1
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Chan SH, Molé CN, Nye D, Mitchell L, Dai N, Buss J, Kneller DW, Whipple JM, Robb GB. Biochemical characterization of mRNA capping enzyme from Faustovirus. RNA (NEW YORK, N.Y.) 2023; 29:1803-1817. [PMID: 37625853 PMCID: PMC10578482 DOI: 10.1261/rna.079738.123] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023]
Abstract
The mammalian mRNA 5' cap structures play important roles in cellular processes such as nuclear export, efficient translation, and evading cellular innate immune surveillance and regulating 5'-mediated mRNA turnover. Hence, installation of the proper 5' cap is crucial in therapeutic applications of synthetic mRNA. The core 5' cap structure, Cap-0, is generated by three sequential enzymatic activities: RNA 5' triphosphatase, RNA guanylyltransferase, and cap N7-guanine methyltransferase. Vaccinia virus RNA capping enzyme (VCE) is a heterodimeric enzyme that has been widely used in synthetic mRNA research and manufacturing. The large subunit of VCE D1R exhibits a modular structure where each of the three structural domains possesses one of the three enzyme activities, whereas the small subunit D12L is required to activate the N7-guanine methyltransferase activity. Here, we report the characterization of a single-subunit RNA capping enzyme from an amoeba giant virus. Faustovirus RNA capping enzyme (FCE) exhibits a modular array of catalytic domains in common with VCE and is highly efficient in generating the Cap-0 structure without an activation subunit. Phylogenetic analysis suggests that FCE and VCE are descended from a common ancestral capping enzyme. We found that compared to VCE, FCE exhibits higher specific activity, higher activity toward RNA containing secondary structures and a free 5' end, and a broader temperature range, properties favorable for synthetic mRNA manufacturing workflows.
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Affiliation(s)
- S Hong Chan
- New England Biolabs, Inc., Ipswich, Massachusetts 01938, USA
| | - Christa N Molé
- New England Biolabs, Inc., Ipswich, Massachusetts 01938, USA
| | - Dillon Nye
- New England Biolabs, Inc., Ipswich, Massachusetts 01938, USA
| | - Lili Mitchell
- New England Biolabs, Inc., Ipswich, Massachusetts 01938, USA
| | - Nan Dai
- New England Biolabs, Inc., Ipswich, Massachusetts 01938, USA
| | - Jackson Buss
- New England Biolabs, Inc., Ipswich, Massachusetts 01938, USA
| | | | | | - G Brett Robb
- New England Biolabs, Inc., Ipswich, Massachusetts 01938, USA
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2
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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: 2] [Impact Index Per Article: 1.0] [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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3
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Brahim Belhaouari D, Pires De Souza GA, Lamb DC, Kelly SL, Goldstone JV, Stegeman JJ, Colson P, La Scola B, Aherfi S. Metabolic arsenal of giant viruses: Host hijack or self-use? eLife 2022; 11:e78674. [PMID: 35801640 PMCID: PMC9270025 DOI: 10.7554/elife.78674] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 06/22/2022] [Indexed: 12/11/2022] Open
Abstract
Viruses generally are defined as lacking the fundamental properties of living organisms in that they do not harbor an energy metabolism system or protein synthesis machinery. However, the discovery of giant viruses of amoeba has fundamentally challenged this view because of their exceptional genome properties, particle sizes and encoding of the enzyme machinery for some steps of protein synthesis. Although giant viruses are not able to replicate autonomously and still require a host for their multiplication, numerous metabolic genes involved in energy production have been recently detected in giant virus genomes from many environments. These findings have further blurred the boundaries that separate viruses and living organisms. Herein, we summarize information concerning genes and proteins involved in cellular metabolic pathways and their orthologues that have, surprisingly, been discovered in giant viruses. The remarkable diversity of metabolic genes described in giant viruses include genes encoding enzymes involved in glycolysis, gluconeogenesis, tricarboxylic acid cycle, photosynthesis, and β-oxidation. These viral genes are thought to have been acquired from diverse biological sources through lateral gene transfer early in the evolution of Nucleo-Cytoplasmic Large DNA Viruses, or in some cases more recently. It was assumed that viruses are capable of hijacking host metabolic networks. But the giant virus auxiliary metabolic genes also may represent another form of host metabolism manipulation, by expanding the catalytic capabilities of the host cells especially in harsh environments, providing the infected host cells with a selective evolutionary advantage compared to non-infected cells and hence favoring the viral replication. However, the mechanism of these genes' functionality remains unclear to date.
