scholarly journals Genetic and functional diversity of double-stranded DNA viruses in a tropical monsoonal estuary, India

2018 ◽  
Vol 8 (1) ◽  
Author(s):  
Vijayan Jasna ◽  
Ammini Parvathi ◽  
Abhinandita Dash
Keyword(s):  
Functional Diversity ◽  
Dna Viruses ◽  
Double Stranded Dna

scholarly journals Extrachromosomal Histone H2B Mediates Innate Antiviral Immune Responses Induced by Intracellular Double-Stranded DNA

2009 ◽  
Vol 84 (2) ◽  
pp. 822-832 ◽  
Author(s):  
Kouji Kobiyama ◽  
Fumihiko Takeshita ◽  
Nao Jounai ◽  
Asako Sakaue-Sawano ◽  
Atsushi Miyawaki ◽  
...  
Keyword(s):  
Immune Responses ◽  
Rna Virus ◽  
Cellular Signaling ◽  
Helical Structure ◽  
Human Cells ◽  
Type I Interferons ◽  
Type I ◽  
Histone H2b ◽  
Dna Viruses ◽  
Double Stranded Dna

ABSTRACT Fragments of double-stranded DNA (dsDNA) forming a right-handed helical structure (B-DNA) stimulate cells to produce type I interferons (IFNs). While an adaptor molecule, IFN-β promoter stimulator 1 (IPS-1), mediates dsDNA-induced cellular signaling in human cells, the underlying molecular mechanism is not fully understood. Here, we demonstrate that the extrachromosomal histone H2B mediates innate antiviral immune responses in human cells. H2B physically interacts with IPS-1 through the association with a newly identified adaptor, CIAO (COOH-terminal importin 9-related adaptor organizing histone H2B and IPS-1), to transmit the cellular signaling for dsDNA but not immunostimulatory RNA. Extrachromosomal histone H2B was biologically crucial for cell-autonomous responses to protect against multiplication of DNA viruses but not an RNA virus. Thus, the present findings provide evidence indicating that the extrachromosomal histone H2B is engaged in the signaling pathway initiated by dsDNA to trigger antiviral innate immune responses.

scholarly journals The Fourth International Symposium on Ranaviruses: Summary of North American Herpetological Content and Points of Interest

2020 ◽  
pp. 29
Author(s):  
Lauren Ash ◽  
Rachel Marschang ◽  
Jolianne Rijks ◽  
Amanda Duffus
Keyword(s):  
North America ◽  
International Symposium ◽  
North American ◽  
Fourth International Symposium ◽  
Dna Viruses ◽  
The North ◽  
Double Stranded Dna ◽  
Points Of Interest ◽  
The Family ◽  
Globally Distributed

Ranaviruses are large double stranded DNA viruses from the family Iridoviridae. They are globally distributed and are currently known to affect fish, reptiles and amphibians. In North America, ranaviruses are also widely distributed, and cause frequent morbidity and mortality events in both wild and cultured populations. This is a synopsys of the North American content of the 4th International Symposium on Ranaviruses held in May 2017 in Budapest, Hungary.

scholarly journals Exceptionally diverse morphotypes and genomes of crenarchaeal hyperthermophilic viruses

2004 ◽  
Vol 32 (2) ◽  
pp. 204-208 ◽  
Author(s):  
D. Prangishvili ◽  
R.A. Garrett
Keyword(s):  
Aquatic Ecosystems ◽  
African Swine Fever Virus ◽  
African Swine Fever ◽  
Open Reading Frames ◽  
Dna Viruses ◽  
Double Stranded Dna ◽  
Sequence Patterns ◽  
Hydrothermal Environments ◽  
Homologous Orfs ◽  
Reading Frames

The remarkable diversity of the morphologies of viruses found in terrestrial hydrothermal environments with temperatures >80°C is unprecedented for aquatic ecosystems. The best-studied viruses from these habitats have been assigned to novel viral families: Fuselloviridae, Lipothrixviridae and Rudiviridae. They all have double-stranded DNA genomes and infect hyperthermophilic crenarchaea of the orders Sulfolobales and Thermoproteales. Representatives of the different viral families share a few homologous ORFs (open reading frames). However, about 90% of all ORFs in the seven sequenced genomes show no significant matches to sequences in public databases. This suggests that these hyperthermophilic viruses have exceptional biochemical solutions for biological functions. Specific features of genome organization, as well as strategies for DNA replication, suggest that phylogenetic relationships exist between crenarchaeal rudiviruses and the large eukaryal DNA viruses: poxviruses, the African swine fever virus and Chlorella viruses. Sequence patterns at the ends of the linear genome of the lipothrixvirus AFV1 are reminiscent of the telomeric ends of linear eukaryal chromosomes and suggest that a primitive telomeric mechanism operates in this virus.

