1
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Hu Y, Schwab S, Deiss S, Escudeiro P, van Heesch T, Joiner J, Vreede J, Hartmann M, Lupas A, Alvarez B, Alva V, Dame R. Bacterial histone HBb from Bdellovibrio bacteriovorus compacts DNA by bending. Nucleic Acids Res 2024; 52:8193-8204. [PMID: 38864377 PMCID: PMC11317129 DOI: 10.1093/nar/gkae485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 05/01/2024] [Accepted: 05/24/2024] [Indexed: 06/13/2024] Open
Abstract
Histones are essential for genome compaction and transcription regulation in eukaryotes, where they assemble into octamers to form the nucleosome core. In contrast, archaeal histones assemble into dimers that form hypernucleosomes upon DNA binding. Although histone homologs have been identified in bacteria recently, their DNA-binding characteristics remain largely unexplored. Our study reveals that the bacterial histone HBb (Bd0055) is indispensable for the survival of Bdellovibrio bacteriovorus, suggesting critical roles in DNA organization and gene regulation. By determining crystal structures of free and DNA-bound HBb, we unveil its distinctive dimeric assembly, diverging from those of eukaryotic and archaeal histones, while also elucidating how it binds and bends DNA through interaction interfaces reminiscent of eukaryotic and archaeal histones. Building on this, by employing various biophysical and biochemical approaches, we further substantiated the ability of HBb to bind and compact DNA by bending in a sequence-independent manner. Finally, using DNA affinity purification and sequencing, we reveal that HBb binds along the entire genomic DNA of B. bacteriovorus without sequence specificity. These distinct DNA-binding properties of bacterial histones, showcasing remarkable similarities yet significant differences from their archaeal and eukaryotic counterparts, highlight the diverse roles histones play in DNA organization across all domains of life.
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Affiliation(s)
- Yimin Hu
- Department of Protein Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Samuel Schwab
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333CC Leiden, The Netherlands; Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands; Centre for Interdisciplinary Genome Research, Leiden University, Leiden, The Netherlands
| | - Silvia Deiss
- Department of Protein Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Pedro Escudeiro
- Department of Protein Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Thor van Heesch
- Van ’t Hoff Institute for Molecular Sciences, University of Amsterdam, The Netherlands
| | - Joe D Joiner
- Department of Protein Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Jocelyne Vreede
- Van ’t Hoff Institute for Molecular Sciences, University of Amsterdam, The Netherlands
| | - Marcus D Hartmann
- Department of Protein Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Andrei N Lupas
- Department of Protein Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Birte Hernandez Alvarez
- Department of Protein Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Vikram Alva
- Department of Protein Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Remus T Dame
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333CC Leiden, The Netherlands; Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands; Centre for Interdisciplinary Genome Research, Leiden University, Leiden, The Netherlands
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2
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Irwin NAT, Richards TA. Self-assembling viral histones are evolutionary intermediates between archaeal and eukaryotic nucleosomes. Nat Microbiol 2024; 9:1713-1724. [PMID: 38806669 PMCID: PMC11222145 DOI: 10.1038/s41564-024-01707-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 04/19/2024] [Indexed: 05/30/2024]
Abstract
Nucleosomes are DNA-protein complexes composed of histone proteins that form the basis of eukaryotic chromatin. The nucleosome was a key innovation during eukaryotic evolution, but its origin from histone homologues in Archaea remains unclear. Viral histone repeats, consisting of multiple histone paralogues within a single protein, may reflect an intermediate state. Here we examine the diversity of histones encoded by Nucleocytoviricota viruses. We identified 258 histones from 168 viral metagenomes with variable domain configurations including histone singlets, doublets, triplets and quadruplets, the latter comprising the four core histones arranged in series. Viral histone repeats branch phylogenetically between Archaea and eukaryotes and display intermediate functions in Escherichia coli, self-assembling into eukaryotic-like nucleosomes that stack into archaeal-like oligomers capable of impacting genomic activity and condensing DNA. Histone linkage also facilitates nucleosome formation, promoting eukaryotic histone assembly in E. coli. These data support the hypothesis that viral histone repeats originated in stem-eukaryotes and that nucleosome evolution proceeded through histone repeat intermediates.
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Affiliation(s)
- Nicholas A T Irwin
- Merton College, University of Oxford, Oxford, UK.
- Department of Biology, University of Oxford, Oxford, UK.
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria.
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3
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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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4
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Upadhyay M, Nair D, Moseley GW, Srivastava S, Kondabagil K. Giant Virus Global Proteomics Innovation: Comparative Evaluation of In-Gel and In-Solution Digestion Methods. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2024; 28:170-181. [PMID: 38621149 DOI: 10.1089/omi.2024.0012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/17/2024]
Abstract
With their unusually large genome and particle sizes, giant viruses (GVs) defy the conventional definition of viruses. Although most GVs isolated infect unicellular protozoans, such as amoeba, studies in the last decade have established their much wider prevalence infecting most eukaryotic supergroups and some giant viral families with the potential to be human pathogens. Their complexity, almost autonomous life cycle, and enigmatic evolution necessitate the study of GVs. The accurate assessment of GV proteome is a veritable challenge. We have compared the coverage of global protein identification using different methods for GVs isolated in Mumbai, Mimivirus Bombay (MVB), Powai Lake Megavirus (PLMV), and Kurlavirus (KV), along with two previously studied GVs, Acanthamoeba polyphaga Mimivirus (APMV) and Marseillevirus (MV). Our study shows that the simultaneous use of in-gel and in-solution digestion methods can significantly increase the coverage of protein identification in the global proteome analysis of purified GV particles. Combining the two methods of analyses, we identified an additional 72 proteins in APMV and 114 in MV compared with what have been previously reported. Similarly, proteomes of MVB, PLMV, and KV were analyzed, and a total of 242 proteins in MVB, 287 proteins in PLMV, and 174 proteins in KV were identified. Our results suggest that a combined methodology of in-gel and in-solution methods is more efficient and opens up new avenues for innovation in global proteome analysis of GVs. Future planetary health research on GVs can benefit from consideration of a broader range of proteomics methodologies as illustrated by the present study.
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Affiliation(s)
- Monica Upadhyay
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Divya Nair
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Gregory W Moseley
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Kiran Kondabagil
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
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5
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Queiroz VF, Tatara JM, Botelho BB, Rodrigues RAL, Almeida GMDF, Abrahao JS. The consequences of viral infection on protists. Commun Biol 2024; 7:306. [PMID: 38462656 PMCID: PMC10925606 DOI: 10.1038/s42003-024-06001-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Accepted: 02/29/2024] [Indexed: 03/12/2024] Open
Abstract
Protists encompass a vast widely distributed group of organisms, surpassing the diversity observed in metazoans. Their diverse ecological niches and life forms are intriguing characteristics that render them valuable subjects for in-depth cell biology studies. Throughout history, viruses have played a pivotal role in elucidating complex cellular processes, particularly in the context of cellular responses to viral infections. In this comprehensive review, we provide an overview of the cellular alterations that are triggered in specific hosts following different viral infections and explore intricate biological interactions observed in experimental conditions using different host-pathogen groups.
