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de Azevedo BL, Queiroz VF, de Aquino ILM, Machado TB, de Assis FL, Reis E, Araújo Júnior JP, Ullmann LS, Colson P, Greub G, Aylward F, Rodrigues RAL, Abrahão JS. The genomic and phylogenetic analysis of Marseillevirus cajuinensis raises questions about the evolution of Marseilleviridae lineages and their taxonomical organization. J Virol 2024; 98:e0051324. [PMID: 38752754 PMCID: PMC11237802 DOI: 10.1128/jvi.00513-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 04/19/2024] [Indexed: 06/14/2024] Open
Abstract
Marseilleviruses (MsV) are a group of viruses that compose the Marseilleviridae family within the Nucleocytoviricota phylum. They have been found in different samples, mainly in freshwater. MsV are classically organized into five phylogenetic lineages (A/B/C/D/E), but the current taxonomy does not fully represent all the diversity of the MsV lineages. Here, we describe a novel strain isolated from a Brazilian saltwater sample named Marseillevirus cajuinensis. Based on genomics and phylogenetic analyses, M. cajuinensis exhibits a 380,653-bp genome that encodes 515 open reading frames. Additionally, M. cajuinensis encodes a transfer RNA, a feature that is rarely described for Marseilleviridae. Phylogeny suggests that M. cajuinensis forms a divergent branch within the MsV lineage A. Furthermore, our analysis suggests that the common ancestor for the five classical lineages of MsV diversified into three major groups. The organization of MsV into three main groups is reinforced by a comprehensive analysis of clusters of orthologous groups, sequence identities, and evolutionary distances considering several MsV isolates. Taken together, our results highlight the importance of discovering new viruses to expand the knowledge about known viruses that belong to the same lineages or families. This work proposes a new perspective on the Marseilleviridae lineages organization that could be helpful to a future update in the taxonomy of the Marseilleviridae family. IMPORTANCE Marseilleviridae is a family of viruses whose members were mostly isolated from freshwater samples. In this work, we describe the first Marseillevirus isolated from saltwater samples, which we called Marseillevirus cajuinensis. Most of M. cajuinensis genomic features are comparable to other Marseilleviridae members, such as its high number of unknown proteins. On the other hand, M. cajuinensis encodes a transfer RNA, which is a gene category involved in protein translation that is rarely described in this viral family. Additionally, our phylogenetic analyses suggested the existence of, at least, three major Marseilleviridae groups. These observations provide a new perspective on Marseilleviridae lineages organization, which will be valuable in future updates to the taxonomy of the family since the current official classification does not capture all the Marseilleviridae known diversity.
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Affiliation(s)
- Bruna Luiza de Azevedo
- Laboratório de Vírus, Departamento de Microbiologia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil
| | - Victória Fulgêncio Queiroz
- Laboratório de Vírus, Departamento de Microbiologia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil
| | - Isabella Luiza Martins de Aquino
- Laboratório de Vírus, Departamento de Microbiologia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil
| | - Talita Bastos Machado
- Laboratório de Vírus, Departamento de Microbiologia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil
| | - Felipe Lopes de Assis
- Laboratório de Vírus, Departamento de Microbiologia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil
| | - Erik Reis
- Laboratório de Vírus, Departamento de Microbiologia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil
| | - João Pessoa Araújo Júnior
- Laboratório de Virologia, Departamento de Microbiologia e Imunologia, Instituto de Biotecnologia, Universidade Estadual Paulista (Unesp), Alameda das Tecomarias s/n, Chácara Capão Bonito, Botucatu, Brazil
| | - Leila Sabrina Ullmann
- Laboratório de Virologia, Departamento de Microbiologia e Imunologia, Instituto de Biotecnologia, Universidade Estadual Paulista (Unesp), Alameda das Tecomarias s/n, Chácara Capão Bonito, Botucatu, Brazil
| | - Philippe Colson
- IHU Méditerranée Infection, Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Aix-Marseille University, Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Marseille, France
| | - Gilbert Greub
- Centre for Research on Intracellular Bacteria and Giant Viruses, Institute of Microbiology, University Hospital Centre and University of Lausanne, Lausanne, Switzerland
| | - Frank Aylward
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA
- Center for Emerging, Zoonotic, and Arthropod-Borne Infectious Disease Virginia Tech, Blacksburg, Virginia, USA
| | - Rodrigo Araújo Lima Rodrigues
- Laboratório de Vírus, Departamento de Microbiologia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil
| | - Jônatas Santos Abrahão
- Laboratório de Vírus, Departamento de Microbiologia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil
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Schulz F, Abergel C, Woyke T. Giant virus biology and diversity in the era of genome-resolved metagenomics. Nat Rev Microbiol 2022; 20:721-736. [PMID: 35902763 DOI: 10.1038/s41579-022-00754-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/25/2022] [Indexed: 11/09/2022]
Abstract
The discovery of giant viruses, with capsids as large as some bacteria, megabase-range genomes and a variety of traits typically found only in cellular organisms, was one of the most remarkable breakthroughs in biology. Until recently, most of our knowledge of giant viruses came from ~100 species-level isolates for which genome sequences were available. However, these isolates were primarily derived from laboratory-based co-cultivation with few cultured protists and algae and, thus, did not reflect the true diversity of giant viruses. Although virus co-cultures enabled valuable insights into giant virus biology, many questions regarding their origin, evolution and ecological importance remain unanswered. With advances in sequencing technologies and bioinformatics, our understanding of giant viruses has drastically expanded. In this Review, we summarize our understanding of giant virus diversity and biology based on viral isolates as laboratory cultivation has enabled extensive insights into viral morphology and infection strategies. We then explore how cultivation-independent approaches have heightened our understanding of the coding potential and diversity of the Nucleocytoviricota. We discuss how metagenomics has revolutionized our perspective of giant viruses by revealing their distribution across our planet's biomes, where they impact the biology and ecology of a wide range of eukaryotic hosts and ultimately affect global nutrient cycles.
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Affiliation(s)
- Frederik Schulz
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Chantal Abergel
- Aix Marseille University, CNRS, IGS UMR7256, IMM FR3479, IM2B, IO, Marseille, France
| | - Tanja Woyke
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. .,University of California Merced, Merced, CA, USA.
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Speciale I, Notaro A, Abergel C, Lanzetta R, Lowary TL, Molinaro A, Tonetti M, Van Etten JL, De Castro C. The Astounding World of Glycans from Giant Viruses. Chem Rev 2022; 122:15717-15766. [PMID: 35820164 PMCID: PMC9614988 DOI: 10.1021/acs.chemrev.2c00118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
![]()
Viruses are a heterogeneous ensemble of entities, all
sharing the
need for a suitable host to replicate. They are extremely diverse,
varying in morphology, size, nature, and complexity of their genomic
content. Typically, viruses use host-encoded glycosyltransferases
and glycosidases to add and remove sugar residues from their glycoproteins.
Thus, the structure of the glycans on the viral proteins have, to
date, typically been considered to mimick those of the host. However,
the more recently discovered large and giant viruses differ from this
paradigm. At least some of these viruses code for an (almost) autonomous
glycosylation pathway. These viral genes include those that encode
the production of activated sugars, glycosyltransferases, and other
enzymes able to manipulate sugars at various levels. This review focuses
on large and giant viruses that produce carbohydrate-processing enzymes.
A brief description of those harboring these features at the genomic
level will be discussed, followed by the achievements reached with
regard to the elucidation of the glycan structures, the activity of
the proteins able to manipulate sugars, and the organic synthesis
of some of these virus-encoded glycans. During this progression, we
will also comment on many of the challenging questions on this subject
that remain to be addressed.
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Affiliation(s)
- Immacolata Speciale
- Department of Agricultural Sciences, University of Napoli, Via Università 100, 80055 Portici, Italy
| | - Anna Notaro
- Department of Agricultural Sciences, University of Napoli, Via Università 100, 80055 Portici, Italy.,Centre National de la Recherche Scientifique, Information Génomique & Structurale, Aix-Marseille University, Unité Mixte de Recherche 7256, IMM, IM2B, 13288 Marseille, Cedex 9, France
| | - Chantal Abergel
- Centre National de la Recherche Scientifique, Information Génomique & Structurale, Aix-Marseille University, Unité Mixte de Recherche 7256, IMM, IM2B, 13288 Marseille, Cedex 9, France
| | - Rosa Lanzetta
- Department of Chemical Sciences, University of Napoli, Via Cintia 4, 80126 Napoli, Italy
| | - Todd L Lowary
- Institute of Biological Chemistry, Academia Sinica, Academia Road, Section 2, Nangang 11529, Taipei, Taiwan
| | - Antonio Molinaro
- Department of Chemical Sciences, University of Napoli, Via Cintia 4, 80126 Napoli, Italy
| | - Michela Tonetti
- Department of Experimental Medicine and Center of Excellence for Biomedical Research, University of Genova, 16132 Genova, Italy
| | - James L Van Etten
- Nebraska Center for Virology, University of Nebraska, Lincoln, Nebraska 68583-0900, United States.,Department of Plant Pathology, University of Nebraska, Lincoln, Nebraska 68583-0722, United States
| | - Cristina De Castro
- Department of Agricultural Sciences, University of Napoli, Via Università 100, 80055 Portici, Italy
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Bellini NK, Thiemann OH, Reyes-Batlle M, Lorenzo-Morales J, Costa AO. A history of over 40 years of potentially pathogenic free-living amoeba studies in Brazil - a systematic review. Mem Inst Oswaldo Cruz 2022; 117:e210373. [PMID: 35792751 PMCID: PMC9252135 DOI: 10.1590/0074-02760210373] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 03/28/2022] [Indexed: 12/17/2022] Open
Abstract
Free-living amoeba (FLA) group includes the potentially pathogenic genera Acanthamoeba, Naegleria, Balamuthia, Sappinia, and Vermamoeba, causative agents of human infections (encephalitis, keratitis, and disseminated diseases). In Brazil, the first report on pathogenic FLA was published in the 70s and showed meningoencephalitis caused by Naegleria spp. FLA studies are emerging, but no literature review is available to investigate this trend in Brazil critically. Thus, the present work aims to integrate and discuss these data. Scopus, PubMed, and Web of Science were searched, retrieving studies from 1974 to 2020. The screening process resulted in 178 papers, which were clustered into core and auxiliary classes and sorted into five categories: wet-bench studies, dry-bench studies, clinical reports, environmental identifications, and literature reviews. The papers dating from the last ten years account for 75% (134/178) of the total publications, indicating the FLA topic has gained Brazilian interest. Moreover, 81% (144/178) address Acanthamoeba-related matter, revealing this genus as the most prevalent in all categories. Brazil’s Southeast, South, and Midwest geographic regions accounted for 96% (171/178) of the publications studied in the present work. To the best of our knowledge, this review is the pioneer in summarising the FLA research history in Brazil.
