1
|
Koonin EV, Fischer MG, Kuhn JH, Krupovic M. The polinton-like supergroup of viruses: evolution, molecular biology, and taxonomy. Microbiol Mol Biol Rev 2024; 88:e0008623. [PMID: 39023254 PMCID: PMC11426020 DOI: 10.1128/mmbr.00086-23] [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] [Indexed: 07/20/2024] Open
Abstract
SUMMARYPolintons are 15-20 kb-long self-synthesizing transposons that are widespread in eukaryotic, and in particular protist, genomes. Apart from a transposase and a protein-primed DNA polymerase, polintons encode homologs of major and minor jelly-roll capsid proteins, DNA-packaging ATPases, and proteases involved in capsid maturation of diverse eukaryotic viruses of kingdom Bamfordvirae. Given the conservation of these structural and morphogenetic proteins among polintons, these elements are predicted to alternate between transposon and viral lifestyles and, although virions have thus far not been detected, are classified as viruses (class Polintoviricetes) in the phylum Preplasmiviricota. Related to polintoviricetes are vertebrate adenovirids; unclassified polinton-like viruses (PLVs) identified in various environments or integrated into diverse protist genomes; virophages (Maveriviricetes), which are part of tripartite hyperparasitic systems including protist hosts and giant viruses; and capsid-less derivatives, such as cytoplasmic linear DNA plasmids of fungi and transpovirons. Phylogenomic analysis indicates that the polinton-like supergroup of viruses bridges bacterial tectivirids (preplasmiviricot class Tectiliviricetes) to the phylum Nucleocytoviricota that includes large and giant eukaryotic DNA viruses. Comparative structural analysis of proteins encoded by polinton-like viruses led to the discovery of previously undetected functional domains, such as terminal proteins and distinct proteases implicated in DNA polymerase processing, and clarified the evolutionary relationships within Polintoviricetes. Here, we leverage these insights into the evolution of the polinton-like supergroup to develop an amended megataxonomy that groups Polintoviricetes, PLVs (new class 'Aquintoviricetes'), and virophages (renamed class 'Virophaviricetes') together with Adenoviridae (new class 'Pharingeaviricetes') in a preplasmiviricot subphylum 'Polisuviricotina' sister to a subphylum including Tectiliviricetes ('Prepoliviricotina').
Collapse
Affiliation(s)
- Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Matthias G Fischer
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - 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, Maryland, USA
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, Archaeal Virology Unit, Paris, France
| |
Collapse
|
2
|
Barth ZK, Hicklin I, Thézé J, Takatsuka J, Nakai M, Herniou EA, Brown AM, Aylward FO. Genomic analysis of hyperparasitic viruses associated with entomopoxviruses. Virus Evol 2024; 10:veae051. [PMID: 39100687 PMCID: PMC11296320 DOI: 10.1093/ve/veae051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 05/17/2024] [Accepted: 07/11/2024] [Indexed: 08/06/2024] Open
Abstract
Polinton-like viruses (PLVs) are a diverse group of small integrative dsDNA viruses that infect diverse eukaryotic hosts. Many PLVs are hypothesized to parasitize viruses in the phylum Nucleocytoviricota for their own propagation and spread. Here, we analyze the genomes of novel PLVs associated with the occlusion bodies of entomopoxvirus (EPV) infections of two separate lepidopteran hosts. The presence of these elements within EPV occlusion bodies suggests that they are the first known hyperparasites of poxviruses. We find that these PLVs belong to two distinct lineages that are highly diverged from known PLVs. These PLVs possess mosaic genomes, and some essential genes share homology with mobile genes within EPVs. Based on this homology and observed PLV mosaicism, we propose a mechanism to explain the turnover of PLV replication and integration genes.
