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Stephens D, Faghihi Z, Moniruzzaman M. Widespread occurrence and diverse origins of polintoviruses influence lineage-specific genome dynamics in stony corals. Virus Evol 2024; 10:veae039. [PMID: 38808038 PMCID: PMC11131425 DOI: 10.1093/ve/veae039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 04/29/2024] [Accepted: 05/12/2024] [Indexed: 05/30/2024] Open
Abstract
Stony corals (Order: Scleractinia) are central to vital marine habitats known as coral reefs. Numerous stressors in the Anthropocene are contributing to the ongoing decline in coral reef health and coverage. While viruses are established modulators of marine microbial dynamics, their interactions within the coral holobiont and impact on coral health and physiology remain unclear. To address this key knowledge gap, we investigated diverse stony coral genomes for 'endogenous' viruses. Our study uncovered a remarkable number of integrated viral elements recognized as 'Polintoviruses' (Class Polintoviricetes) in thirty Scleractinia genomes; with several species harboring hundreds to thousands of polintoviruses. We reveal massive paralogous expansion of polintoviruses in stony coral genomes, alongside the presence of integrated elements closely related to Polinton-like viruses (PLVs), a group of viruses that exist as free virions. These results suggest multiple integrations of polintoviruses and PLV-relatives, along with paralogous expansions, shaped stony coral genomes. Re-analysis of existing gene expression data reveals all polintovirus structural and non-structural hallmark genes are expressed, providing support for free virion production from polintoviruses. Our results, revealing a significant diversity of polintovirus across the Scleractinia order, open a new research avenue into polintovirus and their possible roles in disease, genomic plasticity, and environmental adaptation in this key group of organisms.
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Affiliation(s)
- Danae Stephens
- Department of Marine Biology and Ecology, The Rosenstiel School of Marine, Atmospheric and Earth Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149-1031, USA
| | - Zahra Faghihi
- Department of Marine Biology and Ecology, The Rosenstiel School of Marine, Atmospheric and Earth Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149-1031, USA
| | - Mohammad Moniruzzaman
- Department of Marine Biology and Ecology, The Rosenstiel School of Marine, Atmospheric and Earth Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149-1031, USA
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2
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Koslová A, Hackl T, Bade F, Sanchez Kasikovic A, Barenhoff K, Schimm F, Mersdorf U, Fischer MG. Endogenous virophages are active and mitigate giant virus infection in the marine protist Cafeteria burkhardae. Proc Natl Acad Sci U S A 2024; 121:e2314606121. [PMID: 38446847 PMCID: PMC10945749 DOI: 10.1073/pnas.2314606121] [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: 09/07/2023] [Accepted: 01/14/2024] [Indexed: 03/08/2024] Open
Abstract
Endogenous viral elements (EVEs) are common genetic passengers in various protists. Some EVEs represent viral fossils, whereas others are still active. The marine heterotrophic flagellate Cafeteria burkhardae contains several EVE types related to the virophage mavirus, a small DNA virus that parasitizes the lytic giant virus CroV. We hypothesized that endogenous virophages may act as an antiviral defense system in protists, but no protective effect of virophages in wild host populations has been shown so far. Here, we tested the activity of virophage EVEs and studied their impact on giant virus replication. We found that endogenous mavirus-like elements (EMALEs) from globally distributed Cafeteria populations produced infectious virus particles specifically in response to CroV infection. However, reactivation was stochastic, often inefficient, and poorly reproducible. Interestingly, only one of eight EMALE types responded to CroV infection, implying that other EMALEs may be linked to different giant viruses. We isolated and cloned several reactivated virophages and characterized their particles, genomes, and infection dynamics. All tested virophages inhibited the production of CroV during coinfection, thereby preventing lysis of the host cultures in a dose-dependent manner. Comparative genomics of different C. burkhardae strains revealed that inducible EMALEs are common and are not linked to specific geographic locations. We demonstrate that naturally occurring virophage EVEs reactivate upon giant virus infection, thus providing a striking example that eukaryotic EVEs can become active under specific conditions. Moreover, our results support the hypothesis that virophages can act as an adaptive antiviral defense system in protists.
