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  1 / 23 MEDLINE  
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[PMID]:28759330
[Au] Autor:Colson P; La Scola B; Raoult D
[Ad] Endereço:Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), Aix Marseille Université, UM63, CNRS 7278, IRD 198, INSERM 1095, Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille (AP-HM), 13005 Marseille, France; email: didier.raoult@gmail.com.
[Ti] Título:Giant Viruses of Amoebae: A Journey Through Innovative Research and Paradigm Changes.
[So] Source:Annu Rev Virol;4(1):61-85, 2017 Sep 29.
[Is] ISSN:2327-0578
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Giant viruses of amoebae were discovered serendipitously in 2003; they are visible via optical microscopy, making them bona fide microbes. Their lifestyle, structure, and genomes break the mold of classical viruses. Giant viruses of amoebae are complex microorganisms. Their genomes harbor between 444 and 2,544 genes, including many that are unique to viruses, and encode translation components; their virions contain >100 proteins as well as mRNAs. Mimiviruses have a specific mobilome, including virophages, provirophages, and transpovirons, and can resist virophages through a system known as MIMIVIRE (mimivirus virophage resistance element). Giant viruses of amoebae bring upheaval to the definition of viruses and tend to separate the current virosphere into two categories: very simple viruses and viruses with complexity similar to that of other microbes. This new paradigm is propitious for enhanced detection and characterization of giant viruses of amoebae, and a particular focus on their role in humans is warranted.
[Mh] Termos MeSH primário: Amoeba/virologia
Genoma Viral
Vírus Gigantes/genética
Vírus Gigantes/fisiologia
[Mh] Termos MeSH secundário: DNA Viral
Vírus Gigantes/classificação
Vírus Gigantes/isolamento & purificação
Interações Hospedeiro-Patógeno
Mimiviridae/genética
Filogenia
Vírion/genética
Virófagos/genética
Virófagos/fisiologia
[Pt] Tipo de publicação:JOURNAL ARTICLE; REVIEW
[Nm] Nome de substância:
0 (DNA, Viral)
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171027
[Lr] Data última revisão:
171027
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170801
[St] Status:MEDLINE
[do] DOI:10.1146/annurev-virology-101416-041816


  2 / 23 MEDLINE  
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[PMID]:28525571
[Au] Autor:Mueller L; Bertelli C; Pillonel T; Salamin N; Greub G
[Ad] Endereço:Center for Research on Intracellular Bacteria (CRIB), Institute of Microbiology, Lausanne University Hospital, and University of Lausanne, Switzerland.
[Ti] Título:One Year Genome Evolution of Lausannevirus in Allopatric versus Sympatric Conditions.
[So] Source:Genome Biol Evol;9(6):1432-1449, 2017 Jun 01.
[Is] ISSN:1759-6653
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo: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.
[Mh] Termos MeSH primário: Acanthamoeba castellanii/virologia
Evolução Molecular
Especiação Genética
Genoma Viral
Vírus Gigantes/genética
[Mh] Termos MeSH secundário: Evolução Biológica
Vírus Gigantes/classificação
Mutação
Sistema Fosfotransferase de Açúcar do Fosfoenolpiruvato/genética
Fosfotransferases (Aceptor do Grupo Nitrogenado)/genética
Filogenia
Análise de Sequência de DNA
Simpatria
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
EC 2.7.1.- (Phosphoenolpyruvate Sugar Phosphotransferase System); EC 2.7.3.- (Phosphotransferases (Nitrogenous Group Acceptor)); EC 2.7.3.9 (phosphoenolpyruvate-protein phosphotransferase)
[Em] Mês de entrada:1711
[Cu] Atualização por classe:171101
[Lr] Data última revisão:
171101
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170520
[St] Status:MEDLINE
[do] DOI:10.1093/gbe/evx074