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Affiliation(s)
- Natália Karla Bellini
- Universidade Federal de Minas Gerais, Faculdade de Farmácia, Departamento de Análises Clínicas e Toxicológicas, Belo Horizonte, MG, Brasil
| | - Otavio Henrique Thiemann
- Universidade de São Paulo, Instituto de Física de São Carlos, São Carlos, SP, Brasil.,Universidade Federal de São Carlos, Departamento de Genética e Evolução, São Carlos, SP, Brasil
| | - María Reyes-Batlle
- Universidad de La Laguna, Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias, Departamento de Obstetricia, Ginecología, Pediatría, Medicina Preventiva y Salud Pública, Toxicología, Medicina Legal y Forense y Parasitología, Red de Investigación Cooperativa en Enfermedades Tropicales, Tenerife, Islas Canarias, Spain
| | - Jacob Lorenzo-Morales
- Universidad de La Laguna, Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias, Departamento de Obstetricia, Ginecología, Pediatría, Medicina Preventiva y Salud Pública, Toxicología, Medicina Legal y Forense y Parasitología, Red de Investigación Cooperativa en Enfermedades Tropicales, Tenerife, Islas Canarias, Spain.,Instituto de Salud Carlos III, Consorcio Centro de Investigación Biomédica en Red MP de Enfermedades Infecciosas, Madrid, Spain
| | - Adriana Oliveira Costa
- Universidade Federal de Minas Gerais, Faculdade de Farmácia, Departamento de Análises Clínicas e Toxicológicas, Belo Horizonte, MG, Brasil
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Queiroz VF, Rodrigues RAL, Boratto PVDM, La Scola B, Andreani J, Abrahão JS. Amoebae: Hiding in Plain Sight: Unappreciated Hosts for the Very Large Viruses. Annu Rev Virol 2022; 9:79-98. [DOI: 10.1146/annurev-virology-100520-125832] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
For decades, viruses have been isolated primarily from humans and other organisms. Interestingly, one of the most complex sides of the virosphere was discovered using free-living amoebae as hosts. The discovery of giant viruses in the early twenty-first century opened a new chapter in the field of virology. Giant viruses are included in the phylum Nucleocytoviricota and harbor large and complex DNA genomes (up to 2.7 Mb) encoding genes never before seen in the virosphere and presenting gigantic particles (up to 1.5 μm). Different amoebae have been used to isolate and characterize a plethora of new viruses with exciting details about novel viral biology. Through distinct isolation techniques and metagenomics, the diversity and complexity of giant viruses have astonished the scientific community. Here, we discuss the latest findings on amoeba viruses and how using these single-celled organisms as hosts has revealed entities that have remained hidden in plain sight for ages. Expected final online publication date for the Annual Review of Virology, Volume 9 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Victória Fulgêncio Queiroz
- Laboratório de Vírus, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Rodrigo Araújo Lima Rodrigues
- Laboratório de Vírus, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | - Bernard La Scola
- Department of Microbes, Evolution, Phylogeny and Infection, Institut de Recherche pour le Développement, Assistance Publique-Hôpitaux de Marseille, Aix-Marseille Université, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Julien Andreani
- Department of Microbes, Evolution, Phylogeny and Infection, Institut de Recherche pour le Développement, Assistance Publique-Hôpitaux de Marseille, Aix-Marseille Université, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
- Laboratoire de Virologie, Centre Hospitalier Universitaire Grenoble-Alpes, Grenoble, France
| | - Jônatas Santos Abrahão
- Laboratório de Vírus, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
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Boratto PVM, Serafim MSM, Witt ASA, Crispim APC, de Azevedo BL, de Souza GAP, de Aquino ILM, Machado TB, Queiroz VF, Rodrigues RAL, Bergier I, Cortines JR, de Farias ST, dos Santos RN, Campos FS, Franco AC, Abrahão JS. A Brief History of Giant Viruses’ Studies in Brazilian Biomes. Viruses 2022; 14:v14020191. [PMID: 35215784 PMCID: PMC8875882 DOI: 10.3390/v14020191] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 01/11/2022] [Accepted: 01/15/2022] [Indexed: 02/01/2023] Open
Abstract
Almost two decades after the isolation of the first amoebal giant viruses, indubitably the discovery of these entities has deeply affected the current scientific knowledge on the virosphere. Much has been uncovered since then: viruses can now acknowledge complex genomes and huge particle sizes, integrating remarkable evolutionary relationships that date as early as the emergence of life on the planet. This year, a decade has passed since the first studies on giant viruses in the Brazilian territory, and since then biomes of rare beauty and biodiversity (Amazon, Atlantic forest, Pantanal wetlands, Cerrado savannas) have been explored in the search for giant viruses. From those unique biomes, novel viral entities were found, revealing never before seen genomes and virion structures. To celebrate this, here we bring together the context, inspirations, and the major contributions of independent Brazilian research groups to summarize the accumulated knowledge about the diversity and the exceptionality of some of the giant viruses found in Brazil.
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Affiliation(s)
- Paulo Victor M. Boratto
- Laboratório de Vírus, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Minas Gerais, Brazil; (P.V.M.B.); (M.S.M.S.); (A.S.A.W.); (A.P.C.C.); (B.L.d.A.); (G.A.P.d.S.); (I.L.M.d.A.); (T.B.M.); (V.F.Q.); (R.A.L.R.)
| | - Mateus Sá M. Serafim
- Laboratório de Vírus, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Minas Gerais, Brazil; (P.V.M.B.); (M.S.M.S.); (A.S.A.W.); (A.P.C.C.); (B.L.d.A.); (G.A.P.d.S.); (I.L.M.d.A.); (T.B.M.); (V.F.Q.); (R.A.L.R.)
| | - Amanda Stéphanie A. Witt
- Laboratório de Vírus, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Minas Gerais, Brazil; (P.V.M.B.); (M.S.M.S.); (A.S.A.W.); (A.P.C.C.); (B.L.d.A.); (G.A.P.d.S.); (I.L.M.d.A.); (T.B.M.); (V.F.Q.); (R.A.L.R.)
| | - Ana Paula C. Crispim
- Laboratório de Vírus, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Minas Gerais, Brazil; (P.V.M.B.); (M.S.M.S.); (A.S.A.W.); (A.P.C.C.); (B.L.d.A.); (G.A.P.d.S.); (I.L.M.d.A.); (T.B.M.); (V.F.Q.); (R.A.L.R.)
| | - Bruna Luiza de Azevedo
- Laboratório de Vírus, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Minas Gerais, Brazil; (P.V.M.B.); (M.S.M.S.); (A.S.A.W.); (A.P.C.C.); (B.L.d.A.); (G.A.P.d.S.); (I.L.M.d.A.); (T.B.M.); (V.F.Q.); (R.A.L.R.)
| | - Gabriel Augusto P. de Souza
- Laboratório de Vírus, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Minas Gerais, Brazil; (P.V.M.B.); (M.S.M.S.); (A.S.A.W.); (A.P.C.C.); (B.L.d.A.); (G.A.P.d.S.); (I.L.M.d.A.); (T.B.M.); (V.F.Q.); (R.A.L.R.)
| | - Isabella Luiza M. de Aquino
- Laboratório de Vírus, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Minas Gerais, Brazil; (P.V.M.B.); (M.S.M.S.); (A.S.A.W.); (A.P.C.C.); (B.L.d.A.); (G.A.P.d.S.); (I.L.M.d.A.); (T.B.M.); (V.F.Q.); (R.A.L.R.)
| | - Talita B. Machado
- Laboratório de Vírus, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Minas Gerais, Brazil; (P.V.M.B.); (M.S.M.S.); (A.S.A.W.); (A.P.C.C.); (B.L.d.A.); (G.A.P.d.S.); (I.L.M.d.A.); (T.B.M.); (V.F.Q.); (R.A.L.R.)
| | - Victória F. Queiroz
- Laboratório de Vírus, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Minas Gerais, Brazil; (P.V.M.B.); (M.S.M.S.); (A.S.A.W.); (A.P.C.C.); (B.L.d.A.); (G.A.P.d.S.); (I.L.M.d.A.); (T.B.M.); (V.F.Q.); (R.A.L.R.)
| | - Rodrigo A. L. Rodrigues
- Laboratório de Vírus, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Minas Gerais, Brazil; (P.V.M.B.); (M.S.M.S.); (A.S.A.W.); (A.P.C.C.); (B.L.d.A.); (G.A.P.d.S.); (I.L.M.d.A.); (T.B.M.); (V.F.Q.); (R.A.L.R.)
| | - Ivan Bergier
- Embrapa Pantanal, Corumbá 79320-900, Mato Grosso do Sul, Brazil;
| | - Juliana Reis Cortines
- Departamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-590, Rio de Janeiro, Brazil;
| | - Savio Torres de Farias
- Laboratório de Genética Evolutiva Paulo Leminsk, Departamento de Biologia Molecular, Universidade Federal da Paraíba, João Pessoa 58050-085, Paraíba, Brazil;
| | - Raíssa Nunes dos Santos
- Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre 90.050-170, Rio Grande do Sul, Brazil; (R.N.d.S.); (F.S.C.); (A.C.F.)
| | - Fabrício Souza Campos
- Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre 90.050-170, Rio Grande do Sul, Brazil; (R.N.d.S.); (F.S.C.); (A.C.F.)
| | - Ana Cláudia Franco
- Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre 90.050-170, Rio Grande do Sul, Brazil; (R.N.d.S.); (F.S.C.); (A.C.F.)
| | - Jônatas S. Abrahão
- Laboratório de Vírus, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Minas Gerais, Brazil; (P.V.M.B.); (M.S.M.S.); (A.S.A.W.); (A.P.C.C.); (B.L.d.A.); (G.A.P.d.S.); (I.L.M.d.A.); (T.B.M.); (V.F.Q.); (R.A.L.R.)
- Correspondence:
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Functional genomic analyses reveal an open pan-genome for the chloroviruses and a potential for genetic innovation in new isolates. J Virol 2021; 96:e0136721. [PMID: 34669449 DOI: 10.1128/jvi.01367-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Chloroviruses (family Phycodnaviridae) are large dsDNA viruses that infect unicellular green algae present in inland waters. These viruses have been isolated using three main chlorella-like green algal host cells, traditionally called NC64A, SAG and Pbi, revealing extensive genetic diversity. In this study, we performed a functional genomic analysis on 36 chloroviruses that infected the three different hosts. Phylogenetic reconstruction based on the DNA polymerase B family gene clustered the chloroviruses into three distinct clades. The viral pan-genome consists of 1,345 clusters of orthologous groups of genes (COGs), with 126 COGs conserved in all viruses. 368, 268 and 265 COGs are found exclusively in viruses that infect NC64A, SAG, and Pbi algal hosts, respectively. Two-thirds of the COGs have no known function, constituting the "dark pan-genome" of chloroviruses, and further studies focusing on these genes may identify important novelties. The proportion of functionally characterized COGs composing the pan- and the core-genome are similar, but those related to transcription and RNA processing, protein metabolism, and virion morphogenesis are at least 4-fold more represented in the core-genome. Bipartite network construction evidencing the COG-sharing among host-specific viruses identified 270 COGs shared by at least one virus from each of the different host groups. Finally, our results reveal an open pan-genome for chloroviruses and a well-established core-genome, indicating that the isolation of new chloroviruses can be a valuable source of genetic discovery. Importance Chloroviruses are large dsDNA viruses that infect unicellular green algae distributed worldwide in freshwater environments. They comprise a genetically diverse group of viruses; however, a comprehensive investigation of the genomic evolution of these viruses is still missing. Here we performed a functional pan-genome analysis comprising 36 chloroviruses associated with three different algal hosts in the family Chlorellaceae, referred to as zoochlorellae because of their endosymbiotic lifestyle. We identified a set of 126 highly conserved genes, most of which are related to essential functions in the viral replicative cycle. Several genes are unique to distinct isolates, resulting in an open pan-genome for chloroviruses. This profile is associated with generalist organisms, and new insights into the evolution and ecology of chloroviruses are presented. Ultimately, our results highlight the potential for genetic diversity in new isolates.