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Affiliation(s)
- Victoria Fulgencio Queiroz
- Federal University of Minas Gerais, Institute of Biological Sciences, Department of Microbiology, Belo Horizonte, Minas Gerais, Brazil
| | - Juliana Miranda Tatara
- The Norwegian College of Fishery Science, Faculty of Biosciences, Fisheries and Economics, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Bruna Barbosa Botelho
- Federal University of Minas Gerais, Institute of Biological Sciences, Department of Microbiology, Belo Horizonte, Minas Gerais, Brazil
| | - Rodrigo Araújo Lima Rodrigues
- Federal University of Minas Gerais, Institute of Biological Sciences, Department of Microbiology, Belo Horizonte, Minas Gerais, Brazil
| | - Gabriel Magno de Freitas Almeida
- The Norwegian College of Fishery Science, Faculty of Biosciences, Fisheries and Economics, UiT - The Arctic University of Norway, Tromsø, Norway.
| | - Jonatas Santos Abrahao
- Federal University of Minas Gerais, Institute of Biological Sciences, Department of Microbiology, Belo Horizonte, Minas Gerais, Brazil
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6
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Talbert PB, Henikoff S, Armache KJ. Giant variations in giant virus genome packaging. Trends Biochem Sci 2023; 48:1071-1082. [PMID: 37777391 DOI: 10.1016/j.tibs.2023.09.003] [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: 05/01/2023] [Revised: 09/08/2023] [Accepted: 09/11/2023] [Indexed: 10/02/2023]
Abstract
Giant viruses (Nucleocytoviricota) have a largely conserved lifecycle, yet how they cram their large genomes into viral capsids is mostly unknown. The major capsid protein and the packaging ATPase (pATPase) comprise a highly conserved morphogenesis module in giant viruses, yet some giant viruses dispense with an icosahedral capsid, and others encode multiple versions of pATPases, including conjoined ATPase doublets, or encode none. Some giant viruses have acquired DNA-condensing proteins to compact their genomes, including sheath-like structures encasing folded DNA or densely packed viral nucleosomes that show a resemblance to eukaryotic nucleosomes at the telomeres. Here, we review what is known and unknown about these ATPases and condensing proteins, and place these variations in the context of viral lifecycles.
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Affiliation(s)
- Paul B Talbert
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA.
| | - Steven Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Karim-Jean Armache
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, 10016, USA
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7
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Rigou S, Schmitt A, Alempic JM, Lartigue A, Vendloczki P, Abergel C, Claverie JM, Legendre M. Pithoviruses Are Invaded by Repeats That Contribute to Their Evolution and Divergence from Cedratviruses. Mol Biol Evol 2023; 40:msad244. [PMID: 37950899 PMCID: PMC10664404 DOI: 10.1093/molbev/msad244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 10/31/2023] [Accepted: 11/07/2023] [Indexed: 11/13/2023] Open
Abstract
Pithoviridae are amoeba-infecting giant viruses possessing the largest viral particles known so far. Since the discovery of Pithovirus sibericum, recovered from a 30,000-yr-old permafrost sample, other pithoviruses, and related cedratviruses, were isolated from various terrestrial and aquatic samples. Here, we report the isolation and genome sequencing of 2 Pithoviridae from soil samples, in addition to 3 other recent isolates. Using the 12 available genome sequences, we conducted a thorough comparative genomic study of the Pithoviridae family to decipher the organization and evolution of their genomes. Our study reveals a nonuniform genome organization in 2 main regions: 1 concentrating core genes and another gene duplications. We also found that Pithoviridae genomes are more conservative than other families of giant viruses, with a low and stable proportion (5% to 7%) of genes originating from horizontal transfers. Genome size variation within the family is mainly due to variations in gene duplication rates (from 14% to 28%) and massive invasion by inverted repeats. While these repeated elements are absent from cedratviruses, repeat-rich regions cover as much as a quarter of the pithoviruses genomes. These regions, identified using a dedicated pipeline, are hotspots of mutations, gene capture events, and genomic rearrangements that contribute to their evolution.
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Affiliation(s)
- Sofia Rigou
- Information Génomique & Structurale, Unité Mixte de Recherche 7256 (Institut de Microbiologie de la Méditerranée, FR3479), IM2B, IOM, Aix–Marseille University, Centre National de la Recherche Scientifique, Marseille 13288 Cedex 9, France
| | - Alain Schmitt
- Information Génomique & Structurale, Unité Mixte de Recherche 7256 (Institut de Microbiologie de la Méditerranée, FR3479), IM2B, IOM, Aix–Marseille University, Centre National de la Recherche Scientifique, Marseille 13288 Cedex 9, France
| | - Jean-Marie Alempic
- Information Génomique & Structurale, Unité Mixte de Recherche 7256 (Institut de Microbiologie de la Méditerranée, FR3479), IM2B, IOM, Aix–Marseille University, Centre National de la Recherche Scientifique, Marseille 13288 Cedex 9, France
| | - Audrey Lartigue
- Information Génomique & Structurale, Unité Mixte de Recherche 7256 (Institut de Microbiologie de la Méditerranée, FR3479), IM2B, IOM, Aix–Marseille University, Centre National de la Recherche Scientifique, Marseille 13288 Cedex 9, France
| | - Peter Vendloczki
- Information Génomique & Structurale, Unité Mixte de Recherche 7256 (Institut de Microbiologie de la Méditerranée, FR3479), IM2B, IOM, Aix–Marseille University, Centre National de la Recherche Scientifique, Marseille 13288 Cedex 9, France
| | - Chantal Abergel
- Information Génomique & Structurale, Unité Mixte de Recherche 7256 (Institut de Microbiologie de la Méditerranée, FR3479), IM2B, IOM, Aix–Marseille University, Centre National de la Recherche Scientifique, Marseille 13288 Cedex 9, France
| | - Jean-Michel Claverie
- Information Génomique & Structurale, Unité Mixte de Recherche 7256 (Institut de Microbiologie de la Méditerranée, FR3479), IM2B, IOM, Aix–Marseille University, Centre National de la Recherche Scientifique, Marseille 13288 Cedex 9, France
| | - Matthieu Legendre
- Information Génomique & Structurale, Unité Mixte de Recherche 7256 (Institut de Microbiologie de la Méditerranée, FR3479), IM2B, IOM, Aix–Marseille University, Centre National de la Recherche Scientifique, Marseille 13288 Cedex 9, France
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8
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Moniruzzaman M, Erazo Garcia MP, Farzad R, Ha AD, Jivaji A, Karki S, Sheyn U, Stanton J, Minch B, Stephens D, Hancks DC, Rodrigues RAL, Abrahao JS, Vardi A, Aylward FO. Virologs, viral mimicry, and virocell metabolism: the expanding scale of cellular functions encoded in the complex genomes of giant viruses. FEMS Microbiol Rev 2023; 47:fuad053. [PMID: 37740576 PMCID: PMC10583209 DOI: 10.1093/femsre/fuad053] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 08/29/2023] [Accepted: 09/21/2023] [Indexed: 09/24/2023] Open
Abstract
The phylum Nucleocytoviricota includes the largest and most complex viruses known. These "giant viruses" have a long evolutionary history that dates back to the early diversification of eukaryotes, and over time they have evolved elaborate strategies for manipulating the physiology of their hosts during infection. One of the most captivating of these mechanisms involves the use of genes acquired from the host-referred to here as viral homologs or "virologs"-as a means of promoting viral propagation. The best-known examples of these are involved in mimicry, in which viral machinery "imitates" immunomodulatory elements in the vertebrate defense system. But recent findings have highlighted a vast and rapidly expanding array of other virologs that include many genes not typically found in viruses, such as those involved in translation, central carbon metabolism, cytoskeletal structure, nutrient transport, vesicular trafficking, and light harvesting. Unraveling the roles of virologs during infection as well as the evolutionary pathways through which complex functional repertoires are acquired by viruses are important frontiers at the forefront of giant virus research.
