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1.
Int J Mol Sci ; 22(12)2021 Jun 08.
Artigo em Inglês | MEDLINE | ID: mdl-34201359

RESUMO

Red pepper (Capsicum annuum, L.), is one of the most important spice plants in Korea. Overwintering pepper fruits are a reservoir of various microbial pepper diseases. Here, we conducted metagenomics (DNA sequencing) and metatranscriptomics (RNA sequencing) using samples collected from three different fields. We compared two different library types and three different analytical methods for the identification of microbiomes in overwintering pepper fruits. Our results demonstrated that DNA sequencing might be useful for the identification of bacteria and DNA viruses such as bacteriophages, while mRNA sequencing might be beneficial for the identification of fungi and RNA viruses. Among three analytical methods, KRAKEN2 with raw data reads (KRAKEN2_R) might be superior for the identification of microbial species to other analytical methods. However, some microbial species with a low number of reads were wrongly assigned at the species level by KRAKEN2_R. Moreover, we found that the databases for bacteria and viruses were better established as compared to the fungal database with limited genome data. In summary, we carefully suggest that different library types and analytical methods with proper databases should be applied for the purpose of microbiome study.


Assuntos
Bactérias/genética , Capsicum/genética , Vírus de DNA/genética , Frutas/crescimento & desenvolvimento , Metagenoma , Vírus de RNA/genética , Transcriptoma , Bactérias/classificação , Capsicum/microbiologia , Capsicum/virologia , Vírus de DNA/classificação , Frutas/microbiologia , Frutas/virologia , Vírus de RNA/classificação , Estações do Ano
2.
Viruses ; 13(7)2021 06 27.
Artigo em Inglês | MEDLINE | ID: mdl-34199077

RESUMO

Many viruses, especially RNA viruses, utilize programmed ribosomal frameshifting and/or stop codon readthrough in their expression, and in the decoding of a few a UGA is dynamically redefined to specify selenocysteine. This recoding can effectively increase viral coding capacity and generate a set ratio of products with the same N-terminal domain(s) but different C-terminal domains. Recoding can also be regulatory or generate a product with the non-universal 21st directly encoded amino acid. Selection for translation speed in the expression of many viruses at the expense of fidelity creates host immune defensive opportunities. In contrast to host opportunism, certain viruses, including some persistent viruses, utilize recoding or adventitious frameshifting as part of their strategy to evade an immune response or specific drugs. Several instances of recoding in small intensively studied viruses escaped detection for many years and their identification resolved dilemmas. The fundamental importance of ribosome ratcheting is consistent with the initial strong view of invariant triplet decoding which however did not foresee the possibility of transitory anticodon:codon dissociation. Deep level dynamics and structural understanding of recoding is underway, and a high level structure relevant to the frameshifting required for expression of the SARS CoV-2 genome has just been determined.


Assuntos
Vírus de DNA/genética , Vírus de DNA/imunologia , Antígenos de Histocompatibilidade Classe I/imunologia , Evasão da Resposta Imune , Vírus de RNA/genética , Antivirais/farmacologia , Códon de Terminação , Vírus de DNA/efeitos dos fármacos , Mudança da Fase de Leitura do Gene Ribossômico , Antígenos de Histocompatibilidade Classe I/genética , Conformação de Ácido Nucleico , Peptídeos/imunologia , Biossíntese de Proteínas , Vírus de RNA/efeitos dos fármacos , Vírus de RNA/imunologia
3.
Arch Virol ; 166(7): 2041-2044, 2021 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-33900469

RESUMO

High-throughput sequencing (HTS) was used to construct the virome profile of an old grapevine-leafroll-diseased grapevine (Vitis vinifera). De novo assembly of HTS data showed a complex infection, including a virus sequence with similarity to viruses of the genus Badnavirus, family Caulimoviridae. The complete genome sequence of this virus consists of 7090 nucleotides and has four open reading frames (ORFs). Genome organisation and phylogenetic analysis identify this virus as a divergent variant of grapevine Roditis leaf discoloration-associated virus (GRLDaV) with 90% nucleotide sequence identity to isolate w4 (NC_027131). This is the first genome sequence of a South African variant of GRLDaV.