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Affiliation(s)
- Anna Koslová
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg69120, Germany
| | - Thomas Hackl
- Faculty of Science and Engineering, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen9747 AG, The Netherlands
| | - Felix Bade
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg69120, Germany
| | | | - Karina Barenhoff
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg69120, Germany
| | - Fiona Schimm
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg69120, Germany
| | - Ulrike Mersdorf
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg69120, Germany
| | - Matthias G. Fischer
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg69120, Germany
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3
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Barreat JGN, Katzourakis A. A billion years arms-race between viruses, virophages, and eukaryotes. eLife 2023; 12:RP86617. [PMID: 37358563 DOI: 10.7554/elife.86617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/27/2023] Open
Abstract
Bamfordviruses are arguably the most diverse group of viruses infecting eukaryotes. They include the Nucleocytoplasmic Large DNA viruses (NCLDVs), virophages, adenoviruses, Mavericks and Polinton-like viruses. Two main hypotheses for their origins have been proposed: the 'nuclear-escape' and 'virophage-first' hypotheses. The nuclear-escape hypothesis proposes an endogenous, Maverick-like ancestor which escaped from the nucleus and gave rise to adenoviruses and NCLDVs. In contrast, the virophage-first hypothesis proposes that NCLDVs coevolved with protovirophages; Mavericks then evolved from virophages that became endogenous, with adenoviruses escaping from the nucleus at a later stage. Here, we test the predictions made by both models and consider alternative evolutionary scenarios. We use a data set of the four core virion proteins sampled across the diversity of the lineage, together with Bayesian and maximum-likelihood hypothesis-testing methods, and estimate rooted phylogenies. We find strong evidence that adenoviruses and NCLDVs are not sister groups, and that Mavericks and Mavirus acquired the rve-integrase independently. We also found strong support for a monophyletic group of virophages (family Lavidaviridae) and a most likely root placed between virophages and the other lineages. Our observations support alternatives to the nuclear-escape scenario and a billion years evolutionary arms-race between virophages and NCLDVs.
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Affiliation(s)
| | - Aris Katzourakis
- Department of Biology, University of Oxford, Oxford, United Kingdom
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4
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Chase EE, Desnues C, Blanc G. Integrated Viral Elements Suggest the Dual Lifestyle of Tetraselmis Spp. Polinton-Like Viruses. Virus Evol 2022; 8:veac068. [PMID: 35949392 PMCID: PMC9356565 DOI: 10.1093/ve/veac068] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 06/30/2022] [Accepted: 07/21/2022] [Indexed: 12/03/2022] Open
Abstract
In this study, we aimed at exploring horizontal gene transfer between viruses and Chlorodendraceae green algae (Chlorophyta) using available genomic and transcriptomic sequences for twenty algal strains. We identified a significant number of genes sharing a higher sequence similarity with viral homologues, thus signalling their possible involvement in horizontal gene transfers with viruses. Further characterization showed that many of these genes were clustered in DNA regions of several tens to hundreds of kilobases in size, originally belonging to viruses related to known Tetraselmis spp. viruses (TetV and TsV). In contrast, the remaining candidate HGT genes were randomly dispersed in the algal genomes, were more frequently transcribed, and belonged to large multigene families. The presence of homologues in Viridiplantae suggested that the latter were more likely of algal rather than viral origin. We found a remarkable diversity in polinton-like virus (PLV) elements inserted in Tetraselmis genomes, all of which were most similar to the Tetraselmis striata virus (TsV). The genes of PLV elements are transcriptionally inactive with the notable exception of the homologue of the TVSG_00024 gene of TsV whose function is unknown. We suggest that this gene may be involved in a sentinel process to trigger virus reactivation and excision in response to an environmental stimulus. Altogether, these results provide evidence that TsV-related viruses have a dual lifestyle, alternating between a free viral phase (i.e. virion) and a phase integrated into host genomes.
