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1.
Mol Cell ; 81(17): 3447-3448, 2021 09 02.
Artigo em Inglês | MEDLINE | ID: mdl-34478653

RESUMO

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.


Assuntos
Vírus Gigantes , Vírus , Genoma , Vírus Gigantes/genética , Nucleossomos/genética
3.
EMBO Rep ; 22(8): e53464, 2021 08 04.
Artigo em Inglês | MEDLINE | ID: mdl-34288334

RESUMO

Giant viruses continue to yield fascinating discoveries from ancient eukaryotic immune defenses to viruses' role in the global carbon cycle.


Assuntos
Vírus Gigantes , Vírus , Ecologia , Eucariotos/genética , Células Eucarióticas , Vírus Gigantes/genética , Vírus/genética
4.
Proc Natl Acad Sci U S A ; 118(11)2021 03 16.
Artigo em Inglês | MEDLINE | ID: mdl-33707211

RESUMO

Marine viruses are the most abundant biological entity in the ocean and are considered as major evolutionary drivers of microbial life [C. A. Suttle, Nat. Rev. Microbiol. 5, 801-812 (2007)]. Yet, we lack quantitative approaches to assess their impact on the marine ecosystem. Here, we provide quantification of active viral infection in the bloom forming single-celled phytoplankton Emiliania huxleyi infected by the large virus EhV, using high-throughput single-molecule messenger RNA in situ hybridization (smFISH) of both virus and host transcripts. In natural samples, viral infection reached only 25% of the population despite synchronized bloom demise exposing the coexistence of infected and noninfected subpopulations. We prove that photosynthetically active cells chronically release viral particles through nonlytic infection and that viral-induced cell lysis can occur without viral release, thus challenging major assumptions regarding the life cycle of giant viruses. We could also assess active infection in cell aggregates linking viral infection and carbon export to the deep ocean [C. P. Laber et al., Nat. Microbiol. 3, 537-547 (2018)] and suggest a potential host defense strategy by enrichment of infected cells in sinking aggregates. Our approach can be applied to diverse marine microbial systems, opening a mechanistic dimension to the study of biotic interactions in the ocean.


Assuntos
Eutrofização , Vírus Gigantes/fisiologia , Haptófitas/virologia , Proteínas de Algas/genética , Interações Hospedeiro-Patógeno , Hibridização in Situ Fluorescente , Estágios do Ciclo de Vida , RNA Mensageiro/metabolismo , Água do Mar/microbiologia , Análise de Célula Única , Proteínas Virais/genética , Vírion/metabolismo
6.
Curr Opin Virol ; 47: 79-85, 2021 04.
Artigo em Inglês | MEDLINE | ID: mdl-33647556

RESUMO

The virosphere is fascinatingly vast and diverse, but as mandatory intracellular parasites, viral particles must reach the intracellular space to guarantee their species' permanence on the planet. While most known viruses that infect animals explore the endocytic pathway to enter the host cell, a diverse group of ancient viruses that make up the phylum Nucleocytoviricota appear to have evolved to explore new access' routes to the cell's cytoplasm. Giant viruses of amoeba take advantage of the phagocytosis process that these organisms exploit a lot, while phycodnavirus must actively break through a algal cellulose cell wall. The mechanisms of entry into the cell and the viruses themselves are diverse, varying in the steps of adhesion, entry, and uncoating. These are clues left by evolution about how these organisms shaped and were shaped by convoluting with eukaryotes.


Assuntos
Vírus Gigantes/fisiologia , Internalização do Vírus , Amoeba/virologia , Animais , Coevolução Biológica , Chlorella/virologia , Vírus Gigantes/classificação , Ligação Viral , Desenvelopamento do Vírus
7.
Virus Genes ; 57(2): 222-227, 2021 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-33566217

RESUMO

Giant viruses have brought new perspectives on the virosphere. They have been increasingly described in humans, including in several metagenomic studies. Here, we searched into the metagenome of the 5300-year-old Ötzi mummy for the presence of giant virus-related sequences using MG-Digger pipeline. We found 19 reads (0.00006% of the total read number) that best matched (mean ± standard deviation (range) for e-values of 5.0E-6 ± 1.4E-6 (6.0E-5-4.0E-10) and for amino acid identity of 69.9 ± 8.7% (46.4-84.9%) and most significantly with sequences from various giant viruses, including mostly mimiviruses. This expands current knowledge on the ubiquity and relationship with humans of giant viruses.