Assuntos
Badnavirus/genética , Genoma Viral/genética , Doenças das Plantas/virologia , Folhas de Planta/virologia , Vitis/virologia , Vírus de DNA/genética , DNA Viral/genética , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Fases de Leitura Aberta/genética , Filogenia , Análise de Sequência de DNA/métodos , África do Sul , Sequenciamento Completo do Genoma/métodos
4.
Nat Struct Mol Biol ; 28(5): 413-417, 2021 05.
Artigo em Inglês | MEDLINE | ID: mdl-33927388

RESUMO

Certain large DNA viruses, including those in the Marseilleviridae family, encode histones. Here we show that fused histone pairs Hß-Hα and Hδ-Hγ from Marseillevirus are structurally analogous to the eukaryotic histone pairs H2B-H2A and H4-H3. These viral histones form 'forced' heterodimers, and a heterotetramer of four such heterodimers assembles DNA to form structures virtually identical to canonical eukaryotic nucleosomes.


Assuntos
Vírus de DNA , DNA , Nucleossomos/metabolismo , DNA/química , DNA/metabolismo , Vírus de DNA/genética , Vírus de DNA/metabolismo , Histonas/química , Histonas/metabolismo , Ligação Proteica , Elementos Estruturais de Proteínas , Estrutura Terciária de Proteína
5.
Arch Virol ; 166(6): 1533-1545, 2021 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-33683476

RESUMO

Beekeeping is a widespread activity in Argentina, mainly producing honey that has gained both national and international recognition. There are more than 3,000,000 hives in the country, mainly concentrated in Buenos Aires Province (approximately 1,000,000 hives). In recent decades, worrying rates of hive loss have been observed in many countries around the world. In Latin America, the estimated loss of hives is between 13% (Peru and Ecuador) and 53% (Chile). Argentina had annual losses of 34% for the period of October 1, 2016 to October 1, 2017. The causes of these losses are not clear but probably involve multiple stressors that can act simultaneously. One of the main causes of loss of bee colonies worldwide is infestation by the ectoparasitic mite Varroa destructor in combination with viral infections. To date, 10 viruses have been detected that affect honey bees (Apis mellifera) in Argentina. Of these, deformed wing virus, sacbrood virus, acute bee paralysis virus, chronic bee paralysis virus, and Israeli acute bee paralysis can be transmitted by mites. Deformed wing virus and the AIK complex are the viruses most often associated with loss of hives worldwide. Considering that bee viruses have been detected in Argentina in several hymenopteran and non-hymenopteran insects, these hosts could act as important natural reservoirs for viruses and play an important role in their dispersal in the environment. Further studies to investigate the different mechanisms by which viruses spread in the environment will enable us to develop various strategies for the control of infected colonies and the spread of viruses in the habitat where they are found.


Assuntos
Abelhas/virologia , Animais , Argentina , Vírus de DNA/genética , Vírus de DNA/isolamento & purificação , Interações Hospedeiro-Patógeno , Vírus de RNA/genética , Vírus de RNA/isolamento & purificação
6.
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
7.
Microbiome ; 9(1): 37, 2021 02 01.
Artigo em Inglês | MEDLINE | ID: mdl-33522966