Collapse
Affiliation(s)
- Zachary K Barth
- Department of Biological Sciences, Virginia Tech, 926 West Campus Drive, Blacksburg, VA 24061, USA
| | - Ian Hicklin
- Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, USA
| | - Julien Thézé
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR EPIA, Saint-Genès-Champanelle, France
| | - Jun Takatsuka
- Forestry and Forest Products Research Institute, Matsunosato, Tsukuba, Ibaraki 305-8687, Japan
| | - Madoka Nakai
- Institute of Agriculture, Tokyo University of Agriculture and Technology, Saiwai, Fuchu, Tokyo 183-8509, Japan
| | - Elisabeth A Herniou
- Institut de Recherche sur la Biologie de l’Insecte, UMR7261 CNRS-Université de Tours, 20 Avenue Monge, Parc de Grandmont, Tours 37200, France
| | - Anne M Brown
- Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, USA
- Center for Emerging, Zoonotic, and Arthropod-Borne Pathogens, Virginia Tech, 1981 Kraft Dr, Blacksburg, VA 24061, USA
- Research and Informatics, University Libraries, Virginia Tech, Blacksburg, VA 24061, USA
| | - Frank O Aylward
- Department of Biological Sciences, Virginia Tech, 926 West Campus Drive, Blacksburg, VA 24061, USA
- Center for Emerging, Zoonotic, and Arthropod-Borne Pathogens, Virginia Tech, 1981 Kraft Dr, Blacksburg, VA 24061, USA
| |
Collapse
|
3
|
Tokarz-Deptuła B, Chrzanowska S, Baraniecki Ł, Gurgacz N, Stosik M, Sobolewski J, Deptuła W. Virophages, Satellite Viruses, Virophage Replication and Its Effects and Virophage Defence Mechanisms for Giant Virus Hosts and Giant Virus Defence Systems against Virophages. Int J Mol Sci 2024; 25:5878. [PMID: 38892066 PMCID: PMC11172284 DOI: 10.3390/ijms25115878] [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: 04/16/2024] [Revised: 05/22/2024] [Accepted: 05/24/2024] [Indexed: 06/21/2024] Open
Abstract
In this paper, the characteristics of 40 so far described virophages-parasites of giant viruses-are given, and the similarities and differences between virophages and satellite viruses, which also, like virophages, require helper viruses for replication, are described. The replication of virophages taking place at a specific site-the viral particle factory of giant viruses-and its consequences are presented, and the defence mechanisms of virophages for giant virus hosts, as a protective action for giant virus hosts-protozoa and algae-are approximated. The defence systems of giant viruses against virophages were also presented, which are similar to the CRISPR/Cas defence system found in bacteria and in Archea. These facts, and related to the very specific biological features of virophages (specific site of replication, specific mechanisms of their defensive effects for giant virus hosts, defence systems in giant viruses against virophages), indicate that virophages, and their host giant viruses, are biological objects, forming a 'novelty' in biology.
Collapse
Affiliation(s)
| | - Sara Chrzanowska
- Institute of Biology, University of Szczecin, 71-412 Szczecin, Poland (Ł.B.)
| | - Łukasz Baraniecki
- Institute of Biology, University of Szczecin, 71-412 Szczecin, Poland (Ł.B.)
| | - Natalia Gurgacz
- Institute of Biology, University of Szczecin, 71-412 Szczecin, Poland (Ł.B.)
| | - Michał Stosik
- Institute of Biological Science, Faculty of Biological Sciences, University of Zielona Góra, 65-516 Zielona Góra, Poland;
| | - Jarosław Sobolewski
- Institute of Veterinary Medicine, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University in Toruń, 87-100 Toruń, Poland;
| | - Wiesław Deptuła
- Institute of Veterinary Medicine, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University in Toruń, 87-100 Toruń, Poland;
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Potapov SA, Belykh OI. Virophages Found in Viromes from Lake Baikal. Biomolecules 2023; 13:1773. [PMID: 38136644 PMCID: PMC10741620 DOI: 10.3390/biom13121773] [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: 11/13/2023] [Revised: 12/04/2023] [Accepted: 12/06/2023] [Indexed: 12/24/2023] Open
Abstract
In this study, a previously little-studied group of viruses-virophages-was searched for and identified in the viromes of the ancient oligotrophic Lake Baikal. Virophages are small dsDNA viruses that parasitize giant viruses (e.g., Mimiviridae), which in turn affect unicellular eukaryotes. We analyzed eight viromes obtained from the deep-water areas of three basins of Lake Baikal and the shallow-water strait Maloye More in different seasons. The sequences of virophages were revealed in all viromes and were dominant after bacteriophages and algal viruses. Sixteen putative complete genomes of virophages were assembled, all of which contained four conserved genes encoding major capsid protein (MCP), minor capsid protein (mCP), maturation cysteine protease (PRO), and FtsK-HerA family DNA-packaging ATPase (ATPase). The MCP-based cluster analysis showed a sequence separation according to seasons, and a dependence on the geographical localization was not detected.