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8
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Aoki K, Fukaya S, Takahashi H, Kobayashi M, Sasaki K, Takemura M. Marseilleviridae Lineage B Diversity and Bunch Formation Inhibited by Galactose. Microbes Environ 2021; 36. [PMID: 33612562 PMCID: PMC7966940 DOI: 10.1264/jsme2.me20139] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Marseilleviridae is a family of large double-stranded DNA viruses that is currently divided into five subgroups, lineages A–E. Hokutovirus and kashiwazakivirus, both of which belong to lineage B, have been reported to induce host acanthamoeba cells to form aggregations called “bunches”. This putatively results in increased opportunities to infect acanthamoeba cells, in contrast to lineage A, which has been reported to not form “bunches”. In the present study, we isolated 14 virus strains of the family Marseilleviridae from several Japanese water samples, 11 of which were identified as lineage B viruses. All 11 lineage B strains caused infected amoeba cells to form bunches. We then investigated the involvement of monosaccharides in bunch formation by amoeba cells infected with hokutovirus. Galactose inhibited bunch formation, thereby allowing amoeba cells to delay the process, whereas mannose and glucose did not. A kinetic image analysis of hokutovirus-infected amoeba cells confirmed the inhibition of bunch formation by galactose. The number of hokutovirus-infected amoeba cells increased more rapidly than that of tokyovirus-infected cells, which belongs to lineage A. This result suggests that bunch formation by infected amoeba cells is advantageous for lineage B viruses.
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Affiliation(s)
- Keita Aoki
- Laboratory of Biology, Graduate School of Mathematics and Science Education, Tokyo University of Science
| | - Sho Fukaya
- Laboratory of Biology, Graduate School of Mathematics and Science Education, Tokyo University of Science
| | - Haruna Takahashi
- Laboratory of Biology, Graduate School of Mathematics and Science Education, Tokyo University of Science
| | - Mio Kobayashi
- Laboratory of Biology, Graduate School of Mathematics and Science Education, Tokyo University of Science
| | - Kenta Sasaki
- Laboratory of Biology, Graduate School of Mathematics and Science Education, Tokyo University of Science
| | - Masaharu Takemura
- Laboratory of Biology, Graduate School of Mathematics and Science Education, Tokyo University of Science.,Laboratory of Biology, Faculty of Science Division I, Tokyo University of Science
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9
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Sahmi-Bounsiar D, Rolland C, Aherfi S, Boudjemaa H, Levasseur A, La Scola B, Colson P. Marseilleviruses: An Update in 2021. Front Microbiol 2021; 12:648731. [PMID: 34149639 PMCID: PMC8208085 DOI: 10.3389/fmicb.2021.648731] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Accepted: 04/12/2021] [Indexed: 01/19/2023] Open
Abstract
The family Marseilleviridae was the second family of giant viruses that was described in 2013, after the family Mimiviridae. Marseillevirus marseillevirus, isolated in 2007 by coculture on Acanthamoeba polyphaga, is the prototype member of this family. Afterward, the worldwide distribution of marseilleviruses was revealed through their isolation from samples of various types and sources. Thus, 62 were isolated from environmental water, one from soil, one from a dipteran, one from mussels, and two from asymptomatic humans, which led to the description of 67 marseillevirus isolates, including 21 by the IHU Méditerranée Infection in France. Recently, five marseillevirus genomes were assembled from deep sea sediment in Norway. Isolated marseilleviruses have ≈250 nm long icosahedral capsids and 348–404 kilobase long mosaic genomes that encode 386–545 predicted proteins. Comparative genomic analyses indicate that the family Marseilleviridae includes five lineages and possesses a pangenome composed of 3,082 clusters of genes. The detection of marseilleviruses in both symptomatic and asymptomatic humans in stool, blood, and lymph nodes, and an up-to-30-day persistence of marseillevirus in rats and mice, raise questions concerning their possible clinical significance that are still under investigation.
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Affiliation(s)
- Dehia Sahmi-Bounsiar
- IHU Méditerranée Infection, Marseille, France.,Institut de Recherche pour le Développement (IRD), Assistance Publique- Hôpitaux de Marseille (AP-HM), MEPHI, Aix-Marseille Université, Marseille, France
| | - Clara Rolland
- IHU Méditerranée Infection, Marseille, France.,Institut de Recherche pour le Développement (IRD), Assistance Publique- Hôpitaux de Marseille (AP-HM), MEPHI, Aix-Marseille Université, Marseille, France
| | - Sarah Aherfi
- IHU Méditerranée Infection, Marseille, France.,Institut de Recherche pour le Développement (IRD), Assistance Publique- Hôpitaux de Marseille (AP-HM), MEPHI, Aix-Marseille Université, Marseille, France
| | - Hadjer Boudjemaa
- IHU Méditerranée Infection, Marseille, France.,Department of Biology, Faculty of Natural Science and Life, Hassiba Benbouali University of Chlef, Chlef, Algeria
| | - Anthony Levasseur
- IHU Méditerranée Infection, Marseille, France.,Institut de Recherche pour le Développement (IRD), Assistance Publique- Hôpitaux de Marseille (AP-HM), MEPHI, Aix-Marseille Université, Marseille, France
| | - Bernard La Scola
- IHU Méditerranée Infection, Marseille, France.,Institut de Recherche pour le Développement (IRD), Assistance Publique- Hôpitaux de Marseille (AP-HM), MEPHI, Aix-Marseille Université, Marseille, France
| | - Philippe Colson
- IHU Méditerranée Infection, Marseille, France.,Institut de Recherche pour le Développement (IRD), Assistance Publique- Hôpitaux de Marseille (AP-HM), MEPHI, Aix-Marseille Université, Marseille, France
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10
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Blanca L, Christo-Foroux E, Rigou S, Legendre M. Comparative Analysis of the Circular and Highly Asymmetrical Marseilleviridae Genomes. Viruses 2020; 12:E1270. [PMID: 33171839 PMCID: PMC7695187 DOI: 10.3390/v12111270] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 11/05/2020] [Accepted: 11/05/2020] [Indexed: 12/11/2022] Open
Abstract
Marseilleviridae members are large dsDNA viruses with icosahedral particles 250 nm in diameter infecting Acanthamoeba. Their 340 to 390 kb genomes encode 450 to 550 protein-coding genes. Since the discovery of marseillevirus (the prototype of the family) in 2009, several strains were isolated from various locations, among which 13 are now fully sequenced. This allows the organization of their genomes to be deciphered through comparative genomics. Here, we first experimentally demonstrate that the Marseilleviridae genomes are circular. We then acknowledge a strong bias in sequence conservation, revealing two distinct genomic regions. One gathers most Marseilleviridae paralogs and has undergone genomic rearrangements, while the other, enriched in core genes, exhibits the opposite pattern. Most of the genes whose protein products compose the viral particles are located in the conserved region. They are also strongly biased toward a late gene expression pattern. We finally discuss the potential advantages of Marseilleviridae having a circular genome, and the possible link between the biased distribution of their genes and the transcription as well as DNA replication mechanisms that remain to be characterized.
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Affiliation(s)
| | | | | | - Matthieu Legendre
- CNRS, IGS, Information Génomique & Structurale (UMR7256), Institut de Microbiologie de la Méditerranée (FR 3489), Aix Marseille Univ., 13288 Marseille, France; (L.B.); (E.C.-F.); (S.R.)
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11
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Abstract
DNA methylation is an important epigenetic mark that contributes to various regulations in all domains of life. Giant viruses are widespread dsDNA viruses with gene contents overlapping the cellular world that also encode DNA methyltransferases. Yet, virtually nothing is known about the methylation of their DNA. Here, we use single-molecule real-time sequencing to study the complete methylome of a large spectrum of giant viruses. We show that DNA methylation is widespread, affecting 2/3 of the tested families, although unevenly distributed. We also identify the corresponding viral methyltransferases and show that they are subject to intricate gene transfers between bacteria, viruses and their eukaryotic host. Most methyltransferases are conserved, functional and under purifying selection, suggesting that they increase the viruses' fitness. Some virally encoded methyltransferases are also paired with restriction endonucleases forming Restriction-Modification systems. Our data suggest that giant viruses' methyltransferases are involved in diverse forms of virus-pathogens interactions during coinfections.
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12
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Rodrigues RAL, da Silva LCF, Abrahão JS. Translating the language of giants: translation-related genes as a major contribution of giant viruses to the virosphere. Arch Virol 2020; 165:1267-1278. [DOI: 10.1007/s00705-020-04626-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 03/25/2020] [Indexed: 12/21/2022]
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13
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Rodrigues RAL, Louazani AC, Picorelli A, Oliveira GP, Lobo FP, Colson P, La Scola B, Abrahão JS. Analysis of a Marseillevirus Transcriptome Reveals Temporal Gene Expression Profile and Host Transcriptional Shift. Front Microbiol 2020; 11:651. [PMID: 32390970 PMCID: PMC7192143 DOI: 10.3389/fmicb.2020.00651] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 03/22/2020] [Indexed: 12/17/2022] Open
Abstract
Marseilleviruses comprise a family of large double-stranded DNA viruses belonging to the proposed order "Megavirales." These viruses have a circular genome of ∼370 kbp, coding hundreds of genes. Over a half of their genes are associated with AT-rich putative promoter motifs, which have been demonstrated to be important for gene regulation. However, the transcriptional profile of Marseilleviruses is currently unknown. Here we used RNA sequencing technology to get a general transcriptional profile of Marseilleviruses. Eight million 75-bp-long nucleotide sequences were robustly mapped to all 457 genes initially predicted for Marseillevirus isolate T19, the prototype strain of the family, and we were able to assemble 359 viral contigs using a genome-guided approach with stringent parameters. These reads were differentially mapped to the genes according to the replicative cycle time point from which they were obtained. Cluster analysis indicated the existence of three main temporal categories of gene expression, early, intermediate and late, which were validated by quantitative reverse transcription polymerase chain reaction assays targeting several genes. Genes belonging to different functional groups exhibited distinct expression levels throughout the infection cycle. We observed that the previously predicted promoter motif, AAATATTT, as well as new predicted motifs, were not specifically related to any of the temporal or functional classes of genes, suggesting that other components are involved in temporally regulating virus transcription. Moreover, the host transcription machinery is heavily altered, and many genes are down regulated, including those related to translation process. This study provides an overview of the transcriptional landscape of Marseilleviruses.