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Affiliation(s)
- Mohammad Moniruzzaman
- Rosenstiel School of Marine Atmospheric, and Earth Science, University of Miami, Coral Gables, FL 33149, United States
| | - Maria Paula Erazo Garcia
- Department of Biological Sciences, Virginia Tech, 926 West Campus Drive, Blacksburg, VA 24061, United States
| | - Roxanna Farzad
- Department of Biological Sciences, Virginia Tech, 926 West Campus Drive, Blacksburg, VA 24061, United States
| | - Anh D Ha
- Department of Biological Sciences, Virginia Tech, 926 West Campus Drive, Blacksburg, VA 24061, United States
| | - Abdeali Jivaji
- Department of Biological Sciences, Virginia Tech, 926 West Campus Drive, Blacksburg, VA 24061, United States
| | - Sangita Karki
- Department of Biological Sciences, Virginia Tech, 926 West Campus Drive, Blacksburg, VA 24061, United States
| | - Uri Sheyn
- Department of Biological Sciences, Virginia Tech, 926 West Campus Drive, Blacksburg, VA 24061, United States
| | - Joshua Stanton
- Department of Biological Sciences, Virginia Tech, 926 West Campus Drive, Blacksburg, VA 24061, United States
| | - Benjamin Minch
- Rosenstiel School of Marine Atmospheric, and Earth Science, University of Miami, Coral Gables, FL 33149, United States
| | - Danae Stephens
- Rosenstiel School of Marine Atmospheric, and Earth Science, University of Miami, Coral Gables, FL 33149, United States
| | - Dustin C Hancks
- Department of Immunology, University of Texas Southwestern Medical Center, 6000 Harry Hines Blvd, Dallas, TX, United States
| | - Rodrigo A L Rodrigues
- Laboratório de Vírus, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil
| | - Jonatas S Abrahao
- Laboratório de Vírus, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil
| | - Assaf Vardi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Frank O Aylward
- Department of Biological Sciences, Virginia Tech, 926 West Campus Drive, Blacksburg, VA 24061, United States
- Center for Emerging, Zoonotic, and Arthropod-Borne Infectious Disease, Virginia Tech, Blacksburg, VA 24061, United States
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9
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Du Q, Peng F, Xiong Q, Xu K, Yang KY, Wang M, Wu Z, Li S, Cheng X, Rao X, Wang Y, Tsui SKW, Zeng X. Genomic Analysis of Amphioxus Reveals a Wide Range of Fragments Homologous to Viral Sequences. Viruses 2023; 15:v15040909. [PMID: 37112889 PMCID: PMC10145014 DOI: 10.3390/v15040909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 03/11/2023] [Accepted: 03/28/2023] [Indexed: 04/05/2023] Open
Abstract
Amphioxus species are considered living fossils and are important in the evolutionary study of chordates and vertebrates. To explore viral homologous sequences, a high-quality annotated genome of the Beihai amphioxus (Branchiostoma belcheri beihai) was examined using virus sequence queries. In this study, 347 homologous fragments (HFs) of viruses were identified in the genome of B. belcheri beihai, of which most were observed on 21 genome assembly scaffolds. HFs were preferentially located within protein-coding genes, particularly in their CDS regions and promoters. A range of amphioxus genes with a high frequency of HFs is proposed, including histone-related genes that are homologous to the Histone H4 or Histone H2B domains of viruses. Together, this comprehensive analysis of viral HFs provides insights into the neglected role of viral integration in the evolution of amphioxus.
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Affiliation(s)
- Qiao Du
- Agricultural Bioinformatics Key Laboratory of Hubei Province and 3D Genomics Research Centre, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Fang Peng
- Agricultural Bioinformatics Key Laboratory of Hubei Province and 3D Genomics Research Centre, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Qing Xiong
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong, China
| | - Kejin Xu
- Agricultural Bioinformatics Key Laboratory of Hubei Province and 3D Genomics Research Centre, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Kevin Yi Yang
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong, China
| | - Mingqiang Wang
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Zhitian Wu
- Agricultural Bioinformatics Key Laboratory of Hubei Province and 3D Genomics Research Centre, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Shanying Li
- Agricultural Bioinformatics Key Laboratory of Hubei Province and 3D Genomics Research Centre, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaorui Cheng
- Agricultural Bioinformatics Key Laboratory of Hubei Province and 3D Genomics Research Centre, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Xinjie Rao
- Agricultural Bioinformatics Key Laboratory of Hubei Province and 3D Genomics Research Centre, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Yuyouye Wang
- Agricultural Bioinformatics Key Laboratory of Hubei Province and 3D Genomics Research Centre, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Stephen Kwok-Wing Tsui
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong, China
| | - Xi Zeng
- Agricultural Bioinformatics Key Laboratory of Hubei Province and 3D Genomics Research Centre, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
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10
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Giant Viruses as a Source of Novel Enzymes for Biotechnological Application. Pathogens 2022; 11:pathogens11121453. [PMID: 36558786 PMCID: PMC9787589 DOI: 10.3390/pathogens11121453] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/24/2022] [Accepted: 11/28/2022] [Indexed: 12/05/2022] Open
Abstract
The global demand for industrial enzymes has been increasing in recent years, and the search for new sources of these biological products is intense, especially in microorganisms. Most known viruses have limited genetic machinery and, thus, have been overlooked by the enzyme industry for years. However, a peculiar group of viruses breaks this paradigm. Giant viruses of the phylum Nucleocytoviricota infect protists (i.e., algae and amoebae) and have complex genomes, reaching up to 2.7 Mb in length and encoding hundreds of genes. Different giant viruses have robust metabolic machinery, especially those in the Phycodnaviridae and Mimiviridae families. In this review, we present some peculiarities of giant viruses that infect protists and discuss why they should be seen as an outstanding source of new enzymes. We revisited the genomes of representatives of different groups of giant viruses and put together information about their enzymatic machinery, highlighting several genes to be explored in biotechnology involved in carbohydrate metabolism, DNA replication, and RNA processing, among others. Finally, we present additional evidence based on structural biology using chitinase as a model to reinforce the role of giant viruses as a source of novel enzymes for biotechnological application.