  3 / 23 MEDLINE  
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[PMID]:28496163
[Au] Autor:Heinz E; Domman D
[Ad] Endereço:Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
[Ti] Título:Reshaping the tree of life.
[So] Source:Nat Rev Microbiol;15(6):322, 2017 May 12.
[Is] ISSN:1740-1534
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:This month's Genome Watch highlights how metagenomics is continuing to reveal the diversity of microorganisms in the environment and how it is challenging and expanding our understanding of how life evolved on Earth.
[Mh] Termos MeSH primário: Archaea/classificação
Bactérias/classificação
Evolução Biológica
Eucariotos/classificação
Evolução Molecular
Vírus Gigantes/classificação
[Mh] Termos MeSH secundário: Archaea/genética
Bactérias/genética
Eucariotos/genética
Vírus Gigantes/genética
Metagenômica
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Em] Mês de entrada:1705
[Cu] Atualização por classe:170523
[Lr] Data última revisão:
170523
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170513
[St] Status:MEDLINE
[do] DOI:10.1038/nrmicro.2017.51


  4 / 23 MEDLINE  
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[PMID]:28387730
[Au] Autor:Jain S; Panda A; Colson P; Raoult D; Pontarotti P
[Ad] Endereço:Aix-Marseille Université, Ecole Centrale de Marseille, I2M UMR 7373, CNRS équipe Evolution Biologique et Modélisation, 13284 Marseille, France. sourabh.jain@etu.univ-amu.fr.
[Ti] Título:MimiLook: A Phylogenetic Workflow for Detection of Gene Acquisition in Major Orthologous Groups of Megavirales.
[So] Source:Viruses;9(4), 2017 Apr 07.
[Is] ISSN:1999-4915
[Cp] País de publicação:Switzerland
[La] Idioma:eng
[Ab] Resumo:With the inclusion of new members, understanding about evolutionary mechanisms and processes by which members of the proposed order, Megavirales, have evolved has become a key area of interest. The central role of gene acquisition has been shown in previous studies. However, the major drawback in gene acquisition studies is the focus on few MV families or putative families with large variation in their genetic structure. Thus, here we have tried to develop a methodology by which we can detect horizontal gene transfers (HGTs), taking into consideration orthologous groups of distantly related Megavirale families. Here, we report an automated workflow MimiLook, prepared as a Perl command line program, that deduces orthologous groups (OGs) from ORFomes of Megavirales and constructs phylogenetic trees by performing alignment generation, alignment editing and protein-protein BLAST (BLASTP) searching across the National Center for Biotechnology Information (NCBI) non-redundant (nr) protein sequence database. Finally, this tool detects statistically validated events of gene acquisitions with the help of the T-REX algorithm by comparing individual gene tree with NCBI species tree. In between the steps, the workflow decides about handling paralogs, filtering outputs, identifying Megavirale specific OGs, detection of HGTs, along with retrieval of information about those OGs that are monophyletic with organisms from cellular domains of life. By implementing MimiLook, we noticed that nine percent of Megavirale gene families (i.e., OGs) have been acquired by HGT, 80% OGs were Megaviralespecific and eight percent were found to be sharing common ancestry with members of cellular domains (Eukaryote, Bacteria, Archaea, Phages or other viruses) and three percent were ambivalent. The results are briefly discussed to emphasize methodology. Also, MimiLook is relevant for detecting evolutionary scenarios in other targeted phyla with user defined modifications. It can be accessed at following link 10.6084/m9.figshare.4653622.
[Mh] Termos MeSH primário: Evolução Molecular
Transferência Genética Horizontal
Genes Virais
Vírus Gigantes/genética
Filogenia
[Mh] Termos MeSH secundário: Biologia Computacional/métodos
Fluxo de Trabalho
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Em] Mês de entrada:1709
[Cu] Atualização por classe:170927
[Lr] Data última revisão:
170927
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170408
[St] Status:MEDLINE