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Affiliation(s)
- Rodrigo Araújo Lima Rodrigues
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Microbes, Evolution, Phylogeny and Infection (MEΦI), IRD 198, Assistance Publique-Hopitaux de Marseille (AP-HM), Aix-Marseille Université UM63, Marseille, France
| | - Amina Cherif Louazani
- Microbes, Evolution, Phylogeny and Infection (MEΦI), IRD 198, Assistance Publique-Hopitaux de Marseille (AP-HM), Aix-Marseille Université UM63, Marseille, France
| | - Agnello Picorelli
- Laboratório de Algoritmos em Biologia, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Graziele Pereira Oliveira
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Microbes, Evolution, Phylogeny and Infection (MEΦI), IRD 198, Assistance Publique-Hopitaux de Marseille (AP-HM), Aix-Marseille Université UM63, Marseille, France
| | - Francisco Pereira Lobo
- Laboratório de Algoritmos em Biologia, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Philippe Colson
- Microbes, Evolution, Phylogeny and Infection (MEΦI), IRD 198, Assistance Publique-Hopitaux de Marseille (AP-HM), Aix-Marseille Université UM63, Marseille, France
- Institut Hospitalo-Universitaire (IHU) - Méditerranée Infection, Marseille, France
| | - Bernard La Scola
- Microbes, Evolution, Phylogeny and Infection (MEΦI), IRD 198, Assistance Publique-Hopitaux de Marseille (AP-HM), Aix-Marseille Université UM63, Marseille, France
- Institut Hospitalo-Universitaire (IHU) - Méditerranée Infection, Marseille, France
| | - Jônatas Santos Abrahão
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
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14
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Abstract
Since the discovery of mimivirus, numerous giant viruses associated with free-living amoebae have been described. The genome of giant viruses can be more than 2.5 megabases, and virus particles can exceed the size of many bacteria. The unexpected characteristics of these viruses have made them intriguing research targets and, as a result, studies focusing on their interactions with their amoeba host have gained increased attention. Studies have shown that giant viruses can establish host-pathogen interactions, which have not been previously demonstrated, including the unprecedented interaction with a new group of small viruses, called virophages, that parasitize their viral factories. In this brief review, we present recent advances in virophage-giant virus-host interactions and highlight selected studies involving interactions between giant viruses and amoebae. These unprecedented interactions involve the giant viruses mimivirus, marseillevirus, tupanviruses and faustovirus, all of which modulate the amoeba environment, affecting both their replication and their spread to new hosts.
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15
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Macera L, Spezia PG, Focosi D, Mazzetti P, Antonelli G, Pistello M, Maggi F. Lack of Marseillevirus DNA in immunocompetent and immunocompromised Italian patients. J Med Virol 2019; 92:187-190. [PMID: 31498443 DOI: 10.1002/jmv.25592] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 09/04/2019] [Indexed: 01/21/2023]
Abstract
Marseilleviridae is a family of viruses which have only been propagated in acanthamoeba. Marseillevirus sequences have been recently detected in different human matrices by viral metagenomics. Single-center studies worldwide have estimated a low prevalence of marseillevirus both in symptomatic patients and in healthy donors but, to date, no informations are available on the prevalence of this giant virus in Italy. By a polymerase chain reaction targeting the ORF152 viral sequence, we tested sera from 197 immunosuppressed patients and 285 healthy donors, and 63 and 30 respiratory and cerebrospinal fluid samples, respectively, of patients with various clinical conditions and referring the Virology Division for diagnostic purposes. We observed no evidence of Marseillevirus DNA in all 575 samples tested. Marseillevirus probably does not cause infection in human.
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Affiliation(s)
- Lisa Macera
- Retrovirus Center and Virology Section, Department of Translational Research, University of Pisa, Pisa, Italy.,Virology Division, Pisa University Hospital, Pisa, Italy
| | - Pietro Giorgio Spezia
- Retrovirus Center and Virology Section, Department of Translational Research, University of Pisa, Pisa, Italy
| | - Daniele Focosi
- North-Western Tuscany Blood Bank, Pisa University Hospital, Pisa, Italy
| | - Paola Mazzetti
- Retrovirus Center and Virology Section, Department of Translational Research, University of Pisa, Pisa, Italy.,Virology Division, Pisa University Hospital, Pisa, Italy
| | - Guido Antonelli
- Department of Molecular Medicine, Laboratory of Virology and Pasteur Institute-Cenci Bolognetti Foundation, Sapienza University of Rome, Rome, Italy
| | - Mauro Pistello
- Retrovirus Center and Virology Section, Department of Translational Research, University of Pisa, Pisa, Italy.,Virology Division, Pisa University Hospital, Pisa, Italy
| | - Fabrizio Maggi
- Retrovirus Center and Virology Section, Department of Translational Research, University of Pisa, Pisa, Italy.,Virology Division, Pisa University Hospital, Pisa, Italy
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16
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Protozoal giant viruses: agents potentially infectious to humans and animals. Virus Genes 2019; 55:574-591. [PMID: 31290063 PMCID: PMC6746690 DOI: 10.1007/s11262-019-01684-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 07/02/2019] [Indexed: 12/11/2022]
Abstract
The discovery of giant viruses has revolutionised the knowledge on viruses and transformed the idea of three domains of life. Here, we discuss the known protozoal giant viruses and their potential to infect also humans and animals.
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17
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Aoki K, Hagiwara R, Akashi M, Sasaki K, Murata K, Ogata H, Takemura M. Fifteen Marseilleviruses Newly Isolated From Three Water Samples in Japan Reveal Local Diversity of Marseilleviridae. Front Microbiol 2019; 10:1152. [PMID: 31178850 PMCID: PMC6543897 DOI: 10.3389/fmicb.2019.01152] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 05/06/2019] [Indexed: 11/13/2022] Open
Abstract
The family Marseilleviridae, defined as a group of icosahedral double-stranded DNA viruses with particle size of approximately 250 nm and genome size of 350-380 kbp, belongs to the nucleo-cytoplasmic family of large DNA viruses. The family Marseilleviridae is currently classified into lineages A-E. In this study, we isolated 12 or 15 new members of the family Marseilleviridae from three sampling locations in Japan. Molecular phylogenetic analysis of the MCP genes showed that the new viruses could be further classified into three groups, hokutoviruses, kashiwazakiviruses, and kyotoviruses. Hokutoviruses were closely related to lineage B, kyotoviruses were related to lineage A, and kashiwazakiviruses were also classified into lineage B but a new putative subgroup of lineage B, revealing the diversity of this lineage. Interestingly, more than two viruses with slightly different MCP genes were isolated from a single water sample from a single location, i.e., two hokutoviruses and one kashiwazakivirus were isolated from a small reservoir, five kashiwazakiviruses from the mouth of a river, and five kyotoviruses from fresh water of a river, suggesting that several milliliters of water samples contain several types of giant viruses. Amoeba cells infected with hokutoviruses or kashiwazakiviruses exhibited a "bunch" formation consisting of normal and infected cells similarly to a tupanvirus, whereas cells infected with kyotoviruses or tokyovirus did not. These results suggest the previously unrecognized local diversity of the family Marseilleviridae in aquatic environments.
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Affiliation(s)
- Keita Aoki
- Laboratory of Biology, Graduate School of Mathematics and Science Education, Tokyo University of Science, Tokyo, Japan
| | - Reika Hagiwara
- Laboratory of Biology, Department of Liberal Arts, Faculty of Science, Tokyo University of Science, Tokyo, Japan
| | - Motohiro Akashi
- Laboratory of Biology, Department of Liberal Arts, Faculty of Science, Tokyo University of Science, Tokyo, Japan
| | - Kenta Sasaki
- Laboratory of Biology, Department of Liberal Arts, Faculty of Science, Tokyo University of Science, Tokyo, Japan
| | | | - Hiroyuki Ogata
- Institute for Chemical Research, Kyoto University, Gokasho, Japan
| | - Masaharu Takemura
- Laboratory of Biology, Graduate School of Mathematics and Science Education, Tokyo University of Science, Tokyo, Japan.,Laboratory of Biology, Department of Liberal Arts, Faculty of Science, Tokyo University of Science, Tokyo, Japan
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18
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Brandes N, Linial M. Giant Viruses-Big Surprises. Viruses 2019; 11:v11050404. [PMID: 31052218 PMCID: PMC6563228 DOI: 10.3390/v11050404] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 04/17/2019] [Accepted: 04/23/2019] [Indexed: 12/21/2022] Open
Abstract
Viruses are the most prevalent infectious agents, populating almost every ecosystem on earth. Most viruses carry only a handful of genes supporting their replication and the production of capsids. It came as a great surprise in 2003 when the first giant virus was discovered and found to have a >1 Mbp genome encoding almost a thousand proteins. Following this first discovery, dozens of giant virus strains across several viral families have been reported. Here, we provide an updated quantitative and qualitative view on giant viruses and elaborate on their shared and variable features. We review the complexity of giant viral proteomes, which include functions traditionally associated only with cellular organisms. These unprecedented functions include components of the translation machinery, DNA maintenance, and metabolic enzymes. We discuss the possible underlying evolutionary processes and mechanisms that might have shaped the diversity of giant viruses and their genomes, highlighting their remarkable capacity to hijack genes and genomic sequences from their hosts and environments. This leads us to examine prominent theories regarding the origin of giant viruses. Finally, we present the emerging ecological view of giant viruses, found across widespread habitats and ecological systems, with respect to the environment and human health.
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Affiliation(s)
- Nadav Brandes
- The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
| | - Michal Linial
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
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19
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Rolland C, Andreani J, Louazani AC, Aherfi S, Francis R, Rodrigues R, Silva LS, Sahmi D, Mougari S, Chelkha N, Bekliz M, Silva L, Assis F, Dornas F, Khalil JYB, Pagnier I, Desnues C, Levasseur A, Colson P, Abrahão J, La Scola B. Discovery and Further Studies on Giant Viruses at the IHU Mediterranee Infection That Modified the Perception of the Virosphere. Viruses 2019; 11:E312. [PMID: 30935049 PMCID: PMC6520786 DOI: 10.3390/v11040312] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 03/25/2019] [Accepted: 03/27/2019] [Indexed: 12/17/2022] Open
Abstract
The history of giant viruses began in 2003 with the identification of Acanthamoeba polyphaga mimivirus. Since then, giant viruses of amoeba enlightened an unknown part of the viral world, and every discovery and characterization of a new giant virus modifies our perception of the virosphere. This notably includes their exceptional virion sizes from 200 nm to 2 µm and their genomic complexity with length, number of genes, and functions such as translational components never seen before. Even more surprising, Mimivirus possesses a unique mobilome composed of virophages, transpovirons, and a defense system against virophages named Mimivirus virophage resistance element (MIMIVIRE). From the discovery and isolation of new giant viruses to their possible roles in humans, this review shows the active contribution of the University Hospital Institute (IHU) Mediterranee Infection to the growing knowledge of the giant viruses' field.
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Affiliation(s)
- Clara Rolland
- MEPHI, APHM, IRD 198, Aix Marseille Univ, Department of Medicine, IHU-Méditerranée Infection, 13005 Marseille, France.
| | - Julien Andreani
- MEPHI, APHM, IRD 198, Aix Marseille Univ, Department of Medicine, IHU-Méditerranée Infection, 13005 Marseille, France.
| | - Amina Cherif Louazani
- MEPHI, APHM, IRD 198, Aix Marseille Univ, Department of Medicine, IHU-Méditerranée Infection, 13005 Marseille, France.
| | - Sarah Aherfi
- MEPHI, APHM, IRD 198, Aix Marseille Univ, Department of Medicine, IHU-Méditerranée Infection, 13005 Marseille, France.
- IHU IHU-Méditerranée Infection, 13005 Marseille, France.
| | - Rania Francis
- MEPHI, APHM, IRD 198, Aix Marseille Univ, Department of Medicine, IHU-Méditerranée Infection, 13005 Marseille, France.
| | - Rodrigo Rodrigues
- MEPHI, APHM, IRD 198, Aix Marseille Univ, Department of Medicine, IHU-Méditerranée Infection, 13005 Marseille, France.
