scholarly journals Giant Viruses and the Tree of Life

2021 ◽  
Vol 6 (2) ◽  
Author(s):  
Patrick Forterre
Keyword(s):  
Tree Of Life ◽  
Current Understanding ◽  
Giant Virus ◽  
Giant Viruses

When the first giant virus, the mimivirus, was discovered in 1992, it was misidentified as a bacterium because it was too large to have been a virus by the current understanding. Ever since, biologists have been debating how viruses should be categorized and described. Are they living? Are they something else? What is their place on the tree of life?

scholarly journals Advantages and limits of metagenomic assembly and binning of a giant virus

2020 ◽  
Author(s):  
Frederik Schulz ◽  
Julien Andreani ◽  
Rania Francis ◽  
Jacques Yaacoub Bou Khalil ◽  
Janey Lee ◽  
...  
Keyword(s):  
Size Range ◽  
Sequence Data ◽  
Giant Virus ◽  
Sample Matrix ◽  
Environmental Sequence ◽  
Successful Recovery ◽  
Metagenome Assembly ◽  
Giant Viruses ◽  
Metagenomic Assembly ◽  
Virus Genomes

AbstractGiant viruses have large genomes, often within the size range of cellular organisms. This distinguishes them from most other viruses and demands additional effort for the successful recovery of their genomes from environmental sequence data. Here we tested the performance of genome-resolved metagenomics on a recently isolated giant virus, Fadolivirus, by spiking it into an environmental sample from which two other giant viruses were isolated. At high spike-in levels, metagenome assembly and binning led to the successful genomic recovery of Fadolivirus from the sample. A complementary survey of viral hallmark genes indicated the presence of other giant viruses in the sample matrix, but did not detect the two isolated from this sample. Our results indicate that genome-resolved metagenomics is a valid approach for the recovery of near-complete giant virus genomes given that sufficient clonal particles are present. Our data also underline that a vast majority of giant viruses remain currently undetected, even in an era of terabase-scale metagenomics.

scholarly journals Boiling Acid Mimics Intracellular Giant Virus Genome Release

2019 ◽  
Author(s):  
Jason R. Schrad ◽  
Jônatas S. Abrahão ◽  
Juliana R. Cortines ◽  
Kristin N. Parent
Keyword(s):  
Mass Spectrometry ◽  
Virus Infection ◽  
Virus Genome ◽  
Life Cycles ◽  
Giant Virus ◽  
Infection Mechanisms ◽  
Specific Proteins ◽  
Giant Viruses ◽  
Molecular Forces

SummarySince their discovery, giant viruses have expanded our understanding of the principles of virology. Due to their gargantuan size and complexity, little is known about the life cycles of these viruses. To answer outstanding questions regarding giant virus infection mechanisms, we set out to determine biomolecular conditions that promote giant virus genome release. We generated four metastable infection intermediates in Samba virus (lineage A Mimiviridae) as visualized by cryo-EM, cryo-ET, and SEM. Each of these four intermediates reflects a stage that occurs in vivo. We show that these genome release stages are conserved in other, diverse giant viruses. Finally, we identified proteins that are released from Samba and newly discovered Tupanvirus through differential mass spectrometry. Our work revealed the molecular forces that trigger infection are conserved amongst disparate giant viruses. This study is also the first to identify specific proteins released during the initial stages of giant virus infection.

scholarly journals Giant virus vs amoeba: fight for supremacy

2019 ◽  
Vol 16 (1) ◽  
Author(s):  
Graziele Oliveira ◽  
Bernard La Scola ◽  
Jônatas Abrahão
Keyword(s):  
Giant Virus ◽  
Host Pathogen Interactions ◽  
Free Living ◽  
Host Interactions ◽  
Virus Particles ◽  
Recent Advances ◽  
Host Pathogen ◽  
New Hosts ◽  
Giant Viruses

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.

scholarly journals Discovery and description of the first human Retro-Giant virus

F1000Research ◽  
2018 ◽  
Vol 7 ◽  
pp. 1005 ◽  
Author(s):  
Elena Angela Lusi ◽  
Federico Caicci
Keyword(s):  
T Cell ◽  
Genome Sequence ◽  
Environmental Dna ◽  
Reverse Transcriptase Activity ◽  
Giant Virus ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Cell Tropism ◽  
Giant Viruses ◽  
Human Retrovirus