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Affiliation(s)
- Djamal Brahim Belhaouari
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), IHU Méditerranée Infection, Marseille, France, Aix-Marseille UniversitéMarseilleFrance
| | - Gabriel Augusto Pires De Souza
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), IHU Méditerranée Infection, Marseille, France, Aix-Marseille UniversitéMarseilleFrance
| | - David C Lamb
- Faculty of Medicine, Health and Life Sciences, Institute of Life Science, Swansea UniversitySwanseaUnited Kingdom
| | - Steven L Kelly
- Faculty of Medicine, Health and Life Sciences, Institute of Life Science, Swansea UniversitySwanseaUnited Kingdom
| | - Jared V Goldstone
- Biology Department, Woods Hole Oceanographic InstitutionWoods HoleUnited States
| | - John J Stegeman
- Biology Department, Woods Hole Oceanographic InstitutionWoods HoleUnited States
| | - Philippe Colson
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), IHU Méditerranée Infection, Marseille, France, Aix-Marseille UniversitéMarseilleFrance
- Assistance Publique - Hôpitaux de Marseille (AP-HM)MarseilleFrance
| | - Bernard La Scola
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), IHU Méditerranée Infection, Marseille, France, Aix-Marseille UniversitéMarseilleFrance
- Assistance Publique - Hôpitaux de Marseille (AP-HM)MarseilleFrance
| | - Sarah Aherfi
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), IHU Méditerranée Infection, Marseille, France, Aix-Marseille UniversitéMarseilleFrance
- Assistance Publique - Hôpitaux de Marseille (AP-HM)MarseilleFrance
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4
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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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5
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Geballa-Koukoulas K, La Scola B, Blanc G, Andreani J. Diversity of Giant Viruses Infecting Vermamoeba vermiformis. Front Microbiol 2022; 13:808499. [PMID: 35602053 PMCID: PMC9116030 DOI: 10.3389/fmicb.2022.808499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 03/18/2022] [Indexed: 11/28/2022] Open
Abstract
The discovery of Acanthamoeba polyphaga mimivirus in 2003 using the free-living amoeba Acanthamoeba polyphaga caused a paradigm shift in the virology field. Twelve years later, using another amoeba as a host, i.e., Vermamoeba vermiformis, novel isolates of giant viruses have been discovered. This amoeba–virus relationship led scientists to study the evolution of giant viruses and explore the origins of eukaryotes. The purpose of this article is to review all the giant viruses that have been isolated from Vermamoeba vermiformis, compare their genomic features, and report the influence of these viruses on the cell cycle of their amoebal host. To date, viruses putatively belonging to eight different viral taxa have been described: 7 are lytic and 1 is non-lytic. The comparison of giant viruses infecting Vermamoeba vermiformis has suggested three homogenous groups according to their size, the replication time inside the host cell, and the number of encoding tRNAs. This approach is an attempt at determining the evolutionary origins and trajectories of the virus; therefore, more giant viruses infecting Vermamoeba must be discovered and studied to create a comprehensive knowledge on these intriguing biological entities.