- Laboratório de Vírus, Instituto de Ciêncas Biológicas, Departamento de Microbiologia, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte, Brazil.
| | - Ludmila Santos Silva
- MEPHI, APHM, IRD 198, Aix Marseille Univ, Department of Medicine, IHU-Méditerranée Infection, 13005 Marseille, France.
| | - Dehia Sahmi
- MEPHI, APHM, IRD 198, Aix Marseille Univ, Department of Medicine, IHU-Méditerranée Infection, 13005 Marseille, France.
| | - Said Mougari
- MEPHI, APHM, IRD 198, Aix Marseille Univ, Department of Medicine, IHU-Méditerranée Infection, 13005 Marseille, France.
| | - Nisrine Chelkha
- MEPHI, APHM, IRD 198, Aix Marseille Univ, Department of Medicine, IHU-Méditerranée Infection, 13005 Marseille, France.
| | - Meriem Bekliz
- MEPHI, APHM, IRD 198, Aix Marseille Univ, Department of Medicine, IHU-Méditerranée Infection, 13005 Marseille, France.
| | - Lorena Silva
- MEPHI, APHM, IRD 198, Aix Marseille Univ, Department of Medicine, IHU-Méditerranée Infection, 13005 Marseille, France.
- Laboratório de Vírus, Instituto de Ciêncas Biológicas, Departamento de Microbiologia, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte, Brazil.
| | - Felipe Assis
- MEPHI, APHM, IRD 198, Aix Marseille Univ, Department of Medicine, IHU-Méditerranée Infection, 13005 Marseille, France.
| | - Fábio Dornas
- MEPHI, APHM, IRD 198, Aix Marseille Univ, Department of Medicine, IHU-Méditerranée Infection, 13005 Marseille, France.
| | | | - Isabelle Pagnier
- MEPHI, APHM, IRD 198, Aix Marseille Univ, Department of Medicine, IHU-Méditerranée Infection, 13005 Marseille, France.
- IHU IHU-Méditerranée Infection, 13005 Marseille, France.
| | - Christelle Desnues
- MEPHI, APHM, IRD 198, Aix Marseille Univ, Department of Medicine, IHU-Méditerranée Infection, 13005 Marseille, France.
| | - Anthony Levasseur
- MEPHI, APHM, IRD 198, Aix Marseille Univ, Department of Medicine, IHU-Méditerranée Infection, 13005 Marseille, France.
- IHU IHU-Méditerranée Infection, 13005 Marseille, France.
| | - Philippe Colson
- MEPHI, APHM, IRD 198, Aix Marseille Univ, Department of Medicine, IHU-Méditerranée Infection, 13005 Marseille, France.
- IHU IHU-Méditerranée Infection, 13005 Marseille, France.
| | - Jônatas Abrahão
- MEPHI, APHM, IRD 198, Aix Marseille Univ, Department of Medicine, IHU-Méditerranée Infection, 13005 Marseille, France.
- Laboratório de Vírus, Instituto de Ciêncas Biológicas, Departamento de Microbiologia, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte, Brazil.
| | - Bernard La Scola
- MEPHI, APHM, IRD 198, Aix Marseille Univ, Department of Medicine, IHU-Méditerranée Infection, 13005 Marseille, France.
- IHU IHU-Méditerranée Infection, 13005 Marseille, France.
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Rodrigues RAL, Arantes TS, Oliveira GP, dos Santos Silva LK, Abrahão JS. The Complex Nature of Tupanviruses. Adv Virus Res 2019; 103:135-166. [PMID: 30635075 DOI: 10.1016/bs.aivir.2018.09.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The discovery of giant viruses revealed a new level of complexity in the virosphere, raising important questions about the diversity, ecology, and evolution of these viruses. The family Mimiviridae was the first group of amoebal giant viruses to be discovered (by Bernard La Scola and Didier Raoult team), containing viruses with structural and genetic features that challenged many concepts of classic virology. The tupanviruses are among the newest members of this family and exhibit structural, biological, and genetic features never previously observed in other giant viruses. The complexity of these viruses has put us one step forward toward the comprehension of giant virus biology and evolution, but also has raised important questions that still need to be addressed. In this chapter, we tell the history behind the discovery of one of the most complex viruses isolated to date, highlighting the unique features exhibited by tupanviruses, and discuss how these giant viruses have contributed to redefining limits for the virosphere.
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21
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Zhang QY, Gui JF. Diversity, evolutionary contribution and ecological roles of aquatic viruses. SCIENCE CHINA-LIFE SCIENCES 2018; 61:1486-1502. [DOI: 10.1007/s11427-018-9414-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 09/26/2018] [Indexed: 01/21/2023]
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22
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Clouthier S, Anderson E, Kurath G, Breyta R. Molecular systematics of sturgeon nucleocytoplasmic large DNA viruses. Mol Phylogenet Evol 2018; 128:26-37. [PMID: 30059742 DOI: 10.1016/j.ympev.2018.07.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 07/06/2018] [Accepted: 07/20/2018] [Indexed: 12/23/2022]
Abstract
Namao virus (NV) is a sturgeon nucleocytoplasmic large DNA virus (sNCLDV) that can cause a lethal disease of the integumentary system in lake sturgeon Acipenser fulvescens. As a group, the sNCLDV have not been assigned to any currently recognized taxonomic family of viruses. In this study, a data set of NV DNA sequences was generated and assembled as two non-overlapping contigs of 306,448 bp and then used to conduct a comprehensive systematics analysis using Bayesian inference of phylogeny for NV, other sNCLDV and representative members of six families of the NCLDV superfamily. The phylogeny of NV was reconstructed using protein homologues encoded by nine nucleocytoplasmic virus orthologous genes (NCVOGs): NCVOG0022 - mcp, NCVOG0038 - DNA polymerase B elongation subunit, NCVOG0076 - VV A18-type helicase, NCVOG0249 - VV A32-type ATPase, NCVOG0262 - AL2 VLTF3-like transcription factor, NCVOG0271 - RNA polymerase II subunit II, NCVOG0274 - RNA polymerase II subunit I, NCVOG0276 - ribonucleotide reductase small subunit and NCVOG1117 - mRNA capping enzyme. The accuracy of our phylogenetic method was evaluated using a combination of Bayesian statistical analysis and congruence analysis. Stable tree topologies were obtained with data sets differing in target molecule(s), sequence length and taxa. Congruent topologies were obtained in phylogenies constructed using individual protein data sets. The major capsid protein phylogeny inferred that ten representative sNCLDV form a monophyletic group comprised of four lineages within a polyphyletic Mimi-Phycodnaviridae group of taxa. Overall, the analyses revealed that Namao virus is a member of the Mimiviridae family with strong and consistent support for a clade containing NV and CroV as sister taxa.
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Affiliation(s)
- Sharon Clouthier
- Fisheries & Oceans Canada, Freshwater Institute, 501 University Crescent, Winnipeg, Manitoba R3T 2N6, Canada.
| | - Eric Anderson
- Box 28, Group 30, RR2, Ste Anne, Manitoba R5H 1R2, Canada
| | - Gael Kurath
- U.S. Geological Survey, Western Fisheries Research Center, 6505 NE 65th Street, Seattle, WA 98115, USA
| | - Rachel Breyta
- U.S. Geological Survey, Western Fisheries Research Center, 6505 NE 65th Street, Seattle, WA 98115, USA; Department of Microbiology, Oregon State University, 2820 SW Campus Way, Corvallis, OR 97331, USA
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23
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Aherfi S, Andreani J, Baptiste E, Oumessoum A, Dornas FP, Andrade ACDSP, Chabriere E, Abrahao J, Levasseur A, Raoult D, La Scola B, Colson P. A Large Open Pangenome and a Small Core Genome for Giant Pandoraviruses. Front Microbiol 2018; 9:1486. [PMID: 30042742 PMCID: PMC6048876 DOI: 10.3389/fmicb.2018.01486] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 06/14/2018] [Indexed: 01/09/2023] Open
Abstract
Giant viruses of amoebae are distinct from classical viruses by the giant size of their virions and genomes. Pandoraviruses are the record holders in size of genomes and number of predicted genes. Three strains, P. salinus, P. dulcis, and P. inopinatum, have been described to date. We isolated three new ones, namely P. massiliensis, P. braziliensis, and P. pampulha, from environmental samples collected in Brazil. We describe here their genomes, the transcriptome and proteome of P. massiliensis, and the pangenome of the group encompassing the six pandoravirus isolates. Genome sequencing was performed with an Illumina MiSeq instrument. Genome annotation was performed using GeneMarkS and Prodigal softwares and comparative genomic analyses. The core genome and pangenome were determined using notably ProteinOrtho and CD-HIT programs. Transcriptomics was performed for P. massiliensis with the Illumina MiSeq instrument; proteomics was also performed for this virus using 1D/2D gel electrophoresis and mass spectrometry on a Synapt G2Si Q-TOF traveling wave mobility spectrometer. The genomes of the three new pandoraviruses are comprised between 1.6 and 1.8 Mbp. The genomes of P. massiliensis, P. pampulha, and P. braziliensis were predicted to harbor 1,414, 2,368, and 2,696 genes, respectively. These genes comprise up to 67% of ORFans. Phylogenomic analyses showed that P. massiliensis and P. braziliensis were more closely related to each other than to the other pandoraviruses. The core genome of pandoraviruses comprises 352 clusters of genes, and the ratio core genome/pangenome is less than 0.05. The extinction curve shows clearly that the pangenome is still open. A quarter of the gene content of P. massiliensis was detected by transcriptomics. In addition, a product for a total of 162 open reading frames were found by proteomic analysis of P. massiliensis virions, including notably the products of 28 ORFans, 99 hypothetical proteins, and 90 core genes. Further analyses should allow to gain a better knowledge and understanding of the evolution and origin of these giant pandoraviruses, and of their relationships with viruses and cellular microorganisms.
