus, we observed an increase of Arc protein highly correlated with an increase in fluorescent intensity and the number of mCherry-positive cells. By proximity ligation assay (PLA), we demonstrated that the mCherry-Arc fusion protein retains the Arc function by interacting with the transmembrane protein stargazin in postsynaptic spines. Finally, we recorded mCherry-Arc interaction with presynaptic protein Bassoon in mCherry-negative surrounding neurons at close proximity to mCherry-positive spines of edited neurons. This is the first study to provide support for inter-neuronal in vivo transfer of Arc in the mammalian brain.
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Affiliation(s)
- Martino Avallone
- Molecular Neuromodulation, Wallenberg Neuroscience Center, Lund University, Lund, Sweden
| | - Joaquín Pardo
- Molecular Neuromodulation, Wallenberg Neuroscience Center, Lund University, Lund, Sweden
- Instituto de Investigaciones Bioquímicas de La Plata “Prof. Dr. Rodolfo R. Brenner” (INIBIOLP), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)—Universidad Nacional de La Plata (UNLP), La Plata, Argentina
| | - Tadiwos F. Mergiya
- Department of Biomedicine, University of Bergen, Bergen, Norway
- Mohn Research Center for the Brain, University of Bergen, Bergen, Norway
| | - Jana Rájová
- Molecular Neuromodulation, Wallenberg Neuroscience Center, Lund University, Lund, Sweden
| | - Atte Räsänen
- Molecular Neuromodulation, Wallenberg Neuroscience Center, Lund University, Lund, Sweden
| | - Marcus Davidsson
- Molecular Neuromodulation, Wallenberg Neuroscience Center, Lund University, Lund, Sweden
| | - Malin Åkerblom
- Molecular Neuromodulation, Wallenberg Neuroscience Center, Lund University, Lund, Sweden
| | - Luis Quintino
- CNS Gene Therapy, Department of Experimental Medical Sciences, Lund University, Lund, Sweden
| | | | - Clive R. Bramham
- Department of Biomedicine, University of Bergen, Bergen, Norway
- Mohn Research Center for the Brain, University of Bergen, Bergen, Norway
| | - Tomas Björklund
- Molecular Neuromodulation, Wallenberg Neuroscience Center, Lund University, Lund, Sweden
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4
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Sun B, Kim H, Mello CC, Priess JR. The CERV protein of Cer1, a C. elegans LTR retrotransposon, is required for nuclear export of viral genomic RNA and can form giant nuclear rods. PLoS Genet 2023; 19:e1010804. [PMID: 37384599 PMCID: PMC10309623 DOI: 10.1371/journal.pgen.1010804] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 05/31/2023] [Indexed: 07/01/2023] Open
Abstract
Retroviruses and closely related LTR retrotransposons export full-length, unspliced genomic RNA (gRNA) for packaging into virions and to serve as the mRNA encoding GAG and POL polyproteins. Because gRNA often includes splice acceptor and donor sequences used to splice viral mRNAs, retroelements must overcome host mechanisms that retain intron-containing RNAs in the nucleus. Here we examine gRNA expression in Cer1, an LTR retrotransposon in C. elegans which somehow avoids silencing and is highly expressed in germ cells. Newly exported Cer1 gRNA associates rapidly with the Cer1 GAG protein, which has structural similarity with retroviral GAG proteins. gRNA export requires CERV (C. elegans regulator of viral expression), a novel protein encoded by a spliced Cer1 mRNA. CERV phosphorylation at S214 is essential for gRNA export, and phosphorylated CERV colocalizes with nuclear gRNA at presumptive sites of transcription. By electron microscopy, tagged CERV proteins surround clusters of distinct, linear fibrils that likely represent gRNA molecules. Single fibrils, or groups of aligned fibrils, also localize near nuclear pores. During the C. elegans self-fertile period, when hermaphrodites fertilize oocytes with their own sperm, CERV concentrates in two nuclear foci that are coincident with gRNA. However, as hermaphrodites cease self-fertilization, and can only produce cross-progeny, CERV undergoes a remarkable transition to form giant nuclear rods or cylinders that can be up to 5 microns in length. We propose a novel mechanism of rod formation, in which stage-specific changes in the nucleolus induce CERV to localize to the nucleolar periphery in flattened streaks of protein and gRNA; these streaks then roll up into cylinders. The rods are a widespread feature of Cer1 in wild strains of C. elegans, but their function is not known and might be limited to cross-progeny. We speculate that the adaptive strategy Cer1 uses for the identical self-progeny of a host hermaphrodite might differ for heterozygous cross-progeny sired by males. For example, mating introduces male chromosomes which can have different, or no, Cer1 elements.