scholarly journals Viral Mutation Rates

2010 ◽  
Vol 84 (19) ◽  
pp. 9733-9748 ◽  
Author(s):  
Rafael Sanjuán ◽  
Miguel R. Nebot ◽  
Nicola Chirico ◽  
Louis M. Mansky ◽  
Robert Belshaw
Keyword(s):  
Mutation Rate ◽  
Rna Viruses ◽  
Experimental Testing ◽  
Mutation Rates ◽  
Cell Infection ◽  
Nucleotide Substitutions ◽  
Data Set ◽  
Dna Viruses ◽  
Double Stranded Dna ◽  
Viral Mutation

ABSTRACT Accurate estimates of virus mutation rates are important to understand the evolution of the viruses and to combat them. However, methods of estimation are varied and often complex. Here, we critically review over 40 original studies and establish criteria to facilitate comparative analyses. The mutation rates of 23 viruses are presented as substitutions per nucleotide per cell infection (s/n/c) and corrected for selection bias where necessary, using a new statistical method. The resulting rates range from 10−8 to10−6 s/n/c for DNA viruses and from 10−6 to 10−4 s/n/c for RNA viruses. Similar to what has been shown previously for DNA viruses, there appears to be a negative correlation between mutation rate and genome size among RNA viruses, but this result requires further experimental testing. Contrary to some suggestions, the mutation rate of retroviruses is not lower than that of other RNA viruses. We also show that nucleotide substitutions are on average four times more common than insertions/deletions (indels). Finally, we provide estimates of the mutation rate per nucleotide per strand copying, which tends to be lower than that per cell infection because some viruses undergo several rounds of copying per cell, particularly double-stranded DNA viruses. A regularly updated virus mutation rate data set will be available at www.uv.es/rsanjuan/virmut .

Double-Stranded DNA Viruses

2015 ◽  
pp. 393-406
Author(s):  
Dimitry Konstantinovich Lvov ◽  
Mikhail Yurievich Shchelkanov ◽  
Sergey Vladimirovich Alkhovsky ◽  
Petr Grigorievich Deryabin
Keyword(s):  
Dna Viruses ◽  
Double Stranded Dna

scholarly journals Adintoviruses: A Proposed Animal-Tropic Family of Midsize Eukaryotic Linear dsDNA (MELD) Viruses

2020 ◽  
Author(s):  
Gabriel J Starrett ◽  
Michael J Tisza ◽  
Nicole L Welch ◽  
Anna K Belford ◽  
Alberto Peretti ◽  
...  
Keyword(s):  
Genome Packaging ◽  
Metagenomic Sequence ◽  
Dna Viruses ◽  
Diverse Range ◽  
Integrase Gene ◽  
Data Mining Approach ◽  
Double Stranded Dna ◽  
Wide Range ◽  
Linear Dsdna ◽  
Dsdna Viruses

Abstract Polintons (also known as Mavericks) were initially identified as a widespread class of eukaryotic transposons named for their hallmark type B DNA polymerase and retrovirus-like integrase genes. It has since been recognized that many polintons encode possible capsid proteins and viral genome-packaging ATPases similar to those of a diverse range of double-stranded DNA (dsDNA) viruses. This supports the inference that at least some polintons are actually viruses capable of cell-to-cell spread. At present, there are no polinton-associated capsid protein genes annotated in public sequence databases. To rectify this deficiency, we used a data-mining approach to investigate the distribution and gene content of polinton-like elements and related DNA viruses in animal genomic and metagenomic sequence datasets. The results define a discrete family-like clade of viruses with two genus-level divisions. We propose the family name Adintoviridae, connoting similarities to adenovirus virion proteins and the presence of a retrovirus-like integrase gene. Although adintovirus-class PolB sequences were detected in datasets for fungi and various unicellular eukaryotes, sequences resembling adintovirus virion proteins and accessory genes appear to be restricted to animals. Degraded adintovirus sequences are endogenized into the germlines of a wide range of animals, including humans.