Collapse
Affiliation(s)
- Sergey Anatoljevich Potapov
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya 3, Irkutsk 664033, Russia;
| | | |
Collapse
|
6
|
Cai H, Zhou Y, Li X, Xu T, Ni Y, Wu S, Yu Y, Wang Y. Genomic Analysis and Taxonomic Characterization of Seven Bacteriophage Genomes Metagenomic-Assembled from the Dishui Lake. Viruses 2023; 15:2038. [PMID: 37896815 PMCID: PMC10611076 DOI: 10.3390/v15102038] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 09/27/2023] [Accepted: 09/29/2023] [Indexed: 10/29/2023] Open
Abstract
Viruses in aquatic ecosystems exhibit remarkable abundance and diversity. However, scattered studies have been conducted to mine uncultured viruses and identify them taxonomically in lake water. Here, whole genomes (29-173 kbp) of seven uncultured dsDNA bacteriophages were discovered in Dishui Lake, the largest artificial lake in Shanghai. We analyzed their genomic signatures and found a series of viral auxiliary metabolic genes closely associated with protein synthesis and host metabolism. Dishui Lake phages shared more genes with uncultivated environmental viruses than with reference viruses based on the gene-sharing network classification. Phylogeny of proteomes and comparative genomics delineated three new genera within two known viral families of Kyanoviridae and Autographiviridae, and four new families in Caudoviricetes for these seven novel phages. Their potential hosts appeared to be from the dominant bacterial phyla in Dishui Lake. Altogether, our study provides initial insights into the composition and diversity of bacteriophage communities in Dishui Lake, contributing valuable knowledge to the ongoing research on the roles played by viruses in freshwater ecosystems.
Collapse
Affiliation(s)
- Haoyun Cai
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China; (H.C.); (Y.Z.); (X.L.); (T.X.); (Y.N.); (S.W.); (Y.Y.)
| | - Yifan Zhou
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China; (H.C.); (Y.Z.); (X.L.); (T.X.); (Y.N.); (S.W.); (Y.Y.)
| | - Xiefei Li
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China; (H.C.); (Y.Z.); (X.L.); (T.X.); (Y.N.); (S.W.); (Y.Y.)
| | - Tianqi Xu
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China; (H.C.); (Y.Z.); (X.L.); (T.X.); (Y.N.); (S.W.); (Y.Y.)
| | - Yimin Ni
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China; (H.C.); (Y.Z.); (X.L.); (T.X.); (Y.N.); (S.W.); (Y.Y.)
| | - Shuang Wu
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China; (H.C.); (Y.Z.); (X.L.); (T.X.); (Y.N.); (S.W.); (Y.Y.)
| | - Yongxin Yu
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China; (H.C.); (Y.Z.); (X.L.); (T.X.); (Y.N.); (S.W.); (Y.Y.)
| | - Yongjie Wang
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China; (H.C.); (Y.Z.); (X.L.); (T.X.); (Y.N.); (S.W.); (Y.Y.)
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266000, China
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation, Ministry of Agriculture and Rural Affairs, Shanghai 201306, China
| |
Collapse
|
7
|
Qin S, Wang K, Gao F, Ge B, Cui H, Li W. Biotechnologies for bulk production of microalgal biomass: from mass cultivation to dried biomass acquisition. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:131. [PMID: 37644516 PMCID: PMC10466707 DOI: 10.1186/s13068-023-02382-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 08/11/2023] [Indexed: 08/31/2023]
Abstract
Microalgal biomass represents a sustainable bioresource for various applications, such as food, nutraceuticals, pharmaceuticals, feed, and other bio-based products. For decades, its mass production has attracted widespread attention and interest. The process of microalgal biomass production involves several techniques, mainly cultivation, harvesting, drying, and pollution control. These techniques are often designed and optimized to meet optimal growth conditions for microalgae and to produce high-quality biomass at acceptable cost. Importantly, mass production techniques are important for producing a commercial product in sufficient amounts. However, it should not be overlooked that microalgal biotechnology still faces challenges, in particular the high cost of production, the lack of knowledge about biological contaminants and the challenge of loss of active ingredients during biomass production. These issues involve the research and development of low-cost, standardized, industrial-scale production equipment and the optimization of production processes, as well as the urgent need to increase the research on biological contaminants and microalgal active ingredients. This review systematically examines the global development of microalgal biotechnology for biomass production, with emphasis on the techniques of cultivation, harvesting, drying and control of biological contaminants, and discusses the challenges and strategies to further improve quality and reduce costs. Moreover, the current status of biomass production of some biotechnologically important species has been summarized, and the importance of improving microalgae-related standards for their commercial applications is noted.