Assuntos
Vírus Gigantes/genética , Metagenoma , Múmias/virologia , Conjuntos de Dados como Assunto , Humanos
8.
Cell Host Microbe ; 29(2): 152-154, 2021 02 10.
Artigo em Inglês | MEDLINE | ID: mdl-33571441

RESUMO

Nucleocytoplasmic large DNA viruses (NCLDVs) are widespread in the biosphere. This issue of Cell Host & Microbe, Nelson et al., and a recent Nature paper, Moniruzzaman et al., show NCLDVs can integrate into host genomes, highlighting a mechanism of large-scale virus-mediated horizontal gene transfer (vHGT) driving eukaryotic evolution.


Assuntos
Vírus Gigantes , Microalgas , Vírus , Vírus de DNA/genética , Eucariotos/genética , Transferência Genética Horizontal , Vírus Gigantes/genética , Vírus/genética
9.
Viruses ; 13(2)2021 01 20.
Artigo em Inglês | MEDLINE | ID: mdl-33498382

RESUMO

Kaumoebavirus infects the amoeba Vermamoeba vermiformis and has recently been described as a distant relative of the African swine fever virus. To characterize the diversity and evolution of this novel viral genus, we report here on the isolation and genome sequencing of a second strain of Kaumoebavirus, namely LCC10. Detailed analysis of the sequencing data suggested that its 362-Kb genome is linear with covalently closed hairpin termini, so that DNA forms a single continuous polynucleotide chain. Comparative genomic analysis indicated that although the two sequenced Kaumoebavirus strains share extensive gene collinearity, 180 predicted genes were either gained or lost in only one genome. As already observed in another distant relative, i.e., Faustovirus, which infects the same host, the center and extremities of the Kaumoebavirus genome exhibited a higher rate of sequence divergence and the major capsid protein gene was colonized by type-I introns. A possible role of the Vermamoeba host in the genesis of these evolutionary traits is hypothesized. The Kaumoebavirus genome exhibited a significant gene strand bias over the two-third of genome length, a feature not seen in the other members of the "extended Asfarviridae" clade. We suggest that this gene strand bias was induced by a putative single origin of DNA replication located near the genome extremity that imparted a selective force favoring the genes positioned on the leading strand.


Assuntos
Asfarviridae/genética , Genoma Viral , Vírus Gigantes/genética , Vírus não Classificados/genética , Asfarviridae/classificação , Proteínas do Capsídeo/genética , Replicação do DNA , Vírus de DNA/classificação , Vírus de DNA/genética , Vírus de DNA/isolamento & purificação , DNA Viral/química , DNA Viral/genética , DNA Viral/metabolismo , Evolução Molecular , Genes Virais , Vírus Gigantes/classificação , Vírus Gigantes/isolamento & purificação , Vírus Gigantes/ultraestrutura , Lobosea/virologia , Filogenia , Esgotos/virologia , Proteínas Virais/genética , Vírus não Classificados/isolamento & purificação , Vírus não Classificados/ultraestrutura
10.
Viruses ; 13(2)2021 Jan 20.
Artigo em Inglês | MEDLINE | ID: mdl-33498458