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Affiliation(s)
- Khalil Geballa-Koukoulas
- MEPHI, APHM, IRD 198, Aix Marseille University, IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO UM 110, Marseille, France
- *Correspondence: Khalil Geballa-Koukoulas,
| | - Bernard La Scola
- MEPHI, APHM, IRD 198, Aix Marseille University, IHU-Méditerranée Infection, Marseille, France
| | - Guillaume Blanc
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO UM 110, Marseille, France
| | - Julien Andreani
- MEPHI, APHM, IRD 198, Aix Marseille University, IHU-Méditerranée Infection, Marseille, France
- Julien Andreani,
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6
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Ferravante C, Sanna G, Melone V, Fromentier A, Rocco T, D'Agostino Y, Lamberti J, Alexandrova E, Pecoraro G, Pagliano P, Astorri R, Manzin A, Weisz A, Giurato G, Galdiero M, Rizzo F, Franci G. Nasopharyngeal virome analysis of COVID-19 patients during three different waves in Campania region of Italy. J Med Virol 2022; 94:2275-2283. [PMID: 34989406 PMCID: PMC9015490 DOI: 10.1002/jmv.27571] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 12/14/2021] [Accepted: 12/30/2021] [Indexed: 01/08/2023]
Abstract
From December 2019, severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) infection has spread rapidly, leading to a global pandemic. Little is known about possible relationships between SARS‐CoV‐2 and other viruses in the respiratory system affecting patient prognosis and outcomes. This study aims to characterize respiratory virome profiles in association with SARS‐CoV‐2 infection and disease severity, through the analysis in 89 nasopharyngeal swabs collected in a patient's cohort from the Campania region (Southern Italy). Results show coinfections with viral species belonging to Coronaviridae, Retroviridae, Herpesviridae, Poxviridae, Pneumoviridae, Pandoraviridae, and Anelloviridae families and only 2% of the cases (2/89) identified respiratory viruses. The severe acute respiratory syndrome coronavirus 2 infection is considered a major global threat that is still spreading around the world. Nasopharyngeal swabs samples were collected from the Campania region cohort of 89 Covid‐19 patients. Descriptive analysis of respiratory virome was carried out with the HOME‐BIO pipeline, that performed viral taxonomy profiling. It detected coinfections with viral species belonging to Coronaviridae, Retroviridae, Herpesviridae, Poxviridae, Pneumoviridae, Pandoraviridae, and Anelloviridae family. Only 2% of the cases (2/89) identified respiratory viruses.
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Affiliation(s)
- Carlo Ferravante
- Department of Medicine, Surgery and Dentistry, "Scuola Medica Salernitana", University of Salerno, Baronissi, Italy
| | - Giuseppina Sanna
- Department of Biomedical Sciences, University of Cagliari, Cittadella Universitaria, Monserrato, Cagliari, Italy
| | - Viola Melone
- Department of Medicine, Surgery and Dentistry, "Scuola Medica Salernitana", University of Salerno, Baronissi, Italy
| | - Aurore Fromentier
- Department of Medicine, Surgery and Dentistry, "Scuola Medica Salernitana", University of Salerno, Baronissi, Italy
| | - Teresa Rocco
- Department of Medicine, Surgery and Dentistry, "Scuola Medica Salernitana", University of Salerno, Baronissi, Italy.,Medical Genomics Program, Clinical Microbiology Program, Infectivology and NAT Molecular Biology Units, AOU 'S. Giovanni di Dio e Ruggi d'Aragona' Università di Salerno, Salerno, Italy
| | - Ylenia D'Agostino
- Department of Medicine, Surgery and Dentistry, "Scuola Medica Salernitana", University of Salerno, Baronissi, Italy.,Medical Genomics Program, Clinical Microbiology Program, Infectivology and NAT Molecular Biology Units, AOU 'S. Giovanni di Dio e Ruggi d'Aragona' Università di Salerno, Salerno, Italy
| | - Jessica Lamberti
- Department of Medicine, Surgery and Dentistry, "Scuola Medica Salernitana", University of Salerno, Baronissi, Italy
| | - Elena Alexandrova