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Affiliation(s)
- Bing Sun
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester,United States of America
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Haram Kim
- Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Craig C. Mello
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester,United States of America
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - James R. Priess
- Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
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5
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Kuhn JH, Koonin EV. Viriforms-A New Category of Classifiable Virus-Derived Genetic Elements. Biomolecules 2023; 13:289. [PMID: 36830658 PMCID: PMC9953437 DOI: 10.3390/biom13020289] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
The International Committee on Taxonomy of Viruses (ICTV) recently accepted viriforms as a new polyphyletic category of classifiable virus-derived genetic elements, juxtaposed to the polyphyletic virus, viroid, and satellite nucleic acid categories. Viriforms are endogenized former viruses that have been exapted by their cellular hosts to fulfill functions important for the host's life cycle. While morphologically resembling virions, particles made by viriforms do not package the viriform genomes but instead transport host genetic material. Known viriforms are highly diverse: members of family Polydnaviriformidae (former Polydnaviridae) have thus far been found exclusively in the genomes of braconid and ichneumonid parasitoid wasps, whereas the completely unrelated gene transfer agents (GTAs) are widely distributed among prokaryotes. In addition, recent discoveries likely extend viriforms to mammalian genomes. Here, we briefly outline the properties of these viriform groups and the first accepted and proposed ICTV frameworks for viriform classification.
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Affiliation(s)
- Jens H. Kuhn
- Integrated Research Facility at Fort Detrick, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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6
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W B Jr M, A S R, P M, F B. Cellular and Natural Viral Engineering in Cognition-Based Evolution. Commun Integr Biol 2023; 16:2196145. [PMID: 37153718 PMCID: PMC10155641 DOI: 10.1080/19420889.2023.2196145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023] Open
Abstract
Neo-Darwinism conceptualizes evolution as the continuous succession of predominately random genetic variations disciplined by natural selection. In that frame, the primary interaction between cells and the virome is relegated to host-parasite dynamics governed by selective influences. Cognition-Based Evolution regards biological and evolutionary development as a reciprocating cognition-based informational interactome for the protection of self-referential cells. To sustain cellular homeorhesis, cognitive cells collaborate to assess the validity of ambiguous biological information. That collective interaction involves coordinate measurement, communication, and active deployment of resources as Natural Cellular Engineering. These coordinated activities drive multicellularity, biological development, and evolutionary change. The virome participates as the vital intercessory among the cellular domains to ensure their shared permanent perpetuation. The interactions between the virome and the cellular domains represent active virocellular cross-communications for the continual exchange of resources. Modular genetic transfers between viruses and cells carry bioactive potentials. Those exchanges are deployed as nonrandom flexible tools among the domains in their continuous confrontation with environmental stresses. This alternative framework fundamentally shifts our perspective on viral-cellular interactions, strengthening established principles of viral symbiogenesis. Pathogenesis can now be properly appraised as one expression of a range of outcomes between cells and viruses within a larger conceptual framework of Natural Viral Engineering as a co-engineering participant with cells. It is proposed that Natural Viral Engineering should be viewed as a co-existent facet of Natural Cellular Engineering within Cognition-Based Evolution.
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Affiliation(s)
- Miller W B Jr
- Banner Health Systems - Medicine, Paradise Valley, Arizona, AZ, USA
- CONTACT Miller W B Jr Paradise Valley, Arizona, AZ85253, USA
| | - Reber A S
- Department of Psychology, University of British Columbia, Vancouver, BC, Canada
| | - Marshall P
- Department of Engineering, Evolution 2.0, Oak Park, IL, USA
| | - Baluška F
- Institute of Cellular and Molecular Botany, University of Bonn, Bonn, Germany
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7
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Zhang D, Ma S, Wang L, Ma H, Wang W, Xia J, Liu D. Min pig skeletal muscle response to cold stress. PLoS One 2022; 17:e0274184. [PMID: 36155652 PMCID: PMC9512212 DOI: 10.1371/journal.pone.0274184] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 08/18/2022] [Indexed: 11/18/2022] Open
Abstract
The increased sensitivity of pigs to ambient temperature is due to today’s intensive farming. Frequent climate disasters increase the pressure on healthy pig farming. Min pigs are an indigenous pig breed in China with desirable cold resistance characteristics, and hence are ideal for obtaining cold-resistant pig breeds. Therefore, it is important to discover the molecular mechanisms that are activated in response to cold stress in the Min pig. Here, we conducted a transcriptomic analysis of the skeletal muscle of Min pigs under chronic low-temperature acclimation (group A) and acute short cold stress (group B). Cold exposure caused more genes to be upregulated. Totals of 125 and 96 differentially expressed genes (DEGs) were generated from groups A and B. Sixteen common upregulated DEGs were screened; these were concentrated in oxidative stress (SRXN1, MAFF), immune and inflammatory responses (ITPKC, AREG, MMP25, FOSL1), the nervous system (RETREG1, GADD45A, RCAN1), lipid metabolism (LRP11, LIPG, ITGA5, AMPD2), solute transport (SLC19A2, SLC28A1, SLCO4A1), and fertility (HBEGF). There were 102 and 73 genes that were specifically differentially expressed in groups A and B, respectively. The altered mRNAs were enriched in immune, endocrine, and cancer pathways. There were 186 and 91 differentially expressed lncRNAs generated from groups A and B. Analysis of the target genes suggested that they may be involved in regulating the MAPK signaling pathway for resistance to cold. The results of this study provide a comprehensive overview of cold exposure–induced transcriptional patterns in skeletal muscle of the Min pig. These results can guide future molecular studies of cold stress response in pigs for improving cold tolerance as a goal in breeding programs.