RESUMO

Giant viruses are widespread in the biosphere and play important roles in biogeochemical cycling and host genome evolution. Also known as nucleo-cytoplasmic large DNA viruses (NCLDVs), these eukaryotic viruses harbor the largest and most complex viral genomes known. Studies have shown that NCLDVs are frequently abundant in metagenomic datasets, and that sequences derived from these viruses can also be found endogenized in diverse eukaryotic genomes. The accurate detection of sequences derived from NCLDVs is therefore of great importance, but this task is challenging owing to both the high level of sequence divergence between NCLDV families and the extraordinarily high diversity of genes encoded in their genomes, including some encoding for metabolic or translation-related functions that are typically found only in cellular lineages. Here, we present ViralRecall, a bioinformatic tool for the identification of NCLDV signatures in 'omic data. This tool leverages a library of giant virus orthologous groups (GVOGs) to identify sequences that bear signatures of NCLDVs. We demonstrate that this tool can effectively identify NCLDV sequences with high sensitivity and specificity. Moreover, we show that it can be useful both for removing contaminating sequences in metagenome-assembled viral genomes as well as the identification of eukaryotic genomic loci that derived from NCLDV. ViralRecall is written in Python 3.5 and is freely available on GitHub: https://github.com/faylward/viralrecall.


Assuntos
Biologia Computacional/métodos , Citoplasma/virologia , Células Eucarióticas/virologia , Vírus Gigantes/classificação , Metagenômica , Sequência de Aminoácidos , Biodiversidade , Biblioteca Gênica , Genoma Viral , Vírus Gigantes/genética , Filogenia
11.
Nat Rev Microbiol ; 19(2): 74, 2021 02.
Artigo em Inglês | MEDLINE | ID: mdl-33303930
12.
Sci Rep ; 10(1): 21685, 2020 12 10.
Artigo em Inglês | MEDLINE | ID: mdl-33303919

RESUMO

Proteins with a metallo-beta-lactamase (MBL) fold have been largely studied in bacteria in the framework of resistance to beta-lactams, but their spectrum of activities is broader. We show here that the giant Tupanvirus also encodes a MBL fold-protein that has orthologs in other giant viruses, a deep phylogenetic root and is clustered with tRNases. This protein is significantly associated with translation components in giant viruses. After expression in Escherichia coli, it was found to hydrolyse nitrocefin, a beta-lactam, and penicillin G. This was inhibited by sulbactam, a beta-lactamase inhibitor. In addition, the tupanvirus MBL fold-protein was not active on single- or double-stranded DNA, but degraded RNAs from bacteria and Acanthamoeba castellanii, the tupanvirus amoebal host. This activity was not neutralized by sulbactam. Overall, our results still broaden the host range of MBL fold-proteins, showing dual beta-lactamase/nuclease activities in giant viruses.


Assuntos
Vírus Gigantes/enzimologia , Vírus Gigantes/genética , Hidrolases/genética , Hidrolases/metabolismo , Oxirredutases/genética , Oxirredutases/metabolismo , Biossíntese de Proteínas/genética , Ribonucleases/genética , Ribonucleases/metabolismo , beta-Lactamases/genética , beta-Lactamases/metabolismo , Filogenia
13.
Curr Biol ; 30(24): R1469-R1471, 2020 12 21.
Artigo em Inglês | MEDLINE | ID: mdl-33352125

RESUMO

A new metagenomics study has shown that marine viruses recently acquired genes encoding light-gated ion channels from green algae. These so-called channelrhodopsin genes may allow the viruses to manipulate the swimming behavior of the algae they infect.


Assuntos
Clorófitas , Vírus Gigantes , Ânions , Channelrhodopsins , Clorófitas/genética , Transferência Genética Horizontal , Vírus Gigantes/metabolismo , Rodopsina/genética , Rodopsina/metabolismo
14.
Viruses ; 12(11)2020 11 21.
Artigo em Inglês | MEDLINE | ID: mdl-33233432