Background:Robert Gallo reported the first human retrovirus HLTV in 1980. What we report here is the first human giant virus, Mimivirus-like, with a retroviral core.Methods:  The isolation of human giant viruses from human T cells  Leukaemia was performed on 25% sucrose gradient. The purified viral pellet was examined using electron microscopy (EM), after immunolabelling with anti-FeLV gag p27 moAb, used for its ability to bind conserved epitopes among different mammalian retroviruses. These human giant viruses were tested for reverse transcriptase activity. RNA extracted from the viral  particles was initially amplified with the Pan Retrovirus PCR technique.  In  addition,a shotgun whole genome sequence was performed. Results:EM showed the presence of ~400 nm giant viruses, mimivirus-like, specifically labelled by anti-FeLV gag p27 Ab. The giant viruses had the reverse transcribing property. Whole genome sequence showed the presence of transforming retroviral genes in the large viral genome confirming that the Retro-Giant viruses are a distinct branch, missing from the current classification of retroviruses. Conclusions:Although sharing some of the morphological features with Mimiviruses, this human giant virus differs substantially from environmental DNA-giant viruses isolated so far, in that it manifests a unique mammalian transforming retroviral core and T cell tropism. The virus should not be confused with a classic human retrovirus nor even a large human retrovirus, but an ancestral human giant virus, mimivirus-like, with a mammalian retroviral core. Certainly, the oncogenic potential of the viral particle and its T cell tropism is of concern and further studies are needed to clarify the role of this giant virus in human diseases and evolution of archetypal retroviruses.

scholarly journals Diverse Trajectories Drive the Expression of a Giant Virus in the Oomycete Plant Pathogen Phytophthora parasitica

2021 ◽  
Vol 12 ◽  
Author(s):  
Sihem Hannat ◽  
Pierre Pontarotti ◽  
Philippe Colson ◽  
Marie-Line Kuhn ◽  
Eric Galiana ◽  
...  
Keyword(s):  
Rna Polymerase Ii ◽  
Plant Pathogen ◽  
Transcriptional Repression ◽  
African Swine Fever Virus ◽  
African Swine Fever ◽  
Giant Virus ◽  
Phytophthora Parasitica ◽  
Wide Range ◽  
Viral Genes ◽  
Giant Viruses

Giant viruses of amoebas, recently classified in the class Megaviricetes, are a group of viruses that can infect major eukaryotic lineages. We previously identified a set of giant virus sequences in the genome of Phytophthora parasitica, an oomycete and a devastating major plant pathogen. How viral insertions shape the structure and evolution of the invaded genomes is unclear, but it is known that the unprecedented functional potential of giant viruses is the result of an intense genetic interplay with their hosts. We previously identified a set of giant virus sequences in the genome of P. parasitica, an oomycete and a devastating major plant pathogen. Here, we show that viral pieces are found in a 550-kb locus and are organized in three main clusters. Viral sequences, namely RNA polymerases I and II and a major capsid protein, were identified, along with orphan sequences, as a hallmark of giant viruses insertions. Mining of public databases and phylogenetic reconstructions suggest an ancient association of oomycetes and giant viruses of amoeba, including faustoviruses, African swine fever virus (ASFV) and pandoraviruses, and that a single viral insertion occurred early in the evolutionary history of oomycetes prior to the Phytophthora–Pythium radiation, estimated at ∼80 million years ago. Functional annotation reveals that the viral insertions are located in a gene sparse region of the Phytophthora genome, characterized by a plethora of transposable elements (TEs), effectors and other genes potentially involved in virulence. Transcription of viral genes was investigated through analysis of RNA-Seq data and qPCR experiments. We show that most viral genes are not expressed, and that a variety of mechanisms, including deletions, TEs insertions and RNA interference may contribute to transcriptional repression. However, a gene coding a truncated copy of RNA polymerase II along a set of neighboring sequences have been shown to be expressed in a wide range of physiological conditions, including responses to stress. These results, which describe for the first time the endogenization of a giant virus in an oomycete, contribute to challenge our view of Phytophthora evolution.