Shrinking of repeating unit length in leucine-rich repeats from double-stranded DNA viruses

2020 ◽  
Author(s):  
Norio Matsushima ◽  
Hiroki Miyashita ◽  
Shinsuke Tamaki ◽  
Robert H. Kretsinger
Keyword(s):  
Unit Length ◽  
Dna Viruses ◽  
Double Stranded Dna ◽  
Leucine Rich Repeats

scholarly journals Identification of the Immediate-Early Genes of Cyprinid Herpesvirus 2

Viruses ◽  
2020 ◽  
Vol 12 (9) ◽  
pp. 994
Author(s):  
Ruizhe Tang ◽  
Liqun Lu ◽  
Beiyang Wang ◽  
Jiao Yu ◽  
Hao Wang
Keyword(s):  
Time Course ◽  
Immediate Early ◽  
Viral Pathogen ◽  
Dna Viruses ◽  
Reading Frame ◽  
Double Stranded Dna ◽  
Cyprinid Herpesvirus 3 ◽  
Efficient Expression ◽  
Herpesvirus 1 ◽  
Polymerase Chain

Cyprinid herpesvirus 2 (CyHV-2), which infects goldfish and crucian carp causing high mortality, is an emerging viral pathogen worldwide. The genome of CyHV-2 is large and comprises double-stranded DNA, including several genes similar to cyprinid herpesvirus 1, ictalurid herpesvirus-1, cyprinid herpesvirus 3, and ranid herpesvirus-1. Genes of DNA viruses are expressed in three temporal phases: immediate-early (IE), early (E), and late (L) genes. Viral IE genes initiate transcription as soon as the virus enters the host, without viral DNA replication. IE gene products enable the efficient expression of E and L genes or regulate the host to initiate virus replication. In the present study, five IE genes of CyHV-2 were identified, including open reading frame (ORF)54, ORF121, ORF141, ORF147, and ORF155. Time course analysis and reverse transcription polymerase chain reaction confirmed five IE genes, thirty-four E genes, and thirty-nine L genes. In addition, all 150 ORFs identified in the CyHV-2 genome are transcribed, and are expressed in chronological order, similar to other herpesviruses. This study is the first to identify the IE genes of CyHV-2, which will provide more information for viral molecular characterization.

scholarly journals Amoeba genome reveals dominant host contribution to plastid endosymbiosis

2020 ◽  
Author(s):  
Duckhyun Lhee ◽  
JunMo Lee ◽  
Khaoula Ettahi ◽  
Chung Hyun Cho ◽  
Ji-San Ha ◽  
...  
Keyword(s):  
Stress Response ◽  
Light Stress ◽  
Terrestrial Ecosystems ◽  
Nucleotide Metabolism ◽  
Dna Viruses ◽  
Draft Assembly ◽  
Double Stranded Dna ◽  
Organelle Evolution ◽  
And Oxidative Stress ◽  
Stress Response Gene

Abstract Eukaryotic photosynthetic organelles, plastids, are the powerhouses of many aquatic and terrestrial ecosystems. The canonical plastid in algae and plants originated >1 billion years ago and therefore offers limited insights into the initial stages of organelle evolution. To address this issue, we focus here on the photosynthetic amoeba Paulinella micropora strain KR01 (hereafter, KR01) that underwent a more recent (ca. 124 Mya) primary endosymbiosis, resulting in a photosynthetic organelle termed the chromatophore. Analysis of genomic and transcriptomic data resulted in a high-quality draft assembly of size 707 Mbp and 32,361 predicted gene models. A total of 291 chromatophore targeted proteins were predicted in silico, 206 of which comprise the ancestral organelle proteome in photosynthetic Paulinella species with functions, among others, in nucleotide metabolism and oxidative stress response. Gene co-expression analysis identified networks containing known high light stress response genes as well as a variety of genes of unknown function (“dark” genes). We characterized diurnally rhythmic genes in this species and found that over 51% are dark. It was recently hypothesized that large double-stranded DNA viruses may have driven gene transfer to the nucleus in Paulinella and facilitated endosymbiosis. Our analyses do not support this idea, but rather suggest that these viruses in the KR01 and closely related P. micropora MYN1 genomes resulted from a more recent invasion.

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