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Affiliation(s)
- Dongjie Zhang
- Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Harbin, Heilongjiang, People’s Republic of China
| | - Shouzheng Ma
- Department of Animal Science, Northeast Agricultural University, Harbin, Heilongjiang, People’s Republic of China
| | - Liang Wang
- Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Harbin, Heilongjiang, People’s Republic of China
| | - Hong Ma
- Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Harbin, Heilongjiang, People’s Republic of China
| | - Wentao Wang
- Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Harbin, Heilongjiang, People’s Republic of China
| | - Jiqao Xia
- Department of Animal Science, Northeast Agricultural University, Harbin, Heilongjiang, People’s Republic of China
| | - Di Liu
- Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Harbin, Heilongjiang, People’s Republic of China
- Department of Animal Science, Northeast Agricultural University, Harbin, Heilongjiang, People’s Republic of China
- * E-mail:
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8
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The Role of Transposable Elements of the Human Genome in Neuronal Function and Pathology. Int J Mol Sci 2022; 23:ijms23105847. [PMID: 35628657 PMCID: PMC9148063 DOI: 10.3390/ijms23105847] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/17/2022] [Accepted: 05/19/2022] [Indexed: 12/13/2022] Open
Abstract
Transposable elements (TEs) have been extensively studied for decades. In recent years, the introduction of whole-genome and whole-transcriptome approaches, as well as single-cell resolution techniques, provided a breakthrough that uncovered TE involvement in host gene expression regulation underlying multiple normal and pathological processes. Of particular interest is increased TE activity in neuronal tissue, and specifically in the hippocampus, that was repeatedly demonstrated in multiple experiments. On the other hand, numerous neuropathologies are associated with TE dysregulation. Here, we provide a comprehensive review of literature about the role of TEs in neurons published over the last three decades. The first chapter of the present review describes known mechanisms of TE interaction with host genomes in general, with the focus on mammalian and human TEs; the second chapter provides examples of TE exaptation in normal neuronal tissue, including TE involvement in neuronal differentiation and plasticity; and the last chapter lists TE-related neuropathologies. We sought to provide specific molecular mechanisms of TE involvement in neuron-specific processes whenever possible; however, in many cases, only phenomenological reports were available. This underscores the importance of further studies in this area.