- Department of Medicine, Surgery and Dentistry, "Scuola Medica Salernitana", University of Salerno, Baronissi, Italy
| | - Giovanni Pecoraro
- Department of Medicine, Surgery and Dentistry, "Scuola Medica Salernitana", University of Salerno, Baronissi, Italy
| | - Pasquale Pagliano
- Department of Medicine, Surgery and Dentistry, "Scuola Medica Salernitana", University of Salerno, Baronissi, Italy.,Medical Genomics Program, Clinical Microbiology Program, Infectivology and NAT Molecular Biology Units, AOU 'S. Giovanni di Dio e Ruggi d'Aragona' Università di Salerno, Salerno, Italy
| | - Roberta Astorri
- Department of Mental Health and Public Medicine, Infection Disease Unit, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Aldo Manzin
- Department of Biomedical Sciences, University of Cagliari, Cittadella Universitaria, Monserrato, Cagliari, Italy
| | - Alessandro Weisz
- Department of Medicine, Surgery and Dentistry, "Scuola Medica Salernitana", University of Salerno, Baronissi, Italy.,Medical Genomics Program, Clinical Microbiology Program, Infectivology and NAT Molecular Biology Units, AOU 'S. Giovanni di Dio e Ruggi d'Aragona' Università di Salerno, Salerno, Italy.,Genome Research Center for Health (CRGS), University of Salerno, Baronissi, Italy
| | - Giorgio Giurato
- Department of Medicine, Surgery and Dentistry, "Scuola Medica Salernitana", University of Salerno, Baronissi, Italy.,Genome Research Center for Health (CRGS), University of Salerno, Baronissi, Italy
| | - Massimiliano Galdiero
- Department of Experimental Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Francesca Rizzo
- Department of Medicine, Surgery and Dentistry, "Scuola Medica Salernitana", University of Salerno, Baronissi, Italy.,Genome Research Center for Health (CRGS), University of Salerno, Baronissi, Italy
| | - Gianluigi Franci
- Department of Medicine, Surgery and Dentistry, "Scuola Medica Salernitana", University of Salerno, Baronissi, Italy.,Medical Genomics Program, Clinical Microbiology Program, Infectivology and NAT Molecular Biology Units, AOU 'S. Giovanni di Dio e Ruggi d'Aragona' Università di Salerno, Salerno, Italy
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7
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Incomplete tricarboxylic acid cycle and proton gradient in Pandoravirus massiliensis: is it still a virus? ISME JOURNAL 2021; 16:695-704. [PMID: 34556816 PMCID: PMC8857278 DOI: 10.1038/s41396-021-01117-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 08/24/2021] [Accepted: 09/10/2021] [Indexed: 11/24/2022]
Abstract
The discovery of Acanthamoeba polyphaga Mimivirus, the first isolated giant virus of amoeba, challenged the historical hallmarks defining a virus. Giant virion sizes are known to reach up to 2.3 µm, making them visible by optical microscopy. Their large genome sizes of up to 2.5 Mb can encode proteins involved in the translation apparatus. We have investigated possible energy production in Pandoravirus massiliensis. Mitochondrial membrane markers allowed for the detection of a membrane potential in purified virions and this was enhanced by a regulator of the tricarboxylic acid cycle but abolished by the use of a depolarizing agent. Bioinformatics was employed to identify enzymes involved in virion proton gradient generation and this approach revealed that eight putative P. massiliensis proteins exhibited low sequence identities with known cellular enzymes involved in the universal tricarboxylic acid cycle. Further, all eight viral genes were transcribed during replication. The product of one of these genes, ORF132, was cloned and expressed in Escherichia coli, and shown to function as an isocitrate dehydrogenase, a key enzyme of the tricarboxylic acid cycle. Our findings show for the first time that a membrane potential can exist in Pandoraviruses, and this may be related to tricarboxylic acid cycle. The presence of a proton gradient in P. massiliensis makes this virus a form of life for which it is legitimate to ask the question “what is a virus?”.