Collapse
Affiliation(s)
- Song Qin
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, No. 19, Chunhui Road, Laishan District, Yantai, 264003, Shandong, China.
| | - Kang Wang
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, No. 19, Chunhui Road, Laishan District, Yantai, 264003, Shandong, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fengzheng Gao
- Bioprocess Engineering, AlgaePARC, Wageningen University, P.O. Box 16, 6700 AA, Wageningen, Netherlands
- Laboratory of Sustainable Food Processing, ETH Zürich, 8092, Zurich, Switzerland
- Laboratory of Nutrition and Metabolic Epigenetics, ETH Zürich, 8603, Schwerzenbach, Switzerland
| | - Baosheng Ge
- College of Chemical Engineering and Center for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao, 266580, China
| | - Hongli Cui
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, No. 19, Chunhui Road, Laishan District, Yantai, 264003, Shandong, China
| | - Wenjun Li
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, No. 19, Chunhui Road, Laishan District, Yantai, 264003, Shandong, China
| |
Collapse
|
8
|
Wu Z, Chu T, Sheng Y, Yu Y, Wang Y. Diversity, Relationship, and Distribution of Virophages and Large Algal Viruses in Global Ocean Viromes. Viruses 2023; 15:1582. [PMID: 37515268 PMCID: PMC10385804 DOI: 10.3390/v15071582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 07/10/2023] [Accepted: 07/12/2023] [Indexed: 07/30/2023] Open
Abstract
Virophages are a group of small double-stranded DNA viruses that replicate and proliferate with the help of the viral factory of large host viruses. They are widely distributed in aquatic environments but are more abundant in freshwater ecosystems. Here, we mined the Global Ocean Viromes 2.0 (GOV 2.0) dataset for the diversity, distribution, and association of virophages and their potential host large viruses in marine environments. We identified 94 virophage sequences (>5 kbp in length), of which eight were complete genomes. The MCP phylogenetic tree showed that the GOV virophages were widely distributed on the global virophage tree but relatively clustered on three major branches. The gene-sharing network divided GOV virophages into 21 outliers, 2 overlaps, and 14 viral clusters, of which 4 consisted of only the GOV virophages. We also identified 45 large virus sequences, 8 of which were >100 kbp in length and possibly involved in cell-virus-virophage (C-V-v) trisome relationships. The potential eukaryotic hosts of these eight large viruses and the eight virophages with their complete genomes identified are likely to be algae, based on comparative genomic analysis. Both homologous gene and codon usage analyses support a possible interaction between a virophage (GOVv18) and a large algal virus (GOVLV1). These results indicate that diverse and novel virophages and large viruses are widespread in global marine environments, suggesting their important roles and the presence of complicated unknown C-V-v relationships in marine ecosystems.
Collapse
Affiliation(s)
- Zhenqi Wu
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201304, China
| | - Ting Chu
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201304, China
| | - Yijian Sheng
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201304, China
| | - Yongxin Yu
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201304, China
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture and Rural Affairs, Shanghai 201304, China
| | - Yongjie Wang
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201304, China
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture and Rural Affairs, Shanghai 201304, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266000, China
| |
Collapse
|
9
|
Tokarz-Deptuła B, Chrzanowska S, Gurgacz N, Stosik M, Deptuła W. Virophages-Known and Unknown Facts. Viruses 2023; 15:1321. [PMID: 37376621 PMCID: PMC10301787 DOI: 10.3390/v15061321] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 05/31/2023] [Accepted: 05/31/2023] [Indexed: 06/29/2023] Open
Abstract
The paper presents virophages, which, like their host, giant viruses, are "new" infectious agents whose role in nature, including mammalian health, is important. Virophages, along with their protozoan and algal hosts, are found in fresh inland waters and oceanic and marine waters, including thermal waters and deep-sea vents, as well as in soil, plants, and in humans and animals (ruminants). Representing "superparasitism", almost all of the 39 described virophages (except Zamilon) interact negatively with giant viruses by affecting their replication and morphogenesis and their "adaptive immunity". This causes them to become regulators and, at the same time, defenders of the host of giant viruses protozoa and algae, which are organisms that determine the homeostasis of the aquatic environment. They are classified in the family Lavidaviridae with two genus (Sputnikovirus, Mavirus). However, in 2023, a proposal was presented that they should form the class Maveriviricetes, with four orders and seven families. Their specific structure, including their microsatellite (SSR-Simple Sequence Repeats) and the CVV (cell-virus-virophage, or transpovirion) system described with them, as well as their function, makes them, together with the biological features of giant viruses, form the basis for discussing the existence of a fourth domain in addition to Bacteria, Archaea, and Eukaryota. The paper also presents the hypothetical possibility of using them as a vector for vaccine antigens.