RESUMO

Giant viruses are a group of eukaryotic double-stranded DNA viruses with large virion and genome size that challenged the traditional view of virus. Newly isolated strains and sequenced genomes in the last two decades have substantially advanced our knowledge of their host diversity, gene functions, and evolutionary history. Giant viruses are now known to infect hosts from all major supergroups in the eukaryotic tree of life, which predominantly comprises microbial organisms. The seven well-recognized viral clades (taxonomic families) have drastically different host range. Mimiviridae and Phycodnaviridae, both with notable intrafamilial genome variation and high abundance in environmental samples, have members that infect the most diverse eukaryotic lineages. Laboratory experiments and comparative genomics have shed light on the unprecedented functional potential of giant viruses, encoding proteins for genetic information flow, energy metabolism, synthesis of biomolecules, membrane transport, and sensing that allow for sophisticated control of intracellular conditions and cell-environment interactions. Evolutionary genomics can illuminate how current and past hosts shape viral gene repertoires, although it becomes more obscure with divergent sequences and deep phylogenies. Continued works to characterize giant viruses from marine and other environments will further contribute to our understanding of their host range, coding potential, and virus-host coevolution.


Assuntos
Eucariotos/virologia , Evolução Molecular , Genoma Viral , Vírus Gigantes/genética , Vírus Gigantes/fisiologia , Especificidade de Hospedeiro , Animais , Tamanho do Genoma , Genômica , Humanos , Filogenia
15.
Nature ; 588(7836): 141-145, 2020 12.
Artigo em Inglês | MEDLINE | ID: mdl-33208937

RESUMO

Endogenous viral elements (EVEs)-viruses that have integrated their genomes into those of their hosts-are prevalent in eukaryotes and have an important role in genome evolution1,2. The vast majority of EVEs that have been identified to date are small genomic regions comprising a few genes2, but recent evidence suggests that some large double-stranded DNA viruses may also endogenize into the genome of the host1. Nucleocytoplasmic large DNA viruses (NCLDVs) have recently become of great interest owing to their large genomes and complex evolutionary origins3-6, but it is not yet known whether they are a prominent component of eukaryotic EVEs. Here we report the widespread endogenization of NCLDVs in diverse green algae; these giant EVEs reached sizes greater than 1 million base pairs and contained as many as around 10% of the total open reading frames in some genomes, substantially increasing the scale of known viral genes in eukaryotic genomes. These endogenized elements often shared genes with host genomic loci and contained numerous spliceosomal introns and large duplications, suggesting tight assimilation into host genomes. NCLDVs contain large and mosaic genomes with genes derived from multiple sources, and their endogenization represents an underappreciated conduit of new genetic material into eukaryotic lineages that can substantially impact genome composition.


Assuntos
Clorófitas/genética , Clorófitas/virologia , Genoma/genética , Vírus Gigantes/genética , Genes Virais , Íntrons/genética , Mosaicismo , Phycodnaviridae/genética , Filogenia
16.
Curr Biol ; 30(19): R1108-R1110, 2020 10 05.
Artigo em Inglês | MEDLINE | ID: mdl-33022247

RESUMO

Chantal Abergel and Jean-Michel Claverie introduce giant viruses.


Assuntos
Evolução Biológica , Ecossistema , Genoma Viral , Vírus Gigantes/classificação , Vírus Gigantes/fisiologia , Interações Hospedeiro-Patógeno , Humanos
18.
Curr Biol ; 30(24): 4910-4920.e5, 2020 12 21.
Artigo em Inglês | MEDLINE | ID: mdl-33065010

RESUMO

Channelrhodopsins (ChRs) are light-gated ion channels widely used as optogenetic tools for manipulating neuronal activity. The currently characterized ChR families include green algal and cryptophyte cation-conducting ChRs (CCRs) and cryptophyte, haptophyte, and stramenopile anion-conducting ChRs (ACRs). Here, we report the discovery of a new family of phylogenetically distinct ChRs encoded by marine giant viruses and acquired from their unicellular green algal hosts. These previously unknown viral and green algal ChRs act as ACRs when expressed in cultured neuroblastoma-derived cells and are likely involved in behavioral responses to light.