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8
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Rolland C, Andreani J, Sahmi-Bounsiar D, Krupovic M, La Scola B, Levasseur A. Clandestinovirus: A Giant Virus With Chromatin Proteins and a Potential to Manipulate the Cell Cycle of Its Host Vermamoeba vermiformis. Front Microbiol 2021; 12:715608. [PMID: 34447361 PMCID: PMC8383183 DOI: 10.3389/fmicb.2021.715608] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 07/14/2021] [Indexed: 11/13/2022] Open
Abstract
For several decades, the vast world of DNA viruses has been expanding constantly. Various discoveries in this field have broadened our knowledge and revealed that DNA viruses encode many functional features, which were once thought to be exclusive to cellular life. Here, we report the isolation of a giant virus named "clandestinovirus," grown on the amoebal host Vermamoeba vermiformis. This virus was discovered in a mixed co-culture associated with another giant virus, Faustovirus ST1. Clandestinovirus possesses a linear dsDNA genome of 581,987 base pairs containing 617 genes. Phylogenetically, clandestinovirus is most closely related to Acanthamoeba castellanii medusavirus and was considered a member of the proposed Medusaviridae family. However, clandestinovirus genome is 65% larger than that of medusavirus, emphasizing the considerable genome size variation within this virus family. Functional annotation of the clandestinovirus genes suggests that the virus encodes four core histones. Furthermore, clandestinovirus appears to orchestrate the cell cycle and mitochondrial activities of the infected host by virtue of encoding a panel of protein kinases and phosphatases, and a suite of functionally diverse mitochondrial protein homologs, respectively. Collectively, these observations illuminate a strategy employed by clandestinovirus to optimize the intracellular environment for efficient virus propagation.
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Affiliation(s)
- Clara Rolland
- Aix-Marseille Université (AMU), UMR MEPHI (Microbes, Evolution, Phylogeny and Infections), IRD, APHM, Faculté de Médecine, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Julien Andreani
- Aix-Marseille Université (AMU), UMR MEPHI (Microbes, Evolution, Phylogeny and Infections), IRD, APHM, Faculté de Médecine, Marseille, France
| | - Dehia Sahmi-Bounsiar
- Aix-Marseille Université (AMU), UMR MEPHI (Microbes, Evolution, Phylogeny and Infections), IRD, APHM, Faculté de Médecine, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Mart Krupovic
- Archaeal Virology Unit, Institut Pasteur, Paris, France
| | - Bernard La Scola
- Aix-Marseille Université (AMU), UMR MEPHI (Microbes, Evolution, Phylogeny and Infections), IRD, APHM, Faculté de Médecine, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Anthony Levasseur
- Aix-Marseille Université (AMU), UMR MEPHI (Microbes, Evolution, Phylogeny and Infections), IRD, APHM, Faculté de Médecine, Marseille, France
- IHU Méditerranée Infection, Marseille, France
- Institut Universitaire de France, Paris, France
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9
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Sahmi-Bounsiar D, Baudoin JP, Hannat S, Decloquement P, Chabrieres E, Aherfi S, La Scola B. Generation of Infectious Mimivirus Virions Through Inoculation of Viral DNA Within Acanthamoeba castellanii Shows Involvement of Five Proteins, Essentially Uncharacterized. Front Microbiol 2021; 12:677847. [PMID: 34305841 PMCID: PMC8299487 DOI: 10.3389/fmicb.2021.677847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 06/08/2021] [Indexed: 11/13/2022] Open
Abstract
One of the most curious findings associated with the discovery of Acanthamoeba polyphaga mimivirus (APMV) was the presence of many proteins and RNAs within the virion. Although some hypotheses on their role in Acanthamoeba infection have been put forward, none have been validated. In this study, we directly transfected mimivirus DNA with or without additional proteinase K treatment to extracted DNA into Acanthamoeba castellanii. In this way, it was possible to generate infectious APMV virions, but only without extra proteinase K treatment of extracted DNA. The virus genomes before and after transfection were identical. We searched for the remaining DNA-associated proteins that were digested by proteinase K and could visualize at least five putative proteins. Matrix-assisted laser desorption/ionization time-of-flight and liquid chromatography–mass spectrometry comparison with protein databases allowed the identification of four hypothetical proteins—L442, L724, L829, and R387—and putative GMC-type oxidoreductase R135. We believe that L442 plays a major role in this protein–DNA interaction. In the future, expression in vectors and then diffraction of X-rays by protein crystals could help reveal the exact structure of this protein and its precise role.