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Affiliation(s)
- Emily E Chase
- Microbiologie Environnementale Biotechnologie, Institut Méditerranéen d’Océanologie, Campus de Luminy , 163 Avenue de Luminy, 13009 Marseille, France
- Institut hospitalo-universitaire (IHU) Méditerranée infection , 19-21 Boulevard Jean Moulin, 13005 Marseille, France
| | - Christelle Desnues
- Microbiologie Environnementale Biotechnologie, Institut Méditerranéen d’Océanologie, Campus de Luminy , 163 Avenue de Luminy, 13009 Marseille, France
- Institut hospitalo-universitaire (IHU) Méditerranée infection , 19-21 Boulevard Jean Moulin, 13005 Marseille, France
| | - Guillaume Blanc
- Microbiologie Environnementale Biotechnologie, Institut Méditerranéen d’Océanologie, Campus de Luminy , 163 Avenue de Luminy, 13009 Marseille, France
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5
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Zhao M, Yue C, Yang Z, Li Y, Zhang D, Zhang J, Yang S, Shen Q, Su X, Qi D, Ma R, Xiao Y, Hou R, Yan X, Li L, Zhou Y, Liu J, Wang X, Wu W, Zhang W, Shan T, Liu S. Viral metagenomics unveiled extensive communications of viruses within giant pandas and their associated organisms in the same ecosystem. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 820:153317. [PMID: 35066043 DOI: 10.1016/j.scitotenv.2022.153317] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 01/17/2022] [Accepted: 01/17/2022] [Indexed: 06/14/2023]
Abstract
Cross-species transmission events were commonplace, with numerous cases of host-switching during the viral evolutionary history, but relatively little evidence for onward transmission in different species living in the same ecosystem. For understanding the communications of viruses in giant pandas (Ailuropoda melanoleuca) and their associated organisms, based on a large size of samples (N = 2305) collected between 2015 and 2020 from giant panda (N = 776) and other four giant panda-associated organisms in the same ecosystem, red pandas (N = 700), stray cats (N = 32), wild rats (N = 42), and mosquitoes (N = 755), viromics was used for the virus identification and subsequent virus traceability. The results showed that a feline panleukopenia virus (FPV) was found in giant pandas with clinical signs of vomiting and mild diarrhea. Meanwhile, the same FPV strain was also prevalent in the healthy red panda (Ailurus fulgens) population. From the viromes of the five different organisms, 250 virus genomes were determined. Our data revealed that besides FPV, other putative pathogenic viruses, such as red panda amdoparvoviruses (RPAVs) and Getah viruses (GETVs) were responsible for previous disease or death of some red pandas. We also demonstrated that a number of viruses were involved in potential interspecies jumping events between giant pandas and their associated species. Collectively, our results shed light on the genetic diversity and relationship of diverse viral pathogens in 'Giant pandas-Associated animals-Arthropods' and report some cases of possible viral host-switching among these host species living in the same ecosystem.
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Affiliation(s)
- Min Zhao
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang 212013, Jiangsu, China
| | - Chanjuan Yue
- Chengdu Research Base of Giant Panda Breeding, Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu 610081, Sichuan, China
| | - Zijun Yang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang 212013, Jiangsu, China
| | - Yunli Li
- Chengdu Research Base of Giant Panda Breeding, Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu 610081, Sichuan, China
| | - Dongsheng Zhang
- Chengdu Research Base of Giant Panda Breeding, Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu 610081, Sichuan, China
| | - Ju Zhang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang 212013, Jiangsu, China
| | - Shixing Yang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang 212013, Jiangsu, China
| | - Quan Shen
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang 212013, Jiangsu, China
| | - Xiaoyan Su
- Chengdu Research Base of Giant Panda Breeding, Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu 610081, Sichuan, China
| | - Dunwu Qi
- Chengdu Research Base of Giant Panda Breeding, Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu 610081, Sichuan, China
| | - Rui Ma
- Chengdu Research Base of Giant Panda Breeding, Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu 610081, Sichuan, China
| | - Yuqing Xiao
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang 212013, Jiangsu, China
| | - Rong Hou
- Chengdu Research Base of Giant Panda Breeding, Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu 610081, Sichuan, China
| | - Xia Yan
- Chengdu Research Base of Giant Panda Breeding, Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu 610081, Sichuan, China
| | - Lin Li
- Chengdu Research Base of Giant Panda Breeding, Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu 610081, Sichuan, China
| | - Yanshan Zhou
- Chengdu Research Base of Giant Panda Breeding, Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu 610081, Sichuan, China
| | - Jiabin Liu
- Chengdu Research Base of Giant Panda Breeding, Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu 610081, Sichuan, China
| | - Xiaochun Wang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang 212013, Jiangsu, China
| | - Wei Wu
- Chengdu Research Base of Giant Panda Breeding, Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu 610081, Sichuan, China
| | - Wen Zhang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang 212013, Jiangsu, China.