RESUMO

BACKGROUND: Viruses are a significant player in many biosphere and human ecosystems, but most signals remain "hidden" in metagenomic/metatranscriptomic sequence datasets due to the lack of universal gene markers, database representatives, and insufficiently advanced identification tools. RESULTS: Here, we introduce VirSorter2, a DNA and RNA virus identification tool that leverages genome-informed database advances across a collection of customized automatic classifiers to improve the accuracy and range of virus sequence detection. When benchmarked against genomes from both isolated and uncultivated viruses, VirSorter2 uniquely performed consistently with high accuracy (F1-score > 0.8) across viral diversity, while all other tools under-detected viruses outside of the group most represented in reference databases (i.e., those in the order Caudovirales). Among the tools evaluated, VirSorter2 was also uniquely able to minimize errors associated with atypical cellular sequences including eukaryotic genomes and plasmids. Finally, as the virosphere exploration unravels novel viral sequences, VirSorter2's modular design makes it inherently able to expand to new types of viruses via the design of new classifiers to maintain maximal sensitivity and specificity. CONCLUSION: With multi-classifier and modular design, VirSorter2 demonstrates higher overall accuracy across major viral groups and will advance our knowledge of virus evolution, diversity, and virus-microbe interaction in various ecosystems. Source code of VirSorter2 is freely available ( https://bitbucket.org/MAVERICLab/virsorter2 ), and VirSorter2 is also available both on bioconda and as an iVirus app on CyVerse ( https://de.cyverse.org/de ). Video abstract.


Assuntos
Vírus de DNA/classificação , Genoma Viral/genética , Metagenômica , Vírus de RNA/classificação , Software , Vírus de DNA/genética , Ecossistema , Humanos , Vírus de RNA/genética
8.
Res Vet Sci ; 136: 1-5, 2021 May.
Artigo em Inglês | MEDLINE | ID: mdl-33548686

RESUMO

The laboratory mouse strain C57BL/6 is widely used as an animal model for various applications. It is becoming increasingly clear that the bacterial enteric community highly influences the phenotype. Eukaryotic viruses represent a sparsely investigated member of the enteric microbiome that might also affect the phenotype. We here investigated the presence of enteric eukaryotic DNA viruses (EDVs) in specific pathogen-free (SPF) C57BL/6N mice purchased from three vendors upon arrival and after being fed a low-fat diet (LFD) or high-fat diet (HFD). We detected genetic fragments of EDVs belonging to the viral families of Herpes-, Mimi-, Baculo- and Phycodnaviridae represented by two genera; Chlorovirus and Prasinovirus. The EDVs were detected in the mice upon arrival and persisted for 13 weeks. However, these signals of EDVs were only detected at notable levels in mice fed LFD from 2 out of 3 vendors, which suggested that the enteric composition of these EDVs were affected by both vendor (p < 0.003) and different dietary regimes (p < 0.013). This highlights the need of additional studies assessing the potential function of these EDVs that may influence the mouse phenotype and the reproducibility of animal studies using this C57BL/6N substrain.


Assuntos
Vírus de DNA/isolamento & purificação , Microbioma Gastrointestinal , Camundongos Endogâmicos C57BL/virologia , Animais , Vírus de DNA/genética , Dieta Hiperlipídica , Camundongos , Fenótipo , Reprodutibilidade dos Testes , Organismos Livres de Patógenos Específicos
9.
Microbes Environ ; 36(1)2021.
Artigo em Inglês | MEDLINE | ID: mdl-33612562

RESUMO

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.


Assuntos
Vírus de DNA/classificação , Galactose/metabolismo , Acanthamoeba/virologia , Vírus de DNA/genética , Vírus de DNA/isolamento & purificação , Vírus de DNA/metabolismo , Água Doce/virologia , Japão , Filogenia
10.
Arch Virol ; 166(2): 613-617, 2021 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-33389103

RESUMO

To investigate the viral communities in diarrhoeal faeces of Tibetan pigs, 146 diarrhoeic samples were collected from 16 pigs farms on the Tibetan plateau. Nineteen viruses belonging to eleven viral taxonomic families were identified in a pooled library. Metagenomics analysis revealed that the viruses were mainly small linear and circular DNA viruses. Furthermore, sequences of 10 NS1 genes and two complete genomes of PBuVs were obtained by PCR amplification. Sequence comparisons and phylogenetic analysis showed that the PBuVs from Tibetan pigs displayed more abundant genetic diversity than those from domestic pigs. This is the first description of the faecal viral community in Tibetan pigs associated with diarrhoea.


