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Viruses Jan 2020DNA viruses that replicate in the nucleus encompass a range of ubiquitous and clinically important viruses, from acute pathogens to persistent tumor viruses. These... (Review)
Review
DNA viruses that replicate in the nucleus encompass a range of ubiquitous and clinically important viruses, from acute pathogens to persistent tumor viruses. These viruses must co-opt nuclear processes for the benefit of the virus, whilst evading host processes that would otherwise attenuate viral replication. Accordingly, DNA viruses induce the formation of membraneless assemblies termed viral replication compartments (VRCs). These compartments facilitate the spatial organization of viral processes and regulate virus-host interactions. Here, we review advances in our understanding of VRCs. We cover their initiation and formation, their function as the sites of viral processes, and aspects of their composition and organization. In doing so, we highlight ongoing and emerging areas of research highly pertinent to our understanding of nuclear-replicating DNA viruses.
Topics: Cell Nucleus; DNA Viruses; Host Microbial Interactions; Humans; Viral Proteins; Viral Replication Compartments; Virus Replication
PubMed: 32013091
DOI: 10.3390/v12020151 -
PLoS Pathogens Jun 2018Drosophila melanogaster has played a key role in our understanding of invertebrate immunity. However, both functional and evolutionary studies of host-virus interaction...
Drosophila melanogaster has played a key role in our understanding of invertebrate immunity. However, both functional and evolutionary studies of host-virus interaction in Drosophila have been limited by a dearth of native virus isolates. In particular, despite a long history of virus research, DNA viruses of D. melanogaster have only recently been described, and none have been available for experimental study. Here we report the isolation and comprehensive characterisation of Kallithea virus, a large double-stranded DNA virus, and the first DNA virus to have been reported from wild populations of D. melanogaster. We find that Kallithea virus infection is costly for adult flies, reaching high titres in both sexes and disproportionately reducing survival in males, and movement and late fecundity in females. Using the Drosophila Genetic Reference Panel, we quantify host genetic variance for virus-induced mortality and viral titre and identify candidate host genes that may underlie this variation, including Cdc42-interacting protein 4. Using full transcriptome sequencing of infected males and females, we examine the transcriptional response of flies to Kallithea virus infection and describe differential regulation of virus-responsive genes. This work establishes Kallithea virus as a new tractable model to study the natural interaction between D. melanogaster and DNA viruses, and we hope it will serve as a basis for future studies of immune responses to DNA viruses in insects.
Topics: Animals; Biological Evolution; DNA Virus Infections; DNA Viruses; Drosophila melanogaster; Female; Genetic Variation; Host-Pathogen Interactions; Male; Symbiosis; Viral Proteins; Virus Replication; Wolbachia
PubMed: 29864164
DOI: 10.1371/journal.ppat.1007050 -
The Journal of General Virology Sep 2020is a family of icosahedral, internal membrane-containing bacterial viruses with circular, single-stranded DNA genomes. The family includes the genus, , with the...
is a family of icosahedral, internal membrane-containing bacterial viruses with circular, single-stranded DNA genomes. The family includes the genus, , with the species, . Flavobacterium phage FLiP was isolated with its Gram-negative host bacterium from a boreal freshwater habitat in Central Finland in 2010. It is the first described single-stranded DNA virus with an internal membrane and shares minimal sequence similarity with other known viruses. The virion organization (pseudo =21 ) and major capsid protein fold (double-β-barrel) resemble those of Pseudoalteromonas phage PM2 (family ), which has a double-stranded DNA genome. A similar major capsid protein fold is also found in other double-stranded DNA viruses in the kingdom . This is a summary of the International Committee on Taxonomy of Viruses (ICTV) report on the family , which is available at ictv.global/report/finnlakeviridae.
Topics: Bacteriolysis; Bacteriophages; DNA Viruses; DNA, Single-Stranded; DNA, Viral; Flavobacterium; Genome, Viral; Virion; Virus Replication
PubMed: 32840474
DOI: 10.1099/jgv.0.001488 -
Seminars in Immunology Sep 1990With present technology, nearly any DNA virus can be employed as an expression vector. The characteristics of such vectors are diverse and depend on the intrinsic... (Review)
Review
With present technology, nearly any DNA virus can be employed as an expression vector. The characteristics of such vectors are diverse and depend on the intrinsic biological properties of the parental virus. With some vectors, construction of recombinant viruses is straightforward and expression is routinely obtained. Thus far, the greatest uses of virus vectors have been for determination of the targets of humoral and cell mediated immunity, experimental animal protection studies, protein production in cultured cells, and analysis of protein function and processing. Some recombinant virus vectors are being tested as candidate live vaccines for medical and veterinary purposes; the products of others are being evaluated as subunit vaccines.