Collapse
Affiliation(s)
| | - Sara Chrzanowska
- Institute of Biology, University of Szczecin, 71-412 Szczecin, Poland
| | - Natalia Gurgacz
- Institute of Biology, University of Szczecin, 71-412 Szczecin, Poland
| | - Michał Stosik
- Institute of Biological Science, Faculty of Biological Sciences, University of Zielona Góra, 65-417 Zielona Góra, Poland
| | - Wiesław Deptuła
- Institute of Veterinary Medicine, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University of Toruń, 87-100 Toruń, Poland
| |
Collapse
|
10
|
Bellas C, Hackl T, Plakolb MS, Koslová A, Fischer MG, Sommaruga R. Large-scale invasion of unicellular eukaryotic genomes by integrating DNA viruses. Proc Natl Acad Sci U S A 2023; 120:e2300465120. [PMID: 37036967 PMCID: PMC10120064 DOI: 10.1073/pnas.2300465120] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 03/20/2023] [Indexed: 04/12/2023] Open
Abstract
Eukaryotic genomes contain a variety of endogenous viral elements (EVEs), which are mostly derived from RNA and ssDNA viruses that are no longer functional and are considered to be "genomic fossils." Genomic surveys of EVEs, however, are strongly biased toward animals and plants, whereas protists, which represent the majority of eukaryotic diversity, remain poorly represented. Here, we show that protist genomes harbor tens to thousands of diverse, ~14 to 40 kbp long dsDNA viruses. These EVEs, composed of virophages, Polinton-like viruses, and related entities, have remained hitherto hidden owing to poor sequence conservation between virus groups and their repetitive nature that precluded accurate short-read assembly. We show that long-read sequencing technology is ideal for resolving virus insertions. Many protist EVEs appear intact, and most encode integrases, which suggests that they have actively colonized hosts across the tree of eukaryotes. We also found evidence for gene expression in host transcriptomes and that closely related virophage and Polinton-like virus genomes are abundant in viral metagenomes, indicating that many EVEs are probably functional viruses.
Collapse
Affiliation(s)
| | - Thomas Hackl
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, 9747AGGroningen, The Netherlands
| | | | - Anna Koslová
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, 69120Heidelberg, Germany
| | - Matthias G. Fischer
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, 69120Heidelberg, Germany
| | - Ruben Sommaruga
- Department of Ecology, Universität Innsbruck, 6020Innsbruck, Austria
| |
Collapse
|
11
|
Roitman S, Rozenberg A, Lavy T, Brussaard CPD, Kleifeld O, Béjà O. Isolation and infection cycle of a polinton-like virus virophage in an abundant marine alga. Nat Microbiol 2023; 8:332-346. [PMID: 36702941 DOI: 10.1038/s41564-022-01305-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 12/13/2022] [Indexed: 01/27/2023]
Abstract
Virophages are small double stranded DNA (dsDNA) viruses that can only replicate in a host by co-infecting with another virus. Marine algae are commonly associated with virophage-like elements such as Polinton-like viruses (PLVs) that remain largely uncharacterized. Here we isolated a PLV that co-infects the alga Phaeocystis globosa with the Phaeocystis globosa virus-14T (PgV-14T), a close relative of the "Phaeocystis globosa virus-virophage" genomic sequence. We name this PLV 'Gezel-14T. Gezel is phylogenetically distinct from the Lavidaviridae family where all known virophages belong. Gezel-14T co-infection decreases the fitness of its viral host by reducing burst sizes of PgV-14T, yet insufficiently to spare the cellular host population. Genomic screens show Gezel-14T-like PLVs integrated into Phaeocystis genomes, suggesting that these widespread viruses are capable of integration into cellular host genomes. This system presents an opportunity to better understand the evolution of eukaryotic dsDNA viruses as well as the complex dynamics and implications of viral parasitism.