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9
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Pandey K, Yu XW, Steinmetz A, Alberini CM. Autophagy coupled to translation is required for long-term memory. Autophagy 2021; 17:1614-1635. [PMID: 32501746 PMCID: PMC8354608 DOI: 10.1080/15548627.2020.1775393] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 05/12/2020] [Accepted: 05/22/2020] [Indexed: 02/07/2023] Open
Abstract
An increase in protein synthesis following learning is a fundamental and evolutionarily conserved mechanism of long-term memory. To maintain homeostasis, this protein synthesis must be counterbalanced by mechanisms such as protein degradation. Recent studies reported that macroautophagy/autophagy, a major protein degradation mechanism, is required for long-term memory formation. However, how learning regulates autophagy and recruits it into long-term memory formation remains to be established. Here, we show that inhibitory avoidance in rats significantly increases the levels of autophagy and lysosomal degradation proteins, including BECN1/beclin 1, LC3-II, SQSTM1/p62 and LAMP1, as well as autophagic flux in the hippocampus. Moreover, pharmacological inhibition or targeted molecular disruption of the learning-induced autophagy impairs long-term memory, leaving short-term memory intact. The increase in autophagy proteins results from active translation of their mRNA and not from changes in their total mRNA levels. Additionally, the induction of autophagy requires the immediate early gene Arc/Arg3.1. Finally, in contrast to classical regulation of autophagy in other systems, we found that the increase in autophagy upon learning is dispensable for the increase in protein synthesis. We conclude that coupling between learning-induced translation and autophagy, rather than translation per se, is an essential mechanism of long-term memory.Abbreviations: AAV: adeno-associated virus; ARC/ARG3.1: activity regulated cytoskeletal-associated protein; ATG: autophagy related; DG: dentate gyrus; GFP: green fluorescent protein; IA: inhibitory avoidance; LAMP1: lysosomal-associated membrane protein 1; MAP1LC3B/LC3B: microtubule-associated protein 1 light chain 3 beta; ODN: oligodeoxynucleotide; qPCR: quantitative polymerase chain reaction; SBI: SBI0206965; SQSTM1/p62: sequestosome 1; SUnSET: surface sensing of translation; TRAP: translating ribosome affinity purification; ULK1: unc-51 like kinase 1.
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Affiliation(s)
- Kiran Pandey
- Center for Neural Science, New York University, New York, NY, USA
| | - Xiao-Wen Yu
- Center for Neural Science, New York University, New York, NY, USA
| | - Adam Steinmetz
- Center for Neural Science, New York University, New York, NY, USA
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10
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Villarreal LP, Witzany G. Social Networking of Quasi-Species Consortia drive Virolution via Persistence. AIMS Microbiol 2021; 7:138-162. [PMID: 34250372 PMCID: PMC8255905 DOI: 10.3934/microbiol.2021010] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 04/25/2021] [Indexed: 12/31/2022] Open
Abstract
The emergence of cooperative quasi-species consortia (QS-C) thinking from the more accepted quasispecies equations of Manfred Eigen, provides a conceptual foundation from which concerted action of RNA agents can now be understood. As group membership becomes a basic criteria for the emergence of living systems, we also start to understand why the history and context of social RNA networks become crucial for survival and function. History and context of social RNA networks also lead to the emergence of a natural genetic code. Indeed, this QS-C thinking can also provide us with a transition point between the chemical world of RNA replicators and the living world of RNA agents that actively differentiate self from non-self and generate group identity with membership roles. Importantly the social force of a consortia to solve complex, multilevel problems also depend on using opposing and minority functions. The consortial action of social networks of RNA stem-loops subsequently lead to the evolution of cellular organisms representing a tree of life.
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11
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Mustafin RN, Khusnutdinova EK. Involvement of transposable elements in neurogenesis. Vavilovskii Zhurnal Genet Selektsii 2021; 24:209-218. [PMID: 33659801 PMCID: PMC7893149 DOI: 10.18699/vj20.613] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The article is about the role of transposons in the regulation of functioning of neuronal stem cells and mature neurons of the human brain. Starting from the first division of the zygote, embryonic development is governed by regular activations of transposable elements, which are necessary for the sequential regulation of the expression of genes specific for each cell type. These processes include differentiation of neuronal stem cells, which requires the finest tuning of expression of neuron genes in various regions of the brain. Therefore, in the hippocampus, the center of human neurogenesis, the highest transposon activity has been identified, which causes somatic mosaicism of cells during the formation of specific brain structures. Similar data were obtained in studies on experimental animals. Mobile genetic elements are the most important sources of long non-coding RNAs that are coexpressed with important brain protein-coding genes. Significant activity of long non-coding RNA was detected in the hippocampus, which confirms the role of transposons in the regulation of brain function. MicroRNAs, many of which arise from transposon transcripts, also play an important role in regulating the differentiation of neuronal stem cells. Therefore, transposons, through their own processed transcripts, take an active part in the epigenetic regulation of differentiation of neurons. The global regulatory role of transposons in the human brain is due to the emergence of protein-coding genes in evolution by their exonization, duplication and domestication. These genes are involved in an epigenetic regulatory network with the participation of transposons, since they contain nucleotide sequences complementary to miRNA and long non-coding RNA formed from transposons. In the memory formation, the role of the exchange of virus-like mRNA with the help of the Arc protein of endogenous retroviruses HERV between neurons has been revealed. A possible mechanism for the implementation of this mechanism may be reverse transcription of mRNA and site-specific insertion into the genome with a regulatory effect on the genes involved in the memory.