| | - Tongling Shan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China.
| | - Songrui Liu
- Chengdu Research Base of Giant Panda Breeding, Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu 610081, Sichuan, China.
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6
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Isolation and Identification of a Large Green Alga Virus ( Chlorella Virus XW01) of Mimiviridae and Its Virophage ( Chlorella Virus Virophage SW01) by Using Unicellular Green Algal Cultures. J Virol 2022; 96:e0211421. [PMID: 35262372 DOI: 10.1128/jvi.02114-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Virophages are a group of small double-stranded DNA viruses that infect protist hosts and parasitize the viral factory of host giant/large viruses to propagate. Here, we discover a novel cell-virus-virophage (CVv) tripartite interaction system by using unicellular micro-green algae (Chlorella sp.) as eukaryotic hosts for the first time. Viral particles, resembling known virophages and large alga viruses, are detected in culture supernatants and inside algal cells. Complete genomic sequences of the virophage (Chlorella virus virophage SW01 [CVv-SW01]; 24,744 bp) and large virus (Chlorella virus XW01 [CV-XW01]; 407,612 bp) are obtained from the cocultures. Both genomic and phylogenetic analyses show that CVv-SW01 is closely related to virophages previously found in Dishui Lake. CV-XW01 shares the greatest number of homologous genes (n = 82) with Cafeteria roenbergensis virus (CroV) and phylogenetically represents the closest relative to CroV. This is the first report of a large green alga virus being affiliated with a heterotrophic zooplankton-infecting Cafeteriavirus of the family Mimiviridae. Moreover, the codon usage preferences of CV-XW01 and CVv-SW01 are highly similar to those of CroV and its virophage Mavirus, respectively. The discovery of such a novel CVv system with the green alga Chlorella sp. as the single cellular eukaryotic host paves a way to further investigate the potential interaction mechanism of CVv and its significance in the ecology of green algae and the evolution of large/giant viruses and their parasitic viruses. IMPORTANCE Parasitic virophages are small unicellular eukaryotic dsDNA viruses that rely on the viral factories of coinfecting giant/large dsDNA viruses for propagation. Presently, the identified eukaryotic hosts of isolated virophages were restricted to a free-living amoeba, Acanthamoeba polyphaga, and a widespread marine heterotrophic flagellate, Cafeteria roenbergensis. In this study, we successfully discovered and identified a novel tripartite interaction system comprised of a micro-green alga (Chlorella sp.), Mimiviridae large green alga virus, and virophage at the coculture level, with Chlorella sp. as the eukaryotic host, based on combination analysis of infection, morphotype, genome, and phylogeny. The large green alga virus CV-XW01 represents the closest relative to the Mimiviridae giant virus Cafeteria roenbergensis virus, host virus of the virophage Mavirus, as well as a novel large virus of Mimiviridae that infects a non-protozoan protist host. The virophage CVv-SW01 highly resembles Mavirus in its codon usage frequency and preference, although they are phylogenetically distantly related. These findings give novel insights into the diversity of large/giant viruses and their virophages.