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Affiliation(s)
- Sarah Aherfi
- Microbes Evolution Phylogenie et Infections (MEϕI), Institut Hospitalo-Universitaire Méditerranée Infection, Assistance Publique - Hôpitaux de Marseille, Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France
| | - Julien Andreani
- Microbes Evolution Phylogenie et Infections (MEϕI), Institut Hospitalo-Universitaire Méditerranée Infection, Assistance Publique - Hôpitaux de Marseille, Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France
| | - Emeline Baptiste
- Microbes Evolution Phylogenie et Infections (MEϕI), Institut Hospitalo-Universitaire Méditerranée Infection, Assistance Publique - Hôpitaux de Marseille, Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France
| | - Amina Oumessoum
- Microbes Evolution Phylogenie et Infections (MEϕI), Institut Hospitalo-Universitaire Méditerranée Infection, Assistance Publique - Hôpitaux de Marseille, Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France
| | - Fábio P Dornas
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Ana Claudia Dos S P Andrade
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Eric Chabriere
- Microbes Evolution Phylogenie et Infections (MEϕI), Institut Hospitalo-Universitaire Méditerranée Infection, Assistance Publique - Hôpitaux de Marseille, Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France
| | - Jonatas Abrahao
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Anthony Levasseur
- Microbes Evolution Phylogenie et Infections (MEϕI), Institut Hospitalo-Universitaire Méditerranée Infection, Assistance Publique - Hôpitaux de Marseille, Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France
| | - Didier Raoult
- Microbes Evolution Phylogenie et Infections (MEϕI), Institut Hospitalo-Universitaire Méditerranée Infection, Assistance Publique - Hôpitaux de Marseille, Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France
| | - Bernard La Scola
- Microbes Evolution Phylogenie et Infections (MEϕI), Institut Hospitalo-Universitaire Méditerranée Infection, Assistance Publique - Hôpitaux de Marseille, Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France
| | - Philippe Colson
- Microbes Evolution Phylogenie et Infections (MEϕI), Institut Hospitalo-Universitaire Méditerranée Infection, Assistance Publique - Hôpitaux de Marseille, Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France
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Morphologic and Genomic Analyses of New Isolates Reveal a Second Lineage of Cedratviruses. J Virol 2018; 92:JVI.00372-18. [PMID: 29695424 DOI: 10.1128/jvi.00372-18] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 04/13/2018] [Indexed: 12/22/2022] Open
Abstract
Giant viruses have been isolated and characterized in different environments, expanding our knowledge about the biology of these unique microorganisms. In the last 2 years, a new group was discovered, the cedratviruses, currently composed of only two isolates and members of a putative new family, "Pithoviridae," along with previously known pithoviruses. Here we report the isolation and biological and genomic characterization of two novel cedratviruses isolated from samples collected in France and Brazil. Both viruses were isolated using Acanthamoeba castellanii as a host cell and exhibit ovoid particles with corks at either extremity of the particle. Curiously, the Brazilian cedratvirus is ∼20% smaller and presents a shorter genome of 460,038 bp, coding for fewer proteins than other cedratviruses. In addition, it has a completely asyntenic genome and presents a lower amino acid identity of orthologous genes (∼73%). Pangenome analysis comprising the four cedratviruses revealed an increase in the pangenome concomitant with a decrease in the core genome with the addition of the two novel viruses. Finally, phylogenetic analyses clustered the Brazilian virus in a separate branch within the group of cedratviruses, while the French isolate is closer to the previously reported Cedratvirus lausannensis Taking all together, we propose the existence of a second lineage of this emerging viral genus and provide new insights into the biodiversity and ubiquity of these giant viruses.IMPORTANCE Various giant viruses have been described in recent years, revealing a unique part of the virosphere. A new group among the giant viruses has recently been described, the cedratviruses, which is currently composed of only two isolates. In this paper, we describe two novel cedratviruses isolated from French and Brazilian samples. Biological and genomic analyses showed viruses with different particle sizes, genome lengths, and architecture, revealing the existence of a second lineage of this new group of giant viruses. Our results provide new insights into the biodiversity of cedratviruses and highlight the importance of ongoing efforts to prospect for and characterize new giant viruses.
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Aherfi S, Nappez C, Lepidi H, Bedotto M, Barassi L, Jardot P, Colson P, La Scola B, Raoult D, Bregeon F. Experimental Inoculation in Rats and Mice by the Giant Marseillevirus Leads to Long-Term Detection of Virus. Front Microbiol 2018; 9:463. [PMID: 29619012 PMCID: PMC5871663 DOI: 10.3389/fmicb.2018.00463] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 02/27/2018] [Indexed: 11/13/2022] Open
Abstract
The presence of the giant virus of amoeba Marseillevirus has been identified at many different sites on the human body, including in the bloodstream of asymptomatic subjects, in the lymph nodes of a child with adenitis, in one adult with Hodgkin's disease, and in the pharynx of an adult. A high seroprevalence of the Marseillevirus has been recorded in the general population. Whether Marseillevirus can disseminate and persist within a mammal after entry remains unproven. We aimed to assess the ability of the virus to disseminate and persist into healthy organisms, especially in the lymphoid organs. Parenteral inoculations were performed by intraperitoneal injection (in rats and mice) or intravenous injection (in rats). Airway inoculation was performed by aerosolization (in mice). Dissemination and persistence were assessed by using PCR and amebal co-culture. Serologies were performed by immunofluorescent assay. Pathological examination was conducted after standard and immunohistochemistry staining. After intraperitoneal inoculation in mice and rats, Marseillevirus was detected in the bloodstream during the first 24 h. Persistence was noted until the end of the experiment, i.e., at 14 days in rats. After intravenous inoculation in rats, the virus was first detected in the blood until 48 h and then in deep organs with infectious virus detected until 14 and 21 days in the liver and the spleen, respectively. Its DNA was detected for up to 30 days in the liver and the spleen. After aerosolization in mice, infectious Marseillevirus was present in the lungs and nasal associated lymphoid tissue until 30 days post inoculation but less frequently and at a lower viral load in the lung than in the nasal associated lymphoid tissue. No other site of dissemination was found after aerosol exposure. Despite no evidence of disease being observed, the 30-day long persistence of Marseillevirus in rats and mice, regardless of the route of inoculation, supports the hypothesis of an infective potential of the virus in certain conditions. Its constant and long-term detection in nasal associated lymphoid tissue in mice after an aerosol exposure suggests the involvement of naso-pharyngeal associated lymphoid tissues in protecting the host against environmental Marseillevirus.
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Affiliation(s)
- Sarah Aherfi
- Institut Hospitalo Universitaire Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, Centre Hospitalo Universitaire Timone, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Marseille, France
| | - Claude Nappez
- Institut Hospitalo Universitaire Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, Centre Hospitalo Universitaire Timone, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Marseille, France
| | - Hubert Lepidi
- Institut Hospitalo Universitaire Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, Centre Hospitalo Universitaire Timone, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Marseille, France.,Laboratoire d'Anatomopathologie, Centre Hospitalo Universitaire Timone, Assistance Publique des Hôpitaux de Marseille, Marseille, France
| | - Marielle Bedotto
- Institut Hospitalo Universitaire Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, Centre Hospitalo Universitaire Timone, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Marseille, France
| | - Lina Barassi
- Institut Hospitalo Universitaire Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, Centre Hospitalo Universitaire Timone, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Marseille, France
| | - Priscilla Jardot
- Institut Hospitalo Universitaire Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, Centre Hospitalo Universitaire Timone, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Marseille, France
| | - Philippe Colson
- Institut Hospitalo Universitaire Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, Centre Hospitalo Universitaire Timone, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Marseille, France
| | - Bernard La Scola
- Institut Hospitalo Universitaire Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, Centre Hospitalo Universitaire Timone, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Marseille, France
| | - Didier Raoult
- Institut Hospitalo Universitaire Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, Centre Hospitalo Universitaire Timone, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Marseille, France
| | - Fabienne Bregeon
- Institut Hospitalo Universitaire Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, Centre Hospitalo Universitaire Timone, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Marseille, France.,Service des Explorations Fonctionnelles Respiratoires Centre Hospitalo Universitaire Nord, Pôle Cardio-Vasculaire et thoracique, Assistance Publique des Hôpitaux de Marseille, Marseille, France
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26
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Andrade ACDSP, Arantes TS, Rodrigues RAL, Machado TB, Dornas FP, Landell MF, Furst C, Borges LGA, Dutra LAL, Almeida G, Trindade GDS, Bergier I, Abrahão W, Borges IA, Cortines JR, de Oliveira DB, Kroon EG, Abrahão JS. Ubiquitous giants: a plethora of giant viruses found in Brazil and Antarctica. Virol J 2018; 15:22. [PMID: 29368617 PMCID: PMC5784613 DOI: 10.1186/s12985-018-0930-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 01/12/2018] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Since the discovery of giant viruses infecting amoebae in 2003, many dogmas of virology have been revised and the search for these viruses has been intensified. Over the last few years, several new groups of these viruses have been discovered in various types of samples and environments.In this work, we describe the isolation of 68 giant viruses of amoeba obtained from environmental samples from Brazil and Antarctica. METHODS Isolated viruses were identified by hemacolor staining, PCR assays and electron microscopy (scanning and/or transmission). RESULTS A total of 64 viruses belonging to the Mimiviridae family were isolated (26 from lineage A, 13 from lineage B, 2 from lineage C and 23 from unidentified lineages) from different types of samples, including marine water from Antarctica, thus being the first mimiviruses isolated in this extreme environment to date. Furthermore, a marseillevirus was isolated from sewage samples along with two pandoraviruses and a cedratvirus (the third to be isolated in the world so far). CONCLUSIONS Considering the different type of samples, we found a higher number of viral groups in sewage samples. Our results reinforce the importance of prospective studies in different environmental samples, therefore improving our comprehension about the circulation anddiversity of these viruses in nature.
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Affiliation(s)
- Ana Cláudia Dos S P Andrade
- Laboratorio de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Thalita S Arantes
- Laboratorio de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Rodrigo A L Rodrigues
- Laboratorio de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Talita B Machado
- Laboratorio de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Fábio P Dornas
- Laboratorio de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Melissa F Landell
- Laboratório de Diversidade Molecular, Instituto de Ciências Biológicas e da Saúde, Universidade Federal de Alagoas, Maceió, Brazil
| | - Cinthia Furst
- Departamento de Patologia, Universidade Federal do Espírito Santo, Maruípe, Brazil
| | - Luiz G A Borges
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Instituto do Petróleo e dos Recursos Naturais (IPR), Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Lara A L Dutra
- Department of Biological and Environmental Sciences, University of Jyvaskyla, Jyvaskyla, Finland
| | - Gabriel Almeida
- Department of Biological and Environmental Sciences, University of Jyvaskyla, Jyvaskyla, Finland
| | - Giliane de S Trindade
- Laboratorio de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | | | - Iara A Borges
- Laboratorio de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Juliana R Cortines
- Departamento de Virologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Danilo B de Oliveira
- Faculdade de Medicina, Universidade Federal do dos Vales do Jequitinhonha e Mucuri, Diamantina, Brazil
| | - Erna G Kroon
- Laboratorio de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Jônatas S Abrahão
- Laboratorio de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
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Andreani J, Khalil JYB, Baptiste E, Hasni I, Michelle C, Raoult D, Levasseur A, La Scola B. Orpheovirus IHUMI-LCC2: A New Virus among the Giant Viruses. Front Microbiol 2018; 8:2643. [PMID: 29403444 PMCID: PMC5786535 DOI: 10.3389/fmicb.2017.02643] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 12/19/2017] [Indexed: 02/06/2023] Open
Abstract
Giant viruses continue to invade the world of virology, in gigantic genome sizes and various particles shapes. Strains discoveries and metagenomic studies make it possible to reveal the complexity of these microorganisms, their origins, ecosystems and putative roles. We isolated from a rat stool sample a new giant virus “Orpheovirus IHUMI-LCC2,” using Vermamoeba vermiformis as host cell. In this paper, we describe the main genomic features and replicative cycle of Orpheovirus IHUMI-LCC2. It possesses a circular genome exceeding 1.4 Megabases with 25% G+C content and ovoidal-shaped particles ranging from 900 to 1300 nm. Particles are closed by at least one thick membrane in a single ostiole-like shape in their apex. Phylogenetic analysis and the reciprocal best hit for Orpheovirus show a connection to the proposed Pithoviridae family. However, some genomic characteristics bear witness to a completely divergent evolution for Orpheovirus IHUMI-LCC2 when compared to Cedratviruses or Pithoviruses.