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11
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Rayamajhee B, Willcox MDP, Henriquez FL, Petsoglou C, Subedi D, Carnt N. Acanthamoeba, an environmental phagocyte enhancing survival and transmission of human pathogens. Trends Parasitol 2022; 38:975-990. [PMID: 36109313 DOI: 10.1016/j.pt.2022.08.007] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 08/10/2022] [Accepted: 08/11/2022] [Indexed: 01/13/2023]
Abstract
The opportunistic protist Acanthamoeba, which interacts with other microbes such as bacteria, fungi, and viruses, shows significant similarity in cellular and functional aspects to human macrophages. Intracellular survival of microbes in this microbivorous amoebal host may be a crucial step for initiation of infection in higher eukaryotic cells. Therefore, Acanthamoeba-microbe adaptations are considered an evolutionary model of macrophage-pathogen interactions. This paper reviews Acanthamoeba as an emerging human pathogen and different ecological interactions between Acanthamoeba and microbes that may serve as environmental training grounds and a genetic melting pot for the evolution, persistence, and transmission of potential human pathogens.
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Affiliation(s)
- Binod Rayamajhee
- School of Optometry and Vision Science, Faculty of Medicine and Health, University of New South Wales (UNSW), Sydney, Australia.
| | - Mark D P Willcox
- School of Optometry and Vision Science, Faculty of Medicine and Health, University of New South Wales (UNSW), Sydney, Australia.
| | - Fiona L Henriquez
- Institute of Biomedical and Environmental Health Research, School of Health and Life Sciences, University of the West of Scotland, Blantyre, South Lanarkshire, G72 0LH, UK
| | - Constantinos Petsoglou
- Sydney and Sydney Eye Hospital, Southeastern Sydney Local Health District, Sydney, Australia; Save Sight Institute, University of Sydney, Sydney, Australia
| | - Dinesh Subedi
- School of Biological Sciences, Monash University, Clayton, Australia
| | - Nicole Carnt
- School of Optometry and Vision Science, Faculty of Medicine and Health, University of New South Wales (UNSW), Sydney, Australia
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12
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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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [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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13
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Sato S, Dacher M, Kurumizaka H. Nucleosome Structures Built from Highly Divergent Histones: Parasites and Giant DNA Viruses. EPIGENOMES 2022; 6:22. [PMID: 35997368 PMCID: PMC9396995 DOI: 10.3390/epigenomes6030022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 07/29/2022] [Accepted: 07/29/2022] [Indexed: 02/04/2023] Open
Abstract
In eukaryotes, genomic DNA is bound with histone proteins and packaged into chromatin. The nucleosome, a fundamental unit of chromatin, regulates the accessibility of DNA to enzymes involved in gene regulation. During the past few years, structural analyses of chromatin architectures have been limited to evolutionarily related organisms. The amino acid sequences of histone proteins are highly conserved from humans to yeasts, but are divergent in the deeply branching protozoan groups, including human parasites that are directly related to human health. Certain large DNA viruses, as well as archaeal organisms, contain distant homologs of eukaryotic histone proteins. The divergent sequences give rise to unique and distinct nucleosome architectures, although the fundamental principles of histone folding and DNA contact are highly conserved. In this article, we review the structures and biophysical properties of nucleosomes containing histones from the human parasites Giardia lamblia and Leishmania major, and histone-like proteins from the Marseilleviridae amoeba virus family. The presented data confirm the sharing of the overall DNA compaction system among evolutionally distant species and clarify the deviations from the species-specific nature of the nucleosome.
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Affiliation(s)
| | | | - Hitoshi Kurumizaka
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan; (S.S.); (M.D.)
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14
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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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15
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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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16
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Talbert PB, Armache KJ, Henikoff S. Viral histones: pickpocket's prize or primordial progenitor? Epigenetics Chromatin 2022; 15:21. [PMID: 35624484 PMCID: PMC9145170 DOI: 10.1186/s13072-022-00454-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 04/19/2022] [Indexed: 12/12/2022] Open
Abstract
The common histones H2A, H2B, H3, and H4 are the characteristic components of eukaryotic nucleosomes, which function to wrap DNA and compact the genome as well as to regulate access to DNA for transcription and replication in all eukaryotes. In the past two decades, histones have also been found to be encoded in some DNA viruses, where their functions and properties are largely unknown, though recently histones from two related viruses have been shown to form nucleosome-like structures in vitro. Viral histones can be highly similar to eukaryotic histones in primary sequence, suggesting they have been recently picked up from eukaryotic hosts, or they can be radically divergent in primary sequence and may occur as conjoined histone doublets, triplets, or quadruplets, suggesting ancient origins prior to the divergence of modern eukaryotes. Here, we review what is known of viral histones and discuss their possible origins and functions. We consider how the viral life cycle may affect their properties and histories, and reflect on the possible roles of viruses in the origin of the nucleus of modern eukaryotic cells.
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Affiliation(s)
- Paul B Talbert
- Howard Hughes Medical Institute and Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA, 98109, USA
| | - Karim-Jean Armache
- Skirball Institute of Biomolecular Medicine, Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, 550 First Ave, New York, NY, 10016, USA
| | - Steven Henikoff
- Howard Hughes Medical Institute and Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA, 98109, USA.
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17
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Mueller L, Moreno H, Kunz S, Greub G. Lausannevirus bilevel set-points. New Microbes New Infect 2022; 46:100966. [PMID: 35330592 PMCID: PMC8938865 DOI: 10.1016/j.nmni.2022.100966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 01/28/2022] [Accepted: 02/14/2022] [Indexed: 11/25/2022] Open
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18
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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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19
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Genome chromatinization in giant double-stranded DNA viruses. Trends Biochem Sci 2021; 47:3-5. [PMID: 34657789 DOI: 10.1016/j.tibs.2021.10.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 10/04/2021] [Indexed: 11/22/2022]
Abstract
Giant viruses have extravagantly large double-stranded (ds)DNA genomes that are packaged into exceedingly complex virions. In two recent papers, Liu et al. and Valencia-Sánchez, Abini-Agbomson et al. show that some giant viruses encode unique histone doublets, which form nucleosomes remarkably similar to those found across the eukaryotic domain of life.
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20
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Abstract
Valencia-Sánchez et al. (2021) and Liu et al. (2021) provide structural and biological insights about the existence and importance of a nucleosome-like particle in a family of giant viruses.