Collapse
Affiliation(s)
- Sheila Roitman
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel.
| | - Andrey Rozenberg
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - Tali Lavy
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - Corina P D Brussaard
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Texel, The Netherlands
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - Oded Kleifeld
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - Oded Béjà
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel.
| |
Collapse
|
12
|
Roux S, Fischer MG, Hackl T, Katz LA, Schulz F, Yutin N. Updated Virophage Taxonomy and Distinction from Polinton-like Viruses. Biomolecules 2023; 13:204. [PMID: 36830574 PMCID: PMC9952930 DOI: 10.3390/biom13020204] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 01/02/2023] [Accepted: 01/04/2023] [Indexed: 01/20/2023] Open
Abstract
Virophages are small dsDNA viruses that hijack the machinery of giant viruses during the co-infection of a protist (i.e., microeukaryotic) host and represent an exceptional case of "hyperparasitism" in the viral world. While only a handful of virophages have been isolated, a vast diversity of virophage-like sequences have been uncovered from diverse metagenomes. Their wide ecological distribution, idiosyncratic infection and replication strategy, ability to integrate into protist and giant virus genomes and potential role in antiviral defense have made virophages a topic of broad interest. However, one limitation for further studies is the lack of clarity regarding the nomenclature and taxonomy of this group of viruses. Specifically, virophages have been linked in the literature to other "virophage-like" mobile genetic elements and viruses, including polinton-like viruses (PLVs), but there are no formal demarcation criteria and proper nomenclature for either group, i.e., virophage or PLVs. Here, as part of the ICTV Virophage Study Group, we leverage a large set of genomes gathered from published datasets as well as newly generated protist genomes to propose delineation criteria and classification methods at multiple taxonomic ranks for virophages 'sensu stricto', i.e., genomes related to the prototype isolates Sputnik and mavirus. Based on a combination of comparative genomics and phylogenetic analyses, we show that this group of virophages forms a cohesive taxon that we propose to establish at the class level and suggest a subdivision into four orders and seven families with distinctive ecogenomic features. Finally, to illustrate how the proposed delineation criteria and classification method would be used, we apply these to two recently published datasets, which we show include both virophages and other virophage-related elements. Overall, we see this proposed classification as a necessary first step to provide a robust taxonomic framework in this area of the virosphere, which will need to be expanded in the future to cover other virophage-related viruses such as PLVs.
Collapse
Affiliation(s)
- Simon Roux
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Matthias G. Fischer
- Max Planck Institute for Medical Research, Department of Biomolecular Mechanisms, 69120 Heidelberg, Germany
| | - Thomas Hackl
- Groningen Institute of Evolutionary Life Sciences, University of Groningen, 9700 AB Groningen, The Netherlands
| | - Laura A. Katz
- Department of Biological Sciences, Smith College, Northampton, MA 01063, USA
| | - Frederik Schulz
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Natalya Yutin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| |
Collapse
|
13
|
del Arco A, Fischer M, Becks L. Simultaneous Giant Virus and Virophage Quantification Using Droplet Digital PCR. Viruses 2022; 14:1056. [PMID: 35632796 PMCID: PMC9144729 DOI: 10.3390/v14051056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 04/30/2022] [Accepted: 05/03/2022] [Indexed: 01/27/2023] Open
Abstract
Viruses are an abundant component of aquatic systems, but their detection and quantification remain a challenge. Virophages co-replicate with giant viruses in the shared host cell, and can inhibit the production of new giant virus particles, thereby increasing the survival of the infected host population. Here, we present a protocol for Droplet Digital PCR (ddPCR) to quantify simultaneously giant virus and virophage in a mixed sample, enabling the rapid, culture-free and high throughput detection of virus and virophage. As virophage can be present as free virus particles or integrated into the virus host's genome as well as associated with organic particles, we developed a simple method that enables discrimination between free and particle-associated virophages. The latter include aggregated virophage particles as well as virophage integrated into the host genome. We used, for our experiments, a host-virus-virophage system consisting of Cafeteria burkhardae, CroV and mavirus. Our results show that ddPCR can be an efficient method to quantify virus and virophage, and we discuss potential applications of the method for studying ecological and evolutionary processes of virus and virophages.
Collapse
Affiliation(s)
- Ana del Arco
- Limnology-Aquatic Ecology and Evolution, Limnological Institute, University of Konstanz, 78464 Konstanz, Germany;
| | - Matthias Fischer
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany;
| | - Lutz Becks
- Limnology-Aquatic Ecology and Evolution, Limnological Institute, University of Konstanz, 78464 Konstanz, Germany;
| |
Collapse
|