Topics: Animals; DNA Viruses; Gene Expression Regulation, Viral; Genetic Vectors; Humans; Immunity, Cellular; Immunotherapy, Active; Recombinant Fusion Proteins; Vaccines, Synthetic
PubMed: 2134016
DOI: No ID Found -
Reviews in Medical Virology 1999In the same way as other viral functions, the transcription of viral genes is frequently controlled by cellular regulatory proteins either acting alone or together with... (Review)
Review
In the same way as other viral functions, the transcription of viral genes is frequently controlled by cellular regulatory proteins either acting alone or together with virally encoded factors. In this review, I discuss three examples of such regulation in different types of DNA viruses by different members of the POU family of transcription factors, all of which involve viruses which play a role in the aetiology of specific human diseases. These are the glial cell-specific transcription of JC virus which is controlled by the glial cell specific POU factor Tst-1; the regulation of human papillomavirus gene expression in the cervix by positively and negatively acting POU factors and the manner in which the balance between lytic or latent infection with HSV is controlled by positively and negatively acting POU factors which differ in their ability to interact with the virally encoded transactivator VP16. As well as being of interest in themselves, these processes may offer a therapeutic target for controlling the diseases caused by these very different viruses.
Topics: Amino Acid Sequence; DNA Viruses; DNA-Binding Proteins; Gene Expression Regulation, Viral; Humans; JC Virus; Molecular Sequence Data; POU Domain Factors; Papillomaviridae; Simplexvirus; Transcription Factors; Transcription, Genetic
PubMed: 10371670
DOI: 10.1002/(sici)1099-1654(199901/03)9:1<31::aid-rmv231>3.0.co;2-2 -
Viruses Dec 2022Hibiscus ( spp., family Malvaceae) leaves exhibiting symptoms of mosaic, ringspot, and chlorotic spots were collected in 2020 on Oahu, HI. High-throughput sequencing...
Hibiscus ( spp., family Malvaceae) leaves exhibiting symptoms of mosaic, ringspot, and chlorotic spots were collected in 2020 on Oahu, HI. High-throughput sequencing analysis was conducted on ribosomal RNA-depleted composite RNA samples extracted from symptomatic leaves. About 77 million paired-end reads and 161,970 contigs were generated after quality control, trimming, and de novo assembly. Contig annotation with BLASTX/BLASTN searches revealed a sequence (contig 1) resembling the RNA virus, hibiscus chlorotic ringspot virus (genus ), and one (contig 2) resembling the DNA virus, peanut chlorotic streak virus (genus ). Further bioinformatic analyses of the complete viral genome sequences indicated that these viruses, with proposed names of hibiscus betacarmovirus and hibiscus soymovirus, putatively represent new species in the genera and , respectively. RT-PCR using specific primers, designed based on the retrieved contigs, coupled with Sanger sequencing, further confirmed the presence of these viruses. An additional 54 hibiscus leaf samples from other locations on Oahu were examined to determine the incidence and distribution of these viruses.
Topics: Caulimoviridae; Hibiscus; Hawaii; DNA Viruses; RNA Viruses
PubMed: 36680129
DOI: 10.3390/v15010090 -
Marine Genomics Feb 2022Promoters are key elements for the regulation of gene expression. Recently, we investigated the activity of promoters derived from marine diatom-infecting viruses (DIVs)...
Promoters are key elements for the regulation of gene expression. Recently, we investigated the activity of promoters derived from marine diatom-infecting viruses (DIVs) in marine diatoms. Previously, we focused on potential promoter regions of the replication-associated protein gene and the capsid protein gene of the DIVs. In addition to these genes, two genes of unknown function (VP1 and VP4 genes) have been found in the DIV genomes. In this study, the promoter regions of the VP1 gene and VP4 gene derived from a Chaetoceros lorenzianus-infecting DNA virus (named ClP3 and ClP4, respectively) were newly isolated. ClP4 was found to be a constitutive promoter and displayed the highest activity. In particular, the 3' region of ClP4 (ClP4 3' region) showed a higher promoter activity than full-length ClP4. The ClP4 3' region might involve high-level promoter activity of ClP4. In addition, the ClP4 3' region may be useful for substance production and metabolic engineering of diatoms.