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Affiliation(s)
- Alessandro Vannini
- Division of Structural Biology, The Institute of Cancer Research, London, SW7 3RP, UK; Fondazione Human Technopole, Structural Biology Research Centre, 20157, Milan, Italy.
| | - Ivan Marazzi
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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21
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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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22
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Liu Y, Bisio H, Toner CM, Jeudy S, Philippe N, Zhou K, Bowerman S, White A, Edwards G, Abergel C, Luger K. Virus-encoded histone doublets are essential and form nucleosome-like structures. Cell 2021; 184:4237-4250.e19. [PMID: 34297924 PMCID: PMC8357426 DOI: 10.1016/j.cell.2021.06.032] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 05/25/2021] [Accepted: 06/25/2021] [Indexed: 12/13/2022]
Abstract
The organization of genomic DNA into defined nucleosomes has long been viewed as a hallmark of eukaryotes. This paradigm has been challenged by the identification of “minimalist” histones in archaea and more recently by the discovery of genes that encode fused remote homologs of the four eukaryotic histones in Marseilleviridae, a subfamily of giant viruses that infect amoebae. We demonstrate that viral doublet histones are essential for viral infectivity, localize to cytoplasmic viral factories after virus infection, and ultimately are found in the mature virions. Cryogenic electron microscopy (cryo-EM) structures of viral nucleosome-like particles show strong similarities to eukaryotic nucleosomes despite the limited sequence identify. The unique connectors that link the histone chains contribute to the observed instability of viral nucleosomes, and some histone tails assume structural roles. Our results further expand the range of “organisms” that require nucleosomes and suggest a specialized function of histones in the biology of these unusual viruses. Marseilleviridae encode proteins that resemble fused histones H4-H3 and H2B-H2A These histone doublets assemble into unstable nucleosome-like particles in vitro Histone doublets localize to the viral factory and are highly abundant in the virus They are essential for viral fitness and infectivity, a first for any virus
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Affiliation(s)
- Yang Liu
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80309, USA; Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Hugo Bisio
- Aix-Marseille University, Centre National de la Recherche Scientifique, Information Génomique & Structurale, Unité Mixte de Recherche 7256 (Institut de Microbiologie de la Méditerranée, FR3479, IM2B), 13288 Marseille Cedex 9, France
| | - Chelsea Marie Toner
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Sandra Jeudy
- Aix-Marseille University, Centre National de la Recherche Scientifique, Information Génomique & Structurale, Unité Mixte de Recherche 7256 (Institut de Microbiologie de la Méditerranée, FR3479, IM2B), 13288 Marseille Cedex 9, France
| | - Nadege Philippe
- Aix-Marseille University, Centre National de la Recherche Scientifique, Information Génomique & Structurale, Unité Mixte de Recherche 7256 (Institut de Microbiologie de la Méditerranée, FR3479, IM2B), 13288 Marseille Cedex 9, France
| | - Keda Zhou
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Samuel Bowerman
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Alison White
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Garrett Edwards
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Chantal Abergel
- Aix-Marseille University, Centre National de la Recherche Scientifique, Information Génomique & Structurale, Unité Mixte de Recherche 7256 (Institut de Microbiologie de la Méditerranée, FR3479, IM2B), 13288 Marseille Cedex 9, France.
| | - Karolin Luger
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80309, USA; Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO 80309, USA.
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23
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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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24
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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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25
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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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26
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Legendre M. L’épigénome des virus géants. Med Sci (Paris) 2020; 36:838-840. [DOI: 10.1051/medsci/2020149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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27
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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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28
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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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29
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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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30
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Moniruzzaman M, Martinez-Gutierrez CA, Weinheimer AR, Aylward FO. Dynamic genome evolution and complex virocell metabolism of globally-distributed giant viruses. Nat Commun 2020; 11:1710. [PMID: 32249765 PMCID: PMC7136201 DOI: 10.1038/s41467-020-15507-2] [Citation(s) in RCA: 107] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 03/09/2020] [Indexed: 01/11/2023] Open
Abstract
The discovery of eukaryotic giant viruses has transformed our understanding of the limits of viral complexity, but the extent of their encoded metabolic diversity remains unclear. Here we generate 501 metagenome-assembled genomes of Nucleo-Cytoplasmic Large DNA Viruses (NCLDV) from environments around the globe, and analyze their encoded functional capacity. We report a remarkable diversity of metabolic genes in widespread giant viruses, including many involved in nutrient uptake, light harvesting, and nitrogen metabolism. Surprisingly, numerous NCLDV encode the components of glycolysis and the TCA cycle, suggesting that they can re-program fundamental aspects of their host's central carbon metabolism. Our phylogenetic analysis of NCLDV metabolic genes and their cellular homologs reveals distinct clustering of viral sequences into divergent clades, indicating that these genes are virus-specific and were acquired in the distant past. Overall our findings reveal that giant viruses encode complex metabolic capabilities with evolutionary histories largely independent of cellular life, strongly implicating them as important drivers of global biogeochemical cycles.
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Affiliation(s)
| | | | - Alaina R Weinheimer
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Frank O Aylward
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, 24061, USA.
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31
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Characterization of Mollivirus kamchatka, the First Modern Representative of the Proposed Molliviridae Family of Giant Viruses. J Virol 2020; 94:JVI.01997-19. [PMID: 31996429 DOI: 10.1128/jvi.01997-19] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 01/14/2020] [Indexed: 02/07/2023] Open
Abstract
Microbes trapped in permanently frozen paleosoils (permafrost) are the focus of increasing research in the context of global warming. Our previous investigations led to the discovery and reactivation of two Acanthamoeba-infecting giant viruses, Mollivirus sibericum and Pithovirus sibericum, from a 30,000-year old permafrost layer. While several modern pithovirus strains have since been isolated, no contemporary mollivirus relative was found. We now describe Mollivirus kamchatka, a close relative to M. sibericum, isolated from surface soil sampled on the bank of the Kronotsky River in Kamchatka, Russian Federation. This discovery confirms that molliviruses have not gone extinct and are at least present in a distant subarctic continental location. This modern isolate exhibits a nucleocytoplasmic replication cycle identical to that of M. sibericum Its spherical particle (0.6 μm in diameter) encloses a 648-kb GC-rich double-stranded DNA genome coding for 480 proteins, of which 61% are unique to these two molliviruses. The 461 homologous proteins are highly conserved (92% identical residues, on average), despite the presumed stasis of M. sibericum for the last 30,000 years. Selection pressure analyses show that most of these proteins contribute to virus fitness. The comparison of these first two molliviruses clarify their evolutionary relationship with the pandoraviruses, supporting their provisional classification in a distinct family, the Molliviridae, pending the eventual discovery of intermediary missing links better demonstrating their common ancestry.IMPORTANCE Virology has long been viewed through the prism of human, cattle, or plant diseases, leading to a largely incomplete picture of the viral world. The serendipitous discovery of the first giant virus visible under a light microscope (i.e., >0.3 μm in diameter), mimivirus, opened a new era of environmental virology, now incorporating protozoan-infecting viruses. Planet-wide isolation studies and metagenome analyses have shown the presence of giant viruses in most terrestrial and aquatic environments, including upper Pleistocene frozen soils. Those systematic surveys have led authors to propose several new distinct families, including the Mimiviridae, Marseilleviridae, Faustoviridae, Pandoraviridae, and Pithoviridae We now propose to introduce one additional family, the Molliviridae, following the description of M. kamchatka, the first modern relative of M. sibericum, previously isolated from 30,000-year-old arctic permafrost.