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Affiliation(s)
- Dehia Sahmi-Bounsiar
- IHU Méditerranée Infection, Marseille, France.,Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique- Hôpitaux de Marseille (AP-HM), MEPHI, Marseille, France
| | - Jean-Pierre Baudoin
- IHU Méditerranée Infection, Marseille, France.,Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique- Hôpitaux de Marseille (AP-HM), MEPHI, Marseille, France
| | - Sihem Hannat
- IHU Méditerranée Infection, Marseille, France.,Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique- Hôpitaux de Marseille (AP-HM), MEPHI, Marseille, France
| | - Philippe Decloquement
- IHU Méditerranée Infection, Marseille, France.,Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique- Hôpitaux de Marseille (AP-HM), MEPHI, Marseille, France
| | - Eric Chabrieres
- IHU Méditerranée Infection, Marseille, France.,Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique- Hôpitaux de Marseille (AP-HM), MEPHI, Marseille, France
| | - Sarah Aherfi
- IHU Méditerranée Infection, Marseille, France.,Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique- Hôpitaux de Marseille (AP-HM), MEPHI, Marseille, France
| | - Bernard La Scola
- IHU Méditerranée Infection, Marseille, France.,Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique- Hôpitaux de Marseille (AP-HM), MEPHI, Marseille, France
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10
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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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11
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de Souza GAP, Queiroz VF, Coelho LFL, Abrahão JS. Alohomora! What the entry mechanisms tell us about the evolution and diversification of giant viruses and their hosts. Curr Opin Virol 2021; 47:79-85. [PMID: 33647556 DOI: 10.1016/j.coviro.2021.02.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 02/08/2021] [Accepted: 02/09/2021] [Indexed: 12/18/2022]
Abstract
The virosphere is fascinatingly vast and diverse, but as mandatory intracellular parasites, viral particles must reach the intracellular space to guarantee their species' permanence on the planet. While most known viruses that infect animals explore the endocytic pathway to enter the host cell, a diverse group of ancient viruses that make up the phylum Nucleocytoviricota appear to have evolved to explore new access' routes to the cell's cytoplasm. Giant viruses of amoeba take advantage of the phagocytosis process that these organisms exploit a lot, while phycodnavirus must actively break through a algal cellulose cell wall. The mechanisms of entry into the cell and the viruses themselves are diverse, varying in the steps of adhesion, entry, and uncoating. These are clues left by evolution about how these organisms shaped and were shaped by convoluting with eukaryotes.
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Affiliation(s)
- Gabriel Augusto Pires de Souza
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Belo Horizonte, 31270-901, Brasil
| | - Victória Fulgêncio Queiroz
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Belo Horizonte, 31270-901, Brasil
| | - Luiz Felipe Leomil Coelho
- Laboratório de Vacinas, Departamento de Microbiologia e Imunologia, Instituto de Ciências Biomédicas, Universidade Federal de Alfenas, Rua Gabriel Monteiro da Silva, 700, Alfenas, 37130-001, Brasil
| | - Jônatas Santos Abrahão
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Belo Horizonte, 31270-901, Brasil.