Topics: DNA Viruses; Diatoms; Open Reading Frames; Promoter Regions, Genetic
PubMed: 35030498
DOI: 10.1016/j.margen.2021.100921 -
Viruses Jan 2020The Sonoran Desert tortoise is adapted to the desert, and plays an important ecological role in this environment. There is limited information on the viral diversity...
The Sonoran Desert tortoise is adapted to the desert, and plays an important ecological role in this environment. There is limited information on the viral diversity associated with tortoises (family Testudinidae), and to date no DNA virus has been identified associated with these animals. This study aimed to assess the diversity of DNA viruses associated with the Sonoran Desert tortoise by sampling their fecal matter. A viral metagenomics approach was used to identify the DNA viruses in fecal samples from wild Sonoran Desert tortoises in Arizona, USA. In total, 156 novel single-stranded DNA viruses were identified from 40 fecal samples. Those belonged to two known viral families, the ( = 27) and ( = 119). In addition, 10 genomes were recovered that belong to the unclassified group of circular-replication associated protein encoding single-stranded (CRESS) DNA virus and five circular molecules encoding viral-like proteins.
Topics: Animals; Arizona; DNA Viruses; DNA, Circular; DNA, Single-Stranded; Feces; Genome, Viral; Microviridae; Microvirus; Phylogeny; Recombination, Genetic; Turtles; Viral Proteins
PubMed: 31991902
DOI: 10.3390/v12020143 -
MSphere Apr 2021Nucleocytoplasmic large DNA viruses (NCLDVs) are highly diverse and abundant in marine environments. However, the knowledge of their hosts is limited because only a few...
Nucleocytoplasmic large DNA viruses (NCLDVs) are highly diverse and abundant in marine environments. However, the knowledge of their hosts is limited because only a few NCLDVs have been isolated so far. Taking advantage of the recent large-scale marine metagenomics census, host prediction approaches are expected to fill the gap and further expand our knowledge of virus-host relationships for unknown NCLDVs. In this study, we built co-occurrence networks of NCLDVs and eukaryotic taxa to predict virus-host interactions using Oceans sequencing data. Using the positive likelihood ratio to assess the performance of host prediction for NCLDVs, we benchmarked several co-occurrence approaches and demonstrated an increase in the odds ratio of predicting true positive relationships 4-fold compared to random host predictions. To further refine host predictions from high-dimensional co-occurrence networks, we developed a phylogeny-informed filtering method, Taxon Interaction Mapper, and showed it further improved the prediction performance by 12-fold. Finally, we inferred virophage-NCLDV networks to corroborate that co-occurrence approaches are effective for predicting interacting partners of NCLDVs in marine environments. NCLDVs can infect a wide range of eukaryotes, although their life cycle is less dependent on hosts compared to other viruses. However, our understanding of NCLDV-host systems is highly limited because few of these viruses have been isolated so far. Co-occurrence information has been assumed to be useful to predict virus-host interactions. In this study, we quantitatively show the effectiveness of co-occurrence inference for NCLDV host prediction. We also improve the prediction performance with a phylogeny-guided method, which leads to a concise list of candidate host lineages for three NCLDV families. Our results underpin the usage of co-occurrence approaches for the metagenomic exploration of the ecology of this diverse group of viruses.
Topics: DNA Viruses; Genome, Viral; Host Microbial Interactions; Humans; Metagenomics; Phylogeny
PubMed: 33883262
DOI: 10.1128/mSphere.01298-20 -
Journal of Invertebrate Pathology Jul 2017In this review we provide an overview of the diversity of large DNA viruses known to be pathogenic for invertebrates. We present their taxonomical classification and... (Review)
Review
In this review we provide an overview of the diversity of large DNA viruses known to be pathogenic for invertebrates. We present their taxonomical classification and describe the evolutionary relationships among various groups of invertebrate-infecting viruses. We also indicate the relationships of the invertebrate viruses to viruses infecting mammals or other vertebrates. The shared characteristics of the viruses within the various families are described, including the structure of the virus particle, genome properties, and gene expression strategies. Finally, we explain the transmission and mode of infection of the most important viruses in these families and indicate, which orders of invertebrates are susceptible to these pathogens.
Topics: Animals; DNA Virus Infections; DNA Viruses; Disease Susceptibility; Genetic Variation; Genome, Viral; Invertebrates
PubMed: 27592378
DOI: 10.1016/j.jip.2016.08.001