Assuntos
Channelrhodopsins/genética , Clorófitas/genética , Transferência Genética Horizontal , Genes Virais , Vírus Gigantes/genética , Animais , Ânions/metabolismo , Linhagem Celular , Channelrhodopsins/metabolismo , Clorófitas/metabolismo , Clorófitas/efeitos da radiação , Clorófitas/virologia , Vírus Gigantes/metabolismo , Células Híbridas , Luz , Metagenômica , Camundongos , Optogenética , Filogenia , Ratos
19.
J Virol ; 94(24)2020 11 23.
Artigo em Inglês | MEDLINE | ID: mdl-32999026

RESUMO

We conducted an exhaustive search for three-dimensional structural homologs to the proteins of 20 key phylogenetically distinct nucleocytoplasmic DNA viruses (NCLDV). Structural matches covered 429 known protein domain superfamilies, with the most highly represented being ankyrin repeat, P-loop NTPase, F-box, protein kinase, and membrane occupation and recognition nexus (MORN) repeat. Domain superfamily diversity correlated with genome size, but a diversity of around 200 superfamilies appeared to correlate with an abrupt switch to paralogization. Extensive structural homology was found across the range of eukaryotic RNA polymerase II subunits and their associated basal transcription factors, with the coordinated gain and loss of clusters of subunits on a virus-by-virus basis. The total number of predicted endonucleases across the 20 NCLDV was nearly quadrupled from 36 to 132, covering much of the structural and functional diversity of endonucleases throughout the biosphere in DNA restriction, repair, and homing. Unexpected findings included capsid protein-transcription factor chimeras; endonuclease chimeras; enzymes for detoxification; antimicrobial peptides and toxin-antitoxin systems associated with symbiosis, immunity, and addiction; and novel proteins for membrane abscission and protein turnover.IMPORTANCE We extended the known annotation space for the NCLDV by 46%, revealing high-probability structural matches for fully 45% of the 9,671 query proteins and confirming up to 98% of existing annotations per virus. The most prevalent protein families included ankyrin repeat- and MORN repeat-containing proteins, many of which included an F-box, suggesting extensive host cell modulation among the NCLDV. Regression suggested a minimum requirement for around 36 protein structural superfamilies for a viable NCLDV, and beyond around 200 superfamilies, genome expansion by the acquisition of new functions was abruptly replaced by paralogization. We found homologs to herpesvirus surface glycoprotein gB in cytoplasmic viruses. This study provided the first prediction of an endonuclease in 10 of the 20 viruses examined; the first report in a virus of a phenolic acid decarboxylase, proteasomal subunit, or cysteine knot (defensin) protein; and the first report of a prokaryotic-type ribosomal protein in a eukaryotic virus.


Assuntos
Vírus de DNA/classificação , Vírus de DNA/genética , Vírus Gigantes/genética , Filogenia , Proteoma/genética , Proteínas Virais/genética , Anquirinas/genética , Citoplasma/virologia , RNA Polimerases Dirigidas por DNA , Células Eucarióticas , Evolução Molecular , Tamanho do Genoma , Genoma Viral , Mimiviridae/genética , Vaccinia/genética
20.
Nat Ecol Evol ; 4(12): 1639-1649, 2020 12.
Artigo em Inglês | MEDLINE | ID: mdl-32895519

RESUMO

Nucleocytoplasmic large DNA viruses (NCLDVs) are ubiquitous in marine environments and infect diverse eukaryotes. However, little is known about their biogeography and ecology in the ocean. By leveraging the Tara Oceans pole-to-pole metagenomic data set, we investigated the distribution of NCLDVs across size fractions, depths and biomes, as well as their associations with eukaryotic communities. Our analyses reveal a heterogeneous distribution of NCLDVs across oceans, and a higher proportion of unique NCLDVs in the polar biomes. The community structures of NCLDV families correlate with specific eukaryotic lineages, including many photosynthetic groups. NCLDV communities are generally distinct between surface and mesopelagic zones, but at some locations they exhibit a high similarity between the two depths. This vertical similarity correlates to surface phytoplankton biomass but not to physical mixing processes, which suggests a potential role of vertical transport in structuring mesopelagic NCLDV communities. These results underscore the importance of the interactions between NCLDVs and eukaryotes in biogeochemical processes in the ocean.


Assuntos
Vírus Gigantes , Vírus de DNA , Eucariotos , Vírus Gigantes/genética , Humanos , Oceanos e Mares , Filogenia
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