  5 / 23 MEDLINE  
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[PMID]:28304329
[Au] Autor:Wilhelm SW; Bird JT; Bonifer KS; Calfee BC; Chen T; Coy SR; Gainer PJ; Gann ER; Heatherly HT; Lee J; Liang X; Liu J; Armes AC; Moniruzzaman M; Rice JH; Stough JM; Tams RN; Williams EP; LeCleir GR
[Ad] Endereço:The Department of Microbiology, The University of Tennessee, Knoxville, TN 37996, USA. wilhelm@utk.edu.
[Ti] Título:A Student's Guide to Giant Viruses Infecting Small Eukaryotes: From Acanthamoeba to Zooxanthellae.
[So] Source:Viruses;9(3), 2017 Mar 17.
[Is] ISSN:1999-4915
[Cp] País de publicação:Switzerland
[La] Idioma:eng
[Ab] Resumo:The discovery of infectious particles that challenge conventional thoughts concerning "what is a virus" has led to the evolution a new field of study in the past decade. Here, we review knowledge and information concerning "giant viruses", with a focus not only on some of the best studied systems, but also provide an effort to illuminate systems yet to be better resolved. We conclude by demonstrating that there is an abundance of new host-virus systems that fall into this "giant" category, demonstrating that this field of inquiry presents great opportunities for future research.
[Mh] Termos MeSH primário: Eucariotos/virologia
Vírus Gigantes/isolamento & purificação
[Pt] Tipo de publicação:JOURNAL ARTICLE; REVIEW
[Em] Mês de entrada:1709
[Cu] Atualização por classe:170926
[Lr] Data última revisão:
170926
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170318
[St] Status:MEDLINE


  6 / 23 MEDLINE  
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[PMID]:28282930
[Au] Autor:Wagstaff BA; Vladu IC; Barclay JE; Schroeder DC; Malin G; Field RA
[Ad] Endereço:Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK. ben.wagstaff@live.co.uk.
[Ti] Título:Isolation and Characterization of a Double Stranded DNA Megavirus Infecting the Toxin-Producing Haptophyte Prymnesium parvum.
[So] Source:Viruses;9(3), 2017 Mar 09.
[Is] ISSN:1999-4915
[Cp] País de publicação:Switzerland
[La] Idioma:eng
[Ab] Resumo:is a toxin-producing haptophyte that causes harmful algal blooms globally, leading to large-scale fish kills that have severe ecological and economic implications. For the model haptophyte, , it has been shown that large dsDNA viruses play an important role in regulating blooms and therefore biogeochemical cycling, but much less work has been done looking at viruses that infect , or the role that these viruses may play in regulating harmful algal blooms. In this study, we report the isolation and characterization of a lytic nucleo-cytoplasmic large DNA virus (NCLDV) collected from the site of a harmful bloom. In subsequent experiments, this virus was shown to infect cultures of sp. and showed phylogenetic similarity to the extended family of algal viruses.
[Mh] Termos MeSH primário: DNA Viral/genética
DNA/genética
Vírus Gigantes/classificação
Vírus Gigantes/isolamento & purificação
Haptófitas/virologia
[Mh] Termos MeSH secundário: Vírus Gigantes/genética
Filogenia
Análise de Sequência de DNA
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (DNA, Viral); 9007-49-2 (DNA)
[Em] Mês de entrada:1709
[Cu] Atualização por classe:170926
[Lr] Data última revisão:
170926
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170312
[St] Status:MEDLINE