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Affiliation(s)
- Julien Andreani
- Aix Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - Jacques Y B Khalil
- Aix Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France.,Centre National de la Recherche Scientifique, Marseille, France
| | - Emeline Baptiste
- Aix Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - Issam Hasni
- Aix Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - Caroline Michelle
- Aix Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - Didier Raoult
- Aix Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - Anthony Levasseur
- Aix Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - Bernard La Scola
- Aix Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
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28
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Diesend J, Kruse J, Hagedorn M, Hammann C. Amoebae, Giant Viruses, and Virophages Make Up a Complex, Multilayered Threesome. Front Cell Infect Microbiol 2018; 7:527. [PMID: 29376032 PMCID: PMC5768912 DOI: 10.3389/fcimb.2017.00527] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Accepted: 12/13/2017] [Indexed: 01/28/2023] Open
Abstract
Viral infection had not been observed for amoebae, until the Acanthamoeba polyphaga mimivirus (APMV) was discovered in 2003. APMV belongs to the nucleocytoplasmatic large DNA virus (NCLDV) family and infects not only A. polyphaga, but also other professional phagocytes. Here, we review the Megavirales to give an overview of the current members of the Mimi- and Marseilleviridae families and their structural features during amoebal infection. We summarize the different steps of their infection cycle in A. polyphaga and Acanthamoeba castellani. Furthermore, we dive into the emerging field of virophages, which parasitize upon viral factories of the Megavirales family. The discovery of virophages in 2008 and research in recent years revealed an increasingly complex network of interactions between cell, giant virus, and virophage. Virophages seem to be highly abundant in the environment and occupy the same niches as the Mimiviridae and their hosts. Establishment of metagenomic and co-culture approaches rapidly increased the number of detected virophages over the recent years. Genetic interaction of cell and virophage might constitute a potent defense machinery against giant viruses and seems to be important for survival of the infected cell during mimivirus infections. Nonetheless, the molecular events during co-infection and the interactions of cell, giant virus, and virophage have not been elucidated, yet. However, the genetic interactions of these three, suggest an intricate, multilayered network during amoebal (co-)infections. Understanding these interactions could elucidate molecular events essential for proper viral factory activity and could implicate new ways of treating viruses that form viral factories.
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Affiliation(s)
- Jan Diesend
- Ribogenetics Biochemistry Lab, Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen, Germany
| | - Janis Kruse
- Ribogenetics Biochemistry Lab, Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen, Germany
| | - Monica Hagedorn
- Ribogenetics Biochemistry Lab, Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen, Germany
| | - Christian Hammann
- Ribogenetics Biochemistry Lab, Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen, Germany
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Assis FL, Franco-Luiz APM, Dos Santos RN, Campos FS, Dornas FP, Borato PVM, Franco AC, Abrahao JS, Colson P, Scola BL. Genome Characterization of the First Mimiviruses of Lineage C Isolated in Brazil. Front Microbiol 2017; 8:2562. [PMID: 29312242 PMCID: PMC5743647 DOI: 10.3389/fmicb.2017.02562] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 12/11/2017] [Indexed: 01/01/2023] Open
Abstract
The family Mimiviridae, comprised by giant DNA viruses, has been increasingly studied since the isolation of the Acanthamoeba polyphaga mimivirus (APMV), in 2003. In this work, we describe the genome analysis of two new mimiviruses, each isolated from a distinct Brazilian environment. Furthermore, for the first time, we are reporting the genomic characterization of mimiviruses of group C in Brazil (Br-mimiC), where a predominance of mimiviruses from group A has been previously reported. The genomes of the Br-mimiC isolates Mimivirus gilmour (MVGM) and Mimivirus golden (MVGD) are composed of double-stranded DNA molecules of ∼1.2 Mb, each encoding more than 1,100 open reading frames. Genome functional annotations highlighted the presence of mimivirus group C hallmark genes, such as the set of seven aminoacyl-tRNA synthetases. However, the set of tRNA encoded by the Br-mimiC was distinct from those of other group C mimiviruses. Differences could also be observed in a genome synteny analysis, which demonstrated the presence of inversions and loci translocations at both extremities of Br-mimiC genomes. Both phylogenetic and phyletic analyses corroborate previous results, undoubtedly grouping the new Brazilian isolates into mimivirus group C. Finally, an updated pan-genome analysis of genus Mimivirus was performed including all new genomes available until the present moment. This last analysis showed a slight increase in the number of clusters of orthologous groups of proteins among mimiviruses of group A, with a larger increase after addition of sequences from mimiviruses of groups B and C, as well as a plateau tendency after the inclusion of the last four mimiviruses of group C, including the Br-mimiC isolates. Future prospective studies will help us to understand the genetic diversity among mimiviruses.
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Affiliation(s)
- Felipe L Assis
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Ana P M Franco-Luiz
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Raíssa N Dos Santos
- Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Fabrício S Campos
- College of Veterinary Medicine and Agronomy, University of Brasília, Brasília, Brazil
| | - Fábio P Dornas
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Paulo V M Borato
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Ana C Franco
- Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Jônatas S Abrahao
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Philippe Colson
- CNRS 7278, IRD 198, INSERM 1095, UM63, IHU - Méditerranée Infection, AP-HM, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Aix-Marseille Université, Marseille, France
| | - Bernard La Scola
- CNRS 7278, IRD 198, INSERM 1095, UM63, IHU - Méditerranée Infection, AP-HM, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Aix-Marseille Université, Marseille, France
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Gut Symbiont Bacteroides fragilis Secretes a Eukaryotic-Like Ubiquitin Protein That Mediates Intraspecies Antagonism. mBio 2017; 8:mBio.01902-17. [PMID: 29184019 PMCID: PMC5705921 DOI: 10.1128/mbio.01902-17] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Human gut Bacteroides species produce different types of toxins that antagonize closely related members of the gut microbiota. Some are toxic effectors delivered by type VI secretion systems, and others are non-contact-dependent secreted antimicrobial proteins. Many strains of Bacteroides fragilis secrete antimicrobial molecules, but only one of these toxins has been described to date (Bacteroidales secreted antimicrobial protein 1 [BSAP-1]). In this study, we describe a novel secreted protein produced by B. fragilis strain 638R that mediated intraspecies antagonism. Using transposon mutagenesis and deletion mutation, we identified a gene encoding a eukaryotic-like ubiquitin protein (BfUbb) necessary for toxin activity against a subset of B. fragilis strains. The addition of ubb into a heterologous background strain conferred toxic activity on that strain. We found this gene to be one of the most highly expressed in the B. fragilis genome. The mature protein is 84% similar to human ubiquitin but has an N-terminal signal peptidase I (SpI) signal sequence and is secreted extracellularly. We found that the mature 76-amino-acid synthetic protein has very potent activity, confirming that BfUbb mediates the activity. Analyses of human gut metagenomic data sets revealed that ubb is present in 12% of the metagenomes that have evidence of B. fragilis. As 638R produces both BSAP-1 and BfUbb, we performed a comprehensive analysis of the toxin activity of BSAP-1 and BfUbb against a set of 40 B. fragilis strains, revealing that 75% of B. fragilis strains are targeted by one or the other of these two secreted proteins of strain 638R. We are just beginning to understand some of the important interactions that occur between microbes of the human gut microbiota that dictate the composition and abundance of its constituent members. The ability of one member to produce molecules that directly kill a coresident member has been shown among minor gut species and is just starting to be studied in the abundant Bacteroides species. Here, we show that some strains of Bacteroides fragilis have acquired a gene encoding a secreted eukaryotic-like ubiquitin protein with potent inhibitory activity against other B. fragilis stains. This is the first bacterially encoded ubiquitin-like molecule shown to function like a bacterial toxin. This molecule is an example of a gut symbiont acquiring and adapting a eukaryotic molecule likely to increase its competitiveness in the mammalian gut. Understanding antagonistic factors produced by abundant gut symbionts is an important prerequisite to properly engineer strains to colonize the gut for health benefits.
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The Investigation of Promoter Sequences of Marseilleviruses Highlights a Remarkable Abundance of the AAATATTT Motif in Intergenic Regions. J Virol 2017; 91:JVI.01088-17. [PMID: 28794030 DOI: 10.1128/jvi.01088-17] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 08/04/2017] [Indexed: 12/13/2022] Open
Abstract
Viruses display a wide range of genomic profiles and, consequently, a variety of gene expression strategies. Specific sequences associated with transcriptional processes have been described in viruses, and putative promoter motifs have been elucidated for some nucleocytoplasmic large DNA viruses (NCLDV). Among NCLDV, the Marseilleviridae is a well-recognized family because of its genomic mosaicism. The marseilleviruses have an ability to incorporate foreign genes, especially from sympatric organisms inhabiting Acanthamoeba, its main known host. Here, we identified for the first time an eight-nucleotide A/T-rich promoter sequence (AAATATTT) associated with 55% of marseillevirus genes that is conserved in all marseilleviruses lineages, a higher level of conservation than that of any giant virus described to date. We instigated our prediction about the promoter motif by biological assays and by evaluating how single mutations in this octamer can impact gene expression. The investigation of sequences that regulate the expression of genes relative to lateral transfer revealed that the promoter motifs do not appear to be incorporated by marseilleviruses from donor organisms. Indeed, analyses of the intergenic regions that regulate lateral gene transfer-related genes have revealed an independent origin of the marseillevirus intergenic regions that does not match gene-donor organisms. About 50% of AAATATTT motifs spread throughout intergenic regions of the marseilleviruses are present as multiple copies. We believe that such multiple motifs are associated with increased expression of a given gene or are related to incorporation of foreign genes into the mosaic genome of marseilleviruses.IMPORTANCE The marseilleviruses draw attention because of the peculiar features of their genomes; however, little is known about their gene expression patterns or the factors that regulate those expression patterns. The limited published research on the expression patterns of the marseilleviruses and their unique genomes has led us to study the promoter motif sequences in the intergenic regions of the marseilleviruses. This work is the first to analyze promoter sequences in the genomes of the marseilleviruses. We also suggest a strong capacity to acquire foreign genes and to express those genes mediated by multiple copies of the promoter motifs available in intergenic regions. These findings contribute to an understanding of genomic expansion and plasticity observed in these giant viruses.
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Chatterjee A, Kondabagil K. Complete genome sequence of Kurlavirus, a novel member of the family Marseilleviridae isolated in Mumbai, India. Arch Virol 2017; 162:3243-3245. [PMID: 28685284 DOI: 10.1007/s00705-017-3469-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 06/20/2017] [Indexed: 11/24/2022]
Abstract
The complete genome sequence of Kurlavirus, a new member of the family Marseilleviridae is reported. The Kurlavirus genome was found to encode a remarkable complement of genes homologous to those of other members of the family Marseilleviridae. Interestingly, the Kurlavirus genome contains 71 fewer ORFs than that of Marseillevirus, even though their genome sizes are comparable.
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Affiliation(s)
- Anirvan Chatterjee
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, Maharashtra, 400076, India
| | - Kiran Kondabagil
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, Maharashtra, 400076, India.
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Mounce R, Murray-Rust P, Wills M. A machine-compiled microbial supertree from figure-mining thousands of papers. RESEARCH IDEAS AND OUTCOMES 2017. [DOI: 10.3897/rio.3.e13589] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
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Noumeavirus replication relies on a transient remote control of the host nucleus. Nat Commun 2017; 8:15087. [PMID: 28429720 PMCID: PMC5413956 DOI: 10.1038/ncomms15087] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 02/28/2017] [Indexed: 12/13/2022] Open
Abstract
Acanthamoeba are infected by a remarkable diversity of large dsDNA viruses, the infectious cycles of which have been characterized using genomics, transcriptomics and electron microscopy. Given their gene content and the persistence of the host nucleus throughout their infectious cycle, the Marseilleviridae were initially assumed to fully replicate in the cytoplasm. Unexpectedly, we find that their virions do not incorporate the virus-encoded transcription machinery, making their replication nucleus-dependent. However, instead of delivering their DNA to the nucleus, the Marseilleviridae initiate their replication by transiently recruiting the nuclear transcription machinery to their cytoplasmic viral factory. The nucleus recovers its integrity after becoming leaky at an early stage. This work highlights the importance of virion proteomic analyses to complement genome sequencing in the elucidation of the replication scheme and evolution of large dsDNA viruses. Large dsDNA viruses either replicate in or disrupt the nucleus to gain access to host RNA polymerases, or they rely on virus-encoded, packaged RNA polymerases. Here, the authors show that Noumeavirus replicates in the cytoplasm and relies on a transient recruitment of nuclear proteins to initiate replication.