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Affiliation(s)
| | - E K Khusnutdinova
- Institute of Biochemistry and Genetics - Subdivision of the Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa, Russia
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12
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Function of Drosophila Synaptotagmins in membrane trafficking at synapses. Cell Mol Life Sci 2021; 78:4335-4364. [PMID: 33619613 PMCID: PMC8164606 DOI: 10.1007/s00018-021-03788-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 01/29/2021] [Accepted: 02/09/2021] [Indexed: 12/13/2022]
Abstract
The Synaptotagmin (SYT) family of proteins play key roles in regulating membrane trafficking at neuronal synapses. Using both Ca2+-dependent and Ca2+-independent interactions, several SYT isoforms participate in synchronous and asynchronous fusion of synaptic vesicles (SVs) while preventing spontaneous release that occurs in the absence of stimulation. Changes in the function or abundance of the SYT1 and SYT7 isoforms alter the number and route by which SVs fuse at nerve terminals. Several SYT family members also regulate trafficking of other subcellular organelles at synapses, including dense core vesicles (DCV), exosomes, and postsynaptic vesicles. Although SYTs are linked to trafficking of multiple classes of synaptic membrane compartments, how and when they interact with lipids, the SNARE machinery and other release effectors are still being elucidated. Given mutations in the SYT family cause disorders in both the central and peripheral nervous system in humans, ongoing efforts are defining how these proteins regulate vesicle trafficking within distinct neuronal compartments. Here, we review the Drosophila SYT family and examine their role in synaptic communication. Studies in this invertebrate model have revealed key similarities and several differences with the predicted activity of their mammalian counterparts. In addition, we highlight the remaining areas of uncertainty in the field and describe outstanding questions on how the SYT family regulates membrane trafficking at nerve terminals.
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13
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Eriksen MS, Nikolaienko O, Hallin EI, Grødem S, Bustad HJ, Flydal MI, Merski I, Hosokawa T, Lascu D, Akerkar S, Cuéllar J, Chambers JJ, O'Connell R, Muruganandam G, Loris R, Touma C, Kanhema T, Hayashi Y, Stratton MM, Valpuesta JM, Kursula P, Martinez A, Bramham CR. Arc self-association and formation of virus-like capsids are mediated by an N-terminal helical coil motif. FEBS J 2020; 288:2930-2955. [PMID: 33175445 DOI: 10.1111/febs.15618] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 10/13/2020] [Accepted: 10/26/2020] [Indexed: 12/15/2022]
Abstract
Activity-regulated cytoskeleton-associated protein (Arc) is a protein interaction hub with diverse roles in intracellular neuronal signaling, and important functions in neuronal synaptic plasticity, memory, and postnatal cortical development. Arc has homology to retroviral Gag protein and is capable of self-assembly into virus-like capsids implicated in the intercellular transfer of RNA. However, the molecular basis of Arc self-association and capsid formation is largely unknown. Here, we identified a 28-amino-acid stretch in the mammalian Arc N-terminal (NT) domain that is necessary and sufficient for self-association. Within this region, we identified a 7-residue oligomerization motif, critical for the formation of virus-like capsids. Purified wild-type Arc formed capsids as shown by transmission and cryo-electron microscopy, whereas mutant Arc with disruption of the oligomerization motif formed homogenous dimers. An atomic-resolution crystal structure of the oligomerization region peptide demonstrated an antiparallel coiled-coil interface, strongly supporting NT-NT domain interactions in Arc oligomerization. The NT coil-coil interaction was also validated in live neurons using fluorescence lifetime FRET imaging, and mutation of the oligomerization motif disrupted Arc-facilitated endocytosis. Furthermore, using single-molecule photobleaching, we show that Arc mRNA greatly enhances higher-order oligomerization in a manner dependent on the oligomerization motif. In conclusion, a helical coil in the Arc NT domain supports self-association above the dimer stage, mRNA-induced oligomerization, and formation of virus-like capsids. DATABASE: The coordinates and structure factors for crystallographic analysis of the oligomerization region were deposited at the Protein Data Bank with the entry code 6YTU.