Assuntos
Vírus de DNA/genética , Diarreia/virologia , Variação Genética/genética , Sus scrofa/virologia , Doenças dos Suínos/virologia , Animais , China , Fezes/virologia , Genoma Viral/genética , Metagenômica/métodos , Filogenia , Suínos , Tibet
11.
Microbiome ; 9(1): 13, 2021 01 12.
Artigo em Inglês | MEDLINE | ID: mdl-33436089

RESUMO

BACKGROUND: Polintons are large mobile genetic elements found in the genomes of eukaryotic organisms that are considered the ancient ancestors of most eukaryotic dsDNA viruses. Originally considered as transposons, they have been found to encode virus capsid genes, suggesting they may actually be integrated viruses; however, an extracellular form has yet to be detected. Recently, circa 25 Polinton-like viruses have been discovered in environmental metagenomes and algal genomes, which shared distantly related genes to both Polintons and virophages (Lavidaviridae). These entities could be the first members of a major class of ancient eukaryotic viruses; however, owing to the lack of available genomes for analysis, information on their global diversity, evolutionary relationships, eukaryotic hosts, and status as free virus particles is limited. RESULTS: Here, we analysed the metaviromes of an alpine lake to show that Polinton-like virus genome sequences are abundant in the water column. We identify major capsid protein genes belonging to 82 new Polinton-like viruses and use these to interrogate publicly available metagenomic datasets, identifying 543 genomes and a further 16 integrated into eukaryotic genomes. Using an analysis of shared gene content and major capsid protein phylogeny, we define large groups of Polinton-like viruses and link them to diverse eukaryotic hosts, including a new group of viruses, which possess all the core genes of virophages and infect oomycetes and Chrysophyceae. CONCLUSIONS: Our study increased the number of known Polinton-like viruses by 25-fold, identifying five major new groups of eukaryotic viruses, which until now have been hidden in metagenomic datasets. The large enrichment (> 100-fold) of Polinton-like virus sequences in the virus-sized fraction of this alpine lake and the fact that their viral major capsid proteins are found in eukaryotic host transcriptomes support the hypothesis that Polintons in unicellular eukaryotes are viruses. In summary, our data reveals a diverse assemblage of globally distributed viruses, associated with a wide range of unicellular eukaryotic hosts. We anticipate that the methods we have developed for Polinton-like virus detection and the database of over 20,000 genes we present will allow for continued discovery and analysis of these new viral groups. Video abstract.


Assuntos
Organismos Aquáticos/genética , Organismos Aquáticos/virologia , Vírus de DNA/genética , Eucariotos/genética , Eucariotos/virologia , Genoma Viral/genética , Lagos , Vírus de DNA/classificação , DNA Viral/genética , Ecossistema , Filogenia , Virófagos/genética , Integração Viral/genética
12.
Transbound Emerg Dis ; 68(2): 289-295, 2021 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-32657534