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32
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Ribeiro CL, Conde D, Balmant KM, Dervinis C, Johnson MG, McGrath AP, Szewczyk P, Unda F, Finegan CA, Schmidt HW, Miles B, Drost DR, Novaes E, Gonzalez-Benecke CA, Peter GF, Burleigh JG, Martin TA, Mansfield SD, Chang G, Wickett NJ, Kirst M. The uncharacterized gene EVE contributes to vessel element dimensions in Populus. Proc Natl Acad Sci U S A 2020; 117:5059-5066. [PMID: 32041869 PMCID: PMC7060721 DOI: 10.1073/pnas.1912434117] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The radiation of angiosperms led to the emergence of the vast majority of today's plant species and all our major food crops. Their extraordinary diversification occurred in conjunction with the evolution of a more efficient vascular system for the transport of water, composed of vessel elements. The physical dimensions of these water-conducting specialized cells have played a critical role in angiosperm evolution; they determine resistance to water flow, influence photosynthesis rate, and contribute to plant stature. However, the genetic factors that determine their dimensions are unclear. Here we show that a previously uncharacterized gene, ENLARGED VESSEL ELEMENT (EVE), contributes to the dimensions of vessel elements in Populus, impacting hydraulic conductivity. Our data suggest that EVE is localized in the plasma membrane and is involved in potassium uptake of differentiating xylem cells during vessel development. In plants, EVE first emerged in streptophyte algae, but expanded dramatically among vessel-containing angiosperms. The phylogeny, structure and composition of EVE indicates that it may have been involved in an ancient horizontal gene-transfer event.
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Affiliation(s)
- Cíntia L Ribeiro
- Plant Molecular and Cellular Biology Graduate Program, University of Florida, Gainesville, FL 32611
- School of Forest Resources and Conservation, University of Florida, Gainesville, FL 32611
| | - Daniel Conde
- School of Forest Resources and Conservation, University of Florida, Gainesville, FL 32611
| | - Kelly M Balmant
- School of Forest Resources and Conservation, University of Florida, Gainesville, FL 32611
| | - Christopher Dervinis
- School of Forest Resources and Conservation, University of Florida, Gainesville, FL 32611
| | | | - Aaron P McGrath
- Skaggs School of Pharmacy and Pharmaceutical Science, University of California San Diego, La Jolla, CA 92093
| | - Paul Szewczyk
- Skaggs School of Pharmacy and Pharmaceutical Science, University of California San Diego, La Jolla, CA 92093
| | - Faride Unda
- Department of Wood Science, Faculty of Forestry, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Christina A Finegan
- Plant Molecular and Cellular Biology Graduate Program, University of Florida, Gainesville, FL 32611
| | - Henry W Schmidt
- School of Forest Resources and Conservation, University of Florida, Gainesville, FL 32611
| | - Brianna Miles
- School of Forest Resources and Conservation, University of Florida, Gainesville, FL 32611
| | - Derek R Drost
- Plant Molecular and Cellular Biology Graduate Program, University of Florida, Gainesville, FL 32611
| | - Evandro Novaes
- School of Forest Resources and Conservation, University of Florida, Gainesville, FL 32611
| | | | - Gary F Peter
- Plant Molecular and Cellular Biology Graduate Program, University of Florida, Gainesville, FL 32611
- School of Forest Resources and Conservation, University of Florida, Gainesville, FL 32611
- Genetics Institute, University of Florida, Gainesville, FL 32611
| | - J Gordon Burleigh
- Plant Molecular and Cellular Biology Graduate Program, University of Florida, Gainesville, FL 32611
- Department of Biology, University of Florida, Gainesville, FL 32611
| | - Timothy A Martin
- School of Forest Resources and Conservation, University of Florida, Gainesville, FL 32611
| | - Shawn D Mansfield
- Department of Wood Science, Faculty of Forestry, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Geoffrey Chang
- Skaggs School of Pharmacy and Pharmaceutical Science, University of California San Diego, La Jolla, CA 92093
- Department of Pharmacology, School of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Norman J Wickett
- Plant Science and Conservation, Chicago Botanic Garden, Glencoe, IL 60622
- Plant Biology and Conservation, Northwestern University, Evanston, IL 60208
| | - Matias Kirst
- Plant Molecular and Cellular Biology Graduate Program, University of Florida, Gainesville, FL 32611;
- School of Forest Resources and Conservation, University of Florida, Gainesville, FL 32611
- Genetics Institute, University of Florida, Gainesville, FL 32611
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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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Akashi M, Takemura M. Distribution of SNSs in Mimivirus Genomes and the Classification of Mimiviruses Isolated from Japan. Microbes Environ 2019; 34:451-455. [PMID: 31645535 PMCID: PMC6934397 DOI: 10.1264/jsme2.me19077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Mimiviruses have been detected in various habitats. Analyses of single nucleotide substitutions (SNSs) have revealed that SNSs are mainly localized on both ends of the mimivirus genome, and mimivirus lineage A has been split into three genotype groups; therefore, mimiviruses may be classified into lineages and genotype groups based on SNSs. We isolated 9 mimiviruses from Japan and analyzed SNSs. These isolates were classified as lineage A genotype group type 2, suggesting that the local diversity of members of the family Mimiviridae isolated from Acanthamoeba spp. is lower than that of giant viruses from other families isolated in Japan.
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Affiliation(s)
- Motohiro Akashi
- Laboratory of Biology, Department of Liberal Arts, Faculty of Science, Tokyo University of Science
| | - Masaharu Takemura
- Laboratory of Biology, Department of Liberal Arts, Faculty of Science, Tokyo University of Science
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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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36
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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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Medusavirus, a Novel Large DNA Virus Discovered from Hot Spring Water. J Virol 2019; 93:JVI.02130-18. [PMID: 30728258 PMCID: PMC6450098 DOI: 10.1128/jvi.02130-18] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 01/24/2019] [Indexed: 12/22/2022] Open
Abstract
Recent discoveries of new large DNA viruses reveal high diversity in their morphologies, genetic repertoires, and replication strategies. Here, we report the novel features of medusavirus, a large DNA virus newly isolated from hot spring water in Japan. Medusavirus, with a diameter of 260 nm, shows a T=277 icosahedral capsid with unique spherical-headed spikes on its surface. It has a 381-kb genome encoding 461 putative proteins, 86 of which have their closest homologs in Acanthamoeba, whereas 279 (61%) are orphan genes. The virus lacks the genes encoding DNA topoisomerase II and RNA polymerase, showing that DNA replication takes place in the host nucleus, whereas the progeny virions are assembled in the cytoplasm. Furthermore, the medusavirus genome harbored genes for all five types of histones (H1, H2A, H2B, H3, and H4) and one DNA polymerase, which are phylogenetically placed at the root of the eukaryotic clades. In contrast, the host amoeba encoded many medusavirus homologs, including the major capsid protein. These facts strongly suggested that amoebae are indeed the most promising natural hosts of medusavirus, and that lateral gene transfers have taken place repeatedly and bidirectionally between the virus and its host since the early stage of their coevolution. Medusavirus reflects the traces of direct evolutionary interactions between the virus and eukaryotic hosts, which may be caused by sharing the DNA replication compartment and by evolutionarily long lasting virus-host relationships. Based on its unique morphological characteristics and phylogenomic relationships with other known large DNA viruses, we propose that medusavirus represents a new family, Medusaviridae IMPORTANCE We have isolated a new nucleocytoplasmic large DNA virus (NCLDV) from hot spring water in Japan, named medusavirus. This new NCLDV is phylogenetically placed at the root of the eukaryotic clades based on the phylogenies of several key genes, including that encoding DNA polymerase, and its genome surprisingly encodes the full set of histone homologs. Furthermore, its laboratory host, Acanthamoeba castellanii, encodes many medusavirus homologs in its genome, including the major capsid protein, suggesting that the amoeba is the genuine natural host from ancient times of this newly described virus and that lateral gene transfers have repeatedly occurred between the virus and amoeba. These results suggest that medusavirus is a unique NCLDV preserving ancient footprints of evolutionary interactions with its hosts, thus providing clues to elucidate the evolution of NCLDVs, eukaryotes, and virus-host interaction. Based on the dissimilarities with other known NCLDVs, we propose that medusavirus represents a new viral family, Medusaviridae.