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Dutta D, Ravichandiran V, Sukla S. Virophages: association with human diseases and their predicted role as virus killers. Pathog Dis 2021; 79:6380487. [PMID: 34601577 DOI: 10.1093/femspd/ftab049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 09/27/2021] [Indexed: 11/13/2022] Open
Abstract
The fascinating discovery of the first giant virus, Acanthamoeba polyphaga mimivirus (APMV), belonging to the family Mimiviridae in 2008, and its associated virophage, Sputnik, have left the world of microbiology awestruck. To date, about 18 virophages have been isolated from different environmental sources. With their unique feature of resisting host cell infection and lysis by giant viruses, analogous to bacteriophage, they have been assigned under the family Lavidaviridae. Genome of T-27, icosahedral-shaped, non-enveloped virophages, consist of dsDNA encoding four proteins, namely, major capsid protein, minor capsid protein, ATPase and cysteine protease, which are essential in the formation and assembly of new virophage particles during replication. A few virophage genomes have been observed to contain additional sequences like PolB, ZnR and S3H. Another interesting characteristic of virophage is that Mimivirus lineage A is immune to infection by the Zamilon virophage through a phenomenon termed MIMIVIRE, resembling the CRISPR-Cas mechanism in bacteria. Based on the fact that giant viruses have been found in clinical samples of hospital-acquired pneumonia and rheumatoid arthritis patients, virophages have opened a novel era in the search for cures of various diseases. This article aims to study the prospective role of virophages in the future of human therapeutics.
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Affiliation(s)
- Debrupa Dutta
- National Institute of Pharmaceuticals Education and Research, 168, Maniktala Main Road, Kolkata, PIN-700054, West Bengal, India
| | - Velayutham Ravichandiran
- National Institute of Pharmaceuticals Education and Research, 168, Maniktala Main Road, Kolkata, PIN-700054, West Bengal, India
| | - Soumi Sukla
- National Institute of Pharmaceuticals Education and Research, 168, Maniktala Main Road, Kolkata, PIN-700054, West Bengal, India
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Morphological and Taxonomic Properties of the Newly Isolated Cotonvirus japonicus, a New Lineage of the Subfamily Megavirinae. J Virol 2021; 95:e0091921. [PMID: 34191583 PMCID: PMC8387033 DOI: 10.1128/jvi.00919-21] [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] [Indexed: 12/16/2022] Open
Abstract
Since 2003, various viruses from the subfamily Megavirinae in the family Mimiviridae have been isolated worldwide, including icosahedral mimiviruses and tailed tupanviruses. To date, the evolutionary relationship between tailed and nontailed mimiviruses has not been elucidated. Here, we present the genomic and morphological features of a newly isolated giant virus, Cotonvirus japonicus (cotonvirus), belonging to the family Mimiviridae. It contains a linear double-stranded DNA molecule of 1.47 Mb, the largest among the reported viruses in the subfamily Megavirinae, excluding tupanviruses. Among its 1,306 predicted open reading frames, 1,149 (88.0%) were homologous to those of the family Mimiviridae. Several nucleocytoplasmic large DNA virus (NCLDV) core genes, aminoacyl-tRNA synthetase genes, and the host specificity of cotonvirus were highly similar to those of Mimiviridae lineages A, B, and C; however, lineage A was slightly closer to cotonvirus than the others were. Moreover, based on its genome size, the presence of two copies of 18S rRNA-like sequences, and the period of its infection cycle, cotonvirus is the most similar to the tupanviruses among the icosahedral mimiviruses. Interestingly, the cotonvirus utilizes Golgi apparatus-like vesicles for virion factory (VF) formation. Overall, we showed that cotonvirus is a novel lineage of the subfamily Megavirinae. Our findings support the diversity of icosahedral mimiviruses and provide mechanistic insights into the replication, VF formation, and evolution of the subfamily Megavirinae. IMPORTANCE We have isolated a new virus of an independent lineage belonging to the family Mimiviridae, subfamily Megavirinae, from the fresh water of a canal in Japan, named Cotonvirus. In a proteomic tree, this new nucleocytoplasmic large DNA virus (NCLDV) is phylogenetically placed at the root of three lineages of the subfamily Megavirinae—lineages A (mimivirus), B (moumouvirus), and C (megavirus). Multiple genomic and phenotypic features of cotonvirus are more similar to those of tupanviruses than to those of the A, B, or C lineages, and other genomic features, while the host specificity of cotonvirus is more similar to those of the latter than of the former. These results suggest that cotonvirus is a unique virus that has chimeric features of existing viruses of Megavirinae and uses Golgi apparatus-like vesicles of the host cells for virion factory (VF) formation. Thus, cotonvirus can provide novel insights into the evolution of mimiviruses and the underlying mechanisms of VF formation.
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