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Affiliation(s)
- Maria S Eriksen
- Department of Biomedicine, University of Bergen, Norway.,KG Jebsen Centre for Neuropsychiatric Disorders, University of Bergen, Norway
| | - Oleksii Nikolaienko
- Department of Biomedicine, University of Bergen, Norway.,KG Jebsen Centre for Neuropsychiatric Disorders, University of Bergen, Norway
| | - Erik I Hallin
- Department of Biomedicine, University of Bergen, Norway
| | - Sverre Grødem
- Department of Biomedicine, University of Bergen, Norway.,KG Jebsen Centre for Neuropsychiatric Disorders, University of Bergen, Norway
| | - Helene J Bustad
- Department of Biomedicine, University of Bergen, Norway.,KG Jebsen Centre for Neuropsychiatric Disorders, University of Bergen, Norway
| | - Marte I Flydal
- Department of Biomedicine, University of Bergen, Norway.,KG Jebsen Centre for Neuropsychiatric Disorders, University of Bergen, Norway
| | - Ian Merski
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, MA, USA
| | - Tomohisa Hosokawa
- Department of Pharmacology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Daniela Lascu
- Department of Biomedicine, University of Bergen, Norway.,KG Jebsen Centre for Neuropsychiatric Disorders, University of Bergen, Norway
| | - Shreeram Akerkar
- Department of Biomedicine, University of Bergen, Norway.,KG Jebsen Centre for Neuropsychiatric Disorders, University of Bergen, Norway
| | - Jorge Cuéllar
- Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - James J Chambers
- Institute for Applied Life Sciences, University of Massachusetts Amherst, MA, USA
| | - Rory O'Connell
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, MA, USA
| | - Gopinath Muruganandam
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium.,Structural Biology Brussels, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Belgium
| | - Remy Loris
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium.,Structural Biology Brussels, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Belgium
| | - Christine Touma
- Faculty of Biochemistry and Molecular Biology & Biocenter Oulu, University of Oulu, Finland
| | - Tambudzai Kanhema
- Department of Biomedicine, University of Bergen, Norway.,KG Jebsen Centre for Neuropsychiatric Disorders, University of Bergen, Norway
| | - Yasunori Hayashi
- Department of Pharmacology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Margaret M Stratton
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, MA, USA
| | | | - Petri Kursula
- Department of Biomedicine, University of Bergen, Norway.,Faculty of Biochemistry and Molecular Biology & Biocenter Oulu, University of Oulu, Finland
| | - Aurora Martinez
- Department of Biomedicine, University of Bergen, Norway.,KG Jebsen Centre for Neuropsychiatric Disorders, University of Bergen, Norway
| | - Clive R Bramham
- Department of Biomedicine, University of Bergen, Norway.,KG Jebsen Centre for Neuropsychiatric Disorders, University of Bergen, Norway
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14
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Albagli O, Pelczar H. [The neuronal protein Arc: a retrotransposon capsid domesticated to serve key synaptic functions]. Med Sci (Paris) 2020; 36:980-983. [PMID: 33151858 DOI: 10.1051/medsci/2020178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Olivier Albagli
- Inserm U1016, CNRS UMR8104, Institut Cochin, Groupe hospitalier Cochin-Port-Royal, bâtiment Cassini, 123 boulevard de Port-Royal, 75014 Paris, France
| | - Hélène Pelczar
- Inserm U1016, CNRS UMR8104, Institut Cochin, Groupe hospitalier Cochin-Port-Royal, bâtiment Cassini, 123 boulevard de Port-Royal, 75014 Paris, France
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15
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Bessières B, Jia M, Travaglia A, Alberini CM. Developmental changes in plasticity, synaptic, glia, and connectivity protein levels in rat basolateral amygdala. ACTA ACUST UNITED AC 2019; 26:436-448. [PMID: 31615855 PMCID: PMC6796789 DOI: 10.1101/lm.049866.119] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 08/09/2019] [Indexed: 01/01/2023]
Abstract
The basolateral complex of amygdala (BLA) processes emotionally arousing aversive and rewarding experiences. The BLA is critical for acquisition and storage of threat-based memories and the modulation of the consolidation of arousing explicit memories, that is, the memories that are encoded and stored by the medial temporal lobe. In addition, in conjunction with the medial prefrontal cortex (mPFC), the BLA plays an important role in fear memory extinction. The BLA develops relatively early in life, but little is known about the molecular changes that accompany its development. Here, we quantified relative basal expression levels of sets of plasticity, synaptic, glia, and connectivity proteins in the rat BLA at various developmental ages: postnatal day 17 (PN17, infants), PN24 (juveniles), and PN80 (young adults). We found that the levels of activation markers of brain plasticity, including phosphorylation of CREB at Ser133, CamKIIα at Thr286, pERK1/pERK2 at Thr202/Tyr204, and GluA1 at Ser831 and Ser845, were significantly higher in infant and juvenile compared with adult brain. In contrast, age increase was accompanied by a significant augmentation in the levels of proteins that mark synaptogenesis and synapse maturation, such as synaptophysin, PSD95, SynCAM, GAD65, GAD67, and GluN2A/GluN2B ratio. Finally, we observed significant age-associated changes in structural markers, including MAP2, MBP, and MAG, suggesting that the structural connectivity of the BLA increases over time. The biological differences in the BLA between developmental ages compared with adulthood suggest the need for caution in extrapolating conclusions based on BLA-related brain plasticity and behavioral studies conducted at different developmental stages.