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12
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Pires de Souza GA, Rolland C, Nafeh B, La Scola B, Colson P. Giant virus-related sequences in the 5300-year-old Ötzi mummy metagenome. Virus Genes 2021; 57:222-227. [PMID: 33566217 DOI: 10.1007/s11262-021-01823-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 01/05/2021] [Indexed: 12/20/2022]
Abstract
Giant viruses have brought new perspectives on the virosphere. They have been increasingly described in humans, including in several metagenomic studies. Here, we searched into the metagenome of the 5300-year-old Ötzi mummy for the presence of giant virus-related sequences using MG-Digger pipeline. We found 19 reads (0.00006% of the total read number) that best matched (mean ± standard deviation (range) for e-values of 5.0E-6 ± 1.4E-6 (6.0E-5-4.0E-10) and for amino acid identity of 69.9 ± 8.7% (46.4-84.9%) and most significantly with sequences from various giant viruses, including mostly mimiviruses. This expands current knowledge on the ubiquity and relationship with humans of giant viruses.
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Affiliation(s)
- Gabriel Augusto Pires de Souza
- Institut de Recherche Pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), MEPHI, Aix-Marseille Univ., 27 boulevard Jean Moulin, 13005, Marseille, France.,IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France.,Departamento de Microbiologia, Instituto de Ciencias Biologicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Clara Rolland
- Institut de Recherche Pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), MEPHI, Aix-Marseille Univ., 27 boulevard Jean Moulin, 13005, Marseille, France.,IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France
| | - Bariaa Nafeh
- Institut de Recherche Pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), MEPHI, Aix-Marseille Univ., 27 boulevard Jean Moulin, 13005, Marseille, France
| | - Bernard La Scola
- Institut de Recherche Pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), MEPHI, Aix-Marseille Univ., 27 boulevard Jean Moulin, 13005, Marseille, France.,IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France
| | - Philippe Colson
- Institut de Recherche Pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), MEPHI, Aix-Marseille Univ., 27 boulevard Jean Moulin, 13005, Marseille, France. .,IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France.
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13
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Chelkha N, Levasseur A, La Scola B, Colson P. Host-virus interactions and defense mechanisms for giant viruses. Ann N Y Acad Sci 2020; 1486:39-57. [PMID: 33090482 DOI: 10.1111/nyas.14469] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Revised: 06/28/2020] [Accepted: 07/26/2020] [Indexed: 12/26/2022]
Abstract
Giant viruses, with virions larger than 200 nm and genomes larger than 340 kilobase pairs, modified the now outdated perception of the virosphere. With virions now reported reaching up to 1.5 μm in size and genomes of up to 2.5 Mb encoding components shared with cellular life forms, giant viruses exhibit a complexity similar to microbes, such as bacteria and archaea. Here, we review interactions of giant viruses with their hosts and defense strategies of giant viruses against their hosts and coinfecting microorganisms or virophages. We also searched by comparative genomics for homologies with proteins described or suspected to be involved in defense mechanisms. Our search reveals that natural immunity and apoptosis seem to be crucial components of the host defense against giant virus infection. Conversely, giant viruses possess methods of hijacking host functions to counteract cellular antiviral responses. In addition, giant viruses may encode other unique and complex pathways to manipulate the host machinery and eliminate other competing microorganisms. Notably, giant viruses have evolved defense mechanisms against their virophages and they might trigger defense systems against other viruses through sequence integration. We anticipate that comparative genomics may help identifying genes involved in defense strategies of both giant viruses and their hosts.