RESUMO

In this study, we detected a circular replication-associated protein (Rep)-encoding single-stranded (CRESS) DNA virus (named Po-Circo-like (PCL) virus) in intestinal tissue samples of pigs, and the complete genome sequences of three strains (named PCL viruses GX14, GX15 and GX19) were obtained. Unlike PCL virus strains 21 and 22, whose genome sequences have 3,912 and 3,923 nucleotides (nt), respectively, the strains revealed in this study have a circular genome with 3,944 nt and five major open reading frames (ORFs). Among these ORFs, ORF1 encodes the Rep and not the typical capsid protein encoded in PCV. Furthermore, the strains in this study share 79.2%-96.0% nucleic acid identity and 83.0%-98.1% amino acid identity with ORF1 of the reference strains. Moreover, the Rep of the PCL virus in this study shared 19.9%-22.2% (<30%) identity of its amino acid sequence with PCV but shared 34.9%-94.8% (>30%) identity of its amino acid sequence with sequences of five proteins that are expressed by the family Kirkoviridae. [Correction added on 24 December 2020 after first online publication: The preceding sentence has been corrected in this version.] Interestingly, the stem loop of the PCL virus has one nucleotide substitution, T1328G. The Bo-Circo-like CH strain shares high nucleic acid and amino acid similarity (>80%) with the PCL virus. Moreover, Bo-Circo-like CH and GX-19 had similar stem-loop sequences. The PCL virus might therefore be transmitted to non-porcine hosts by cross-species transmission routes. Phylogenetic analysis classified the PCL virus into the new family Kirkoviridae and indicated its close relationship with the Bo-Circo-like virus. A phylogenetic divergence analysis based on the rep gene classified all PCL virus strains into two genotypes (PCLa and PCLb). In conclusion, the present study is the first detailed report of the PCL virus, which is a potential new virus in pigs that might be involved in cross-species transmission. Further investigation is needed to determine the pathogenesis of this virus and its epidemiologic impact.


Assuntos
Infecções por Vírus de DNA/veterinária , Vírus de DNA/classificação , Vírus de DNA/genética , Diarreia/veterinária , Genoma Viral , Doenças dos Suínos/virologia , Sequência de Aminoácidos , Animais , Sequência de Bases , Proteínas do Capsídeo/genética , China , Circovirus/genética , Infecções por Vírus de DNA/virologia , Vírus de DNA/isolamento & purificação , DNA Viral/genética , Diarreia/virologia , Fases de Leitura Aberta , Filogenia , Suínos , Proteínas Virais/genética
13.
J Gen Virol ; 102(1)2021 01.
Artigo em Inglês | MEDLINE | ID: mdl-33258767

RESUMO

Viruses in the family Redondoviridae have a circular genome of 3.0 kb with three open reading frames. The packaged genome is inferred to be single-stranded DNA by analogy to related viruses. Redondoviruses were discovered through metagenomic sequencing methods in samples from human subjects and are inferred to replicate in humans. Evidence of redondovirus infection is associated with periodontitis and critical illness, but redondoviruses have not been shown to be the causative agent of any diseases. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Redondoviridae, which is available at ictv.global/report/redondoviridae.


Assuntos
Vírus de DNA/classificação , Vírus de DNA/genética , Vírus de DNA/patogenicidade , Vírus de DNA/fisiologia , DNA Circular , DNA de Cadeia Simples , DNA Viral , Genoma Viral/genética , Humanos , Metagenômica , Fases de Leitura Aberta , Replicação Viral
14.
J Gen Virol ; 102(3)2021 03.
Artigo em Inglês | MEDLINE | ID: mdl-33331812

RESUMO

Ovaliviridae is a family of enveloped viruses with a linear dsDNA genome. The virions are ellipsoidal, and contain a multi-layered spool-like capsid. The viral genome is presumably replicated through protein priming by a putative DNA polymerase encoded by the virus. Progeny virions are released through hexagonal openings resulting from the rupture of virus-associated pyramids formed on the surface of infected cells. The only known host is a hyperthermophilic archaeon of the genus Sulfolobus. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Ovaliviridae, which is available at ictv.global/report/ovaliviridae.