  7 / 23 MEDLINE  
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[PMID]:28247094
[Au] Autor:Kerepesi C; Grolmusz V
[Ad] Endereço:PIT Bioinformatics Group, Eötvös University, Pázmány Péter stny. 1/C, Budapest, 1117, Hungary.
[Ti] Título:The "Giant Virus Finder" discovers an abundance of giant viruses in the Antarctic dry valleys.
[So] Source:Arch Virol;162(6):1671-1676, 2017 Jun.
[Is] ISSN:1432-8798
[Cp] País de publicação:Austria
[La] Idioma:eng
[Ab] Resumo:Mimivirus was identified in 2003 from a biofilm of an industrial water-cooling tower in England. Later, numerous new giant viruses were found in oceans and freshwater habitats, some of them having 2,500 genes. We have demonstrated their likely presence in four soil samples taken from the Kutch Desert (Gujarat, India). Here we describe a bioinformatics work-flow, called the "Giant Virus Finder" that is capable of discovering the likely presence of the genomes of giant viruses in metagenomic shotgun-sequenced datasets. The new workflow is applied to numerous hot and cold desert soil samples as well as some tundra- and forest soils. We show that most of these samples contain giant viruses, especially in the Antarctic dry valleys. The results imply that giant viruses could be frequent not only in aqueous habitats, but in a wide spectrum of soils on our planet.
[Mh] Termos MeSH primário: Vírus Gigantes/isolamento & purificação
Mimiviridae/isolamento & purificação
Microbiologia do Solo
[Mh] Termos MeSH secundário: Regiões Antárticas
Vírus Gigantes/classificação
Vírus Gigantes/genética
Mimiviridae/classificação
Mimiviridae/genética
Filogenia
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Em] Mês de entrada:1706
[Cu] Atualização por classe:170630
[Lr] Data última revisão:
170630
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170302
[St] Status:MEDLINE
[do] DOI:10.1007/s00705-017-3286-4


  8 / 23 MEDLINE  
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[PMID]:28239153
[Au] Autor:Colson P; La Scola B; Levasseur A; Caetano-Anollés G; Raoult D
[Ad] Endereço:Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), Aix-Marseille University, UM63, CNRS 7278, IRD 198, INSERM 1095, Institut Hospitalo-Universitaire (IHU) - Méditerranée Infection, AP-HM, 19-21 Boulevard Jean Moulin, 13385 Marseille, France.
[Ti] Título:Mimivirus: leading the way in the discovery of giant viruses of amoebae.
[So] Source:Nat Rev Microbiol;15(4):243-254, 2017 Apr.
[Is] ISSN:1740-1534
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:The accidental discovery of the giant virus of amoeba - Acanthamoeba polyphaga mimivirus (APMV; more commonly known as mimivirus) - in 2003 changed the field of virology. Viruses were previously defined by their submicroscopic size, which probably prevented the search for giant viruses, which are visible by light microscopy. Extended studies of giant viruses of amoebae revealed that they have genetic, proteomic and structural complexities that were not thought to exist among viruses and that are comparable to those of bacteria, archaea and small eukaryotes. The giant virus particles contain mRNA and more than 100 proteins, they have gene repertoires that are broader than those of other viruses and, notably, some encode translation components. The infection cycles of giant viruses of amoebae involve virus entry by amoebal phagocytosis and replication in viral factories. In addition, mimiviruses are infected by virophages, defend against them through the mimivirus virophage resistance element (MIMIVIRE) system and have a unique mobilome. Overall, giant viruses of amoebae, including mimiviruses, marseilleviruses, pandoraviruses, pithoviruses, faustoviruses and molliviruses, challenge the definition and classification of viruses, and have increasingly been detected in humans.
[Mh] Termos MeSH primário: Acanthamoeba/virologia
Amoeba/virologia
Vírus Gigantes/ultraestrutura
Mimiviridae/ultraestrutura
[Mh] Termos MeSH secundário: Genoma Viral/genética
Vírus Gigantes/genética
Vírus Gigantes/metabolismo
Mimiviridae/genética
Mimiviridae/metabolismo
Virófagos/genética
Internalização do Vírus
[Pt] Tipo de publicação:JOURNAL ARTICLE; REVIEW
[Em] Mês de entrada:1705
[Cu] Atualização por classe:170523
[Lr] Data última revisão:
170523
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170228
[St] Status:MEDLINE
[do] DOI:10.1038/nrmicro.2016.197