scholarly journals Isolation of Yasminevirus, the First Member of Klosneuvirinae Isolated in Coculture with Vermamoeba vermiformis, Demonstrates an Extended Arsenal of Translational Apparatus Components

2019 ◽  
Vol 94 (1) ◽  
Author(s):  
Leena Hussein Bajrai ◽  
Saïd Mougari ◽  
Julien Andreani ◽  
Emeline Baptiste ◽  
Jeremy Delerce ◽  
...  
Keyword(s):  
Gc Content ◽  
Sewage Water ◽  
Giant Virus ◽  
Content Type ◽  
Translational Machinery ◽  
Trna Synthetases ◽  
Double Stranded Dna ◽  
Vermamoeba Vermiformis ◽  
Giant Viruses ◽  
Translational Apparatus

ABSTRACT The family of giant viruses is still expanding, and evidence of a translational machinery is emerging in the virosphere. The Klosneuvirinae group of giant viruses was first reconstructed from in silico studies, and then a unique member was isolated, Bodo saltans virus. Here we describe the isolation of a new member in this group using coculture with the free-living amoeba Vermamoeba vermiformis. This giant virus, called Yasminevirus, has a 2.1-Mb linear double-stranded DNA genome encoding 1,541 candidate proteins, with a GC content estimated at 40.2%. Yasminevirus possesses a nearly complete translational machinery, with a set of 70 tRNAs associated with 45 codons and recognizing 20 amino acids (aa), 20 aminoacyl-tRNA synthetases (aaRSs) recognizing 20 aa, as well as several translation factors and elongation factors. At the genome scale, evolutionary analyses placed this virus in the Klosneuvirinae group of giant viruses. Rhizome analysis demonstrated that the genome of Yasminevirus is mosaic, with ∼34% of genes having their closest homologues in other viruses, followed by ∼13.2% in Eukaryota, ∼7.2% in Bacteria, and less than 1% in Archaea. Among giant virus sequences, Yasminevirus shared 87% of viral hits with Klosneuvirinae. This description of Yasminevirus sheds light on the Klosneuvirinae group in a captivating quest to understand the evolution and diversity of giant viruses. IMPORTANCE Yasminevirus is an icosahedral double-stranded DNA virus isolated from sewage water by amoeba coculture. Here its structure and replicative cycle in the amoeba Vermamoeba vermiformis are described and genomic and evolutionary studies are reported. This virus belongs to the Klosneuvirinae group of giant viruses, representing the second isolated and cultivated giant virus in this group, and is the first isolated using a coculture procedure. Extended translational machinery pointed to Yasminevirus among the quasiautonomous giant viruses with the most complete translational apparatus of the known virosphere.

scholarly journals On the occurrence of cytochrome P450 in viruses

2019 ◽  
Vol 116 (25) ◽  
pp. 12343-12352 ◽  
Author(s):  
David C. Lamb ◽  
Alec H. Follmer ◽  
Jared V. Goldstone ◽  
David R. Nelson ◽  
Andrew G. Warrilow ◽  
...  
Keyword(s):  
Cytochrome P450 ◽  
Acanthamoeba Castellanii ◽  
Giant Virus ◽  
Gene Products ◽  
Cytochrome P450 Reductase ◽  
P450 Gene ◽  
Redox Partners ◽  
Genes Encoding ◽  
Giant Viruses ◽  
And Function

Genes encoding cytochrome P450 (CYP; P450) enzymes occur widely in the Archaea, Bacteria, and Eukarya, where they play important roles in metabolism of endogenous regulatory molecules and exogenous chemicals. We now report that genes for multiple and unique P450s occur commonly in giant viruses in the Mimiviridae, Pandoraviridae, and other families in the proposed order Megavirales. P450 genes were also identified in a herpesvirus (Ranid herpesvirus 3) and a phage (Mycobacterium phage Adler). The Adler phage P450 was classified as CYP102L1, and the crystal structure of the open form was solved at 2.5 Å. Genes encoding known redox partners for P450s (cytochrome P450 reductase, ferredoxin and ferredoxin reductase, and flavodoxin and flavodoxin reductase) were not found in any viral genome so far described, implying that host redox partners may drive viral P450 activities. Giant virus P450 proteins share no more than 25% identity with the P450 gene products we identified in Acanthamoeba castellanii, an amoeba host for many giant viruses. Thus, the origin of the unique P450 genes in giant viruses remains unknown. If giant virus P450 genes were acquired from a host, we suggest it could have been from an as yet unknown and possibly ancient host. These studies expand the horizon in the evolution and diversity of the enormously important P450 superfamily. Determining the origin and function of P450s in giant viruses may help to discern the origin of the giant viruses themselves.