Assuntos
Vírus de Archaea/classificação , Vírus de Archaea/fisiologia , Vírus de DNA/classificação , Vírus de DNA/fisiologia , Vírus de Archaea/genética , Vírus de Archaea/ultraestrutura , Capsídeo/ultraestrutura , Vírus de DNA/genética , Vírus de DNA/ultraestrutura , Genoma Viral , Sulfolobus/virologia , Vírion/genética , Vírion/fisiologia , Vírion/ultraestrutura , Replicação Viral
15.
Viruses ; 13(1)2020 12 22.
Artigo em Inglês | MEDLINE | ID: mdl-33375071

RESUMO

Bats are often claimed to be a major source for future viral epidemics, as they are associated with several viruses with zoonotic potential. Here we describe the presence and biodiversity of bats associated with intensive pig farms devoted to the production of heavy pigs in northern Italy. Since chiropters or signs of their presence were not found within animal shelters in our study area, we suggest that fecal viruses with high environmental resistance have the highest likelihood for spillover through indirect transmission. In turn, we investigated the circulation of mammalian orthoreoviruses (MRVs), coronaviruses (CoVs) and astroviruses (AstVs) in pigs and bats sharing the same environment. Results of our preliminary study did not show any bat virus in pigs suggesting that spillover from these animals is rare. However, several AstVs, CoVs and MRVs circulated undetected in pigs. Among those, one MRV was a reassortant strain carrying viral genes likely acquired from bats. On the other hand, we found a swine AstV and a MRV strain carrying swine genes in bat guano, indicating that viral exchange at the bat-pig interface might occur more frequently from pigs to bats rather than the other way around. Considering the indoor farming system as the most common system in the European Union (EU), preventive measures should focus on biosecurity rather than displacement of bats, which are protected throughout the EU and provide critical ecosystem services for rural settings.


Assuntos
Quirópteros , Suínos , Animais , Biodiversidade , Quirópteros/virologia , Vírus de DNA/classificação , Vírus de DNA/genética , Ecossistema , Filogenia , Vírus de RNA/classificação , Vírus de RNA/genética , Vírus Reordenados/genética , Suínos/virologia , Doenças dos Suínos/epidemiologia , Doenças dos Suínos/transmissão , Doenças dos Suínos/virologia , Viroses/veterinária
16.
Viruses ; 12(11)2020 11 07.
Artigo em Inglês | MEDLINE | ID: mdl-33171839

RESUMO

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.


Assuntos
Vírus de DNA/genética , Genoma Viral , Filogenia , Acanthamoeba/virologia , Sequência de Bases , DNA Viral/genética , Genômica , Análise de Sequência de DNA
17.
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
18.
Int J Mol Sci ; 21(19)2020 Oct 02.
Artigo em Inglês | MEDLINE | ID: mdl-33023222

RESUMO

Recognition of the non-self signature of invading pathogens is a crucial step for the initiation of the innate immune mechanisms of the host. The host response to viral and bacterial infection involves sets of pattern recognition receptors (PRRs), which bind evolutionarily conserved pathogen structures, known as pathogen-associated molecular patterns (PAMPs). Recent advances in the identification of different types of PRRs in teleost fish revealed a number of cytosolic sensors for recognition of viral and bacterial nucleic acids. These are DExD/H-box RNA helicases including a group of well-characterized retinoic acid inducible gene I (RIG-I)-like receptors (RLRs) and non-RLR DExD/H-box RNA helicases (e.g., DDX1, DDX3, DHX9, DDX21, DHX36 and DDX41) both involved in recognition of viral RNAs. Another group of PRRs includes cytosolic DNA sensors (CDSs), such as cGAS and LSm14A involved in recognition of viral and intracellular bacterial dsDNAs. Moreover, dsRNA-sensing protein kinase R (PKR), which has a role in antiviral immune responses in higher vertebrates, has been identified in fish. Additionally, fish possess a novel PKR-like protein kinase containing Z-DNA binding domain, known as PKZ. Here, we review the current knowledge concerning cytosolic sensors for recognition of viral and bacterial nucleic acids in teleosts.