  9 / 23 MEDLINE  
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[PMID]:28117696
[Au] Autor:Gallot-Lavallée L; Blanc G
[Ad] Endereço:Structural and Genomic Information Laboratory (IGS), Aix-Marseille Université, CNRS UMR7256 (IMM FR3479), 13288 Marseille cedex 09, France. lucie.gallot-lavallee@igs.cnrs-mrs.fr.
[Ti] Título:A Glimpse of Nucleo-Cytoplasmic Large DNA Virus Biodiversity through the Eukaryotic Genomics Window.
[So] Source:Viruses;9(1), 2017 Jan 20.
[Is] ISSN:1999-4915
[Cp] País de publicação:Switzerland
[La] Idioma:eng
[Ab] Resumo:The nucleocytoplasmic large DNA viruses (NCLDV) are a group of extremely complex double-stranded DNA viruses, which are major parasites of a variety of eukaryotes. Recent studies showed that certain eukaryotes contain fragments of NCLDV DNA integrated in their genome, when surprisingly many of these organisms were not previously shown to be infected by NCLDVs. We performed an update survey of NCLDV genes hidden in eukaryotic sequences to measure the incidence of this phenomenon in common public sequence databases. A total of 66 eukaryotic genomic or transcriptomic datasets-many of which are from algae and aquatic protists-contained at least one of the five most consistently conserved NCLDV core genes. Phylogenetic study of the eukaryotic NCLDV-like sequences identified putative new members of already recognized viral families, as well as members of as yet unknown viral clades. Genomic evidence suggested that most of these sequences resulted from viral DNA integrations rather than contaminating viruses. Furthermore, the nature of the inserted viral genes helped predicting original functional capacities of the donor viruses. These insights confirm that genomic insertions of NCLDV DNA are common in eukaryotes and can be exploited to delineate the contours of NCLDV biodiversity.
[Mh] Termos MeSH primário: Biodiversidade
Eucariotos/genética
Eucariotos/virologia
Vírus Gigantes/classificação
Vírus Gigantes/genética
[Mh] Termos MeSH secundário: Genômica
Recombinação Genética
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Em] Mês de entrada:1709
[Cu] Atualização por classe:170926
[Lr] Data última revisão:
170926
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170125
[St] Status:MEDLINE


  10 / 23 MEDLINE  
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[PMID]:28117683
[Au] Autor:Oliveira GP; Andrade AC; Rodrigues RA; Arantes TS; Boratto PV; Silva LK; Dornas FP; Trindade GS; Drumond BP; La Scola B; Kroon EG; Abrahão JS
[Ad] Endereço:Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Minas Gerais, Brazil. graziufmg@yahoo.com.br.
[Ti] Título:Promoter Motifs in NCLDVs: An Evolutionary Perspective.
[So] Source:Viruses;9(1), 2017 Jan 20.
[Is] ISSN:1999-4915
[Cp] País de publicação:Switzerland
[La] Idioma:eng
[Ab] Resumo:For many years, gene expression in the three cellular domains has been studied in an attempt to discover sequences associated with the regulation of the transcription process. Some specific transcriptional features were described in viruses, although few studies have been devoted to understanding the evolutionary aspects related to the spread of promoter motifs through related viral families. The discovery of giant viruses and the proposition of the new viral order Megavirales that comprise a monophyletic group, named nucleo-cytoplasmic large DNA viruses (NCLDV), raised new questions in the field. Some putative promoter sequences have already been described for some NCLDV members, bringing new insights into the evolutionary history of these complex microorganisms. In this review, we summarize the main aspects of the transcription regulation process in the three domains of life, followed by a systematic description of what is currently known about promoter regions in several NCLDVs. We also discuss how the analysis of the promoter sequences could bring new ideas about the giant viruses' evolution. Finally, considering a possible common ancestor for the NCLDV group, we discussed possible promoters' evolutionary scenarios and propose the term "MEGA-box" to designate an ancestor promoter motif ('TATATAAAATTGA') that could be evolved gradually by nucleotides' gain and loss and point mutations.
[Mh] Termos MeSH primário: Vírus Gigantes/genética
Regiões Promotoras Genéticas
Transcrição Genética
[Pt] Tipo de publicação:JOURNAL ARTICLE; REVIEW
[Em] Mês de entrada:1709
[Cu] Atualização por classe:170926
[Lr] Data última revisão:
170926
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170125
[St] Status:MEDLINE



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