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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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Abstract
Flaviviruses are positive-sense single-stranded RNA viruses, including some well-known human pathogens such as Zika, dengue, and yellow fever viruses, which are primarily associated with mosquito and tick vectors. The vast majority of flavivirus research has focused on terrestrial environments; however, recent findings indicate that a range of flaviviruses are also present in aquatic environments, both marine and freshwater. These flaviviruses are found in various hosts, including fish, crustaceans, molluscs, and echinoderms. Although the effects of aquatic flaviviruses on the hosts they infect are not all known, some have been detected in farmed species and may have detrimental effects on the aquaculture industry. Exploration of the evolutionary history through the discovery of the Wenzhou shark flavivirus in both a shark and crab host is of particular interest since the potential dual-host nature of this virus may indicate that the invertebrate-vertebrate relationship seen in other flaviviruses may have a more profound evolutionary root than previously expected. Potential endogenous viral elements and the range of novel aquatic flaviviruses discovered thus shed light on virus origins and evolutionary history and may indicate that, like terrestrial life, the origins of flaviviruses may lie in aquatic environments.
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Li Y, Bletsa M, Zisi Z, Boonen I, Gryseels S, Kafetzopoulou L, Webster JP, Catalano S, Pybus OG, Van de Perre F, Li H, Li Y, Li Y, Abramov A, Lymberakis P, Lemey P, Lequime S. Endogenous Viral Elements in Shrew Genomes Provide Insights into Pestivirus Ancient History. Mol Biol Evol 2022; 39:6692409. [PMID: 36063436 PMCID: PMC9550988 DOI: 10.1093/molbev/msac190] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
As viral genomic imprints in host genomes, endogenous viral elements (EVEs) shed light on the deep evolutionary history of viruses, ancestral host ranges, and ancient viral-host interactions. In addition, they may provide crucial information for calibrating viral evolutionary timescales. In this study, we conducted a comprehensive in silico screening of a large data set of available mammalian genomes for EVEs deriving from members of the viral family Flaviviridae, an important group of viruses including well-known human pathogens, such as Zika, dengue, or hepatitis C viruses. We identified two novel pestivirus-like EVEs in the reference genome of the Indochinese shrew (Crocidura indochinensis). Homologs of these novel EVEs were subsequently detected in vivo by molecular detection and sequencing in 27 shrew species, including 26 species representing a wide distribution within the Crocidurinae subfamily and one in the Soricinae subfamily on different continents. Based on this wide distribution, we estimate that the integration event occurred before the last common ancestor of the subfamily, about 10.8 million years ago, attesting to an ancient origin of pestiviruses and Flaviviridae in general. Moreover, we provide the first description of Flaviviridae-derived EVEs in mammals even though the family encompasses numerous mammal-infecting members. This also suggests that shrews were past and perhaps also current natural reservoirs of pestiviruses. Taken together, our results expand the current known Pestivirus host range and provide novel insight into the ancient evolutionary history of pestiviruses and the Flaviviridae family in general.
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Affiliation(s)
- Yiqiao Li
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Magda Bletsa
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Zafeiro Zisi
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Ine Boonen
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Sophie Gryseels
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium,Belgium Evolutionary Ecology Group, University of Antwerp, 2610 Wilrijk, Belgium
| | - Liana Kafetzopoulou
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium,Virology Department, Belgium Bernhard Nocht Institute for Tropical Medicine, 20359 Hamburg, Germany
| | - Joanne P Webster
- Department of Pathobiology and Population Science, Royal Veterinary College, University of London, Herts, AL9 7TA, UK
| | - Stefano Catalano
- Department of Pathobiology and Population Science, Royal Veterinary College, University of London, Herts, AL9 7TA, UK
| | - Oliver G Pybus
- Department of Pathobiology and Population Science, Royal Veterinary College, University of London, Herts, AL9 7TA, UK
| | | | - Haotian Li
- Marine College, Shandong University (Weihai), 264209 Weihai, China
| | - Yaoyao Li
- Marine College, Shandong University (Weihai), 264209 Weihai, China
| | - Yuchun Li
- Marine College, Shandong University (Weihai), 264209 Weihai, China
| | - Alexei Abramov
- Laboratory of Theriology, Zoological Institute of the Russian Academy of Sciences, 190121 Saint Petersburg, Russia
| | | | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
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Nishihara H. Transposable elements as genetic accelerators of evolution: contribution to genome size, gene regulatory network rewiring and morphological innovation. Genes Genet Syst 2020; 94:269-281. [PMID: 31932541 DOI: 10.1266/ggs.19-00029] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
In the current era, as a growing number of genome sequence assemblies have been reported in animals, an in-depth analysis of transposable elements (TEs) is one of the most fundamental and essential studies for evolutionary genomics. Although TEs have, in general, been regarded as non-functional junk/selfish DNA, parasitic elements or harmful mutagens, studies have revealed that TEs have had a substantial and sometimes beneficial impact on host genomes in several ways. First, TEs are themselves diverse and thus provide lineage-specific characteristics to the genomes. Second, because TEs constitute a substantial fraction of animal genomes, they are a major contributing factor to evolutionary changes in genome size and composition. Third, host organisms have co-opted many repetitive sequences as genes, cis-regulatory elements and chromatin domain boundaries, which alter gene regulatory networks and in addition are partly involved in morphological evolution, as has been well documented in mammals. Here, I review the impact of TEs on various aspects of the genome, such as genome size and diversity in animals, as well as the evolution of gene networks and genome architecture in mammals. Given that a number of TE families probably remain to be discovered in many non-model organisms, unknown TEs may have contributed to gene networks in a much wider variety of animals than considered previously.
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