Assuntos
Bactérias/isolamento & purificação , Técnicas Biossensoriais , Ácidos Nucleicos/isolamento & purificação , Vírus/isolamento & purificação , Animais , Bactérias/patogenicidade , Citosol/microbiologia , Citosol/virologia , Vírus de DNA/genética , Vírus de DNA/isolamento & purificação , DNA Bacteriano/genética , DNA Bacteriano/isolamento & purificação , Proteínas de Ligação a DNA/química , Peixes/genética , Peixes/microbiologia , Peixes/virologia , Ácidos Nucleicos/genética , Proteínas com Motivo de Reconhecimento de RNA/química , RNA Bacteriano/genética , RNA Bacteriano/isolamento & purificação , RNA Viral/genética , RNA Viral/isolamento & purificação , Vírus/patogenicidade
19.
Elife ; 92020 10 28.
Artigo em Inglês | MEDLINE | ID: mdl-33112738

RESUMO

Hosts and viruses are constantly evolving in response to each other: as a host attempts to suppress a virus, the virus attempts to evade and suppress the host's immune system. Here, we describe the recurrent evolution of a virulent strain of a DNA virus, which infects multiple Drosophila species. Specifically, we identified two distinct viral types that differ 100-fold in viral titer in infected individuals, with similar differences observed in multiple species. Our analysis suggests that one of the viral types recurrently evolved at least four times in the past ~30,000 years, three times in Arizona and once in another geographically distinct species. This recurrent evolution may be facilitated by an effective mutation rate which increases as each prior mutation increases viral titer and effective population size. The higher titer viral type suppresses the host-immune system and an increased virulence compared to the low viral titer type.


Assuntos
Evolução Biológica , Infecções por Vírus de DNA/veterinária , Infecções por Vírus de DNA/virologia , Vírus de DNA/patogenicidade , Drosophila/virologia , Animais , Vírus de DNA/genética , Vírus de DNA/isolamento & purificação , Vírus de DNA/fisiologia , Feminino , Humanos , Masculino , Virulência
20.
NPJ Biofilms Microbiomes ; 6(1): 45, 2020 10 30.
Artigo em Inglês | MEDLINE | ID: mdl-33127920

RESUMO

Plant disease is one of the most important causes of crop losses worldwide. The effective control of plant disease is related to food security. Sclerotinia stem rot (SSR) caused by Sclerotinia sclerotiorum leads to serious yield losses in rapeseed (Brassica napus) production. Hypovirulent strain DT-8 of S. sclerotiorum, infected with Sclerotinia sclerotiorum hypovirulence-associated DNA virus 1 (SsHADV-1), has the potential to control SSR. In this study, we found rapeseed bio-priming with strain DT-8 could significantly decrease the disease severity of SSR and increase yield in the field. After bio-priming, strain DT-8 could be detected on the aerial part of the rapeseed plant. By 16S rRNA gene and internal transcribed spacer (ITS) sequencing technique, the microbiome on different parts of the SSR lesion on bioprimed and non-bioprimed rapeseed stem was determined. The results indicated that SSR and bio-priming treatment could influence the structure and composition of fungal and bacterial communities. Bio-priming treatment could reduce the total abundance of possible plant pathogens and enhance the connectivity and robustness of the interaction network at the genus level. This might be one of the mechanisms that rapeseed bioprimed with strain DT-8 had excellent tolerance on SSR. It might be another possible mechanism of biocontrol and will provide a theoretical guide for agricultural practical production.


Assuntos
Ascomicetos/genética , Bactérias/classificação , Brassica napus/microbiologia , DNA Fúngico/genética , Doenças das Plantas/prevenção & controle , Ascomicetos/classificação , Ascomicetos/patogenicidade , Bactérias/genética , Bactérias/isolamento & purificação , Brassica napus/crescimento & desenvolvimento , Produtos Agrícolas/crescimento & desenvolvimento , Produtos Agrícolas/microbiologia , Vírus de DNA/genética , DNA Bacteriano/genética , DNA Ribossômico/genética , Interações Microbianas , Filogenia , Doenças das Plantas/microbiologia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA
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