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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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Abstract
Organisms display astonishing levels of cell and molecular diversity, including genome size, shape, and architecture. In this chapter, we review how the genome can be viewed as both a structural and an informational unit of biological diversity and explicitly define our intended meaning of genetic information. A brief overview of the characteristic features of bacterial, archaeal, and eukaryotic cell types and viruses sets the stage for a review of the differences in organization, size, and packaging strategies of their genomes. We include a detailed review of genetic elements found outside the primary chromosomal structures, as these provide insights into how genomes are sometimes viewed as incomplete informational entities. Lastly, we reassess the definition of the genome in light of recent advancements in our understanding of the diversity of genomic structures and the mechanisms by which genetic information is expressed within the cell. Collectively, these topics comprise a good introduction to genome biology for the newcomer to the field and provide a valuable reference for those developing new statistical or computation methods in genomics. This review also prepares the reader for anticipated transformations in thinking as the field of genome biology progresses.
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40
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Cryo-EM structure of a Marseilleviridae virus particle reveals a large internal microassembly. Virology 2018; 516:239-245. [PMID: 29407382 DOI: 10.1016/j.virol.2018.01.021] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 01/24/2018] [Accepted: 01/25/2018] [Indexed: 02/07/2023]
Abstract
Nucleocytoplasmic large DNA viruses (NCLDVs) blur the line between viruses and cells. Melbournevirus (MelV, family Marseilleviridae) belongs to a new family of NCLDVs. Here we present an electron cryo-microscopy structure of the MelV particle, with the large triangulation number T = 309 constructed by 3080 pseudo-hexagonal capsomers. The most distinct feature of the particle is a large and dense body (LDB) consistently found inside all particles. Electron cryo-tomography of 147 particles shows that the LDB is preferentially located in proximity to the probable lipid bilayer. The LDB is 30 nm in size and its density matches that of a genome/protein complex. The observed LDB reinforces the structural complexity of MelV, setting it apart from other NCLDVs.
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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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42
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Chen H, Zhang W, Li X, Pan Y, Yan S, Wang Y. The genome of a prasinoviruses-related freshwater virus reveals unusual diversity of phycodnaviruses. BMC Genomics 2018; 19:49. [PMID: 29334892 PMCID: PMC5769502 DOI: 10.1186/s12864-018-4432-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 01/03/2018] [Indexed: 11/10/2022] Open
Abstract
Background Phycodnaviruses are widespread algae-infecting large dsDNA viruses and presently contain six genera: Chlorovirus, Prasinovirus, Prymnesiovirus, Phaeovirus, Coccolithovirus and Raphidovirus. The members in Prasinovirus are identified as marine viruses due to their marine algal hosts, while prasinovirus freshwater relatives remain rarely reported. Results Here we present the complete genomic sequence of a novel phycodnavirus, Dishui Lake Phycodnavirus 1 (DSLPV1), which was assembled from Dishui Lake metagenomic datasets. DSLPV1 harbors a linear genome of 181,035 bp in length (G + C content: 52.7%), with 227 predicted genes and 2 tRNA encoding regions. Both comparative genomic and phylogenetic analyses indicate that the freshwater algal virus DSLPV1 is closely related to the members in Prasinovirus, a group of marine algae infecting viruses. In addition, a complete eukaryotic histone H3 variant was identified in the genome of DSLPV1, which is firstly detected in phycodnaviruses and contributes to understand the interaction between algal virus and its eukaryotic hosts. Conclusion It is in a freshwater ecosystem that a novel Prasinovirus-related viral complete genomic sequence is discovered, which sheds new light on the evolution and diversity of the algae infecting Phycodnaviridae. Electronic supplementary material The online version of this article (10.1186/s12864-018-4432-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hao Chen
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Weijia Zhang
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China.,Present address: Archaea Center, Department of Biology, Copenhagen University, DK2000, Copenhagen, Denmark
| | - Xiefei Li
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Yingjie Pan
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China.,Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation, Ministry of Agriculture, Shanghai, China
| | - Shuling Yan
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China.,Institute of Biochemistry and Molecular Cell Biology, University of Göttingen, Göttingen, Germany
| | - Yongjie Wang
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China. .,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China. .,Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation, Ministry of Agriculture, Shanghai, China.
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43
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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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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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Erives AJ. Phylogenetic analysis of the core histone doublet and DNA topo II genes of Marseilleviridae: evidence of proto-eukaryotic provenance. Epigenetics Chromatin 2017; 10:55. [PMID: 29179736 PMCID: PMC5704553 DOI: 10.1186/s13072-017-0162-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Accepted: 11/15/2017] [Indexed: 11/15/2022] Open
Abstract
Background While the genomes of eukaryotes and Archaea both encode the histone-fold domain, only eukaryotes encode the core histone paralogs H2A, H2B, H3, and H4. With DNA, these core histones assemble into the nucleosomal octamer underlying eukaryotic chromatin. Importantly, core histones for H2A and H3 are maintained as neofunctionalized paralogs adapted for general bulk chromatin (canonical H2 and H3) or specialized chromatin (H2A.Z enriched at gene promoters and cenH3s enriched at centromeres). In this context, the identification of core histone-like “doublets” in the cytoplasmic replication factories of the Marseilleviridae (MV) is a novel finding with possible relevance to understanding the origin of eukaryotic chromatin. Here, we analyze and compare the core histone doublet genes from all known MV genomes as well as other MV genes relevant to the origin of the eukaryotic replisome. Results Using different phylogenetic approaches, we show that MV histone domains encode obligate H2B-H2A and H4-H3 dimers of possible proto-eukaryotic origin. MV core histone moieties form sister clades to each of the four eukaryotic clades of canonical and variant core histones. This suggests that MV core histone moieties diverged prior to eukaryotic neofunctionalizations associated with paired linear chromosomes and variant histone octamer assembly. We also show that MV genomes encode a proto-eukaryotic DNA topoisomerase II enzyme that forms a sister clade to eukaryotes. This is a relevant finding given that DNA topo II influences histone deposition and chromatin compaction and is the second most abundant nuclear protein after histones. Conclusions The combined domain architecture and phylogenomic analyses presented here suggest that a primitive origin for MV histone genes is a more parsimonious explanation than horizontal gene transfers + gene fusions + sufficient divergence to eliminate relatedness to eukaryotic neofunctionalizations within the H2A and H3 clades without loss of relatedness to each of the four core histone clades. We thus suggest MV histone doublet genes and their DNA topo II gene possibly were acquired from an organism with a chromatinized replisome that diverged prior to the origin of eukaryotic core histone variants for H2/H2A.Z and H3/cenH3. These results also imply that core histones were utilized ancestrally in viral DNA compaction and/or protection from host endonucleases. Electronic supplementary material The online version of this article (10.1186/s13072-017-0162-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Albert J Erives
- Department of Biology, University of Iowa, Iowa City, IA, 52242-1324, USA.