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Schrad JR, Young EJ, Abrahão JS, Cortines JR, Parent KN. Microscopic Characterization of the Brazilian Giant Samba Virus. Viruses 2017; 9:v9020030. [PMID: 28216551 PMCID: PMC5332949 DOI: 10.3390/v9020030] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 01/25/2017] [Accepted: 02/02/2017] [Indexed: 12/13/2022] Open
Abstract
Prior to the discovery of the mimivirus in 2003, viruses were thought to be physically small and genetically simple. Mimivirus, with its ~750-nm particle size and its ~1.2-Mbp genome, shattered these notions and changed what it meant to be a virus. Since this discovery, the isolation and characterization of giant viruses has exploded. One of the more recently discovered giant viruses, Samba virus, is a Mimivirus that was isolated from the Rio Negro in the Brazilian Amazon. Initial characterization of Samba has revealed some structural information, although the preparation techniques used are prone to the generation of structural artifacts. To generate more native-like structural information for Samba, we analyzed the virus through cryo-electron microscopy, cryo-electron tomography, scanning electron microscopy, and fluorescence microscopy. These microscopy techniques demonstrated that Samba particles have a capsid diameter of ~527 nm and a fiber length of ~155 nm, making Samba the largest Mimivirus yet characterized. We also compared Samba to a fiberless mimivirus variant. Samba particles, unlike those of mimivirus, do not appear to be rigid, and quasi-icosahedral, although the two viruses share many common features, including a multi-layered capsid and an asymmetric nucleocapsid, which may be common amongst the Mimiviruses.
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Affiliation(s)
- Jason R Schrad
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, 48824 MI, USA.
| | - Eric J Young
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, 48824 MI, USA.
| | - Jônatas S Abrahão
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901 Minas Gerais, Brazil.
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE) UM63 CNRS 7278 IRD 198 INSERM U1095, Aix-Marseille University, 13385 Marseille Cedex 05, France.
| | - Juliana R Cortines
- Departamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902 Rio de Janeiro, Brazil.
| | - Kristin N Parent
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, 48824 MI, USA.
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Takemura M. Morphological and Taxonomic Properties of Tokyovirus, the First Marseilleviridae Member Isolated from Japan. Microbes Environ 2016; 31:442-448. [PMID: 27867160 PMCID: PMC5158117 DOI: 10.1264/jsme2.me16107] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Members of the Marseilleviridae family are large DNA viruses with icosahedral particle structures that infect Acanthamoeba cells. The first Marseillevirus to be discovered was isolated in 2009. Since then, several other members of the Marseilleviridae family have been reported, including Lausannevirus, Senegalvirus, Cannes 8 virus, Insectomime virus, Tunisvirus, Melbournevirus, Port-Miou virus, and Brazilian Marseillevirus, which have been isolated from Europe, Africa, Australia, and South America. The morphological and genomic properties of a new Marseilleviridae family member, Tokyovirus, discovered in a water/soil sample from a Japanese river in Tokyo, were described in the present study. Tokyovirus possesses icosahedral particles of up to 200 nm in diameter, as revealed by a transmission electron microscopy (TEM) analysis, which form a giant virion factory in Acanthamoeba cells. A preliminary genome analysis predicted 487 coding sequences. A dot plot analysis and phylogenetic analysis using family B DNA polymerase, proliferating cell nuclear antigen (PCNA), and DNA-directed RNA polymerase alpha subunit genes revealed that Tokyovirus shares similarities with Marseillevirus, Melbournevirus, and Cannes 8 virus (Marseilleviridae subclade A), but not with Lausannevirus and Port-Miou virus (subclade B), Tunisvirus and Insectomime virus (subclade C), or Brazilian Marseillevirus (subclade D), suggesting that Tokyovirus has evolved separately from the previously described Marseilleviridae members.
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Affiliation(s)
- Masaharu Takemura
- Laboratory of Biology, Department of Liberal Arts, Faculty of Science, Tokyo University of Science (RIKADAI)
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Andreani J, Aherfi S, Bou Khalil JY, Di Pinto F, Bitam I, Raoult D, Colson P, La Scola B. Cedratvirus, a Double-Cork Structured Giant Virus, is a Distant Relative of Pithoviruses. Viruses 2016; 8:v8110300. [PMID: 27827884 PMCID: PMC5127014 DOI: 10.3390/v8110300] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 10/24/2016] [Accepted: 10/26/2016] [Indexed: 11/16/2022] Open
Abstract
Most viruses are known for the ability to cause symptomatic diseases in humans and other animals. The discovery of Acanthamoeba polyphaga mimivirus and other giant amoebal viruses revealed a considerable and previously unknown area of uncharacterized viral particles. Giant viruses have been isolated from various environmental samples collected from very distant geographic places, revealing a ubiquitous distribution. Their morphological and genomic features are fundamental elements for classifying them. Herein, we report the isolation and draft genome of Cedratvirus, a new amoebal giant virus isolated in Acanthamoeba castellanii, from an Algerian environmental sample. The viral particles are ovoid-shaped, resembling Pithovirus sibericum, but differing notably in the presence of two corks at each extremity of the virion. The draft genome of Cedratvirus-589,068 base pairs in length-is a close relative of the two previously described pithoviruses, sharing 104 and 113 genes with P. sibericum and Pithovirus massiliensis genomes, respectively. Interestingly, analysis of these viruses' core genome reveals that only 21% of Cedratvirus genes are involved in best reciprocal hits with the two pithoviruses. Phylogeny reconstructions and comparative genomics indicate that Cedratvirus is most closely related to pithoviruses, and questions their membership in an enlarged putative Pithoviridae family.
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Affiliation(s)
- Julien Andreani
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), UM63 CNRS 7278 IRD 198 INSERM U1095, Facultés de Médecine et de Pharmacie, 13385 cedex 05 Marseille, France.
| | - Sarah Aherfi
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), UM63 CNRS 7278 IRD 198 INSERM U1095, Facultés de Médecine et de Pharmacie, 13385 cedex 05 Marseille, France.
- Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Centre Hospitalo-Universitaire Timone, Assistance Publique-Hôpitaux de Marseille,13005 Marseille, France.
| | - Jacques Yaacoub Bou Khalil
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), UM63 CNRS 7278 IRD 198 INSERM U1095, Facultés de Médecine et de Pharmacie, 13385 cedex 05 Marseille, France.
| | - Fabrizio Di Pinto
- Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Centre Hospitalo-Universitaire Timone, Assistance Publique-Hôpitaux de Marseille,13005 Marseille, France.
| | - Idir Bitam
- Laboratoire Biodiversité et Environnement: Interactions Génomes, Faculté des Sciences Biologiques Université des Sciences et de la Technologie Houari Boumediene, BP 32 EL ALIA 16111 Bab Ezzouar Alger, Algeria.
| | - Didier Raoult
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), UM63 CNRS 7278 IRD 198 INSERM U1095, Facultés de Médecine et de Pharmacie, 13385 cedex 05 Marseille, France.
- Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Centre Hospitalo-Universitaire Timone, Assistance Publique-Hôpitaux de Marseille,13005 Marseille, France.
| | - Philippe Colson
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), UM63 CNRS 7278 IRD 198 INSERM U1095, Facultés de Médecine et de Pharmacie, 13385 cedex 05 Marseille, France.
- Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Centre Hospitalo-Universitaire Timone, Assistance Publique-Hôpitaux de Marseille,13005 Marseille, France.
| | - Bernard La Scola
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), UM63 CNRS 7278 IRD 198 INSERM U1095, Facultés de Médecine et de Pharmacie, 13385 cedex 05 Marseille, France.
- Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Centre Hospitalo-Universitaire Timone, Assistance Publique-Hôpitaux de Marseille,13005 Marseille, France.
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A new marseillevirus isolated in Southern Brazil from Limnoperna fortunei. Sci Rep 2016; 6:35237. [PMID: 27739526 PMCID: PMC5064363 DOI: 10.1038/srep35237] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 09/06/2016] [Indexed: 11/13/2022] Open
Abstract
Members of the family Marseilleviridae are giant viruses that have the ability to infect amoebas. Such viruses were initially described in 2009. Since then, this family has grown, and diverse members have been found in different environments and geographic locations. Previous phylogenetic analyses suggested the existence of four marseillevirus lineages. A fourth lineage was described with the discovery of the Brazilian marseillevirus (BrMr), isolated from Pampulha Lake, Brazil. Here we describe the isolation and characterization of the Golden marseillevirus (GMar), a new marseillevirus isolated from golden mussels (Limnoperna fortunei) in South of Brazil. This new representative of Marseilleviridae has circular, double-stranded (dsDNA) that contains 360, 610 base pairs and encodes 483 open read frames (ORFs). The complete virus genome was sequenced and phylogenic analyses indicated clear differences between this virus and other marseilleviruses. In addition, this is the only marseillevirus so far that has been isolated from mussels, and this report expands the diversity of environments from which giant viruses could be recovered.
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Draft Genome Sequence of Tokyovirus, a Member of the Family Marseilleviridae Isolated from the Arakawa River of Tokyo, Japan. GENOME ANNOUNCEMENTS 2016; 4:4/3/e00429-16. [PMID: 27284144 PMCID: PMC4901213 DOI: 10.1128/genomea.00429-16] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Members of the Marseilleviridae family are large DNA viruses with icosahedral particles that infect Acanthamoeba cells. This report presents a new Marseilleviridae family member discovered in a water/soil sample from a river in Tokyo, named Tokyovirus, with genome size of 370 to 380 kb.
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40
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Infection and Proliferation of Giant Viruses in Amoeba Cells. Uirusu 2016; 66:135-146. [PMID: 29081465 DOI: 10.2222/jsv.66.135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Acanthamoeba polyphaga mimivirus, the first discovered giant virus with genome size and particle size much larger than previously discovered viruses, possesses several genes for translation and CRISPER Cas system-like defense mechanism against virophages, which co-infect amoeba cells with the giant virus and which inhibit giant virus proliferation. Mimiviruses infect amoeba cells by phagocytosis and release their DNA into amoeba cytoplasm through their stargate structure. After infection, giant virion factories (VFs) form in amoeba cytoplasm, followed by DNA replication and particle formation at peripheral regions of VF. Marseilleviruses, the smallest giant viruses, infect amoeba cells by phagocytosis or endocytosis, form larger VF than Mimivirus's VF in amoeba cytoplasm, and replicate their particles. Pandoraviruses found in 2013 have the largest genome size and particle size among all viruses ever found. Pandoraviruses infect amoeba cells by phagocytosis and release their DNA into amoeba cytoplasm through their mouth-like apical pores. The proliferation of Pandoraviruses occurs along with nucleus disruption. New virions form at the periphery of the region formerly occupied by the amoeba cell nucleus.
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