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Affiliation(s)
- Benjamin Bessières
- Center for Neural Science, New York University, New York, New York 10003, USA
| | - Margaret Jia
- Center for Neural Science, New York University, New York, New York 10003, USA
| | - Alessio Travaglia
- Center for Neural Science, New York University, New York, New York 10003, USA
| | - Cristina M Alberini
- Center for Neural Science, New York University, New York, New York 10003, USA
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16
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Abstract
Alzheimer's disease (AD) dementia refers to a particular onset and course of cognitive and functional decline associated with age together with a particular neuropathology. It was first described by Alois Alzheimer in 1906 about a patient whom he first encountered in 1901. Modern clinical diagnostic criteria have been developed, and criteria have also been proposed to recognize preclinical (or presymptomatic) stages of the disease with the use of biomarkers. The primary neuropathology was described by Alzheimer, and in the mid-1980s subsequently evolved into a more specific neuropathologic definition that recognizes the comorbid neuropathologies that frequently contribute to clinical dementia. Alzheimer's disease is now the most common form of neurodegenerative dementia in the United States with a disproportionate disease burden in minority populations. Deficits in the ability to encode and store new memories characterizes the initial stages of the disease. Subsequent progressive changes in cognition and behavior accompany the later stages. Changes in amyloid precursor protein (APP) cleavage and production of the APP fragment beta-amyloid (Aβ) along with hyperphosphorylated tau protein aggregation coalesce to cause reduction in synaptic strength, synaptic loss, and neurodegeneration. Metabolic, vascular, and inflammatory changes, as well as comorbid pathologies are key components of the disease process. Symptomatic treatment offers a modest, clinically measurable effect in cognition, but disease-modifying therapies are desperately needed.
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Affiliation(s)
- Jose A Soria Lopez
- Department of Neurosciences, University of California San Diego, La Jolla, CA, United States; Shiley-Marcos Alzheimer's Disease Research Center, University of California San Diego, La Jolla, CA, United States
| | - Hector M González
- Department of Neurosciences, University of California San Diego, La Jolla, CA, United States; Shiley-Marcos Alzheimer's Disease Research Center, University of California San Diego, La Jolla, CA, United States
| | - Gabriel C Léger
- Department of Neurosciences, University of California San Diego, La Jolla, CA, United States; Shiley-Marcos Alzheimer's Disease Research Center, University of California San Diego, La Jolla, CA, United States.
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17
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Gray JM, Spiegel I. Cell-type-specific programs for activity-regulated gene expression. Curr Opin Neurobiol 2018; 56:33-39. [PMID: 30529822 DOI: 10.1016/j.conb.2018.11.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 11/04/2018] [Accepted: 11/05/2018] [Indexed: 12/20/2022]
Abstract
Experience leaves a lasting mark on neural circuit function in part through activity-regulated gene (ARG) expression. New genome wide approaches have revealed that ARG programs are highly cell-type-specific, raising the possibility that they mediate different forms of experience-dependent plasticity in different cell types. The cell-type specificity of these gene programs is achieved by a combination of cell-intrinsic mechanisms that determine the transcriptional response of each neuronal subtype to a given stimulus and by cell-extrinsic mechanisms that influence the nature of the stimulus a cell receives. A better understanding of these mechanisms could usher in an era of molecular systems neuroscience in which genetic perturbations of cell-type-specific plasticities are assessed using electrophysiology and in vivo imaging to reveal the neural basis of adaptive behaviors.
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Affiliation(s)
- Jesse M Gray
- Department of Genetics, Harvard Medical School, Boston, United States.
| | - Ivo Spiegel
- Department of Neurobiology, Weizmann Institute of Science, 76100 Rehovot, Israel.