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Mueller L, Bertelli C, Pillonel T, Salamin N, Greub G. One Year Genome Evolution of Lausannevirus in Allopatric versus Sympatric Conditions. Genome Biol Evol 2017; 9:1432-1449. [PMID: 28525571 PMCID: PMC5513546 DOI: 10.1093/gbe/evx074] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/17/2017] [Indexed: 02/07/2023] Open
Abstract
Amoeba-resisting microorganisms raised a great interest during the last decade. Among them, some large DNA viruses present huge genomes up to 2.5 Mb long, exceeding the size of small bacterial genomes. The rate of genome evolution in terms of mutation, deletion, and gene acquisition in these genomes is yet unknown. Given the suspected high plasticity of viral genomes, the microevolution of the 346 kb genome of Lausannevirus, a member of Megavirales, was studied. Hence, Lausannevirus was co-cultured within the amoeba Acanthamoeba castellanii over one year. Despite a low number of mutations, the virus showed a genome reduction of 3.7% after 12 months. Lausannevirus genome evolution in sympatric conditions was investigated by its co-culture with Estrella lausannensis, an obligate intracellular bacterium, in the amoeba A. castellanii during one year. Cultures were split every 3 months. Genome sequencing revealed that in these conditions both, Lausannevirus and E. lausannensis, show stable genome, presenting no major rearrangement. In fact, after one year they acquired from 2 to 7 and from 4 to 10 mutations per culture for Lausannevirus and E. lausannensis, respectively. Interestingly, different mutations in the endonuclease encoding genes of Lausannevirus were observed in different subcultures, highlighting the importance of this gene product in the replication of Lausannevirus. Conversely, mutations in E. lausannensis were mainly located in a gene encoding for a phosphoenolpyruvate–protein phosphotransferase (PtsI), implicated in sugar metabolism. Moreover, in our conditions and with our analyses we detected no horizontal gene transfer during one year of co-culture.
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Affiliation(s)
- Linda Mueller
- Center for Research on Intracellular Bacteria (CRIB), Institute of Microbiology, Lausanne University Hospital, and University of Lausanne, Switzerland
| | - Claire Bertelli
- Center for Research on Intracellular Bacteria (CRIB), Institute of Microbiology, Lausanne University Hospital, and University of Lausanne, Switzerland.,SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Trestan Pillonel
- Center for Research on Intracellular Bacteria (CRIB), Institute of Microbiology, Lausanne University Hospital, and University of Lausanne, Switzerland
| | - Nicolas Salamin
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Department of Ecology and Evolution, Biophore, University of Lausanne, Switzerland
| | - Gilbert Greub
- Center for Research on Intracellular Bacteria (CRIB), Institute of Microbiology, Lausanne University Hospital, and University of Lausanne, Switzerland
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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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Bertelli C, Mueller L, Thomas V, Pillonel T, Jacquier N, Greub G. Cedratvirus lausannensis - digging into Pithoviridae diversity. Environ Microbiol 2017; 19:4022-4034. [PMID: 28618143 DOI: 10.1111/1462-2920.13813] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 05/24/2017] [Accepted: 05/30/2017] [Indexed: 12/13/2022]
Abstract
Amoeba-infecting viruses have raised scientists' interest due to their novel particle morphologies, their large genome size and their genomic content challenging previously established dogma. We report here the discovery and the characterization of Cedratvirus lausannensis, a novel member of the Megavirales, with a 0.75-1 µm long amphora-shaped particle closed by two striped plugs. Among numerous host cell types tested, the virus replicates only in Acanthamoeba castellanii leading to host cell lysis within 24 h. C. lausannensis was resistant to ethanol, hydrogen peroxide and heating treatments. Like 30 000-year-old Pithovirus sibericum, C. lausannensis enters by phagocytosis, releases its genetic content by fusion of the internal membrane with the inclusion membrane and replicates in intracytoplasmic viral factories. The genome encodes 643 proteins that confirmed the grouping of C. lausannensis with Cedratvirus A11 as phylogenetically distant members of the family Pithoviridae. The 575,161 bp AT-rich genome is essentially devoid of the numerous repeats harbored by Pithovirus, suggesting that these non-coding repetitions might be due to a selfish element rather than particular characteristics of the Pithoviridae family. The discovery of C. lausannensis confirms the contemporary worldwide distribution of Pithoviridae members and the characterization of its genome paves the way to better understand their evolution.
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Affiliation(s)
- Claire Bertelli
- Institute of Microbiology, University Hospital Center and University of Lausanne, 1011 Lausanne, Switzerland.,SIB Swiss Institute of Bioinformatics, Lausanne, 1015, Switzerland
| | - Linda Mueller
- Institute of Microbiology, University Hospital Center and University of Lausanne, 1011 Lausanne, Switzerland
| | - Vincent Thomas
- Technology Research Institute Bioaster, 28, Rue du Docteur Roux, Paris, 75015, France
| | - Trestan Pillonel
- Institute of Microbiology, University Hospital Center and University of Lausanne, 1011 Lausanne, Switzerland
| | - Nicolas Jacquier
- Institute of Microbiology, University Hospital Center and University of Lausanne, 1011 Lausanne, Switzerland
| | - Gilbert Greub
- Institute of Microbiology, University Hospital Center and University of Lausanne, 1011 Lausanne, Switzerland
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Phaeocystis globosa Virus DNA Polymerase X: a "Swiss Army knife", Multifunctional DNA polymerase-lyase-ligase for Base Excision Repair. Sci Rep 2017; 7:6907. [PMID: 28761124 PMCID: PMC5537341 DOI: 10.1038/s41598-017-07378-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 06/27/2017] [Indexed: 01/04/2023] Open
Abstract
Phaeocystis globosa virus 16T is a giant virus that belongs to the so-called nucleo-cytoplasmic large DNA virus (NCLDV) group. Its linear dsDNA genome contains an almost full complement of genes required to participate in viral base excision repair (BER). Among them is a gene coding for a bimodular protein consisting of an N-terminal Polβ-like core fused to a C-terminal domain (PgVPolX), which shows homology with NAD+-dependent DNA ligases. Analysis of the biochemical features of the purified enzyme revealed that PgVPolX is a multifunctional protein that could act as a “Swiss army knife” enzyme during BER since it is endowed with: 1) a template-directed DNA polymerization activity, preferentially acting on DNA structures containing gaps; 2) 5′-deoxyribose-5-phosphate (dRP) and abasic (AP) site lyase activities; and 3) an NAD+-dependent DNA ligase activity. We show how the three activities act in concert to efficiently repair BER intermediates, leading us to suggest that PgVPolX may constitute, together with the viral AP-endonuclease, a BER pathway. This is the first time that this type of protein fusion has been demonstrated to be functional.
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50
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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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