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Affiliation(s)
- Nisrine Chelkha
- Aix-Marseille University, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
| | - Anthony Levasseur
- Aix-Marseille University, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Bernard La Scola
- Aix-Marseille University, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Philippe Colson
- Aix-Marseille University, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
- IHU Méditerranée Infection, Marseille, France
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14
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Schulz F, Andreani J, Francis R, Boudjemaa H, Bou Khalil JY, Lee J, La Scola B, Woyke T. Advantages and Limits of Metagenomic Assembly and Binning of a Giant Virus. mSystems 2020; 5:e00048-20. [PMID: 32576649 PMCID: PMC7311315 DOI: 10.1128/msystems.00048-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 05/26/2020] [Indexed: 12/31/2022] Open
Abstract
Giant viruses have large genomes, often within the size range of cellular organisms. This distinguishes them from most other viruses and demands additional effort for the successful recovery of their genomes from environmental sequence data. Here, we tested the performance of genome-resolved metagenomics on a recently isolated giant virus, Fadolivirus, by spiking it into an environmental sample from which two other giant viruses were isolated. At high spike-in levels, metagenome assembly and binning led to the successful genomic recovery of Fadolivirus from the sample. A complementary survey of the major capsid protein indicated the presence of other giant viruses in the sample matrix but did not detect the two isolated from this sample. Our results indicate that genome-resolved metagenomics is a valid approach for the recovery of near-complete giant virus genomes given that sufficient clonal particles are present. However, our data also underline that a vast majority of giant viruses remain currently undetected, even in an era of terabase-scale metagenomics.IMPORTANCE The discovery of large and giant nucleocytoplasmic large DNA viruses (NCLDV) with genomes in the megabase range and equipped with a wide variety of features typically associated with cellular organisms was one of the most unexpected, intriguing, and spectacular breakthroughs in virology. Recent studies suggest that these viruses are highly abundant in the oceans, freshwater, and soil, impact the biology and ecology of their eukaryotic hosts, and ultimately affect global nutrient cycles. Genome-resolved metagenomics is becoming an increasingly popular tool to assess the diversity and coding potential of giant viruses, but this approach is currently lacking validation.
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Affiliation(s)
| | - Julien Andreani
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Rania Francis
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Hadjer Boudjemaa
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
- Department of Biology, Hassiba Ben Bouali University Chlef, Chlef, Algeria
| | | | - Janey Lee
- DOE Joint Genome Institute, Berkeley, California, USA
| | - Bernard La Scola
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Tanja Woyke
- DOE Joint Genome Institute, Berkeley, California, USA
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15
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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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16
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Mougari S, Sahmi-Bounsiar D, Levasseur A, Colson P, La Scola B. Virophages of Giant Viruses: An Update at Eleven. Viruses 2019; 11:v11080733. [PMID: 31398856 PMCID: PMC6723459 DOI: 10.3390/v11080733] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 07/31/2019] [Accepted: 08/02/2019] [Indexed: 12/19/2022] Open
Abstract
The last decade has been marked by two eminent discoveries that have changed our perception of the virology field: The discovery of giant viruses and a distinct new class of viral agents that parasitize their viral factories, the virophages. Coculture and metagenomics have actively contributed to the expansion of the virophage family by isolating dozens of new members. This increase in the body of data on virophage not only revealed the diversity of the virophage group, but also the relevant ecological impact of these small viruses and their potential role in the dynamics of the microbial network. In addition, the isolation of virophages has led us to discover previously unknown features displayed by their host viruses and cells. In this review, we present an update of all the knowledge on the isolation, biology, genomics, and morphological features of the virophages, a decade after the discovery of their first member, the Sputnik virophage. We discuss their parasitic lifestyle as bona fide viruses of the giant virus factories, genetic parasites of their genomes, and then their role as a key component or target for some host defense mechanisms during the tripartite virophage–giant virus–host cell interaction. We also present the latest advances regarding their origin, classification, and definition that have been widely discussed.
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Affiliation(s)
- Said Mougari
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), 27 boulevard Jean Moulin, 13005 Marseille, France
- Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005 Marseille, France
| | - Dehia Sahmi-Bounsiar
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), 27 boulevard Jean Moulin, 13005 Marseille, France
- Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005 Marseille, France
| | - Anthony Levasseur
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), 27 boulevard Jean Moulin, 13005 Marseille, France
- Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005 Marseille, France
| | - Philippe Colson
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), 27 boulevard Jean Moulin, 13005 Marseille, France.
- Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005 Marseille, France.
| | - Bernard La Scola
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), 27 boulevard Jean Moulin, 13005 Marseille, France.
- Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005 Marseille, France.
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17
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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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