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18
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Nakahata Y, Yasuda R. Plasticity of Spine Structure: Local Signaling, Translation and Cytoskeletal Reorganization. Front Synaptic Neurosci 2018; 10:29. [PMID: 30210329 PMCID: PMC6123351 DOI: 10.3389/fnsyn.2018.00029] [Citation(s) in RCA: 133] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 08/07/2018] [Indexed: 12/31/2022] Open
Abstract
Dendritic spines are small protrusive structures on dendritic surfaces, and function as postsynaptic compartments for excitatory synapses. Plasticity of spine structure is associated with many forms of long-term neuronal plasticity, learning and memory. Inside these small dendritic compartments, biochemical states and protein-protein interactions are dynamically modulated by synaptic activity, leading to the regulation of protein synthesis and reorganization of cytoskeletal architecture. This in turn causes plasticity of structure and function of the spine. Technical advances in monitoring molecular behaviors in single dendritic spines have revealed that each signaling pathway is differently regulated across multiple spatiotemporal domains. The spatial pattern of signaling activity expands from a single spine to the nearby dendritic area, dendritic branch and the nucleus, regulating different cellular events at each spatial scale. Temporally, biochemical events are typically triggered by short Ca2+ pulses (~10–100 ms). However, these signals can then trigger activation of downstream protein cascades that can last from milliseconds to hours. Recent imaging studies provide many insights into the biochemical processes governing signaling events of molecular assemblies at different spatial localizations. Here, we highlight recent findings of signaling dynamics during synaptic plasticity and discuss their roles in long-term structural plasticity of dendritic spines.
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Affiliation(s)
- Yoshihisa Nakahata
- Neuronal Signal Transduction, Max Planck Florida Institute for Neuroscience (MPFI), Jupiter, FL, United States
| | - Ryohei Yasuda
- Neuronal Signal Transduction, Max Planck Florida Institute for Neuroscience (MPFI), Jupiter, FL, United States
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19
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Pastuzyn ED, Day CE, Kearns RB, Kyrke-Smith M, Taibi AV, McCormick J, Yoder N, Belnap DM, Erlendsson S, Morado DR, Briggs JAG, Feschotte C, Shepherd JD. The Neuronal Gene Arc Encodes a Repurposed Retrotransposon Gag Protein that Mediates Intercellular RNA Transfer. Cell 2018; 172:275-288.e18. [PMID: 29328916 PMCID: PMC5884693 DOI: 10.1016/j.cell.2017.12.024] [Citation(s) in RCA: 286] [Impact Index Per Article: 47.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 08/15/2017] [Accepted: 12/18/2017] [Indexed: 12/25/2022]
Abstract
The neuronal gene Arc is essential for long-lasting information storage in the mammalian brain, mediates various forms of synaptic plasticity, and has been implicated in neurodevelopmental disorders. However, little is known about Arc's molecular function and evolutionary origins. Here, we show that Arc self-assembles into virus-like capsids that encapsulate RNA. Endogenous Arc protein is released from neurons in extracellular vesicles that mediate the transfer of Arc mRNA into new target cells, where it can undergo activity-dependent translation. Purified Arc capsids are endocytosed and are able to transfer Arc mRNA into the cytoplasm of neurons. These results show that Arc exhibits similar molecular properties to retroviral Gag proteins. Evolutionary analysis indicates that Arc is derived from a vertebrate lineage of Ty3/gypsy retrotransposons, which are also ancestors to retroviruses. These findings suggest that Gag retroelements have been repurposed during evolution to mediate intercellular communication in the nervous system.
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Affiliation(s)
- Elissa D Pastuzyn
- Department of Neurobiology and Anatomy, The University of Utah, Salt Lake City, UT, USA
| | - Cameron E Day
- Department of Neurobiology and Anatomy, The University of Utah, Salt Lake City, UT, USA
| | - Rachel B Kearns
- Department of Neurobiology and Anatomy, The University of Utah, Salt Lake City, UT, USA
| | - Madeleine Kyrke-Smith
- Department of Neurobiology and Anatomy, The University of Utah, Salt Lake City, UT, USA
| | - Andrew V Taibi
- Department of Neurobiology and Anatomy, The University of Utah, Salt Lake City, UT, USA
| | - John McCormick
- Department of Human Genetics, The University of Utah, Salt Lake City, UT, USA
| | - Nathan Yoder
- Department of Neurobiology and Anatomy, The University of Utah, Salt Lake City, UT, USA
| | - David M Belnap
- Department of Biochemistry, The University of Utah, Salt Lake City, UT, USA; Department of Biology, The University of Utah, Salt Lake City, UT, USA
| | - Simon Erlendsson
- Department of Biology, University of Copenhagen, Copenhagen, Denmark; MRC Laboratory of Molecular Biology, Cambridge, UK
| | | | | | - Cédric Feschotte
- Department of Human Genetics, The University of Utah, Salt Lake City, UT, USA
| | - Jason D Shepherd
- Department of Neurobiology and Anatomy, The University of Utah, Salt Lake City, UT, USA; Department of Biochemistry, The University of Utah, Salt Lake City, UT, USA.
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