scholarly journals Exploration of the propagation of transpovirons within Mimiviridae reveals a unique example of commensalism in the viral world

2019 ◽  
Vol 14 (3) ◽  
pp. 727-739 ◽  
Author(s):  
Sandra Jeudy ◽  
Lionel Bertaux ◽  
Jean-Marie Alempic ◽  
Audrey Lartigue ◽  
Matthieu Legendre ◽  
...  
Keyword(s):  
Dominance Effect ◽  
Giant Virus ◽  
Adaptation Process ◽  
Lower Efficiency ◽  
Ongoing Process ◽  
Host Cytoplasm ◽  
Giant Viruses ◽  
Infectious Cycle

AbstractAcanthamoeba-infecting Mimiviridae are giant viruses with dsDNA genome up to 1.5 Mb. They build viral factories in the host cytoplasm in which the nuclear-like virus-encoded functions take place. They are themselves the target of infections by 20-kb-dsDNA virophages, replicating in the giant virus factories and can also be found associated with 7-kb-DNA episomes, dubbed transpovirons. Here we isolated a virophage (Zamilon vitis) and two transpovirons respectively associated to B- and C-clade mimiviruses. We found that the virophage could transfer each transpoviron provided the host viruses were devoid of a resident transpoviron (permissive effect). If not, only the resident transpoviron originally isolated from the corresponding virus was replicated and propagated within the virophage progeny (dominance effect). Although B- and C-clade viruses devoid of transpoviron could replicate each transpoviron, they did it with a lower efficiency across clades, suggesting an ongoing process of adaptive co-evolution. We analysed the proteomes of host viruses and virophage particles in search of proteins involved in this adaptation process. This study also highlights a unique example of intricate commensalism in the viral world, where the transpoviron uses the virophage to propagate and where the Zamilon virophage and the transpoviron depend on the giant virus to replicate, without affecting its infectious cycle.

scholarly journals Virophages of Giant Viruses: An Update at Eleven

Viruses ◽  
2019 ◽  
Vol 11 (8) ◽  
pp. 733 ◽  
Author(s):  
Said Mougari ◽  
Dehia Sahmi-Bounsiar ◽  
Anthony Levasseur ◽  
Philippe Colson ◽  
Bernard La Scola
Keyword(s):  
Defense Mechanisms ◽  
Ecological Impact ◽  
Cell Interaction ◽  
The Body ◽  
Giant Virus ◽  
New Members ◽  
Microbial Network ◽  
Parasitic Lifestyle ◽  
Bona Fide ◽  
Giant Viruses

The last decade has been marked by two eminent discoveries that have changed our perception of the virology field: The discovery of giant viruses and a distinct new class of viral agents that parasitize their viral factories, the virophages. Coculture and metagenomics have actively contributed to the expansion of the virophage family by isolating dozens of new members. This increase in the body of data on virophage not only revealed the diversity of the virophage group, but also the relevant ecological impact of these small viruses and their potential role in the dynamics of the microbial network. In addition, the isolation of virophages has led us to discover previously unknown features displayed by their host viruses and cells. In this review, we present an update of all the knowledge on the isolation, biology, genomics, and morphological features of the virophages, a decade after the discovery of their first member, the Sputnik virophage. We discuss their parasitic lifestyle as bona fide viruses of the giant virus factories, genetic parasites of their genomes, and then their role as a key component or target for some host defense mechanisms during the tripartite virophage–giant virus–host cell interaction. We also present the latest advances regarding their origin, classification, and definition that have been widely discussed.

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